Microarray-based ultra-high resolution discovery of genomic deletion mutations

BACKGROUND: Oligonucleotide microarray-based comparative genomic hybridization (CGH) offers an attractive possible route for the rapid and cost-effective genome-wide discovery of deletion mutations. CGH typically involves comparison of the hybridization intensities of genomic DNA samples with microarray chip representations of entire genomes, and has widespread potential application in experimental research and medical diagnostics. However, the power to detect small deletions is low. RESULTS: Here we use a graduated series of Arabidopsis thaliana genomic deletion mutations (of sizes ranging from 4 bp to ~5 kb) to optimize CGH-based genomic deletion detection. We show that the power to detect smaller deletions (4, 28 and 104 bp) depends upon oligonucleotide density (essentially the number of genome-representative oligonucleotides on the microarray chip), and determine the oligonucleotide spacings necessary to guarantee detection of deletions of specified size. CONCLUSIONS: Our findings will enhance a wide range of research and clinical applications, and in particular will aid in the discovery of genomic deletions in the absence of a priori knowledge of their existence

Two Decades of Income Inequality in Britain: The Role of Wages, Household Earnings and Redistribution

We study earnings and income inequality in Britain over the past two decades, including the period of relatively 'inclusive' growth from 1997 to 2004, and the Great Recession. We focus on the middle 90%, where trends have contrasted strongly with the 'new inequality' at the very top. Household earnings inequality has risen, driven by male earnings-although a 'catch-up' of female earnings did hold down individual earnings inequality and reduce within-household inequality. Nevertheless, net household income inequality fell due to deliberate increases in redistribution, the tax and transfer system's insurance role during the Great Recession, falling household worklessness, and rising pensioner incomes

Two-Photon Interferometry for High-Resolution Imaging

We discuss advantages of using non-classical states of light for two aspects of optical imaging: creating of miniature images on photosensitive substrates, which constitutes the foundation for optical lithography, and imaging of micro objects. In both cases, the classical resolution limit given by the Rayleigh criterion is approximately a half of the optical wavelength. It has been shown, however, that by using multi-photon quantum states of the light field, and multi-photon sensitive material or detector, this limit can be surpassed. We give a rigorous quantum mechanical treatment of this problem, address some particularly widespread misconceptions and discuss the requirements for turning the research on quantum imaging into a practical technology.Comment: Presented at PQE 2001. To appear in Special Issue of Journal of Modern Optic

Accelerating Community College Graduation Rates: A Benefit–Cost Analysis

This article reports a benefit–cost evaluation of the Accelerated Study in Associate Programs (ASAP) of the City University of New York (CUNY). ASAP was designed to accelerate associate degree completion within 3 years of degree enrollment at CUNY’s community colleges. The program evaluation revealed that the completion rate for the examined cohort increased from 24.1% to 54.9%, and cost per graduate declined considerably (Levin & Garcia, 2012; Linderman & Kolenovic, 2012). The returns on investment to the taxpayer include the benefits from higher tax revenues and lower costs of spending on public health, criminal justice, and public assistance. For each dollar of investment in ASAP by taxpayers, the return was $3 to$4. For each additional graduate, the taxpayer gained an amount equal to a certificate of deposit with a value of $146,000 (net of the costs of the investment). Based on these estimated returns, a cohort of 1,000 students enrolled in ASAP would generate net fiscal benefits for the taxpayer of more than$46 million relative to enrolling in the conventional degree program. ASAP results demonstrate that an effective educational policy can generate returns to the taxpayer that vastly exceed the public investment required

Two-Photon Fluorescence Microscopy Imaging of Cellular Oxidative Stress Using Profluorescent Nitroxides

A range of varying chromophore nitroxide free radicals and their nonradical methoxyamine analogues were synthesized and their linear photophysical properties examined. The presence of the proximate free radical masks the chromophore’s usual fluorescence emission, and these species are described as profluorescent. Two nitroxides incorporating anthracene and fluorescein chromophores (compounds 7 and 19, respectively) exhibited two-photon absorption (2PA) cross sections of approximately 400 G.M. when excited at wavelengths greater than 800 nm. Both of these profluorescent nitroxides demonstrated low cytotoxicity toward Chinese hamster ovary (CHO) cells. Imaging colocalization experiments with the commercially available CellROX Deep Red oxidative stress monitor demonstrated good cellular uptake of the nitroxide probes. Sensitivity of the nitroxide probes to H2O2-induced damage was also demonstrated by both one- and two-photon fluorescence microscopy. These profluorescent nitroxide probes are potentially powerful tools for imaging oxidative stress in biological systems, and they essentially “light up” in the presence of certain species generated from oxidative stress. The high ratio of the fluorescence quantum yield between the profluorescent nitroxide species and their nonradical adducts provides the sensitivity required for measuring a range of cellular redox environments. Furthermore, their reasonable 2PA cross sections provide for the option of using two-photon fluorescence microscopy, which circumvents commonly encountered disadvantages associated with one-photon imaging such as photobleaching and poor tissue penetration

Excimer formation by steric twisting in carbazole and triphenylamine-based host materials

This paper presents a detailed spectroscopic investigation of luminescence properties of 4,4′-Bis(N-carbazolyl)-1,1′-biphenyl (CBP) and N,N,N’,N’-tetraphenylbenzidine (TAD) in solutions and neat films. These compounds are compared to their derivatives CDBP and TDAD that contain methyl groups in the 2 and 2’ position of the biphenyl core. We find that whereas steric twisting in CDBP and TDAD leads to a high triplet energy of about 3.0 and 3.1 eV, respectively, these compounds also tend to form triplet excimers in a neat film, in contrast to CBP and TAD. By comparison with N-phenylcarbazole (NPC) and triphenylamine (TPA), on which these compounds are based, as well as with the rigid spiro analogs to CBP and TAD we show that the reduced excimer formation in CBP and TAD can be attributed to a localization of the excitation onto the central biphenyl part of the molecule.We acknowledge support from the Federal Ministry of Education and Research (BMBF) through the project ‘Trip-Q’, the German Science Foundation (DFG) through the Research and Training Group GRK 1640 and the UK Engineering and Physical Sciences Research Council (grant number EP/G060738/1).This is the final published version. It first appeared at http://pubs.acs.org/doi/abs/10.1021/jp512772j

Identifying patterns of alumni commitment in key strategic relationship programmes

Higher education institutions (HEIs) need to understand their alumni when drawing strategic relationship programmes. This paper aims to identify clusters of alumni based on their commitment relationship and to analyse factors influencing their intention to collaborate with the HEI. The study took place at a Portuguese university, considering a dataset of 1075 of alumni asserting intention to collaborate. First, a cluster analysis was conducted to identify patterns of commitment relationship. Secondly, a logistic regression was run to identify determinants of intention to collaborate. Both techniques revealed the decisive role of HEI commitment in the process. Relationship advantages and positive feelings towards the HEI were also pointed out as important. Alumni asserted recommendations, further training, sharing experiences and giving help as ways to collaborate with HEI. Regression results suggest that sociodemographic variables such as gender, marital status and volunteering are significantly associated with a probability to collaborate. Results also show that affiliation in sororities/fraternities and participation in extracurricular activities are significantly associated with that collaborative intention. The findings provide clues to support strategic relationship programmes based on consistent marketing campaigns, while bringing value to the literature in the European context, where alumni culture requires real insights to evolve.info:eu-repo/semantics/publishedVersio

Inhibition of N1-Src kinase by a specific SH3 peptide ligand reveals a role for N1-Src in neurite elongation by L1-CAM

In the mammalian brain the ubiquitous tyrosine kinase, C-Src, undergoes splicing to insert short sequences in the SH3 domain to yield N1- and N2-Src. We and others have previously shown that the N-Srcs have altered substrate specificity and kinase activity compared to C-Src. However, the exact functions of the N-Srcs are unknown and it is likely that N-Src signalling events have been misattributed to C-Src because they cannot be distinguished by conventional Src inhibitors that target the kinase domain. By screening a peptide phage display library, we discovered a novel ligand (PDN1) that targets the unique SH3 domain of N1-Src and inhibits N1-Src in cells. In cultured neurons, PDN1 fused to a fluorescent protein inhibited neurite outgrowth, an effect that was mimicked by shRNA targeting the N1-Src microexon. PDN1 also inhibited L1-CAM-dependent neurite elongation in cerebellar granule neurons, a pathway previously shown to be disrupted in Src(−/−) mice. PDN1 therefore represents a novel tool for distinguishing the functions of N1-Src and C-Src in neurons and is a starting point for the development of a small molecule inhibitor of N1-Src