Selectivity over coverage in de novo sequencing of IgGs

Although incredibly diverse in specificity, millions of unique Immunoglobulin G (IgG) molecules in the human antibody repertoire share most of their amino acid sequence. These constant parts of IgG do not yield any useful information in attempts to sequence antibodies de novo. Therefore, methods focusing solely on the variable regions and providing unambiguous sequence reads are strongly advantageous. We report a mass spectrometry-based method that uses electron capture dissociation (ECD) to provide straightforward-to-read sequence ladders for the variable parts of both the light and heavy chains, with a preference for the functionally important CDR3. We optimized this method on the therapeutic antibody Trastuzumab and demonstrate its applicability on two monoclonal quartets of the four IgG subclasses, IgG1, IgG2, IgG3 and IgG4. The method is based on proteolytically separating the variable F(ab′)₂ part from the conserved Fc part, whereafter the F(ab′)₂ portions are mass-analyzed and fragmented by ECD. Pure ECD, without additional collisional activation, leads to straightforward-to-read sequence tags covering the CDR3 of both the light and heavy chains. Using molecular modelling and structural analysis, we discuss and explain this selective fragmentation behavior and describe how structural features of the different IgG subclasses lead to distinct fragmentation patterns. Overall, we foresee that pure ECD on F(ab′)₂ or Fab molecules can become a valuable tool for the de novo sequencing of serum antibodies.     

Synthesis of functionalized CF3-containing heterocycles via [2,3]-sigmatropic rearrangement and sequential catalytic carbocyclization

A new efficient access to functionalized CF₃-substituted and nitrogen or sulfur-containing heterocycles has been developed directly from diazocompounds CF₃C(N₂)Z (Z=CO₂Me, P(O)(OEt)₂). The method is based on the direct selective synthesis of doubly unsaturated substrates followed by metal-mediated carbocylization. The first step has been performed by Cu(II)-catalyzed [2,3]-sigmatropic rearrangement of propargyl- or/and allyl-containing sulfur and nitrogen ylides leading to fluorinated enynes, diolefins, and especially allenynes derivatives. The second step involves their carbocyclization via ring closing metathesis and Pauson-Khand reaction.     

The Molecular Basis of Different Approaches for the Study of Cancer Stem Cells and the Advantages and Disadvantages of a Three-Dimensional Culture

Cancer stem cells (CSCs) are a rare tumor subpopulation with high differentiation, proliferative and tumorigenic potential compared to the remaining tumor population. CSCs were first discovered by Bonnet and Dick in 1997 in acute myeloid leukemia. The identification and isolation of these cells in this pioneering study were carried out through the flow cytometry, exploiting the presence of specific cell surface molecular markers (CD34⁺/CD38⁻). In the following years, different strategies and projects have been developed for the study of CSCs, which are basically divided into surface markers assays and functional assays; some of these techniques also allow working with a cellular model that better mimics the tumor architecture. The purpose of this mini review is to summarize and briefly describe all the current methods used for the identification, isolation and enrichment of CSCs, describing, where possible, the molecular basis, the advantages and disadvantages of each technique with a particular focus on those that offer a three-dimensional culture.     

Improved Sensing Performance of Amperometric Urea Biosensor by Using Platinum Nanoparticles

A novel Platinum nanoparticle (PtNPs) modified Poly(pyrrole-co-1-(2-Aminophenyl)pyrrole)/Urease film coated Au electrode was designed for amperometric detection of urea. PtNPs quantity, film density and pH were optimized and interference effect of some substances readily found in municipal wastewater and blood was investigated. The biosensor responded to urea with a measurement concentration range of 0.1 to 30 mM, a sensitivity of 31.8 μA mM⁻¹ cm⁻², a LOD of 7.58 μM, an accuracy of 104 % and a RSD% of only 0.82. It sensed the concentration of urea in the municipal sewage water with recovery of 97.6 % (n=3) and remained 78 % of its initial response at 28^th day. Results confirmed that PtNPs with strong conductivity improved the electron transfer ability of the working electrode.