The Ca2+ permeability of sarcoplasmic reticulum vesicles I. Ca2+ outflow in the non-energized state of the calcium pump

Passive Ca²⁺ permeability of sarcoplasmic reticulum vesicles has been studied after maximal loading with Ca²⁺ (150–200 nmol/mg protein) in the presence of Ca²⁺, MgATP and an ATP generating system of limited capacity. Outflow of accumulated Ca²⁺ in the non-energized state of the system was studied by depletion of the medium of one of the substrates, either MgATP (by complete consumption) or Ca²⁺ (by complexation with EGTA). It was found that Ca²⁺ outflow under these conditions is relatively slow and independent of the medium concentration of Ca²⁺ (5·10^?9–5·10^?5 M) or MgATP (0.7–730 μM). Outflow curves were steep at the beginning of the outflow phase (30–60 nmol/min per mg protein), and outflow proceeded at a much lower rate below 100 nmol Ca²⁺/mg protein. Outflow could be completely inhibited by La³⁺. The Ca²⁺ release curves are not compatible with simple diffusion, and cannot be accounted for by Ca²⁺ binding inside the vesicles. Neither are our observations consistent with permeation mediated via the Ca²⁺ translocation sites involved in active transport. We suggest that non-energized Ca²⁺ outflow may proceed by a process of ion-exchange through negatively charged, water-filled channels in the membrane, the properties of which are altered by a high intravesicular concentration of Ca²⁺.     

The transition to self-compatibility in Arabidopsis thaliana and evolution within S-haplotypes over 10 Myr

A recent investigation found evidence that the transition of Arabidopsis thaliana from ancestral self-incompatibility (SI) to full self-compatibility occurred very recently and suggested that this occurred through a selective fixation of a nonfunctional allele (PsiSCR1) at the SCR gene, which determines pollen specificity in the incompatibility response. The main evidence is the lack of polymorphism at the SCR locus in A. thaliana. However, the nearby SRK gene, which determines stigma specificity in self-incompatible Brassicaceae species, has extremely high sequence diversity, with 3 very divergent SRK haplotypes, 2 of them present in multiple strains. Such high diversity is extremely unusual in this species, and it suggests the possibility that multiple, different SRK haplotypes may have been preserved from A. thaliana's self-incompatible ancestor. To study the evolution of S-haplotypes in the A. thaliana lineage, we searched the 2 most closely related Arabidopsis species Arabidopsis lyrata and Arabidopsis halleri, in which most populations have retained SI, and found SRK sequences corresponding to all 3 A. thaliana haplogroup sequences. Our molecular evolutionary analyses of these 3 S-haplotypes provide an independent estimate of the timing of the breakdown of SI and again exclude an ancient transition to selfing in A. thaliana. Comparing sequences of each of the 3 haplogroups between species, we find that 2 of the 3 SRK sequences (haplogroups A and B) are similar throughout their length, suggesting that little or no recombination with other SRK alleles has occurred since these species diverged. The diversity difference between the SCR and SRK loci in A. thaliana, however, suggests crossing-over, either within SRK or between the SCR and SRK loci. If the loss of SI involved fixation of the PsiSCR1 sequence, the exchange must have occurred during its fixation. Divergence between the species is much lower at the S-locus, compared with reference loci, and we discuss two contributory possibilities. Introgression may have occurred between A. lyrata and A. halleri and between their ancestral lineage and A. thaliana, at least for some period after their split. In addition, the coalescence times of sequences of individual S-haplogroups are expected to be less than those of alleles at non-S-loci.     

Modulation of i-motif thermodynamic stability by the introduction of UNA (unlocked nucleic acid) monomers

The influence of acyclic RNA derivatives, UNA (unlocked nucleic acid) monomers, on i-DNA thermodynamic stability has been investigated. The 22 nt human telomeric fragment was chosen as the model sequence for stability studies. UNA monomers modulate i-motif stability in a position-depending manner. The largest destabilization is observed for position C14, while UNA placed in position A12 causes significant increase of i-DNA thermodynamic stability. CD curves of UNA-modified variants imply no structural changes relative to the native i-motif.     

AllelicImbalance: an R/ bioconductor package for detecting,managing, and visualizing allele expression imbalance data from RNA sequencing

Background

One aspect in which RNA sequencing is more valuable than microarray-based methods is the ability to examine the allelic imbalance of the expression of a gene. This process is often a complex task that entails quality control, alignment, and the counting of reads over heterozygous single-nucleotide polymorphisms. Allelic imbalance analysis is subject to technical biases, due to differences in the sequences of the measured alleles. Flexible bioinformatics tools are needed to ease the workflow while retaining as much RNA sequencing information as possible throughout the analysis to detect and address the possible biases.

Results

We present AllelicImblance, a software program that is designed to detect, manage, and visualize allelic imbalances comprehensively. The purpose of this software is to allow users to pose genetic questions in any RNA sequencing experiment quickly, enhancing the general utility of RNA sequencing. The visualization features can reveal notable, non-trivial allelic imbalance behavior over specific regions, such as exons.

Conclusions

The software provides a complete framework to perform allelic imbalance analyses of aligned RNA sequencing data, from detection to visualization, within the robust and versatile management class, ASEset.

Electronic supplementary material

The online version of this article (doi:10.1186/s12859-015-0620-2) contains supplementary material, which is available to authorized users.     

Specific Activation of the Plant P-type Plasma Membrane H+-ATPase by Lysophospholipids Depends on the Autoinhibitory N- and C-terminal Domains

Eukaryotic P-type plasma membrane H⁺-ATPases are primary active transport systems that are regulated at the post-translation level by cis-acting autoinhibitory domains, which can be relieved by protein kinase-mediated phosphorylation or binding of specific lipid species. Here we show that lysophospholipids specifically activate a plant plasma membrane H⁺-ATPase (Arabidopsis thaliana AHA2) by a mechanism that involves both cytoplasmic terminal domains of AHA2, whereas they have no effect on the fungal counterpart (Saccharomyces cerevisiae Pma1p). The activation was dependent on the glycerol backbone of the lysophospholipid and increased with acyl chain length, whereas the headgroup had little effect on activation. Activation of the plant pump by lysophospholipids did not involve the penultimate residue, Thr-947, which is known to be phosphorylated as part of a binding site for activating 14-3-3 protein, but was critically dependent on a single autoinhibitory residue (Leu-919) upstream of the C-terminal cytoplasmic domain in AHA2. A corresponding residue is absent in the fungal counterpart. These data indicate that plant plasma membrane H⁺-ATPases evolved as specific receptors for lysophospholipids and support the hypothesis that lysophospholipids are important plant signaling molecules.     

Getting the measure of eutrophication in the Baltic Sea: towards improved assessment principles and methods

The eutrophication status of the entire Baltic Sea is classified using a multi-metric indicator-based assessment tool. A total of 189 areas are assessed using indicators where information on reference conditions (RefCon), and acceptable deviation (AcDev) from reference condition could be combined with national monitoring data from the period 2001?C2006. Most areas (176) are classified as ??affected by eutrophication?? and only two open water areas and 11 coastal areas are classified as ??unaffected by eutrophication??. The classification is made by application of the recently developed HELCOM Eutrophication Assessment Tool (HEAT), which is described in this paper. The use of harmonized assessment principles and the HEAT tool allows for direct comparisons between different parts of the Baltic Sea despite variations in monitoring activities. The impaired status of 176 areas is directly related to nutrient enrichment and elevated loads from upstream catchments. Baltic Sea States have implemented nutrient management strategies since years which have reduced nutrient inputs. However, eutrophication is still a major problem for large parts of the Baltic Sea. The 2007 Baltic Sea Action Plan is projected to further reduce nutrient inputs aiming for a Baltic Sea unaffected by eutrophication by 2021.     

Water loss in insects: an environmental change perspective

In the context of global environmental change much of the focus has been on changing temperatures. However, patterns of rainfall and water availability have also been changing and are expected to continue doing so. In consequence, understanding the responses of insects to water availability is important, especially because it has a pronounced influence on insect activity, distribution patterns, and species richness. Here we therefore provide a critical review of key questions that either are being or need to be addressed in this field. First, an overview of insect behavioural responses to changing humidity conditions and the mechanisms underlying sensing of humidity variation is provided. The primary sensors in insects belong to the temperature receptor protein superfamily of cation channels. Temperature-activated transient receptor potential ion channels, or thermoTRPs, respond to a diverse range of stimuli and may be a primary integrator of sensory information, such as environmental temperature and moisture. Next we touch briefly on the components of water loss, drawing attention to a new, universal model of the water costs of gas exchange and its implications for responses to a warming, and in places drying, world. We also provide an overview of new understanding of the role of the sub-elytral chamber for water conservation, and developments in understanding of the role of cuticular hydrocarbons in preventing water loss. Because of an increasing focus on the molecular basis of responses to dehydration stress we touch briefly on this area, drawing attention to the role of sugars, heat shock proteins, aquaporins, and LEA proteins. Next we consider phenotypic plasticity or acclimation responses in insect water balance after initial exposures to altered humidity, temperature or nutrition. Although beneficial acclimation has been demonstrated in several instances, this is not always the case. Laboratory studies show that responses to selection for enhanced ability to survive water stress do evolve and that genetic variation for traits underlying such responses does exist in many species. However, in others, especially tropical, typically narrowly distributed species, this appears not to be the case. Using the above information we then demonstrate that habitat alteration, climate change, biological invasions, pollution and overexploitation are likely to be having considerable effects on insect populations mediated through physiological responses (or the lack thereof) to water stress, and that these effects may often be non-intuitive.