Increased transgenerational epigenetic variation,but not predictable epigenetic variants,after environmental exposure in two apomictic dandelion lineages

DNA methylation is one of the mechanisms underlying epigenetic modifications. DNA methylations can be environmentally induced and such induced modifications can at times be transmitted to successive generations. However, it remains speculative how common such environmentally induced transgenerational DNA methylation changes are and if they persist for more than one offspring generation. We exposed multiple accessions of two different apomictic dandelion lineages of the Taraxacum officinale group (Taraxacum alatum and T. hemicyclum) to drought and salicylic acid (SA) treatment. Using methylation‐sensitive amplified fragment length polymorphism markers (MS‐AFLPs) we screened anonymous methylation changes at CCGG restriction sites throughout the genome after stress treatments and assessed the heritability of induced changes for two subsequent unexposed offspring generations. Irrespective of the initial stress treatment, a clear buildup of heritable DNA methylation variation was observed across three generations, indicating a considerable background rate of heritable epimutations. Less evidence was detected for environmental effects. Drought stress showed some evidence for accession‐specific methylation changes, but only in the exposed generation and not in their offspring. By contrast, SA treatment caused an increased rate of methylation change in offspring of treated plants. These changes were seemingly undirected resulting in increased transgenerational epigenetic variation between offspring individuals, but not in predictable epigenetic variants. While the functional consequences of these MS‐AFLP‐detected DNA methylation changes remain to be demonstrated, our study shows that (1) stress‐induced transgenerational DNA methylation modification in dandelions is genotype and context‐specific; and (2) inherited environmental DNA methylation effects are mostly undirected and not targeted to specific loci.     

On the detection of environmental effects on complex matrices combining off-line liquid chromatography and 1H-NMR

An off-line combination of 400 MHz proton (1H)-NMR spectroscopy and liquid chromatography (LC) has been used for the multi-component comparison of low-molecular weight compounds (i.e., chemical fingerprinting) in model fluid broths and (processed) tomato. The focus of the research described is on (i) devising GLP-like methods for sample handling and NMR measurements that will ensure reproducibility, (ii) an automated handling of data, (iii) validity of the designed methodology and (iv) the interpretation of large amounts of data.     

Novel genetic tools for Hansenula polymorpha

Hansenula polymorpha is an important yeast in industrial biotechnology. In addition, it is extensively used in fundamental research devoted to unravel the principles of peroxisome biology and nitrate assimilation. Here we present an overview of key components of the genetic toolbox for H.?polymorpha. In addition, we present new selection markers that we recently implemented in H. polymorpha. We describe novel strategies for the efficient creation of targeted gene deletions and integrations in H.?polymorpha. For this, we generated a yku80 mutant, deficient in non-homologous end joining, resulting in strongly enhanced efficiency of gene targeting relative to the parental strain. Finally, we show the implementation of Gateway technology and a single-step PCR strategy to create deletions in H.?polymorpha.     

Evaluating the ecological realism of plant species distribution models with ecological indicator values

Species distribution models (SDMs) are routinely applied to assess current as well as future species distributions, for example to assess impacts of future environmental change on biodiversity or to underpin conservation planning. It has been repeatedly emphasized that SDMs should be evaluated based not only on their goodness of fit to the data, but also on the realism of the modeled ecological responses. However, possibilities for the latter are hampered by limited knowledge on the true responses as well as a lack of quantitative evaluation methods. Here we compared modeled niche optima obtained from European-scale SDMs of 1476 terrestrial vascular plant species with empirical ecological indicator values indicating the preferences of plant species for key environmental conditions. For each plant species we first fitted an ensemble SDM including three modeling techniques (GLM, GAM and BRT) and extracted niche optima for climate, soil, land use and nitrogen deposition variables with a large explanatory power for the occurrence of that species. We then compared these SDM-derived niche optima with the ecological indicator values by means of bivariate correlation analysis. We found weak to moderate correlations in the expected direction between the SDM-derived niche optima and ecological indicator values. The strongest correlation occurred between the modeled optima for growing degree days and the ecological indicator values for temperature. Correlations were weaker for SDM-derived niche optima with a more distal relationship to ecological indicator values (notably precipitation and soil moisture). Further, correlations were consistently highest for BRT, followed by GLM and GAM. Our method gives insight into the ecological realism of modeled niche optima and projected core habitats and can be used to improve SDMs by making a more informed selection of environmental variables and modeling techniques.     

Serotonin and dopamine protect from hypothermia/rewarming damage through the CBS/H2S pathway

Biogenic amines have been demonstrated to protect cells from apoptotic cell death. Herein we show for the first time that serotonin and dopamine increase H(2)S production by the endogenous enzyme cystathionine-β-synthase (CBS) and protect cells against hypothermia/rewarming induced reactive oxygen species (ROS) formation and apoptosis. Treatment with both compounds doubled CBS expression through mammalian target of rapamycin (mTOR) and increased H(2)S production in cultured rat smooth muscle cells. In addition, serotonin and dopamine treatment significantly reduced ROS formation. The beneficial effect of both compounds was minimized by inhibition of their re-uptake and by pharmacological inhibition of CBS or its down-regulation by siRNA. Exogenous administration of H(2)S and activation of CBS by Prydoxal 5'-phosphate also protected cells from hypothermic damage. Finally, serotonin and dopamine pretreatment of rat lung, kidney, liver and heart prior to 24 h of hypothermia at 3°C followed by 30 min of rewarming at 37°C upregulated the expression of CBS, strongly reduced caspase activity and maintained the physiological pH compared to untreated tissues. Thus, dopamine and serotonin protect cells against hypothermia/rewarming induced damage by increasing H(2)S production mediated through CBS. Our data identify a novel molecular link between biogenic amines and the H(2)S pathway, which may profoundly affect our understanding of the biological effects of monoamine neurotransmitters.     

Co‐expression of the protease furin in Nicotiana benthamiana leads to efficient processing of latent transforming growth factor‐β1 into a biologically active protein

Transforming growth factor beta (TGF‐β) is a signalling molecule that plays a key role in developmental and immunological processes in mammals. Three TGF‐β isoforms exist in humans, and each isoform has unique therapeutic potential. Plants offer a platform for the production of recombinant proteins, which is cheap and easy to scale up and has a low risk of contamination with human pathogens. TGF‐β3 has been produced in plants before using a chloroplast expression system. However, this strategy requires chemical refolding to obtain a biologically active protein. In this study, we investigated the possibility to transiently express active human TGF‐β1 in Nicotiana benthamiana plants. We successfully expressed mature TGF‐β1 in the absence of the latency‐associated peptide (LAP) using different strategies, but the obtained proteins were inactive. Upon expression of LAP‐TGF‐β1, we were able to show that processing of the latent complex by a furin‐like protease does not occur in planta. The use of a chitinase signal peptide enhanced the expression and secretion of LAP‐TGF‐β1, and co‐expression of human furin enabled the proteolytic processing of latent TGF‐β1. Engineering the plant post‐translational machinery by co‐expressing human furin also enhanced the accumulation of biologically active TGF‐β1. This engineering step is quite remarkable, as furin requires multiple processing steps and correct localization within the secretory pathway to become active. Our data demonstrate that plants can be a suitable platform for the production of complex proteins that rely on specific proteolytic processing.     

Timing of simulated aboveground herbivory influences population dynamics of root-feeding nematodes

Aims

A soil-plant-atmosphere continuum (SPAC) model for simulating tree transpiration (Ep) with variable water stress and water distribution in the soil is presented. The model couples a sun/shade approach for the canopy with a discrete representation of the soil in different layers and compartments.

Methods

To test its performance, the outputs from the simulations are compared to those from an experiment using trees of olive ‘Picual’ and almond ‘Marinada’ with the root system split into two. Trees are subjected to different irrigation phases in which one side of the root system is dried out while the other is kept wet.

Results

The model is able to accurately predict Ep (R² and the efficiency factor (EF) around 0.9) in the two species studied. The use of a function that modulates the uptake capacity of a root according to the soil water content was necessary to track the fluxes observed from each split part. It was also appropriate to account for root clumping to match the measured and modelled leaf water potential.

Conclusions

Coupling the sun/shade approach with the soil multi-compartment solution provides a useful tool to explore tree Ep for different degrees of water availability and distribution.

     

Short Term Depression Unmasks the Ghost Frequency

Short Term Plasticity (STP) has been shown to exist extensively in synapses throughout the brain. Its function is more or less clear in the sense that it alters the probability of synaptic transmission at short time scales. However, it is still unclear what effect STP has on the dynamics of neural networks. We show, using a novel dynamic STP model, that Short Term Depression (STD) can affect the phase of frequency coded input such that small networks can perform temporal signal summation and determination with high accuracy. We show that this property of STD can readily solve the problem of the ghost frequency, the perceived pitch of a harmonic complex in absence of the base frequency. Additionally, we demonstrate that this property can explain dynamics in larger networks. By means of two models, one of chopper neurons in the Ventral Cochlear Nucleus and one of a cortical microcircuit with inhibitory Martinotti neurons, it is shown that the dynamics in these microcircuits can reliably be reproduced using STP. Our model of STP gives important insights into the potential roles of STP in self-regulation of cortical activity and long-range afferent input in neuronal microcircuits.