Heat and phosphate starvation effects on the proteome, morphology and chemical composition of the biomining bacteria Acidithiobacillusferrooxidans

Acidithiobacillus ferrooxidans is a Gram negative, acidophilic, chemolithoautotrophic bacterium that plays an important role in metal bioleaching. During bioleaching, the cells are subjected to changes in the growth temperature and nutrients starvation. The aim of this study was to gather information about the response of the A. ferrooxidans Brazilian strain LR to K₂HPO₄ starvation and heat stress through investigation of cellular morphology, chemical composition and differential proteome. The scanning electron microscopic results showed that under the tested stress conditions, A. ferrooxidans cells became elongated while the Fourier transform infrared spectroscopy (FT-IR) analysis showed alterations in the wavenumbers between 850 and 1,275 cm⁻¹, which are related to carbohydrates, phospholipids and phosphoproteins. These findings indicate that the bacterial cell surface is affected by the tested stress conditions. A proteomic analysis, using 2-DE and tandem mass spectrometry, enabled the identification of 44 differentially expressed protein spots, being 30 due to heat stress (40°C) and 14 due to K₂HPO₄ starvation. The identified proteins belonged to 11 different functional categories, including protein fate, energy metabolism and cellular processes. The upregulated proteins were mainly from protein fate and energy metabolism categories. The obtained results provide evidences that A. ferrooxidans LR responds to heat stress and K₂HPO₄ starvation by inducing alterations in cellular morphology and chemical composition of the cell surface. Also, the identification of several proteins involved in protein fate suggests that the bacteria cellular homesostasis was affected. In addition, the identification of proteins from different functional categories indicates that the A. ferrooxidans response to higher than optimal temperatures and phosphate starvation involves global changes in its physiology.     

Intra‐clutch pattern of albumen δ13C and δ15N in yellow‐legged gulls Larus michahellis: female dietary shift or resource allocation strategy?

Energy or nutritional constraints associated to female dietary shifts during the clutch production period may play a role in generating intra‐clutch egg size variation in yellow‐legged gulls Larus michahellis. To explore this possibility, we determined albumen δ¹³C and δ¹⁵N values in three‐egg clutches (modal clutch size) from three different breeding episodes: Ebro Delta 2004 and 2006, and Columbretes Islands 2004. Rather than a shift in females’ diet, consistent intra‐clutch patterns of variation in egg size and albumen isotopic values (particularly in the case of albumen δ¹³C, which values held constant throughout the laying sequence) pointed to an intrinsic mechanism as the most feasible cause for the relatively smaller size of third/last‐laid eggs. However, diet “quality” for breeding females seemed to affect intra‐clutch egg size variation. In particular, a deficit of specific nutrients for egg formation associated to refuse scraps exploitation (as suggested by depleted albumen isotopic values) likely resulted in the more apparent intra‐clutch egg size profile for the Ebro Delta 2004. In the absence of dietary shifts, the observation of consistently higher δ¹⁵N values for third‐albumens suggested a greater contribution of endogenous resources to their synthesis, as conversion of stored reserves into egg proteins results in greater isotopic fractionation, thereby yielding enriched isotopic signatures (particularly for δ¹⁵N that shows greater isotopic fractionation with respect to that commonly assumed for δ¹³C). We point to reabsorbed material derived from the hormonally‐mediated regression of the female reproductive system (which is likely the intrinsic mechanisms resulting in the intra‐clutch pattern of egg size variation: the hormonal hypothesis) as the most feasible endogenous source of nutrients for the synthesis of last‐laid eggs, as optimize reproductive investment and maximize female fitness.     

Nitrogen removal efficiencies in a free water surface constructed wetland in relation to plant coverage

Vegetation coverage is considered to be a key factor controlling nitrogen removal in wetlands. We describe the use of newly designed stainless steel incubation chambers to detect shifts in the in situ nitrate reduction activities associated to areas covered with common reed (Phragmites australis) and cattail (Typha latifolia) in the sediment of a free water surface constructed wetland (FWS-CW). Activities were measured at six different positions and times of the year and were related to physicochemical and hydraulic variables. Mean nitrate + nitrite reduction activities varied from 11.1 to 69.4 mg N/m²/h and showed a high variability within sediment types. Ammonification rates accounted for roughly 10% of the total nitrate reduction and were especially relevant in vegetated areas. Measured activities were highly above total nitrogen removal efficiencies estimated in the three parallel treatment cells of the Empuriabrava FWS-CW, indicating the potentiality of the system. In situ nitrate reduction activities correlated well with physichochemical characteristics such as pH and temperature. Additionally, differences in the total nitrogen removal efficiencies were detected between the three treatment cells and were related to changes in the water retention time. The plant species effect was detected in treatment cells of comparable hydraulic loads in which vegetation belts dominated by Typha latifolia were shown to have greater nitrogen removal efficiencies.     

Saturated fat intake and alcohol consumption modulate the association between the APOE polymorphism and risk of future coronary heart disease: a nested case-control study in the Spanish EPIC cohort

The association is still not clear between the common APOE polymorphism and coronary heart disease (CHD) risk, nor its modulation by diet. Thus, our aim was to study the association between the APOE genotypes and incident CHD and how dietary fat and alcohol consumption modify these effects. We performed a nested case-control study in the Spanish European Prospective Investigation into Cancer and Nutrition cohort. Healthy men and women (41?440, 30-69 years) were followed up over a 10-year period, with the incident CHD cases being identified. We analyzed 534 incident CHD cases and 1123 controls. APOE, dietary intake and plasma lipids were determined at baseline. The APOE polymorphism was significantly associated with low-density lipoprotein cholesterol (LDL-C), and gene-alcohol interactions in determining LDL-C were detected. In the whole population, the E2 allele was significantly associated with a lower CHD risk than E3/E3 subjects [odds ratio (OR), 0.58; 95% confidence interval (CI), 0.38-0.89]. The E4 allele did not reach statistical significance vs. E3/E3 (OR, 1.17; 95% CI, 0.88-1.58). However, saturated fat intake modified the effect of the APOE polymorphism in determining CHD risk. When saturated fat intake was low (<10% of energy), no statistically significant association between the APOE polymorphism and CHD risk was observed (P=.682). However, with higher intake (≥10%), the polymorphism was significant (P=.005), and the differences between E2 and E4 carriers were magnified (OR for E4 vs. E2, 3.33; 95% CI, 1.61-6.90). Alcohol consumption also modified the effect of the APOE on CHD risk.In conclusion, in this Mediterranean population, the E2 allele is associated with lower CHD risk, and this association is modulated by saturated fat and alcohol consumption.     

Integrating the intrinsic conformational preferences of noncoded α-amino acids modified at the peptide bond into the noncoded amino acids database

Recently, we reported a database (Noncoded Amino acids Database; http://recerca.upc.edu/imem/index.htm) that was built to compile information about the intrinsic conformational preferences of nonproteinogenic residues determined by quantum mechanical calculations, as well as bibliographic information about their synthesis, physical and spectroscopic characterization, the experimentally established conformational propensities, and applications (Revilla-López et al., J Phys Chem B 2010;114:7413-7422). The database initially contained the information available for α-tetrasubstituted α-amino acids. In this work, we extend NCAD to three families of compounds, which can be used to engineer peptides and proteins incorporating modifications at the--NHCO--peptide bond. Such families are: N-substituted α-amino acids, thio-α-amino acids, and diamines and diacids used to build retropeptides. The conformational preferences of these compounds have been analyzed and described based on the information captured in the database. In addition, we provide an example of the utility of the database and of the compounds it compiles in protein and peptide engineering. Specifically, the symmetry of a sequence engineered to stabilize the 3(10)-helix with respect to the α-helix has been broken without perturbing significantly the secondary structure through targeted replacements using the information contained in the database.     

A character‐based approach in the Mexican cycads supports diverse multigene combinations for DNA barcoding

A DNA barcoding study was conducted to determine the optimal combination of loci needed for successful species‐level molecular identification in three extant cycad genera—Ceratozamia, Dioon, and Zamia—that occur in Mexico. Based on conclusions of a previous multigene study in representative species of all genera in the Cycadales, we tested the DNA barcoding performance of seven chloroplast coding (matK, rpoB, rpoC1, and rbcL) and non‐coding (atpF/H, psbK/I, and trnH‐psbA) regions, plus sequences of the nuclear internal transcribed spacer. We analysed data under the assumptions of the “character attributes organization system” (CAOS), a character‐based approach in which species are identified through the presence of ‘DNA diagnostics’. In Ceratozamia, four chloroplast regions and one nuclear region were needed to achieve > 70% unique species identification. In contrast, the two‐gene combination atpF/H + psbK/I and the four‐gene combination atpF/H + psbK/I + rpoC1 + ITS2 were needed to reach 79% and 75% unique species identification in Dioon and Zamia, respectively. The combinations atpF/H + psbK/I and atpF/H + psbK/I + rpoC1 + ITS2 include loci previously considered by the international DNA barcoding community. However, none of the three combinations of potential DNA barcoding loci found to be optimal with a character‐based approach in the Mexican cycads coincides with the ‘core barcode’ of chloroplast markers (matK + rbcL) recently proposed for universal use in the plant kingdom.     

Effects of extreme habitat conditions on otolith morphology: a case study on extremophile live bearing fishes (Poecilia mexicana, P. sulphuraria)

Our study was designed to evaluate if, and to what extent, restrictive environmental conditions affect otolith morphology. As a model, we chose two extremophile livebearing fishes: (i) Poecilia mexicana, a widespread species in various Mexican freshwater habitats, with locally adapted populations thriving in habitats characterized by the presence of one (or both) of the natural stressors hydrogen sulphide and darkness, and (ii) the closely related Poecilia sulphuraria living in a highly sulphidic habitat (Baños del Azufre). All three otolith types (lapilli, sagittae, and asterisci) of P. mexicana showed a decrease in size ranging from the non-sulphidic cave habitat (Cueva Luna Azufre), to non-sulphidic surface habitats, to the sulphidic cave (Cueva del Azufre), to sulphidic surface habitats (El Azufre), to P. sulphuraria. Although we found a distinct differentiation between ecotypes with respect to their otolith morphology, no clear-cut pattern of trait evolution along the two ecological gradients was discernible. Otoliths from extremophiles captured in the wild revealed only slight similarities to aberrant otoliths found in captive-bred fish. We therefore hypothesize that extremophile fishes have developed coping mechanisms enabling them to avoid aberrant otolith growth – an otherwise common phenomenon in fishes reared under stressful conditions.     

Anti-inflammatory and cytotoxic activities of chichipegenin, peniocerol, and macdougallin isolated from Myrtillocactus geometrizans (Mart. ex Pfeiff.) Con

The oleanane-type triterpene chichipegenin and the sterols peniocerol and macdougallin, isolated from Myrtillocactus geometrizans, showed anti-inflammatory activities in both the 12-O-tetradecanoylphorbol-13-acetate (TPA)-induced mouse ear edema model and the carrageenan-induced rat paw edema model. All tested compounds inhibited the TPA-induced edema in a dose-dependent manner, with ED50 values less than or equal to that shown by indomethacin. Among them, peniocerol was the most active compound. However, only peniocerol and macdougallin reduced carrageenan-induced rat paw edema. On the other hand, peniocerol and macdougallin showed cytotoxicity against several human cancer cell lines. These results indicate that compounds isolated from M. geometrizans possess antiinflammatory and cytotoxic properties, and the presence of chichipegenin in the aerial parts could justify the medicinal uses attributed to the plant.     

Genetic evidence for multiple events of hybridization between wolves and domestic dogs in the Iberian Peninsula

Hybridization between wild species and their domestic counterparts may represent a major threat to natural populations. However, high genetic similarity between the hybridizing taxa makes the detection of hybrids a difficult task and may hinder attempts to assess the impact of hybridization in conservation biology. In this work, we used a combination of 42 autosomal microsatellites together with Y-chromosome microsatellite-defined haplotypes and mtDNA sequences to investigate the occurrence and dynamics of wolf-dog hybridization in the Iberian Peninsula. To do this, we applied a variety of Bayesian analyses and a parallel set of simulation studies to evaluate (i) the differences between Iberian wolves and dogs, (ii) the frequency and geographical distribution of hybridization and (iii) the directionality of hybridization. First, we show that Iberian wolves and dogs form two well-differentiated genetic entities, suggesting that introgressive hybridization is not a widespread phenomenon shaping both gene pools. Second, we found evidence for the existence of hybridization that is apparently restricted to more peripheral and recently expanded wolf populations. Third, we describe compelling evidence suggesting that the dynamics of hybridization in wolf populations is mediated by crosses between male dogs and female wolves. More importantly, the observation of a population showing the occurrence of a continuum of hybrid classes forming mixed packs may indicate that we have underestimated hybridization. If future studies confirm this pattern, then an intriguing avenue of research is to investigate how introgression from free-ranging domestic dogs is enabling wolf populations to adapt to the highly humanized habitats of southern Europe while still maintaining their genetic differentiation.     

Stable linkage disequilibrium owing to sexual antagonism

Linkage disequilibrium (LD) is an association between genetic loci that is typically transient. Here, we identify a previously overlooked cause of stable LD that may be pervasive: sexual antagonism. This form of selection produces unequal allele frequencies in males and females each generation, which upon admixture at fertilization give rise to an excess of haplotypes that couple male-beneficial with male-beneficial and female-beneficial with female-beneficial alleles. Under sexual antagonism, LD is obtained for all recombination frequencies in the absence of epistasis. The extent of LD is highest at low recombination and for stronger selection. We provide a partition of the total LD into distinct components and compare our result for sexual antagonism with Li and Nei''s model of LD owing to population subdivision. Given the frequent observation of sexually antagonistic selection in natural populations and the number of traits that are often involved, these results suggest a major contribution of sexual antagonism to genomic structure.