Identification of novel stress-responsive biomarkers from gene expression datasets in tomato roots

Published by CSIRO Publishing. This is the Author Accepted Manuscript. This article may be used for personal use only.Abiotic stresses such as heat, drought or salinity have been widely studied individually. Nevertheless, in the nature and in the field, plants and crops are commonly exposed to a different combination of stresses, which often result in a synergistic response mediated by the activation of several molecular pathways that cannot be inferred from the response to each individual stress. By screening microarray data obtained from different plant species and under different stresses, we identified several conserved stress-responsive genes whose expression was differentially regulated in tomato (Solanum lycopersicum L.) roots in response to one or several stresses. We validated 10 of these genes as reliable biomarkers whose expression levels are related to different signalling pathways involved in adaptive stress responses. In addition, the genes identified in this work could be used as general salt-stress biomarkers to rapidly evaluate the response of salt-tolerant cultivars and wild species for which sufficient genetic information is not yet available

Guidelines to use tomato in experiments with a controlled environment

Domesticated tomato (Solanum lycopersicum) is the most important horticultural crop worldwide. Low polymorphism at the DNA level conflicts with the wealth of morphological variation. Fruits vary widely in size, shape, and color. In contrast, genetic variation between the 16 wild relatives is tremendous. Several large seed banks provide tomato germplasm for both domesticated and wild accessions of tomato. Recently, the genomes of the inbred cultivar “Heinz 1706” (≈900 Mb), and S. pimpinellifolium (739 Mb) were sequenced. Genomic markers and genome re-sequencing data are available for >150 cultivars and accessions. Transformation of tomato is relatively easy and T-DNA insertion line collections are available. Tomato is widely used as a model crop for fruit development but also for diverse physiological, cellular, biochemical, molecular, and genetic studies. It can be easily grown in greenhouses or growth chambers. Plants grow, flower, and develop fruits well at daily light lengths between 8 and 16 h. The required daily light integral of an experiment depends on growth stage and temperature investigated. Temperature must be 10–35°C, relative humidity 30–90%, and, CO2 concentration 200–1500 μmol mol−1. Temperature determines the speed of the phenological development while daily light integral and CO2 concentration affect photosynthesis and biomass production. Seed to seed cultivation takes 100 days at 20°C and can be shortened or delayed by temperature. Tomato may be cultivated in soil, substrates, or aeroponically without any substrate. Root volume, and water uptake requirements are primarily determined by transpiration demands of the plants. Many nutrient supply recipes and strategies are available to ensure sufficient supply as well as specific nutrient deficits/surplus. Using appropriate cultivation techniques makes tomato a convenient model plant for researchers, even for beginners

Cnemidophorus hyperythrus

Number of Pages: 6Integrative BiologyGeological Science

Using quantum theory to reduce the complexity of input-output processes

All natural things process and transform information. They receive environmental information as input, and transform it into appropriate output responses. Much of science is dedicated to building models of such systems -- algorithmic abstractions of their input-output behavior that allow us to simulate how such systems can behave in the future, conditioned on what has transpired in the past. Here, we show that classical models cannot avoid inefficiency -- storing past information that is unnecessary for correct future simulation. We construct quantum models that mitigate this waste, whenever it is physically possible to do so. This suggests that the complexity of general input-output processes depends fundamentally on what sort of information theory we use to describe them.Comment: 10 pages, 5 figure

Multidecadal warming of Antarctic waters

Decadal trends in the properties of seawater adjacent to Antarctica are poorly known, and the mechanisms responsible for such changes are uncertain. Antarctic ice sheet mass loss is largely driven by ice shelf basal melt, which is influenced by ocean-ice interactions and has been correlated with Antarctic Continental Shelf Bottom Water (ASBW) temperature. We document the spatial distribution of long-term large-scale trends in temperature, salinity, and core depth over the Antarctic continental shelf and slope. Warming at the seabed in the Bellingshausen and Amundsen seas is linked to increased heat content and to a shoaling of the mid-depth temperature maximum over the continental slope, allowing warmer, saltier water greater access to the shelf in recent years. Regions of ASBW warming are those exhibiting increased ice shelf melt

Orientation-sensitivity to facial features explains the Thatcher illusion

The Thatcher illusion provides a compelling example of the perceptual cost of face inversion. The Thatcher illusion is often thought to result from a disruption to the processing of spatial relations between face features. Here, we show the limitations of this account and instead demonstrate that the effect of inversion in the Thatcher illusion is better explained by a disruption to the processing of purely local facial features. Using a matching task, we found that participants were able to discriminate normal and Thatcherized versions of the same face when they were presented in an upright orientation, but not when the images were inverted. Next, we showed that the effect of inversion was also apparent when only the eye region or only the mouth region was visible. These results demonstrate that a key component of the Thatcher illusion is to be found in orientation-specific encoding of the expressive features (eyes and mouth) of the face

The muscarinic antagonists scopolamine and atropine are competitive antagonists at 5-HT3 receptors.

Scopolamine is a high affinity muscarinic antagonist that is used for the prevention of post-operative nausea and vomiting. 5-HT3 receptor antagonists are used for the same purpose and are structurally related to scopolamine. To examine whether 5-HT3 receptors are affected by scopolamine we examined the effects of this drug on the electrophysiological and ligand binding properties of 5-HT3A receptors expressed in Xenopus oocytes and HEK293 cells, respectively. 5-HT3 receptor-responses were reversibly inhibited by scopolamine with an IC50 of 2.09 μM. Competitive antagonism was shown by Schild plot (pA2 = 5.02) and by competition with the 5-HT3 receptor antagonists [(3)H]granisetron (Ki = 6.76 μM) and G-FL (Ki = 4.90 μM). The related molecule, atropine, similarly inhibited 5-HT evoked responses in oocytes with an IC50 of 1.74 μM, and competed with G-FL with a Ki of 7.94 μM. The reverse experiment revealed that granisetron also competitively bound to muscarinic receptors (Ki = 6.5 μM). In behavioural studies scopolamine is used to block muscarinic receptors and induce a cognitive deficit, and centrally administered concentrations can exceed the IC50 values found here. It is therefore possible that 5-HT3 receptors are also inhibited. Studies that utilise higher concentrations of scopolamine should be mindful of these potential off-target effects.Our thanks are given to John Peters (University of Dundee) for the 5-HT3A subunit. ML thanks the Swiss National Science Foundation for financial support (SNSF- professorship PP00P2_123536 and PP00P2_146321). AJT thanks the British Heart Foundation for financial support (PG/13/39/30293).This is final version of the article. It first appeared from Elsevier via http://dx.doi.org/10.1016/j.neuropharm.2016.04.02

The case for statins: Has it really been made?

Statin drugs are a modern success story. They are the medical treatment for coronary disease and the star of the pharmaceutical industry. Worldwide, sales of statins are running at about $19 billion a year and growing quickly.1 This success profits not only the pharmaceutical industry but also all those whose finances and careers are furthered by the research and the sales. But to what extent is it also a success for the general public? To answer this we will look at the major long-term (five to six year) clinical trials of statins. We start with the treatment offered to the participants, then look at the endpoints that were selected, and continue with a look at how the results have been reported. We conclude with a discussion of the costeffectiveness of statins for people at different levels of risk of coronary heart disease (CHD)

Quinine blocks 5-HT and 5-HT3 receptor mediated peristalsis in both guinea pig and mouse ileum tissue

Introduction. Quinine is commonly used to treat malaria; however one of the principal side effects is gastrointestinal disturbances (White, 1992). 5-HT3 receptors modulate gut peristalsis (Chetty et al., 2006), and, as quinine has been shown to act as a 5-HT3 receptor antagonist (Thompson and Lummis, 2008) it is possible that these side effects result from actions at gut 5-HT3 receptors. To address this question, we examined the ability of quinine to antagonise 5-HT and 5-HT3 mediated peristalsis in guinea pig and mouse ileum. Methods. Ileum was excised from male guinea pigs (200-300g) and C57BL/6 mice (25-35g) following cervical dislocation. Ileum segments (3-5 cm) were mounted in 50 ml organ baths containing Tryode’s solution at 35-37 °C. Concentration-response curves were constructed for 5-HT and the selective 5-HT3 agonist 2-Me-5-HT (non-cumulative doses). Quinine was pre-applied for 10 min and inhibition measured using agonist concentrations that elicited a submaximal response. Results. Concentration-dependent contractions produced by 5-HT (pEC50 = 5.45 ± 0.17, n = 8) and the selective 5-HT3 agonist 2-Me-5-HT (5.01 ± 0.17, n = 11) were not significantly different (Student’s t-test, t = 0.619, df = 17, p = 0.544) in guinea pig ileum. Increasing concentrations of quinine were able to antagonise the activities of both 5-HT (pIC50 = 5.03 ± 0.2, n = 6) and 2-Me-5HT (pIC50 = 4.59 ± 0.26, n = 4). At mouse ileum, 5-HT (pEC50 = 7.57 ± 0.33, n = 9) was more potent (Student’s t-test, t = 3.6, df = 12, p = 0.004) than 2-Me-5-HT (pEC50 = 5.45 ± 0.58, n = 5). Quinine antagonised both the 5-HT (pIC50 = 4.87 ± 0.31, n = 7) and 2-Me-5-HT-induced (pIC50 = 6.18 ± 1.14, n = 4) contractions. Conclusions. These results support previous electrophysiological studies that identified quinine as an antagonist at recombinant 5-HT3 receptors with IC50 values comparable with those reported here (pIC50 = 4.87, Thompson et al., 2007). Further, we found that quinine completely blocked 5-HT induced contractions in mouse and guinea pig, raising the possibility that quinine targets other 5-HT receptors in the gut (e.g., 5-HT4 receptors) and may influence intestinal function