Microbial population genomes from the Amazon River reveal possible modulation of the organic matter degradation process in tropical freshwaters

Rivers connect the carbon cycle in land with that in aquatic ecosystems by transporting and transforming terrestrial organic matter (TeOM). The Amazon River receives huge loads of TeOM from the surrounding rainforest, promoting a substantial microbial heterotrophic activity and consequently, CO₂ outgassing. In the Amazon River, microbes degrade up to 55% of the lignin present in the TeOM. Yet, the main microbial genomes involved in TeOM degradation were unknown. Here, we characterize 51 population genomes (PGs) representing some of the most abundant microbes in the Amazon River deriving from 106 metagenomes. The 51 reconstructed PGs are among the most abundant microbes in the Amazon River, and 53% of them are not able to degrade TeOM. Among the PGs capable of degrading TeOM, 20% were exclusively cellulolytic, while the others could also oxidize lignin. The transport and consumption of lignin oxidation byproducts seemed to be decoupled from the oxidation process, being apparently performed by different groups of microorganisms. By connecting the genomic features of abundant microbes in the Amazon River with the degradation machinery of TeOM, we suggest that a complex microbial consortium could explain the quick turnover of TeOM previously observed in this ecosystem.     

Hybridization and pre-zygotic reproductive barriers in Plasmodium

Sexual reproduction is an obligate step in the life cycle of many parasites, including the causative agents of malaria (Plasmodium). Mixed-species infections are common in nature and consequently, interactions between heterospecific gametes occur. Given the importance of managing gene flow across parasite populations, remarkably little is understood about how reproductive isolation between species is maintained. We use the rodent malaria parasites P. berghei and P. yoelii to investigate the ecology of mixed-species mating groups, identify proteins involved in pre-zygotic barriers, and examine their evolution. Specifically, we show that (i) hybridization occurs, but at low frequency; (ii) hybridization reaches high levels when female gametes lack the surface proteins P230 or P48/45, demonstrating that these proteins are key for pre-zygotic reproductive isolation; (iii) asymmetric reproductive interference occurs, where the fertility of P. berghei gametes is reduced in the presence of P. yoelii and (iv) as expected for gamete recognition proteins, strong positive selection acts on a region of P230 and P47 (P48/45 paralogue). P230 and P48/45 are leading candidates for interventions to block malaria transmission. Our results suggest that depending on the viability of hybrids, applying such interventions to populations where mixed-species infections occur could either facilitate or hinder malaria control.     

Increased p wave dispersion in elite athletes

Background

Few studies have been performed on P wave indices in athletes. The aim of this study was to determine the behaviour of maximum P wave duration (Pmax), minimum P wave duration (Pmin) and P wave dispersion (PWD) in young high performance athletes, as well as the relationship of PWD with training history, heart rate (HR) and echocardiographic parameters.

Methods

We performed a cross-sectional observational study in 38 athletes of high performance in sports: water polo, distance running and weight lifting compared with 34 sedentary controls.

Results

The average age in both groups was 20.6 years. Note that PWD was increased in athletes (57 ± 14 ms vs. 40 ± 12 ms, p <0.001) while Pmin was significantly lower (57 ± 13 ms vs. 72 ± 13 ms, p <0.001), and there was no difference when comparing Pmax (114 ± 9 ms vs. 117 ± 14 ms, p> 0.05). The correlation between the duration of training (r = 0.511) and resting HR (r = 0.461) with PWD was significant (p <0.01).

Conclusions

PWD is increased in young athletes of high performance and was positively correlated with duration of training and baseline HR. The increase in PWD was secondary to a significant decrease in Pmin.     

Resolving the phylogenetic relationships and evolutionary history of the Drosophila virilis group using multilocus data

The Drosophila virilis group is one of the major lineages of Drosophila previously recognised and it has been used as a model for different types of studies. It comprises 13 species whose phylogenetic relationships are not well resolved. In the present study, six nuclear genes (Adh, fused, Gpdh, NonA, CG9631 and CG7219) and the mitochondrial ribosomal RNA genes (12S-16S) have been used to estimate the evolutionary tree of the group using different methods of phylogenetic reconstruction. Different competing evolutionary hypotheses have also been compared using the Approximately Unbiased test to further evaluate the robustness of the inferred trees. Results are, in general, consistent with previous studies in recovering the four major lineages of the group (D. virilis phylad, Drosophila montana subphylad, Drosophila kanekoi subphylad and Drosophila littoralis subphylad), although D. kanekoi, D. littoralis and Drosophila ezoana are here inferred to be more closely related to the D. virilis phylad than to the D. montana subphylad. The age of the crown group, estimated with a Bayesian method that assumes a relaxed molecular clock, is placed in the late Miocene (～ 10 Mya). The oldest lineages also appeared during this period (～ 7.5 to ～ 8.9 Mya), while the ages of the basal nodes of the montana subphylad and the virilis phylad are located in the early Pliocene (～ 4.9 and ～ 4.1 Mya). Major cladogenesis events correlate to geological and palaeoclimatic occurrences that most likely affected the freshwater and deciduous forests where these species are found. The inferred biogeographical history of the group, based on the statistical dispersal-vicariance analysis, indicates that the last common ancestor of the group had a Holarctic distribution from which the North American and the Eurasian lineages evolved as a result of a vicariant event.     

Effect of a native tree on seedling establishment of two exotic invasive species in a semiarid ecosystem

Theory predicts that in more stressful environments, positive plant-plant interactions should be more important than negative ones. For instance, in arid and semiarid regions, amelioration of soil drought produced by the shade of established plants could facilitate establishment of other species, in spite of light reduction. However, this theory has not been tested widely in the context of plant invasion. In this paper we evaluated the hypothesis that in a semiarid ecosystem of central Chile, the native tree, Lithrea caustica, should facilitate through positive shading effects, the seedling establishment of two widely planted and invasive forestry species, Pinus radiata and Eucalyptus globulus. We assessed the seedling establishment examining two processes: seedling recruitment (including germination) and subsequent seedling survival. We sowed seeds (to assess recruitment) and planted 8 months old seedlings (to assess seedling survival) of each exotic species under Lithrea patches, open sites and under an artificial shade mimicking Lithrea shading. The study was repeated in a north-facing and a south-facing slope in the study area located in a xeric zone within the distribution range of plantations of these species in central Chile. Our results show that in a north-facing slope Lithrea had positive effects on recruitment of both species, which was produced by shading. These effects were counteracted by negative effects on seedling survival but through a different mechanism, which suggests that Lithrea would have no significant effect on the whole seedling establishment process of Pinus radiata nor Eucalyptus globulus in this habitat. In turn, in a south-facing slope Lithrea had no significant effect on recruitment but had a negative effect on seedling survival, which was not produced by shading. This suggests that in this habitat Lithrea has a negative effect on the seedling establishment of these exotic species. Our results suggest that the effect of the native Lithrea caustica on the seedling establishment of these exotic species is dependent upon the life-cycle phase (recruitment or seedling survival) and habitat even within the same semiarid ecosystem. In contrast to the expected positive effects Lithrea is unlikely to facilitate seedling establishment of these exotic species in this area, and in fact in some habitats this effect could be negative. However, our results also suggest that a common mechanism proposed to resist invasion in forest ecosystems such as shading, probably is not sufficient to inhibit invasion in a semiarid region.     

Using shifts in amino acid frequency and substitution rate to identify latent structural characters in base-excision repair enzymes

Protein evolution includes the birth and death of structural motifs. For example, a zinc finger or a salt bridge may be present in some, but not all, members of a protein family. We propose that such transitions are manifest in sequence phylogenies as concerted shifts in substitution rates of amino acids that are neighbors in a representative structure. First, we identified rate shifts in a quartet from the Fpg/Nei family of base excision repair enzymes using a method developed by Xun Gu and coworkers. We found the shifts to be spatially correlated, more precisely, associated with a flexible loop involved in bacterial Fpg substrate specificity. Consistent with our result, sequences and structures provide convincing evidence that this loop plays a very different role in other family members. Second, then, we developed a method for identifying latent protein structural characters (LSC) given a set of homologous sequences based on Gu's method and proximity in a high-resolution structure. Third, we identified LSC and assigned states of LSC to clades within the Fpg/Nei family of base excision repair enzymes. We describe seven LSC; an accompanying Proteopedia page (http://proteopedia.org/wiki/index.php/Fpg_Nei_Protein_Family) describes these in greater detail and facilitates 3D viewing. The LSC we found provided a surprisingly complete picture of the interaction of the protein with the DNA capturing familiar examples, such as a Zn finger, as well as more subtle interactions. Their preponderance is consistent with an important role as phylogenetic characters. Phylogenetic inference based on LSC provided convincing evidence of independent losses of Zn fingers. Structural motifs may serve as important phylogenetic characters and modeling transitions involving structural motifs may provide a much deeper understanding of protein evolution.     

ARP2 a novel protein involved in apoptosis of LNCaP cells shares a high degree homology with splicing factor Prp8

The mechanism of apoptosis has been recognized as an important event in processes such as cellular development and homeostasis, as well as degenerative conditions like cancer. Prostate cancer during its advanced stages develops androgen independent cells that ultimately overgrow and promote metastatic events. Our group employing androgen independent LNCaP cells have previously proposed, based on electrophysiological findings, that apoptosis induced cells overexpress a cell death calcium channel-like molecule. Here we report the cloning and expression in Xenopus laevis oocytes of apoptosis regulated protein 2 (ARP2), a protein overexpressed in apoptosis induced LNCaP cells capable to induce calcium inward currents and apoptosis typical morphology changes in oocytes injected with arp2 mRNA. Our results also indicate that clone arp2 cDNA (1.3Kb) shares a 99% homology with a small fragment that corresponds to 18% of the complete sequence of Prp8 cDNA (7.0 Kb), a molecule that codifies for an important protein in the assembly of the spliceosome. We propose that protein ARP2 as a fragment of protein Prp8, corresponds to a molecule with a new function in apoptosis related phenomena. (Mol Cell Biochem 269: 189–201, 2005)     

Uterine and fetal asphyxia monitoring in parturient sows treated with oxytocin

Oxytocin is used to induce and control parturition, nevertheless, the increase of uterine contractions decreases blood flow and gaseous exchange through the womb predisposing to intra-partum mortality. The objective of the present study was to evaluate the effect of oxytocin on myometrial activity, fetal intrauterine hypoxia and postnatal asphyxia in sows during farrowing. Hybrid (n = 120) sows approaching the time of farrowing were randomly assigned in two groups of 60 animals each. Group I (G(1): control) was treated IM with saline solution and Group II (G(2)) was injected IM with oxytocin (1IU/6kg LW) as a single dose at birth of the first piglet. Both average number of myometrial contractions and intensity in G(2) were greater (P < 0.01) as compared with G(1). The mean of intra-partum stillbirths (IPS's) and those where fetal cardiac frequency (FCF) or heart beats, could not be detected after birth, were greater (P < 0.01) in G(2) as compared with G(1). The average decelerations of FCF known as dips II, which indicate severe hypoxia, was greater in G(2) (P < 0.01) as compared with that of G(1). There was a greater (P < 0.01) number of intra-partum stillbirths, stained with severe meconium in G(2) when compared with G(1). Oxytocin treatment increased (P < 0.01) the number of pigs born alive with ruptured umbilical cords and those with different grades of meconium staining on their skin. It was concluded that administration of oxytocin at the onset of parturition increased the myometrial activity, decreased fetal cardiac frequency, predisposed the rupture of umbilical cords and the degree of meconium staining, and increased intra-partum mortality.     

The 1.49 A resolution crystal structure of PsbQ from photosystem II of Spinacia oleracea reveals a PPII structure in the N-terminal region

We report the high-resolution structure of the spinach PsbQ protein, one of the main extrinsic proteins of higher plant photosystem II (PSII). The crystal structure shows that there are two well-defined regions in PsbQ, the C-terminal region (residues 46-149) folded as a four helix up-down bundle and the N-terminal region (residues 1-45) that is loosely packed. This structure provides, for the first time, insights into the crucial N-terminal region. First, two parallel beta-strands cross spatially, joining the beginning and the end of the N-terminal region of PsbQ. Secondly, the residues Pro9-Pro10-Pro11-Pro12 form a left-handed helix (or a polyproline type II (PPII) structure), which is stabilized by hydrogen bonds between the Pro peptide carbonyl groups and solvent water molecules. Thirdly, residues 14-33 are not visible in the electron density map, suggesting that this loop might be very flexible and presumably extended when PsbQ is free in solution. On the basis of the essential role of the N-terminal region of PsbQ in binding to PSII, we propose that both the PPII structure and the missing loop are key secondary structure elements in the recognition of specific protein-protein interactions between PsbQ and other oxygen-evolving complex extrinsic and/or intrinsic proteins of PSII. In addition, the PsbQ crystal coordinates two zinc ions, one of them is proposed to have a physiological role in higher plants, on the basis of the full conservation of the ligand protein residues in the sequence subfamily.