scholarly journals Wolbachia Detection in Field-Collected Mosquitoes from Cameroon

Insects ◽  
2021 ◽  
Vol 12 (12) ◽  
pp. 1133
Author(s):  
Roland Bamou ◽  
Adama Zan Diarra ◽  
Marie Paul Audrey Mayi ◽  
Borel Djiappi-Tchamen ◽  
Christophe Antonio-Nkondjio ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
Aedes Albopictus ◽  
Culex Quinquefasciatus ◽  
Wolbachia Infection ◽  
23S Rrna ◽  
Intracellular Bacteria ◽  
Rna Sequences ◽  
16S Rna

Wolbachia spp., known to be maternally inherited intracellular bacteria, are widespread among arthropods, including mosquitoes. Our study assessed the presence and prevalence of Wolbachia infection in wild mosquitoes collected in Cameroon, using the combination of 23s rRNA Anaplasmatacea and 16s rRNA Wolbachia genes. Mosquitoes that were positive for Wolbachia were sequenced for subsequent phylogenetic analysis. Out of a total of 1740 individual mosquitoes belonging to 22 species and five genera screened, 33 mosquitoes (1.87%) belonging to eight species (namely, Aedes albopictus, A. contigus, Culex quinquefasciatus, C. perfuscus, C. wigglesworthi, C. duttoni, Anopheles paludis and Coquillettidia sp.) were found to be positive for Wolbachia infections. Wolbachia spp. were absent in A. gambiae and A. aegypti, the main vectors of malaria and dengue, respectively. Phylogenetic analysis of the 16S RNA sequences showed they belong mainly to two distinct subgroups (A and B). This study reports the presence of Wolbachia in about eight species of mosquitoes in Cameroon and suggests that future characterisation of the strains is needed.

Scytolyngbya timoleontis, gen. et sp. nov. (Leptolyngbyaceae, Cyanobacteria): a novel false branching Cyanobacteria from China

Phytotaxa ◽  
2015 ◽  
Vol 224 (1) ◽  
pp. 72 ◽  
Author(s):  
Gaofei Song ◽  
Yongguang Jiang ◽  
Renhui Li
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
Type Species ◽  
Intergenic Spacer ◽  
Secondary Structures ◽  
Sensu Stricto ◽  
Polyphasic Approach ◽  
23S Rrna ◽  
Rrna Sequences ◽  
16S Rrna Sequences

A novel genus within Leptolyngbyaceae related to Leptolyngbya morphotypes, Scytolyngbya, gen. nov., is described based on a polyphasic approach in the present study. From a freshwater sample with filaments of oscillatorean cyanobacteria from a well in Hubei Province, China, Scytolyngbya (type species: Scytolyngbya timoleontis, sp. nov.) was found to possess richly and repeatedly false branches and thick sheaths, which distinguishs this genus from Leptolyngbya sensu stricto. Phylogenetic analysis based on 16S rRNA sequences showed that this species was clustered into the Leptolyngbyaceae and separated from the type species Leptolyngbya boryana. The secondary structures of 16S-23S rRNA intergenic spacer of Scytolyngbya timoleontis did not correspond to any previously described species in cyanobacteria.

scholarly journals Multilocus sequence analysis of the family Halomonadaceae

2012 ◽  
Vol 62 (Pt_3) ◽  
pp. 520-538 ◽  
Author(s):  
Rafael R. de la Haba ◽  
M. Carmen Márquez ◽  
R. Thane Papke ◽  
Antonio Ventosa
Keyword(s):  
Phylogenetic Analysis ◽  
Sequence Analysis ◽  
16S Rrna ◽  
Halophilic Bacteria ◽  
Multilocus Sequence Analysis ◽  
23S Rrna ◽  
Rrna Gene ◽  
The Family ◽  
Micro Organisms ◽  
The Impact

Multilocus sequence analysis (MLSA) protocols have been developed for species circumscription for many taxa. However, at present, no studies based on MLSA have been performed within any moderately halophilic bacterial group. To test the usefulness of MLSA with these kinds of micro-organisms, the family Halomonadaceae, which includes mainly halophilic bacteria, was chosen as a model. This family comprises ten genera with validly published names and 85 species of environmental, biotechnological and clinical interest. In some cases, the phylogenetic relationships between members of this family, based on 16S rRNA gene sequence comparisons, are not clear and a deep phylogenetic analysis using several housekeeping genes seemed appropriate. Here, MLSA was applied using the 16S rRNA, 23S rRNA, atpA, gyrB, rpoD and secA genes for species of the family Halomonadaceae. Phylogenetic trees based on the individual and concatenated gene sequences revealed that the family Halomonadaceae formed a monophyletic group of micro-organisms within the order Oceanospirillales. With the exception of the genera Halomonas and Modicisalibacter, all other genera within this family were phylogenetically coherent. Five of the six studied genes (16S rRNA, 23S rRNA, gyrB, rpoD and secA) showed a consistent evolutionary history. However, the results obtained with the atpA gene were different; thus, this gene may not be considered useful as an individual gene phylogenetic marker within this family. The phylogenetic methods produced variable results, with those generated from the maximum-likelihood and neighbour-joining algorithms being more similar than those obtained by maximum-parsimony methods. Horizontal gene transfer (HGT) plays an important evolutionary role in the family Halomonadaceae; however, the impact of recombination events in the phylogenetic analysis was minimized by concatenating the six loci, which agreed with the current taxonomic scheme for this family. Finally, the findings of this study also indicated that the 16S rRNA, gyrB and rpoD genes were the most suitable genes for future taxonomic studies using MLSA within the family Halomonadaceae.

scholarly journals Molecular Characterization of the 16S rRNA Gene ofHelicobacter fennelliaeIsolated from Stools and Blood Cultures from Paediatric Patients in South Africa

2011 ◽  
Vol 2011 ◽  
pp. 1-9 ◽  
Author(s):  
Heidi E. M. Smuts ◽  
Albert Joseph Lastovica
Keyword(s):  
South Africa ◽  
Phylogenetic Analysis ◽  
16S Rrna ◽  
South African ◽  
Rpob Gene ◽  
Australian Isolate ◽  
23S Rrna ◽  
Rrna Gene ◽  
Separate Branch ◽  
Primary Stem

Forty strains ofH. fennelliaecollected from paediatric blood and stool samples over an 18 year period at a children's hospital in Cape Town, South Africa, were amplified by PCR of the 16S rRNA. Two distinct genotypes ofH. fennelliaewere identified based on the phylogenetic analysis. This was confirmed by sequencing a portion of the beta subunit of the RNA polymerase (rpoB) gene. All isolates from South Africa clustered with a proposed novelHelicobacterstrain (accession number AF237612) isolated in Australia, while threeH. fennelliaetype strains from the northern hemisphere, NCTC 11612, LMG 7546 and CCUG 18820, formed a separate branch. A large (355bp) highly conserved intervening sequence (IVS) in the 16S rRNA was found in all isolates. Predicted secondary structures of the IVS from the 16S rRNA and 23S rRNA were characterised by a primary stem structure formed by base pairing of the 3′and 5′ends and internal loops and stems. This phylogenetic analysis is the largest undertaken ofH. fennelliae. The South AfricanH. fennelliaeisolates are closely related to an Australian isolate previously reported to be a possible novel species of Helicobacter. This study suggests that the latter is strain ofH. fennelliae.

scholarly journals Taxonomy of the canine Mollicutes by 16S rRNA gene and 16S/23S rRNA intergenic spacer region sequence comparison

2004 ◽  
Vol 54 (2) ◽  
pp. 537-542 ◽  
Author(s):  
Victoria J. Chalker ◽  
Joe Brownlie
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Comparison ◽  
Intergenic Spacer ◽  
23S Rrna ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Intergenic Spacer Region ◽  
The 16S Rrna Gene

The taxonomy of canine Mollicutes is described, based on phylogenetic analysis of 16S rRNA gene and 16S/23S rRNA intergenic spacer (IGS) region sequences. The nucleotide sequences of the 16S rRNA gene of two untyped mycoplasmas and the IGS region of 11 Mycoplasma species were determined and used for phylogenetic analysis. The two untyped Mycoplasma strains, HRC 689 and VJC 358, were found to be distinct from all known canine mycoplasmas and all published mycoplasma 16S rRNA gene sequences.

Protein-induced conformational changes in 16S rRNA during assembly of the Escherichia Coli 30S ribosomal subunit: A STEM study

1987 ◽  
Vol 45 ◽  
pp. 910-911
Author(s):  
M. Boublik ◽  
V. Mandiyan ◽  
J.F. Hainfeld ◽  
J.S. Wall
Keyword(s):  
16S Rrna ◽  
Conformational Changes ◽  
Ribosomal Proteins ◽  
Structural Changes ◽  
Ribosomal Subunit ◽  
Compact Structure ◽  
E Coli ◽  
Freeze Dried ◽  
16S Rna ◽  
30S Subunit

The aim of this study is to understand the mechanism of 16S rRNA folding into the compact structure of the small 30S subunit of E. coli ribosome. The assembly of the 30S E. coli ribosomal subunit is a sequence of specific interactions of 16S rRNA with 21 ribosomal proteins (S1-S21). Using dedicated high resolution STEM we have monitored structural changes induced in 16S rRNA by the proteins S4, S8, S15 and S20 which are involved in the initial steps of 30S subunit assembly. S4 is the first protein to bind directly and stoichiometrically to 16S rRNA. Direct binding also occurs individually between 16S RNA and S8 and S15. However, binding of S20 requires the presence of S4 and S8. The RNA-protein complexes are prepared by the standard reconstitution procedure, dialyzed against 60 mM KCl, 2 mM Mg(OAc)2, 10 mM-Hepes-KOH pH 7.5 (Buffer A), freeze-dried and observed unstained in dark field at -160°.

Imaging of ribosomal RNA-protein interactions by dark-field STEM

1989 ◽  
Vol 47 ◽  
pp. 250-251
Author(s):  
M. Boublik ◽  
V. Mandiyan ◽  
S. Tumminia ◽  
J.F. Hainfeld ◽  
J.S. Wall
Keyword(s):  
Nucleic Acid ◽  
16S Rrna ◽  
Dark Field ◽  
Radius Of Gyration ◽  
Central Domain ◽  
The Core ◽  
16S Rna ◽  
30S Subunit ◽  
Core Particles

Success in protein-free deposition of native nucleic acid molecules from solutions of selected ionic conditions prompted attempts for high resolution imaging of nucleic acid interactions with proteins, not attainable by conventional EM. Since the nucleic acid molecules can be visualized in the dark-field STEM mode without contrasting by heavy atoms, the established linearity between scattering cross-section and molecular weight can be applied to the determination of their molecular mass (M) linear density (M/L), mass distribution and radius of gyration (RG). Determination of these parameters promotes electron microscopic imaging of biological macromolecules by STEM to a quantitative analytical level. This technique is applied to study the mechanism of 16S rRNA folding during the assembly process of the 30S ribosomal subunit of E. coli. The sequential addition of protein S4 which binds to the 5'end of the 16S rRNA and S8 and S15 which bind to the central domain of the molecule leads to a corresponding increase of mass and increased coiling of the 16S rRNA in the core particles. This increased compactness is evident from the decrease in RG values from 114Å to 91Å (in “ribosomal” buffer consisting of 10 mM Hepes pH 7.6, 60 mM KCl, 2 m Mg(OAc)2, 1 mM DTT). The binding of S20, S17 and S7 which interact with the 5'domain, the central domain and the 3'domain, respectively, continues the trend of mass increase. However, the RG values of the core particles exhibit a reverse trend, an increase to 108Å. In addition, the binding of S7 leads to the formation of a globular mass cluster with a diameter of about 115Å and a mass of ∽300 kDa. The rest of the mass, about 330 kDa, remains loosely coiled giving the particle a “medusa-like” appearance. These results provide direct evidence that 16S RNA undergoes significant structural reorganization during the 30S subunit assembly and show that its interactions with the six primary binding proteins are not sufficient for 16S rRNA coiling into particles resembling the native 30S subunit, contrary to what has been reported in the literature.

scholarly journals Assessment of Genetic Diversity and Symbiotic Efficiency of Selected Rhizobia Strains Nodulating Lentil (Lens culinaris Medik.)

Plants ◽  
2020 ◽  
Vol 10 (1) ◽  
pp. 15
Author(s):  
Badreddine Sijilmassi ◽  
Abdelkarim Filali-Maltouf ◽  
Hassan Boulahyaoui ◽  
Aymane Kricha ◽  
Kenza Boubekri ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
16S Rrna ◽  
Rhizobium Leguminosarum ◽  
Sequence Similarity ◽  
P Value ◽  
Rrna Gene ◽  
Research Station ◽  
Symbiotic Efficiency ◽  
Rhizobium Strains

A total of 14 Rhizobium strains were isolated from lentil accessions grown at the ICARDA experimental research station at Marchouch in Morocco and used for molecular characterization and symbiotic efficiency assessment. Individual phylogenetic analysis using the 16S rRNA gene, house-keeping genes rpoB, recA, and gyrB, and symbiotic genes nodD and nodA along with Multilocus Sequence Analysis (MLSA) of the concatenated genes (16S rRNA-rpoB-recA-gyrB) was carried out for the identification and clustering of the isolates. The symbiotic efficiency of the strains was assessed on three Moroccan lentil cultivars (Bakria, Chakkouf, and Zaria) based on the number of nodules, plant height, plant dry weight, and total nitrogen content in leaves. The results showed that the individual phylogenetic analysis clustered all the strains into Rhizobium laguerreae and Rhizobium leguminosarum with sequence similarity ranging from 94 to 100%, except one strain which clustered with Mesorhizobium huakuii with sequence similarity of 100%. The MLSA of the concatenated genes and the related percentages of similarity clustered these strains into two groups of Rhizobium species, with one strain as a new genospecies when applying the threshold of 96%. For symbiotic efficiency, the Bakria variety showed the best association with 10 strains compared to its non-inoculated control (p-value ≤ 0.05), followed by Chakkouf and Zaria. The present study concluded that the genetic diversity and the symbiotic efficiency of Rhizobium strains appeared to be mainly under the control of the lentil genotypes.

scholarly journals The Termite Group I Phylum Is Highly Diverse and Widespread in the Environment

2007 ◽  
Vol 73 (20) ◽  
pp. 6682-6685 ◽  
Author(s):  
Daniel P. R. Herlemann ◽  
Oliver Geissinger ◽  
Andreas Brune
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Specific Primers ◽  
Environmental Distribution ◽  
Data Set ◽  
Group I

ABSTRACT The bacterial candidate phylum Termite Group I (TG-1) presently consists mostly of “Endomicrobia,” which are endosymbionts of flagellate protists occurring exclusively in the hindguts of termites and wood-feeding cockroaches. Here, we show that public databases contain many, mostly undocumented 16S rRNA gene sequences from other habitats that are affiliated with the TG-1 phylum but are only distantly related to “Endomicrobia.” Phylogenetic analysis of the expanded data set revealed several diverse and deeply branching lineages comprising clones from many different habitats. In addition, we designed specific primers to explore the diversity and environmental distribution of bacteria in the TG-1 phylum.

scholarly journals Diversity unearthed by the estimated molecular phylogeny and ecologically quantitative characteristics of uncultured Ehrlichia bacteria in Haemaphysalis ticks, Japan

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Hongru Su ◽  
Eri Onoda ◽  
Hitoshi Tai ◽  
Hiromi Fujita ◽  
Shigetoshi Sakabe ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
Core Genome ◽  
Phylogenetic Analyses ◽  
Taxonomic Status ◽  
Housekeeping Genes ◽  
Pcr Screening ◽  
Taxonomic Profiling ◽  
Quantitative Characteristics

AbstractEhrlichia species are obligatory intracellular bacteria transmitted by arthropods, and some of these species cause febrile diseases in humans and livestock. Genome sequencing has only been performed with cultured Ehrlichia species, and the taxonomic status of such ehrlichiae has been estimated by core genome-based phylogenetic analysis. However, many uncultured ehrlichiae exist in nature throughout the world, including Japan. This study aimed to conduct a molecular-based taxonomic and ecological characterization of uncultured Ehrlichia species or genotypes from ticks in Japan. We first surveyed 616 Haemaphysalis ticks by p28-PCR screening and analyzed five additional housekeeping genes (16S rRNA, groEL, gltA, ftsZ, and rpoB) from 11 p28-PCR-positive ticks. Phylogenetic analyses of the respective genes showed similar trees but with some differences. Furthermore, we found that V1 in the V1–V9 regions of Ehrlichia 16S rRNA exhibited the greatest variability. From an ecological viewpoint, the amounts of ehrlichiae in a single tick were found to equal approx. 6.3E+3 to 2.0E+6. Subsequently, core-partial-RGGFR-based phylogenetic analysis based on the concatenated sequences of the five housekeeping loci revealed six Ehrlichia genotypes, which included potentially new Ehrlichia species. Thus, our approach contributes to the taxonomic profiling and ecological quantitative analysis of uncultured or unidentified Ehrlichia species or genotypes worldwide.

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