BackgroundThe Firmicutes often possess three conspicuous genome features: marked Purine Asymmetry (PAS) across two strands of replication, Strand-biased Gene Distribution (SGD) and presence of two isoforms of DNA polymerase III alpha subunit, PolC and DnaE. Despite considerable research efforts, it is not clear whether the co-existence of PAS, PolC and/or SGD is an essential and exclusive characteristic of the Firmicutes. The nature of correlations, if any, between these three features within and beyond the lineages of Firmicutes has also remained elusive. The present study has been designed to address these issues.ResultsA large-scale analysis of diverse bacterial genomes indicates that PAS, PolC and SGD are neither essential nor exclusive features of the Firmicutes. PolC prevails in four bacterial phyla: Firmicutes, Fusobacteria, Tenericutes and Thermotogae, while PAS occurs only in subsets of Firmicutes, Fusobacteria and Tenericutes. There are five major compositional trends in Firmicutes: (I) an explicit PAS or G + A-dominance along the entire leading strand (II) only G-dominance in the leading strand, (III) alternate stretches of purine-rich and pyrimidine-rich sequences, (IV) G + T dominance along the leading strand, and (V) no identifiable patterns in base usage. Presence of strong SGD has been observed not only in genomes having PAS, but also in genomes with G-dominance along their leading strands – an observation that defies the notion of co-occurrence of PAS and SGD in Firmicutes. The PolC-containing non-Firmicutes organisms often have alternate stretches of R-dominant and Y-dominant sequences along their genomes and most of them show relatively weak, but significant SGD. Firmicutes having G + A-dominance or G-dominance along LeS usually show distinct base usage patterns in three codon sites of genes. Probable molecular mechanisms that might have incurred such usage patterns have been proposed.ConclusionCo-occurrence of PAS, strong SGD and PolC should not be regarded as a genome signature of the Firmicutes. Presence of PAS in a species may warrant PolC and strong SGD, but PolC and/or SGD not necessarily implies PAS.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-430) contains supplementary material, which is available to authorized users.

Comparative analyses of codon/amino acid usage in Leishmania major, Trypanosoma brucei and Trypanosoma cruzi reveal that gene expressivity and GC-bias play key roles in shaping the gene composition of all three parasites, and protein composition of L. major only. In T. brucei and T. cruzi, the major contributors to the variation in protein composition are hydropathy and/or aromaticity. Principle of Cost Minimization is followed by T. brucei, disregarded by T. cruzi and opposed by L. major. Slowly evolving highly expressed gene-products of L. major bear signatures of relatively AT-rich ancestor, while faster evolution under GC-bias has characterized the lowly expressed genes of the species by higher GC 12 -content.

In the transition to a society based on renewable energy, flexibility is important in balancing the energy supply as more intermittent sources like wind and solar are included in the energy mix. The storage-based hydropower systems are a renewable energy source that provides the needed flexibility since a hydropower plant can be started and stopped in minutes, and the reservoirs provide stored energy that can be utilized when the demand arises. Thereby, the hydropower plants can balance the variability in other energy sources, e.g., when there is no wind or when solar input is low. This need for increased flexibility has led research toward new hydropower turbines to provide larger ramping rates, more frequent starts and stops, and other system services. A possible drawback of the ramping operation of hydropower plants (often termed “hydropeaking”) are the adverse effects on the environment in receiving water bodies downstream of the power plant outlet, particularly when the hydropower outlets are in rivers. Rapid changes in flow can lead to stranding of fish and other biota during the shutdown of turbines and flushing of biota during the start of turbines. These effects can also be caused by other sudden episodes of water withdrawal, such as during accidental turbine shutdowns. The main objective of this study is to describe a method of designing the necessary volume of water required to mitigate a fast ramping turbine, and present the effect this has on the downstream river reach. We used a 2D hydraulic model to find the areas affected by hydropeaking operation and, furthermore, to define areas with a faster ramping rate than 13 cm/h which is used as a limit in Norwegian guidelines. Based on this, we developed a ramping regime that would prevent fast dewatering of critical areas and provide this as a basis for mitigating the effects of fast dewatering in the downstream river (River Nidelva in Norway was used as a test case). Furthermore, the effect of increasing the frequency of start–stop cycles was studied, and the proposed mitigation was evaluated for the new operational regime.

A strong purine asymmetry, along with strand-biased gene distribution and the presence of PolC, prevails in Bacillus and some other members of Firmicutes, Fusobacteria and Tenericutes. The analysis of protein features in 21 Bacillus species of diverse metabolic, virulence and ecological traits revealed that purine asymmetry in conjunction with lineage/niche specific constraints significantly influences protein evolution in Bacillus. All Bacillus species, except for Se-respiring Bacillus selenitireducens, display distinct strand-specific biases in amino acid usage, which may affect the isoelectric point or surface charge distribution of proteins with prevalence of acidic and basic residues in the leading and lagging strand proteins, respectively.

No abstract