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High-resolution yeast phenomics resolves different physiological features in the saline response.

ABSTRACT: We present a methodology for gene functional prediction based on extraction of physiologically relevant growth variables from all viable haploid yeast knockout mutants. This quantitative phenomics approach, here applied to saline cultivation, identified marginal but functionally important phenotypes and allowed the precise determination of time to adapt to an environmental challenge, rate of growth, and efficiency of growth. We identified approximately 500 salt-sensitive gene deletions, the majority of which were previously uncharacterized and displayed salt sensitivity for only one of the three physiological features. We also report a high correlation to protein-protein interaction data; in particular, several salt-sensitive subcellular networks indicating functional modules were revealed. In contrast, no correlation was found between gene dispensability and gene expression. It is proposed that high-resolution phenomics will be instrumental in systemwide descriptions of intragenomic functional networks.

SUBMITTER: Warringer J

PROVIDER: S-EPMC307635 | biostudies-literature | 2003 Dec

REPOSITORIES: biostudies-literature

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High-resolution yeast phenomics resolves different physiological features in the saline response.

Warringer Jonas J Ericson Elke E Fernandez Luciano L Nerman Olle O Blomberg Anders A

Proceedings of the National Academy of Sciences of the United States of America 20031215 26

We present a methodology for gene functional prediction based on extraction of physiologically relevant growth variables from all viable haploid yeast knockout mutants. This quantitative phenomics approach, here applied to saline cultivation, identified marginal but functionally important phenotypes and allowed the precise determination of time to adapt to an environmental challenge, rate of growth, and efficiency of growth. We identified approximately 500 salt-sensitive gene deletions, the majo ...[more]

PMID: 14676322

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Project description:BackgroundPhysiological saline (0.9% NaCl) and acetone are extensively used for storage (as well as hydration) and removal of bone marrow, respectively, of cancellous bone during preparation and mechanical testing. Our study aimed to investigate the mechanical properties of cancellous bone subjected to short-term immersion in saline and acetone treatment with subsequent immersion in saline.MethodsCylindrical samples (Ø6 × 12 mm) were harvested from three positions (left, middle, and right) of 1 thoracic vertebral body, 19 lumbar vertebral bodies, and 5 sacral bones, as well as from 9 femoral heads. All samples were divided into two groups according to the different treatments, (i) samples from the left and middle sides were immersed in saline at 4℃ for 43 h (saline-immersed group, n = 48); (ii) samples from the respective right side were treated with a combination of acetone and ultrasonic bath (4 h), air-dried at room temperature (21℃, 15 h), and then immersed in saline at room temperature (21℃, 24 h) (acetone and saline-treated group, n = 38). All samples were subjected, both before and after treatment, to a non-destructive compression test with a strain of 0.45%, and finally destructive tests with a strain of 50%. Actual density (ρact), initial modulus (E0), maximum stress (σmax), energy absorption (W), and plateau stress (σp) were calculated as evaluation indicators.ResultsBased on visual observation, a combination of acetone and ultrasonic bath for 4 h failed to completely remove bone marrow from cancellous bone samples. The mean values of ρact, σmax, W, and σp were significantly higher in the femoral head than in the spine. There was no significant difference in E0 between non-treated and saline-immersed samples (non-treated 63.98 ± 20.23 vs. saline-immersed 66.29 ± 20.61, p = 0.132). The average E0 of acetone and saline-treated samples was significantly higher than that of non-treated ones (non-treated 62.17 ± 21.08 vs. acetone and saline-treated 74.97 ± 23.98, p = 0.043).ConclusionShort-term storage in physiological saline is an appropriate choice and has no effect on the E0 of cancellous bone. Treatment of cancellous bone with acetone resulted in changes in mechanical properties that could not be reversed by subsequent immersion in physiological saline.

Project description:The use of more salt stress-tolerant vine rootstocks can be a sustainable strategy for adapting traditional grapevine cultivars to future conditions. However, how the new M1 and M4 rootstocks perform against salinity compared to conventional ones, such as the 1103-Paulsen, had not been previously assessed under real field conditions. Therefore, a field trial was carried out in a young 'Tempranillo' (Vitis vinifera L.) vineyard grafted onto all three rootstocks under a semi-arid and hot-summer Mediterranean climate. The vines were irrigated with two kinds of water: a non-saline Control with EC of 0.8 dS m-1 and a Saline treatment with 3.5 dS m-1. Then, various physiological parameters were assessed in the scion, and, additionally, gene expression was studied by high throughput sequencing in leaf and berry tissues. Plant water relations evidenced the osmotic effect of water quality, but not that of the rootstock. Accordingly, leaf-level gas exchange rates were also reduced in all three rootstocks, with M1 inducing significantly lower net photosynthesis rates than 1103-Paulsen. Nevertheless, the expression of groups of genes involved in photosynthesis and amino acid metabolism pathways were not significantly and differentially expressed. The irrigation with saline water significantly increased leaf chloride contents in the scion onto the M-rootstocks, but not onto the 1103P. The limitation for leaf Cl- and Na+ accumulation on the scion was conferred by rootstock. Few processes were differentially regulated in the scion in response to the saline treatment, mainly, in the groups of genes involved in the flavonoids and phenylpropanoids metabolic pathways. However, these transcriptomic effects were not fully reflected in grape phenolic ripeness, with M4 being the only one that did not cause reductions in these compounds in response to salinity, and 1103-Paulsen having the highest overall concentrations. These results suggest that all three rootstocks confer short-term salinity tolerance to the scion. The lower transcriptomic changes and the lower accumulation of potentially phytotoxic ions in the scion grafted onto 1103-Paulsen compared to M-rootstocks point to the former being able to maintain this physiological response in the longer term. Further agronomic trials should be conducted to confirm these effects on vine physiology and transcriptomics in mature vineyards.

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High-resolution yeast phenomics resolves different physiological features in the saline response.

Publications

High-resolution yeast phenomics resolves different physiological features in the saline response.

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