Search results for "FLP"

Quality controls for cell cultures: identification of interspecies cross-contamination by PCR-RFLP analysis of the cytochrome b gene

2012

Cross-contaminations of a cell line with cells of different species represent a potential risk in laboratories handling human and animal cells. Therefore, it is necessary to control such contaminations. Tests based on mitochondrial DNA (mtDNA) are used in forensic analysis, phylogenetic studies and in food authentication. However, the use of mtDNA in quality controls of cell cultures is recent. Mitochondrial sequence differences of closely related animal species are five- to tenfold higher than those of nuclear genes. On the contrary, intraspecies variation in mitochondrial sequences is low in most animal species. Moreover, each cell contains 100–10.000 mitochondrial genomes. The amount of …

Effects of the introduction of a biocontrol strain of Trichoderma atroviride on non target soil micro-organisms

2009

International audience; The main objective of this study was to assess the impact of the application of an antagonistic strain of Trichoderma atroviride on the native microbial soil communities. The structures of the fungal and bacterial communities were assessed by T-RFLP (terminal restriction fragment length polymorphism) method, based on T-RFLP analysis of 18S and 16S rRNA genes, respectively. Results showed that the introduction of the strain I-1237 into two soils slightly modified the microbial diversity, only for a short period of time. Nine months post-inoculation resilience took place, resulting in similar structures of the fungal and bacterial communities in the inoculated and cont…

Evaluation of a modified single-enzyme amplified fragment length polymorphism (SE-AFLP) technique for subtyping Salmonella enterica serotype Enteriti…

2006

Salmonella enterica subsp. enterica serotype Enteritidis is not readily subtyped beyond the level of phage type (PT). Pulsed field gel electrophoresis (PFGE) is generally acknowledged to be the most discriminating typing method for Salmonella, but only a restricted variety of PFGE types has been described for S. enterica serotype Enteritidis. In the present study, a modification of the SE-AFLP typing method was used to investigate both outbreak and apparently sporadic isolates of S. enterica serotype Enteritidis belonging to different PTs and/or PFGE types. The method proved to be as discriminatory as PFGE when combined with phage typing, and provided subtyping data consistent with epidemio…

Genetic population structure of Epinephelus marginatus (Pisces, Serranidae) revealed by two molecular markers

2006

In this paper, data are presented regarding the population structure of dusky grouper (Epinephelus marginatus) which was sampled in the Mediterranean Sea and Atlantic Ocean using two different molecular markers, ND2 RFLP and cytochrome b (cyt b) sequence analysis. The main objective of the study is to analyse the genetic variability of E. marginatus in the Mediterranean Sea to define how the biological characteristics of the species, such as the dispersal capability of pelagic larvae and the benthonic-sedentary life style, can affect the genetic population structure or maintaining the gene flow or determining genetic differences. Furthermore, we considered an Atlantic sample to establish th…

Genotyping of GII.4 and GIIb norovirus RT-PCR amplicons by RFLP analysis

2007

GII.4 and GIIb/Hilversum norovirus (NoV) strains appear to have a prominent epidemiological role in outbreaks or sporadic cases of human gastroenteritis. Sequence analysis, although laborious, is the reference method used for characterization of noroviruses. In this study a screening test is proposed to characterize GIIb and GII.4 NoVs based on restriction fragment length polymorphism (RFLP) analysis of amplicons obtained from the RNA-dependent RNA polymerase (RdRp) region. Virtual analysis of 793 RdRp sequences of GGI and GGII NoVs, retrieved from GenBank, and representative of global geographical origins on a long-time period, permitted the selection of four restriction enzymes, XmnI, Ahd…

Use of pulsed field gel electrophoresis (PFGE) and single-enzyme amplified fragment lenght polymorphism (SE-AFLP) to subtype isolates of Salmonella e…

2005

Spatial microbial community structure and biodiversity analysis in "extreme" hypersaline soils of a semiarid Mediterranean area

2015

In recent years specific attention has been paid on the biotechnological potential of microorganisms in extreme soils, in particular in saline soils. Salinity is one of the most widespread soil degradation processes on the Earth, and saline soils can be defined as extreme soils or border line habitats in which several factors, as high salt content, may limit the growth of organisms. In this study, the physical, chemical and microbiological soil properties were investigated in the shallower horizon of natural saltaffected soils in Sicily (Italy). The main aim of the research was to evaluate the structure and diversity of bacterial and archaeal communities by terminal-restriction fragment len…

FLP estimation of semi-parametric models for space-time point processes and diagnostic tools

2015

Abstract The conditional intensity function of a space–time branching model is defined by the sum of two main components: the long-run term intensity and short-run term one. Their simultaneous estimation is a complex issue that usually requires the use of hard computational techniques. This paper deals with a new mixed estimation approach for a particular space–time branching model, the Epidemic Type Aftershock Sequence model. This approach uses a simultaneous estimation of the different model components, alternating a parametric step for estimating the induced component by Maximum Likelihood and a non-parametric estimation step, for the background intensity, by FLP (Forward Predictive Like…

Mixed Non-Parametric and Parametric Estimation Techniques in R Package etasFLP for Earthquakes’ Description

2017

etasFLP is an R package which fits an epidemic type aftershock sequence (ETAS) model to an earthquake catalog; non-parametric background seismicity can be estimated through a forward predictive likelihood approach, while parametric components of triggered seismicity are estimated through maximum likelihood; estimation steps are alternated until convergence is obtained and for each event the probability of being a background event is estimated. The package includes options which allow its wide use. Methods for plot, summary and profile are defined for the main output class object. The paper provides examples of the package's use with description of the underlying R and Fortran routines.

Windowed Etas Models With Application To The Chilean Seismic Catalogs

2015

Abstract The seismicity in Chile is estimated using an ETAS (Epidemic Type Aftershock sequences) space–time point process through a semi-parametric technique to account for the estimation of parametric and nonparametric components simultaneously. The two components account for triggered and background seismicity respectively, and are estimated by alternating a ML estimation for the parametric part and a forward predictive likelihood technique for the nonparametric one. Given the geographic and seismological characteristics of Chile, the sensitivity of the technique with respect to different geographical areas is examined in overlapping successive windows with varying latitude. A different b…