Influence of organic solvents and temperature on the micellization of conventional and gemini surfactants: a conductometric study

<p>The micellar behaviour of similar hydrophobic chain length conventional (cetyltrimethyl ammonium bromide, CTAB; cetyl pyridinium chloride, CPC; cetyldimethylbenzyl ammonium chloride, C16BCl) and gemini surfactant (16-2-16) in water and polar non-aqueous solvents has been investigated in the temperature range 288.15–318.15 K with the help of conductivity measurements. The method proposed by Carpena <i>et al</i>. has been used to analyse the conductivity–concentration to determine the micellization parameters using critical micelle concentration (CMC) and degree of counter-ion dissociation (α) of the micelle. It shows much better performance than the conventional methods and the effect of experimental errors on the evaluation of the micellization parameters has been shown to be minimal by using this procedure. It was observed that the micellization tendency of the surfactant decreases in the presence of solvents. Thermodynamic parameters were also evaluated from the temperature dependence of the CMC values.</p

Quantitative Proteomic Analysis of Mouse Embryonic Fibroblasts and Induced Pluripotent Stem Cells Using ¹⁶O/¹⁸O Labeling

Induced pluripotent stem cells (iPSC) hold great promise for regenerative medicine as well as for investigations into the pathogenesis and treatment of various diseases. Understanding of key intracellular signaling pathways and protein targets that control development of iPSC from somatic cells is essential for designing new approaches to improve reprogramming efficiency. Here, we report the development and application of an integrated quantitative proteomics platform for investigating differences in protein expressions between mouse embryonic fibroblasts (MEF) and MEF-derived iPSC. This platform consists of ¹⁶O/¹⁸O labeling, multidimensional peptide separation coupled with tandem mass spectrometry, and data analysis with UNiquant software. With this platform, a total of 2481 proteins were identified and quantified from the ¹⁶O/¹⁸O-labeled MEF-iPSC proteome mixtures with a false discovery rate of 0.01. Among them, 218 proteins were significantly upregulated, while 247 proteins were significantly downregulated in iPSC compared to MEF. Many nuclear proteins, including Hdac1, Dnmt1, Pcna, Ccnd1, Smarcc1, and subunits in DNA replication and RNA polymerase II complex, were found to be enhanced in iPSC. Protein network analysis revealed that Pcna functions as a hub orchestrating complicated mechanisms including DNA replication, epigenetic inheritance (Dnmt1), and chromatin remodeling (Smarcc1) to reprogram MEF and maintain stemness of iPSC

Accurate Sequence Analysis of a Monoclonal Antibody by Top-Down and Middle-Down Orbitrap Mass Spectrometry Applying Multiple Ion Activation Techniques

Targeted top-down (TD) and middle-down (MD) mass spectrometry (MS) offer reduced sample manipulation during protein analysis, limiting the risk of introducing artifactual modifications to better capture sequence information on the proteoforms present. This provides some advantages when characterizing biotherapeutic molecules such as monoclonal antibodies, particularly for the class of biosimilars. Here, we describe the results obtained analyzing a monoclonal IgG1, either in its ∼150 kDa intact form or after highly specific digestions yielding ∼25 and ∼50 kDa subunits, using an Orbitrap mass spectrometer on a liquid chromatography (LC) time scale with fragmentation from ion–photon, ion–ion, and ion–neutral interactions. Ultraviolet photodissociation (UVPD) used a new 213 nm solid-state laser. Alternatively, we applied high-capacity electron-transfer dissociation (ETD HD), alone or in combination with higher energy collisional dissociation (EThcD). Notably, we verify the degree of complementarity of these ion activation methods, with the combination of 213 nm UVPD and ETD HD producing a new record sequence coverage of ∼40% for TD MS experiments. The addition of EThcD for the >25 kDa products from MD strategies generated up to 90% of complete sequence information in six LC runs. Importantly, we determined an optimal signal-to-noise threshold for fragment ion deconvolution to suppress false positives yet maximize sequence coverage and implemented a systematic validation of this process using the new software TDValidator. This rigorous data analysis should elevate confidence for assignment of dense MS² spectra and represents a purposeful step toward the application of TD and MD MS for deep sequencing of monoclonal antibodies

The uses and abuses of Elinor Ostrom’s concept of commons in urban theorizing

Any urban setting will contain privately owned spaces, public space and different aspects of mixed space that are not wholly public or private but which constitute common resources. Some urban common resources are tangible such as parks, sidewalks and libraries and some are intangible like a sense of security allowing people to move freely in the city, a sense of belonging, or general buzz. The notion of commons has been given an important upswing in popularity after Elinor Ostrom’s 2009 Nobel Prize. Her work on common-pool resources seems to provide a starting point for grappling with issues of urban commons. However, Ostrom’s earlier work (Ostrom 1990) deals with subtractive and tangible resources (like fish, water and forests). And one important design principle for governance of these commons is that the group of appropriators can erect clear boundary rules. A central characteristic of urban settings however is mobility, permeable boundaries and perhaps that at least occasionally resources are less clearly subtractible. It is therefore questionable to what extent theories of governing the commons relying on Ostrom’s models can be applied in urban settings. However, it may also be that urban commons may have somewhat different character but may be fruitfully approached using the same basic framework. Inroads have been made for instance on informational commons (Ostrom 2007) which also seem radically different from fisheries or water basins. This paper presents are review (in process) of how Ostrom's theories have been applied in urban studies and to highlight the potential and limitations of these approaches

ISPTM: An Iterative Search Algorithm for Systematic Identification of Post-translational Modifications from Complex Proteome Mixtures

Identifying protein post-translational modifications (PTMs) from tandem mass spectrometry data of complex proteome mixtures is a highly challenging task. Here we present a new strategy, named iterative search for identifying PTMs (ISPTM), for tackling this challenge. The ISPTM approach consists of a basic search with no variable modification, followed by iterative searches of many PTMs using a small number of them (usually two) in each search. The performance of the ISPTM approach was evaluated on mixtures of 70 synthetic peptides with known modifications, on an 18-protein standard mixture with unknown modifications and on real, complex biological samples of mouse nuclear matrix proteins with unknown modifications. ISPTM revealed that many chemical PTMs were introduced by urea and iodoacetamide during sample preparation and many biological PTMs, including dimethylation of arginine and lysine, were significantly activated by Adriamycin treatment in nuclear matrix associated proteins. ISPTM increased the MS/MS spectral identification rate substantially, displayed significantly better sensitivity for systematic PTM identification compared with that of the conventional all-in-one search approach, and offered PTM identification results that were complementary to InsPecT and MODa, both of which are established PTM identification algorithms. In summary, ISPTM is a new and powerful tool for unbiased identification of many different PTMs with high confidence from complex proteome mixtures