MALDI MSI of MeLiM melanoma: Searching for differences in protein profiles

Background Treatment of advanced cutaneous melanoma remains challenging, and new data on melanoma biology are required. The most widely accepted criteria for the prognostic evaluation of melanoma are histopathological and clinical parameters, and the identification of additional tumor markers is thus of paramount importance. Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI MSI), an important tool in cancer research, is useful for unraveling the molecular profile of melanoma. Methodology/Principal findings In this report, we used the melanoma-bearing Libechov minipig (MeLiM), a unique animal model that allows observation of the complete spontaneous regression of invasive cutaneous melanoma, to investigate i) the differences between melanoma and healthy skin protein profiles and ii) the proteins potentially involved in spontaneous regression. The MeLiM tissues were cryosected, histologically characterized, analyzed by MALDI MSI, and immunohistologically stained. Multivariate statistical analyses of the MALDI MSI data revealed ten relevant m/z ions, of which the expression levels varied significantly among the studied MeLiM tissues. These ion peaks were used to create mass ion images/maps and visualize the differences between tumor and healthy skin specimens, as well as among histologically characterized tissue regions. Conclusions/Significance Protein profiles comprising ten statistically significant mass ion peaks useful for differentiating cutaneous melanoma and healthy skin tissues were determined. Peaks at m/z 3044, 6011, 6140 and 10180 were overexpressed in melanoma compared with healthy skin tissue. More specifically, m/z 6140 was expressed at significantly (p < 0.05) higher levels in normally growing melanoma regions than in regions with early and late spontaneous regression. This study demonstrates the clinical utility of MALDI MSI for the analysis of tissue cryosections at a molecular level

Metrics of Growth Habit Derived from the 3D Tree Point Cloud Used for Species Determination-A New Approach in Botanical Taxonomy Tested on Dragon Tree Group Example

Detailed, three-dimensional modeling of trees is a new approach in botanical taxonomy. Representations of individual trees are a prerequisite for accurate assessments of tree growth and morphological metronomy. This study tests the abilities of 3D modeling of trees to determine the various metrics of growth habit and compare morphological differences. The study included four species of the genus Dracaena: D. draco, D. cinnabari, D. ombet, and D. serrulata. Forty-nine 3D tree point clouds were created, and their morphological metrics were derived and compared. Our results indicate the possible application of 3D tree point clouds to dendrological taxonomy. Basic metrics of growth habit and coefficients derived from the 3D point clouds developed in the present study enable the statistical evaluation of differences among dragon tree species.O

Cuticular hydrocarbons corroborate the distinction between lowland and highland Natal fruit fly (Tephritidae, Ceratitis rosa) populations

The cuticular hydrocarbons (CHs) and morphology of two Ceratitis rosa Karsch (Diptera: Tephritidae) populations, putatively belonging to two cryptic taxa, were analysed. The chemical profiles were characterised by two-dimensional gas chromatography with mass spectrometric detection. CHs of C. rosa that originated from the lowlands and highlands of Kenya comprised of n-alkanes, monomethylalkanes, dimethylalkanes and unsaturated hydrocarbons in the range of the carbon backbone from C14 to C37. Hydrocarbons containing C29, C31, C33 and C35 carbon atoms predominated in these two populations. 2-Methyltriacontane was the predominant compound in both populations. Quantitative differences in the distribution of hydrocarbons of different chain lengths, mainly the C22, C32, C33 and C34 compounds of these two populations, were observed despite indistinct qualitative differences in these hydrocarbons. Morphological analyses of male legs confirmed that the flies belong to different morphotypes of C. rosa previously labelled as R1 and R2 for lowland and highland populations, respectively. A statistical analysis of the CH compositions of the putative R1 and R2 species showed distinct interspecific identities, with several CHs specific for each of the lowland and highland populations. This study supports a hypothesis that the taxon C. rosa consists of at least two biological species

MFA of transformed GC×GC/MS data of 59 compounds identified in five <i>Bactrocera</i> entities.

<p>M = male, F = female, DOR = <i>B</i>. <i>dorsalis</i>, CAR = <i>B</i>. <i>carambolae</i>, INV = <i>B</i>. ‘syn. <i>invadens</i>’, PAP = <i>B</i>. ‘syn. <i>papayae</i>’, PHI = <i>B</i>. ‘syn. <i>philippinensis</i>’. (A) Score plot describing the species and chemical class modalities of the first two factors, (B) projection of variables onto the plane defined by the first two principal components of the MFA. The coordinates for each variable are the correlation coefficients with the two first principal components (red Ac01–03 = fatty acid, blue Al01–02 = aldehyde, violet CH01–32 = cuticular hydrocarbon, green E01–22 = fatty acid ester). The compounds are assigned according to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0184102#pone.0184102.s001" target="_blank">S1 Table</a>.</p

Epicuticular chemistry reinforces the new taxonomic classification of the <i>Bactrocera dorsalis</i> species complex (Diptera: Tephritidae, Dacinae)

<div><p><i>Bactrocera invadens</i> Drew, Tsuruta & White, <i>Bactrocera papayae</i> Drew & Hancock, and <i>Bactrocera philippinensis</i> Drew & Hancock, key pest species within the <i>Bactrocera dorsalis</i> species complex, have been recently synonymized under the name <i>Bactrocera dorsalis</i> (Hendel). The closely related <i>Bactrocera carambolae</i> Drew & Hancock remains as a discrete taxonomic entity. Although the synonymizations have been accepted by most researchers, debate about the species limits remains. Because of the economic importance of this group of taxa, any new information available to support or deny the synonymizations is valuable. We investigated the chemical epicuticle composition of males and females of <i>B</i>. <i>dorsalis</i>, <i>B</i>. <i>invadens</i>, <i>B</i>. <i>papayae</i>, <i>B</i>. <i>philippinensis</i>, and <i>B</i>. <i>carambolae</i> by means of one- and two-dimensional gas chromatography–mass spectrometry, followed by multiple factor analyses and principal component analysis. Clear segregation of complex cuticule profiles of both <i>B</i>. <i>carambolae</i> sexes from <i>B</i>. <i>dorsalis</i> (Hendel) was observed. In addition to cuticular hydrocarbons, abundant complex mixtures of sex-specific oxygenated lipids (three fatty acids and 22 fatty acid esters) with so far unknown function were identified in epicuticle extracts from females of all species. The data obtained supports both taxonomic synonymization of <i>B</i>. <i>invadens</i>, <i>B</i>. <i>papayae</i>, and <i>B</i>. <i>philippinensis</i> with <i>B</i>. <i>dorsalis</i>, as well as the exclusion of <i>B</i>. <i>carambolae</i> from <i>B</i>. <i>dorsalis</i>.</p></div

Two-dimensional chromatogram of GC×GC/MS analysis of <i>Bactrocera dorsalis</i> and <i>B</i>. <i>carambolae</i> cuticular profiles.

<p>Cuticular profiles of <i>B</i>. <i>carambolae</i> female (A) and male (B) and of <i>B</i>. <i>dorsalis</i> female (C), male (D). Intensity of the signals is colour coded from blue (zero) to red (maximum). The compounds are assigned according to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0184102#pone.0184102.s001" target="_blank">S1 Table</a>.</p

MFA of transformed GC×GC/MS data of 32 cuticular hydrocarbons identified in five <i>Bactrocera</i> entities.

<p>M = male, DOR = <i>B</i>. <i>dorsalis</i>, CAR = <i>B</i>. <i>carambolae</i>, INV = <i>B</i>. ‘syn. <i>invadens</i>’, PAP = <i>B</i>. ‘syn. <i>papayae</i>’, PHI = <i>B</i>. ‘syn. <i>philippinensis</i>’. (A) Representation of groups of variables, (B) score plot describing the species and chemical class modalities of the first two factors, (C) projection of variables onto the plane defined by the first two principal components of the MFA. The coordinates of each variable are the correlation coefficients for the two first principal components (linear CH = red, methyl-branched CH = green, unsaturated CH = blue). The compounds are assigned according to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0184102#pone.0184102.s001" target="_blank">S1 Table</a>.</p

Heat map of all 59 compounds and the five <i>Bactrocera</i> entities from the GC×GC/MS data set.

<p>M = male, F = female, DOR = <i>B</i>. <i>dorsalis</i>, CAR = <i>B</i>. <i>carambolae</i>, INV = <i>B</i>. ‘syn. <i>invadens</i>’, PAP = <i>B</i>. ‘syn. <i>papayae</i>’, PHI = <i>B</i>. ‘syn. <i>philippinensis</i>’. Columns are colour coded according to chemical classes (i.e. red = fatty acid Ac01–03, green = fatty acid ester E01–22, violet = cuticular hydrocarbon CH01–32, blue = aldehyde Al01–02). The dendrograms are created using correlation-based distances and the Ward method of hierarchical clustering (<i>P</i> < 0.05). The compounds are assigned according to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0184102#pone.0184102.s001" target="_blank">S1 Table</a>.</p