Data _PONE-D-16-32451

Data underlying main figures and supplement

Species discrimination by barcode marker for complete samples.

<p>Squares indicate means for <i>matK</i> (blue; m), <i>rbcL</i> (red; r), nrITS2 (yellow; i), <i>matK</i> combined with <i>rbcL</i> (purple; mr), <i>matK</i> combined with nrITS2 (green; mi), <i>rbcL</i> combined with nrITS2 (orange, ri), and all markers combined (black; mri). Error bars indicate 95% confidence intervals.</p

Diagnostic barcode variation for complete samples of Podocarpaceae.

<p>Diagnostic barcode variation for complete samples of Podocarpaceae.</p

Barcode variation within and among species for complete samples.

<p>Circles represent the set of <i>matK</i> (blue), <i>rbcL</i> (red), and nrITS2 (yellow) sequences for each species. Opaque filled circles denote diagnostic sequence sets. Non–diagnostic sequence sets are indicated with semi–transparent filled circles. Equal intra– and inter–specific variation is marked by the gray line. Points above the gray line indicate species with ‘barcode gaps’.</p

DNA Barcode Identification of Podocarpaceae—The Second Largest Conifer Family

<div><p>We have generated <i>matK</i>, <i>rbcL</i>, and nrITS2 DNA barcodes for 320 specimens representing all 18 extant genera of the conifer family Podocarpaceae. The sample includes 145 of the 198 recognized species. Comparative analyses of sequence quality and species discrimination were conducted on the 159 individuals from which all three markers were recovered (representing 15 genera and 97 species). The vast majority of sequences were of high quality (<i>B</i>₃₀ = 0.596–0.989). Even the lowest quality sequences exceeded the minimum requirements of the BARCODE data standard. In the few instances that low quality sequences were generated, the responsible mechanism could not be discerned. There were no statistically significant differences in the discriminatory power of markers or marker combinations (<i>p</i> = 0.05). The discriminatory power of the barcode markers individually and in combination is low (56.7% of species at maximum). In some instances, species discrimination failed in spite of ostensibly useful variation being present (genotypes were shared among species), but in many cases there was simply an absence of sequence variation. Barcode gaps (maximum intraspecific p–distance > minimum interspecific p–distance) were observed in 50.5% of species when all three markers were considered simultaneously. The presence of a barcode gap was not predictive of discrimination success (<i>p</i> = 0.02) and there was no statistically significant difference in the frequency of barcode gaps among markers (<i>p</i> = 0.05). In addition, there was no correlation between number of individuals sampled per species and the presence of a barcode gap (<i>p</i> = 0.27).</p></div

Rates of discriminatory success for barcoding studies that analyzed <i>matK</i>, <i>rbcL</i>, and nrITS2 sequences using algorithms comparable to BRONX.

<p>Rates of discriminatory success for barcoding studies that analyzed <i>matK</i>, <i>rbcL</i>, and nrITS2 sequences using algorithms comparable to BRONX.</p

Phylogenetic relationships among complete samples.

<p>Strict consensus of 3600 most parsimonious trees (L = 1205; CI = 0.59; RI = 0.93; all tree statistics exclude uninformative nucleotide positions) obtained from the simultaneous analysis of <i>matK</i>, <i>rbcL</i>, and nrITS2 sequence data. Numbers at nodes indicated jackknife support above 50%. Species that can be distinguished from all other species using the ‘least inclusive clade’ method are in boldface (the least inclusive clade method cannot be applied to species with only one sample). Genera have been abbreviated: <i>Ac.</i>  =  <i>Acmopyle</i>, <i>Af.</i>  =  <i>Afrocarpus</i>, <i>Dc.</i>  =  <i>Dacrycarpus</i>, <i>Dd.</i>  =  <i>Dacrydium</i>, <i>F.</i>  =  <i>Falcatifolium</i>, <i>La.</i>  =  <i>Lagarostrobos</i>, <i>Le.</i>  =  <i>Lepidothamnus</i>, <i>Ma.</i>  =  <i>Manoao</i>, <i>Mi.</i>  =  <i>Microcachrys</i>, <i>N.</i>  =  <i>Nageia</i>, <i>Ph.</i>  =  <i>Pherosphaera</i>, <i>Po.</i>  =  <i>Podocarpus</i>, <i>Pr.</i>  =  <i>Prumnopitys</i>, <i>R.</i>  =  <i>Retrophyllum</i>, and <i>S.</i>  =  <i>Saxegothaea</i>. Sample codes correspond to those used in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0081008#pone.0081008.s001" target="_blank">Dataset S1</a>.</p

Barcode sequence quality (<i>B₃₀</i>) versus linguistic complexity (<i>LC</i>) for complete samples.

<p>Circles represent individual <i>matK</i> (blue; m), <i>rbcL</i> (red; r), and nrITS2 (yellow; i) sequences. Black squares indicate marker means. Error bars span three standard deviations.</p

The Role of Hydrogen on the Adsorption Behavior of Carboxylic Acid on TiO₂ Surfaces

In this work, we present binding energies of acetic acid on the (110), (100), and (011) surfaces of rutile TiO₂ calculated with the two density functional theory (DFT) exchange-correlation functionals PBE and PBEsol. It is shown that the binding energies can be influenced, in this case slightly reduced for all three surfaces, via preadsorption of hydrogen. Additionally, we tested the performance of the density-functional based tight-binding (DFTB) method applied to these adsorbate systems. Analysis of the electronic density of states shows that DFTB provides qualitatively comparable results to DFT calculations as long as the Fermi energy level remains within the band gap

Modification of Surfaces by Chemical Transfer Printing Using Chemically Patterned Stamps

The preparation of well-defined molecular monolayers and their patterning on the microscale and nanoscale are key aspects of surface science and chemical nanotechnology. In this article, we describe the modification of amine-functionalized surfaces using a new type of contact printing based on chemically patterned, flat PDMS stamps. The stamps have discrete areas with surface-bond tetrafluorophenol (TFP) groups, which allow the attachment of carboxylic acids in the presence of coupling agents such as diisopropylcarbodiimide (DIC). The generated active esters can be reacted by placing the stamps in contact with amine-functionalized surfaces. The process leads to the transfer of acyl residues from the stamp to the substrate and therefore to a covalent attachment. Patterning occurs because of the fact that reaction and transfer take place only in areas with TFP groups present on the stamp surface. Different types of amine-decorated surfaces were successfully modified, and the transfer was visualized by fluorescence microscopy. To the best of our knowledge, the covalent transfer printing (CTP) of an immobilized molecular monolayer from one surface to another surface is unprecedented