Search results for "PCR"

Impact of maize mucilage on atrazine mineralization andatzC abundance

2005

Soil was amended with maize mucilage, a major rhizodeposit, to study its role on the number of culturable soil micro-organisms, the structure of the bacterial community, atrazine mineralization and atzC abundance. The maximal percentage of atrazine mineralization was lower for mucilage-amended than for water-amended soil. Total culturable soil bacteria and 16S rDNA copy number, measured by RT-PCR, presented similar values and were not significantly (P < 0.05) different among treatments. Mucilage applied at a rate of 70 mu g C g(-1) dry soil day(-1) over two weeks did not modify the abundance of the total soil microflora. Global structure of soil bacterial communities revealed by RISA analys…

A real-time PCR assay for detection and quantification of 2-branched (1,3)-β-D–glucan producing lactic acid bacteria in cider

2010

28 p.-1 fig.-4 tab.

Population Data of Nine STR Loci From Western Sicily, Italy

2008

Salt drying: a low-cost, simple and efficient method for storing plants in the field and preserving biological repositories for DNA diversity researc…

2013

Although a variety of methods have been optimized for the collection and storage of plant specimens, most of these are not suited for field expeditions for a variety of logistic reasons. Drying specimens with silica gel in polyethylene bags is currently the standard for field-sampling methods that are suitable for subsequent DNA extraction. However, silica-gel repositories are not readily available in remote areas, and its use is not very cost-effective for the long-term storage of collections or in developing countries with limited research budgets. Salting is an ancient and traditional drying process that preserves food samples by dehydrating tissues and inhibiting water-dependent cellula…

Characterization of denitrification gene clusters of soil bacteria via a metagenomic approach

2009

International audience; Denitrification is a microbial respiratory process contributing to the emission of greenhouse gas. The study of denitrifying bacteria, like that of others, is hindered by characteristics that can prevent up to 99% of soil bacteria from being cultivated in vitro. New approaches based on the direct extraction of DNA from the natural environment and PCR amplifications can overcome limitations due to bacterial unculturability, but until now their application to denitrification genes has led only to the recovery of partial sequences for some of these genes.Our goals in this study were to apply a metagenomic approach characterized by cloning of DNA extracted from soil and …

On extremal cases of Hopcroft’s algorithm

2010

AbstractIn this paper we consider the problem of minimization of deterministic finite automata (DFA) with reference to Hopcroft’s algorithm. Hopcroft’s algorithm has several degrees of freedom, so there can exist different executions that can lead to different sequences of refinements of the set of the states up to the final partition. We find an infinite family of binary automata for which such a process is unique, whatever strategy is chosen. Some recent papers (cf. Berstel and Carton (2004) [3], Castiglione et al. (2008) [6] and Berstel et al. (2009) [1]) have been devoted to find families of automata for which Hopcroft’s algorithm has its worst execution time. They are unary automata as…

Hopcroft’s Algorithm and Cyclic Automata

2008

Minimization of deterministic finite automata is a largely studied problem of the Theory of Automata and Formal Languages. It consists in finding the unique (up to isomorphism) minimal deterministic automaton recognizing a set of words. The first approaches to this topic can be traced back to the 1950’s with the works of Huffman and Moore (cf. [12,15]). Over the years several methods to solve this problem have been proposed but the most efficient algorithm in the worst case was given by Hopcroft in [11]. Such an algorithm computes in O(n log n) the minimal automaton equivalent to a given automaton with n states. The Hopcroft’s algorithm has been widely studied, described and implemented by …

Hopcroft's algorithm and tree-like automata

2011

Minimizing a deterministic finite automata (DFA) is a very important problem in theory of automata and formal languages. Hopcroft's algorithm represents the fastest known solution to the such a problem. In this paper we analyze the behavior of this algorithm on a family binary automata, called tree-like automata, associated to binary labeled trees constructed by words. We prove that all the executions of the algorithm on tree-like automata associated to trees, constructed by standard words, have running time with the same asymptotic growth rate. In particular, we provide a lower and upper bound for the running time of the algorithm expressed in terms of combinatorial properties of the trees…

Circular sturmian words and Hopcroft’s algorithm

2009

AbstractIn order to analyze some extremal cases of Hopcroft’s algorithm, we investigate the relationships between the combinatorial properties of a circular sturmian word (x) and the run of the algorithm on the cyclic automaton Ax associated to (x). The combinatorial properties of words taken into account make use of sturmian morphisms and give rise to the notion of reduction tree of a circular sturmian word. We prove that the shape of this tree uniquely characterizes the word itself. The properties of the run of Hopcroft’s algorithm are expressed in terms of the derivation tree of the automaton, which is a tree that represents the refinement process that, in the execution of Hopcroft’s alg…

On Extremal Cases of Hopcroft’s Algorithm

2009

In this paper we consider the problem of minimization of deterministic finite automata (DFA) with reference to Hopcroft’s algorithm. Hopcroft’s algorithm has several degrees of freedom, so there can exist different sequences of refinements of the set of the states that lead to the final partition. We find an infinite family of binary automata for which such a process is unique. Some recent papers (cf. [3,7,1]) have been devoted to find families of automata for which Hopcroft’s algorithm has its worst execution time. They are unary automata associated to circular words. However, automata minimization can be achieved also in linear time when the alphabet has only one letter (cf. [14]), so in …