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Summer freezing resistance of high-elevation plant species changes with ontogeny

admin — Sun, 05 Feb 2012 21:59:30 +0000

Publication year: 2012
Source: Environmental and Experimental Botany, Available online 4 February 2012

Angela Sierra-Almeida, Lohengrin A. Cavieres

In high-elevation habitats, an apparent trade-off between high growth-rates and freezing resistance has led some authors to assume that seedlings are less freezing resistant than adults. However, because seedlings are exposed to lower and longer freezing events near the ground, they could be more freezing-resistant than adults. As freezing resistance is related to plant height, ontogenetic changes in the intensity of freezing resistance and the mechanism involved should differ between seedlings and adults of tallvs. short plants, with those changes being greater for tall plants. We evaluated differences between seedlings and adult plants in the ability to resist freezing temperatures in 13 high-Andean species from central Chile. In a field laboratory, we determined the low temperature damage, ice nucleation temperature and freezing resistance mechanisms in their leaves. Seedlings were on average 3.4 K less freezing resistant than adults with greater differences found for tall plant species. Six species changed their freezing resistance mechanism with ontogeny, including short and tall plants, although changes were greater for tall plant species. Ontogenetic changes in the freezing resistance of high-Andean species seem to be more related to a trade-off between plant-growth and stress resistance than to differences in thermal microhabitats between seedlings and adults.

Highlights

► We evaluated ontogenetic changes in the freezing resistance of 13 high-Andean species. ► We determined the magnitude and mechanisms of freezing resistance in their leaves. Seedlings were 4 K less freezing resistant than adults, particularly for tall plants. ► Six species changed their mechanism with ontogeny, including short and tall plants. ► Ontogenetic changes are related to a trade-off between growth and resistance to stress.

Photomorphogenic effects of UVB and UVA radiation on leaves of six Mediterranean sclerophyllous woody species subjected to two different watering regimes at the seedling stage

admin — Fri, 03 Feb 2012 23:31:19 +0000

Publication year: 2012
Source: Environmental and Experimental Botany, Available online 2 February 2012

Dolors Verdaguer, Laura Llorens, Meritxell Bernal, Jordi Badosa

We aimed to investigate the effects of UV radiation and drought on the leaf morphology and anatomy of six native Mediterranean species with different degrees of sclerophylly (Phillyrea angustifolia,Pistacia lentiscus,Daphne gnidium,Ilex aquifolium,Laurus nobilis,Rosa sempervirens). One-year-old seedlings of these species were grown in a glasshouse under three different UV conditions: UVB plus UVA radiation (UVBA), UVA radiation (UVA) and without UV radiation (UV0), and under two watering regimes (low- and well-watered). We observed a significant reduction in leaf area and thickness in response to drier conditions in all the species. The combination of UVB and UVA radiation resulted in leaves with a higher leaf mass area (LMA) and thickness, basically as a consequence of an increase in the thickness of the palisade parenchyma. UVA radiation specifically affected the adaxial epidermal cells, which were thicker and longer than those grown without UV. However, when UV radiation effects were analyzed within each watering treatment, well-watered plants showed a higher sensitivity to UV while UV did not affect significantly the leaf parameters measured in low-watered plants. Lastly, the more sclerophyllous plants were the least sensitive to UV radiation which suggests that leaf sclerophylly would influence the UV plant response.

Highlights

► UVB and UVA treated leaves showed higher leaf mass area and thickness basically due to thicker palisade parenchyma ► UVA radiation specifically affected the adaxial epidermal cells, which were thicker and longer than those grown without UV ► Leaf morpho-anatomical traits of well-watered plants showed a higher sensitivity to UV than those of low-watered plants ► The more sclerophyllous the leaves were, the more insensitive they were to UV radiation or drought.

Nonparametric Bayesian inference of the fiber orientation distribution from diffusion-weighted MR images

admin — Fri, 03 Feb 2012 23:30:32 +0000

Publication year: 2012
Source: Medical Image Analysis, Available online 31 January 2012

Enrico Kaden, Frithjof Kruggel

Diffusion MR imaging provides a unique tool to probe the microgeometry of nervous tissue and to explore the wiring diagram of the neural connections noninvasively. Generally, a forward model is established to map the intra-voxel fiber architecture onto the observable diffusion signals, which is reformulated in this article by adopting a measure-theoretic approach. However, the inverse problem, i.e., the spherical deconvolution of the fiber orientation density from noisy MR measurements, is ill-posed. We propose a nonparametric representation of the tangential distribution of the nerve fibers in terms of a Dirichlet process mixture. Given a second-order approximation of the impulse response of a fiber segment, the specified problem is solved by Bayesian statistics under a Rician noise model, using an adaptive reversible jump Markov chain Monte Carlo sampler. The density estimation framework is demonstrated by various experiments with a diffusion MR dataset featuring high angular resolution, uncovering the fiber orientation field in the cerebral white matter of the living human brain.

Graphical abstract

Bayesian density estimation allows us to disentangle three crossing fiber bundles in the centrum semiovale.

Highlights

► The spherical convolution model is reformulated by adopting a measure-theoretic approach. ► The fiber orientation density is represented by a Dirichlet process mixture, which may be used for realistic simulations. ► The inverse problem is solved by nonparametric Bayesian statistics under a Rician noise model. ► The density estimation framework is demonstrated with HARDI datasets.

Brain Tissue Segmentation in MR Images based on a Hybrid of MRF and Social Algorithms

admin — Fri, 03 Feb 2012 23:30:32 +0000

Publication year: 2012
Source: Medical Image Analysis, Available online 31 January 2012

Sahar Yousefi, Reza Azmi, Morteza Zahedi

Effective abnormality detection and diagnosis in Magnetic Resonance Images (MRIs) requires a robust segmentation strategy. Since manual segmentation is a time-consuming task which engages valuable human resources, automatic MRI segmentations received an enormous amount of attention. For this goal, various techniques have been applied. However, Markov Random Field (MRF) based algorithms have produced reasonable results in noisy images compared to other methods. MRF seeks a label field which minimizes an energy function. The traditional minimization method, simulated annealing (SA), uses Monte Carlo simulation to access the minimum solution with heavy computation burden. For this reason, MRFs are rarely used in real time processing environments. This paper proposed a novel method based on MRF and a hybrid of social algorithms that contain an ant colony optimization (ACO) and a Gossiping algorithm which can be used for segmenting single and multispectral MRIs in real time environments. Combining ACO with the Gossiping algorithm helps find the better path using neighborhood information. Therefore, this interaction causes the algorithm to converge to an optimum solution faster. Several experiments on phantom and real images were performed. Results indicate that the proposed algorithm outperforms the traditional MRF and hybrid of MRF-ACO in speed and accuracy.

Graphical abstract

Effective abnormality detection and diagnosis in Magnetic Resonance Images (MRIs) requires a robust segmentation strategy. Since manual segmentation is a so time-consuming task which engages valuable human resources, automatic MRI segmentation have been received an enormous amount of attention. For this purpose various techniques have been applied however Markov Random Field (MRF) based algorithms have produced better results in noisy images compared to other methods. MRF seeks for a label field which minimizes energy function. Traditional minimization method, simulated annealing (SA), uses Monte Carlo simulation to access the minimum solution with heavy computation burden. For this reason MRFs never be used in real time processing environments. This paper proposed a novel method based on MRF and hybrid of social algorithms contains ant colony optimization (ACO) and Gossiping algorithm. Combining ACO with Gossiping algorithm assists ants to find the better path using the information of their neighbors. Therefore, this interaction causes the algorithm converges to optimum solution faster. Several experiments on phantom and real images were performed. Results indicate the proposed algorithm outperforms the traditional MRF in speed and accuracy.

Highlights

► This article presents a novel unsupervised MRF-based model for MRI segmentation. ► The proposed method uses ACO and gossiping algorithm to speed up the classic MRF. ► Tackling Gossiping algorithm, the proposed method assists ants in smart decision. ► The IBSR and Brainweb datasets have been used for testing the method. ► Results. ► demonstrate the novel method outperforms other models in speed and quality.

Understanding the Phase Contrast Optics to Restore Artifact-free Microscopy Images for Segmentation

admin — Fri, 03 Feb 2012 23:30:32 +0000

Publication year: 2012
Source: Medical Image Analysis, Available online 2 February 2012

Zhaozheng Yin, Takeo Kanade, Mei Chen

Phase contrast, a noninvasive microscopy imaging technique, is widely used to capture time-lapse images to monitor the behavior of transparent cells without staining or altering them. Due to the optical principle, phase contrast microscopy images contain artifacts such as the halo and shade-off that hinder image segmentation, a critical step in automated microscopy image analysis. Rather than treating phase contrast microscopy images as general natural images and applying generic image processing techniques on them, we propose to study the optical properties of the phase contrast microscope to model its image formation process. The phase contrast imaging system can be approximated by a linear imaging model. Based on this model and input image properties, we formulate a regularized quadratic cost function to restore artifact-free phase contrast images that directly correspond to the specimen’s optical path length. With artifacts removed, high quality segmentation can be achieved by simply thresholding the restored images. The imaging model and restoration method are quantitatively evaluated on microscopy image sequences with thousands of cells captured over several days. We also demonstrate that accurate restoration lays the foundation for high performance in cell detection and tracking.

Graphical abstract

Highlights

► Understand the phase contrast optics and its artifacts. ► Derive the computational imaging model for phase contrast optics. ► Design an effective algorithm to restore artifact-free phase contrast images. ► Facilitate high-performance microscopy image analysis such as cell segmentation.

Salinity-induced changes in phenolic compounds in leaves and roots of four olive cultivars (Olea europaeaL.) and their relationship to antioxidant activity

admin — Sun, 29 Jan 2012 02:14:49 +0000

Publication year: 2012
Source: Environmental and Experimental Botany, Available online 28 January 2012

Antonios Petridis, Ioannis Therios, Georgios Samouris, Chrisoula Tananaki

Phenolic compounds are constituents of all higher plants. However, their biosynthesis is often induced when plants are exposed to environmental stresses, such as salinity. The aim of the present research was to determine the phenolic status (total phenol content, oleuropein and hydroxytyrosol) and antioxidant activity of four olive cultivars under saline conditions in two different plant parts (leaves and root). We also tested the possible relationship between oleuropein and glucose, since the latter compound is a part of the former molecule and accumulates under saline conditions. The data indicate that salinity stimulated the biosynthesis of phenols and oleuropein, especially in leaves, whereas the hydroxytyrosol concentration was either negatively or not affected by the salt stress. Oleuropein was the main phenolic compound in both tissues regardless of NaCl treatments. In leaves, glucose showed a totally inverse response to salinity than that of oleuropein, while a highly negative correlation existed between these two substances (R = -0.90, -0.80, -0.88 and -0.84 for ‘Zard’, ‘Ascolana’, ‘Koroneiki’ and ‘Arbequina’, respectively). A possible explanation for this relationship is that oleuropein acts as a glucose-reservoir for osmoregulation or high energy-consuming processes required for plant adaptation to salinity. A highly significant correlation was recorded between total phenol content and antioxidant activity in both leaves and roots. Finally, there is no indication pointing to translocation of phenolic compounds between leaves and root owing to exposure to salt stress

Highlights

► Salinity induced phenylpropanoid metabolism in the olive tree ► Oleuropein was the main phenolic compound in olive tree involved in protection against salinity stress ► Oleuropein in the leaves could act as a glucose reservoir ► There is no indication of a transport mechanism between leaves and root ► Oleuropein may act as an additional constituent of the antioxidant defense system of olive tree

Oxidation of dimethylsulfoniopropionate (DMSP) in response to oxidative stress inSpartina alternifloraand protection of a non-DMSP producing grass by exogenous DMSP+acrylate

admin — Sun, 29 Jan 2012 02:14:49 +0000

Publication year: 2012
Source: Environmental and Experimental Botany, Available online 28 January 2012

Joseph D. Husband, Ronald P. Kiene, Timothy D. Sherman

We investigated the possible role of dimethylsulfoniopropionate (DMSP) as an antioxidant inSpartina alterniflora(Smooth cordgrass). Experimentally-applied oxidative stress caused by application of the herbicides, 1,1′-dimethyl-4,4′-bipyridinediium dichloride (Paraquat), and 1,1-dimethyl-3-(3,4-dichlorophenyl)urea(DCMU)to the leaves ofS. alternifloraresulted in increased oxidation of DMSP to dimethylsulfoxide (DMSO). We did not see an increase in DMSP synthesis and accumulation in response to herbicide induced oxidative stress. The role of DMSP in oxidative stress protection was further investigated via the exogenous application of Paraquat and DMSP + acrylate to leaf discs of the non-DMSP producing grassPanicum commutatum(Panic grass). Inclusion of DMSP + acrylate in the treatment medium resulted in significantly less tissue damage as indicated by decreased tissue necrosis, and chlorophyll bleaching.While the lack of enhanced synthesis of DMSP suggests that DMSP may not function solely as an antioxidant inS. alterniflora, ourresults show that the ability ofS. alterniflorato synthesize DMSP may partially explain its ability to thrive in the stressful low marsh environment.

Highlights

► Oxidative stress did not resultin increasedDMSP levels inS. alterniflora leaves ► Oxidative stress increased oxidation of DMSP to DMSO in S. alterniflora leaves ► Addition of DMSP to paraquat treatments resulted in less damage to treated tissue

Linking root traits to plant physiology and growth inFraxinus angustifoliaVahl. seedlings under soil compaction conditions

admin — Fri, 27 Jan 2012 22:18:01 +0000

Publication year: 2012
Source: Environmental and Experimental Botany, Available online 24 January 2012

David Alameda, Rafael Villar

Roots are immersed in a soil matrix with different and contrasting conditions that may affect their anatomy, structure and function. Soil chemical factors, texture and compaction are some of the main factors experienced by roots. This study investigates how soil compaction and soil type can modify root anatomy and morphology, and, thus, plant physiology and growth. Seedlings of a woody species (Fraxinus angustifoliaVahl.) were grown in a greenhouse with two types of soil (loam and sandy-loam) under a wide range of soil compaction. Despite intrinsic differences in the chemical properties of the two soils, soil compaction explained much of the variation in root morphology and anatomy. We found, in a single species, a high root plasticity in different key root traits as a response to soil compaction. Soil compaction affected negatively the proportion of fine roots, specific root length and proportion of the root xylem vessels. These effects on root traits had an influence on plant physiology and growth. A causal model (by d-sep method) found that soil compaction affected specific root length, and this affects transpiration and photoysinthesis rates. Also, the effect of soil compaction on xylem vessel proportion and xylem vessel diameter affected plant area and plant biomass. In conclusion, soil compaction shows an important effect on root anatomy and morphology during the seedling stage, with consequences on plant physiology and growth.

Highlights

► Soil compaction explained much of the variation in root morphology and anatomy. ► A single species can show a high root plasticity in key root traits as a response to soil compaction. ► Soil compaction affected negatively the percentage of fine roots and specific root length. ► Soil compaction decreases the proportion of root xylem vessels. ► These effects on root traits had an influence on plant physiology and growth.

On price discrimination, parallel trade and the availability of patented drugs in developing countries

admin — Fri, 27 Jan 2012 22:07:42 +0000

Publication year: 2012
Source: International Review of Law and Economics, Available online 25 January 2012

Mainak Mazumdar, Dyuti S. Banerjee

This paper examines the effect of product patent act and parallel trade on the availability of an essential drug in the developing countries. Price discrimination by a Multinational Corporation (MNC) alleviates the problem of non-availability of the drug in a developing country compared to uniform pricing strategy. Incorporating an upstream -downstream market structure we show that in the presence of parallel trade ‘a form of arbitrage’ by traders the MNC cannot successfully discriminate the prices for its product. The analysis however, indicate that if the market size of the developing nation is relatively large, then with Cournot competition among the traders, the manufacturer earns higher profit by allowing parallel trade than by perfectly discriminating the prices for its product. Under Bertrand competition, the strategy to allow parallel trade always dominates the strategy to restrain it.

Summer heat and drought extremes trigger unexpected changes in productivity of a temperate annual/biannual plant community

admin — Wed, 25 Jan 2012 01:18:26 +0000

Publication year: 2012
Source: Environmental and Experimental Botany, Available online 24 January 2012

Freja E. Dreesen, Hans J. De Boeck, Ivan A. Janssens, Ivan Nijs

One consequence of climate warming is an increase in frequency and intensity of heat and drought extremes. The need for realistic experiments examining the effects of extreme events, including their possible interaction, is therefore high. Here, we imposed heat and drought events in a full factorial design, on experimental plant communities consisting of three temperate, annual or biannual herbaceous species. The extremes were simulated in either early or late summer (July or August), as summer is the season where they are expected to have the greatest impact. The 10-day heat waves were simulated with infrared lamps and drought (either 20 or 17 days) was created by withholding water input and removing the water table.During exposure, effects of drought extremes on leaf physiology were predominantly negative in July, and absent in August. Effects of heat extremes were positive, negative or neutral depending on species and period. Heat and drought were additive in July, but interacted in August. The aforementioned negative effects were not reflected in total (aboveground plus belowground) end-of-season community biomass, which, surprisingly, was stimulated in response to drought extremes in both periods. Effects of heat extremes varied but never reduced biomass, likewise to combined heat and drought. This increase in total community biomass originated exclusively from stimulated root growth. The exact mechanism for this unexpected result could not be ascertained, but greater whole-plant nitrogen stocks clearly indicated enhanced nutrient availability. The latter may have arisen from increased net mineralization or from greater root exploration under the influence of “mid-season drought”. Shifts in species dominance apparently also played a role, as species with pronounced allocation to roots were released from competition.This study demonstrates that community responses to climate extremes are not necessarily negative. The observed responses depended on the soil moisture conditions they induced, which in our experiments varied with the timing of the imposed extremes, even within the same season.

Highlights

► Temperate plant communities were exposed to summer heat and/or drought extremes ► Drought extremes stimulated total biomass even when short term effects were negative ► Heat extremes and the combined extremes stimulated or did not affect total biomass ► Changes in soil biogeochemistry and/or species dominance can explain these unexpected biomass increases ► Effects of climate extremes are not necessarily negative.

A Probabilistic Framework for Image Information Fusion with An Application to Mammographic Analysis

admin — Wed, 25 Jan 2012 01:17:55 +0000

Publication year: 2012
Source: Medical Image Analysis, Available online 24 January 2012

Marina Velikova, Peter J.F. Lucas, Maurice Samulski, Nico Karssemeijer

The recent increased interest in information fusion methods for solving complex problem, such as in image analysis, is motivated by the wish to better exploit the multitude of information, available from different sources, to enhance decision-making. In this paper, we propose a novel method, that advances the state of the art of fusing image information from different views, based on a special class of probabilistic graphical models, called causal independence models. The strength of this method is its ability to systematically and naturally capture uncertain domain knowledge, while performing information fusion in a computationally efficient way. We examine the value of the method for mammographic analysis and demonstrate its advantages in terms of explicit knowledge representation and accuracy (increase of at least 6.3% and 5.2% of true positive detection rates at 5% and 10% false positive rates) in comparison with previous single-view and multi-view systems, and benchmark fusion methods such as naïve Bayes and logistic regression.

Graphical abstract

Highlights

► We develop a multi-stage probabilistic framework for multi-view image analysis. ► The framework is computationally efficient and quite general to apply to any domain. ► A sound unbiased evaluation procedure for multi-stage models is proposed. ► Comparison with previous mammographic CAD systems show improved performance.

Editorial board

admin — Wed, 25 Jan 2012 01:17:55 +0000

Publication year: 2012
Source: Medical Image Analysis, Volume 16, Issue 2, February 2012, Pages IFC

[No author name available]

Cd-induced signaling pathways in plants: Regulation of Phytochelatin synthase by protein phosphatase PP1

admin — Sun, 22 Jan 2012 02:51:57 +0000

Publication year: 2012
Source: Environmental and Experimental Botany, Available online 21 January 2012

Ana Isabel Gusmão Lima, Edgar Da Cruz e Silva, Etelvina Maria Paula Almeida Figueira

Phyhtochelatins (PCS) are non-protein thiolssynthesised through glutathione transpeptidation, due to the enzymatic activity of phytochelatin synthase, and are one of the most important metal tolerance mechanisms in plants. The present work was designed to identify the importance of plant protein phosphatase 1 in Cd signaling and PC production, by analyzing its role on GSH production and PC synthesis, as well as on Cd absorption and metal tolerance. Throughout the time-course development of PC synthesis and Cd chelation, we monitored PP1 expression and also assessed its importance for PC synthesis and Cd tolerance by using a specific PP1 inhibitor, CantharidinResultsprovided here show that PC synthase activity can be modulated by protein phosphorylation. PP1 inhibition induced a prominent increase in PC synthesis, mostly by influencing PCS activity, buthad no influence on GSH synthesis. Altogether, results suggest that under Cd-free conditions, PP1 maybe responsible for maintaining PCS inactive in the cells, and that during Cd stress it gets inhibited, enhancing PCS activity. Our findings can open new possibilities for further studies on Cd tolerance regulation in plants, where regulators of protein phosphorylation can be used to specific target PCS activity and enhance Cd uptake and tolerance.

Highlights

► The present work was designed to identify the importance of plant protein phosphatase PP1 in Cd signalling and PC production ► Results provided showed that PC synthase activity can be modulated by protein phosphorilation ► These findings can open new possibilities for further studies on Cd tolerance regulation in plants, where regulators of protein phosphorylation can be used to specific target PCS activity and enhance Cd uptake and tolerance

Editorial Board

admin — Sun, 22 Jan 2012 02:51:57 +0000

Publication year: 2012
Source: Environmental and Experimental Botany, Volume 77, April 2012, Pages CO2

[No author name available]

A CANDLE for a deeperin-vivoinsight

admin — Thu, 19 Jan 2012 03:28:54 +0000

Publication year: 2012
Source: Medical Image Analysis, Available online 18 January 2012

Pierrick Coupé, Martin Munz, Jose V. Manjon, Edward Ruthazer, D. Louis Collins

A newCollaborativeApproach for eNhancedDenoising underLow-lightExcitation (CANDLE) is introduced for the processing of 3D laser scanning multiphoton microscopy images. CANDLE is designed to be robust for low signal-to-noise ratio (SNR) conditions typically encountered when imaging deep in scattering biological specimens. Based on an optimized non-local means filter involving the comparison of filtered patches, CANDLE locally adapts the amount of smoothing in order to deal with the noise inhomogeneity inherent to laser scanning fluorescence microscopy images. An extensive validation on synthetic data, images acquired on microspheres andin vivoimages is presented. These experiments show that the CANDLE filter obtained competitive results compared to a state-of-the-art method and a locally adaptive optimized nonlocal means filter, especially under low SNR conditions (PSNR<8dB). Finally, the deeper imaging capabilities enabled by the proposed filter are demonstrated on deep tissuein vivoimages of neurons and fine axonal processes in the Xenopus tadpole brain.

Graphical abstract

Highlights

► A new method for the denoising of confocal and multiphoton images is proposed. ► An extensive validation demonstrates the high denoising performance of our filter. ► The deeperin vivoimaging capabilities enabled by our filter are presented.

Cinnamic acid pretreatment enhances heat tolerance of cucumber leaves through modulating antioxidant enzyme activity

admin — Wed, 18 Jan 2012 00:38:54 +0000

Publication year: 2012
Source: Environmental and Experimental Botany, Available online 16 January 2012

Ai-Hua Dai, Yong-Xin Nie, Bin Yu, Qian Li, Ling-Yun Lu, …

To investigate the physiological mechanism of heat stress mitigated by exogenous cinnamic acid (CA), seedlings of a cucumber cultivar (Cucumis sativuscv. Jinchun no. 4) were pretreated with CA for 2 d and then were exposed to normal (25/18 °C) and elevated (42/38 °C) temperatures for 3 d. 50 μM CA was chosen since it improved growth more than other CA concentrations under heat stress. At 2 d, supply of 50 μM CA elevated the activities of antioxidant enzymes superoxide dismutase (SOD, EC 1.15.1.1), catalase (CAT, EC 1.11.1.6), guaiacol peroxidase (GPX, EC 1.11.1.7), glutathione peroxidase (GSH-Px, EC 1.11.1.9), ascorbate peroxidase (APX, EC 1.11.1.11), monodehydroascorbate reductase (MDHAR, EC 1.6.5.4), dehydroascorbate reductase (DHAR, EC 1.8.5.1) and glutathione reductase (GR, EC 1.6.4.2) in cucumber leaves, and it also increased the contents of reduced glutathione (GSH) and ascorbate (AsA). When the CA-pretreated cucumber seedlings have been exposed to heat stress, their antioxidant activities were changed further and were higher than heat treatment alone. Compared to heat treatment, the combination of CA pretreatment and heat also increased relative water content (RWC) of leaves, enhanced levels of proline and soluble sugars, elevated contents of CA and vanillic acid (VA) in leaves, and decreased levels of malonaldehyde (MDA), superoxide radical (O2) and hydrogen peroxide (H2O2), while it resulted in 8.33 percent of leaf edges being dried up. Meantime, heat had adverse effects on plant growth, RWC, CA and VA contents in leaves, and it as well increased the levels of MDA, O2and H2O2and made the dried leaf edges to be 79.17 percent. We conclude that pretreatment with 50 μM CA elevates CA and VA contents in leaves, enhances antioxidant activities under heat stress and decreases lipid peroxidation to some extent, accompanying with increasing proline and soluble sugar levels in heat-stressed leaves, thus the pretreatment enhances heat tolerance of cucumber seedlings.

Highlights

► In this study CA-pretreated cucumber seedlings are exposed to heat stress. ► CA pretreatment increases antioxidant activities in heat-stressed leaves. ► CA elevates proline and soluble sugar levels in leaves under heat stress. ► CA also improves growth inhibition and decreases MDA levels under heat stress. ► Exogenous CA mitigates heat stress through regulating antioxidant activities.

Effects of Drought Preconditioning on Freezing Tolerance of Perennial Ryegrass

admin — Wed, 18 Jan 2012 00:38:54 +0000

Publication year: 2012
Source: Environmental and Experimental Botany, Available online 16 January 2012

Lindsey Hoffman, Michelle DaCosta, J. Scott Ebdon, Jiuzhou Zhao

Predicted increases in winter temperatures may negatively impact winter survival by preventing maximal cold acclimation prior to freezing temperatures. Accordingly, research is needed to identify strategies that may help promote cold acclimation and increase freezing tolerance. Therefore, the objectives of this research were to (i) examine the effects of drought preconditioning (DP) on freezing tolerance of two perennial ryegrass (Lolium perenneL.) cultivars (‘Buccaneer’ and ‘Sunkissed’) under both non-cold acclimating (20 °C) and cold acclimating (2 °C) conditions; and (ii) examine the physiological and biochemical changes in leaves and crowns of perennial ryegrass in response to DP. Plants of ‘Buccaneer’ and ‘Sunkissed’ perennial ryegrass were subjected to the following treatments in a controlled environment chamber: (i) well-watered at 20 °C, (ii) DP at 20 °C, (iii) well-watered at 2 °C, and (iv) DP at 2 °C. Leaf and crown tissues were harvested for analysis of freezing tolerance (lethal temperature resulting in 50% mortality, LT50), nonstructural carbohydrates, proline, soluble protein, and antioxidant enzyme activities. Drought preconditioning resulted in an improvement in freezing tolerance (lower LT50) for Buccaneer, but had no significant effect on freezing tolerance of Sunkissed. Furthermore, DP resulted in increases in carbohydrate, proline, and soluble protein contents, but this response was dependent upon cultivar, tissue, and temperature regime

Highlights

► The incidence of freezing injury is likely to increase under future climate changes ► Drought preconditioning may be useful for enhancing plant freezing tolerance ► In one cultivar, drought preconditioning increased freezing tolerance at 20 °C and 2 °C ► Drought preconditioning increased crown fructan, proline, and soluble protein content at 2 °C

Protective responses induced by herbicide safeners in wheat

admin — Wed, 18 Jan 2012 00:38:54 +0000

Publication year: 2012
Source: Environmental and Experimental Botany, Available online 16 January 2012

Victoria L. Taylor, Ian Cummins, Melissa Brazier-Hicks, Robert Edwards

Safeners are agrochemicals which enhance tolerance to herbicides in cereals including wheat (Triticum aestivumL.) by elevating the expression of xenobiotic detoxifying enzymes, such as glutathione transferases (GSTs). When wheat plants were spray-treated with three safener chemistries, namely cloquintocet mexyl, mefenpyr diethyl and fenchlorazole ethyl, an apparently identical subset of GSTs derived from the tau, phi and lambda classes accumulated in the foliage. Treatment with the closely related mefenpyr diethyl and fenchlorazole ethyl enhanced seedling shoot growth, but this effect was not determined with the chemically-unrelated cloquintocet mexyl. Focussing on cloquintocet mexyl, treatments were found to only give a transient induction of GSTs, with the period of elevation being dose dependent. Examining the role of safener metabolism in controlling these responses, it was determined that cloquintocet mexyl was rapidly hydrolysed to the respective carboxylic acid. Studies with cloquintocet showed that the acid was equally effective at inducing GSTs as the ester and appeared to be the active safener. Studies on the tissue induction of GSTs showed that while phi and tau class enzymes were induced in all tissues, the induction of the lambda enzymes was restricted to the meristems. To test the potential protective effects of cloquintocet mexyl in wheat on chemicals other than herbicides, seeds were pre-soaked in safeners prior to sowing on soil containing oil and a range of heavy metals. While untreated seeds were unable to germinate on the contaminated soil, safener treatments resulted in seedlings briefly growing before succumbing to the pollutants. Our results show that safeners exert a range of protective and growth promoting activities in wheat that extend beyond enhancing tolerance to herbicides.

Highlights

► Wheat treated with 3 safeners induced identical glutathione transferases (GSTs). ► Two safeners caused an enhancement in seedling growth. ► GST induction was transient, saturable and tissue dependent. ► Seeds treated with safeners were able to germinate on chemically contaminated soil.

Mass Preserving Image Registration for Lung CT

admin — Sun, 15 Jan 2012 02:57:31 +0000

Publication year: 2012
Source: Medical Image Analysis, Available online 13 January 2012

Vladlena Gorbunova, Jon Sporring, Pechin Lo, Martine Loeve, Harm A Tiddens, …

This paper presents a mass preserving image registration algorithm for lung CT images. To account for the local change in lung tissue intensity during the breathing cycle, a tissue appearance model based on the principle of preservation of total lung mass is proposed. This model is incorporated into a standard image registration framework with a composition of a global affine and several free-form B-Spline transformations with increasing grid resolution. The proposed mass preserving registration method is compared to registration using the sum of squared intensity differences as a similarity function on four groups of data: 44 pairs of longitudinal inspiratory chest CT scans with small difference in lung volume; 44 pairs of longitudinal inspiratory chest CT scans with large difference in lung volume; 16 pairs of expiratory and inspiratory CT scans; and 5 pairs of images extracted at end exhale and end inhale phases of 4D-CT images. Registration errors, measured as the average distance between vessel tree centerlines in the matched images, are significantly lower for the proposed mass preserving image registration method in the second, third and fourth group, while there is no statistically significant difference between the two methods in the first group. Target registration error, assessed via a set of manually annotated landmarks in the last group, was significantly smaller for the proposed registration method.

Graphical abstract

Highlights

► Preservation of mass is a plausible model of lung parenchyma. ► Mass preserving model simulates lung tissue density change related to the change in regional ventilation. ► Incorporating mass preserving model into an image registration leads to more accurate results.

Strategic Delegation And “Judicial Couples” In The Italian Constitutional Court

admin — Sat, 14 Jan 2012 02:05:32 +0000

Publication year: 2012
Source: International Review of Law and Economics, Available online 13 January 2012

Fabio Padovano, Nadia Fiorino

We analyze the selection of the Justice Reporter by the Justice President of the Italian Constitutional Court, the most important form of agenda setting power and act of delegation in decisions of constitutional (il)legitimacy. We estimate a series of econometric models that evaluate the relative importance of the determinants of the creation of these “judicial couples”, namely, professional background, political affiliation, age etc. Professional background is shown to be an important determinant of the creation of the couples, more so with time, although the onset of the Second Republic has reduced its importance. This analysis sheds light into the inner workings of the Italian Constitutional Court and the actual processes through which its jurisprudence is generated.

Highlights

► We analyze the selection of the Justice Reporter by the Justice President of the Italian Constitutional Court, the most important form of agenda setting power and act of delegation in decisions of constitutional (il)legitimacy. ► This paper is probably the first, or one of the very few, to empirically analyze the internal relationships within a Kelsenian Court, their drivers and to what extent they affect the jurisprudence of the Court. ► Specifically, we estimate an econometric model that evaluates the relative importance of the determinants of the creation of these “judicial couples”, namely, professional background, political affiliation, age etc. ► Professional background is shown to be an important determinant of the creation of the couples, more so with time, although the onset of the Second Republic has reduced its importance. ► The paper also discusses the reasons why the Italian Constitutional Court is an especially suited testing ground for analyzing issues of delegation within Kelsenian Courts.

Relative contribution of photoprotection and anti-oxidative mechanisms to differential drought adaptation ability in grapevines

admin — Thu, 12 Jan 2012 23:05:33 +0000

Publication year: 2012
Source: Environmental and Experimental Botany, Available online 12 January 2012

Alexandros Beis, Angelos Patakas

A comparative study on contribution of photoprotective and anti-oxidative mechanisms to combined drought and high radiation intensity stress adaptation was conducted on two grapevine varieties (Vitis viniferaL., cvs Sabatiano and Mavrodafni), differing in their ability for drought adaptation. Plants of both varieties were subjected to two different deficit irrigation regimes receiving either 50% (DI50) or 25% (DI25) of fully irrigated control plants. Sabatiano, which is considered as more drought resistant variety, maintained significant higher values of photosynthetic rate (PN), stomatal conductance (gs) and predawn water potential (ΨPD) compared to Mavrodafni at the beginning of the drought period. Furthermore, Sabatiano showed significantly lower electron transport rate (ETR), PSII maximum (Φexc) efficiency and significantly higher non-photochemical quenching (NPQ) values for the same values of ΨPDand gsrespectively, which implies a more efficient dissipation of excess energy via the xanthophyll cycle. On the other hand, photorespiration was higher in Mavrodafni suggesting a possible contribution of this mechanism in this variety photoprotection. Drought-induced hydrogen peroxide (H2O2) concentration increased rapidly in Mavrodafni resulting in higher lipid peroxidation. No significant differences in the up-regulation of ascorbic peroxidase (APX, EC 1.11.1.11) and superoxidase dismutase (SOD, EC 1.15.1.1) enzyme activities in response to drought were observed whereas catalase (CAT, EC 1.11.1.6) activity changes in response to gsfollowed completely different patterns in two varieties. The similarity between nitric oxide (NO) accumulation and CAT activity increase at the early stages of drought suggests a positive role of NO in catalase up-regulation.

Highlights

► The contribution of photoprotection mechanisms to differential drought adaptation in grapevines was examined ► The more drought resistant variety dissipates more efficiently the excess energy via the xanthophyll cycle ► In the more susceptible to drought variety photoprotection is mainly based on photorespiration ► Catalase changes in response to drought followed completely different patterns in the two varieties ► Results suggest a positive role of nitric oxide in catalase up-regulation

Explaininguniformity in rule design: The role of citizen participation in enforcement

admin — Thu, 12 Jan 2012 22:55:38 +0000

Publication year: 2012
Source: International Review of Law and Economics, Available online 11 January 2012

Timo Goeschl, Ole Jürgens

Uniform rules incur high aggregate compliance costs when agents are sufficiently heterogeneous. Despite this, uniformity remains a common feature in regulation. Focusing on the monitoring stage of enforcement, this paper highlights an underappreciated benefit of uniform rules: Uniformity of regulation can enhance the productivity of monitoring. We illustrate the general mechanism by showing that in the presence of members of the public that are willing and able to report violations to the regulator at a cost to themselves, uniform rules allow substituting third-party participation for costly own monitoring. However, socially desirable acts may have to be punished to generate deterrence for undesirable acts. Individualizing monitoring and enforcement and citizens acting on welfare considerations do not improve on the outcome.

Highlights

► The paper highlights an underappreciated benefit of uniformity in regulation. ► Motivated citizens can participate in the monitoring of agents. ► Subjecting all agents to the same rule makes detection of violations easier for citizens. ► The reduced monitoring costs for the regulator can outweigh the losses from uniformity. ► Individualized enforcement and welfare-oriented citizens do not improve on the outcome.

Cardiac MR perfusion image processing techniques: A survey

admin — Wed, 11 Jan 2012 02:54:55 +0000

Publication year: 2012
Source: Medical Image Analysis, Available online 10 January 2012

Vikas Gupta, Hortense A. Kirişli, Emile A. Hendriks, Rob J. van der Geest, Martijn van de Giessen, …

First-pass cardiac MR perfusion (CMRP) imaging has undergone rapid technical advancements in recent years. Although the efficacy of CMRP imaging in the assessment of coronary artery diseases (CAD) has been proven, its clinical use is still limited. This limitation stems, in part, from manual interaction required to quantitatively analyze the large amount of data. This process is tedious, time-consuming, and prone to operator bias. Furthermore, acquisition and patient related image artifacts reduce the accuracy of quantitative perfusion assessment. With the advent of semi- and fully automatic image processing methods, not only the challenges posed by these artifacts have been overcome to a large extent, but a significant reduction has also been achieved in analysis time and operator bias. Despite an extensive literature on such image processing methods, to date, no survey has been performed to discuss this dynamic field. The purpose of this article is to provide an overview of the current state of the field with a categorical study, along with a future perspective on the clinical acceptance of image processing methods in the diagnosis of CAD.

Graphical abstract

Highlights

► Survey of semi- and fully automatic image processing methods for cardiac MR perfusion quantification. ► Classification of image processing methods based on their registration, segmentation and multimodality fusion and visualization algorithms. ► Investigation of the advantages and drawbacks of the surveyed methods and their robustness to acquisition artifacts. ► Extensive literature overview of the last 20 years.

Transpiration response of de-rooted peanut plants to aquaporin inhibitors

admin — Tue, 10 Jan 2012 00:53:37 +0000

Publication year: 2012
Source: Environmental and Experimental Botany, Available online 9 January 2012

M. Jyostna Devi, Walid Sadok, Thomas R. Sinclair

Selected genotypes of peanut (Arachis hypogaeaL.) have been identified that show constrained transpiration rates (TR) at high atmospheric vapor pressure deficits (VPD) in contrast to genotypes that exhibit continually increasing TR with increasing VPD. The constraint of TR has been proposed as a putative trait for soil water conservation and improved crop performance during late-season water deficits. In soybean (Glycine max(L.) Merr.), limited TR at high VPD has been found to be related to a decreased hydraulic conductance in leaves. A different population of water-transport-mediating proteins, i.e., aquaporins (AQP), was indicated in soybean by measuring the response of shoot TR to treatment with a silver AQP inhibitor. The objective of this study was to test the shoots of four peanut genotypes for a transpiration response when treated with four inhibitors of AQP, which appear to have differing modes of action in inhibiting AQP. Transpiration rate of all four genotypes were equally sensitive to exposure to cycloheximide and mercuric chloride (HgCl2). Treatment of the shoots of three genotypes (ICGS 44, TMV 2 and ICGV 86699) with silver nitrate (AgNO3) and hydrogen tetrachloroaurate (HAuCl4) resulted in decreased TR while treatment of genotype ICGV 91284, which had constrained TR at high VPD, resulted in little or no decrease of TR. In fact, the AgNO3treatment of this fourth genotype resulted in a stimulation of TR at higher AgNO3concentrations. Among the three genotypes with TR not constrained at high VPD, two genotypes had less decrease in TR with HAuCl4treatment than the third genotype. These results identified major differences in shoot response to AQP inhibitors, which were hypothesized to indicate different populations of AQP in the leaves of these peanut genotypes

Highlights

► Genotypes identified for transpiration response differences to vapor pressure deficit ► Shoots of four genotypes treated with four aquaporin inhibitors ► One genotype responsive to silver and gold inhibitors, three unresponsive ► Inhibitor response correlated with vapor pressure deficit response ► Aquaporin inhibitors useful to discriminate hydraulic traits among peanut genotypes

Canopy position determines the photoprotective demand and antioxidant protection of leaves in salt-stressedSalvia officinalisL. plants

admin — Tue, 10 Jan 2012 00:53:37 +0000

Publication year: 2012
Source: Environmental and Experimental Botany, Available online 8 January 2012

Taïeb Tounekti, Maria Elizabeth Abreu, Habib Khemira, Sergi Munné-Bosch

The effects of salt stress and leaf canopy position on mechanisms of photo- and antioxidant protection, including changes in photosynthetic pigments and low-molecular-weight chloroplastic antioxidants, were examined in sage (Salvia officinalisL.) plants exposed to two doses of NaCl (50 mM and 100 mM) for five weeks. Sage appeared to be a moderately salt-resistant glycophyte. The addition of 100 mM NaCl to the nutrient solution reduced total leaf biomass, the number of leaves, leaf water potential, net photosynthesis, stomatal conductance and chlorophyll levels. However, the malondialdehyde levels, which indicate the extent of lipid peroxidation, did not increase in plants treated with either 50 mM or 100 mM NaCl, relative to controls. In the plants treated with 100 mM NaCl, the accumulation of Nain the leaves occurred in parallel with a drastic reduction in the net CO2assimilation rates, but also with the activation of mechanisms of photo- and antioxidant protection, including xanthophyll cycle de-epoxidation and the accumulation of tocopherols and phenolic diterpenes. Furthermore, we examined the extent to which canopy position determines the photoprotective demand and antioxidant protection of leaves, and how salinity affects this demand. The lower leaves showed a lower photoprotective demand than the upper leaves. However, the former showed higher lipid peroxidation than the latter under salt stress, which suggests that the lower, older leaves suffer from greater photo-oxidative stress than the upper, younger ones, despite being located in areas with a lower photoprotective demand within the canopy. We concluded that leaf position in the canopy should be carefully considered in studies aimed at unravelling mechanisms of salt-stress tolerance in plants.

Highlights

► Salt tolerance is achieved through activation of photoprotection mechanisms ► Leaf position in the canopy determines the photoprotective demand of leaves ► Lower leaves suffer photo-oxidative stress despite receiving low light intensities ► Leaf position should be considered in studies of salt stress tolerance in plants

Temperature Effect on Transpiration Response of Maize Plants to Vapour Pressure Deficit

admin — Sat, 07 Jan 2012 01:59:19 +0000

Publication year: 2012
Source: Environmental and Experimental Botany, Available online 4 January 2012

Zongjian Yang, Thomas R. Sinclair, MaggieZhu, Carlos D. Messina, Mark Cooper, …

Breeding for drought tolerance can benefit from a better understanding of possible responses of transpiration to various environmental variables. Temperature and vapour pressure deficit (VPD) are two important factors influencing stomatal conductance and transpiration. In this study, maize (Zea maysL.) plants of four hybrids were grown under three day/night temperature regimes (30/26, 26/22 and 22/18 °C) in glasshouses, and the response of transpiration rate to changes in atmospheric VPD was measured at two different temperatures in a growth chamber. For all the hybrids examined, increases in transpiration rate with increasing VPD were similar and well described by a two-segment linear regression. There was little further increase in transpiration as VPD increased beyond a breakpoint. When measured at high temperature, the breakpoint in transpiration response to VPD occurred at significantly higher VPD and transpiration rate than at low temperature. The effect of growth temperature on transpiration was evident when plants were grown at low temperature (22/18 °C) and measured at higher temperature (30 °C). However, on the second day under the measurement temperature, the transpiration rate of these plants increased to the same level as those grown in higher day/night temperature environments. Limitation on transpiration at high VPD is a promising trait that could be incorporated into breeding programs to improve drought tolerance in maize.

Graphical abstract

Highlights

► The response of transpiration rate (TR) to increase in VPD was investigated in maize ► Hybrids examined showedlimitation on increase in TR at high VPD above a breakpoint ► The breakpoints occurred at high VPD and TR when measured at high temperature ► TR response acclimated quickly from growth temperature to measurement temperature

Exogenous nitric oxide effect on fructan accumulation andFBEsexpression in chilling-sensitive and chilling-resistant wheat

admin — Sat, 07 Jan 2012 01:59:19 +0000

Publication year: 2012
Source: Environmental and Experimental Botany, Available online 4 January 2012

Chunxi Li, Tingting Li, Daijing Zhang, Lina Jiang, Yun Shao

This study was to investigate the effect of exogenous nitric oxide (NO) on fructan accumulation and fructan biosynthesic enzymes (FBEs) expression in seedlings leaves of two wheat (Triticum aestivumL.) cultivars, winter wheat (Zhoumai18, ZM) and spring wheat (Yanzhan4110, YZ), under 4 °C. The seedlings of two wheat cultivars were subjected to different concentrations of sodium nitroprussiate (SNP) for 0, 24, 48, and 96 h. Relative water content (RWC) was increased by exogenous NO in YZ, but decreased in ZM. Except for glucose, fructose and fructans of degree of polymerization (DP) 3 in YZ, other soluble carbohydrates contents in the two wheat cultivars all increased to different degrees. The activities of FS (including sucrose: sucrose 1-fructosyltransferase (1-SST, EC: 2.4.1.99) and sucrose: fructan 6-fructosyltransferase (6-SFT, EC: 2.4.1.10)) were significantly higher than fructan: fructan 1-fructosyltransferase (1-FFT, EC: 2.4.1.100) in the seedlings of two wheat cultivars. The same phenomenon occurred to FBEs expression. In addition, sucrose content decreased while fructans content increased under low temperature, which was in accordance with the improved 1-FFT activity in ZM. Moreover, fructans content increased to a high level under high concentration of NO in ZM while kept at a constant low level in YZ. The expression levels of FBEs were universally higher in ZM than in YZ, which identified with the high frost resistance of the winter cultivar. It is concluded that exogenous NO treatment on wheat may be a good option to reduce chilling injury by regulating fructan accumulation in leaves. This is the first report owing that exogenous NO alleviated the negative effects of chilling stress by accumulating fructans in wheat.

Highlights

► A high level of fructans would play a key role in wheat resistance against the injury caused by chilling stress. ► Exogenous NO plays a role in adjusting the fructans content to alleviate the damage caused by chilling stress. ► High DP fructans may play a key role in high frost-resistance of winter wheat, while low DP fructans were likely more important in response of spring wheat to low temperature stress.

Osmotic and saline effect on growth, water relations, and ion uptake and translocation inPhlomis purpureaplants

admin — Sat, 07 Jan 2012 01:59:19 +0000

Publication year: 2012
Source: Environmental and Experimental Botany, Available online 4 January 2012

Sara Álvarez, Mª José Gómez-Bellot, Marco Castillo, Sebastián Bañón, Mª Jesús Sánchez-Blanco

The effect of different levels of water deficit and saline stress on physiological and morphological parameters inPhlomis purpureaplants was studied to evaluate their adaptability to such conditions.P. purpureaplants, grown under greenhouse conditions, were subjected to four irrigation treatments lasting 26 weeks: control (C, 1 dS m, 100% water holding capacity), moderate water deficit (MWD, 1dS m, 60% of the control level of irrigation water), severe water deficit (SWD, 1 dS m, 40% of the control level of irrigation water) and saline (S, 4dS m, nutrient solution containing 44 mM NaCl). Aerial dry weight decreased in all three treatments, although this response was more marked in the water deficit treatments, especially SWD. Stem diameter, leaf number and leaf area were similarly reduced in both water deficit treatments, while only leaf area decreased in saline treated plants. Throughout the experiment, plant height remained similar in both control and saline treated plants but was inhibited 10 weeks after the beginning of the deficit irrigation. At the end of the experiment there were significant differences in plant height between the control and saline treatment. The control treatment produced a higher number of plants with flowers. Plants irrigated with saline water had higher Naconcentrations in their leaves than in their roots and shoots, while the increase in the Clconcentrations were similar in leaves and roots, suggesting some resistance to the movement of the latter ions from root to shoots. There was a negative relationship between leaf growth and Naconcentration in the saline treated plants, in which the accumulation of salt in leaves was associated with osmotic adjustment, which was responsible for maintaining predawn and midday leaf turgor. However, no osmotic adjustment was observed in plants submitted to water stress. Root hydraulic resistance increased in SWD plants, in which the lowest leaf water potential values were recorded. In water stressed plants, in general the decrease of photosynthesis rate was mainly related with stomata factors, although the reductions observed in saline-stressed plants suggest that non-stomatal limitations to photosynthesis could also have been operating

Highlights

► The responses ofP. purpureadiffer significantly between salinity and water stress ► Growth decrease was more marked in the drought treatments than in saline treatment ► Phlomis plants under salinity increased Naconcentration, especially in leaves ► While the increase in the Clconcentration was similarly for roots and leaves ► The use of saline water is feasible for growingP. purpureacommercially

Differences in copper accumulation and copper stress between eight populations ofHaumaniastrum katangense

admin — Wed, 04 Jan 2012 01:24:52 +0000

Publication year: 2012
Source: Environmental and Experimental Botany, Available online 2 January 2012

Hongyun Peng, Qiyan Wang-Müller, Timo Witt, François Malaisse, Hendrik Küpper

Haumaniastrum katangense is well known as the “copper flower” of the Katangan Copper Belt. Few studies, however, are available on the physiology of this remarkable plant, including questions like stress responses and population-dependent differences. In the current study, we compared the response to copper for eight populations of this species in terms of copper accumulation, copper resistance, and various physiological parameters that might change under copper toxicity stress (biophysics of photosynthesis, growth, chlorophylls and carotenoids). Among six populations growing well under experimental conditions, three were found to be copper sensitive in terms of a strong inhibition of growth by 10 μM copper, while the other three were rather resistant. As the most prominent copper tolerance associated difference, copper resistant populations (as judged by their growth, photosynthetic activity and pigmentation) showed a decrease of iron accumulation in response to increased copper supply, while copper sensitive populations increased their Fe accumulation in response under these conditions. Copper sensitive populations showed the expected loss of pigments under copper toxicity stress, while two of the three copper tolerant populations even showed an enhancement of chlorophylls and violaxanthin in response to toxic copper. Also for other pigments population-specific differences in copper response were found, but they did not correlate with copper tolerance. Photosynthesis biophysics was affected by copper stress like in other species, no clearly tolerance/population-specific differences were found.

Highlights

► We compared the Cu-response for 8 H. katangense populations from different habitats ► Cu-tolerant populations decreased Fe-accumulation in response to increased copper ► Cu-sensitive populations increased Fe-accumulation in response to elevated Cu. ► Cu-toxicity in sensitive populations led to enhanced loss of pigments ► In Cu-tolerant populations, chlorophylls & violaxanthin increased at high copper.

The continental-oceanic climatic gradient impose clinal variation in vernalization response inArabidopsis thaliana

admin — Sun, 01 Jan 2012 23:04:48 +0000

Publication year: 2011
Source: Environmental and Experimental Botany, Available online 31 December 2011

Anna M. Lewandowska-Sabat, Siri Fjellheim, Odd Arne Rognli

Flowering time is a major determinant of plant reproductive success and adaptation to local climatic conditions. Vernalization, i.e. a prolonged period of low temperature, is one of the processes controlling flowering time. This study investigates vernalization responses in natural populations ofA. thalianafrom higher latitudes and their significance for local adaptation. Twenty-sevenA. thalianapopulations were collected across latitudinal (59-68N) and altitudinal gradients (2-850 m a.s.l.) in Norway, and the populations were screened for responses to 5 different vernalization treatments. These populations represent the northernmost limit of the species distribution worldwide. Variations in vernalization sensitivity and vernalization saturation were tested for relationships with altitude, distance from the ocean and climatic factors associated with the site of origin. The results showed that these traits were associated with both altitude and distance from the ocean. Populations originating from higher altitudes and inland locations were more sensitive and required less time to saturate their vernalization requirement than populations from lower altitudes at coastal locations. Analyses among inland populations revealed higher contribution of distance from the ocean than altitude to the variation in vernalization responses. These results indicate that the continental–oceanic climatic gradient generate clinal variation in adaptive traits.

Highlights

► This study investigates vernalization responses in natural populations ofA. thalianafrom higher latitudes. ► Vernalization sensitivity and vernalization saturation were associated with both altitude and distance from the ocean. ► Populations from higher altitudes and inland locations were more sensitive to vernalization than populations from lower altitudes at coastal locations. ► Analyses among inland populations revealed higher contribution of distance from the ocean than altitude to the variation in vernalization responses. ► These results indicate that the continental–oceanic climatic gradient generate clinal variation in adaptive traits.

Interspecific variability of plant stomatal response to step changes of [CO2]

admin — Sat, 31 Dec 2011 22:01:35 +0000

Publication year: 2011
Source: Environmental and Experimental Botany, Available online 29 December 2011

Dominik Vodnik, Jože Hladnik, Martina Vrešak, Klemen Eler

The kinetics of a stomatal response to sudden increases or decreases of CO2concentrations ([CO2]) was studied in 13 plant species growing in the field. Plants were well supplied with water. In each plant, gas exchange measurements were made on a fully-developed leaf that was first left to achieve steady-state stomatal conductance (gs) at 400 μmol(CO2) mol) and then exposed to a step change of [CO2] (to 700 μmol molin one experiment; and to 700 and back to 400 μmol molin a second experiment). Porometric data were captured in intervals of 3 sec until a new steady state was reached.A comparison oft½, the half-time needed to achieve newgs, indicates similar responses of stomata in grasses when compared to herbs. The stomata of C4plants responded in approximately five minutes, while the highest closure rate was detected inEchinochloa crus-galliandDigitaria sanguinalis. Opening rates were similar to closing rates and the response as a whole was rather symmetric. In C3plants, the full response of stomata was much slower. Analysis revealed differences in absolute rates ofgschange between C3and C4plants. These differences can be related to the specificities of the type of photosynthetic metabolism. C4photosynthesis enables plants to reducegs, which can hasten further changes of diffusivity in response to the environmental signals. A possible coupling of C4metabolism to the regulation of guard cells also has to be taken into account when explaining the observed results.

Highlights

► stomatal opening and closing at step [CO2] change have similar kinetics. ► C4plant species can be recognized as fast responders to step [CO2] changes. ► differences in stomatal kinetics of C4and C3might have implications in time-averaged stomatal conductance in the environments with fluctuating carbon dioxide concentrations.

The exclusion of ambient aerosols changes the water relations of sunflower (Helianthus annuus) and bean (Vicia faba) plants

admin — Sat, 31 Dec 2011 22:01:35 +0000

Publication year: 2011
Source: Environmental and Experimental Botany, Available online 30 December 2011

S. Pariyar, T. Eichert, H.E. Goldbach, M. Hunsche, J. Burkhardt

Aerosols are an ubiquitous component of the atmospheric environment of plants but their ecophysiological role is largely unknown. Here we address this role by comparing the water relations of plants grown in ventilated greenhouses with ambient air (AA), and filtered air (FA) where particle concentrations had been reduced by more than 99%. Beans and sunflowers were grown in well watered soil or hydroponics. Humidity response curves of gas exchange were recorded along with sap flow, water potentials, and osmotic potentials.Hydroponically grown FA sunflowers and FA beans showed 20 to 40% lower stomatal conductance and lower transpiration compared to the respective AA plants under identical conditions. In sap flow measurements, the leaf-area related transpiration of soil-grown FA sunflowers was about 20 to 30% lower than for AA plants, partially due to lower night time values. Midday water potentials as well as osmotic potentials of FA plants were higher compared to the respective AA plants, while pre-dawn water potentials did not differ.Reduced transpiration of FA plants with stable photosynthesis was observed for beans and can be explained by the ‘hydraulic activation of stomata”, where deposited hygroscopic aerosols form liquid water connections along the stomatal walls, thereby forming a second, liquid-water type of stomatal transpiration. Simultaneously decreased transpiration and photosynthesis were observed for sunflower and point to a smaller stomatal aperture of FA plants. To our knowledge, this is the first study allocating an important functional role to natural aerosol concentrations. It further supports the idea that particulate air pollution may decrease the water use efficiency and the drought tolerance of plants.

Highlights

► First reported experiment on effects of ambient aerosols on plant water relations ► The exclusion of ambient aerosols decreased the transpiration of sunflowers and beans ► Stomatal conductance and transpiration were lowered by 20 to 40%

Copper tolerance strategies involving the root cell wall pectins inSilene paradoxaL.

admin — Sat, 31 Dec 2011 22:01:35 +0000

Publication year: 2011
Source: Environmental and Experimental Botany, Available online 30 December 2011

Ilaria Colzi, Miluscia Arnetoli, Alessia Gallo, Saer Doumett, Massimo Del Bubba, …

New insights were provided on the function of root cell wall pectin concentration and methylation degree in copper tolerance studying contrasting ecotypes of Silene paradoxa. A metallicolous copper tolerant population and a non-metallicolous sensitive population were grown in hydroponics and exposed to different CuSO4treatments to evaluate copper accumulation in relation to pectin concentration and methylation degree of the root cell wall. In short-term exposure experiments the tolerant population decreased root cell wall pectin concentration and increased their methylation degree, while the sensitive population did not respond. Moreover, a positive correlation between root pectin concentration and metal accumulation in root apoplast and symplast was found. In addition, a negative correlation between pectin methylation degree and apoplastic copper concentration were found to be negatively correlated. In long-term exposure experiments, the sensitive population increased the concentration of pectins with the same methylation degree and consequently the ability of its root cell wall to bind the metal. The opposite phenomenon was shown by the tolerant population. Moreover, pectin methylation degree was higher in the tolerant population in respect to the sensitive one, possibly to limit metal binding to the root cell wall. Therefore, in the copper tolerant population of S. paradoxa the generation of metal-excluding root cell walls was suggested to be one of the factors concurring to guarantee a low apoplastic copper accumulation and probably also to limit symplastic copper uptake by the root cells.

Highlights

► Cu induced a change in root cell wall pectins in Cu-tolerantSilene paradoxa. ► During copper exposure, total concentration of root pectins decreased. ► Root pectin methylation degree increased under copper treatment. ► We propose Cu-tolerantSilene paradoxato have metal-excluding root cell walls.

INFLUENCE OF SALINITY ON PIP GENE EXPRESSION IN CITRUS ROOTS AND ITS RELATIONSHIP WITH ROOT HYDRAULIC CONDUCTANCE, TRANSPIRATION AND CHLORIDE EXCLUSION FROM LEAVES

admin — Fri, 30 Dec 2011 02:45:56 +0000

Publication year: 2011
Source: Environmental and Experimental Botany, Available online 29 December 2011

Juan Rodríguez-Gamir, Gema Ancillo, Francisco Legaz, Eduardo Primo-Millo, M. Angeles Forner-Giner

The present work studies the effect of salinity on PIP aquaporins gene expression in citrus roots and its relationship with root hydraulic conductance (Kr), transpiration rate (E) and chloride transport to leaves. To this end, ten-month-old seedlings of Cleopatra mandarin (CM), Carrizo citrange (CC) andPoncirus trifoliata(PT) were tested.No effect was detected of salt treatments on PIP1 and PIP2 aquaporin mRNA transcript abundances from citrus roots, although PIP1 expression in CM roots was lower than in CC and PT.The lowest Kr and E values were detected in CM, whereas PT had the highest. CC seedlings presented intermediate values for these parameters. Addition of HgCl2to either control or salt solution (200 mM NaCl) led to a decrease in Kr and E, thus implying aquaporin involvement. By contrast, salinity strongly reduced Kr and E in all plants, with this effect being unrelated to aquaporin activity.In salinised seedlings, E values appear to be related with Clconcentration in leaves. Thus, CM seedlings treated with 80 mM NaCl presented a lower Cluptake by leaves than PT, whereas this trend was intermediate in CC. Moreover, Hgtreatments significantly reduced leaf Clconcentration in salt stressed plants, probably through the reduction of E.We can conclude that differences among genotypes in PIP1 expression affects Clexclusion from leaves, probably due to effects on water movement. Nevertheless, long-term salt treatments did not affect PIP expression in citrus plants, but reduced root hydraulic conductance and transpiration.

Highlights

► The present work studies the effect of salinity on root hydraulic conductance and aquaporin gene expression in citrus roots. ► It determines the influence of aquaporins gene expression on chloride uptake and transport. ► Long-term salt treatments did not affect aquaporin expression in citrus plants, though they reduced transpiration and root hydraulic conductance.

Ethylene-stimulated photosynthesis results from increased nitrogen and sulfur assimilation in mustard types that differ in photosynthetic capacity

admin — Fri, 30 Dec 2011 02:45:56 +0000

Publication year: 2011
Source: Environmental and Experimental Botany, Available online 29 December 2011

Noushina Iqbal, Nafees A. Khan, Rahat Nazar, Jaime A. Teixeira da Silva

In this study, we have shown that application of ethephon (an ethylene source) resulted in increased activity of nitrate reductase (NR, EC 1.6.6.1) and ATP-sulfurylase (ATPS, EC 2.7.7.4), which accounted for enhanced N and S assimilation, resulting in increased photosynthetic responses in two mustard (Brassica junceaL.) cultivars that differ in photosynthetic capacity. These results were further substantiated by the effects of 100 μM norbornadiene (NBD; an ethylene action inhibitor) treatment. The application of NBD to ethephon-treated plants reduced ethylene sensitivity of plants and inhibited ethylene action by binding to the ethylene receptors, suppressing ethylene-induced N and S assimilation and photosynthetic responses in both the cultivars. Ethylene could be potentially used to increase available N and S resources, photosynthetic-NUE and -SUE and photosynthesis of mustard.

Highlights

► The role of ethylene in regulating photosynthesis at the whole plant level is not clear. ► Ethylene increases photosynthesis via its influence on N and S assimilation enzymes and subsequent incorporation of N and S into photosynthetic machinery. ► The influence of ethylene was on stomatal response and photosynthetic machinery. ► The differential photosynthetic capacity of genotypes was a result of variation in ethylene sensitivity.

Cold hardiness ofPinus nigraArnold as influenced by geographic origin, warming, and extreme summer drought

admin — Fri, 30 Dec 2011 02:45:56 +0000

Publication year: 2011
Source: Environmental and Experimental Botany, Available online 29 December 2011

Juergen Kreyling, Guido L.B. Wiesenberg, Daniel Thiel, Christian Wohlfart, Gerhard Huber, …

Adaptation to the adverse effects of climate change is being investigated more and more through the introduction of species from warmer and drier climates, such as the (sub-) mediterraneanPinus nigrato dry sites in temperate Central Europe. Winter survival, however, may pose a serious threat to this strategy as cold extremes, which naturally determine the poleward range limits of forest trees, are not expected to follow the general warming trend in the near future.Here, juveniles ofP. nigrafrom eight provenances throughout Europe were exposed to different climate change scenarios (factorial combinations of 42 days of drought and warming by 1.6 °C) in a common garden experiment in Bayreuth, Germany. Cold hardiness (LT50) was determined by the Relative Electrolyte Leakage method (REL) in two consecutive winters.Cold hardiness of foliage differed by 10 °C between the provenances studied and a local adaptation to minimum temperature was found. Cold hardiness was further affected by extreme summer drought, increasing cold hardiness by 3.9 °C on average in the subsequent winter, and by summer warming, increasing cold hardiness by 3.4 °C. Year-round warming had no significant effect on cold hardiness. Cold hardiness was related to the content of soluble carbohydrates and to the composition of fatty acids and alkanes in the needles. Juveniles ofP. nigraexhibited a comparable cold hardiness as juveniles of species native to Central Europe (P. sylvestris, Picea abies, Fagus sylvaticaandQuercus petraea) under the same climatic conditions. Cold hardiness of the fine roots ofP. nigraaveraged -16.5 °C compared to -23.8 °C on average for needles.Our results imply that the cold hardiness of the foliage is adaptive to both long-term growing conditions at the seed origin (genetic heritage) and short-term alterations of these conditions (individual plasticity), while first hints suggest that cold hardiness of the roots is high and might not be adaptive. ForP. nigra, below- and above-ground cold hardiness of selected provenances in mid-winter appear suitable for cultivation in temperate regions.

Highlights

► Cold hardiness ofPinus nigrashows local adaptation to climate at its geographic origin ► Winter cold hardiness increases with summer drought and summer warming ► Cold hardiness is related to the content of soluble carbohydrates and composition of fatty acids and alkanes ►Pinus nigrashows similar cold hardiness as the native Central European forest trees

Effect Of Fluoranthene On Plant Cell Model – Tobacco By-2 Suspension Culture

admin — Wed, 28 Dec 2011 00:07:34 +0000

Publication year: 2011
Source: Environmental and Experimental Botany, Available online 26 December 2011

Petr Babula, Ondrej Vodicka, Vojtech Adam, Marie Kummerova, Ladislav Havel, …

Polycyclic aromatic hydrocarbons (PAHs) belong to the group of the most important pollutants of the living environment, which are present in air, soils, freshwater, seawater and sediments. They have very substantial effects on all living organisms including plants and animals. Plants represent important point in PAHs food chain entry. Despite the fact that PAHs influence on animals is intensively studied, effect on plants is almost unknown. In our study, action of polycyclic aromatic hydrocarbon fluoranthene on a plant cell experimental model–tobacco BY-2 cell suspension culture–was studied. BY-2 cells were exposed to the fluoranthene in concentration range from 0 to 1000 μM, duration of treatment was 120 hours, respectively 5 days. Samples were collected in the strictly defined time intervals of 24 hours. Exposure of the BY-2 cells led to significant changes in viability, changes in autofluorescence due to accumulation of fluoranthene in lipophilic cell compartments, especially biomembranes, and production of reactive oxygen species, which resulted in damage of biomembranes and disruption of their semipermeability and initiation of process of programmed cell death. Obtained results bring new knowledge about phytotoxicity of fluoranthene and mechanism of its action

Highlights

► Fluoranthene as cytotoxic compound tested on BY-2 cells. ► Fluoranthene deposition and accumulation in cells were demonstrated. ► Changes in cell viability as well as apoptic changes were detected. ► New knowledge about cytotoxic action of fluoranthene on cell model BY-2.

A fast analysis method for non-invasive imaging of blood flow in individual cerebral arteries using vessel-encoded arterial spin labeling angiography

admin — Wed, 28 Dec 2011 00:07:05 +0000

Publication year: 2011
Source: Medical Image Analysis, Available online 27 December 2011

Michael A. Chappell, Thomas W. Okell, Stephen J. Payne, Peter Jezzard, Mark W. Woolrich

Arterial spin labeling (ASL) MRI offers a non-invasive means to create blood-borne contrastin vivofor dynamic angiographic imaging. By spatial modulation of the ASL process it is possible to uniquely label individual arteries over a series of measurements, allowing each to be separately identified in the resulting angiographic images. This separation requires appropriate analysis for which a general Bayesian framework has previously been proposed. Here this framework is adapted for clinical dynamic angiographic imaging. This specifically addresses the issues of computational speed of the algorithm and the robustness required to deal with real patient data. An algorithm is proposed that can incorporate planning information about the arteries being imaged whilst adapting for subsequent patient movement. A fast maximuma priorisolution is adopted and shown to be only marginally less accurate than Monte Carlo sampling under simulation. The final algorithm is demonstrated onin vivodata with analysis on a time scale of the order of 10 minutes, from both a healthy control and a patient with a vertebro-basilar occlusion.

Graphical abstract

Highlights

► Non-invasive vessel selective MR angiography. ► Fast Bayesian analysis for artery flow contributions. ► Robust treatment of imperfect artery location specification e.g. due to patient movement. ► Robust to clinical scenarios e.g. occluded arteries.

Fire-mobilized nutrients from hydrophyte leaves favor differentiallyTypha domingensisseedling growth

admin — Mon, 26 Dec 2011 23:37:24 +0000

Publication year: 2011
Source: Environmental and Experimental Botany, Available online 26 December 2011

Dilia López-Arcos, Mariela Gómez-Romero, Roberto Lindig-Cisneros, Paul H. Zedler

In wetlands, altered disturbance regimes can change species composition and favor the expansion of invasive species. In Central Mexico,Typha domingensisexpands after fires to colonize areas previously dominated by other natives, but the mechanisms are unknown. To explore if the invasion is facilitated by nutrient release after fire, we tested the effect of ash fromSchoenoplectus americanusandT. domingensisplants on the growth ofT. domingensisseedlings.Schoenoplectusash had higher concentration of soluble phosphates (0.68 ± 0.23 mg/g) thanTyphaash (0.36 ± 0.08 mg/g). At two monthsTyphaseedlings were taller (48 ± 8 cm) in the treatment withSchoenoplectusash added than in either the treatment withTyphaash (29 ± 7 cm) or in the control (25 ± 6 cm). Aboveground biomass (1.03 ± 0.42 g, 0.36 ± 0.17 g, 0.27 ± 0.11 g) and belowground biomass (0.65 ± 0.24 g, 0.32 ± 0.11 g, 0.27 ± 0.11 g) showed the same trends.Typhaseedlings fertilized withSchoenoplectusash had the lowest root: shoot ratios, but the largest rhizomes (dry weight 0.07 ± 0.03 g), followed by those fertilized withTyphaash (0.04 ± 0.01 g) and control plants (0.03 ± 0.01 g). These results show thatT. domingensisresponds to increased phosphate availability from ash of other species by growing larger and allocating more to storage tissues. We conclude that fire promotes the spread ofTyphaby facilitating seedling growth especially in areas dominated byS. americanus

Highlights

► In wetlands altered disturbance regimes can favor the expansion of invasive species ► Invasion ofTypha domingensisseedlings was facilitated by nutrient release after fire ► Phosphorus in the ash increasedTypha domingensisleave and root growth ► Phosphorus content in ash is hignly dependant on the species burned.

Enhanced Sensitivity of the Photosynthetic Apparatus to Heat Stress in Digalactosyl-diacylglycerol DeficientArabidopsis

admin — Mon, 26 Dec 2011 23:37:24 +0000

Publication year: 2011
Source: Environmental and Experimental Botany, Available online 26 December 2011

Jemâa Essemine, Sridharan Govindachary, Saïda Ammar, Sadok Bouzid, Robert Carpentier

The effect of short-term heat stress on photosynthetic electron transport (Photosystem I and II) in chloroplasts ofArabidopsis thalianadeficient in digalactosyl diacylglycerol was investigated. PS II electron transport was characterized by chlorophyll fluorescence rise kinetics while the oxidation-reduction reactions of PSI complexes were studied using leaf-absorbance changes. In wild type plants exposed to temperatures above 36 °C, a progressive damping of the fluorescence rise kinetics, and thus of Fv/Fmand Fv/F0, revealed the marked decline in the quantum yield of PSII. This temperature-dependent inactivation of water photolysis and light-induced plastoquinone reduction was more pronounced inArabidopsismutants,dgd1-2anddgd1-3. At light intensities above 600 μmol m sunder normal temperatures for growth,Arabidopsis dgd1-3was also deficient in its capacity to quench the absorbed light energy nonphotochemically (NPQ) if compared to the NPQ efficiencies of the other two genotypes. The measurements of leaf absorbance changes at 820 nm illustrated the temperature-dependent decline in PSI activity. However, the magnitudes of PSI inhibition were only half of the PSII inhibition, regardless of the plants used. These measurements also showed the suppression of cyclic electron flow around PSI which was temperature-dependent. Leaf exposure above 40 °C resulted in the diversion of electron flow through Mehler reaction in which molecular oxygen acts as terminal acceptor. Notably, in the absence of fully operational PSII and cyclic electron transport around PSI, the decay of the leaf absorption at 820 nm after the cessation of far-red illumination illustrated an enhanced charge recombination in PSI complexes

Highlights

►Arabidopsis thalianadeficient in digalactosyl diacylglycerol was more sensitive to heat stress. ► The quantum yields of PSI in DGDG deficient mutants were several folds higher. ► The major route of P700reduction in the dark inArabidopsissubmitted to 44 °C for 5 min is charge recombination.

Differential activation of defense genes and enzymes in maize genotypes with contrasting levels of resistance to Fusarium verticillioides

admin — Sat, 24 Dec 2011 21:57:47 +0000

Publication year: 2011
Source: Environmental and Experimental Botany, Available online 23 December 2011

Alessandra Lanubile, Jamila Bernardi, Adriano Marocco, Antonio Logrieco, Costantino Paciolla

Fusarium ear rot is one of the most important diseases of maize, that is of concern because Fusarium verticillioides produces the mycotoxins known as fumonisins. F. verticillioides can be transmitted either through infected silks or seed-to-kernel. In order to better understand the virulence of F. verticillioides, the effect of the fungus on the defense systems was investigated both in immature kernels and in seedlings. The molecular mechanisms involved in compatible and incompatible responses were also studied. Gene expression data were obtained from microarray hybridizations, comparing healthy and infected kernels of resistant and susceptible maize inbreds 48 h after infection with a fumonisin-producing strain of F. verticillioides. A total of 739 transcripts were differentially expressed between the two inbred lines at one time point after infection. Among all the differentially regulated genes, 7.3% of encoded proteins play a role in cell rescue and defense. The qRT-PCR analysis confirmed that most of the defense genes had already been transcribed before infection occurred in the maize-resistant line. The study was extended to the analysis of enzymes involved in removing reactive oxygen species, namely ascorbate peroxidase, catalase, total peroxidase and superoxide dismutase. In resistant seedlings, before infection, ascorbate peroxidase and superoxide dismutase enzyme activities were higher than in the susceptible ones and, five days after treatment, they remained unchanged. On the other hand, in the susceptible seedlings, except for superoxide dismutase, all enzymes assayed were activated after pathogen attack. These results support our previous findings of a basal defense response provided by maize genotypes resistant against F. verticillioides infection, both in kernels and seedlings

Highlights

► This work provides novel information on theF. verticillioides-maize pathosystem ► Using gene expression and enzymatic activity analysis multiple defense mechanisms are detected in the resistant maize genotype ► The resistant line, as compared to susceptible line, has an higher antioxidant level before infection and provides basic defense to the fungus ► Plant basal defense genes in maize may be involved in reducing colonization ofF. verticilliodes.

High-light acclimation inQuercus roburL. seedlings upon over-topping a shaded environment

admin — Sat, 24 Dec 2011 21:57:47 +0000

Publication year: 2011
Source: Environmental and Experimental Botany, Available online 24 December 2011

Anna M. Jensen, Emile S. Gardiner, Kevin C. Vaughn

High developmental plasticity at the seedling-level during acclimation to the light environment may be an important determinant of seedling establishment and growth in temperate broadleaf forests, especially in dense understories where spatial light availability can vary greatly. Pedunculate oak (Quercus roburL.) seedlingswere raised beneath a range of artificial light environments(high light, partial high lightand low light) to examine morphological and photosynthetic acclimation to vertically stratified light availability. Acclimation observed at the seedling levelincluded changes inproportional distribution of biomass and leaf area ratio to enhance either light gathering under low light availability or reduction of moisture stress under high light availability. Seedling-level acclimation was partially driven by plasticity at the flush level, but plasticity of traits determining flush morphology, such as leaf number, area, and mass, was largely controlled during bud formation rather than during shoot development. Therefore, flush-level acclimation was restricted when shoots elongated from a shaded environment into a high light environment. In contrast, traits influencing leaf-level acclimation, such as leaf thickness, specific leaf area, and pigment concentrationsappeared to be driven primarily by the prevailing light environment during leaf development. The plastic response in leaf traits to light environments during shoot development enabled immediate acclimation of photosynthetic capacity to the prevailing light environment. In conclusion, oak seedlings displayed a large phenotypical plasticity on multiple levels that maximized whole seedling performance.

Highlights

► Oaks acclimate to stratified light with great phenotypical plasticity. ► Plasticity of traits determining flush morphology was controlled during bud formation. ► Light environment of developing shoot determined phenotypical leaf development. ► Photosynthetic mechanism of oaks exhibited high plasticity to light availability.

The early response ofArabidopsis thalianato cadmium- and copper-induced stress

admin — Sat, 24 Dec 2011 21:57:47 +0000

Publication year: 2011
Source: Environmental and Experimental Botany, Available online 24 December 2011

Ana Martínez-Peñalver, Elisa Graña, Manuel J. Reigosa, Adela M. Sánchez-Moreiras

To investigate the early (first day) effects of cadmium and copper poisoning, adult plants of thale cress (Arabidopsis thalianaL.) were treated with nutrient solution containing 50-100 μM Cdor Cu. The main effect of Cutreatment was a temporary reduction inFv/Fmwith respect to controls, which is suggestive of transient damage to the antenna. By contrast, within 3 h of Cdtreatment, leaf chlorophyll and carotenoid contents and photochemical operating efficiency (φII) fell with respect to controls, whileqNand ETR rose andFv/Fmremained essentially unaltered. Protein content fell initially and rose within 24 h, and a transient widespread increase in H2O2production around hour 6 evolved by hour 24 to more intense production around leaf veins when plants were watered with Cd. These alterations were not due to induced nutrient deficiency, and are interpreted as suggestive of damage to the biochemical phase of photosynthesis. The loss of pigment, and fall inφIIwithout an accompanying fall inFv/Fm, might be used as early signs of cadmium poisoning. It is assumed that Cuwas less harmful than Cdbecause of its tendency to remain in roots and because, as a fairly abundant essential micronutrient, it is subject to endogenous mechanisms of regulation.

Highlights

►Arabidopsis thalianaresponses to Cd and Cu root application monitored for 24 hours. Cd increased H2O2in veins and reduced pigments and photosynthetic efficiency. ► Cu was less translocated than Cd and its effects were less important. ► Cd poisoning and Cu effects were not atributable to nutrients imbalance.

Leaf-level responses to ultraviolet-B radiation inTrifolium repenspopulations under defoliation pressure

admin — Sat, 24 Dec 2011 21:57:47 +0000

Publication year: 2011
Source: Environmental and Experimental Botany, Available online 24 December 2011

Rainer W. Hofmann, Bruce D. Campbell

Pasture plants such asTrifolium repensL. (white clover) are exposed to high levels of ultraviolet-B (UV-B) radiation in summer, as well as to frequent defoliation events from grazing animals and pests. This study examined responses in twoT. repenspopulations exposed to 16 weeks supplementation of 0 or 13.3 kJ mdUV-B radiation under controlled environmental conditions. During that period, plants were exposed to two large defoliation events that lasted two and three weeks, respectively. We investigated a number of leaf morphological characteristics, photochemical attributes, as well as aspects of cellular leaf structure. In particular, we sought to explore whether possible differences in these attributes between the twoT. repenspopulations could be related to their UV-B responsiveness. Leaf dry mass decreased by 16% in the UV-B-sensitive cultivar ‘Huia’ under UV-B, whereas the tolerant ecotype ‘Tienshan’ was unaffected. This differential UV-B response was related to constitutive differences in leaf mass and in leaf area between the two populations. UV-B did not affect specific leaf mass, whereas leaf dry matter content was reduced by 8% in response to UV-B. Measurements of chlorophyll fluorescence revealed no significant effects of UV-B on photochemistry. Results from light microscopy showed that the cellular leaf structure of theT. repenspopulations was not damaged by UV-B. Population-specific structural features included more dome-shaped epidermal cells for ‘Tienshan’. We conclude that differential UV-B-responses inT. repenspopulations can occur after defoliation pressure and can be related to differences in leaf characteristics.

Highlights

► Addresses gap in the literature by examining and demonstrating UV-B effects in plants exposed to defoliation pressure ► First long-term controlled environment UV-B study examining cellular structure in a UV-B-tolerant and -sensitive plant population ► Differential intraspecific UV-B responses are related to constitutive differences in leaf morphology ► Epidermal cell structure further helps explain differential UV-B responses ► Results show a trade-off between competitive strategy under productive conditions and reduced plant biomass accumulation under UV-B1AgResearch, Grasslands Research Centre, Palmerston North, New Zealand.

Low temperature inhibits pollen viability by alteration of actin cytoskeleton and regulation of pollen plasma membrane ion channels inPyrus pyrifolia

admin — Sat, 24 Dec 2011 21:57:47 +0000

Publication year: 2011
Source: Environmental and Experimental Botany, Available online 24 December 2011

Ju-You Wu, Cong Jin, Hai-Yong Qu, Shu-Tian Tao, Guo-Hua Xu, …

Low temperature (LT) generally inhibits pollen germination and pollen tube growth, but the cellular mechanism(s) of this response are still largely unknown. Here we report that LT induced alterations in pear (Pyrus pyrifolia) pollen in the actin cytoskeleton and increased cytosolic free calcium ([Ca]cyt). The increased [Ca]cytcame from extracellular Cainflux and intracellular Carelease. Extracellular Cainflux occurred within a short time of sensing LT. Intracellular Carelease was followed by, but independent of, the extracellular Cainflux. Outward Kcurrent was also activated during LT in the mediation of increased [Ca]cyt. Moreover, the LT-induced Caconductance was regulated by cytoskeleton depolymerization. Our data provide evidence of a signal transduction pathway for the early stage of LT stress in pear pollen. Thus, LT induced depolymerization of the actin cytoskeleton, which induced the extracellular Cainflux, and the increased [Ca]cytpromoted a Koutward flux; these reactions finally inhibited pear pollen germination and tube growth.

Highlights

► Low temperature-induced pear pollen alterations in the actin cytoskeleton ► Low temperature evoked the plasma membrane Cachannel ► Outward Kcurrent was induced by low temperature in the mediation of [Ca]cyt► Low temperature-induced Cainflux was regulated by cytoskeleton depolymerization.

Adaptive diversity inCastanea sativaMill. half-sib progenies in response to drought stress

admin — Sat, 24 Dec 2011 21:57:47 +0000

Publication year: 2011
Source: Environmental and Experimental Botany, Available online 24 December 2011

M. Ciordia, I. Feito, S. Pereira-Lorenzo, A. Fernández, J. Majada

Variation patterns in phenotypic expression after cultivation in two water regimes: 50% and 90% substrate saturation were studied in progenies of chestnut (Castanea sativaMill.) cultivars originating from two main origins in the Iberian Peninsula: North (specifically from Asturias and Galicia) and Central Iberian Peninsula (specifically from the Canary Islands and Andalusia in Southern Spain related to this gene pool). The restricted water supply reduced the water potential of all the families as well as their growth, both in terms of height and weight. Root development increased whilst leaf area decreased as a result of reduction in number and surface area of individual leaves as well as sprouting rather than through defoliation. Drought stress also modified the morphology of the leaves and the relationships indicating the rate of relative development of the leaves compared to the rest of the plant. A correlation with the minimum summer rainfall in the regions of provenance was observed for several traits. The phenotypic variation observed was greater than expected from progenies of selected fruit cultivars. The results of this study show that i) phenotypic variation exists between the two origins of variability corresponding to the two identified gene pools ii) the Northern group might be considered more tolerant to drought stress when considering plantlets’ ability to recover water potential, though important phenotypic plasticity was found in both origins of variability and iii) the pattern of variation found in some physiological and morphological traits suggests that Spanish chestnut stands have great potential to respond to the expected increase in drought in the Iberian Peninsula over the present century.

Highlights

► Progenies of Spanish chestnut cultivars were assesed under drought stress trials ► Water potential and key morphological and growth traits varied between progenies in response to drought ► A variation gradient, reflected in growth and morphological traits, was found between the two origins of variability due to genetic differentiation.

Heat tolerance and suppression of oxidative stress: comparative analysis of 25 cultivars of the C3grassLolium perenne

admin — Fri, 23 Dec 2011 02:55:45 +0000

Publication year: 2011
Source: Environmental and Experimental Botany, Available online 22 December 2011

Wagdi Saber Soliman, Masahiro Fujimori, Kazuhiro Tase, Shu-ichi Sugiyama

Plants exposed to high temperatures frequently suffer from oxidative stress. A large difference was observed among cultivars ofLolium perenneL. in the extent to which their growth in field had been damaged during summer. This study seeks to clarify the relationships between the heat tolerance and tolerance to oxidative stress among the cultivars in this species. Twenty-five cultivars ofL. perennewith different degrees of field tolerance to high summer temperatures were exposed to moderately high temperatures (36/30 °C) for 40 days in a growth chamber. The field tolerance showed a negative correlation with H2O2content (r = -0.66**) and with the degree of lipid peroxidation (r = -0.65**) in leaves after 40 days of exposure to stress, which suggest involvement of oxidative stress in the field tolerance. The H2O2content was positively correlated with electron transport rate (r = 0.56**) and negatively correlated with leaf thickness (r = -0.63**). Tetraploid cultivars, because of their thicker leaves, had higher field tolerance and lower H2O2content than diploid cultivars. These results suggest that the balance between electron transport and CO2reduction in photosynthetic response, which is largely influenced by leaf thickness, plays a pivotal role in determining H2O2generation and resulting oxidative damage under prolonged exposure to moderate to high temperatures

Highlights

► Twenty-five cultivars ofL. perennewith different degrees of field summer tolerance were examined in relation to tolerance to oxidative stress. ► All cultivars were exposed to 36/30 °C for 40 days in a growth chamber. ► Cultivars with low field tolerance had higher H2O2content and higher degree of lipid peroxidation than those with high tolerance. ► The results showed that both H2O2production and H2O2scavenging contribute to cultivar differences in heat tolerance

Similarity and Distinction between Organ-Specific Gibberellin-Modulated Genome Expression between Arabidopsis and Rice

admin — Fri, 23 Dec 2011 02:55:45 +0000

Publication year: 2011
Source: Environmental and Experimental Botany, Available online 22 December 2011

Xiaoyan Feng, Xing Fu, Zhi-Yu Peng, Huiyong Zhang, Songgang Li, …

Gibberellins (GAs) regulate plant growth and development, at least in part, by modulating downstream gene expression. Different plant species and plant organs are differentially responsive to GAs, though it remains unclear whether there exist organ and species specificities of GA responses at the genome expression level. Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa) are model dicot and monocot plants. Microarray analyses indicate that in different organs of both species, small portions of the genomes are affected by GA3or paclobutrazol (PAC), a gibberellin biosynthetic inhibitor. Gene Ontology analyses reveal that GA3regulates genes in almost all major functional categories of both species. Functional categorization of GA3-responsive homologous genes suggests that some features of GA3regulation of genome expression are conserved between the two species. Venn diagrams and cluster display analyses show that only a small gene portion is shared between each pair of rice and Arabidopsis organs, strongly supporting the presence of organ specificity of GA3-regulated gene expression in both species

Highlights

► We show that in different organs of Arabidopsis and rice, small portions of the genomes are affected by GA or paclobutrazol, a gibberellin biosynthetic inhibitor. ► Gene Ontology analyses reveal that GA regulates genes in almost all major functional categories of both species. ► Functional categorization of GA-responsive homologous genes suggests that some features of GA regulation of genome expression are conserved between the two species. ► Venn diagrams and cluster display analyses show that only a small gene portion is shared between each pair of rice and Arabidopsis organs, strongly supporting the presence of organ specificity of GA-regulated gene expression in both species

Nonlinear Dimensionality Reduction Combining MR Imaging with Non-Imaging Information

admin — Fri, 23 Dec 2011 02:55:16 +0000

Publication year: 2011
Source: Medical Image Analysis, Available online 22 December 2011

Robin Wolz, Paul Aljabar, Joseph V. Hajnal, Jyrki Lötjönen, Daniel Rueckert

We propose a framework for the extraction of biomarkers from low-dimensional manifolds representing inter-subject brain variation. Manifold coordinates of each image capture information about structural shape and appearance and, when a phenotype exists, about the subject’s clinical state. Our framework incorporates subject meta-information into the manifold learning step. Apart from gender and age, information such as genotype or a derived biomarker is often available in clinical studies and can inform the classification of a query subject. Such information, whether discrete or continuous, is used as an additional input to manifold learning, extending the Laplacian eigenmap objective function and enriching a similarity measure derived from pairwise image similarities. The biomarkers identified with the proposed method are data-driven in contrast to a-priori defined biomarkers derived from, e.g., manual or automated segmentations. They form a unified representation of both the imaging and non-imaging measurements, providing a natural use for data analysis and visualization. We test the method to classify subjects with Alzheimer’s disease (AD), mild cognitive impairment (MCI) and healthy controls enrolled in the ADNI study. Non-imaging metadata used are ApoE genotype, a risk factor associated with AD, and the CSF-concentration of Aβ1-42, an established biomarker for AD. In addition, we use hippocampal volume as a derived imaging-biomarker to enrich the learned manifold. Our classification results compare favorably to what has been reported in a recent meta-analysis using established neuroimaging methods on the same database.

Graphical abstract

The top figure shows a 2D manifold embedding of images acquired from subjects with AD (squares) and healthy controls (circles) using pairwise image similarities with Laplacian Eigenmaps. The bottom figure shows an embedding obtained with the proposed method incorporating metadata (color-coded) into the manifold learning process. A better separation between the two groups can be obtained when considering both measures. Misclassiclassified subjects are marked by a black outline.

Highlights

► We propose an extension to nonlinear dimensionality reduction with Laplacian Eigenmaps. ► MR imaging information is combined with clinical metadata. ► The representation of subjects in the low-dimensional space is interpreted as biomarker. ► We use this biomarker to classify AD subjects from healthy controls. ► We evaluate the method on the ADNI study.

Physiological and morphological responses to flooding with fresh or saline water inJatropha curcas

admin — Thu, 22 Dec 2011 02:24:13 +0000

Publication year: 2011
Source: Environmental and Experimental Botany, Available online 21 December 2011

Vicente Gimeno, James P. Syvertsen, Inmaculada Simón, Manuel Nieves, Leyanes Díaz-López, …

Jatropha curcasL. has recently drawn the attention of the international research community due to its potential as a biodiesel crop. AlthoughJatrophais relatively tolerant to drought and salinity, poorly drained production areas have suffered increasing problems associated with flooding by saline water. Since the combined effects of flooding and salinity stress are not known, the objective in this work was to investigate physiological and morphological responses ofJatropha curcasplants to flooding by fresh water or salt water. Plant growth, leaf water relations, leaf gas exchange, chlorophyll fluorescence parameters, carbohydrate and organic solutes, and leaf mineral nutrients were determined in three month-old plants exposed to flooding for 10 days with water containing 0, 150 or 300 mM NaCl. Flooding decreased shoot and root growth but there were no significant difference between 0 and 300 mM NaCl treatments. In 0 mM NaCl flooded plants, leaves suffered dehydration as relative water content (RWC) and leaf water potential (Ψw) decreased progressively resulting in decreased leaf turgor potential (ΨP). In 300 mM NaCl flooded plants, however, Ψwremained high as leaf osmotic potential (Ψπ) decreased and ΨPincreased. Increased leaf Cland Naconcentration enabled this osmotic adjustment avoiding leaf dehydration but toxic values were reached in leaves. Leaf gas exchange parameters [net assimilation of CO2(ACO2), stomatal conductance (gs)] and quantum efficiency of PSII (ΦPSII) were reduced similarly by flooding but internal CO2concentration was highest in the 300 mM NaCl treatment. Soluble sugars and starch was reduced in leaves and roots, and leaf Ca, Mg and P concentration was increased in plants under flooding.Jatropha curcasplants are sensitive to flooding condition regardless of the level of salinity confirming their salinity tolerance even under flooded conditions.

Highlights

►J. curcasplants are a flood-sensitive species in freshwater and saltwater condition ► The flooding reduced leaf gas exchange and chlorophyll fluorescence parameters ► In freshwater, leaf dehydration is caused by decreased root hydraulic conductance ► In saltwater, Cl- and Na+ toxicity reduced ACO2 and carbohydrate concentrations ►J. curcasplants are sensitive to flooding regardless of the level of salinity

Lead accumulation and synthesis of non-protein thiolic peptides in selected clones ofMelilotus albaandMelilotus officinalis

admin — Thu, 22 Dec 2011 02:24:13 +0000

Publication year: 2011
Source: Environmental and Experimental Botany, Available online 21 December 2011

R. Fernández, A. Bertrand, J.I. García, R.S. Tamés, A. González

The accumulation of Pb, its effect on plant growth, and the synthesis of non-protein thiolic peptides were evaluated in clone MA-X ofMelilotus albaand clone MO-A ofMelilotus officinaliscultured in a greenhouse in artificially-polluted substrate with 200 and 1000 mg Pb kg. At 90 days of Pb exposure root growth was not affected, except at 1000 mg Pb kgin MA-X. At this concentration hyperaccumulation value was exceeded in both clones, reaching more than 4800 mg Pb kgdry wt. in shoots of MA-X and more than 3400 mg Pb kgdry wt. in shoots of MO-A. Phytochelatins (PCs) and homophytochelatins (hPCs) were found in all cases for both species. Clone MA-X showed an increase in constitutive hPCs content in shoots whereas PC2, PC3and hPC3were synthesized in roots after 90 days of culture in 1000 mg Pb kg. On the other hand, MO-A synthesized a new PC (PC4) in shoots while in roots only hPC2was found. Our results suggest that clones MA-X and MO-A show high Pb accumulation ability and that this capability can be related to the synthesis of PCs and hPCs

Highlights

► Selected clones MA-X and MO-A hyperaccumulate Pb in the shoots. ► Pb accumulation is related to the synthesis of thiolic peptides in MA-X and MO-A. ► MA-X synthesizedde novoPC2, PC3and hPC3in roots treated with 1000 mg Pb kg► MO-A synthesized hPC2in Pb-treated roots and PC4in shoots at 1000 mg Pb kg

Quantitative trait locus analyses of ozone-induced grain yield reduction in rice

admin — Wed, 21 Dec 2011 01:57:32 +0000

Publication year: 2011
Source: Environmental and Experimental Botany, Available online 19 December 2011

Keita Tsukahara, Hiroko Sawada, Hideyuki Matsumura, Yoshihisa Kohno, Masanori Tamaoki

Reduction of grain yield (total seed weight) by ozone in rice (Oryza sativaL.) is believed to be caused by ozone-induced reduction of photosynthetic activity followed by growth inhibition. Here,japonicarice cultivar Sasanishiki andindicarice cultivar Habataki showed different responses to ozone. When exposed to ozone, the leaves of Habataki exhibited no critical damage, whereas those of Sasanishiki developed lesions. Conversely, ozone exposure reduced total seed weight by 19% in Habataki, but not significantly in Sasanishiki. Chronic ozone exposure also significantly decreased culm length, number of primary rachis branch, and number of spikelets per panicle in Habataki. QTL analysis in Sasanishiki/Habataki chromosome segment substitution lines identified a single locus associated with the yield loss caused by ozone on chromosome 6 of Habataki close to marker RM3430 (107.6 cM). A QTL for reduction of primary rachis branch number and total spikelet number was found in the same position. These results indicate that a QTL on chromosome 6 has an important role in ozone-induced yield loss, and is also involved in primary rachis branch formation and total spikelet number in ozone-exposed rice

Highlights

► Ozone caused significant leaf lesions in ajaponicarice cv. Sasanishiki ► Total seed weight of an indica rice cv. Habataki was reduced by ozone ► Ozone also reduced number of primary rachis branch and total spikelet number in Habataki ► The QTL participating in total seed weight loss by ozone was found on chromosome 6 ► Ozone-exposure decreasedAPO1expression level in Habataki.

Silicon availability changes structural carbon ratio and phenol content of grasses

admin — Wed, 21 Dec 2011 01:57:32 +0000

Publication year: 2011
Source: Environmental and Experimental Botany, Available online 19 December 2011

Jörg Schaller, Carsten Brackhage, E. Gert Dudel

Silicon is not an essential element insensu strictobut affects the productivity ofPoaceae. Recent field studies has shown the effect of silicon on cellulose and lignin content in bulk analyses of green compartments of different species, sampled before matter translocation in the course of senescence. Nevertheless, there is a gap in information about silicon availability and its effect on cellulose, lignin and phenol content in different plant tissues after nutrient resorption.In order to prove the effect of controlled silica supply on functional relevant carbon compoundsPhragmites australisTrin. was grown in pot trials under three different levels of silicon surplus. After resorption of nutrients into rhizomes the content of silicon, lignin, cellulose and phenol were measured in different plant tissues.The results show that different levels of silicon surplus changed the plant cellulose, lignin and phenol content depending on plant tissue function. Cellulose content in tissues with stabilization function is reduced contrasting enhanced cellulose content in tissues without stabilization function. Furthermore, higher silicon surplus decreased the phenol content in photosynthetic active tissues and increased the phenol content in culm. Only weak silicon to lignin interaction was found.It is concluded that silicon affects the cellulose and phenol metabolism and the tradeoff between productivity and stabilization/defense. Considering these compounds as crucial factors in decay processes, silicon may be very important for the terrestrial and semi-terrestrial carbon turnover

Highlights

► Silicon availability changes the cellulose, lignin and phenol content of grasses ► Silicon surplus affect the cellulose content: reduced (culm) and enhanced (leaf) ► Silicon addition altered phenol content: decreased (leaf) and increased (culm) ► Only weak silicon to lignin interaction was found.

3D Segmentation of SBFSEM Images of Neuropil by a Graphical Model over Supervoxel Boundaries

admin — Tue, 20 Dec 2011 01:30:10 +0000

Publication year: 2011
Source: Medical Image Analysis, Available online 19 December 2011

Bjoern Andres, Ullrich Koethe, Thorben Kroeger, Moritz Helmstaedter, Kevin L. Briggman, …

The segmentation of large volume images of neuropil acquired by serial sectioning electron microscopy is an important step towards the 3D reconstruction of neural circuits. The only cue provided by the data at hand are boundaries between otherwise indistinguishable objects. This indistinguishability, combined with the boundaries becoming very thin or faint in places, makes the large body of work on region based segmentation methods inapplicable. On the other hand, boundary-based methods that exploit purely local evidence do not reach the extremely high accuracy required by the application domain that cannot tolerate the global topological errors arising from false local decisions.As a consequence, we propose a supervoxel merging method which arrives at itsdecisions in a non-local fashion, by posing and approximately solving ajointcombinatorial optimization problem overallfaces between supervoxels. The use of supervoxels allows the extraction of expressive geometric features. These are used by the higher-order potentials in a graphical model that assimilate knowledge about the geometry of neural surfaces by automated training on a gold standard.The scope of this improvement is demonstrated on the benchmark dataset E1088 (Helmstaedter et al.,2011) of 7.5 billion voxels from the inner plexiform layer of rabbit retina. We provide C++ source code for annotation, geometry extraction, training and inference.

Graphical abstract

Highlights

► We propose a supervoxel merging method for segmenting 3D SBFSEM images of neuropil. ► All merging decisions are coupled in a graphical model. ► Knowledge about correct segments is incorporated in higher-order potentials. ► These potentials are learned automatically from training data. ► The scope of this improvement is demonstrated on the benchmark dataset E1088.

Saline and osmotic stress differentially affects apoplastic and intracellular reactive oxygen species production, curling and death of root hair duringGlycine maxL.-Bradyrhizobium japonicuminteraction

admin — Sat, 17 Dec 2011 23:37:51 +0000

Publication year: 2011
Source: Environmental and Experimental Botany, Available online 17 December 2011

Nacira Muñoz, German Robert, Mariana Melchiorre, Roberto Racca, Ramiro Lascano

In the present study, the production of apoplastic and intracellular reactive oxygen species (ROS) and deformations of young soybean root hairs inoculated withBradyrhizobium japonicumstrain USDA138 were analyzed under saline and osmotic stress. Sustained and transient increase of apoplastic and intracellular ROS production, respectively, were observed in inoculated root hairs. The apical production of apoplastic superoxide in growing root hairs colocalized with flavonoid autofluorescence and both were relocated to the zone of maximum curvature in curled root hairs. Saline and osmotic stress had differential effects on both the production of apoplastic ROS and curling: only saline stress inhibited both processes in a dose-dependent manner. Intracellular ROS production was not altered by osmotic stress but was inhibited completely by 150 mM NaCl. In inoculated root hairs under 50 mM NaCl, the intracellular ROS levels was initially increased, but not decrease at later stages, as occurred in control conditions. Root hair death was induced by 150 mM NaCl in bothinoculated and noninoculated roots and by 50 mM NaCl only in inoculated roots.Saline, but not osmotic stress, marked affects both apoplastic and intracellular ROS production, inhibiting root hair curling and inducing root hair death

Highlights

► Sustained increase of apoplastic ROS production is necessary for root hairs curling ► Apoplastic ROS production is relocated from the tip to the zone of maximum curvature ► Apoplastic ROS co localized with flavonoid autofluorescence ► Transient increase of intracellular ROS production is necessary root hairs for curling ► Saline, but not osmotic stress, affects ROS and curling; and induces root hair death

Influence of Microbial Associations on Selenium Localization and Speciation in Roots ofAstragalusandStanleyaHyperaccumulators

admin — Sat, 17 Dec 2011 23:37:51 +0000

Publication year: 2011
Source: Environmental and Experimental Botany, Available online 17 December 2011

Stormy Dawn Lindblom, Jose R. Valdez-Barillas, Sirine C. Fakra, Matthew A. Marcus, Ami L. Wangeline, …

Selenium (Se) hyperaccumulator plants can accumulate and tolerate Se up to 1% of their dry weight. Since little is known about below-ground processes of Se uptake and metabolism in hyperaccumulators, X-ray absorption spectromicroscopy was used to characterize the chemical composition and spatial distribution of Se in roots ofAstragalusandStanleyahyperaccumulators. Selenium was present throughout the roots, with the highest levels in the cortex. The main form of Se (48-95%) in both species collected from naturally seleniferous soil was an organic C-Se-C compound, likely methyl-selenocysteine. In addition, surprisingly high fractions (up to 35%) of elemental Se (Se) were found, a form so far not reported in plants but commonly produced by Se-tolerant bacteria and fungi. Four fungi collected from hyperaccumulator roots were characterized with respect to their Se tolerance and ability to produce Se, and then used to inoculate hyperaccumulators in a controlled greenhouse study. The roots of the greenhouse-grownAstragalusandStanleyacontained mainly C-Se-C; in most plants no Sewas detected, with the exception ofAstragalusnodules and roots ofAstragalusinoculated withAlternaria astragali, an Se-producing fungus. Apparently, Se- producing endosymbionts including nitrogen-fixing bacteria and endophytic fungi or bacteria in the root can affect Se speciation in hyperaccumulator roots. Microbes that affect plant Se speciation may be applicable in phytoremediation and biofortification, especially if they are promiscuous and affect Se tolerance in crop species

Highlights

► Selenium inStanleyaandAstragalusroots is most concentrated in the cortex ► In field roots, 46-95% of Se was C-Se-C, with up to 35% elemental Se (Se) ► Three fungi from field roots produced mainly Se; these were used to inoculate ► In greenhouse-grown plants Sewas found only in nodules and some inoculated roots ► Microbial symbionts appear to affect Se speciation in hyperaccumulator roots

Grain quality characteristics of spring wheat (Triticum aestivum) as affected by free-air CO2enrichment

admin — Sat, 17 Dec 2011 23:37:51 +0000

Publication year: 2011
Source: Environmental and Experimental Botany, Available online 17 December 2011

P. Högy, M. Brunnbauer, P. Koehler, K. Schwadorf, J. Breuer, …

Spring wheat (Triticum aestivumL. cv. Triso) was grown in a free-air carbon dioxide (CO2) enrichment (FACE) system at Stuttgart-Hohenheim (Germany) in 2008 to examine effects on crop yield and grain quality. Elevated CO2had no significant impacts on aboveground biomass and grain yield components except for an increase in thousand grain weight by 5.4% with size distribution shifted towards larger grains. Total grain protein concentration decreased by 7.9% under CO2enrichment, and protein composition was altered. Total gliadins and their single types (ω5-gliadins, ω1,2-gliadins, α-gliadins, γ-gliadins) were reduced, while albumins/globulins, total glutenins and their subunits were not influenced. The gluten proteins (gliadins plus glutenins) were lowered by 11.3% in the high-CO2treatment, whereas proportions of gluten protein types were slightly affected as only ω1,2-gliadins decreased. Accordingly, all proteinogenic amino acids were decreased by 4.2 to 7.9% in concentrations per unit flour mass, although partly below the level of statistical significance. In contrast, the composition of amino acids on a per protein basis remained unaffected except for a decline in serine. Among the minerals, the concentrations of calcium, magnesium, iron and cobalt decreased, while an increase was observed for boron. The concentrations of total non-structural carbohydrates and starch decreased, whereas fructose, raffinose and fructan increased. Total lipid concentration remained unaffected by the CO2enrichment, whereas the grain carbon/nitrogen relation was increased by 8.5%. Implications may occur for consumer nutrition and health, and for industrial processing, thus breeding of new wheat cultivars that exploit CO2fertilisation and maintain grain quality properties is regarded as one potential option to assure the supply chain for the future

Highlights

► In a free-air CO2experiment with wheat, thousand grain weight increased, while several grain quality parameters were negatively affected ► Most importantly, concentrations of proteins and amino acids decreased and their compositions changed as well ► The CO2-induced decrease in iron and calcium may aggravate nutrient deficiencies in terms of cereal-based diets

Effects Of Climate Change On Leaf Litter Decomposition Across Post-Fire Plant Regenerative Groups

admin — Wed, 14 Dec 2011 22:15:49 +0000

Publication year: 2011
Source: Environmental and Experimental Botany, Available online 13 December 2011

S. Saura-Mas, M. Estiarte, J. Peñuelas, F. Lloret

Decomposition is a determining factor for the functioning of ecosystems because litter dynamics (litter fall and litter decomposition) constitute a key process in the regulation of the recycling of carbon and nutrients. We studied the litter decomposition properties of a set of 19 Mediterranean-basin woody species with different post-fire regenerative strategies (resprouters and non-resprouters), under experimental climate manipulation (simulating warming and drought) over a 2-year period. We show that climate change modifies litter decomposition of these Mediterranean woody species as litter contributions to the soil (g/year) were lower under drought experimental conditions. Species with different post-fire regeneration performance showed different leaf decomposition patterns, though these patterns were influenced by the taxonomical affiliation of the species. As expected, the mass loss of the non-resprouter litter, after two years, was higher than in resprouters. Non-resprouters showed higher nutrient concentration per mass of leaf litter after 2 years of experiment than resprouters, possibly because they have lost more C-rich biomass, allowing high nutrients concentration in the remaining litter. That would apply particularly to P as litter N:P ratio was lower in non-resprouters than in resprouters. This study suggests that, in Mediterranean ecosystems, nutrients’ return from leaf litter to the soil will be slower under the projected future drier conditions. Furthermore, changes in fire regimes that lead to modifications in the abundance of post-fire regenerative groups are likely to affect ecosystem’s functional properties. Thus, if new fire regimes enhance non-resprouters’ abundance, we can expect a greater return of organic matter contributions to the soil and a lower litter N:P.

Highlights

► We studied the litter decomposition of 19 Mediterranean-basin woody species during two years. ► Litter decomposition has been studied under experimental climate manipulation. Differences among post-fire regenerative strategies has been also considered. ► Litter contributions to the soil (g/year) are lower under drought conditions. ► The mass loss of the non-resprouter litter, after two years, was higher than in resprouters, while the litter N:P ratio was lower in non-resprouters than in resprouters. ► Climate change and changes in wildfire regimes are expected to affect litter decomposition processes.

Citrate assisted phytoextraction of uranium by sunflowers: study of fluxes in soils and plants and resultingintra-plantadistribution of Fe and U

admin — Wed, 14 Dec 2011 22:15:49 +0000

Publication year: 2011
Source: Environmental and Experimental Botany, Available online 13 December 2011

Ján Mihalík, Pascale Henner, Sandrine Frelon, Virginie Camilleri, Laureline Février

This study aimed to determine how the citric acid assisted phytoextraction of uranium (U) by sunflowers impacted on the remobilisation of U in soil, its subsequent transfer to plants and its further distributionintra-planta. Consequences of the flux of nutrient elements [iron (Fe) and zinc (Zn)] able to interfere with U during this process were also specifically addressed. A U-contaminated soil receiving different citric acid treatments in terms of dose delivered and frequency of delivery was studied. Dynamics of remobilisation in soil were assessed using DGT (Diffusive Gradient in Thin-film) measurements, and phytoextraction experiments were conducted in a Rhizoplan device. All treatments induced a remobilisation of U and Fe from the soil solid-phase to the soil solution. Consequently, sunflower uptake of U was greatly enhanced, whereas the uptake of Fe was not affected–in accordance with the high regulation of this nutrient in the plant. As for U, the Zn uptake increased due to the citric acid treatment. The DGT-measured concentration correlated well with the concentration taken up by plants for U. Nevertheless, under all conditions, U fluxes to DGT were higher than U fluxes to plants, suggesting that DGT did not mimic the plant uptake mechanism for U. There was no correlation found for Fe, due to its plant uptake regulation. Distribution of these elementsin plantawas strongly impacted by citric acid, with an increase in translocation from root-to-shoot of both U and Fe, whereas Zn remained mainly in the roots. Such an increase was expected for U but was very surprising for Fe, suggesting that the presence of U in plants may have interfered with mechanisms that regulate Fe homeostasis

Graphical abstract

Highlights

► U and Fe fluxes in soils and plants induced by citric acid assisted phytoextraction ► Citric acid increase mobility of U and Fe in soils ► DGT is a useful tool to predict U phytoavailability, but not Fe one ► Citric acid enhance bioaccumulation of U, Zn and Fe in sunflowers ► Citric acid increase root to shoot translocation of U and Fe, but not that of Zn

Alfalfa yield under elevated CO2and temperature depends on theSinorhizobiumstrain and growth season

admin — Wed, 14 Dec 2011 22:15:49 +0000

Publication year: 2011
Source: Environmental and Experimental Botany, Available online 13 December 2011

Álvaro Sanz-Sáez, Gorka Erice, Jone Aguirrolea, Juan José Irigoyen, Manuel Sánchez-Díaz

The aim of the present study was to analyze the effect of elevated CO2at different temperature, inoculation with threeSinorhizobium melilotistrains and growth in two seasons (summer and autumn) on plant growth, photosynthesis and N2fixation (estimated as apparent nitrogenase activity, ANA). One of the objectives was to demonstrate that most efficient N2-fixing strains could improve alfalfa forage production. The second objective was to test ifS. melilotistrains alter their efficiency under climate change conditions. The third objective was to show if seasonal changes may modify alfalfa productivity. Interaction of CO2and temperature enhanced alfalfa dry matter in both seasons; however, plants produced more dry matter in autumn than in summer, due to the negative effect of elevated summer temperature on N2-fixation. Higher yield in summer corresponded to plants in symbiosis with 102F78 strain being not related to enhanced nodule dry matter or apparent nitrogenase activity but to putative lower carbon consumption for N2fixing process. Contrariwise, in autumn the highest yield was obtained by 102F34 as a consequence of increased nodule dry matter induced under elevated CO2and temperature.

Highlights

► CO2and T enhanced plant DM in summer and autumn regardless of theS. melilotistrain ► Alfalfa was less productive in summer due to the negative effect of high T on N2fixation ► In summer, growth of nodulated alfalfa under elevated CO2was limited by N availability ► Higher yield of alfalfa with 102F78 was related to lower C cost for N2fixation in summer ► Higher yield with 102F34 was related to increased nodule DM induced by CO2in autumn.

Consistent Segmentation using a Rician Classifier

admin — Wed, 14 Dec 2011 22:15:18 +0000

Publication year: 2011
Source: Medical Image Analysis, Available online 13 December 2011

Snehashis Roy, Aaron Carass, Pierre-Louis Bazin, Susan Resnick, Jerry L. Prince

Several popular classification algorithms used to segment magnetic resonance brain images assume that the image intensities, or log-transformed intensities, satisfy a finite Gaussian mixture model. In these methods, the parameters of the mixture model are estimated and the posterior probabilities for each tissue class are used directly as soft segmentations or combined to form a hard segmentation. It is suggested and shown in this paper that a Rician mixture model fits the observed data better than a Gaussian model. Accordingly, a Rician mixture model is formulated and used within an expectation maximization (EM) framework to yield a new tissue classification algorithm called RiCE (Rician Classifier using EM). It is shown using both simulated and real data that RiCE yields comparable or better performance to that of algorithms based on the finite Gaussian mixture model. As well, we show that RiCE yields more consistent segmentation results when used on images of the same individual acquired with different T1-weighted pulse sequences. Therefore, RiCE has the potential to stabilize segmentation results in brain studies involving heterogeneous acquisition sources as is typically found in both multi-center and longitudinal studies.

Graphical abstract

Highlights

► Noise in magnetic resonance images should be modeled as Rician distribution. ► Rician distribution fits the MR image histogram better than a Gaussian one. ► Cortical surfaces from the brain MR images can be better delineated using Rician models in a segmentation algorithm compared to a Gaussian one. ► Segmentations between same brain MR images acquired under different pulse sequences are more consistent using Rician modeling.

Don’t Say You’re Sorry Unless You Mean It: Pricing Apologies to Achieve Credibility

admin — Wed, 14 Dec 2011 22:07:55 +0000

Publication year: 2011
Source: International Review of Law and Economics, Available online 13 December 2011

Murat C. Mungan

Remorse and apologies by offenders have not been rigorously analyzed in the law and economics literature. This is perhaps because apologies are regarded as’cheap talk’and are deemed to be non-informative of an individual’s conscious state. In this paper, I develop a formal framework in which one can analyze remorse and apologies. I argue that legal procedures can be designed topriceapologies, such that only truly remorseful individuals apologize. Hence, apologies would not be mere ’cheap talk’ and could send correct signals regarding an offender’s true conscious state, making them credible. This will lead victims, upon receiving apologies, to forgive offenders more frequently. Moreover, pricing apologies does not negatively impact the possibility of achieving optimal deterrence. An (arguably negative) effect of pricing apologies is its elimination of insincere apologies. If it is assumed that apologies, even if insincere, carry rehabilitative and/or palliative benefits, then the optimality of pricing apologies depends on a trade-off between achieving credibility and increasing such rehabilitative and palliative benefits.

Highlights

► A credible apology system can be designed by pricing apologies. ► When apologies are priced, remorseful offenders can relieve their guilty consciences by sending credible signals to their victims, which will lead victims to forgive remorseful offenders more frequently. ► When there are no sizeable benefits attached to insincere apologies, pricing regimes are optimal. ► When there are rehabilitative and palliative benefits attached to insincere apologies, the optimality of pricing regimes depends on a trade-off between achieving credibility and increasing rehabilitative and palliative benefits attached to insincere apologies. ► Results hold regardless of whether or not sanctions are costly to impose.

Both ozone exposure and soil water stress are able to induce stomatal sluggishness

admin — Sun, 11 Dec 2011 02:05:04 +0000

Publication year: 2011
Source: Environmental and Experimental Botany, Available online 9 December 2011

Yasutomo Hoshika, Kenji Omasa, Elena Paoletti

We tested whether short-term exposure to realistic ozone pollution (≤150 ppb, 1 h) and soil water stress (soil water content ≤ 15%) slow stomatal dynamics in an ozone-sensitive cultivar of snapbean. Both ozone exposure and water stress caused stomata to be sluggish in the degree of closure after leaf severing, while ozone also delayed the time the closing signal was perceived. Ozone-induced aberrations lasted up to the night and caused incomplete closure of stomata. No synergic effect was observed in the dynamic measurements. In contrast, at steady-state, water-stress protected the plants from the negative ozone effects on stomatal conductance. Ambient ozone peaks may thus cause sluggish stomatal response and increase leaf water loss both under well watered and drought conditions.

Highlights

► We tested whether realistic ozone and soil water stress slow stomatal dynamics. ► Both ozone exposure and water stress caused stomata to be sluggish. ► At steady-state, water-stress protected from the negative ozone effects. ► Complex static and dynamic stomatal responses to ozone and drought arise.

Understanding crop physiology to select breeding targets and improve crop management under increasing atmospheric CO2concentrations

admin — Sun, 11 Dec 2011 02:05:04 +0000

Publication year: 2011
Source: Environmental and Experimental Botany, Available online 9 December 2011

Michael Tausz, Sabine Tausz-Posch, Robert M. Norton, Glenn J. Fitzgerald, Marc E. Nicolas, …

The present overview paper reviews knowledge on plant metabolism under elevated atmospheric CO2concentrations (e[CO2]) with regard to underpinning options for the management of crop production systems and the selection of crop traits beneficial for future conditions.Better understanding of intra-specific variability in responses to e[CO2] is of great importance to breed or select best possible genotypes for future conditions. Yield increases per 100 μL Lincrease in [CO2] varied between none and over 30% among varieties of important crops. Carbon source-sink relationships are believed to play a major role in determining the ability of a plant to utilise e[CO2] and avoid downward acclimation of photosynthesis upon prolonged e[CO2] exposure. Corresponding traits (e.g. tillering capacity, stem carbohydrate storage capacity, or seed size and numbers) are currently under investigation in Free Air Carbon dioxide Enrichment (FACE) facilities, such as AGFACE (Australian Grains FACE).The stimulatory effect of e[CO2] on plant growth is dependent on adequate nutrient supply. For example, N concentrations in plant tissues generally decrease under e[CO2], which in leaves is commonly related to a decrease in Rubisco concentration and activity, and therefore linked to photosynthetic downward acclimation. This effect is also of direct concern for food production where decreased N and protein content can have negative effects on product quality (e.g., grain protein). Plant nutrient metabolism appears to adjust to a new physiological equilibrium under e[CO2] which limits the extent to which nutrient application can ameliorate the situation. What the control points are for an adjustment of plant N metabolism is unclear. Rubisco metabolism in leaves, N assimilation, N translocation or N uptake are all potential key steps that may be inhibited or downregulated under e[CO2]. To achieve the best possible growth response while maintaining product quality, it is important to understand plant nutrient metabolism under e[CO2].Comparatively little is known about mechanisms of potential changes in plant stress tolerance under e[CO2]. Defence metabolites such as antioxidants are, in part, directly linked to primary carbohydrate mechanism and so potentially impacted by e[CO2]. It is unknown whether photoprotective and antioxidative defence systems, key to plant stress tolerance, will be affected, and if so, whether the response will be strengthened or weakened by e[CO2]. Better understanding of underlying principles is particularly important because it is virtually impossible to test all possible stress factor combinations with e[CO2] in realistic field settings.

Highlights

► Maximum crop yield response to elevated CO2is needed for food security. ► Source sink relations may determine CO2response and provide selection targets. ► Crop nutrition traits must ensure food quality under elevated CO2. ► Elevated CO2effects on antioxidants may affect crop stress tolerance.

The effect of elevated CO2on photochemistry and antioxidative defence capacity in wheat depends on environmental growing conditions – A FACE study

admin — Sun, 11 Dec 2011 02:05:04 +0000

Publication year: 2011
Source: Environmental and Experimental Botany, Available online 9 December 2011

Sabine Tausz-Posch, Klaudia Borowiak, Raymond W. Dempsey, Robert M. Norton, Saman Seneweera, …

The present study examines photosynthesis, photochemistry and low weight molecular antioxidants (ascorbic acid and glutathione) of twoTriticum aestivumL. cultivars (H45 and Yitpi) in response to growth under two CO2concentrations (elevated CO2, e[CO2]vs. ambient CO2, a[CO2]), two sowing times (time of sowing 1, TOS1, less stressful growing conditionsvs.time of sowing 2, TOS2, more stressful growing conditions) and two water treatments (rain-fedvs. irrigated). The objective was to evaluate (1) if growth under e[CO2] will alleviate climate stresses such as higher temperature and/or limited water supply thereby reducing the need for photoprotection and concentrations of low weight molecular antioxidants and (2) cultivar-specific responses to combined climate change factors which may be useful to identify intra-specific variation in stress tolerance for future breeding. We compared gas exchange, chlorophyll fluorescence and antioxidative defence compounds (ascorbic acid, glutathione) of flag leaves of Australian Grains Free Air Carbon dioxide Enrichment (AGFACE) grown wheat. When plants were grown under the less stressful growing conditions of TOS1, e[CO2] increased light saturated net assimilation rates (Asat) and quantum yield of PSII electron transport (ΦPSII) but decreased thermal energy dissipation (indicated by increased efficiency of open PSII centres, Fv’/Fm’), while antioxidant concentrations did not change. Under the more stressful growing conditions of TOS2, e[CO2] also increased Asat(like at TOS1), however, photochemical processes were not affected while antioxidant concentrations (especially ascorbic acid) were decreased. Cultivar specific responses also varied between sowing dates: Only at TOS2 and additional irrigation, antioxidant concentrations were lower in e[CO2] grown H45 as compared to Yitpi indicating decreased photo-oxidative pressure in H45. These results suggest a photo-protective role of e[CO2] as well as some intra-specific variability between investigated cultivars in their stress responsiveness, all strongly modified by environmental growing conditions.

Highlights

► We compared effects of elevated CO2on photochemistry and antioxidants in wheat. ► Effects were tested under a range of environmental growing conditions. ► Results suggest a photo-protective role of e[CO2] and intra-specific variability. ► Responses were strongly modified by environmental growing conditions.

Spatially Variable Rician Noise in Magnetic Resonance Imaging

admin — Sun, 11 Dec 2011 02:04:37 +0000

Publication year: 2011
Source: Medical Image Analysis, Available online 9 December 2011

Ivan I. Maximov, Ezequiel A. Farrher, Farida Grinberg, N. Jon Shah

Magnetic resonance images tend to be influenced by various random factors usually referred to as “noise”. The principal sources of noise and related artefacts can be divided into two types: arising from hardware (acquisition coil arrays, gradient coils, field inhomogeneity); and arising from the subject (physiological noise including body motion, cardiac pulsation or respiratory motion). These factors negatively affect the resolution and reproducibility of the images. Therefore, a proper noise treatment is important for improving the performance of clinical and research investigations. Noise reduction becomes especially critical for the images with a low signal-to-noise ratio, such as those typically acquired in diffusion tensor imaging at high diffusion weightings. The standard methods of signal correction usually assume a uniform distribution of the standard deviation of the noise across the image and evaluate a single correction parameter for the whole image. We pursue a more advanced approach based on the assumption of an inhomogeneous distribution of noise in space and evaluate correction factors for each voxel individually. The Rician nature of the underlying noise is considered for low and high signal-to-noise ratios. The approach developed here has been examined using numerical simulations andin vivobrain diffusion tensor imaging experiments. The efficacy and usefulness of this approach is demonstrated here and the resultant effective tool is described.

Graphical abstract

Highlights

► Spatially variable noise correction algorithm is applied with the Rician correction. ► Automatic detection of a regions with the Gaussian or Rician noise distributions. ► Improved noise correction scheme for the diffusion-weighted imaging.

Who Walks Out? Entrepreneurship in a Global Economy

admin — Sun, 11 Dec 2011 01:57:21 +0000

Publication year: 2011
Source: International Review of Law and Economics, Available online 9 December 2011

Juan Pablo Couyoumdjian

Modern entrepreneurially-driven capitalism is embedded in a global economy. Crucially, in this environment entrepreneurship must be viewed as a mobile resource. Entrepreneurs can thus “vote-with-their-feet” when deciding where to establish their businesses. The institutional context for entrepreneurship is a key determinant of an agent’s decision to migrate. In this paper we put forward a new framework for an examination of the relationship between institutional quality and entrepreneurship. We then offer an exploration on the problem of entrepreneurship in an economy that is open to the international movement of goods and services, capital and, above all, labor, especially talented labor.

Highlights

► In a global economy entrepreneurship must be viewed as a mobile resource ► Entrepreneurs can “vote-with-their-feet” when deciding where to establish their businesses ► The institutional context for entrepreneurship is a key determinant of an agent’s decision to migrate ► We put forward a new framework for an examination of the relationship between institutional quality and entrepreneurship ► The migration of entrepreneurs is an important issue.

Manifold Learning for Image-Based Breathing Gating in Ultrasound and MRI

admin — Sat, 10 Dec 2011 00:55:05 +0000

Publication year: 2011
Source: Medical Image Analysis, Available online 8 December 2011

Christian Wachinger, Mehmet Yigitsoy, Erik-Jan Rijkhorst, Nassir Navab

Respiratory motion is a challenging factor for image acquisition and image-guided procedures in the abdominal and thoracic region. In order to address the issues arising from respiratory motion, it is often necessary to detect the respiratory signal. In this article, we propose a novel, purely image-based retrospective respiratory gating method for ultrasound and MRI. Further, we apply this technique to acquire breathing-affected 4D ultrasound with a wobbler probe and, similarly, to create 4D MR with a slice stacking approach. We achieve the gating with Laplacian eigenmaps, a manifold learning technique, to determine the low-dimensional manifold embedded in the high-dimensional image space. Since Laplacian eigenmaps assign to each image frame a coordinate in low-dimensional space by respecting the neighborhood relationship, they are well suited for analyzing the breathing cycle. We perform the image-based gating on several 2D and 3D ultrasound datasets over time, and quantify its very good performance by comparing it to measurements from an external gating system. For MRI, we perform the manifold learning on several datasets for various orientations and positions. We achieve very high correlations by a comparison to an alternative gating with diaphragm tracking.

Graphical abstract

Highlights

► Automatic, image-based gating in ultrasound and MRI. ► Application of Laplacian eigenmaps for gating. ► Creation of 4D ultrasound data with wobbler transducer. ► Validation by comparison to alternative gating approaches.

Talent Matters: Judicial Productivity and Speed in Japan

admin — Thu, 08 Dec 2011 23:45:22 +0000

Publication year: 2011
Source: International Review of Law and Economics, Available online 8 December 2011

J. Mark Ramseyer

To study the determinants of judicial productivity and speed (measured by published opinions), I examine all 348 trial-court civil medical malpractice opinions published in Japan between 1995 and 2004. For comparative purposes, I add 120 randomly selected civil judgments from the same period. The data cover 706 judges (about a third of the Japanese bench). I find: (A) Productivity (measured as published opinions per year on the bench) correlates with apparent intellectual ability and effort. The judges who attended the most selective universities, who passed the bar exam most quickly, and who were chosen by the courts for an elite career track publish the most opinions. (B) Adjudicatory speed (measured as time from filing to decision, for published opinions) may correlate with apparent ability and effort too (the evidence is weaker), but institutional experience counts as well. As the courts acquired increasing experience with malpractice cases, the pace of adjudication quickened.

On the Optimal Number of Courts

admin — Thu, 08 Dec 2011 23:45:22 +0000

Publication year: 2011
Source: International Review of Law and Economics, Available online 8 December 2011

Stefan Voigt

This is the first paper to investigate whether the number of high courts in a country has systematic effects both on the quality of its legal system and on its level of economic development more generally. It is theorized that due to the division of labor and a higher degree of specialization, high courts might be advantageous in terms of court productivity. Yet, they might also be disadvantageous in terms of a less coherent legal system. It is empirically tested whether the positive or the negative effects prevail. Results show that a larger number of high courts never has any positive effects on very broad outcome variables; indeed, with regard to some of these, a greater number of high courts is correlated with worse outcomes.

Optimization, Path Dependence And The Law: Can Judges Promote Efficiency?

admin — Thu, 08 Dec 2011 23:45:22 +0000

Publication year: 2011
Source: International Review of Law and Economics, Available online 8 December 2011

Alain Marciano, Elias L. Khalil

The thesis that judges could (voluntarily or not) promote efficiency through their decisions has largely been discussed since Posner put it forward in the early 1970 s. There nonetheless remains a methodological aspect that has never (to our knowledge) been analyzed and that we address in this paper. We thus show that both promoters and critics of the judge-and-efficiency thesis similarly use a definition of optimization in which history, constraints and path-dependency are viewed as obstacles that must be removed to reach the most efficient outcome. This is misleading. Efficiency cannot be defined in absolute terms, as a “global ideal” that would mean being free from any constraint, including historically deposited ones. That judges are obliged to refer to the past does not mean that they are unable to make the most efficient decision because constraints are part of the optimization process; or optimization is necessarily path-dependent. Thus, the output of legal systems cannot be efficient or inefficientper se. This is what we argue in this paper.

Aggregate Litigation and Regulatory Innovation: Another View of Judicial Efficiency

admin — Thu, 08 Dec 2011 23:45:22 +0000

Publication year: 2011
Source: International Review of Law and Economics, Available online 8 December 2011

Giovanni B. Ramello

In this article, we argue that aggregate litigation and the court system can not only restore the protection of victims and the production of deterrence, but also play a pivotal role in stimulating regulatory innovation. This is accomplished through a reward system that seems largely to mimic the institutional devices used in other domains, such as intellectual property rights, by defining a proper set of incentives. Precisely the described solution relies on creating a specific economic framework able to foster economies of scale and grant a valuable property right over a specific litigation to an entrepreneurial individual, who in exchange provides the venture capital needed for the legal action, and produces inputs and focal points for amending regulations. In this light, aggregate litigation thus can be equally seen as an incubator for regulation.

The Effect of Rules Shifting Supreme Court Jurisdiction from Mandatory to Discretionary-An Empirical Lesson from Taiwan

admin — Thu, 08 Dec 2011 23:45:22 +0000

Publication year: 2011
Source: International Review of Law and Economics, Available online 8 December 2011

Theodore Eisenberg, Kuo-Chang Huang

Theoretical works suggest that granting a supreme court discretion in choosing the cases to be decided on the merits could shift dockets away from traditional case-based adjudication and towards issue-based adjudication. According to this prediction, legislatures can recast supreme courts’ roles in society by modifying jurisdictional rules. This study tests this prediction empirically. Using a newly assembled data set on appeals terminated by the Taiwan Supreme Court for the period 1996-2008, we study the effect of jurisdictional-source procedural reform, a switch from mandatory jurisdiction to discretionary jurisdiction in 2003, on the Taiwan Supreme Court’s performance. Our study shows that the 2003 reform failed to transform the function of the Court from correcting error to a greater role in leading the development of legal doctrine as intended by the legislature. Our findings suggest that a supreme court can adjust the way it conducts business according to its own preference and the role it defines for itself, which are influenced both by the background against which it operates and the inertia of its members’ working habits. Our study informs policy-makers that merely amending procedural rules, without more, is unlikely to change the function of a supreme court. Our findings also suggest that statutorily dictated mandatory jurisdiction may not be implemented by a high court faced with caseload pressure.

Examining the Efficiency of the U.S. Courts of Appeals: Pathologies and Prescriptions

admin — Thu, 08 Dec 2011 23:45:22 +0000

Publication year: 2011
Source: International Review of Law and Economics, Available online 8 December 2011

Robert K. Christensen, John Szmer

Until recently (e.g., Lindquist 2007), few studies have examined the factors that might affect aspects of judicial efficiency, including the time it takes a court to decide a case. In our analysis of a sample o f U.S. Courts of Appeals decisions from 1971-1996, we examine a variety of potential causes of inefficiency, or pathologies, before suggesting a series of prescriptions.

Court Output, Judicial Staffing, and the Demand for Court Services: Evidence from Slovenian Courts of First Instance

admin — Thu, 08 Dec 2011 23:45:22 +0000

Publication year: 2011
Source: International Review of Law and Economics, Available online 8 December 2011

Valentina Dimitrova-Grajzl, Peter Grajzl, Janez Sustersic, Katarina Zajc

We contribute to the scant empirical literature on court activity by examining how judicial staffing and caseload influence court output in Slovenia, a post-socialist EU member state struggling with implementing an effective judicial system. Unlike the majority of the existing literature, we attempt to tackle endogeneity problems that arise in estimation of the determinants of court output. In addition to controlling for court fixed effects to address endogeneity due to unobserved court-level heterogeneity, an instrumental variables approach based on a plausible assumption of sequential exogeneity of our regressors allows us to address the problem of reverse causality between court output and both caseload and judicial staffing. Our findings suggest that ignoring endogeneity issues may lead to erroneous policy conclusions about the expected impact of resources, as proxied by judicial appointments, devoted to the court system. Our results imply that the primary driving force of output of Slovenian courts is the demand for their services.

The Economics of Efficiency and the Judicial System

admin — Wed, 07 Dec 2011 23:01:28 +0000

Publication year: 2011
Source: International Review of Law and Economics, Available online 7 December 2011

Giovanni B. Ramello, Stefan Voigt

Construction of 3D MR image-based computer models of pathologic hearts, augmented with histology and optical fluorescence imaging to characterize action potential propagation

admin — Tue, 06 Dec 2011 22:13:30 +0000

Publication year: 2011
Source: Medical Image Analysis, Available online 6 December 2011

Mihaela Pop, Maxime Sermesant, Garry Liu, Jatin Relan, Tommaso Mansi, …

Cardiac computer models can help us understand and predict the propagation of excitation waves (i.e., action potential, AP) in healthy and pathologic hearts. Our broad aim is to develop accurate 3D MR image-based computer models of electrophysiology in large hearts (translatable to clinical applications) and to validate them experimentally. The specific goals of this paper were to match models with maps of the propagation of optical AP on the epicardial surface using large porcine hearts with scars, estimating several parameters relevant to macroscopic reaction-diffusion electrophysiological models. We used voltage-sensitive dyes to image AP in large porcine hearts with scars (3 specimens had chronic myocardial infarct, and 3 had radiofrequency RF acute scars). We first analyzed the main AP waves’ characteristics: duration (APD) and propagation under controlled pacing locations and frequencies as recorded from 2D optical images. We further built 3D MR image-based computer models that have information derived from the optical measures, as well as morphologic MRI data (i.e., myocardial anatomy, fiber directions and scar definition). The scar morphology from MR images was validated against corresponding whole-mount histology. We also compared the measured 3D isochronal maps of depolarization to simulated isochrones (the latter replicating precisely the experimental conditions), performing model customization and 3D volumetric adjustments of the local conductivity. Our results demonstrated that mean APD in the border zone (BZ) of the infarct scars was reduced by ∼13% (compared to ∼318 ms measured in normal zone, NZ), but APD did not change significantly in the thin BZ of the ablation scars. A generic value for velocity ratio (1:2.7) in healthy myocardial tissue was derived from measured values of transverse and longitudinal conduction velocities relative to fibers direction (22cm/s and 60cm/s, respectively). The model customization and 3D volumetric adjustment reduced the differences between measurements and simulations; for example, from one pacing location, the adjustment reduced the absolute error in local depolarization times by a factor of 5 (i.e., from 58 ms to 11 ms) in the infarcted heart, and by a factor of 6 (i.e., from 60 ms to 9 ms) in the heart with the RF scar. Moreover, the sensitivity of adjusted conductivity maps to different pacing locations was tested, and the errors in activation times were found to be of approximately 10-12 ms independent of pacing location used to adjust model parameters, suggesting that any location can be used for model predictions.

Graphical abstract

Highlights

► Successful construction of 3D MRI-based models of pathologic pig hearts. ► 3D model accurately depicts anatomy, scar heterogeneity and fiber directions. ► Categorization of heterogeneous zones was validated using histology. ► Model parameterization used action potential waves from optical imaging.

Mitral annulus segmentation from four-dimensional ultrasound using a valve state predictor and constrained optical flow

admin — Sun, 04 Dec 2011 21:50:23 +0000

Publication year: 2011
Source: Medical Image Analysis, Available online 3 December 2011

Robert J. Schneider, Douglas P. Perrin, Nikolay V. Vasilyev, Gerald R. Marx, Pedro J. del Nido, …

Measurement of the shape and motion of the mitral valve annulus has proven useful in a number of applications, including pathology diagnosis and mitral valve modeling. Current methods to delineate the annulus from four-dimensional (4D) ultrasound, however, either require extensive overhead or user-interaction, become inaccurate as they accumulate tracking error, or they do not account for annular shape or motion. This paper presents a new 4D annulus segmentation method to account for these deficiencies. The method builds on a previously published three-dimensional (3D) annulus segmentation algorithm that accurately and robustly segments the mitral annulus in a frame with a closed valve. In the 4D method, a valve state predictor determines when the valve is closed. Subsequently, the 3D annulus segmentation algorithm finds the annulus in those frames. For frames with an open valve, a constrained optical flow algorithm is used to the track the annulus. The only inputs to the algorithm are the selection of one frame with a closed valve and one user-specified point near the valve, neither of which needs to be precise. The accuracy of the tracking method is shown by comparing the tracking results to manual segmentations made by a group of experts, where an average RMS difference of 1.67 ±0.63mm was found across 30 tracked frames.

Graphical abstract

Highlights

► 4D mitral annulus segmentation algorithm changes methods based on the valve state. ► Valve state is automatically determined from the 3D ultrasound images. ► Closed valve annuli are directly segmented, whereas open valve annuli are tracked. ► Tracking is done using a geometrically constrained optical flow algorithm. ► Annulus delineations are user-independent given reasonable user inputs.

Sequence diversity in haloalkane dehalogenases, as revealed by PCR using family-specific primers

admin — Sat, 03 Dec 2011 21:41:34 +0000

Publication year: 2011
Source: Journal of Microbiological Methods, Available online 2 December 2011

Michael Kotik, Veronika Faměrová

Haloalkane dehalogenases (HLDs) are hydrolytic enzymes that cleave carbon-halogen bonds in various halogenated compounds. Interest initially grew in HLDs as biocatalysts for bioremediation and later for biotransformation applications; each specific HLD within the HLD family has its own substrate specificity, enantioselectivity and product inhibition characteristics. We developed degenerate oligonucleotide primers for HLD-encoding genes and used these to PCR-amplify largehldgene fragments using genomic DNA from the microbial community of a chlorinated-solvent-contaminated aquifer as a template. An analysis of small subunit ribosomal RNA genes revealed a high complexity in the eubacterial population, dominated by α-, β- and γ-Proteobacteria, andAcidobacteria. Using HLD-family-specific primers, we also retrieved transcribedhldhomologues from the microbial consortium of this contaminated site. The DNA-derivedhldsequences were phylogenetically broadly distributed over both HLD subclasses I and II. Mosthldsequences of the environmental RNA data set clustered in three groups within both HLD subclasses, indicating that a considerable proportion of the microbial consortium carryinghldgenes was actively involved in haloalkane dehalogenation. The small sequence variation inhldgenes and transcripts within each HLD cluster inferred the presence of a substantial pool of highly related HLD genes. The sequence variability appeared to be unevenly distributed over the HLD genes, however, with no apparent preference for a particular protein segment or domain.

Highlights

► We developed degenerate haloalkane dehalogenase (HLD)-specific primers. ► Large fragments of HLD-encoding genes and transcripts were retrieved from a microbial community. ► The retrieved sequences were phylogenetically broadly distributed over both HLD subfamilies I and II.

Corrigendum to “Immunological detection of UV induced cyclobutane pyrimidine dimers and (6-4) photoproducts in DNA from reference bacteria and natural aquatic populations” [Journal of Microbiological Methods 84 (2011) 435–441]

admin — Sat, 03 Dec 2011 21:41:34 +0000

Publication year: 2011
Source: Journal of Microbiological Methods, Available online 1 December 2011

Kraft Stephanie, Obst Ursula, Schwartz Thomas

Re-localisation of a Biopsy Site in Endoscopic Images and Characterisation of its Uncertainty

admin — Sat, 03 Dec 2011 03:14:28 +0000

Publication year: 2011
Source: Medical Image Analysis, Available online 1 December 2011

Baptiste Allain, Mingxing Hu, Laurence B. Lovat, Richard J. Cook, Tom Vercauteren, …

Endoscopy guided probe-based optical biopsy is a new method for detecting sites for tissue biopsy and treatment. After detection, it can be useful to provide a visual aid in the endoscopic images to the endoscopist for example for guidance of forceps to the biopsy sites detected optically. A new method for re-localisation of these sites during the endoscopic examination is presented in this paper. It makes use of a sequence of endoscopic images, where the biopsy site location is known, in order to derive the same number of epipolar lines as images in the sequence projected onto a subsequent target image where the re-localised biopsy site needs to be computed. The location of the re-localised biopsy site is found by minimisation of the sum of squared distances to the epipolar lines. The method also determines analytically the uncertainty of the re-localised biopsy site. This provides the endoscopist with a confidence region around the re-localised biopsy site and a measure of the re-localisation precision. Simulations confirmed that the analytical uncertainty has the potential to be a good estimation of the experimental uncertainty. The method was tested on a physical phantom and on real data from 4 patients with 8 sequences of images acquired during gastroscopy. The re-localisation precision and accuracy were estimated at 1 millimetre or better, which is sufficient for re-localisation of optical biopsy sites.

Graphical abstract

Highlights

► A biopsy site is re-localised in endoscopic images using epipolar geometry. ► The uncertainty of the re-localised biopsy site is computed analytically. ► Biopsy sites were re-localised with accuracies greater than 1mm in patient data. ► The analytical uncertainty approximates accurately the experimental uncertainty.

A new typing technique for the RickettsialesEhrlichia ruminantium: Multiple-Locus variable number tandem repeat analysis

admin — Thu, 01 Dec 2011 03:01:38 +0000

Publication year: 2011
Source: Journal of Microbiological Methods, Available online 29 November 2011

Héloïse Pilet, Nathalie Vachiéry, Moez Berrich, Rim Bouchouicha, Benoît Durand, …

Ehrlichia ruminantium(ER) is a member of the order Rickettsiales transmitted byAmblyommaticks. This obligatory intracellular bacterium is the causative agent of a fatal disease in ruminants, named heartwater. It represents a constraint on breeding development in sub-Saharan Africa and in the Caribbean. The genetic diversity of the strains ofER, which could be a limiting factor to obtain effective vaccines, needs to be better characterized. For this purpose, we developed a molecular typing technique based on the polymorphism of variable number tandem repeat (VNTR) sequences, MLVA (Multiple Locus VNTR Analysis).Eight (out of 21) VNTR candidates were validated using 17 samples representing a panel ofERstrains from different geographical origins from West, South Africa, and Caribbean areas and inERinfected ticks and goat tissues. This result demonstrated the ability of these VNTRs to type a wide range of strains. The stability of the selected VNTR markers was very good, at the time scale needed for epidemiological purposes: in particular, no difference in the VNTR profiles was observed between virulent and attenuated strains (for Gardel and Senegal strains) and between strains (Gardel and Blonde strains) isolated in the same area 19 years apart. We validated the strong discriminatory power of MLVA forERand found a high level of polymorphism between the available strains, with 10 different profiles out of 13ERstrains.The MLVA scheme described in this study is a rapid and efficient molecular typing tool forER,which allows rapid and direct typing of this intracellular pathogen without preliminary culture and gives reliable results that can be used for further epidemiological studies.

Highlights

► Ehrlichia ruminantiumcauses heartwater, a fatal tickborne disease of livestock. ► We develop a new molecular typing tool, MLVA, forEhrlichia ruminantium(ER). ► MLVA is very discriminatory (10 profiles/13 strains, D.I. = 0.97). ► As ER grows only intracellularly, we adapt MLVA to direct typing from field samples. ► Certain profiles could be associated to certain geographic locations.

Editorial Board

admin — Thu, 01 Dec 2011 02:30:38 +0000

Publication year: 2011
Source: International Review of Law and Economics, Volume 31, Issue 4, December 2011, Pages CO2

[No author name available]

Author Index (Volume 31, 2011)

admin — Thu, 01 Dec 2011 02:30:38 +0000

Publication year: 2011
Source: International Review of Law and Economics, Volume 31, Issue 4, December 2011, Pages I-II

[No author name available]

Evaluation of nitrate reduction assay, resazurin microtitre assay and microscopic observation drug susceptibility assay for first line antitubercular drugs susceptibility testing of clinical isolates ofM. tuberculosis

admin — Sun, 27 Nov 2011 01:48:35 +0000

Publication year: 2011
Source: Journal of Microbiological Methods, Available online 25 November 2011

Pratima Dixit, Urmila Singh, Pratibha Sharma, Amita Jain

BackgroundDrug resistant tuberculosis (TB) is a growing concern worldwide. Early detection of multidrug-resistantMycobacterium tuberculosisis of primary importance for both patient management and infection control. Optimal method for identifying drug-resistantMycobacterium tuberculosisin a timely and affordable way in resource-limited settings is not yet available.AimThis study evaluated; nitrate reductase assay (NRA), resazurin microtitre assay (REMA) and microscopic observation drug susceptibility assay (MODS) against the conventional 1% proportion method (PM) for the detection of resistance to first line antitubercular drugs, inM. tuberculosisclinical isolates.MethodsTotal one hundred and five clinical isolates ofM. tuberculosis;50 pan sensitive and 55 pan resistant were tested with NRA, REMA and MODS. The 1% proportion method on Lowenstein-Jensen medium was used as reference test.ResultsOf all three methods which were tested NRA was found to be most sensitive and specific. Sensitivity for rifampicin resistance detection was 100%, 94.55% and 92.73% by NRA, REMA and MODS respectively. NRA and REMA were found to be 100% specific, while the MODS was 98% specific for detection of rifampicin resistance. Test results with all these methods were obtained within 8–14 days.ConclusionRapid non-conventional & inexpensive methods may serve as a replacement for 1% proportion method in resource limited settings.

Highlights

► We evaluated 3 rapid methods NRA, REMA and MODS against conventional 1% PM method. ► These methods are simple, inexpensive, accurate and rapid (results available within 8–14 days). ► Among 3 methods NRA was most sensitive, specific and accurate. ► These methods may replace 1% PM for rapid detection of MDR-TB in resource limited settings. ► Early detection of drug resistance will help in patient management and support tuberculosis control programmes.

Corrigendum to Development of a real-time SYBRGreen PCR assay for rapid detection of acquired AmpC in Enterobacteriaceae [J. Microbiol. Methods. 82 (2010) 229–233]

admin — Sun, 27 Nov 2011 01:48:35 +0000

Publication year: 2011
Source: Journal of Microbiological Methods, Available online 25 November 2011

Alma Brolund, Karin Tegmark Wisell, Petra J. Edquist, Lisbeth Elfström, Mats Walder, …

Analysis of fMRI Time Series with Mutual Information

admin — Sat, 26 Nov 2011 00:56:03 +0000

Publication year: 2011
Source: Medical Image Analysis, Available online 25 November 2011

Vanessa Gómez-Verdejo, Manel Martínez-Ramón, José Florensa-Vila, Antonio Oliviero

Neuroimaging plays a fundamental role in the study of human cognitive neuroscience. Functional magnetic resonance imaging (fMRI), based on the Blood Oxygenation Level Dependent signal, is currently considered as a standard technique for a system level understanding of the human brain. The problem of identifying regionally specific effects in neuroimaging data is usually solved by applying Statistical Parametric Mapping (SPM). Here, a mutual information (MI) criterion is used to identify regionally specific effects produced by a task. In particular, two MI estimators are presented for its use in fMRI data. The first one uses a Parzen probability density estimation, and the second one is based on a K Nearest Neighbours (KNN) estimation. Additionally, a statistical measure has been introduced to automatically detect the voxels which are relevant to the fMRI task. Experiments demonstrate the advantages of MI estimators over SPM maps; firstly, providing more significant differences between relevant and irrelevant voxels; secondly, presenting more focalized activation; and, thirdly, detecting small areas related to the task. These findings, and the improved performance of KNN MI estimator in multisubject and multistimuli studies, make the proposed methods a good alternative to SPM.

Graphical abstract

Multisubject brain response estimated using the 3 methods under study, KNN maps are shown in serial and parallel versions. Raw maps (left panel) and their responses after thresholding them (at a 95% confidence level) are displayed. Talairach coordinates of axial slices are 66 mm, 55 mm, -20 mm and -23 mm.Vanessa Gómez-Verdejo, Manel Martínez-Ramón, José Florensa-Vila and Antonio Oliviero.

Highlights

► A mutual information method is used to identify specific effects produced by a task. ► Two MI estimators are proposed for fMRI brain mapping: Parzen windows and KNN. ► A statistical measure has been introduced to automatically threshold the MI maps. ► MI estimators outperform SPM in single subject studies. ► KNN MI shows improved performance in multisubject studies.

Editorial board

admin — Sat, 26 Nov 2011 00:56:03 +0000

Publication year: 2012
Source: Medical Image Analysis, Volume 16, Issue 1, January 2012, Pages IFC

[No author name available]

Acknowledgements to Reviewers

admin — Sat, 26 Nov 2011 00:56:03 +0000

Publication year: 2012
Source: Medical Image Analysis, Volume 16, Issue 1, January 2012, Pages I-II

[No author name available]

A polyphasic approach for the characterization of endophyticAlternariastrains isolates from grapevines

admin — Thu, 24 Nov 2011 00:53:38 +0000

Publication year: 2011
Source: Journal of Microbiological Methods, Available online 23 November 2011

Rachele Polizzotto, Birgitte Andersen, Marta Martini, Simone Grisan, Gemma Assante, …

A polyphasic approach was set up and applied to characterize 20 fungal endophytes belonging to the genusAlternaria, recovered from grapevine in different Italian regions.Morphological, microscopical, molecular and chemical investigations were performed and the obtained results were combined in a pooled cluster analysis. Following morphological analyses, all strains were grouped according to their three-dimensional sporulation pattern on PCA and to the colony characteristics on different substrates. After DNA extraction, all strains were analyzed by RAPD-PCR and the resulting profiles were subjected to cluster analysis. The metabolites extracted from the 20Alternariaendophytes were analyzed by a HPLC and the resulting metabolite profiles were subjected to multivariate statistic analyses. In comparison with reference ‘small-spored’Alternariaspecies, the 20 strains were segregated into two morphological groups: one belonging to theA. arborescensspecies-group and a second to theA. tenuissimaspecies-group. RAPD analysis also showed that grapevine endophytes belonged to either theA.arborescensor theA. tenuissimaspecies-group and that they were molecularly distinct from strains belonging toA. alternata. Chemotaxonomy gave the same grouping: the grapevine endophytic strains belong toA.arborescensorA. tenuissimaspecies-groups producing known metabolites typical of these species-groups. Interestingly, the 20 grapevine endophytes were able to produce also a number of unknown metabolites, whose characterization could be useful for a more precise segregation of the two species-groups.The results show how complementary morphological, molecular and chemical data can clarify relationships among endophyte species-groups of low morphological divergence.

Highlights

► Small-sporedAlternariaspecies often dominate among endophytic fungi.► Alternariagrapevine endophytic fungi have been described by a polyphasic approach. ► Morphological, microscopical, molecular and chemical investigations were set up. ► The obtained results were combined in a pooled cluster analysis. ► Relationships among species-groups of low morphological divergence are established.

The Rise and Fall of the Polluter-Pays Principle in Developing Countries

admin — Sun, 20 Nov 2011 23:45:20 +0000

Publication year: 2011
Source: International Review of Law and Economics, Available online 19 November 2011

Barbara Luppi, Francesco Parisi, Shruti Rajagopalan

The polluter-pays principle stipulates that the person who damages the environment must bear the cost of such damage. A number of developing countries have recently extended this principle to create an obligation on the state to compensate the victims of environmental harm. This variation of the polluter-pays principle is aimed at ensuring victims’ compensation when polluters cannot be identified or are insolvent and at providing stronger incentives for local governments’ monitoring of environmentally risky activities. These regimes hold local governments primarily or jointly-and-severally liable for environmental damage and allow them to act in subrogation against the polluters. In this paper we study the effect of these forms of governmental liability on the polluters’ incentives and on aggregate levels of environmental harm. We develop an economic model to study the conditions under which governmental liability may be preferable to direct polluters’ liability as an instrument of environmental protection. We conclude by suggesting that these variations of the polluter-pays regime may be desirable in environments characterized by widespread poverty, high interest rates, judicial delays and uncertainty in adjudication.

Highlights

► A number of developing countries have extended the polluter-pays principle to create an obligation on the state to compensate the victims of environmental harm. ► The paper examines the effect of these forms of governmental liability on the polluters’ incentives and on aggregate levels of environmental harm. ► The paper shows that governmental liability may be preferable to direct polluters’ liability in environments characterized by widespread poverty, high interest rates, judicial delays and uncertainty in adjudication.

A ‘bacteriocin PCR array’ for identification of bacteriocin-related structural genes in lactic acid bacteria

admin — Sat, 19 Nov 2011 00:19:05 +0000

Publication year: 2011
Source: Journal of Microbiological Methods, Available online 18 November 2011

Sunita J. Macwana, Peter M. Muriana

Bacteriocins have been identified in many strains of lactic acid bacteria (LAB) which are a source of natural food preservatives and microbial inhibitors. Our objectives were to use a PCR array of primers to identify bacteriocin structural genes in BacLAB . DNA sequence homology at the 5’- and 3’-ends of the various structural genes indicated that non-specific priming may allow PCR amplification of heterologous bacteriocin genes. Successful amplification was obtained by real-time PCR and confirmed by melting curve and agarose gel analysis. Sequence information specific to targeted bacteriocin structural genes from the intra-primer regions of amplimers was compared to sequences residing in GenBank. The bacteriocin PCR array allowed the successful amplification of bacteriocin structural genes from strains ofLactobacillus, Lactococcus, and Pediococcusincluding one whose amino acid sequence was unable to be determined by Edman degradation analysis. DNA sequence analysis identified as many as 3 bacteriocin structural genes within a given strain, identifying ten unique bacteriocin sequences that were previously uncharacterized (partial homology) and one that was 100% identical to sequences in GenBank. This study provides a rapid approach to sequence and identify bacteriocin structural genes among BacLAB using a microplate bacteriocin PCR array.

Highlights

► A bacteriocin PCR array to identify bacteriocin genes in lactic acid bacteria. ► Assay to identify bacteriocin structural genes in LAB without any prior genetic information. ► Assay can identify 3 bacteriocin structural genes within the same strain.

Feature-Based Interpolation of Diffusion Tensor Fields and Application to Human Cardiac DT-MRI

admin — Thu, 17 Nov 2011 23:54:51 +0000

Publication year: 2011
Source: Medical Image Analysis, Available online 17 November 2011

Feng Yang, Yuemin Zhu, Isabelle E. Magnin, Jian-Hua Luo, Pierre Croisille, …

Diffusion tensor interpolation is an important issue in the application of diffusion tensor magnetic resonance imaging (DT-MRI) to the human heart, all the more as the points representing the myocardium of the heart are often sparse. We propose a feature-based interpolation framework for the tensor fields from cardiac DT-MRI, by taking into account inherent relationships between tensor components. In this framework, the interpolation consists in representing a diffusion tensor in terms of two tensor features, eigenvalues and orientation, interpolating the Euler angles or the quaternion relative to tensor orientation and the logarithmically transformed eigenvalues, and reconstructing the tensor to be interpolated from the interpolated eigenvalues and tensor orientations. The results obtained with the aid of both synthetic and real cardiac DT-MRI data demonstrate that the feature-based schemes based on Euler angles or quaternions not only maintain the advantages of Log-Euclidean and Riemannian interpolation as for preserving the tensor’s symmetric positive-definiteness and the monotonic determinant variation, but also preserve, at the same time, the monotonicity of fractional anisotropy (FA) and mean diffusivity (MD) values, which is not the case with Euclidean, Cholesky and Log-Euclidean methods. As a result, both interpolation schemes remove the phenomenon of FA collapse, and consequently avoid introducing artificial fiber crossing, with the difference that the quaternion is independent of coordinate system while Euler angles have the property of being more suitable for sophisticated interpolations.

Graphical abstract

Feature-Based Interpolation of Tensor Fields in Human Cardiac DT-MRI (red circledtensors are original tensors before interpolation, the color of a tensor represent its principal eigenvector orientation)

Highlights

► A novel method for diffusion tensor interpolation. ► A diffusion tensor is represented by tensor eigenvalues and tensor orientation. ► Eliminate swelling effect, preserve simultaneously the monotonicity of FA and MD. ► No artificial crossing fibers introduced.

Rapid detection ofblaIMP-6by Amplification Refractory Mutation System

admin — Thu, 17 Nov 2011 00:00:11 +0000

Publication year: 2011
Source: Journal of Microbiological Methods, Available online 15 November 2011

Shizuo Kayama, Norifumi Shigemoto, Ryuichi Kuwahara, Makoto Onodera, Michiya Yokozaki, …

Klebsiella pneumoniaeresistant to almost all ß-lactams except imipenem designated as ISMRK (imipenem-susceptible meropenem-resistant Klebsiella) is emerging in Japan. All ISMRK carriesblaIMP-6which differs fromblaIMP-1by only a single nucleotide at position 640. We devised a rapid detection system ofblaIMP-6by using ARMS PCR.

Real-time image-based rigid registration of three-dimensional ultrasound

admin — Tue, 15 Nov 2011 23:42:00 +0000

Publication year: 2011
Source: Medical Image Analysis, Available online 15 November 2011

Robert J. Schneider, Douglas P. Perrin, Nikolay V. Vasilyev, Gerald R. Marx, Pedro J. del Nido, …

Registration of three-dimensional ultrasound (3DUS) volumes is necessary in several applications, such as when stitching volumes to expand the field of view or when stabilizing a temporal sequence of volumes to cancel out motion of the probe or anatomy. Current systems that register 3DUS volumes either use external tracking systems (electromagnetic or optical), which add expense and impose limitations on acquisitions, or are image-based methods that operate offline and are incapable of providing immediate feedback to clinicians. This paper presents a real-time image-based algorithm for rigid registration of 3DUS volumes designed for acquisitions in which small probe displacements occur between frames. Described is a method for feature detection and descriptor formation that takes into account the characteristics of 3DUS imaging. Volumes are registered by determining a correspondence between these features. A global set of features is maintained and integrated into the registration, which limits the accumulation of registration error. The system operates in real-time (i.e. volumes are registered as fast or faster than they are acquired) by using an accelerated framework on a graphics processing unit. The algorithm’s parameter selection and performance is analyzed and validated in studies which use both water tank and clinical images. The resulting registration accuracy is comparable to similar feature-based registration methods, but in contrast to these methods, can register 3DUS volumes in real-time.

Graphical abstract

Highlights

► Presented is a fast image-based rigid registration method for 3D ultrasound. ► Registrations are computed in real-time (i.e. ► as fast as volumes are acquired). ► Feature detection and descriptor formation account for 3D ultrasound characteristics. ► Efficient use of a global feature set limits the accumulation of registration error. ► Accuracy of the method is comparable to existing rigid registration methods.

Temporal Diffeomorphic Free-Form Deformation: Application to Motion and Strain Estimation from 3D Echocardiography

admin — Tue, 15 Nov 2011 23:42:00 +0000

Publication year: 2011
Source: Medical Image Analysis, Available online 15 November 2011

Mathieu De Craene, Gemma Piella, Oscar Camara, Nicolas Duchateau, Etelvino Silva, …

This paper presents a new registration algorithm, called Temporal Diffeomorphic Free Form Deformation (TDFFD), and its application to motion and strain quantification from a sequence of 3D ultrasound (US) images. The originality of our approach resides in enforcing time consistency by representing the 4D velocity field as the sum of continuous spatiotemporal B-Spline kernels. The spatiotemporal displacement field is then recovered through forward Eulerian integration of the non-stationary velocity field. The strain tensor is computed locally using the spatial derivatives of the reconstructed displacement field. The energy functional considered in this paper weighs two terms: the image similarity and a regularization term. The image similarity metric is the sum of squared differences between the intensities of each frame and a reference one. Any frame in the sequence can be chosen as reference. The regularization term is based on the incompressibility of myocardial tissue. TDFFD was compared to pairwise 3D FFD and 3D+t FFD, both on displacement and velocity fields, on a set of synthetic 3D US images with different noise levels. TDFFD showed increased robustness to noise compared to these two state-of-the-art algorithms. TDFFD also proved to be more resistant to a reduced temporal resolution when decimating this synthetic sequence. Finally, this synthetic dataset was used to determine optimal settings of the TDFFD algorithm. Subsequently, TDFFD was applied to a database of cardiac 3D US images of the left ventricle acquired from 9 healthy volunteers and 13 patients treated by Cardiac Resynchronization Therapy (CRT). On healthy cases, uniform strain patterns were observed over all myocardial segments, as physiologically expected. On all CRT patients, the improvement in synchrony of regional longitudinal strain correlated with CRT clinical outcome as quantified by the reduction of end-systolic left ventricular volume at follow-up (6 and 12 months), showing the potential of the proposed algorithm for the assessment of CRT.

Graphical abstract

Highlights

► We propose a new diffeomorphic temporal registration algorithm. ► It recovers strain and motion from an input 3D ultrasound image sequence. ► Longitudinal strain was quantified on 9 healthy volunteers and 13 CRT patients. ► On volunteers, results are in agreement with clinical literature. ► On patients, results match CRT outcome as quantified by reverse remodeling.

Tumor Invasion Margin on the Riemannian Space of Brain Fibers

admin — Tue, 15 Nov 2011 23:42:00 +0000

Publication year: 2011
Source: Medical Image Analysis, Available online 15 November 2011

Parisa Mosayebi, Dana Cobzas, Albert Murtha, Martin Jagersand

Glioma is one of the most challenging types of brain tumors to treat or control locally. One of the main problems is to determine which areas of the apparently normal brain contain glioma cells, as gliomas are known to infiltrate several centimetres beyond the clinically apparent lesion that is visualized on standard Computed Tomography scans (CT) or Magnetic Resonance Images (MRI). To ensure that radiation treatment encompasses the whole tumor, including the cancerous cells not revealed by MRI, doctors treat the volume of brain that extends 2 cm out from the margin of the visible tumor. This approach does not consider varying tumor-growth dynamics in different brain tissues, thus it may result in killing some healthy cells while leaving cancerous cells alive in the other areas. These cells may cause recurrence of the tumor later in time, which limits the effectiveness of the therapy. Knowing that glioma cells preferentially spread along nerve fibers, we propose the use of a geodesic distance on the Riemannian manifold of brain diffusion tensors to replace the Euclidean distance used in the clinical practice and to correctly identify the tumor invasion margin. This mathematical model results in a first-order Partial Differential Equation (PDE) that can be numerically solved in a stable and consistent way. To compute the geodesic distance, we use actual Diffusion Weighted Imaging (DWI) data from 11 patients with glioma and compare our predicted infiltration distance map with actual grwoth in follow-up MRI scans. Results show improvement in predicting the invasion margin when using the geodesic distance as opposed to the 2 cm conventional Euclidean distance.

Graphical abstract

Highlights

► Glioma cells infiltrate for several cm beyond the margin visible in MRI. ► Doctors treat the brain volume that extends 2cm out from the visible margin. ► Tumour cells preferentially move in the direction of brain fibres. ► Use a geodesic distance on DTI to define a better anisotropic radiation margin

Multiplex allele-specific PCR combined with PCR-RFLP analysis for rapid detection ofgyrAgene fluoroquinolone resistance mutations inMycobacterium tuberculosis

admin — Mon, 14 Nov 2011 23:58:57 +0000

Publication year: 2011
Source: Journal of Microbiological Methods, Available online 13 November 2011

Li-li Zhao, Qiang Xia, Nan Lin, Zhi-guang Liu, Xiu-qin Zhao, …

A modified multiplex allele-specific (MAS) PCR, which combines MAS-PCR and restriction fragment length polymorphism (RFLP) analysis, was established to detect mutations in codons 90, 91 and 94 of thegyrAgene inMycobacterium tuberculosis(M. tuberculosis). With conventional phenotypic drug susceptibility testing as a reference standard, the sensitivity, specificity and accuracy of the modified method forgyrAgene mutation detection was 70.8%, 100% and 84.8% respectively.

Highlights

► We established MAS-PCR combined with RFLP analysis to detect flouroquinolone resistance in M. tuberculosis. ► The method could find out the possible mutations in codons 90, 91 and 94 of the gyrA in M. tuberculosis. ► The performance of the method was evaluated with 125 clinical isolates of M. tuberculosis from China. ► The method is sensitive, specific and accurate enough to permit rapid detection of flouroquinolone resistant M. tuberculosis.

Hollow-Fiber Ultrafiltration for Simultaneous Recovery of Viruses, Bacteria and Parasites from Reclaimed Water

admin — Sat, 12 Nov 2011 23:40:42 +0000

Publication year: 2011
Source: Journal of Microbiological Methods, Available online 12 November 2011

Pengbo Liu, Vincent R. Hill, Donghyun Hahn, Trisha B. Johnson, Yi Pan, …

Hollow-fiber ultrafiltration (UF) is a technique that has been reported to be effective for recovering a diverse array of microbes from water, and may also be potentially useful for microbial monitoring of effluent from water reclamation facilities. However, few data are available to indicate the potential limitations and efficacy of the UF technique for treated wastewater. In this study, recovery efficiencies were determined for various options available for performing the tangential-flow UF technique, including hollow-fiber ultrafilter (i.e., dialyzer) type, ultrafilter pre-treatment (i.e., blocking), and elution. MS2 and ΦX174 bacteriophages,Clostridium perfringensspores,Escherichia coli, andCryptosporidium parvumoocysts were seeded into 10-L reclaimed water samples to evaluate UF options. Then a single UF protocol was established and studied using seeded and non-seeded 100-L samples from two water reclamation facilities in Georgia, USA. Baxter Exeltra Plus 210 and Fresenius F200NR dialyzers were found to provide significantly higher microbial recovery than Minntech HPH 1400 hemoconcentrators. The selected final UF method incorporated use of a non-blocked ultrafilter for UF followed by elution using a surfactant-based solution. For 10-L samples, this method achieved recovery efficiencies of greater than 50% recovery of seeded viruses, bacteria, and parasites. There was no significant difference in overall microbial recovery efficiency when the method was applied to 10- and 100-L samples. In addition, detection levels for pathogens in seeded 100-L reclaimed water samples were 1,000 PFU HAV, 10,000 GI norovirus particles, < 500Salmonellaand < 200Cryptosporidiumoocysts. These data demonstrate that UF can be an effective technique for recovering diverse microbes in reclaimed water to monitor and improve effluent water quality in wastewater treatment plants.

Highlights

► Calf serum blocking was ineffective for the recovery of bacteria, viruses, and parasites in reclaimed water samples using the Fresenius F200NR and Baxter Exeltra Plus 210 ultrafilters. ► Elution procedure was found to significantly increase the recovery efficiency of the ultrafiltration method for both the Fresenius and Baxter ultrafilters. ► Ultrafiltration procedure in this study can be effectively used in conjunction with secondary concentration and multiple analytical techniques to enable sensitive detection of pathogens and microbial indicators in 10-L and 100-L reclaimed water samples.

High-throughput analysis of growth differences among phage strains

admin — Sat, 12 Nov 2011 23:40:42 +0000

Publication year: 2011
Source: Journal of Microbiological Methods, Available online 12 November 2011

Paul E. Turner, Jeremy A. Draghi, Regina Wilpiszeski

Although methods such as spectrophotometry are useful for identifying growth differences among bacterial strains, it is currently difficult to similarly determine whether bacteriophage strains differ in growth using high throughput methods. Here we use automated spectrophotometry to develop anin vitromethod for indirectly distinguishing fitness (growth) differences among virus strains, based on direct measures of their infected bacterial hosts. We used computer simulations of a mathematical model for phage growth to predict which features of bacterial growth curves were best associated with differences in growth among phage strains. We then tested these predictions using thein vitromethod to confirm which of the inferred viral growth traits best reflected known fitness differences among genotypes of the RNA phage phi-6, when infecting aPseudomonas syringaehost. Results showed that the inferred phage trait of time-to-extinction (time required to drive bacterial density below detectable optical density) reliably correlated with genotype rankings based on absolute fitness (phage titer per ml). These data suggested that the high-throughput analysis was valuable for identifying growth differences among virus strains, and that the method may be especially useful for high throughput analyses of fitness differences among phage strains cultured and/or evolved in liquid (unstructured) environments.

Highlights

► Automated spectrophotometry of host bacteria as indicator of phage fitness ► Math model and computer simulation predict phage fitness from host growth ► Theory predictions confirmed by phage and bacteria experiments ► Automated results correlate with known phage fitness rankings using classic methods