RepeatAround: a software tool for finding and visualizing repeats in circular genomes and its application to a human mtDNA database

RepeatAround is a Windows based software tool designed to find "direct repeats", "inverted repeats", "mirror repeats" and "complementary repeats", from 3 to 64bp length, in circular genomes. It processes input files directly extracted from GenBank database, providing visualisation of the repeats location in the genomic structure, so that for instance, in most mtDNAs the user can check if the repeats are located in coding or non-coding region (and in the first case in which gene), and how far apart the repeat pair(s) are. Besides the visual tool, it provides other outputs in a spreadsheet containing information on the number and location of the repeats, facilitating graphic analyses. Several genomes can be inputed simultaneously, for phylogenetic comparison purposes. Other capabilities of the software are the generation of random circular genomes, for statistical evaluation of comparison between observed repeats distributions with their shuffled counterparts, as well as the search for specific motifs, allowing an easy confirmation of repeats flanking a newly detected rearrangement. As an example of the programme's applications we analysed the Direct Repeats distribution in a large human mtDNA database. Results showed that Direct Repeats, even the larger ones, are evenly distributed among the human mtDNA haplogroups, enabling us to state that, based only on the repetitive motifs, no haplogroup is particularly more or less prone to mtDNA macrodeletions.     

Night and day service: Distyly and mixed pollination system in Faramea cyanea (Rubiaceae)

Currently, pollination is seen as involving more generalist interactions than specialized ones. Supporting this trend, some nocturnal distylous flowers may also receive floral visitors during the day, and since the latter contribute to fruit set, the pollination system is mixed and less specialized. Common among the Rubiaceae, distyly has been regarded as a reproductive strategy which requires a precise and specialized pollination system, and in this important tropical family, environmental disturbance and pollination failure have been used to explain anomalies in distylous features. Faramea cyanea Müll. Arg. is a common tree species in forest formations in the increasingly threatened Cerrado biome, the Neotropical savannas in Central Brazil. We evaluated the floral morphology, pollination biology and breeding system of a population of F. cyanea. Despite their moth pollination features, flowers were visited by diurnal (bees) as well as nocturnal (moths) pollinators. Experimental results showed that both pollinator groups contributed equally to pollen flow and legitimate pollination. The population presented distyly, isoplethy and heteromorphic self-incompatibility. Although F. cyanea did not present exact reciprocal herkogamy between floral morphs, pollination and reproductive success were not impaired. Floral features, which allowed pollination by complementary groups of pollinators, may explain the absence of anomalies in the isoplethy and distylous features in the studied population, anomalies which have been observed in other sympatric distylous Rubiaceae.     

Synthesis and anti-inflammatory activity of new arylidene-thiazolidine-2,4-diones as PPARγ ligands

Eight new 5-arylidene-3-benzyl-thiazolidine-2,4-diones with halide groups on their benzyl rings were synthesized and assayed in vivo to investigate their anti-inflammatory activities. These compounds showed considerable biological efficacy when compared to rosiglitazone, a potent and well-known agonist of PPARγ, which was used as a reference drug. This suggests that the substituted 5-arylidene and 3-benzylidene groups play important roles in the anti-inflammatory properties of this class of compounds. Docking studies with these compounds indicated that they exhibit specific interactions with key residues located in the site of the PPARγ structure, which corroborates the hypothesis that these molecules are potential ligands of PPARγ. In addition, competition binding assays showed that four of these compounds bound directly to the ligand-binding domain of PPARγ, with reduced affinity when compared to rosiglitazone. An important trend was observed between the docking scores and the anti-inflammatory activities of this set of molecules. The analysis of the docking results, which takes into account the hydrophilic and hydrophobic interactions between the ligands and the target, explained why the 3-(2-bromo-benzyl)-5-(4-methanesulfonyl-benzylidene)-thiazolidine-2,4-dione compound had the best activity and the best docking score. Almost all of the stronger hydrophilic interactions occurred between the substituted 5-arylidene group of this compound and the residues of the binding site.     

Genetic signatures of a Mediterranean influence in Iberian Peninsula sheep husbandry

Highly adaptable and versatile populations of domestic sheep, the result of millennia of intense husbandry, are found in almost every corner of the world. Here we describe a genetic survey of sheep from the western fringe of its European distribution. We studied the mitochondrial DNA control region sequences from 161 individuals belonging to 7 Portuguese sheep breeds. Our study revealed a high level of genetic diversity, with an average breed haplotype diversity of 0.983, substantially above that observed in central European breeds, as well as the presence of maternal lineages until now only found in the Middle East and Asia. A broad north-south pattern describes the most important trend in the Portuguese sheep population with a southern population clearly distinct from most other breeds. A recurrent influx of new genetic diversity, probably via the Mediterranean Sea, may explain these patterns and appears to corroborate the importance of this maritime route in the history of both mankind and livestock. Zooarchaeological studies of sheep bones from southern Portugal indicate a marked size increase during the Moslem period that may reflect an improvement of this animal--perhaps part of the well known "Arab agricultural revolution" in Andalusia. This could have been a time when the gene pool of Iberian sheep was substantially enriched and may help to explain the history of modern sheep breeds in this peninsula.     

Effect of uroguanylin on potassium and bicarbonate transport in rat renal tubules

The effect of uroguanylin (UGN) on K+ and H+ secretion in the renal tubules of the rat kidney was studied using in vivo stationary microperfusion. For the study of K+ secretion, a tubule was punctured to inject a column of FDC-green-colored Ringer's solution with 0.5 mmol KCl/L+/-10(-6) mol UGN/L, and oil was used to block fluid flow. K+ activity and transepithelial potential differences (PD) were measured with double microelectrodes (K+ ion-selective resin vs. reference) in the distal tubules of the same nephron. During perfusion, K+ activity rose exponentially, from 0.5 mmol/L to stationary concentration, allowing for the calculation of K+ secretion (JK). JK increased from 0.63+/-0.06 nmol.cm-2.s-1 in the control group to 0.85+/-0.06 in the UGN group (p<0.01). PD was -51.0+/-5.3 mV in the control group and -50.3+/-4.98 mV in the UGN group. In the presence of 10(-7) mol iberiotoxin/L, the UGN effect was abolished: JK was 0.37+/-0.038 nmol.cm-2.s-1 in the absence of, and 0.38+/-0.025 in the presence of, UGN, indicating its action on maxi-K channels. In another series of experiments, renal tubule acidification was studied, using a similar method: proximal and distal tubules were perfused with solutions containing 25 mmol NaHCO3/L. Acidification half-time was increased both in proximal and distal segments and, as a consequence, bicarbonate reabsorption decreased in the presence of UGN (in proximal tubules, from 2.40+/-0.26 to 1.56+/-0.21 nmol.cm-2.s-1). When the Na+/H+ exchanger was inhibited by 10(-4) mol hexamethylene amiloride (HMA)/L, the control and UGN groups were not significantly different. In the late distal tubule, after HMA, UGN significantly reduced JHCO3-, indicating an effect of UGN on H+-ATPase. These data show that UGN stimulated JK+ by acting on maxi-K channels, and decreased JHCO3- by acting on NHE3 in proximal and H+-ATPase in distal tubules.     

The distribution and evolutionary history of the PRP8 intein

Background  

We recently described a mini-intein in the PRP8 gene of a strain of the basidiomycete Cryptococcus neoformans, an important fungal pathogen of humans. This was the second described intein in the nuclear genome of any eukaryote; the first nuclear encoded intein was found in the VMA gene of several saccharomycete yeasts. The evolution of eukaryote inteins is not well understood. In this report we describe additional PRP8 inteins (bringing the total of these to over 20). We compare and contrast the phylogenetic distribution and evolutionary history of the PRP8 intein and the saccharomycete VMA intein, in order to derive a broader understanding of eukaryote intein evolution. It has been suggested that eukaryote inteins undergo horizontal transfer and the present analysis explores this proposal.     

Refining the genetic portrait of Portuguese Roma through X-chromosomal markers

Due to differences in transmission between X-chromosomal and autosomal DNA, the comparison of data derived from both markers allows deeper insight into the forces that shape the patterns of genetic diversity in populations. In this study, we applied this comparative approach to a sample of Portuguese Roma (Gypsies) by analyzing 43 X-chromosomal markers and 53 autosomal markers. Portuguese individuals of non-Gypsy ancestry were also studied. Compared with the host population, reduced levels of diversity on the X chromosome and autosomes were detected in Gypsies; this result was in line with known patterns of genetic diversity typical of Roma groups. As a consequence of the complex demographic past of the Roma, during which admixture and genetic drift played major roles, the amount of linkage disequilibrium (LD) on the X chromosome in Gypsies was considerably higher than that observed in non-Gypsies. When the pattern of differentiation on the X chromosome was compared with that of autosomes, there was evidence for asymmetries in female and male effective population sizes during the admixture between Roma and non-Roma. This result supplements previous data provided by mtDNA and the Y chromosome, underlining the importance of using combined information from the X chromosome and autosomes to dissect patterns of genetic diversity. Following the out-of-India dispersion, the Roma acquired a complex genetic pattern that was influenced by drift and introgression with surrounding populations, with important contributions from both males and females. We provide evidence that a sex-biased admixture with Europeans is probably associated with the founding of the Portuguese Gypsies.     

Degradation of difluorobenzenes by the wild strain Labrys portucalensis

This study focuses on the biodegradation of difluorobenzenes (DFBs), compounds commonly used as intermediates in the industrial synthesis of various pharmaceutical and agricultural chemicals. A previously isolated microbial strain (strain F11), identified as Labrys portucalensis, able to degrade fluorobenzene (FB) as sole carbon and energy source, was tested for its capability to degrade 1,2-, 1,3- and 1,4-DFB in batch cultures. Strain F11 could use 1,3-DFB as a sole carbon and energy source, with quantitative release of fluoride, but 1,4-DFB was only degraded and defluorinated when FB was supplied simultaneously. Growth of strain F11 with 0.5 mM of 1,3-DFB led to stoichiometric release of fluoride ion. The same result was obtained in cultures fed with 1 mM of 1,3-DFB or 0.5 mM of 1,4-DFB, in the presence of 1 mM of FB. No growth occurred with 1,2-DFB as substrate, and degradation of FB was inhibited when supplied simultaneously with 1,2-DFB. To our knowledge, this is the first time biodegradation of 1,3-DFB as a sole carbon and energy source, and cometabolic degradation of 1,4-DFB, by a single bacterium, is reported.     

Whole-genome sequencing of the efficient industrial fuel-ethanol fermentative Saccharomyces cerevisiae strain CAT-1

The Saccharomyces cerevisiae strains widely used for industrial fuel-ethanol production have been developed by selection, but their underlying beneficial genetic polymorphisms remain unknown. Here, we report the draft whole-genome sequence of the S. cerevisiae strain CAT-1, which is a dominant fuel-ethanol fermentative strain from the sugarcane industry in Brazil. Our results indicate that strain CAT-1 is a highly heterozygous diploid yeast strain, and the ~12-Mb genome of CAT-1, when compared with the reference S228c genome, contains ~36,000 homozygous and ~30,000 heterozygous single nucleotide polymorphisms, exhibiting an uneven distribution among chromosomes due to large genomic regions of loss of heterozygosity (LOH). In total, 58 % of the 6,652 predicted protein-coding genes of the CAT-1 genome constitute different alleles when compared with the genes present in the reference S288c genome. The CAT-1 genome contains a reduced number of transposable elements, as well as several gene deletions and duplications, especially at telomeric regions, some correlated with several of the physiological characteristics of this industrial fuel-ethanol strain. Phylogenetic analyses revealed that some genes were likely associated with traits important for bioethanol production. Identifying and characterizing the allelic variations controlling traits relevant to industrial fermentation should provide the basis for a forward genetics approach for developing better fermenting yeast strains.