Historical biogeography and speciation in the reef fish genus Haemulon (Teleostei: Haemulidae)

The high biodiversity of tropical marine hotspots has long intrigued evolutionary biologists and biogeographers. The genus Haemulon (grunts) is one of the most important (numerically, ecologically, and economically) reef fish groups in the New World and an excellent candidate to test hypotheses of speciation and diversity generation in the Greater Caribbean, the richest Atlantic biodiversity hotspot, as well as the eastern Pacific. To elucidate the phylogenetic relationships among the species of Haemulon, we obtained a combined total of 2639 base pairs from two mitochondrial genes (cytochrome b and cytochrome oxidase I), and two nuclear genes (TMO-4C4 and RAG2) from all nominal species. Parsimony, Maximum likelihood, and Bayesian analyses resulted in a well-resolved phylogeny with almost identical topologies. Previous phylogenetic hypotheses based on adult morphology, such as the close relationship among H. aurolineatum, H. boschmae, and H. striatum were not supported, whereas others using developmental characters, such as the relationship between H. plumieri and H. sciurus, were confirmed. Our data also indicate that the populations of the nominal H. steindachneri from the two sides of the Isthmus of Panama are genetically divergent at the species level in each ocean, and that the boga, Inermia vittata (family Inermiidae), belongs in the genus Haemulon. This evidence implies that there are 21 valid species of Haemulon, two more than previously recognized. The Amazon barrier and the Isthmus of Panama seem to have played roles in allopatric speciation of Haemulon. However, the majority of sister species pairs have completely overlapping distributions, indicating that vicariance is not the only process driving speciation in this genus. We conclude that both vicariance between biogeographic provinces, and ecological mechanisms of speciation within provinces contribute to species richness in the genus Haemulon.     

Effects of training exercises for the development of strength and endurance in soccer

A training program designed to increase strength and aerobic endurance in 1 season was tested on 16 professional soccer players from Spain with a mean age of 28 +/- 3.37 years. The schedule comprised 4 macrocycles of 12 weeks of aerobic endurance and strength training. As much for the strength training as for the aerobic endurance, the program used a sequence of general, special, and specific exercises. Assessments were made with routine tests (i.e., squat jumps [SJs], countermovement jumps [CMJs], and countermovement jumps with arm swing [CMJas]) at the end of each macrocycle, and the Probst test was used to assess aerobic endurance as a function of running speed and distance, at the start and end of the training schedule and at the start of the third macrocycle. Jumps were performed on an infrared platform fitted to the MuscleLab system. The Probst test showed differences between the first evaluation and the second and third evaluations: 3,550 +/- 411.59 m vs. 2,006 +/- 207.20 m (P < 0.01). For 2 of the 3 jumps analyzed, the results were better in the last 2 than in the first 2 evaluations (SJ, 43.13 +/- 3.77 vs. 39.47 +/- 3.4 [P < 0.05]; CMJ, 49.80 +/- 3.77 vs. 46.67 +/- 3.76 [P < 0.05]; CMJas, 56.24 +/- 5.2 vs. 52.98 +/- 4.54 [P > 0.05]). Improvement of aerobic endurance was produced on the first phase of the season as a consequence of the training. To increase strength, it is necessary to augment the number of training sessions of this type. It is convenient to separate aerobic endurance and strength training to create more ample blocks during the last 2 macrocycles.     

Invasive pulmonary aspergillosis due to a mixed infection caused by Aspergillus flavus and Aspergillus fumigatus

Invasive pulmonary aspergillosis is typically caused by a single Aspergillus species, most frequently Aspergillus fumigatus. Here we report that a lung transplant recipient developed invasive aspergillosis due to a mixed infection caused by Aspergillus flavus and A. fumigatus. The implications for this unusual finding are discussed.     

Gaining confidence in biological interpretation of the microarray data: the functional consistence of the significant GO categories

MOTIVATION: In microarray studies, numerous tools are available for functional enrichment analysis based on GO categories. Most of these tools, due to their requirement of a prior threshold for designating genes as differentially expressed genes (DEGs), are categorized as threshold-dependent methods that often suffer from a major criticism on their changing results with different thresholds. RESULTS: In the present article, by considering the inherent correlation structure of the GO categories, a continuous measure based on semantic similarity of GO categories is proposed to investigate the functional consistence (or stability) of threshold-dependent methods. The results from several datasets show when simply counting overlapping categories between two groups, the significant category groups selected under different DEG thresholds are seemingly very different. However, based on the semantic similarity measure proposed in this article, the results are rather functionally consistent for a wide range of DEG thresholds. Moreover, we find that the functional consistence of gene lists ranked by SAM metric behaves relatively robust against changing DEG thresholds. AVAILABILITY: Source code in R is available on request from the authors.     

Eupafolin: Effect on mitochondrial energetic metabolism

This study evaluated the effects of flavone eupafolin (6-methoxy 5,7,3',4'-tetrahydroxyflavone), extracted from dry leaves of Eupatorium litoralle. Eupafolin (25-200microM) promoted inhibition of the respiratory rate in state 3, in the presence of glutamate or succinate. During succinate oxidation, it was found that only state 4 respiratory rate was stimulated approximately 30% by eupafolin (100microM) and ADP/O ratio and RCC were reduced with all doses. When glutamate was used as substrate, RCC was similarly reduced. Eupafolin caused a reduction of enzymatic activities between complexes I and III of the respiratory chain. Cytochrome c oxidase and ATPase activities were not affected. Using voltammetry cyclic analysis, eupafolin give rise to irreversible oxidation with an anodic peak potential at +0.08V (SHE). We also observed that eupafolin can undergo oxidation catalyzed by EDTA-Fe, promoting cytochrome c reduction in the presence of NADH, resulting in the production of the superoxide radical and hydrogen peroxide. All together, the results could explain the cytotoxic effects observed previously with the eupafolin.     

DAVID gene ID conversion tool

Our current biological knowledge is spread over many independent bioinformatics databases where many different types of gene and protein identifiers are used. The heterogeneous and redundant nature of these identifiers limits data analysis across different bioinformatics resources. It is an even more serious bottleneck of data analysis for larger datasets, such as gene lists derived from microarray and proteomic experiments. The DAVID Gene ID Conversion Tool (DICT), a web-based application, is able to convert user's input gene or gene product identifiers from one type to another in a more comprehensive and high-throughput manner with a uniquely enhanced ID-ID mapping database.     

An assessment of the impacts of molecular oxygen on the evolution of proteomes

Oxygen is not only one of life's essential elements but also a source of protein damage, mutagenesis, and ageing. Many proteome adaptations have been proposed to tackle such stresses and we assessed them using comparative genomics in a phylogenetic context. First, we find that aerobiosis is a trait with important phylogenetic inertia but that oxygen content in proteins is not. Instead, oxygen content is close to the expected values given the nucleotide composition. Accordingly, we find no evidence of oxygen being a scarce resource for protein synthesis even among anaerobes. Second, we searched for counterselection of amino acids more prone to oxidation among aerobes. Only cysteine follows the expected trend, whereas tryptophan follows the inverse one. When analyzing composition in the context of protein structures and residue accessibility, we find that all oxidable residues are avoided at the surface of proteins. Yet, there is no difference between aerobes and anaerobes in this respect, and the effect might be explained by the hydrophobicity of these residues. Third, we revisited the hypothesis that atmospheric enrichment in molecular oxygen led to the development of the communication capabilities of eukaryotes. With a larger data set and adequate controls, we confirm the trend of longer oxygen-rich outer domains in transmembrane proteins of eukaryotes. Yet, we find no significant association between oxygen concentration in the environment and this trait within prokaryotes, suggesting that this difference is clade specific and independent of oxygen availability. We find that genes involved in cellular responses to oxygen are much more frequent among aerobes, and we suggest that they erase most expected differences in terms of proteome composition between organisms facing high and low oxygen concentrations.     

Cross-cultural perspectives on physician and lay models of the common cold

We compare physicians and laypeople within and across cultures, focusing on similarities and differences across samples, to determine whether cultural differences or lay-professional differences have a greater effect on explanatory models of the common cold. Data on explanatory models for the common cold were collected from physicians and laypeople in South Texas and Guadalajara, Mexico. Structured interview materials were developed on the basis of open-ended interviews with samples of lay informants at each locale. A structured questionnaire was used to collect information from each sample on causes, symptoms, and treatments for the common cold. Consensus analysis was used to estimate the cultural beliefs for each sample. Instead of systematic differences between samples based on nationality or level of professional training, all four samples largely shared a single-explanatory model of the common cold, with some differences on subthemes, such as the role of hot and cold forces in the etiology of the common cold. An evaluation of our findings indicates that, although there has been conjecture about whether cultural or lay-professional differences are of greater importance in understanding variation in explanatory models of disease and illness, systematic data collected on community and professional beliefs indicate that such differences may be a function of the specific illness. Further generalizations about lay-professional differences need to be based on detailed data for a variety of illnesses, to discern patterns that may be present. Finally, a systematic approach indicates that agreement across individual explanatory models is sufficient to allow for a community-level explanatory model of the common cold.     

Diurnal Rhythms of Plasma Ions and Metabolites Levels in Thoroughbred Racehorses

The purposes of this study were to observe the presence of diurnal rhythms in plasma ions and metabolites levels in Thoroughbred racehorses under physical training, and to determine the time of blood sampling in clinical investigations. Plasma calcium, phosphorus, potassium, sodium, chloride, magnesium, iron, glucose, cholesterol, triglycerides, and total proteins levels were studied over a 72-h period. Blood samples were taken every 4 hours from five male and five female Thoroughbred racehorses under physical training. COSINOR analyses (P = 0.05) were done. Plasma potassium and triglycerides showed significant diurnal rhythms, with its acrophases occurring at dark period. No significant diurnal rhythms of other variables were found. It was concluded that, in Thoroughbred racehorses, the optimum time for potassium, and triglycerides sampling seems to be light period. And for other variables, time of diagnosis is not important.     

Linkage analysis for mapping genes of sex-influenced traits

Abstract Statistical methods are developed to estimate gender-specific and gender-average recombination frequencies between a biallelic or multiallelic marker and a sex-influenced gene. Iterative solutions are developed for intercross (or F-2 design). For biallelic markers, two iterative solutions are required, one for coupling and repulsion parental linkage phases and one for mixed parental linkage phases. For multiallelic markers, one set of iterative equations applies to all possible parental linkage phases. The resulting formulae for estimating recombination frequency use the full data set and yield estimates that are exactly the same as the true parameters if the observed and expected phenotypic distributions are equal. When one parent is homozygous for the sex-influenced gene as is expected with the backcross design, simple solutions exist for estimating recombination frequencies. However, offspring of one gender (male or female) do not have linkage information depending on whether the homozygous parent has two male-dominant or male-recessive alleles. Consequently, an F-2 design is more efficient than a backcross design for mapping a sex-influenced gene. Knowing each parental linkage phase is important to apply the methods developed in this article. It is shown that an individual's linkage phase of the sex-influenced locus can be determined based on allele transmission from the parents for all crosses except under the mating between an expressed male and an unexpressed female.