The Experts below are selected from a list of 3102 Experts worldwide ranked by ideXlab platform
Floyd E. Dewhirst - One of the best experts on this subject based on the ideXlab platform.
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WPS-2 Phyla/candidate divisions
2016Co-Authors: Anuj Camanocha, Floyd E. DewhirstAbstract:contain species from the lesser-known phyla or candidate divisions, including Synergistetes, TM7, Chlorobi, Chloroflexi, GN02, SR1, and WPS-2. The objectives of this study were to create phyla-selective 16S rDNA PCR primer pairs, create selective 16S rDNA clone libraries, identify novel oral taxa, and update canine and human oral microbiome databases. Design: 16S rRNA gene sequences for members of the lesser-known phyla were downloaded from GenBank and Greengenes databases and aligned with sequences in our RNA databases. Primers with potential phylum level selectivity were designed heuristically with the goal of producing nearly full-length 16S rDNA amplicons. The specificity of primer pairs was examined by making clone libraries from PCR amplicons and determining phyla identity by BLASTN analysis. Results: Phylum-selective primer pairs were identified that allowed construction of clone libraries with 96100 % specificity for each of the lesser-known phyla. From these clone libraries, seven human and two canine novel oral taxa were identified and added to their respective taxonomic databases. For each phylum, genome sequences closest to human oral taxa were identified and added to the Human Oral Microbiome Database to facilitate metagenomic, transcriptomic, and proteomic studies that involve tiling sequences to the most closely related taxon. While examining ribosomal operons in lesser-known phyla from single-cel
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host associated bacterial taxa from chlorobi chloroflexi gn02 synergistetes sr1 tm7 and wps 2 phyla candidate divisions
Journal of Oral Microbiology, 2014Co-Authors: Anuj Camanocha, Floyd E. DewhirstAbstract:Background and objective : In addition to the well-known phyla Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria, Spirochaetes, Fusobacteria, Tenericutes, and Chylamydiae, the oral microbiomes of mammals contain species from the lesser-known phyla or candidate divisions, including Synergistetes, TM7, Chlorobi, Chloroflexi, GN02, SR1, and WPS-2. The objectives of this study were to create phyla-selective 16S rDNA PCR primer pairs, create selective 16S rDNA clone libraries, identify novel oral taxa, and update canine and human oral microbiome databases. Design : 16S rRNA gene sequences for members of the lesser-known phyla were downloaded from GenBank and Greengenes databases and aligned with sequences in our RNA databases. Primers with potential phylum level selectivity were designed heuristically with the goal of producing nearly full-length 16S rDNA amplicons. The specificity of primer pairs was examined by making clone libraries from PCR amplicons and determining phyla identity by BLASTN analysis. Results : Phylum-selective primer pairs were identified that allowed construction of clone libraries with 96–100% specificity for each of the lesser-known phyla. From these clone libraries, seven human and two canine novel oral taxa were identified and added to their respective taxonomic databases. For each phylum, genome sequences closest to human oral taxa were identified and added to the Human Oral Microbiome Database to facilitate metagenomic, transcriptomic, and proteomic studies that involve tiling sequences to the most closely related taxon. While examining ribosomal operons in lesser-known phyla from single-cell genomes and metagenomes, we identified a novel rRNA operon order (23S-5S-16S) in three SR1 genomes and the splitting of the 23S rRNA gene by an I-CeuI-like homing endonuclease in a WPS-2 genome. Conclusions : This study developed useful primer pairs for making phylum-selective 16S rRNA clone libraries. Phylum-specific libraries were shown to be useful for identifying previously unrecognized taxa in lesser-known phyla and would be useful for future environmental and host-associated studies. Keywords : microbiome; primers; cloning; phylogeny; 16S rRNA (Published: 8 October 2014) Citation: Journal of Oral Microbiology 2014, 6 : 25468 - http://dx.doi.org/10.3402/jom.v6.25468
Stefan Stoll - One of the best experts on this subject based on the ideXlab platform.
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temperature drives asymmetric competition between alien and indigenous freshwater snail species Physa acuta and Physa fontinalis
Aquatic Sciences, 2017Co-Authors: Denise Fruh, Peter Haase, Stefan StollAbstract:Biological invasion represents one of the major threats to global biodiversity as alien species often displace indigenous species. Knowledge of the mechanisms behind such displacements and the driving factors of the competitive superiority of the alien species remain limited. We combined analysis of field data and laboratory experiments examining species interactions to investigate the impact of temperature in the case of the alien freshwater snail Physa acuta and the indigenous snail Physa fontinalis. From field data, we identified higher temperature as the most important difference between sites populated by P. acuta and P. fontinalis. Results of the species interaction experiment conducted at 15, 20, and 25 °C revealed that the competitive superiority of P. acuta over P. fontinalis increases at warmer temperatures. In single species treatments, increasing temperature stimulated growth rates in both species. Coexistence treatments revealed an asymmetric competitive interaction between the two snail species. In both species, the density of conspecifics did not affect growth rates; however, density of heterospecifics did. This effect of heterospecifics varied with temperature. At 15 °C, the presence of heterospecifics stimulated the growth rates of both species, while at higher temperatures the presence of heterospecifics stimulated the growth rate in P. acuta only, but inhibited the growth rate in P. fontinalis. Our study shows that temperature can be a powerful driver of competitive outcomes between alien and indigenous species and highlight that the environmental context influences species interactions and impacts of alien species.
Jérôme Goudet - One of the best experts on this subject based on the ideXlab platform.
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Experimental evidence of inbreeding avoidance in the hermaphroditic snail Physa acuta
Evolutionary Ecology, 2006Co-Authors: Benoît Facon, Virginie Ravigné, Jérôme GoudetAbstract:Inbreeding depression should select for inbreeding avoidance behaviours. Here we test this hypothesis in two populations of the simultaneous hermaphroditic freshwater snail Physa acuta . We recorded the copulatory behaviour of 288 pairs of sib-mates, non-kin mates from the same population, or non-kin mates from two different populations. We find that kin discriminatory behaviours exist in this species, exclusively expressed by individuals playing the female role. We discuss the relevance of our finding in the context of the evolution of recognition systems and the consequences of such a behaviour in natural populations.
Masakazu Shimada - One of the best experts on this subject based on the ideXlab platform.
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body size dependent gender role in a simultaneous hermaphrodite freshwater snail Physa acuta
Behavioral Ecology, 2004Co-Authors: Kako Ohbayashihodoki, Fumiko Ishihama, Masakazu ShimadaAbstract:We examined whether gender role in the simultaneous hermaphrodite freshwater snail, Physa acuta, is determined by relative body size in a manner predicted by the size-advantage model. We observed the body-size combinations of pairs in the laboratory by using field-collected populations. Smaller individuals tended to play the "male" role (sperm donor), and larger snails the "female" (sperm recipient). Next, we analyzed the mating behaviors involved in gender-role decision in snail pairs of three different body-size combinations, using "large" and "small" snails. Smaller snails were more likely to approach the partner as a male in different-size combination (large/small), whereas frequent initial approaches as a male and rejection behavior as a female were observed in the large/large combination. Third, we examined the body size preference when a snail can freely choose the partner from two other individuals of different body sizes (large/large/small or large/small/small). Small individuals had a significant tendency to act as the male and positively selected large snails as the female partner in both triple combinations. However, the large individual acted as both the male and the female with nearly equal frequency. In the size-differing pairings, copulations occurred after fewer male approaches and fewer rejections than in pairings involving two large snails, suggesting that body size difference is one of the behavioral solutions in gender conflict. Clear gender-role switching associated with body size was not seen. Smaller snails thus have a tendency to play the male role more frequently but adopt both gender roles when their body size is sufficiently large. Copyright 2004.
Anuj Camanocha - One of the best experts on this subject based on the ideXlab platform.
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WPS-2 Phyla/candidate divisions
2016Co-Authors: Anuj Camanocha, Floyd E. DewhirstAbstract:contain species from the lesser-known phyla or candidate divisions, including Synergistetes, TM7, Chlorobi, Chloroflexi, GN02, SR1, and WPS-2. The objectives of this study were to create phyla-selective 16S rDNA PCR primer pairs, create selective 16S rDNA clone libraries, identify novel oral taxa, and update canine and human oral microbiome databases. Design: 16S rRNA gene sequences for members of the lesser-known phyla were downloaded from GenBank and Greengenes databases and aligned with sequences in our RNA databases. Primers with potential phylum level selectivity were designed heuristically with the goal of producing nearly full-length 16S rDNA amplicons. The specificity of primer pairs was examined by making clone libraries from PCR amplicons and determining phyla identity by BLASTN analysis. Results: Phylum-selective primer pairs were identified that allowed construction of clone libraries with 96100 % specificity for each of the lesser-known phyla. From these clone libraries, seven human and two canine novel oral taxa were identified and added to their respective taxonomic databases. For each phylum, genome sequences closest to human oral taxa were identified and added to the Human Oral Microbiome Database to facilitate metagenomic, transcriptomic, and proteomic studies that involve tiling sequences to the most closely related taxon. While examining ribosomal operons in lesser-known phyla from single-cel
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host associated bacterial taxa from chlorobi chloroflexi gn02 synergistetes sr1 tm7 and wps 2 phyla candidate divisions
Journal of Oral Microbiology, 2014Co-Authors: Anuj Camanocha, Floyd E. DewhirstAbstract:Background and objective : In addition to the well-known phyla Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria, Spirochaetes, Fusobacteria, Tenericutes, and Chylamydiae, the oral microbiomes of mammals contain species from the lesser-known phyla or candidate divisions, including Synergistetes, TM7, Chlorobi, Chloroflexi, GN02, SR1, and WPS-2. The objectives of this study were to create phyla-selective 16S rDNA PCR primer pairs, create selective 16S rDNA clone libraries, identify novel oral taxa, and update canine and human oral microbiome databases. Design : 16S rRNA gene sequences for members of the lesser-known phyla were downloaded from GenBank and Greengenes databases and aligned with sequences in our RNA databases. Primers with potential phylum level selectivity were designed heuristically with the goal of producing nearly full-length 16S rDNA amplicons. The specificity of primer pairs was examined by making clone libraries from PCR amplicons and determining phyla identity by BLASTN analysis. Results : Phylum-selective primer pairs were identified that allowed construction of clone libraries with 96–100% specificity for each of the lesser-known phyla. From these clone libraries, seven human and two canine novel oral taxa were identified and added to their respective taxonomic databases. For each phylum, genome sequences closest to human oral taxa were identified and added to the Human Oral Microbiome Database to facilitate metagenomic, transcriptomic, and proteomic studies that involve tiling sequences to the most closely related taxon. While examining ribosomal operons in lesser-known phyla from single-cell genomes and metagenomes, we identified a novel rRNA operon order (23S-5S-16S) in three SR1 genomes and the splitting of the 23S rRNA gene by an I-CeuI-like homing endonuclease in a WPS-2 genome. Conclusions : This study developed useful primer pairs for making phylum-selective 16S rRNA clone libraries. Phylum-specific libraries were shown to be useful for identifying previously unrecognized taxa in lesser-known phyla and would be useful for future environmental and host-associated studies. Keywords : microbiome; primers; cloning; phylogeny; 16S rRNA (Published: 8 October 2014) Citation: Journal of Oral Microbiology 2014, 6 : 25468 - http://dx.doi.org/10.3402/jom.v6.25468