Acclimation responses to short‐term temperature treatments during early life stages causes long lasting changes in spontaneous activity of adult Drosophila melanogaster

Ecotherms adjust their physiology to environmental temperatures. Long‐term exposures to heat or cold typically induce acclimation responses that generate directional, but reversible shifts in thermal tolerance and performance. However, less is known about how short exposure in different life stages will affect the adult phenotype. In the present study, we compared the effects of long‐term temperature exposure to 15, 19 and 31 °C with that of brief (16 h) exposure periods at the same temperatures in Drosophila melanogaster eggs, larvae, pupae, or adults, respectively. The acclimation responses are evaluated using activity measurements at 11, 15, 19, 27, 31 and 33 °C and by measuring upper and lower thermal limits (CT_max and CT_min) in 5‐day‐old adult males. As expected, long‐term cold exposure reduces relative CT_min, whereas long‐term heat exposure increases relative CT_max. By contrast, we find little effect on thermal limits when using short‐term exposures at different life stages. Long‐term exposures to 31 and 15 °C both suppressed activity relative to the 19 °C control, suggesting that development at high and low temperatures may lead to reduced activity later in life. Short‐term cold exposure early in development reduces activity in the adult stage, whereas the effects of short‐term heat exposure on behaviour are dependent on life stage and test temperature. Together, our results highlight how the thermal sensitivity of the trait measured determines the ability to detect acclimation responses.     

Retention of the Native Epigenome in Purified Mammalian Chromatin

A protocol is presented for the isolation of native mammalian chromatin as fibers of 25–250 nucleosomes under conditions that preserve the natural epigenetic signature. The material is composed almost exclusively of histones and DNA and conforms to the structure expected by electron microscopy. All sequences probed for were retained, indicating that the material is representative of the majority of the genome. DNA methylation marks and histone marks resembled the patterns observed in vivo. Importantly, nucleosome positions also remained largely unchanged, except on CpG islands, where nucleosomes were found to be unstable. The technical challenges of reconstituting biochemical reactions with native mammalian chromatin are discussed.     

Postglacial migration supplements climate in determining plant species ranges in Europe

The influence of dispersal limitation on species ranges remains controversial. Considering the dramatic impacts of the last glaciation in Europe, species might not have tracked climate changes through time and, as a consequence, their present-day ranges might be in disequilibrium with current climate. For 1016 European plant species, we assessed the relative importance of current climate and limited postglacial migration in determining species ranges using regression modelling and explanatory variables representing climate, and a novel species-specific hind-casting-based measure of accessibility to postglacial colonization. Climate was important for all species, while postglacial colonization also constrained the ranges of more than 50 per cent of the species. On average, climate explained five times more variation in species ranges than accessibility, but accessibility was the strongest determinant for one-sixth of the species. Accessibility was particularly important for species with limited long-distance dispersal ability, with southern glacial ranges, seed plants compared with ferns, and small-range species in southern Europe. In addition, accessibility explained one-third of the variation in species' disequilibrium with climate as measured by the realized/potential range size ratio computed with niche modelling. In conclusion, we show that although climate is the dominant broad-scale determinant of European plant species ranges, constrained dispersal plays an important supplementary role.     

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.     

Photoligation of self-assembled DNA constructs containing anthracene-functionalized 2'-amino-LNA monomers

Efficient synthesis of a novel anthracene-functionalized 2′-amino-LNA phosphoramidite derivative is described together with its incorporation into oligodeoxynucleotides. Two DNA strands with the novel 2′-N-anthracenylmethyl-2′-amino-LNA monomers can be effectively cross-linked by photoligation at 366 nm in various types of DNA constructs. Successful application of three differently functionalized 2′-amino-LNA monomers in self-assembled higher ordered structures for simultaneous cross-linking and monitoring of assembly formation is furthermore demonstrated.     

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.     

COX-1 dependent biosynthesis of 15-hydroxyeicosatetraenoic acid in human mast cells

15-hydroxyeicosatetraenoic acid (15-HETE) is an arachidonic acid derived lipid mediator which can originate both from 15-lipoxygenase (15-LOX) activity and cyclooxygenase (COX) activity. The enzymatic source determines the enantiomeric profile of the 15-HETE formed. 15-HETE is the most abundant arachidonic acid metabolite in the human lung and has been suggested to influence the pathophysiology of asthma. Mast cells are central effectors in asthma, but there are contradictory reports on whether 15-HETE originates from 15-LOX or COX in human mast cells. This prompted the current study where the pathway of 15-HETE biosynthesis was examined in three human mast cell models; the cell line LAD2, cord blood derived mast cells (CBMC) and tissue isolated human lung mast cells (HLMC). Levels and enantiomeric profiles of 15-HETE and levels of the downstream metabolite 15-KETE, were analyzed by UPLC-MS/MS after stimulation with anti-IgE or calcium ionophore A23187 in the presence and absence of inhibitors of COX isoenzymes. We found that 15-HETE was produced by COX-1 in human mast cells under these experimental conditions. Unexpectedly, chiral analysis showed that the 15(R) isomer was predominant and gradually accumulated, whereas the 15(S) isomer was metabolized by the 15-hydroxyprostaglandin dehydrogenase. We conclude that during physiological conditions, i.e., without addition of exogenous arachidonic acid, both enantiomers of 15-HETE are produced by COX-1 in human mast cells but that the 15(S) isomer is selectively depleted by undergoing further metabolism. The study highlights that 15-HETE cannot be used as an indicator of 15-LOX activity for cellular studies, unless chirality and sensitivity to pharmacologic inhibition is determined.