72 research outputs found
Independent Expansion of Zincin Metalloproteinases in Onygenales Fungi May Be Associated with Their Pathogenicity
<div><p>To get a comprehensive view of fungal M35 family (deuterolysin) and M36 family (fungalysin) genes, we conducted genome-wide investigations and phylogenetic analyses of genes in these two families from 50 sequenced Ascomycota fungi with different life styles. Large variations in the number of M35 family and M36 family genes were found among different fungal genomes, indicating that these two gene families have been highly dynamic through fungal evolution. Moreover, we found obvious expansions of Meps in two families of Onygenales: Onygenaceae and Arthodermataceae, whereas species in family Ajellomycetace did not show expansion of these genes. The strikingly different gene duplication and loss patterns in Onygenales may be associated with the different pathogenicity of these species. Interestingly, likelihood ratio tests (LRT) of both M35 family and M36 family genes suggested that several branches leading to the duplicated genes in dermatophytic and <i>Coccidioides</i> fungi had signatures of positive selection, indicating that the duplicated <i>Mep</i> genes have likely diverged functionally to play important roles during the evolution of pathogenicity of dermatophytic and <i>Coccidioides</i> fungi. The potentially positively selected residues discovered by our analysis may have contributed to the development of new physiological functions of the duplicated <i>Mep</i> genes in dermatophytic fungi and <i>Coccidioides</i> species. Our study adds to the current knowledge of the evolution of Meps in fungi and also establishes a theoretical foundation for future experimental investigations.</p></div
ML tree based on amino acid sequences of 105 M35 family genes.
<p>The tree was performed using PHYML 3.0<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090225#pone.0090225-Guindon1" target="_blank">[17]</a>. The best-fitting model WAG+I+G and their parameters (I = 0.03, G = 1.912) which were estimated by program ProtTest <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090225#pone.0090225-Galgiani1" target="_blank">[50]</a> were used in the ML analysis. The reliability of the tree topology was evaluated using bootstrap support <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090225#pone.0090225-Felsenstein1" target="_blank">[20]</a> with 100.</p
Duplication and loss events of M35 family genes in Eurotiales fungi.
<p>The reconciliation between species tree and gene tree of Eurotiales fungi along with the confirmation of the gene loss/duplication scenario were determined by using Notung 2.6 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090225#pone.0090225-Chen1" target="_blank">[21]</a>. The species tree of Eurotiale fungi is shown as <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090225#pone.0090225.s008" target="_blank">Fig. S8</a>. Putative duplication events are indicated with solid cycles, while loss events are indicated with thick branches. 1, the lineage includes species of <i>A. fumigatus, N. fischeri</i> and <i>A. clavatus</i>. 2, the lineage includes species of <i>A. nidulans</i>, <i>A. terreus, A. oryza</i> and <i>A. flavus</i>.</p
Duplication and loss events of M35 family genes and M36 family genes in Onygenales fungi.
<p>The reconciliation between species tree and gene tree of Onygenales fungi along with the confirmation of the gene loss/duplication scenario were determined by using Notung 2.6 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090225#pone.0090225-Chen1" target="_blank">[21]</a>. The species tree of Onygenales fungi is shown as <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090225#pone.0090225.s007" target="_blank">Fig. S7</a>. Putative duplication events are indicated with solid cycles, while loss events are indicated with thick branches. a, duplication and loss events of M35 family genes. b, duplication and loss events of M36 family genes.</p
Number of both M35 family and M36 family genes in different fungal species.
<p>Number of both M35 family and M36 family genes in different fungal species.</p
CODEML analyses of selective pattern for M36 family genes.
a<p>In<i>L</i> is the log-likelihood scores.</p>b<p>LRT to detect adaptive evolution. *** P<0.001</p>c<p>Posterior probabilities value of each codon site were showed in parentheses.</p
Phylogenetic tree of 62 M35 family genes used for codon-based maximum likelihood analysis in PAML.
<p>Phylogenetic trees were collapsed with inconsistent nodes from different tree-building methods and poor statistical supports into polytomy. Branches <i>a-s</i> indicated putative duplication events in Onygenales fungi. The branches with significant evidence of positive selection are indicated as a thick branch. The putative positively selected residues along these branches were shaded in grey.</p
Phylogenetic tree of 38 M36 family genes used for codon-based maximum likelihood analysis in PAML.
<p>Phylogenetic trees were collapsed with inconsistent nodes from different tree-building methods and poor statistical supports into polytomy. Branches <i>a-j</i> indicated putative duplication events in Onygenales fungi. The branches with significant evidence of positive selection are indicated as a thick branch. The putative positively selected residues along these branches were shaded in grey.</p
CODEML analyses of selective pattern for M35 family genes.
a<p>In<i>L</i> is the log-likelihood scores.</p>b<p>LRT to detect adaptive evolution. *** P<0.001</p>c<p>Posterior probabilities value of each codon site were showed in parentheses.</p
Fabrication of Structurally-Colored Fibers with Axial Core–Shell Structure via Electrophoretic Deposition and Their Optical Properties
Structurally colored fibers were fabricated using different-sized
polystyrene (PS) nanospheres via electrophoretic deposition on conductive
carbon fiber surfaces. The reflective spectra corresponding to different
colors were taken by microzone and angle-resolved spectrometers from
a single colloidal fiber. As confirmed by structural analysis, the
outer layer of the core–shell colloidal fibers consisted of
face-centered cubic (f.c.c.) domains without long-range order. It
is revealed that the absence of long-range order in the colloidal
assembly caused isotropic reflection in radial and longitudinal directions
on the colloidal fibers. Furthermore, due to the incorporation of
random defects during growth process, the experimental spectra are
blue-shifted and broad compared to reflective spectra calculations
based on the curved f.c.c. structure. This technique is speculated
to have potential application in structural coloration and radiation-proof
fabrics
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