Genetic Differentiation of the Mitochondrial Cytochrome Oxidase <i>c</i> Subunit I Gene in Genus <i>Paramecium</i> (Protista, Ciliophora)

<div><p>Background</p><p>The mitochondrial cytochrome <i>c</i> oxidase subunit I (<i>COI</i>) gene is being used increasingly for evaluating inter- and intra-specific genetic diversity of ciliated protists. However, very few studies focus on assessing genetic divergence of the <i>COI</i> gene within individuals and how its presence might affect species identification and population structure analyses.</p><p>Methodology/Principal findings</p><p>We evaluated the genetic variation of the <i>COI</i> gene in five <i>Paramecium</i> species for a total of 147 clones derived from 21 individuals and 7 populations. We identified a total of 90 haplotypes with several individuals carrying more than one haplotype. Parsimony network and phylogenetic tree analyses revealed that intra-individual diversity had no effect in species identification and only a minor effect on population structure.</p><p>Conclusions</p><p>Our results suggest that the <i>COI</i> gene is a suitable marker for resolving inter- and intra-specific relationships of <i>Paramecium</i> spp.</p></div

Phylogenetic tree of the barcoding region of 263 cytochrome <i>c</i> oxidase subunit I (<i>COI</i>) gene sequences of the genus <i>Paramecium</i> and genera <i>Lembadion</i> and, <i>Tetrahymena</i> inferred by Bayesian Inference (BI) analysis based on dataset <i>COI</i>-f.

<p>The branches are shaded according to subgenera <i>Chloroparamecium</i>, <i>Helianter</i>, <i>Cypriostomum</i>, <i>Paramecium</i>, proposed by Fokin <i>et al. </i><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0077044#pone.0077044-Fokin1" target="_blank">[28]</a>. The scale bar corresponds to 30 substitutions per 100 nucleotide positions. For <i>P. bursaria</i>, Clade H includes populations sampled from Australia, Germany, and Poland; Clade I and J include populations sampled from Russia and Poland, Germany, Ukraine, and Canada; Clade K includes populations sampled from China (Pb1C1-4 & Pb2C &Pb3C2-3), Austria, Japan, and Italy; Clade L includes populations sampled from China (Pb3C1), Russia, and Japan (see details in Fig. S2 in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0077044#pone.0077044.s003" target="_blank">file S3</a>). For <i>P.caudatum</i>, Clade A includes populations sampled from China (PcC1-4 and AM072774), Australia, USA, and Brazil while members of Clade B were sampled from Germany, Italy, Russia, UK, Norway, Hungary, Slovenia, and Austria (see details in Fig. S3 in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0077044#pone.0077044.s003" target="_blank">file S3</a>). Inconsistent sequences (FJ905146, FJ905147, EU056259, EU056258, DQ837977, DQ837982, JF741258, JF304183) are marked in red <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0077044#pone.0077044-Tarcz1" target="_blank">[14]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0077044#pone.0077044-Barth3" target="_blank">[42]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0077044#pone.0077044-StrderKypke2" target="_blank">[47]</a>.</p

Haplotype network of <i>Paramecium bursaria</i> generated on the basis of the maximum-likelihood tree.

<p>Black circles indicate intermediate or unsampled haplotypes, while lines between points represent nucleotide substitutions. Wherever there are more than four substitutions, they are indicated by numbers. Clades K, L, H, I, J are marked to match the corresponding clades in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0077044#pone-0077044-g004" target="_blank">Figure 4</a>. Colored circles and squares indicate haplotypes whose size is proportional to the number of individuals showing that haplotype. Haplotype_7 is represented by 4 clones of Pb1C1; haplotype_14 is represented by 4 clones of Pb1C2 and 7 clones of Pb1C3; haplotype_22 is represented by 5 clones of Pb1C4 and 3 clones of Pb2C1; haplotype_25 is represented by 3 clones of Pb3C1.</p

Haplotype network of <i>Paramecium</i> sp. (A) based on the dataset <i>COI</i>_nw, <i>P. nephridiatum</i> (B) based on dataset <i>COI</i>_nn, <i>P. duboscqui</i> (C), based on dataset <i>COI</i>_nd and <i>P. caudatum</i> (D) based on dataset <i>COI</i>_nc generated on the basis of the maximum-likelihood tree.

<p>Each line between points represents a single mutational step. A haplotype is represented by a circle whose size is proportional to the number of individuals showing that haplotype. Haplotypes are colored to match the respective population in the map. A) Haplotype_1 is represented by 2 clones of PwC1; Haplotype_3 is represented by 4 clones of PwC1 and 2 clones of PwC2; B) Haplotype_4 is represented by 1 clone of PdC1, 1 clone of PdC2, 1 clone of PdC3 and 2 clones of PdC4; C) Haplotype_2 is represented by 4 clones of PnC1 and 1 clone of PnC3; D) Haplotype_6 is represented by 4 clones of PcC1 and 5 clones of PcC3; Haplotype_9 is represented by 6 clones of PcC2 and 5 clones of PcC4; Haplotype_13 is represented by 3 clones of PcC3.</p

Variable site details of <i>Paramecium bursaria</i> and <i>Paramecium caudatum</i>.

<p>Alignment of amplified <i>COI</i> sequences (primer binding regions excluded) based on datasets <i>COI</i>_nb and <i>COI</i>_nc. The nucleotides shaded with rectangles and circles are used to illustrate the levels of diversity found among different clones.</p

Survey of Intraocular Antibiotics Prophylaxis Practice after Open Globe Injury in China

<div><p>Purpose</p><p>To elucidate the Chinese practice of intraocular antibiotics administration for prophylaxis after open globe injury.</p><p>Methods</p><p>A cross-sectional questionnaire survey was performed online by scanning a Quickmark (QR) code with smartphones at the 20^th Chinese National Conference of Ocular Trauma in November 2014.</p><p>Results</p><p>A total of 153 (30.6%) of all participators at the conference responded. Of the respondents, 20.9% were routinely administered with prophylactic intraocular injection of antibiotics at the conclusion of the primary eye repair, and 56.9% were used only in cases with high risk of endophthalmitis development. The intraocular route of delivery was mainly included with intracameral injection (47.9%) and intravitreal injection (42.0%). Cephalosporins (53.8%) and vancomycin (42.0%) were the main choices of antibiotic agents, followed by fluoroquinolones (24.3%), and aminoglycosides (13.4%). Only 21.9% preferred a combination of two or more two drugs routinely. In addition, significantly more respondents from the referral eye hospital (92.7%) replied using intraocular antibiotics injection for prophylaxis compared to those respondents from the primary hospital (69.4%) (<i>p</i> = 0.001, Fisher’s exact test).</p><p>Conclusions</p><p>Intraocular antibiotics injection for post-traumatic endophthalmitis prophylaxis is widely used in China. However, the choice of antibiotic agents and the intraocular route of delivery vary. A well-designed clinical trial is needed to establish a standardized protocol of intraocular antibiotics administration for post-traumatic endophthalmitis prophylaxis.</p></div

Prophylactic intraocular injection of antibiotics at the end of primary eye repair.

<p>Prophylactic intraocular injection of antibiotics at the end of primary eye repair.</p

Intraocular route of antibiotic agents delivery in open globe injuries.

<p>Intraocular route of antibiotic agents delivery in open globe injuries.</p

The most common causative pathogen in post-traumatic endophthalmitis.

<p>The most common causative pathogen in post-traumatic endophthalmitis.</p

Distribution of respondents by annual eye repair volume.

<p>Distribution of respondents by annual eye repair volume.</p