A qualitative assessment of direct-labeled cDNA products prior to microarray analysis

BACKGROUND: The success of the microarray process in determining differential gene expression of thousands of genes is dependent upon the quality and integrity of the starting RNA, this being particularly true of direct labeling via a reverse transcription procedure. Furthermore, an RNA of reasonable quality still may not yield reliable hybridization data if the labeling efficiency was poor. RESULTS: Here we present a novel assay for assessing the quality of directly labeled fluorescent cDNA prior to microarray hybridization utilizing the Agilent 2100 Bioanalyzer, which employs microfluidic technology for the analysis of nucleic acids and proteins. Using varying amounts of RNase to simulate RNA degradation, we show the strength of this un-advertised assay in determining the relative amounts of cDNA obtained from a direct labeling reaction. CONCLUSION: Utilization of this method in the lab will help to prevent the costly mistake of hybridizing poor quality direct labeled products to expensive arrays

Biofilm formation is a risk factor for mortality in patients with Candida albicans bloodstream infection-Scotland, 2012-2013

Acknowledgements This work was supported by the Wellcome Trust Strategic Award for Medical Mycology and Fungal Immunology 097377/Z/11/Z. Data collection was supported by a grant from Pfizer. G. Ramage was also supported by a research fellowship grant from Gilead Sciences. We are grateful to microbiology colleagues throughout Scotland for submitting isolates.Peer reviewedPublisher PD

On The Theoretical Foundation for Data Flow Analysis in Workflow Management

In workflow management, the data flow perspective specifies how data are produced and consumed by activities in a workflow. Data flow analysis can detect data flow anomalies occurring in a workflow while its control flow can be syntactically error-free. Currently, most commercial workflow management systems do not provide the tools for data flow analysis at design time. We have previously proposed a data flow analysis approach and developed the basic concepts and the essential algorithms. As another step forward, this paper examines the issues of data flow anomalies and their verification from a theoretical point of view and validates the correctness of the proposed approach

Are There Place Cells in the Avian Hippocampus?

Birds possess a hippocampus that serves many of the same spatial and mnemonic functions as the mammalian hippocampus but achieves these outcomes with a dramatically different neuroanatomical organization. The properties of spatially responsive neurons in birds and mammals are also different. Much of the contemporary interest in the role of the mammalian hippocampus in spatial representation dates to the discovery of place cells in the rat hippocampus. Since that time, cells that respond to head direction and cells that encode a grid-like representation of space have been described in the rat brain. Research with homing pigeons has discovered hippocampal cells, including location cells, path cells, and pattern cells, that share some but not all properties of spatially responsive neurons in the rodent brain. We have recently used patterns of immediate-early gene expression, visualized by the catFISH method, to investigate how neurons in the hippocampus of brood-parasitic brown-headed cowbirds respond to spatial context. We have found cells that discriminate between different spatial environments and are re-activated when the same spatial environment is re-experienced. Given the differences in habitat and behaviour between birds and rodents, it is not surprising that spatially responsive cells in their hippocampus and other brain regions differ. The enormous diversity of avian habitats and behaviour offers the potential for understanding the general principles of neuronal representation of space

Context-Dependent Egr1 Expression in the Avian Hippocampus.

In mammals, episodic memory and spatial cognition involve context-specific recruitment of unique ensembles in the hippocampal formation (HF). Despite their capacity for sophisticated spatial (e.g., for migration) and episodic-like (e.g., for food-caching) memory, the mechanisms underlying contextual representation in birds is not well understood. Here we demonstrate environment-specific Egr1 expression as male brown-headed cowbirds (Molothrus ater) navigate environments for food reward, showing that the avian HF, like its mammalian counterpart, recruits distinct neuronal ensembles to represent different contexts

Can the Renormalization Group Improved Effective Potential be used to estimate the Higgs Mass in the Conformal Limit of the Standard Model?

We consider the effective potential $V$ in the standard model with a single Higgs doublet in the limit that the only mass scale $\mu$ present is radiatively generated. Using a technique that has been shown to determine $V$ completely in terms of the renormalization group (RG) functions when using the Coleman-Weinberg (CW) renormalization scheme, we first sum leading-log (LL) contributions to $V$ using the one loop RG functions, associated with five couplings (the top quark Yukawa coupling $x$, the quartic coupling of the Higgs field $y$, the SU(3) gauge coupling $z$, and the $SU(2) \times U(1)$ couplings $r$ and $s$). We then employ the two loop RG functions with the three couplings $x$, $y$, $z$ to sum the next-to-leading-log (NLL) contributions to $V$ and then the three to five loop RG functions with one coupling $y$ to sum all the $N^2LL...N^4LL$ contributions to $V$. In order to compute these sums, it is necessary to convert those RG functions that have been originally computed explicitly in the minimal subtraction (MS) scheme to their form in the CW scheme. The Higgs mass can then be determined from the effective potential: the $LL$ result is $m_{H}=219\;GeV/c^2$ decreases to $m_{H}=188\;GeV/c^2$ at $N^{2}LL$ order and $m_{H}=163\;GeV/c^2$ at $N^{4}LL$ order. No reasonable estimate of $m_H$ can be made at orders $V_{NLL}$ or $V_{N^3LL}$. This is taken to be an indication that this mechanism for spontaneous symmetry breaking is in fact viable, though one in which there is slow convergence towards the actual value of $m_H$. The mass $163\;GeV/c^2$ is argued to be an upper bound on $m_H$.Comment: 24 pages, 5 figures. Updated version contains new discussion, references, figures, and corrects errors in reference

Kepler Observations of the Three Pre-Launch Exoplanet Candidates: Discover of Two Eclipsing Binaries and a New Exoplanet

Three transiting exoplanet candidate stars were discovered in a ground-based photometric survey prior to the launch of NASA's Kepler mission. Kepler observations of them were obtained during Quarter 1 of the Kepler mission. All three stars are faint by radial velocity follow-up standards, so we have examined these candidates with regard to eliminating false positives and providing high confidence exoplanet selection. We present a first attempt to exclude false positives for this set of faint stars without high-resolution radial velocity analysis. This method of exoplanet confirmation will form a large part of the Kepler mission follow-up for Jupiter-sized exoplanet candidates orbiting faint stars. Using the Kepler light curves and pixel data, as well as medium-resolution reconnaissance spectroscopy and speckle imaging, we find that two of our candidates are binary stars. One consists of a late-F star with an early M companion, while the other is a K0 star plus a late M-dwarf/brown dwarf in a 19 day elliptical orbit. The third candidate (BOKS-1) is an r = 15 G8V star hosting a newly discovered exoplanet with a radius of 1.12 R_(Jupiter) in a 3.9 day orbit

Surface inspection by monitoring spectral shifts of localized plasmon resonances

We present a numerical study of the spectral variations of localized surface plasmon resonances (LSPR) in a 3D-probe metallic nanoparticle scanned over an inhomoegeneous dielectric surface. The possibilities for both, index monitoring and lateral resolution at nanoscale level are explored, with special attention paid to the shape of the probe and the profile of the near field underneath