Fluorescence imaging of light acclimation of brazilian atlantic forest tree species

In the pursuit of knowledge on the biological behavior of Brazilian Atlantic Forest tree species, this study evaluated the susceptibility of the light-demanding species, Schinus terebinthifolia Raddi., Pseudobombax grandiflorum (Cav.) A. Robyns and Joannesia princeps Vell., and of the shade-tolerant species, Hymenaea courbaril L. var. stilbocarpa and Lecythis pisonis Camb, to photoinhibition and acclimation capacity. These species were first cultivated under two irradiance conditions, I₂₀ (20% direct sunlight radiation) and I₁₀₀ (all-sky or direct sunlight) and then transferred from I₂₀ to I₁₀₀. The effects of the sudden increase in light radiation intensity on photosynthetic activity were then evaluated through chlorophyll (Chl) fluorescence imaging, HPLC xanthophylls analysis, and cell membrane lipid peroxidation measurements. Light-demanding species were found to present a higher photochemical efficiency and higher acclimation capacity under high light irradiance than shade-tolerant species. The higher photoinhibition tolerance observed in light-demanding species was associated to their higher capacity for photochemical dissipation and dissipation of excess excitation energy via the xanthophyll cycle, leading to a lower ROS generation. The obtained results suggested that a knowledge of acclimation capacity, by means of Chl fluorescence imaging yields, is a useful indicator of species successional grouping.     

Caesium,potassium and ammonium distributions in different organs of tropical plants

In the present work the distribution of ions in aboveground plant parts was studied in order to establish the suitability of using radiocaesium as a tracer for the plant absorption of nutrients, such as potassium (K⁺) and ammonium (NH₄⁺). We present the results for the distributions of ¹³⁷Cs, ⁴⁰K and NH₄⁺ from four tropical plant species: lemon (Citrus aurantifolia), orange (Citrus sinensis), guava (Psidium guajava) and chili pepper (Capsicum frutescens). Activity concentrations of ¹³⁷Cs and ⁴⁰K were measured by gamma spectrometry and concentrations of free NH₄⁺ ions by a colorimetric method. Similarly to potassium and ammonium, caesium showed a high mobility within the plants, exhibiting the highest values of concentration in the growing parts of the tree (fruits, new leaves, twigs, and barks). A significant correlation between activity concentrations of ¹³⁷Cs and ⁴⁰K was observed in these tropical plants. The K/Cs discrimination ratios were approximately equal to unity in different compartments of each individual plant, suggesting that caesium could be a good tracer for ⁴⁰K in tropical woody fruit species. Despite the similarity observed for the behaviour of caesium and ammonium in the newly grown plant compartments, ¹³⁷Cs was not well correlated with NH₄⁺. Significant temporal changes in the NH₄⁺ concentrations were observed during the development of fruits, while the ¹³⁷Cs activity concentration alterations were not of great importance, indicating, therefore, that Cs⁺ and free NH₄⁺ ions could have distinct concentration ratios for each particular plant organ.     

Non-native interactions play an effective role in protein folding dynamics

Systematic Monte Carlo simulations of simple lattice models show that the final stage of protein folding is an ordered process where native contacts get locked (i.e., the residues come into contact and remain in contact for the duration of the folding process) in a well‐defined order. The detailed study of the folding dynamics of protein‐like sequences designed as to exhibit different contact energy distributions, as well as different degrees of sequence optimization (i.e., participation of non‐native interactions in the folding process), reveals significant differences in the corresponding locking scenarios—the collection of native contacts and their average locking times, which are largely ascribable to the dynamics of non‐native contacts. Furthermore, strong evidence for a positive role played by non‐native contacts at an early folding stage was also found. Interestingly, for topologically simple target structures, a positive interplay between native and non‐native contacts is observed also toward the end of the folding process, suggesting that non‐native contacts may indeed affect the overall folding process. For target models exhibiting clear two‐state kinetics, the relation between the nucleation mechanism of folding and the locking scenario is investigated. Our results suggest that the stabilization of the folding transition state can be achieved through the establishment of a very small network of native contacts that are the first to lock during the folding process.     

Statistical modeling of biomedical corpora: mining the Caenorhabditis Genetic Center Bibliography for genes related to life span

Background  

The statistical modeling of biomedical corpora could yield integrated, coarse-to-fine views of biological phenomena that complement discoveries made from analysis of molecular sequence and profiling data. Here, the potential of such modeling is demonstrated by examining the 5,225 free-text items in the Caenorhabditis Genetic Center (CGC) Bibliography using techniques from statistical information retrieval. Items in the CGC biomedical text corpus were modeled using the Latent Dirichlet Allocation (LDA) model. LDA is a hierarchical Bayesian model which represents a document as a random mixture over latent topics; each topic is characterized by a distribution over words.     

The shape of human gene family phylogenies

Background  

The shape of phylogenetic trees has been used to make inferences about the evolutionary process by comparing the shapes of actual phylogenies with those expected under simple models of the speciation process. Previous studies have focused on speciation events, but gene duplication is another lineage splitting event, analogous to speciation, and gene loss or deletion is analogous to extinction. Measures of the shape of gene family phylogenies can thus be used to investigate the processes of gene duplication and loss. We make the first systematic attempt to use tree shape to study gene duplication using human gene phylogenies.     

Uric acid oxidation by peroxynitrite: multiple reactions, free radical formation, and amplification of lipid oxidation

Uric acid has been considered to be an efficient scavenger of peroxynitrite but the reaction between urate and peroxynitrite has been only partially characterized. Also, previous studies have indicated that urate may increase peroxynitrite-mediated oxidation of low density lipoprotein (LDL). Here, we examined the reaction between urate and peroxynitrite by combining kinetic, oxygen consumption, spin trapping, and product identification studies; in parallel, we tested the effect of urate upon peroxynitrite-mediated lipid oxidation. Our results demonstrated that urate reacts with peroxynitrite with an apparent second order rate constant of 4.8 x 10(2) M(-1). s(-1) in a complex process, which is accompanied by oxygen consumption and formation of allantoin, alloxan, and urate-derived radicals. The main radical was identified as the aminocarbonyl radical by the electrospray mass spectra of its 5, 5-dimethyl-l-pyrroline N-oxide adduct. Mechanistic studies suggested that urate reacts with peroxynitrous acid and with the radicals generated from its decomposition to form products that can further react with peroxynitrite anion. These many reactions may explain the reported efficiency of urate in inhibiting some peroxynitrite-mediated processes. Production of the aminocarbonyl radical, however, may propagate oxidative reactions. We demonstrated that this radical is likely to be the species responsible for the effects of urate in amplifying peroxynitrite-mediated oxidation of liposomes and LDL, which was monitored by the formation of lipid peroxides and thiobarbituric acid-reactive substances. The aminocarbonyl radical was not detectable during urate attack by other oxidants and consequently it is unlikely to be responsible for all previously described prooxidant effects of uric acid.     

Quality determination and the repair of poor quality spots in array experiments

Background  

A common feature of microarray experiments is the occurence of missing gene expression data. These missing values occur for a variety of reasons, in particular, because of the filtering of poor quality spots and the removal of undefined values when a logarithmic transformation is applied to negative background-corrected intensities. The efficiency and power of an analysis performed can be substantially reduced by having an incomplete matrix of gene intensities. Additionally, most statistical methods require a complete intensity matrix. Furthermore, biases may be introduced into analyses through missing information on some genes. Thus methods for appropriately replacing (imputing) missing data and/or weighting poor quality spots are required.     

A Taxonomic Search Engine: Federating taxonomic databases using web services

Background  

The taxonomic name of an organism is a key link between different databases that store information on that organism. However, in the absence of a single, comprehensive database of organism names, individual databases lack an easy means of checking the correctness of a name. Furthermore, the same organism may have more than one name, and the same name may apply to more than one organism.     

Radiographic joint damage in rheumatoid arthritis is associated with differences in cartilage turnover and can be predicted by serum biomarkers: an evaluation from 1 to 4 years after diagnosis

Introduction  

The objective of this study was to determine whether serum biomarkers for degradation and synthesis of the extracellular matrix of cartilage are associated with, and can predict, radiographic damage in patients with rheumatoid arthritis (RA).