Search results for "Ribosomal"
showing 10 items of 851 documents
The impact of arthropods on fungal community structure in Lascaux Cave
2009
Aims: To determine the major components of the fungal population present in Lascaux Cave, France. The ceiling, walls, sediments and soil were colonized by Fusarium solani in 2001 and later, in 2006, black stains appeared. However, the origin of the successive fungal invasions is unknown as well as the ecology of the cave. Methods and Results: The primers nu-SSU-0817F and nu-SSU-1536R were used for the direct amplification of fungal 18S-rDNA sequences from 11 samples. A total of 607 clones were retrieved. Eight out of the ten most abundant phylotypes corresponded to fungi associated with arthropods and represented about 50% of the clones. Conclusions: Entomophilous fungi play an important ro…
Partial Sequence Homogenization in the 5S Multigene Families May Generate Sequence Chimeras and Spurious Results in Phylogenetic Reconstructions
2014
Multigene families have provided opportunities for evolutionary biologists to assess molecular evolution processes and phylogenetic reconstructions at deep and shallow systematic levels. However, the use of these markers is not free of technical and analytical challenges. Many evolutionary studies that used the nuclear 5S rDNA gene family rarely used contiguous 5S coding sequences due to the routine use of head-to-tail polymerase chain reaction primers that are anchored to the coding region. Moreover, the 5S coding sequences have been concatenated with independent, adjacent gene units in many studies, creating simulated chimeric genes as the raw data for evolutionary analysis. This practice…
Plant-associated microbiota as a source of antagonistic bacteria against the phytopathogen Erwinia amylovora.
2022
Control of bacterial plant diseases is a major concern, as they affect economically important species and spread easily, such as the case of fire blight of rosaceous caused by Erwinia amylovora. In the search for alternatives to the use of agrochemicals and antibiotics, this work presents a screening of natural bacterial antagonists of this relevant and devastating phytopathogen. We recovered bacterial isolates from different plant tissues and geographical origins and then selected those with the strongest ability to reduce fire blight symptoms ex vivo and remarkable in vitro antagonistic activity against E. amylovora. None of them elicited a hypersensitivity reaction in tobacco leaves, mos…
Secondary structure determination of conserved SARS-CoV-2 RNA elements by NMR spectroscopy
2020
AbstractThe current pandemic situation caused by the Betacoronavirus SARS-CoV-2 (SCoV2) highlights the need for coordinated research to combat COVID-19. A particularly important aspect is the development of medication. In addition to viral proteins, structured RNA elements represent a potent alternative as drug targets. The search for drugs that target RNA requires their high-resolution structural characterization. Using nuclear magnetic resonance (NMR) spectroscopy, a worldwide consortium of NMR researchers aims to characterize potential RNA drug targets of SCoV2. Here, we report the characterization of 15 conserved RNA elements located at the 5′ end, the ribosomal frameshift segment and t…
Hemoprotozoa of domestic animals in France: Prevalence and molecular characterization
2008
Very limited information is available on epizootiology of haematozoan infections in French domestic animals. In an attempt to address this issue, prevalence of piroplasmida was studied in carnivores and ruminants, whereas prevalence of Hepatozoon spp. was only investigated in carnivores. In total, 383 animals were included in the survey (namely 116 cats, 108 dogs, 91 sheep and 68 cows). Parasite diagnosis was carried out using molecular methods such as PCR and sequencing of the 18S rRNA gene. In addition, ruminant samples were analyzed with the reverse line blotting technique (RLB). Results of RLB and PCR plus sequencing were in total agreement. In carnivores, haematozoan prevalence was clo…
[Molecular methods in the epidemiology of gram-negative bacterial infections]
1999
Identification and typing of bacterial isolates from patients and environment are necessary in order to detect the sources of infections. In recent years different molecular typing methods have been carried out and proved more reliable than methods based on phenotypical characters. We have applied two methods of genotyping, i. e. ribotyping and rrnARDRA (Amplified Ribosomal DNA Restriction Analysis) methods, to the study of different bacterial species. Ribotyping was the first universal method for molecular typing of bacteria. We have succeded both in typing various species of enterobacteria (Salmonella Wien, S. Enteritidis, Shigella sonnei, Proteus spp., Morganella morganii, Providencia sp…
Vigna mungo, V. radiata and V. unguiculata plants sampled in different agronomical-ecological-climatic regions of India are nodulated by Bradyrhizobi…
2009
International audience; Vigna mungo, Vigna radiata and Vigna unguiculata are important legume crops cultivated in India, but little is known about the genetic resources in native rhizobia that nodulate these species. To identify these bacteria, a core collection of 76 slow-growing isolates was built from root nodules of V. mungo, V. radiata and V. unguiculata plants grown at different sites within three agro-ecological-climatic regions of India. The genetic diversity of the bacterial collection was assessed by restriction fragment length polymorphism (RFLP) analysis of PCR-amplified DNA fragments of the 16S–23S rDNA intergenic spacer (IGS) region, and the symbiotic genes nifH and nodC. One …
A New Method for Extracting Skin Microbes Allows Metagenomic Analysis of Whole-Deep Skin
2013
In the last decade, an extensive effort has been made to characterize the human microbiota, due to its clinical and economic interests. However, a metagenomic approach to the skin microbiota is hampered by the high proportion of host DNA that is recovered. In contrast with the burgeoning field of gut metagenomics, skin metagenomics has been hindered by the absence of an efficient method to avoid sequencing the host DNA. We present here a method for recovering microbial DNA from skin samples, based on a combination of molecular techniques. We have applied this method to mouse skin, and have validated it by standard, quantitative PCR and amplicon sequencing of 16S rRNA. The taxonomic diversit…
Corynebacterium aquatimens sp. nov., a lipophilic Corynebacterium isolated from blood cultures of a patient with bacteremia
2012
An unknown lipophilic coryneform bacterium isolated from the blood cultures of a patient with bacteremia was characterized by phenotypic and molecular genetic methods. Chemical analysis revealed the presence of short chain mycolic acids consistent with the genus Corynebacterium. The DNA G+C content was 60.8 mol%. Comparative 16S rRNA gene sequence analysis demonstrated that the isolate represents a new subline within the genus Corynebacterium. The closely phylogenetic relative of the unknown bacterium was found to be C. tuscaniense (97.8% sequence similarity). Partial rpoB gene sequence revealed that strain IMMIB L-2475(T) exhibited 13.5% sequence divergence with C. tuscaniense. The unknown…
Phylogenetic and genomic relationships in Setaria italica and its close relatives based on the molecular diversity and chromosomal organization of 5S…
2001
We have analyzed the phylogenetic and genomic relationships in the genus Setaria Beauv. including diploid and tetraploid species, by means of the molecular diversity of the 5S rDNA spacer and chromosomal organization of the 5S and 18S-5.8S-25S rDNA genes. PCR amplification of the 5S rDNA sequences gave specific patterns. All the species studied here share a common band of about 340 bp. An additional band of an approximately 300-bp repeat unit was found for Setaria verticillata and the Chinese accessions of Setaria italica and Setaria viridis. An additional band of 450 bp was found in the sole species Setaria faberii. Fluorescent in situ hybridization was used for physical mapping of the 5S …