Tissue specific labeling in proteomics

Mass spectrometry-based proteomics is a powerful tool for identifying and quantifying proteins in biological samples. While it is routinely used for the characterization of simple cell line systems, the analysis of the cell specific proteome in multicellular organisms and tissues poses a significant challenge. Isolating a subset of cells from tissues requires mechanical and biochemical separation or sorting, a process which can alter cellular signaling, and thus, the composition of the proteome. Recently, several approaches for cell selective labeling of proteins, that include bioorthogonal amino acids, biotinylating enzymes, and genetic tools, have been developed. These tools facilitate the selective labeling of proteins, their interactome, or of specific cell types within a tissue or an organism, while avoiding the difficult and contamination-prone biochemical separation of cells from the tissue. In this review, we give an overview of existing techniques and their application in cell culture models and whole animals

Normal-Conducting Separation and Compensation Dipoles for the LHC Experimental Insertions

The experimental insertions of the LHC make use of normal-conducting magnets to provide for part of the beam separation and to compensate the effect of two large spectrometer dipoles. Three different types with respect to the length were designed and are based on the same type of lamination. The main type of magnet MBXW has a core length of 3.4 m while the MBXWT and MBXWS magnets are 1.5 m and 0.75 m long versions respectively. The magnet design was done in collaboration between CERN and BINP and the dipole magnets are produced by BINP. So far all three MBXWS magnets, all three MBXWT magnets and fifteen of twenty-nine MBXW magnets have been manufactured and delivered to CERN. The report presents the main design issues and results of the acceptance tests including mechanical, electrical and magnetic field measurements

Translation of circRNAs

Circular RNAs (circRNAs) are abundant and evolutionarily conserved RNAs of largely unknown function. Here, we show that a subset of circRNAs is translated in vivo. By performing ribosome footprinting from fly heads, we demonstrate that a group of circRNAs is associated with translating ribosomes. Many of these ribo-circRNAs use the start codon of the hosting mRNA, are bound by membrane-associated ribosomes, and have evolutionarily conserved termination codons. In addition, we found that a circRNA generated from the muscleblind locus encodes a protein, which we detected in fly head extracts by mass spectrometry. Next, by performing in vivo and in vitro translation assays, we show that UTRs of ribo-circRNAs (cUTRs) allow cap-independent translation. Moreover, we found that starvation and FOXO likely regulate the translation of a circMbl isoform. Altogether, our study provides strong evidence for translation of circRNAs, revealing the existence of an unexplored layer of gene activity

Crystal-Chemical Origins of the Ultrahigh Conductivity of Metallic Delafossites

Despite their highly anisotropic complex-oxidic nature, certain delafossite compounds (e.g., PdCoO2, PtCoO2) are the most conductive oxides known, for reasons that remain poorly understood. Their room-temperature conductivity can exceed that of Au, while their low-temperature electronic mean-free-paths reach an astonishing 20 microns. It is widely accepted that these materials must be ultrapure to achieve this, although the methods for their growth (which produce only small crystals) are not typically capable of such. Here, we first report a new approach to PdCoO2 crystal growth, using chemical vapor transport methods to achieve order-of-magnitude gains in size, the highest structural qualities yet reported, and record residual resistivity ratios (>440). Nevertheless, the first detailed mass spectrometry measurements on these materials reveal that they are not ultrapure, typically harboring 100s-of-parts-per-million impurity levels. Through quantitative crystal-chemical analyses, we resolve this apparent dichotomy, showing that the vast majority of impurities are forced to reside in the Co-O octahedral layers, leaving the conductive Pd sheets highly pure (~1 ppm impurity concentrations). These purities are shown to be in quantitative agreement with measured residual resistivities. We thus conclude that a previously unconsidered "sublattice purification" mechanism is essential to the ultrahigh low-temperature conductivity and mean-free-path of metallic delafossites

Magnet Acceptance and Allocation at the LHC Magnet Evaluation Board

The normal and superconducting magnets for the LHC ring have been carefully examined to insure that each of about 1900 assemblies is suitable for the operation in the accelerator. Hardware experts and accelerator physicists have contributed to this work that consisted in magnet acceptance, and sorting according to geometry, field quality and quench level. This paper gives a description of the magnet approval mechanism that has been running since four years, reporting in a concise summary the main results achieved

Small Polarons in Transition Metal Oxides

The formation of polarons is a pervasive phenomenon in transition metal oxide compounds, with a strong impact on the physical properties and functionalities of the hosting materials. In its original formulation the polaron problem considers a single charge carrier in a polar crystal interacting with its surrounding lattice. Depending on the spatial extension of the polaron quasiparticle, originating from the coupling between the excess charge and the phonon field, one speaks of small or large polarons. This chapter discusses the modeling of small polarons in real materials, with a particular focus on the archetypal polaron material TiO2. After an introductory part, surveying the fundamental theoretical and experimental aspects of the physics of polarons, the chapter examines how to model small polarons using first principles schemes in order to predict, understand and interpret a variety of polaron properties in bulk phases and surfaces. Following the spirit of this handbook, different types of computational procedures and prescriptions are presented with specific instructions on the setup required to model polaron effects.Comment: 36 pages, 12 figure

Investigation on different materials after pulsed high field conditioning and low-energy H- irradiation

During operation, the radio-frequency quadrupole (RFQ) of the LINAC4 at CERN is exposed to high electric fields, which can lead to vacuum breakdown. It is also subject to beam loss, which can cause surface modification, including blistering, which can result in reduced electric field holding and an increased breakdown rate. First, experiments to study the high-voltage conditioning process and electrical breakdown statistics have been conducted using pulsed high-voltage DC systems in order to identify materials with high electric field handling capability and robustness to low-energy irradiation. In this paper, we discuss the results obtained for the different materials tested. To complement these, an investigation of their metallurgical properties using advanced microscopic techniques was done to observe and characterize the different materials and to compare results before and after irradiation and breakdown testing

Pan-claudin family interactome analysis reveals shared and specific interactions

Claudins are a family of transmembrane proteins expressed in epithelial tissues and are the major components of tight junctions (TJs), which define barrier properties in epithelia and maintain cell polarity. How claudins regulate the formation of TJs and which functions they exert outside of them is not entirely understood. Although the long and unstructured C-terminal tail is essential for regulation, it is unclear how it is involved in these functions beyond interacting with TJ-associated proteins such as TJ protein ZO-1 (TJP1). Here, we present an interactome study of the pan-claudin family in Madin-Darby canine kidney (MDCK)-C7 cells by combining two complementary mass spectrometry-based pull-down techniques creating an interaction landscape of the entire claudin family. The interaction partners of the claudins' C termini reveal their possible implications in localized biological processes in epithelial cells and their regulation by post-translational modifications (PTMs)