Large Scale Biology Laboratory

We describe the designand optimization of polyfunctional scaffoldsbased on a fluorescent indolizine core derivatized with various orthogonalgroups (amines, esters, oximes, alkynes, etc.). To show one applicationas tools in biology, the scaffold was used to prepare drug–biotinconjugates that were then immobilized onto avidin-agarose for affinitychromatography. More specifically, the antiangiogenic drug COB223,whose mechanism of action remained unclear, was chosen as a proof-of-conceptdrug. The drug-selective discrimination of proteins observed afterelution of the cell lysates through the affinity columns, functionalizedeither with the biologically active COB223 or a structurally relatedinactive analogue (COB236), is a clear indication that the presenceof the indolizine core does not limit drug–protein interactionand confirms the usefulness of the indolizine scaffold. Furthermore,the separation of COB223-interacting proteins from human placentalextracts unveiled unanticipated protein targets belonging to the familyof regulatory RNA-binding proteins, which opens the way to new hypotheseson the mode of action of this antiangiogenic drug.

The Chromosome-Centric Human Proteome Project (C-HPP) aims to identify "missing" proteins in the neXtProt knowledgebase. We present an in-depth proteomics analysis of the human sperm proteome to identify testis-enriched missing proteins. Using protein extraction procedures and LC-MS/MS analysis, we detected 235 proteins (PE2-PE4) for which no previous evidence of protein expression was annotated. Through LC-MS/MS and LC-PRM analysis, data mining, and immunohistochemistry, we confirmed the expression of 206 missing proteins (PE2-PE4) in line with current HPP guidelines (version 2.0). Parallel reaction monitoring acquisition and sythetic heavy labeled peptides targeted 36 ≪one-hit wonder≫ candidates selected based on prior peptide spectrum match assessment. 24 were validated with additional predicted and specifically targeted peptides. Evidence was found for 16 more missing proteins using immunohistochemistry on human testis sections. The expression pattern for some of these proteins was specific to the testis, and they could possibly be valuable markers with fertility assessment applications. Strong evidence was also found of four "uncertain" proteins (PE5); their status should be re-examined. We show how using a range of sample preparation techniques combined with MS-based analysis, expert knowledge, and complementary antibody-based techniques can produce data of interest to the community. All MS/MS data are available via ProteomeXchange under identifier PXD003947. In addition to contributing to the C-HPP, we hope these data will stimulate continued exploration of the sperm proteome.

In chick embryos, observations were made on serial semithin transverse sections of the wing level. In addition homo- or heterotopic replacements of the wing or leg somitic mesoderm by labelled somitic or nonsomitic mesoderm were made in 2-to 2.5-day embryos. The nuclear label used was either natural (quail donor embryos in heterotopic transplantations) or isotopic (chick donors labelled with tritiated thymidine).Histological examination revealed that the first somitic cells to leave somite 15 apparently did so at the 20 to 22 somite stage, while the last ones to leave somite 20 apparently did so shortly before the 36 somite stage.Transplantation experiments with labelled donor cells revealed the routes of migratory somitic cells and the time-course of their invasion into the outgrowing limb bud (non-somitic graft cells did not noticeably invade the limb anlage). They showed furthermore that the somitic mesoderm is not regionalized with respect to its limb myogenic properties.These results are compared with those obtained in other classes of vertebrates.

Removal of the apical ectodermal ridge causes a reduction in the rate of outgrowth of the wing-bud and the loss of distal parts. More specifically it causes a short-term increase in cell density and cell death and a decrease in the rate of cell proliferation. The evidence supports the hypothesis of density-dependent control of cell division and suggests that there may also be a mechanism regulating skeletal length at the time of differentiation. An informal model is presented to explain the observations.