Springer protocols feed by Plant Sciences 
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This is an RSS file. You can use it to subscribe to this data in your favourite RSS reader or to display this data on your own website or blog.Viral Detection by High-Throughput Sequencing
We applied a high-throughput sequencing platform, Ion PGM, for viral detection in fecal samples from adult cows collected in Hokkaido, Japan. Random RT-PCR was performed to amplify RNA extracted from 0.25 ml of fecal specimens (N = 8), and more than 5 μg of cDNA was synthesized. Unbiased high-throughput sequencing using the 318 v2 semiconductor chip of these eight samples yielded 57–580 K (average: 270 K, after data analysis) reads in a single run. As a result, viral genome sequences were detected in each specimen. In addition to bacteriophage, mammal- and insect-derived viruses, partial genome seque...
Source: Springer protocols feed by Plant Sciences - October 9, 2014 Category: Biology Source Type: news
Drawing siRNAs of Viral Origin Out from Plant siRNAs Libraries
Viruses are obligate intracellular entities that infect all forms of life. In plants, invading viral nucleic acids trigger RNA silencing machinery and it results in the accumulation of viral short interfering RNAs (v-siRNAs). The study of v-siRNAs population in biological samples has become a major part of many research projects aiming to identify viruses infecting them, including unknown viruses, even at extremely low titer. Currently, siRNA populations are investigated by high-throughput sequencing approaches, which generate very large data sets. The major difficulty in these studies is to properly analyze such huge amou...
Source: Springer protocols feed by Plant Sciences - October 9, 2014 Category: Biology Source Type: news
Infrared Thermal Analysis of Plant Freezing Processes
Infrared thermal analysis is an invaluable technique to study the plant freezing process. In the differential mode infrared thermal analysis allows to localize ice nucleation and ice propagation in whole plants or plant samples at the tissue level. Ice barriers can be visualized, and supercooling of cells, tissues, and organs can be monitored. Places where ice masses are accommodated in the apoplast can be identified. Here, we describe an experimental setting developed in the laboratory in Innsbruck, give detailed information on the practical procedure and preconditions, and give additionally an idea of the problems that c...
Source: Springer protocols feed by Plant Sciences - May 27, 2014 Category: Biology Source Type: news
Identification of Arabidopsis Mutants with Altered Freezing Tolerance
Low temperature is an important determinant in the configuration of natural plant communities and defines the range of distribution and growth of important crops. Some plants, including Arabidopsis, have evolved sophisticated adaptive mechanisms to tolerate low and freezing temperatures. Central to this adaptation is the process of cold acclimation. By means of this process, many plants from temperate regions are able to develop or increase their freezing tolerance in response to low, nonfreezing temperatures. The identification and characterization of factors involved in freezing tolerance are crucial to understand the mo...
Source: Springer protocols feed by Plant Sciences - May 27, 2014 Category: Biology Source Type: news
Common Garden Experiments to Characterize Cold Acclimation Responses in Plants from Different Climatic Regions
Cold acclimation is a crucial factor to consider in the context of ongoing climate change. Maladaptation with regard to frost damage and use of the growing season may occur depending on cold acclimation cues. Importance of photoperiod and preceding temperatures as cues needs therefore to be evaluated within (ecotypes) and among species. Common garden designs, in particular the (1) establishment of multiple common gardens along latitudinal/altitudinal gradients, (2) with in situ additional climate manipulations and (3) with manipulations in climate chambers are proposed as tools for the detection of local adaptations and re...
Source: Springer protocols feed by Plant Sciences - May 27, 2014 Category: Biology Source Type: news
Mapping of Quantitative Trait Loci (QTL) Associated with Plant Freezing Tolerance and Cold Acclimation
Most agronomic traits are determined by quantitative trait loci (QTL) and exhibit continuous distribution in segregating populations. The genetic architecture and the hereditary characteristics of these traits are much more complicated than those of oligogenic traits and need adapted strategies for deciphering. The model plant Arabidopsis thaliana is widely studied for quantitative traits, especially via the utilization of natural genetic diversity. Here we describe a QTL-mapping protocol for analyzing freezing tolerance after cold acclimation in this species based on its specific genetic tools. Nevertheless, this approach...
Source: Springer protocols feed by Plant Sciences - May 27, 2014 Category: Biology Source Type: news
A Whole-Plant Screening Test to Identify Genotypes with Superior Freezing Tolerance
Freezing tolerance is a determinant factor of persistence of perennials grown in northern climate. Selection for winterhardiness in field nurseries is difficult because of the unpredictability of occurrence of test winters allowing the identification of hardy genotypes. Here we describe a whole-plant assay entirely performed indoor in growth chambers and walk-in freezers to identify genotypes with superior tolerance to freezing within populations of open pollinated species. Three successive freezing stresses are applied to progressively eliminate 90 % of the population and to retain only the 10 % best performing genotypes....
Source: Springer protocols feed by Plant Sciences - May 27, 2014 Category: Biology Source Type: news
Conducting Field Trials for Frost Tolerance Breeding in Cereals
Cereal species can be damaged by frost either during winter or at flowering stage. Frost tolerance per se is only a part of the mechanisms that allow the plants to survive during winter; winterhardiness also considers other biotic or physical stresses that challenge the plants during the winter season limiting their survival rate. While frost tolerance can also be tested in controlled environments, winterhardiness can be determined only with field evaluations. Post-heading frost damage occurs from radiation frost events in spring during the reproductive stages. A reliable evaluation of winterhardiness or of post-heading fr...
Source: Springer protocols feed by Plant Sciences - May 27, 2014 Category: Biology Source Type: news
Measuring Freezing Tolerance: Electrolyte Leakage and Chlorophyll Fluorescence Assays
Quantitative assessment of freezing tolerance is essential to unravel plant adaptations to cold temperatures. Not only the survival of whole plants but also impairment of detached leaves after a freeze–thaw cycle can be used to accurately quantify plant freezing tolerance in terms of LT50 values. Here we describe two methods to determine the freezing tolerance of detached leaves using different physiological parameters. Firstly, we illustrate how to assess the integrity of (predominantly) the plasma membrane during freezing using an electrolyte leakage assay. Secondly, we provide a chlorophyll fluorescence imaging pr...
Source: Springer protocols feed by Plant Sciences - May 27, 2014 Category: Biology Source Type: news
Measuring Freezing Tolerance: Survival and Regrowth Assays
Screening plants for freezing tolerance under tightly controlled conditions is an invaluable technique for studying freezing tolerance and selecting for improved winterhardiness. Artificial freezing tests of cereal plants historically have used isolated crown and stem tissue prepared by “removing all plant parts 3 cm above and 0.5 cm below the crown tissue” (Fowler et al., Crop Sci 21:896–901, 1981). Here, we describe a method of conducting freezing tolerance tests using intact plants grown in small horticultural containers, including suggested methods for collecting and analyzing the data. (Source: Sprin...
Source: Springer protocols feed by Plant Sciences - May 27, 2014 Category: Biology Source Type: news
Introduction: Plant Cold Acclimation and Freezing Tolerance
This introductory chapter provides a brief overview of plant freezing tolerance and cold acclimation and describes the basic concepts and approaches that are currently followed to investigate these phenomena. We highlight the multidisciplinary nature of these investigations and the necessity to use methodologies from different branches of science, such as ecology, genetics, physiology, biochemistry, and biophysics, to come to a complete understanding of the complex adaptive mechanisms underlying plant cold acclimation. (Source: Springer protocols feed by Plant Sciences)
Source: Springer protocols feed by Plant Sciences - May 27, 2014 Category: Biology Source Type: news
Isolation and Characterization of Ice-Binding Proteins from Higher Plants
The characterization of ice-binding proteins from plants can involve many techniques, only a few of which are presented here. Chief among these methods are tests for ice recrystallization inhibition activity. Two distinct procedures are described; neither is normally used for precise quantitative assays. Thermal hysteresis assays are used for quantitative studies but are also useful for ice crystal morphologies, which are important for the understanding of ice-plane binding. Once the sequence of interest is cloned, recombinant expression, necessary to verify ice-binding protein identity can present challenges, and a strate...
Source: Springer protocols feed by Plant Sciences - May 27, 2014 Category: Biology Source Type: news
Characterization of Ice Binding Proteins from Sea Ice Algae
Several polar microalgae are able to live and thrive in the extreme environment found within sea ice, where growing ice crystals may cause mechanical damage to the cells and reduce the organisms’ living space. Among the strategies adopted by these organisms to cope with the harsh conditions in their environment, ice binding proteins (IBPs) seem to play a key role and possibly contribute to their success in sea ice. IBPs have the ability to control ice crystal growth. In nature they are widespread among sea ice microalgae, and their mechanism of function is of interest for manifold potential applications. Here we desc...
Source: Springer protocols feed by Plant Sciences - May 27, 2014 Category: Biology Source Type: news
Estimating Ice Encasement Tolerance of Herbage Plants
One of the key stresses acting on herbage plants during winter is ice encasement, when plants are enclosed in compact ice and turn from aerobic to anaerobic respiration. The cause of cell death is related to the accumulation of metabolites to toxic levels during winter and perhaps also to production of reactive oxygen species (ROS) when plants escape from long-lasting ice cover. The process of ice encasement damage has been studied by sampling studies, indirect measurements of ice tolerance, field tests and provocation methods by increasing stress in the field artificially, thus increasing the ice stress. Here we describe ...
Source: Springer protocols feed by Plant Sciences - May 27, 2014 Category: Biology Source Type: news
Quantification of Superoxide and Hydrogen Peroxide in Leaves
Reactive oxygen species (ROS) are produced in plants under both non-stressful and stressful conditions. Various histochemical staining methods have been developed and are widely used to visualize ROS accumulation sites. In contrast to qualitative analysis, quantification of ROS has been time- and labor consuming. As a consequence, the number of samples, which could be analyzed in parallel, has been limited. To overcome this problem, we introduce an improved semiquantitative method, in which ROS levels are quantified after histochemical staining in plant organs with the digital image analysis package ImageJ. (Source: Spring...
Source: Springer protocols feed by Plant Sciences - May 27, 2014 Category: Biology Source Type: news
