42,058 research outputs found
Selection of reference genes suitable for normalization of qPCR data under abiotic stresses in bioenergy crop Arundo donax L.
No full textAbstract Suitable reference gene selection in qRT-PCR is a key pre-requisite to produce reliable data in gene expression analyses. In this study, novel primers for six commonly used reference genes (AC1, TLF, Act2, TUB α, EF-1α and GAPDH) plus two new candidates (pDUF221 and RPN6) were designed and comparatively tested for expression stability under abiotic stresses (osmotic, heavy metal and heat shock) in shoot, root and their combination of Arundo donax L., a raising non-food energy crop. Expression stability rankings from the most to the least stable gene in each condition and in two tissues (young shoots and roots) were generated with geNorm, NormFinder and BestKeeper programs. All programs provided similar rankings and, strikingly, in most cases identified one of the new candidates, RPN6, as the most suitable reference gene. This novel set of reliable references allows to choose either the best combination of reference genes across multiple stress/organ conditions or to select condition-specific genes that can improve the quality of qRT-PCR analysis. This work provides a solid basis for the functional characterization of A. donax, by enabling accurate quantification of the transcriptional responsiveness under a series of common stress conditions of any gene of interest in this promising biomass/bioenergy species
Rates of evolution in stress-related genes are associated with habitat preference in two <it>Cardamine </it>lineages
No full textAbstract Background Elucidating the selective and neutral forces underlying molecular evolution is fundamental to understanding the genetic basis of adaptation. Plants have evolved a suite of adaptive responses to cope with variable environmental conditions, but relatively little is known about which genes are involved in such responses. Here we studied molecular evolution on a genome-wide scale in two species of Cardamine with distinct habitat preferences: C. resedifolia, found at high altitudes, and C. impatiens, found at low altitudes. Our analyses focussed on genes that are involved in stress responses to two factors that differentiate the high- and low-altitude habitats, namely temperature and irradiation. Results High-throughput sequencing was used to obtain gene sequences from C. resedifolia and C. impatiens. Using the available A. thaliana gene sequences and annotation, we identified nearly 3,000 triplets of putative orthologues, including genes involved in cold response, photosynthesis or in general stress responses. By comparing estimated rates of molecular substitution, codon usage, and gene expression in these species with those of Arabidopsis, we were able to evaluate the role of positive and relaxed selection in driving the evolution of Cardamine genes. Our analyses revealed a statistically significant higher rate of molecular substitution in C. resedifolia than in C. impatiens, compatible with more efficient positive selection in the former. Conversely, the genome-wide level of selective pressure is compatible with more relaxed selection in C. impatiens. Moreover, levels of selective pressure were heterogeneous between functional classes and between species, with cold responsive genes evolving particularly fast in C. resedifolia, but not in C. impatiens. Conclusions Overall, our comparative genomic analyses revealed that differences in effective population size might contribute to the differences in the rate of protein evolution and in the levels of selective pressure between the C. impatiens and C. resedifolia lineages. The within-species analyses also revealed evolutionary patterns associated with habitat preference of two Cardamine species. We conclude that the selective pressures associated with the habitats typical of C. resedifolia may have caused the rapid evolution of genes involved in cold response.</p
High-throughput, robust and highly time-flexible method for surface sterilization of Arabidopsis seeds
No full textArabidopsis is by far the plant model species most widely used for functional studies.
The surface sterilization of Arabidopsis seeds is a fundamental step required towards
this end. Thus, it is paramount to establish high-throughput Arabidopsis seed surface
sterilization methods to handle tens to hundreds of samples (e.g., transgenic lines,
ecotypes, or mutants) at once. A seed surface sterilization method based on the
efficient elimination of liquid in tubes with a homemade suction device constructed
from a common vacuum pump is presented in this study. By dramatically reducing
labor-intensive hands-on time with this method handling several hundreds of samples
in one day is possible with little effort. Series time-course analyses further indicated a
highly flexible time range of surface sterilization by maintaining high germination rates.
This method could be easily adapted for surface sterilization of other kinds of small
seeds with simple customization of the suction device according to the seed size, and
the speed desired to eliminate the liquid
Genetic drift linked to heterogeneous landscape and ecological specialization drives diversification in the Alpine endemic columbine Aquilegia thalictrifolia
No full textThe European Alpine system is an extensive mountain range, whose heterogeneous landscape together with Quaternary climatic oscillations significantly affected organismal diversity and distribution in Europe. The model genus Aquilegia representsa textbook example of a rapid and recent radiation through the Northern hemisphere, with the majority of the European taxa occuring in the Alpine system. However, the processes governing genetic differentiation of the genus in this complex geographicarea are still widely unexplored. In this work, we used 9 microsatellite loci to study the genetic structure and diversity of 11 populations of Aquilegia thalictrifolia Schott & Kotschy, an alpine taxon characterized by a marked ecological specificity.We found that, despite the endemic and fragmented distribution, A. thalictrifolia has overall high levels of heterozygosity, which is consistent to the substantial inbreeding depression that characterizes the genus. Strong spatial genetic structuring ofpopulations suggests a historical prevalence of genetic drift over gene flow, with natural barriers and ecological niche hindering migration. An analytical comparison of fixation and population differentiation indexes allowed us to infer hypothesesof the postglacial history and more recent demographic events that have influenced the genetics of the species. Overall, ourresults indicate allopatry as a major force of differentiation in the European scenario, likely to underlie the development oftaxonomic boundaries in a broader geographic context. This adds to previous notions on the primary evolutionary forcesshaping the Aquilegia radiation in Europ
In silico identification and characterization of a diverse subset of conserved microRNAs in bioenergy crop Arundo donax L.
No full textMicroRNAs (miRNAs) are small non-coding RNA molecules involved in the post-transcriptional regulation of gene expression in plants. Arundo donax L. is a perennial C-3 grass considered one of the most promising bioenergy crops. Despite its relevance, many fundamental aspects of its biology still remain to be elucidated. In the present study we carried out the first in silico mining and tissue-specific characterization of microRNAs and their putative targets in A. donax. We identified a total of 141 miRNAs belonging to 14 families along with the corresponding primary miRNAs, precursor miRNAs and a total of 462 high-confidence predicted targets and novel target sites were validated by 5'-race. Gene Ontology functional annotation showed that miRNA targets are constituted mainly by transcription factors, but three of the newly validated targets are enzymes involved in novel functions like RNA editing, acyl lipid metabolism and post-Golgi trafficking. Folding variability of pre-miRNA loops and phylogenetic analyses indicate variable selective pressure acting on the different miRNA families. The set of miRNAs identified in this study will pave the road to further miRNA research in Arundo donax and contribute towards a better understanding of miRNA-mediated gene regulatory processes in other bioenergy crops.Peer reviewe
Assessment of Self-Archiving in Institutional Repositories: Depositorship and Full-Text Availability
No full textThis research evaluates the success of open access self-archiving in several well-known institutional repositories. Two assessment factors have been applied to examine the current practice of self-archiving: depositorship and the availability of full text. This research discovers that the rate of author self-archiving is low and that the majority of documents have been deposited by a librarian or administrative staff. Similarly, the rate of full-text availability is relatively low, except for Australian repositories. By identifying different practices of self-archiving, repository managers can create new strategies for the operation of their repositories and the development of archiving policies
Isolation and preliminary characterization of the phytochelatin synthase from the liverwort Marchantia polymorpha
No full textThe enzyme phytochelatin synthase (PCS) is a ubiquitous enzyme in land plants, and it is responsible for the synthesis of phytochelatins (PC). Previous studies suggest that PCS likely plays a pivotal role in the response to metal homeostatic needs and toxicity in all tracheopytes, but until now only a few handful investigations have been addressed to functional characterization of PCS from bryophytes. In the study performed here, we cloned the only PCS gene present in the genome of the model liverwort Marchantia polymorpha. The gene (MpPCS) codes for a predicted protein of 530 aminoacids with an overall identity of 49% to Arabidopsis thaliana PCS1 protein. In line with all other known PCS, also MpPCS has a highly conserved N-terminal domain and a poorly conserved C-terminus encompassing approximately half of the protein. Overexpression of MpPCS in a mutant yeast strain susceptible to heavy metal toxicity increases its tolerance to both cadmium and excess zinc. We are now going to verify, by mass-spectrophotometry, if significantly higher amounts of PCs are synthesized both in cadmium-exposed M. polymorpha gametophytes and in the overexpressor yeast strain, compared respectively with metal-untreated gametophytes and yeast transformed with an empty vector, thus demonstrating that the liverwort possesses the ability of producing PCs and that the encoded enzyme is indeed a functional PCS. Even more so, we want to demonstrate that, when overexpressed in Arabidopsis thaliana cad1-3 mutant (which is lacking PCS1), MpPCS can rescue the mutant phenotype of increased susceptibility to cadmium, indicating a remarkable evolutionary conservation of PCS function between A. thaliana and M. polymorpha
Metal Detoxification in Land Plants: From Bryophytes to Vascular Plants. STATE of the Art and Opportunities
No full textPotentially toxic elements are a widespread concern due to their increasing diffusion into the environment. To counteract this problem, the relationship between plants and metal(loid)s has been investigated in the last 30 years. In this field, research has mainly dealt with angiosperms, whereas plant clades that are lower in the evolutive scale have been somewhat overlooked. However, recent studies have revealed the potential of bryophytes, pteridophytes and gymnosperms in environmental sciences, either as suitable indicators of habitat health and elemental pollution or as efficient tools for the reclamation of degraded soils and waters. In this review, we summarize recent research on the interaction between plants and potentially toxic elements, considering all land plant clades. The focus is on plant applicability in the identification and restoration of polluted environments, as well as on the characterization of molecular mechanisms with a potential outlet in the engineering of element tolerance and accumulation
Information Literacy and Librarian-Faculty Collaboration: A Model for Success:
No full textIn the age of information explosion and technological advancement, issues of information storage, organization, access, and evaluation have become necessarily important in our societies. Addressing issues of information literacy and designing how they can be best integrated in students' learning process are of critical importance. Library professionals in the United States, particularly in the academia, have realized the importance of information literacy and have attempted in various ways to address these issues. The ultimate goal is to make information literacy an integral part of the academic curriculum, thus helping students to succeed not only during their years in college but also for their lifelong career choices. This article will look at ways of how information literacy can best be incorporated into students' academic experience, and how this process can make students' learning meaningful and successful. Specifically, the author will examine the model of librarian-faculty collaboration in integrating information literacy into the curriculum, as demonstrated in the Ohio Five Colleges' Information Literacy Program.Publisher version of this article is available at: http://www.white-clouds.com/iclc/cliej/cl24.ht
Factors to Assess Self-Archiving in Institutional Repositories
No full textThis paper proposes a group of factors that may be used to assess the success of open access self-archiving. It concentrates on self-archiving in institutional repositories. The authors emphasize the importance of examining content materials, particularly the availability of full text versus abstracts and the deposits archived by authors versus by others.Peer reviewe
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