Manual for starch gel electrophoresis: A method for the detection of genetic variation

The procedure to conduct horizontal starch gel electrophoresis on enzymes is described in detail. Areas covered are (I) collection and storage of specimens, (2) preparation of tissues, (3) preparation of a starch gel, (4) application of enzyme extracts to a gel, (5) setting up a gel for electrophoresis, (6) slicing a gel, and (7) staining a gel. Recipes are also included for 47 enzyme stains and 3 selected gel buffers. (PDF file contains 26 pages.

Disentangling genetic and environmental effects on the proteotypes of individuals

Proteotypes, like genotypes, have been found to vary between individuals in several studies, but consistent molecular functional traits across studies remain to be quantified. In a meta-analysis of 11 proteomics datasets from humans and mice, we use co-variation of proteins in known functional modules across datasets and individuals to obtain a consensus landscape of proteotype variation. We find that individuals differ considerably in both protein complex abundances and stoichiometry. We disentangle genetic and environmental factors impacting these metrics, with genetic sex and specific diets together explaining 13.5% and 11.6% of the observed variation of complex abundance and stoichiometry, respectively. Sex-specific differences, for example, include various proteins and complexes, where the respective genes are not located on sex-specific chromosomes. Diet-specific differences, added to the individual genetic backgrounds, might become a starting point for personalized proteotype modulation toward desired features

Enhanced flux pinning in neutron irradiated MgB2

We study the effect of neutron irradiation on the critical current density Jc of isotopically pure polycrystalline Mg11B2 samples. For fluences in the range 1017-1018 cm-2, Jc is enhanced and its dependence on magnetic field is significantly improved: we demonstrate that, in this regime, point-like pinning centers are effectively introduced in the system proportionally to the neutron fluence. Instead, for larger fluences, a strong suppression of the critical temperature accompanied by a decrease of both the upper critical field Bc2 and Jc is found.Comment: 13 pages, 3 igure

Neutron Irradiation of Mg11B2 : From the Enhancement to the Suppression of Superconducting Properties

In this letter we present the effect of neutron irradiation up to fluences of 3.9 1019 n/cm2 on the superconducting properties of MgB2. In order to obtain a disorder structure homogeneously distributed, the experiment was carried out on bulk samples prepared with the 11B isotope. Up to fluences of 1018 n/cm2 the critical temperature is slightly diminished (36 K) and the superconducting properties are significantly improved; the upper critical field is increased from 13.5 T to 20.3 T at 12 K and the irreversibility field is doubled at 5 K. For larger neutron fluences the critical temperature is suppressed down to 12 K and the superconducting properties come out strongly degraded.Comment: 13 pages, 4 figures. Submitted to Appl.Phys.Let

Whole cell proteome regulation by microRNAs captured in a pulsed SILAC mass spectrometry approach

Since gene expression is controlled on many different levels in a cell, capturing a comprehensive snapshot of all regulatory processes is a difficult task. One possibility to monitor effective changes within a cell is to directly quantify changes in protein synthesis, which reflects the accumulative impact of regulatory mechanisms on gene expression. Pulsed stable isotope labeling by amino acids in cell culture (pSILAC) has been shown to be a viable method to investigate de novo protein synthesis on a proteome-wide scale (Schwanhausser et al., Proteomics 9:205-209, 2009; Selbach et al., Nature 455:58-63, 2008). One application of pSILAC is to study the regulation of protein expression by microRNAs. Here, we describe how pSILAC in conjunction with shotgun mass spectrometry can assess differences in the protein profile between cells transfected with a microRNA and non-transfected cells

Excitation Spectrum and Superexchange Pathways in the Spin Dimer VODPO_4 . 1/2 D_2O

Magnetic excitations have been investigated in the spin dimer material VODPO_4 \cdot 1/2 D_2O using inelastic neutron scattering. A dispersionless magnetic mode was observed at an energy of 7.81(4) meV. The wavevector dependence of the scattering intensityfrom this mode is consistent with the excitation of isolated V^{4+} spin dimers with a V-V separation of 4.43(7) \AA. This result is unexpected since the V-V pair previously thought to constitute themagnetic dimer has a separation of 3.09 \AA. We identify an alternative V-V pair as the likely magnetic dimer, which involves superexchange pathways through a covalently bonded PO_4 group. This surprising result casts doubt on the interpretation of (VO)_2P_2O_7 as a spin ladder.Comment: 4 pages, 4 postscript figures - identical to previous paper but figure 2 and 3 hopefully more compatible .p

Impact of the gradient in gantry-table rotation on dynamic trajectory radiotherapy plan quality.

BACKGROUND To improve organ at risk (OAR) sparing, dynamic trajectory radiotherapy (DTRT) extends VMAT by dynamic table and collimator rotation during beam-on. However, comprehensive investigations regarding the impact of the gantry-table (GT) rotation gradient on the DTRT plan quality have not been conducted. PURPOSE To investigate the impact of a user-defined GT rotation gradient on plan quality of DTRT plans in terms of dosimetric plan quality, dosimetric robustness, deliverability, and delivery time. METHODS The dynamic trajectories of DTRT are described by GT and gantry-collimator paths. The GT path is determined by minimizing the overlap of OARs with planning target volume (PTV). This approach is extended to consider a GT rotation gradient by means of a maximum gradient of the path ( ) between two adjacent control points ( ) and maximum absolute change of G ( ). Four DTRT plans are created with different maximum G&∆G: &  = 0.5&0.125 (DTRT-1), 1&0.125 (DTRT-2), 3&0.125 (DTRT-3) and 3&1‍(DTRT-4), including 3-4 dynamic trajectories, for three clinically motivated cases in the head and neck and brain region (A, B, and C). A reference VMAT plan for each case is created. For all plans, plan quality is assessed and compared. Dosimetric plan quality is evaluated by target coverage, conformity, and OAR sparing. Dosimetric robustness is evaluated against systematic and random patient-setup uncertainties between in the lateral, longitudinal, and vertical directions, and machine uncertainties between in the dynamically rotating machine components (gantry, table, collimator rotation). Delivery time is recorded. Deliverability and delivery accuracy on a TrueBeam are assessed by logfile analysis for all plans and additionally verified by film measurements for one case. All dose calculations are Monte Carlo based. RESULTS The extension of the DTRT planning process with user-defined to investigate the impact of the GT rotation gradient on plan quality is successfully demonstrated. With increasing , slight (case C, : up to‍-1‍Gy) and substantial (case A, : up to -9.3 Gy, case‍B, : up to -4.7‍Gy) improvements in OAR sparing are observed compared to VMAT, while maintaining similar target coverage. All plans are delivered on the TrueBeam. Expected and actual machine position values recorded in the logfiles deviated by 96% (2%‍global/2 mm Gamma passing rate) with the dose calculation. With increasing , delivery time is prolonged by <2 min/trajectory (DTRT-4) compared to VMAT and DTRT-1. The DTRT plans for case A and B and the VMAT plan for case C plan reveal the best dosimetric robustness for the considered uncertainties. CONCLUSION The impact of the GT rotation gradient on DTRT plan quality is comprehensively investigated for three cases in the head and neck and brain region. Increasing freedom in this gradient improves dosimetric plan quality at the cost of increased delivery time for the investigated cases. No clear dependency of GT rotation gradient on dosimetric robustness is observed

Mol. Cell. Proteomics

The term “proteomics” encompasses the large-scale detection and analysis of proteins and their post-translational modifications. Driven by major improvements in mass spectrometric instrumentation, methodology, and data analysis, the proteomics field has burgeoned in recent years. It now provides a range of sensitive and quantitative approaches for measuring protein structures and dynamics that promise to revolutionize our understanding of cell biology and molecular mechanisms in both human cells and model organisms. The Proteomics Specification in Time and Space (PROSPECTS) Network is a unique EU-funded project that brings together leading European research groups, spanning from instrumentation to biomedicine, in a collaborative five year initiative to develop new methods and applications for the functional analysis of cellular proteins. This special issue of Molecular and Cellular Proteomics presents 16 research papers reporting major recent progress by the PROSPECTS groups, including improvements to the resolution and sensitivity of the Orbitrap family of mass spectrometers, systematic detection of proteins using highly characterized antibody collections, and new methods for absolute as well as relative quantification of protein levels. Manuscripts in this issue exemplify approaches for performing quantitative measurements of cell proteomes and for studying their dynamic responses to perturbation, both during normal cellular responses and in disease mechanisms. Here we present a perspective on how the proteomics field is moving beyond simply identifying proteins with high sensitivity toward providing a powerful and versatile set of assay systems for characterizing proteome dynamics and thereby creating a new “third generation” proteomics strategy that offers an indispensible tool for cell biology and molecular medicine

Proteome Profiling of Breast Tumors by Gel Electrophoresis and Nanoscale Electrospray Ionization Mass Spectrometry

We have conducted proteome-wide analysis of fresh surgery specimens derived from breast cancer patients, using an approach that integrates size-based intact protein fractionation, nanoscale liquid separation of peptides, electrospray ion trap mass spectrometry, and bioinformatics. Through this approach, we have acquired a large amount of peptide fragmentation spectra from size-resolved fractions of the proteomes of several breast tumors, tissue peripheral to the tumor, and samples from patients undergoing noncancer surgery. Label-free quantitation was used to generate protein abundance maps for each proteome and perform comparative analyses. The mass spectrometry data revealed distinct qualitative and quantitative patterns distinguishing the tumors from healthy tissue as well as differences between metastatic and non-metastatic human breast cancers including many established and potential novel candidate protein biomarkers. Selected proteins were evaluated by Western blotting using tumors grouped according to histological grade, size, and receptor expression but differing in nodal status. Immunohistochemical analysis of a wide panel of breast tumors was conducted to assess expression in different types of breast cancers and the cellular distribution of the candidate proteins. These experiments provided further insights and an independent validation of the data obtained by mass spectrometry and revealed the potential of this approach for establishing multimodal markers for early metastasis, therapy outcomes, prognosis, and diagnosis in the future. © 2008 American Chemical Society