Ixodes chilensis Kohls, 1956 (Acari: Ixodida: Ixodidae): re-description of the female, description of the nymph, and phylogenetic position inferred from mitochondrial DNA sequences of the 16S rRNA gene

2018 ◽  
Vol 95 (8-9) ◽  
pp. 959-967 ◽  
Author(s):  
Daniel González-Acuña ◽  
María N. Saracho-Bottero ◽  
Gonzalo Ossa ◽  
Alberto A. Guglielmone ◽  
Santiago Nava
Keyword(s):  
Mitochondrial Dna ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Sequences ◽  
Phylogenetic Position ◽  
Rrna Gene ◽  
The 16S Rrna Gene

scholarly journals Seasonal changes in bacterial communities associated with healthy and diseasedPoritescoral in southern Taiwan

2016 ◽  
Vol 62 (12) ◽  
pp. 1021-1033 ◽  
Author(s):  
Chorng-Horng Lin ◽  
Chih-Hsiang Chuang ◽  
Wen-Hung Twan ◽  
Shu-Fen Chiou ◽  
Tit-Yee Wong ◽  
...  
Keyword(s):  
Health Status ◽  
Bacterial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Sequences ◽  
Bacterial Communities ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Rrna Gene ◽  
Southern Taiwan ◽  
The 16S Rrna Gene

We compared the bacterial communities associated with healthy scleractinian coral Porites sp. with those associated with coral infected with pink spot syndrome harvested during summer and winter from waters off the coast of southern Taiwan. Members of the bacterial community associated with the coral were characterized by means of denaturing gradient gel electrophoresis (DGGE) of a short region of the 16S rRNA gene and clone library analysis. Of 5 different areas of the 16S rRNA gene, we demonstrated that the V3 hypervariable region is most suited to represent the coral-associated bacterial community. The DNA sequences of 26 distinct bands extracted from DGGE gels and 269 sequences of the 16S rRNA gene from clone libraries were determined. We found that the communities present in diseased coral were more heterogeneous than the bacterial communities of uninfected coral. In addition, bacterial communities associated with coral harvested in the summer were more diverse than those associated with coral collected in winter, regardless of the health status of the coral. Our study suggested that the compositions of coral-associated bacteria communities are complex, and the population of bacteria varies greatly between seasons and in coral of differing health status.

scholarly journals A novel PCR-clamping assay reducing plant host DNA amplification significantly improves prokaryotic endo-microbiome community characterization

2020 ◽  
Vol 96 (7) ◽  
Author(s):  
Emilie Lefèvre ◽  
Courtney M Gardner ◽  
Claudia K Gunsch
Keyword(s):  
Mitochondrial Dna ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Sequences ◽  
High Throughput Sequencing ◽  
Dna Amplification ◽  
Rrna Gene ◽  
Plant Host ◽  
Plant Chloroplast

ABSTRACT Due to the sequence homology between the bacterial 16S rRNA gene and plant chloroplast and mitochondrial DNA, the taxonomic characterization of plant microbiome using amplicon-based high throughput sequencing often results in the overwhelming presence of plant-affiliated reads, preventing the thorough description of plant-associated microbial communities. In this work we developed a PCR blocking primer assay targeting the taxonomically informative V5-V6 region of the 16S rRNA gene in order to reduce plant DNA co-amplification, and increase diversity coverage of associated prokaryotic communities. Evaluation of our assay on the characterization of the prokaryotic endophytic communities of Zea mays, Pinus taeda and Spartina alternifora leaves led to significantly reducing the proportion of plant reads, yielded 20 times more prokaryotic reads and tripled the number of detected OTUs compared to a commonly used V5-V6 PCR protocol. To expand the application of our PCR-clamping assay across a wider taxonomic spectrum of plant hosts, we additionally provide an alignment of chloroplast and mitochondrial DNA sequences encompassing more than 200 terrestrial plant families as a supporting tool for customizing our blocking primers.

scholarly journals Isolation and Characterization of Two European Strains of Ehrlichia phagocytophila of Equine Origin

2002 ◽  
Vol 9 (2) ◽  
pp. 341-343 ◽  
Author(s):  
Anneli Bjöersdorff ◽  
Bodil Bagert ◽  
Robert F. Massung ◽  
Asiya Gusa ◽  
Ingvar Eliasson
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Sequences ◽  
Rrna Gene ◽  
Granulocytic Ehrlichiosis ◽  
Ehrlichia Phagocytophila ◽  
Isolation And Characterization ◽  
Operon Gene ◽  
The 16S Rrna Gene

ABSTRACT We report the isolation and partial genetic characterization of two equine strains of granulocytic Ehrlichia of the genogroup Ehrlichia phagocytophila. Frozen whole-blood samples from two Swedish horses with laboratory-verified granulocytic ehrlichiosis were inoculated into HL-60 cell cultures. Granulocytic Ehrlichia was isolated and propagated from both horses. DNA extracts from the respective strains were amplified by PCR using primers directed towards the 16S rRNA gene, the groESL heat shock operon gene, and the ank gene. The amplified gene fragments were sequenced and compared to known sequences in the GenBank database. With respect to the 16S rRNA gene, the groESL gene, and the ank gene, the DNA sequences of the two equine Ehrlichia isolates were identical to sequences found in isolates from clinical cases of granulocytic ehrlichiosis in humans and domestic animals in Sweden. However, compared to amplified DNA from an American Ehrlichia strain of the E. phagocytophila genogroup, differences were found in the groESL gene and ank gene sequences.

Characterization ofPaenibacillus popilliaerRNA operons

2004 ◽  
Vol 50 (10) ◽  
pp. 779-791 ◽  
Author(s):  
Douglas W Dingman
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Sequences ◽  
Genomic Dna ◽  
5S Rrna ◽  
Rrna Genes ◽  
23S Rrna ◽  
Rrna Gene ◽  
Hybridization Probe ◽  
The 16S Rrna Gene

The terminal 39 nucleotides on the 3' end of the 16S rRNA gene, along with the complete DNA sequences of the 5S rRNA, 23S rRNA, tRNAIle, and tRNAAlagenes were determined for Paenibacillus popilliae using strains NRRL B-2309 and Dutky 1. Southern hybridization analysis with a 16S rDNA hybridization probe and restriction-digested genomic DNA demonstrated 8 copies of the 16S rRNA gene in P. popilliae strains KLN 3 and Dutky 1. Additionally, the 23S rRNA gene in P. popilliae strains NRRL B-2309, KLN 3, and Dutky 1 was shown by I-CeuI digestion and pulsed-field gel electrophoresis of genomic DNA to occur as 8 copies. It was concluded that these 3 P. popilliae strains contained 8 rrn operons. The 8 operon copies were preferentially located on approximately one-half of the chromosome and were organized into 3 different patterns of genes, as follows: 16S-23S-5S, 16S-ala-23S-5S, and 16S-5S-ile-ala-23S-5S. This is the first report to identify a 5S rRNA gene between the 16S and 23S rRNA genes of a bacterial rrn operon. Comparative analysis of the nucleotides on the 3' end of the 16S rRNA gene suggests that translation of P. popilliae mRNA may occur in Bacillus subtilis and Escherichia coli.Key words: Paenibacillus, milky disease, rrn operon, rRNA, tRNA.

scholarly journals Integral Characterization of the 16S rRNA Gene of Non-sporulating Bacteria and Its Action Against Anticarsia gemmatalis Hübner (Lepidoptera: Erebidae)

2020 ◽  
Vol 12 (12) ◽  
pp. 61
Author(s):  
Higor de Oliveira Alves ◽  
Mariana Davanzo Miranda ◽  
Ricardo Antônio Polanczyk ◽  
Joacir do Nascimento ◽  
Janete Apparecida Desiderio ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Marker Gene ◽  
Anticarsia Gemmatalis ◽  
Phylogenetic Position ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Velvetbean Caterpillar ◽  
The 16S Rrna Gene

Brazil is the world’s largest producer of soybean (Glycine max), an extremely important legume due to its source of proteins and essential oils for humans and animals, besides to its applications in the various branches of industry. The velvetbean caterpillar [Anticarsia gemmatalis Hübner (Lepidoptera: Erebidae)] is a great pest that affects this crop and has been controlled by chemical and biological pesticides based on Bacillus thuringiensis. The objectives of this work were to prospect soil microorganisms, to characterize them using the 16S rRNA gene and to perform bioassays to analyze the lethality or subletality of these isolates against A. gemmatalis larvae. The DNA sequencing of the marker gene was complete, covering all conserved regions of it to determine the phylogenetic position of the isolates. Regarding to bioassays, subletality efficacy were low both for sporulant and for the non-sporulant bacterial strains tested. However, based on the signature by complete 16S rRNA analyses of the non-sporulating bacterial isolates, new characteristics worth of studying and prospecting biotechnologically became available.

scholarly journals Phyllobacterium loti sp. nov. isolated from nodules of Lotus corniculatus

2014 ◽  
Vol 64 (Pt_3) ◽  
pp. 781-786 ◽  
Author(s):  
Maximo Sánchez ◽  
Martha-Helena Ramírez-Bahena ◽  
Alvaro Peix ◽  
María J. Lorite ◽  
Juan Sanjuán ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Carbon Sources ◽  
Lotus Corniculatus ◽  
Culture Conditions ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
The 16S Rrna Gene

Strain S658T was isolated from a Lotus corniculatus nodule in a soil sample obtained in Uruguay. Phylogenetic analysis of the 16S rRNA gene and atpD gene showed that this strain clustered within the genus Phyllobacterium . The closest related species was, in both cases, Phyllobacterium trifolii PETP02T with 99.8 % sequence similarity in the 16S rRNA gene and 96.1 % in the atpD gene. The 16S rRNA gene contains an insert at the beginning of the sequence that has no similarities with other inserts present in the same gene in described rhizobial species. Ubiquinone Q-10 was the only quinone detected. Strain S658T differed from its closest relatives through its growth in diverse culture conditions and in the assimilation of several carbon sources. It was not able to reproduce nodules in Lotus corniculatus. The results of DNA–DNA hybridization, phenotypic tests and fatty acid analyses confirmed that this strain should be classified as a representative of a novel species of the genus Phyllobacterium , for which the name Phyllobacterium loti sp. nov. is proposed. The type strain is S658T( = LMG 27289T = CECT 8230T).

scholarly journals Diagnosis of Fulminant Pneumonia Caused by Legionella pneumophila Serogroup 8 with the Sequence Analysis of the 16S rRNA Gene

2011 ◽  
Vol 225 (1) ◽  
pp. 65-69 ◽  
Author(s):  
Toshinori Kawanami ◽  
Kazuhiro Yatera ◽  
Kazumasa Fukuda ◽  
Kei Yamasaki ◽  
Masamizu Kunimoto ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Legionella Pneumophila ◽  
Rrna Gene ◽  
The 16S Rrna Gene
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