Two applications of 3D semi-landmark morphometrics implying different template designs: the theropod pelvis and the shrew skull

Geometric morphometrics involves defining landmark points to generate a discrete representation of an object. This crucial step is strongly influenced by the biological question guiding the analysis, and even more when using curve and surface semi-landmarks methods, because these require to generate a template of reference. We exemplify these constraints using two datasets from projects with very different backgrounds. The Theropod Dataset is a functional morphometric analysis of different extinct and extant theropod pelves. The Shrew Dataset is a populational morphometric analysis of the white-toothed shrew with very small variations in skull shape. We propose a novel procedure to generate a regular template configuration, using polygonal modelling tools. This method allows us to control the template geometry and adapt its complexity to the morphological variation in the sample. More studies are necessary to assess the morphometric and statistical importance of template design in curve and surface analyses.     

Darwin and sexual selection: One hundred years of misunderstanding

Darwin's book on the Descent of Man and Selection in Relation to Sex (1871) is often viewed as the continuation of TheOrigin of Species published 12 years earlier (1859), both because of the implicit parallelism between natural selection and sexual selection, and because Darwin himself presents the book as developing a subject (man) which he intentionally omitted in the Origin. But the Descent can also be viewed as the continuation of his book on Variation published three years earlier (1868). Firstly because Darwin's hypothesis of pangenesis links the selection process to the origin of variation through use and disuse, an idea underlying his speculations on the origin of moral sense in humans. Second because like the action of the horticulturist on his domestic crops, sexual selection exerted by one sex on the other sex can develop fancy traits that are not easily accounted for by their utility to the selected organism itself, such as artistic taste, pride, courage, and the morphological differences between human populations. These traits are difficult to reconcile with pangenesis. They add up to other contradictions of the book possibly resulting from Darwin's erroneous inference about the mechanism of inheritance, like those on the determination of sex-ratio, or the confusion between individual adaptation and the advantage to the species. These inconsistencies inaugurate a weakening of the Darwinian message, which will last 50 years after his death. They contributed to the neglect of sexual selection for a century. Darwin however maintained a logical distinction between evolutionary mechanisms and hereditary mechanisms, and an epistemological distinction between evolutionary theory and Pangenesis hypothesis. In the modern context of Mendelian genetics, Darwin's sexual selection retrospectively appears as luminous an idea in its pure principle as natural selection, even though the mechanisms governing the evolution of sexual choice in animals remain largely unresolved.     

The Neandertal lower right deciduous second molar from Trou de l'Abîme at Couvin, Belgium

A human lower right deciduous second molar was discovered in 1984 at the entrance of Trou de l'Abîme at Couvin (Belgium). In subsequent years the interpretation of this fossil remained difficult for various reasons: (1) the lack of taxonomically diagnostic elements which would support its attribution to either Homo (sapiens) neanderthalensis or H. s. sapiens; (2) the absence of any reliable chronostratigraphic interpretation of the sedimentary sequence of the site; (3) the contradiction between archaeological interpretations, which attributed the lithic industry to a transitional facies between the Middle and Early Upper Palaeolithic, and the radiocarbon date of 46,820 ± 3,290 BP obtained from animal bone remains associated with the tooth and the flint tools.Thanks to recent progress regarding these three aspects, the tooth from Trou de l'Abîme may now be studied in detail. Analyses of the morphology and enamel thickness of the fossil yielded diagnostic characters consistent with an attribution to Neandertals. Re-examination of the lithic industry of Couvin shows that it corresponds to the late Middle Palaeolithic rather than a transitional facies. Furthermore, a new analysis of the site stratigraphy indicates that the unit situated above the archaeological layer in which the tooth was found is probably a palaeosol of brown soil type. Comparison with the regional cave sequences as well as with the reference sequence from the Belgian loess belt tends to show that the most recent palaeosol of this type is dated between 42,000 and 40,000 BP. This is consistent with both a recently obtained AMS result at 44,500 BP and the published conventional date.     

Activation-induced cytidine deaminase targets DNA at sites of RNA polymerase II stalling by interaction with Spt5

Activation-induced cytidine deaminase (AID) initiates antibody gene diversification by creating U:G mismatches. However, AID is not specific for antibody genes; Off-target lesions can activate oncogenes or cause chromosome translocations. Despite its importance in these transactions little is known about how AID finds its targets. We performed an shRNA screen to identify factors required for class switch recombination (CSR) of antibody loci. We found that Spt5, a factor associated with stalled RNA polymerase II (Pol II) and single stranded DNA (ssDNA), is required for CSR. Spt5 interacts with AID, it facilitates association between AID and Pol II, and AID recruitment to its Ig and non-Ig targets. ChIP-seq experiments reveal that Spt5 colocalizes with AID and stalled Pol II. Further, Spt5 accumulation at sites of Pol II stalling is predictive of AID-induced mutation. We propose that AID is targeted to sites of Pol II stalling in part via its association with Spt5.     

Proteomic analysis of <Emphasis Type="Italic">Parietaria judaica</Emphasis> pollen and allergen profiling by an immunoproteomic approach

Parietaria judaica pollen is a common cause of airway allergic disease in the Mediterranean area. Proteome analysis of mature Parietaria judaica pollen by two-dimensional gel electrophoresis (2-DE) and mass spectrometry has established the first reference proteome map of this weed. Proteins involved in a variety of cellular functions as well as the occurrence of allergens were detected. By using 2-DE and immunoblotting with sera from Parietaria judaica allergic patients we obtained a more detailed characterization of Parietaria judaica allergen profile so to improve our comprehension of the pathogenesis of pollen-induced allergic reaction.     

Multiplexing of multicolor bioluminescence resonance energy transfer

Bioluminescence resonance energy transfer (BRET) is increasingly being used to monitor protein-protein interactions and cellular events in cells. However, the ability to monitor multiple events simultaneously is limited by the spectral properties of the existing BRET partners. Taking advantage of newly developed Renilla luciferases and blue-shifted fluorescent proteins (FPs), we explored the possibility of creating novel BRET configurations using a single luciferase substrate and distinct FPs. Three new (to our knowledge) BRET assays leading to distinct color bioluminescence emission were generated and validated. The spectral properties of two of the FPs used (enhanced blue (EB) FP2 and mAmetrine) and the selection of appropriate detection filters permitted the concomitant detection of two independent BRET signals, without cross-interference, in the same cells after addition of a unique substrate for Renilla luciferase-II, coelentrazine-400a. Using individual BRET-based biosensors to monitor the interaction between G-protein-coupled receptors and G-protein subunits or activation of different G-proteins along with the production of a second messenger, we established the proof of principle that two new BRET configurations can be multiplexed to simultaneously monitor two dependent or independent cellular events. The development of this new multiplexed BRET configuration opens the way for concomitant monitoring of various independent biological processes in living cells.     

Copper(I) and copper(II) binding to β-amyloid 16 (Aβ16) studied by electrospray ionization mass spectrometry

Copper-β-amyloid 16 (Aβ16) complexes were investigated by electrospray ionization mass spectrometry (ESI-MS). Copper(i) and (ii) complexes were formed on-line in a microchip electrospray emitter by using a sacrificial copper electrode as the anode in positive ionization mode. In the presence of ascorbic acid in the peptide solution, the amount of Cu(i)-Aβ16 generated electrochemically was even higher. A kinetic model is proposed to account for the generation of copper complexes. The structure of Cu(i)-Aβ16 was investigated by tandem mass spectrometry (MS/MS), and the binding site of Cu(i) to Aβ16 was identified at the His13, His14 residues. Cu(ii)-Aβ16 was also investigated by MS/MS and, based on the unusual observations of a-ions, the two binding residues of His13 and His14 of Aβ16 to Cu(ii) were also confirmed. This approach provides direct information on Cu(i)-Aβ16 complexes generated in solution from metallic copper and gives evidence that both His13 and His14 are involved in the coordination of both Cu(i)- and Cu(ii)-Aβ16 complexes.