Preparation and characterization of antibacterial cobalt-exchanged natural zeolite/poly(vinyl alcohol) hydrogels

In the present study, potential application of the local clinoptilolite-rich natural zeolite in formulation of antibacterial hydrogels was investigated. The zeolite powder exchanged with cobalt(II) ions was used in preparation of the zeolite/poly(vinyl alcohol) hydrogel films in different amounts. The films were physically crosslinked by the freezing-thawing method and characterized for their crystallinity, surface and cross sectional morphology, chemical composition, thermal behaviour, mechanical properties, swelling and dissolution behaviours, and antibacterial activities against a Gram-negative bacteria. The films with 0.48 wt% and higher cobalt-exchanged zeolite contents showed antibacterial activity. Addition of the zeolite powder in the formulations did not cause significant changes in the other properties of the films.Turkish Republic Prime Ministry State Planning Organization (DPT-2006 K120690

Maximum clade credibility phylogeny, reconstructed in BEAST, with mean divergence times for whole genome sequences from 32 Malagasy <i>Yersinia pestis</i> strains and reference strain CO92.

<p>A maximum clade credibility phylogeny based upon SNPs identified among the 31 Malagasy <i>Y</i>. <i>pestis</i> strains sequenced here and the previously sequenced Malagasy strain IP275 and reference strain CO92. Malagasy strain branches are labeled with the SNP nodes from <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0005887#pntd.0005887.g001" target="_blank">Fig 1</a>, the strain IDs from <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0005887#pntd.0005887.s004" target="_blank">S1 Table</a>, and the year of isolation of the strain. Colors of the clades and/or branches indicate identified subgroups and correspond to the subgroup color designations in <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0005887#pntd.0005887.g001" target="_blank">Fig 1</a>. A timeline indicates the estimated mean divergence times for the various branch points. Estimated mean divergence times for various nodes of interest are also indicated on the phylogeny. Yellow circles indicate the posterior probabilities for each of the clades, where larger circles indicate higher confidence.</p

Divergence time estimates for nodes of interest.

<p>Divergence time estimates for nodes of interest.</p

Geographic distribution of 45 Malagasy <i>Yersinia pestis</i> samples from 2009 to 2012.

<p>The geographic distribution of identified subgroups is presented in separate panels for each year, with symbols and colors as in <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0005887#pntd.0005887.g002" target="_blank">Fig 2</a>.</p

Geographic distribution of 355 Malagasy <i>Yersinia pestis</i> samples from 1995 to 2000.

<p>The map of Madagascar in the upper left indicates elevation, all of the geographic points in this study (small black points), and the portion of Madagascar represented in the other panels (rectangle). The geographic distribution of identified subgroups is presented in separate panels for each year. Circles in the panels represent the locations of the fokontany (i.e., villages) or commune centroids (when the fokontany was unknown) where samples were collected. In some cases where separate circles were too close together to be visibly distinguished at this scale, a single circle indicating the overlapping circles was substituted. This occurred primarily for fokontany within communes Mahajanga and Mahabibo within district Mahajanga I, and for fokontany within the various arrondissements (i.e., administrative divisions) within district Antananarivo Renivohitra, but also occasionally occurred at other locations. Colors of the mapped circles indicate identified subgroups and correspond to the subgroup color designations in <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0005887#pntd.0005887.g001" target="_blank">Fig 1</a>. Divisions within circles indicate that multiple subgroups were found at that location in that year. Unaffiliated Group I and II samples (i.e., I.NONE and II.NONE) are indicated by a “*” and a “+”, respectively.</p

MLVA diversity within SNP nodes.

<p>MLVA diversity within SNP nodes.</p

Geographic distribution of 93 Malagasy <i>Y</i>. <i>pestis</i> clinical samples from 2007.

<p>Light gray shaded polygons indicate Madagascar districts where <i>Y</i>. <i>pestis</i> samples used in this study were obtained (<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0003844#pntd.0003844.s001" target="_blank">S1 Table</a>, column E,F). Circles represent the locations of the communes where samples were collected. Colors within the mapped circles correspond to the MLVA subclade color designations in <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0003844#pntd.0003844.g001" target="_blank">Fig 1</a>. Divisions within circles indicate that multiple MLVA subclades were found at that location. Numbers within MLVA subclade I.A (red) and I.B (orange) circles and pie chart slices indicate the node within lineages s and q, respectively, of the SNP phylogeny in <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0003844#pntd.0003844.g001" target="_blank">Fig 1</a> that the mapped samples belong to. Where the SNP genotype could not be definitively determined for any of the subclade I.A or I.B samples from a particular location, no number is shown. Unaffiliated Group I and II samples (i.e., subclades I.NONE and II.NONE) are indicated by a “*” and a “+,” respectively.</p

SNP and MLVA phylogenies depicting 18 major phylogenetic subgroups identified among 773 Malagasy <i>Yersinia pestis</i> samples.

<p>(A) SNP phylogeny based on 212 informative SNPs identifying 100 individual nodes (circles and stars) among 770 Malagasy <i>Y</i>. <i>pestis</i> samples (only the lineage could be identified for the remaining 3 samples, and not the specific node). Stars indicate terminal nodes defined by a sequenced strain. Circles indicate intermediary nodes (i.e., collapsed branch points) along the lineages containing groups of samples. Branch points that did not contain any samples are labeled in black italics. A dashed arrow indicates a branch leading to a single, previously identified, terminal node not represented among the samples in this analysis. Lineages (lower case letters) and nodes within lineages (numbers within circles and stars) were named as in [<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0005887#pntd.0005887.ref017" target="_blank">17</a>–<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0005887#pntd.0005887.ref019" target="_blank">19</a>], with new letters and numbers assigned to newly identified lineages and nodes, respectively. Basal nodes d and k are represented by pie charts, indicating the presence of multiple MLVA identified subgroups within these nodes. Color shading indicates the 18 identified phylogenetic subgroups and, to the extent possible, corresponds to the subgroup colors used in reference [<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0005887#pntd.0005887.ref019" target="_blank">19</a>]. Solid pale green and striped pale green, respectively, indicate the new SNP lineage (w) and remaining subset of samples within basal node d that were split in this analysis from a single previously identified subgroup. The number of SNPs on branches with >1 SNP are indicated in red. The single SNP differentiating between Groups I and II is indicated by a perpendicular red line on the branch between nodes d and k. (B) MLVA phylogenies of 10 and 38 Malagasy <i>Y</i>. <i>pestis</i> samples from basal SNP nodes d and k, respectively. The MLVA phylogenies consist of neighbor-joining dendrograms constructed in MEGA6 [<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0005887#pntd.0005887.ref035" target="_blank">35</a>] using mean character based distance matrices. Bootstrap values ≥50 (generated in PAUP 4.0b10 (D. Swofford, Sinauer Associates, Inc., Sunderland, MA) based upon 1,000 simulations) supporting MLVA phylogeny branches are indicated. One and four additional phylogenetic subgroups consistent with previous analyses [<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0005887#pntd.0005887.ref019" target="_blank">19</a>] were identified within the MLVA phylogenies of nodes d and k, respectively. In addition, 1 and 3 samples within nodes d and k, respectively, did not fall into any identified phylogenetic subgroup and were labeled with a “+” or an “*”, and classified as II.NONE and I.NONE, respectively.</p

MLVA (A), SNP (B), and CRISPR (C) based phylogenies of 93 <i>Y</i>. <i>pestis</i> clinical samples from Madagascar in 2007.

<p>MLVA subclades were named as in reference [<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0003844#pntd.0003844.ref012" target="_blank">12</a>] for the 8 of 15 previously described subclades identified here, except for subclade II.A, which was subdivided into subclades II.A.1 and II.A.2 in this analysis. Two new subclades described here, including II.A.2, are bolded and marked with stars. One Group I sample and one Group II sample did not fall into any recognized MLVA subclade and so were classified as I.NONE and II.NONE, respectively (A). SNP phylogeny nodes were named as in references [<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0003844#pntd.0003844.ref011" target="_blank">11</a>–<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0003844#pntd.0003844.ref013" target="_blank">13</a>] and include 13 of the 31 nodes described there. Previously described nodes that were not represented in this study are indicated by gray circles and arrows in the SNP phylogeny (B). The numbers of samples in each MLVA subclade and SNP phylogeny node with >1 sample as well as the total number of samples in each CRISPR genotype are indicated. Asterisks indicate 7 samples with incomplete SNP data that were assigned to a SNP phylogeny lineage or node based upon MLVA data (B). Color shading in each phylogeny is based upon the identified MLVA subclade and corresponds to the MLVA subclade colors in reference [<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0003844#pntd.0003844.ref012" target="_blank">12</a>] for the 8 previously described MLVA subclades. Bootstrap values ≥50 supporting MLVA phylogeny branches (A) and specific CRISPR mutations marking CRISPR phylogeny branches (C) are also indicated. Note that CRISPR genotypes I.1 and II.1 are identical and consist of the following CRISPR pattern: a1-a2-a3-a4-a5-a6-a7-a8 b1-b2-b3-b4-b5 c1-c2-c3 (C). An updated CRISPR dictionary is available in <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0003844#pntd.0003844.s002" target="_blank">S2 Table</a>.</p

Geographic distribution of 373 Malagasy <i>Yersinia pestis</i> samples from 2001 to 2008.

<p>The geographic distribution of identified subgroups is presented in separate panels for each year, with symbols and colors as in <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0005887#pntd.0005887.g002" target="_blank">Fig 2</a>.</p