Post alignment clustering procedure for comparative quantitative proteomics LC-MS data

Comparative LC-MS is a powerful method for detailed quantitative comparison of complex protein mixtures. Dedicated software is required for detection, matching, and alignment of peaks in multiple LC-MS datasets. However, retention time shifts, saturation effects, limitations of experimental accuracy, and possible occurrence of split peaks make it difficult for software to perfectly match all chromatograms. We describe a procedure to assess the above problems and show that dataset quality can be enhanced with the aid of cluster analysis.     

Absence of carbon transfer between Medicago truncatula plants linked by a mycorrhizal network, demonstrated in an experimental microcosm

Carbon transfer between plants via a common extraradical network of arbuscular mycorrhizal (AM) fungal hyphae has been investigated abundantly, but the results remain equivocal. We studied the transfer of carbon through this fungal network, from a Medicago truncatula donor plant to a receiver (1) M. truncatula plant growing under decreased light conditions and (2) M. truncatula seedling. Autotrophic plants were grown in bicompartmented Petri plates, with their root systems physically separated, but linked by the extraradical network of Glomus intraradices. A control Myc-/Nod- M. truncatula plant was inserted in the same compartment as the receiver plant. Following labeling of the donor plant with 13CO2, 13C was recovered in the donor plant shoots and roots, in the extraradical mycelium and in the receiver plant roots. Fatty acid analysis of the receiver's roots further demonstrated 13C enrichment in the fungal-specific lipids, while almost no label was detected in the plant-specific compounds. We conclude that carbon was transferred from the donor to the receiver plant via the AM fungal network, but that the transferred carbon remained within the intraradical AM fungal structures of the receiver's root and was not transferred to the receiver's plant tissues.     

Effects of isoflurane on measurements of delayed lumininescence in Acetabularia acetabulum.

The volatile halogenated methyl ethyl ether, isoflurane, used as an anaesthetic, inhibits actin-based dynamics directly or indirectly in animal cells. In plant cells, most intracellular movements are related to actin pathways. We have used isoflurane in a unicellular alga, Acetabularia acetabulum, to test the dynamics of choloroplast organization. By measuring the delayed luminescence, we found that isoflurane worked efficiently in the unicellular organism and showed dose- and time-course-dependent actin-inhibition patterns. When A. acetabulum was treated with saturated solutions of isoflurane in artificial seawater (defined as 100% isoflurane) for 3 or 6 min, the delayed luminescence (DL) was decreased and was never recovered. In contrast, if treated with 75% diluted isoflurane, the DL was firstly inhibited and then recovered several hours later, and if treated with 50% diluted isoflurane, the change of DL was small. Our work proved that isoflurane can affect actin-related pathways in both animals and plants.     

Interrelations Among Habitat Use, Behavior, and Flight-Related Morphology in Two Cooccurring Satyrine Butterflies, Maniola jurtina and Pyronia tithonus

Mobility, activity patterns, habitat use, and some morphological traits of two often cooccurring satyrine butterflies of grasslands—the meadow brown (Maniola jurtina) and the hedge brown (Pyronia tithonus)—were studied by a mark-release-recapture method at two sites. Additionally, someflight-related morphological traits of a series of collected females of P. tithonus were compared between recently colonized and permanent populations. The more active, but less mobile P. tithonus got faster wing damage than did M. jurtina and had more, and more symmetrically spread eyespots onthe wings. For both species, the microdistribution was affected by shelter, long vegetation, and nectar, but this was more pronounced in P. tithonus. It is hypothesized that P. tithonus may traverse the same landscape at a slower rate than M. jurtina.     

Aphid populations showing differential levels of virulence on Capsicum accessions

The green peach aphid,Myzus persicae,is one of the most threatening pests in pepper cultivation and growers would benefit from resistant varietices.Previously,we identified two Capsicum acessions as susceptible and three as resistant to M.persicae using an aphid population originating from the Netherlands(NL).Later on we identified an aphid population originating from a diferent gcographical region(Switserland,SW)that was virulent on all tested Capsicum acessions.The objeetive of the current work is to describe in detail diferent aspects of the interaction between two aphid populations and two sclected Capsicum acessions(one that was susceptible[PB2013046]and one that was resistant[PB2013071]to population NL),including biochemical processes involved.Electrical penetration graph(EPG)recordings showed similar feeding activities for both aphid populations on PB2013046.On acession PB2013071 the aphid population sw was able to devote significantly more time to phloem ingestion than population NL.We also studied plant defense response and found that plants of acession PB2013046 could not induce an accumulation of reactive oxygen species and callose formation after infestation with either aphid population.However,plants of PB2013071 induced a stronger defense response after infestation by population NL than after infestation by population SW.Based on these results,population SW of M.persicae seems to have overcome the resistance of PB2013071 that prevented feeding of aphids from NL population.The potential mechanism by which SW population overcomes the resistance is discussed.     

Transcranial direct current stimulation of cerebellum alters spiking precision in cerebellar cortex: A modeling study of cellular responses

Transcranial direct current stimulation (tDCS) of the cerebellum has rapidly raised interest but the effects of tDCS on cerebellar neurons remain unclear. Assessing the cellular response to tDCS is challenging because of the uneven, highly stratified cytoarchitecture of the cerebellum, within which cellular morphologies, physiological properties, and function vary largely across several types of neurons. In this study, we combine MRI-based segmentation of the cerebellum and a finite element model of the tDCS-induced electric field (EF) inside the cerebellum to determine the field imposed on the cerebellar neurons throughout the region. We then pair the EF with multicompartment models of the Purkinje cell (PC), deep cerebellar neuron (DCN), and granule cell (GrC) and quantify the acute response of these neurons under various orientations, physiological conditions, and sequences of presynaptic stimuli. We show that cerebellar tDCS significantly modulates the postsynaptic spiking precision of the PC, which is expressed as a change in the spike count and timing in response to presynaptic stimuli. tDCS has modest effects, instead, on the PC tonic firing at rest and on the postsynaptic activity of DCN and GrC. In Purkinje cells, anodal tDCS shortens the repolarization phase following complex spikes (-14.7 ± 6.5% of baseline value, mean ± S.D.; max: -22.7%) and promotes burstiness with longer bursts compared to resting conditions. Cathodal tDCS, instead, promotes irregular spiking by enhancing somatic excitability and significantly prolongs the repolarization after complex spikes compared to baseline (+37.0 ± 28.9%, mean ± S.D.; max: +84.3%). tDCS-induced changes to the repolarization phase and firing pattern exceed 10% of the baseline values in Purkinje cells covering up to 20% of the cerebellar cortex, with the effects being distributed along the EF direction and concentrated in the area under the electrode over the cerebellum. Altogether, the acute effects of tDCS on cerebellum mainly focus on Purkinje cells and modulate the precision of the response to synaptic stimuli, thus having the largest impact when the cerebellar cortex is active. Since the spatiotemporal precision of the PC spiking is critical to learning and coordination, our results suggest cerebellar tDCS as a viable therapeutic option for disorders involving cerebellar hyperactivity such as ataxia.     

Partial preferential chromosome pairing is genotype dependent in tetraploid rose

It has long been recognised that polyploid species do not always neatly fall into the categories of auto‐ or allopolyploid, leading to the term ‘segmental allopolyploid’ to describe everything in between. The meiotic behaviour of such intermediate species is not fully understood, nor is there consensus as to how to model their inheritance patterns. In this study we used a tetraploid cut rose (Rosa hybrida) population, genotyped using the 68K WagRhSNP array, to construct an ultra‐high‐density linkage map of all homologous chromosomes using methods previously developed for autotetraploids. Using the predicted bivalent configurations in this population we quantified differences in pairing behaviour among and along homologous chromosomes, leading us to correct our estimates of recombination frequency to account for this behaviour. This resulted in the re‐mapping of 25 695 SNP markers across all homologues of the seven rose chromosomes, tailored to the pairing behaviour of each chromosome in each parent. We confirmed the inferred differences in pairing behaviour among chromosomes by examining repulsion‐phase linkage estimates, which also carry information about preferential pairing and recombination. Currently, the closest sequenced relative to rose is Fragaria vesca. Aligning the integrated ultra‐dense rose map with the strawberry genome sequence provided a detailed picture of the synteny, confirming overall co‐linearity but also revealing new genomic rearrangements. Our results suggest that pairing affinities may vary along chromosome arms, which broadens our current understanding of segmental allopolyploidy.