Spectrophotometric assessment of nuclear proteins: a preliminary study

Qualitative evaluation of protein content in formalin fixed, paraffin-embedded tissues is usually performed by means of cytofluorimetric analysis. On the other hand, several studies underline the opportunity to measure the concentration of nuclear proteins, which is often accomplished by using complex techniques and instrumentation. In the present work, we suggest a new application for the spectrophotometric evaluation of protein content on extracted and isolated nuclei, based on EDTA treatment of specimens and chemical extraction of proteins, followed by direct spectrophotometric measurement at UV wavelengths. We also demonstrate how this parameter correlates with other diagnostic factors, such as the proliferation index (MIB-1) and the DNA content (ploidy) of cells. This method is simple and effective, yet less expensive than other protein quantitation protocols

Radiative distortion of kinematic edges in cascade decays

Kinematic edges of cascade decays of new particles produced in high-energy collisions may provide important constraints on the involved particles' masses. For the exemplary case of gluino decay g˜→qq¯χ˜ into a pair of quarks and a neutralino through a squark resonance, we study the hadronic invariant mass distribution in the vicinity of the kinematic edge. We perform a next-to-leading order calculation in the strong coupling αs and the ratio of squark width and squark mass Γq˜/mq˜, based on a systematic expansion in Γq˜/mq˜. The separation into hard, collinear and soft contributions elucidates the process-dependent and universal features of distributions in the edge region, represented by on-shell decay matrix elements, universal jet functions and a soft function that depends on the resonance propagator and soft Wilson lines.The work of M.B. has been supported in part by the Bundesministerium für Bildung und Forschung (BMBF) under project no. 05H15W0CAA. L.J. was partially supported by the DFG contract STU 615/1-1, and M.U. is partially supported by the STFC grant ST/L000385/1 and her research is funded by a Royal Society Dorothy Hodgkin Research Fellowship

The impact of the LHC Z-boson transverse momentum data on PDF determinations

The LHC has recently released precise measurements of the transverse momentum distribution of the Z-boson that provide a unique constraint on the structure of the proton. Theoretical developments now allow the prediction of these observables through next-to-next-to-leading order (NNLO) in perturbative QCD. In this work we study the impact of incorporating these latest advances into a determination of parton distribution functions (PDFs) through NNLO including the recent ATLAS and CMS 7 TeV and 8 TeV pTZ data. We investigate the consistency of these measurements in a global fit to the available data and quantify the impact of including the pTZ distributions on the PDFs. The inclusion of these new data sets significantly reduces the uncertainties on select parton distributions and the corresponding parton-parton luminosities. In particular, we find that the pTZ data ultimately leads to a reduction of the PDF uncertainty on the gluon-fusion and vector-boson fusion Higgs production cross sections by about 30%, while keeping the central values nearly unchanged.This research was supported in part by the National Science Foundation under Grant No. NSF PHY11-25915 to the Kavli Institute of Theoretical Physics in Santa Barbara. R. B. is supported by the DOE contract DE-AC02-06CH11357. F. P. is supported by the DOE grants DE-FG02- 91ER40684 and DE-AC02-06CH11357. M. U. is supported by a Royal Society Dorothy Hodgkin Research Fellowship and partially supported by the STFC grant ST/L000385/1. A. G. is supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Sk lodowska-Curie grant agreement No 659128 - NEXTGENPDF. This research used resources of the Argonne Leadership Computing Facility, which is a DOE Office of Science User Facility supported under Contract DE-AC02-06CH11357

Progress on neural parton distributions

We give a status report on the determination of a set of parton distributions based on neural networks. In particular, we summarize the determination of the nonsinglet quark distribution up to NNLO, we compare it with results obtained using other approaches, and we discuss its use for a determination of $\alpha_s$.Comment: 4 pages, 2 figs, uses dis2007.cls, to appear in the DIS 2007 workshop proceeding

Recent progress on NNPDF for LHC

We present recent results of the NNPDF collaboration on a full DIS analysis of Parton Distribution Functions (PDFs). Our method is based on the idea of combining a Monte Carlo sampling of the probability measure in the space of PDFs with the use of neural networks as unbiased universal interpolating functions. The general structure of the project and the features of the fit are described and compared to those of the traditional approaches.Comment: 4 pages, 6 figures, contribution for the proceedings of the conference "Rencontres de Moriond, QCD and High Energy Interactions

The impact of heavy quark mass effects in the NNPDF global analysis

We discuss the implementation of the FONLL general-mass scheme for heavy quarks in deep-inelastic scattering in the FastKernel framework, used in the NNPDF series of global PDF analysis. We present the general features of FONLL and benchmark the accuracy of its implementation in FastKernel comparing with the Les Houches heavy quark benchmark tables. We then show preliminary results of the NNPDF2.1 analysis, in which heavy quark mass effects are included following the FONLL-A GM scheme.Comment: 5 pages, 3 figures; to appear in the proceedings of DIS 2010, Firenz

Progress in the Neural Network Determination of Polarized Parton Distributions

We review recent progress towards a determination of a set of polarized parton distributions from a global set of deep-inelastic scattering data based on the NNPDF methodology, in analogy with the unpolarized case. This method is designed to provide a faithful and statistically sound representation of parton distributions and their uncertainties. We show how the FastKernel method provides a fast and accurate method for solving the polarized DGLAP equations. We discuss the polarized PDF parametrizations and the physical constraints which can be imposed. Preliminary results suggest that the uncertainty on polarized PDFs, most notably the gluon, has been underestimated in previous studies.Comment: 5 pages, 2 figures; to appear in the proceedings of DIS 2010, Firenz

High-level detection of gene amplification and chromosome aneuploidy in extracted nuclei from paraffin-embedded tissue of human cancer using FISH: a new approach for retrospective studies

A novel application of fluorescence in situ hybridization (FISH) to isolated nuclei is described. The method detects gene amplification and chromosome aneuploidy in extracted nuclei from paraffin-embedded tissue of human cancer with greater sensitivity and specificity than existing FISH methods. In this study, the method is applied to signal detection of the HER-2/neu (c-erbB-2) gene, whose amplification is one of the most common genetic alterations associated with human breast cancer. Nuclei were extracted and isolated from formalin fixed, paraffin embedded tissue of 43 different carcinomas (breast, ovary, endometrium, gastrointestinal stromal tumor and malignant mesothelioma). FISH was performed both on sections and extracted nuclei of each tissue using chromosome enumeration probes (CEP) for the centromeric regions of chromosomes 8 and 17, and a locus specific identifier (LSI) for the HER-2/neu oncogene. Differences between ploidy calculated in sections and extracted nuclei were seen in 3 breast carcinomas and 1 gastrointestinal stromal tumor (GIST). Furthermore, 1 breast cancer, previously considered to be borderline for HER-2/neu gene amplification turned out to be clearly amplified. Nuclei extraction and isolation bypass all the problems related to signal interpretation in tissue sections, and the adoption of this new technique, which improves the signal quality in several neoplastic samples, is suggested

New active site oriented glyoxyl-agarose derivatives of Escherichia coli penicillin G acylase

<p>Abstract</p> <p>Background</p> <p>Immobilized Penicillin G Acylase (PGA) derivatives are biocatalysts that are industrially used for the hydrolysis of Penicillin G by fermentation and for the kinetically controlled synthesis of semi-synthetic β-lactam antibiotics. One of the most used supports for immobilization is glyoxyl-activated agarose, which binds the protein by reacting through its superficial Lys residues. Since in <it>E. coli </it>PGA Lys are also present near the active site, an immobilization that occurs through these residues may negatively affect the performance of the biocatalyst due to the difficult diffusion of the substrate into the active site. A preferential orientation of the enzyme with the active site far from the support surface would be desirable to avoid this problem.</p> <p>Results</p> <p>Here we report how it is possible to induce a preferential orientation of the protein during the binding process on aldehyde activated supports. A superficial region of PGA, which is located on the opposite side of the active site, is enriched in its Lys content. The binding of the enzyme onto the support is consequently forced through the Lys rich region, thus leaving the active site fully accessible to the substrate. Different mutants with an increasing number of Lys have been designed and, when active, immobilized onto glyoxyl agarose. The synthetic performances of these new catalysts were compared with those of the immobilized wild-type (wt) PGA. Our results show that, while the synthetic performance of the wt PGA sensitively decreases after immobilization, the Lys enriched mutants have similar performances to the free enzyme even after immobilization.</p> <p>We also report the observations made with other mutants which were unable to undergo a successful maturation process for the production of active enzymes or which resulted toxic for the host cell.</p> <p>Conclusion</p> <p>The desired orientation of immobilized PGA with the active site freely accessible can be obtained by increasing the density of Lys residues on a predetermined region of the enzyme. The newly designed biocatalysts display improved synthetic performances and are able to maintain a similar activity to the free enzymes. Finally, we found that the activity of the immobilized enzyme proportionally improves with the number of introduced Lys.</p

Liquid phase microextraction techniques combined with chromatography analysis: A review

Sample pretreatment is the first and the most important step of an analytical procedure. In routine analysis, liquid-liquid microextraction (LLE) is the most widely used sample pre-treatment technique, whose goal is to isolate the target analytes, provide enrichment, with cleanup to lower the chemical noise, and enhance the signal. The use of extensive volumes of hazardous organic solvents and production of large amounts of waste make LLE procedures unsuitable for modern, highly automated laboratories, expensive, and environmentally unfriendly. In the past two decades, liquid-phase microextraction (LPME) was introduced to overcome these drawbacks. Thanks to the need of only a few microliters of extraction solvent, LPME techniques have been widely adopted by the scientific community. The aim of this review is to report on the state-of-the-art LPME techniques used in gas and liquid chromatography. Attention was paid to the classification of the LPME operating modes, to the historical contextualization of LPME applications, and to the advantages of microextraction in methods respecting the value of green analytical chemistry. Technical aspects such as description of methodology selected in method development for routine use, specific variants of LPME developed for complex matrices, derivatization, and enrichment techniques are also discussed