Dioxygen affinity in heme proteins investigated by computer simulation

We present an investigation of the molecular basis of the modulation of oxygen affinity in heme proteins using computer simulation. QM-MM calculations are applied to explore distal and proximal effects on O(2) binding to the heme, while classical molecular dynamics simulations are employed to investigate ligand migration across the polypeptide to the active site. Trends in binding energies and in the kinetic constants are illustrated through a number of selected examples highlighting the virtues and the limitations of the applied methodologies. These examples cover a wide range of O(2)-affinities, and include: the truncated-N and truncated-O hemoglobins from Mycobacterium tuberculosis, the mammalian muscular O(2) storage protein: myoglobin, the hemoglobin from the parasitic nematode Ascaris lumbricoides, the oxygen transporter in the root of leguminous plants: leghemoglobin, the Cerebratulus lacteus nerve tissue hemoglobin, and the Alcaligenes xyloxidans cytochrome c'.     

Melatonin and lipid uptake by murine fibroblasts: clinical implications

The current study was undertaken to uncover the role of melatonin in lipid metabolism in the murine fibroblasts. The results show melatonin in vitro enhances lipid accumulation and lipid droplet formation in this cell line. Using oil red O staining, it was found that when oleic acid was present in the culture media, melatonin at doses of 0.1-2mM, significantly increased the lipid concentrations in the cells. However, low levels of melatonin, with or without oleic acid, did not influence lipid metabolism in the cultured fibroblasts. When a non-specific melatonin receptor antagonist, luzindole 10 microM was co-incubated with 1mM melatonin, the stimulatory effects of melatonin on lipid accumulation in these cells was significantly reduced. It appears that the effects of melatonin on lipid metabolism in murine fibroblasts is mediated by melatonin membrane receptors.     

Nuclear DNA from old collections of avian study skins reveals the evolutionary history of the Old World suboscines (Aves, Passeriformes)

Museum study skins represent an invaluable source of DNA for phylogenetics, phylogeography and population genetics. This becomes evident by comparing the number of study skins of birds housed in museums worldwide ( c . 10 million) with the corresponding number of tissue samples (probably fewer than 500 000). While the laboratory techniques used hitherto have primarily allowed PCR-based studies of mitochondrial genes from museum skins, we present here the first avian phylogeny based on a large number of nuclear sequences. The targeted fragment sizes and the properties of the primers used are important contributory factors to obtain good amplification results. In this study we routinely amplified fragments of c. 350 bp nuclear DNA. This advance in methodology opens up a new avenue for the use of avian museum skins, as nuclear DNA is especially useful when studying ancient patterns of diversification. The phylogenetic hypothesis of the Old World suboscines (Eurylaimides) presented herein strongly supports a monophyletic origin of the pittas (Pittidae). The phylogeny further suggests that pittas could be divided into three major groups, in agreement with the external morphological variation found in this group. The broadbills (Eurylaimidae) as currently defined are, on the other hand, found to be a paraphyletic family, as both Sapayoa aenigma and the asities (Philepittidae) are nested among them. Based on the phylogenetic results we suggest a revised classification of the Old World suboscines (Eurylaimides).     

Abundantly and rarely expressed Lhc protein genes exhibit distinct regulation patterns in plants

We have analyzed gene regulation of the Lhc supergene family in poplar (Populus spp.) and Arabidopsis (Arabidopsis thaliana) using digital expression profiling. Multivariate analysis of the tissue-specific, environmental, and developmental Lhc expression patterns in Arabidopsis and poplar was employed to characterize four rarely expressed Lhc genes, Lhca5, Lhca6, Lhcb7, and Lhcb4.3. Those genes have high expression levels under different conditions and in different tissues than the abundantly expressed Lhca1 to 4 and Lhcb1 to 6 genes that code for the 10 major types of higher plant light-harvesting proteins. However, in some of the datasets analyzed, the Lhcb4 and Lhcb6 genes as well as an Arabidopsis gene not present in poplar (Lhcb2.3) exhibited minor differences to the main cooperative Lhc gene expression pattern. The pattern of the rarely expressed Lhc genes was always found to be more similar to that of PsbS and the various light-harvesting-like genes, which might indicate distinct physiological functions for the rarely and abundantly expressed Lhc proteins. The previously undetected Lhcb7 gene encodes a novel plant Lhcb-type protein that possibly contains an additional, fourth, transmembrane N-terminal helix with a highly conserved motif. As the Lhcb4.3 gene seems to be present only in Eurosid species and as its regulation pattern varies significantly from that of Lhcb4.1 and Lhcb4.2, we conclude it to encode a distinct Lhc protein type, Lhcb8.     

Parasites of the Central American tapir Tapirus bairdii (Perissodactyla: Tapiridae) in Chiapas, Mexico

We analyzed 19 samples of Baird's tapir feces from La Sepultura Biosphere Reserve, collected between March and July 1999. We also took samples directly from a male tapir captured at the Montes Azules Biosphere Reserve. Both reserves are in Chiapas, Mexico. We used five techniques: flotation, MacMaster, micrometric, Ritchie's sedimentation and Ferreira's quantitative. In addition, we collected ectoparasites from animals captured in both reserves and from a captive couple from Tuxtla Gutierrez, Chiapas. These nematodes and protozoans were found: Agriostomun sp., Lacandoria sp., Neomurshidia sp., Trichostrongylus sp., Strongylus sp., Brachylumus sp, and an unidentified species of ancilostomaide. We also found Eimeria sp. and Balantidium coli, as well as the mites Dermacentor halli, Dermacentor latus, Amblyomma cajannense, Amblyomma coelebs, Amblyomma ovale, Anocentor nitens and Ixodes bicornis.     

Carotenoid-bacteriochlorophyll energy transfer in LH2 complexes studied with 10-fs time resolution

In this report, we present a study of carotenoid-bacteriochlorophyll energy transfer processes in two peripheral light-harvesting complexes (known as LH2) from purple bacteria. We use transient absorption spectroscopy with approximately 10 fs temporal resolution, which is necessary to observe the very fast energy relaxation processes. By comparing excited-state dynamics of the carotenoids in organic solvents and inside the LH2 complexes, it has been possible to directly evaluate their energy transfer efficiency to the bacteriochlorophylls. In the case of okenone in the LH2 complex from Chromatium purpuratum, we obtained an energy transfer efficiency of etaET2=63+/-2.5% from the optically active excited state (S2) and etaET1=61+/-2% from the optically dark state (S1); for rhodopin glucoside contained in the LH2 complex from Rhodopseudomonas acidophila these values become etaET2=49.5+/-3.5% and etaET1=5.1+/-1%. The measurements also enabled us to observe vibrational energy relaxation in the carotenoids' S1 state and real-time collective vibrational coherence initiated by the ultrashort pump pulses. Our results are important for understanding the dynamics of early events of photosynthesis and relating it to the structural arrangement of the chromophores.     

Pollen germination and pollen tube growth in Fraxinus pennsylvanica

With regard to adaptation of green ash (Fraxinus pennsylvanica Marshall) to ecological conditions in Croatia, pollen germination and pollen tube length after 2, 4 and 6 hours were examined in vitro at 10, 15, 20 and 25°C during two years 2001 and 2002. Narrow leaved ash (F. angustifolia Vahl) pollen served as a control in 2002. The year, time and temperature, and the interaction between time and temperature were significant for both germination percentage and pollen tube length. Interactions year × temperature and year × time were significant for pollen tube length only. The highest germination percentage (17.86% in 2001 and 19.40% in 2002) of green ash pollen was at 15°C after 6 hours. The pollen tube length was greatest at 20°C (393.46 μm) in 2001 and 25°C (899.50 μm) in 2002 after 6 hours. Narrow leaved ash pollen had the highest germination percentage (19.22%) at 20°C after 6 hours and was significantly reduced at 25°C. The pollen tube length was greatest at 25°C (518.90 μm) after 6 hours. It can be concluded that green ash pollen has satisfactory germination in ecological conditions in Croatia and that the optimum temperature for pollen germination is higher than 20°C.     

Performance of marker-based relatedness estimators in natural populations of outbred vertebrates

Knowledge of relatedness between pairs of individuals plays an important role in many research areas including evolutionary biology, quantitative genetics, and conservation. Pairwise relatedness estimation methods based on genetic data from highly variable molecular markers are now used extensively as a substitute for pedigrees. Although the sampling variance of the estimators has been intensively studied for the most common simple genetic relationships, such as unrelated, half- and full-sib, or parent-offspring, little attention has been paid to the average performance of the estimators, by which we mean the performance across all pairs of individuals in a sample. Here we apply two measures to quantify the average performance: first, misclassification rates between pairs of genetic relationships and, second, the proportion of variance explained in the pairwise relatedness estimates by the true population relatedness composition (i.e., the frequencies of different relationships in the population). Using simulated data derived from exceptionally good quality marker and pedigree data from five long-term projects of natural populations, we demonstrate that the average performance depends mainly on the population relatedness composition and may be improved by the marker data quality only within the limits of the population relatedness composition. Our five examples of vertebrate breeding systems suggest that due to the remarkably low variance in relatedness across the population, marker-based estimates may often have low power to address research questions of interest.     

Primate-specific evolution of an LDLR enhancer

Background  

Sequence changes in regulatory regions have often been invoked to explain phenotypic divergence among species, but molecular examples of this have been difficult to obtain.