Real-time PCR based on SYBR-Green I fluorescence: An alternative to the TaqMan assay for a relative quantification of gene rearrangements, gene amplifications and micro gene deletions

BACKGROUND: Real-time PCR is increasingly being adopted for RNA quantification and genetic analysis. At present the most popular real-time PCR assay is based on the hybridisation of a dual-labelled probe to the PCR product, and the development of a signal by loss of fluorescence quenching as PCR degrades the probe. Though this so-called 'TaqMan' approach has proved easy to optimise in practice, the dual-labelled probes are relatively expensive. RESULTS: We have designed a new assay based on SYBR-Green I binding that is quick, reliable, easily optimised and compares well with the published assay. Here we demonstrate its general applicability by measuring copy number in three different genetic contexts; the quantification of a gene rearrangement (T-cell receptor excision circles (TREC) in peripheral blood mononuclear cells); the detection and quantification of GLI, MYC-C and MYC-N gene amplification in cell lines and cancer biopsies; and detection of deletions in the OPA1 gene in dominant optic atrophy. CONCLUSION: Our assay has important clinical applications, providing accurate diagnostic results in less time, from less biopsy material and at less cost than assays currently employed such as FISH or Southern blotting

Coronaviruses and Australian bats: a review in the midst of a pandemic

Australia’s 81 bat species play vital ecological and economic roles via suppression of insect pests and maintenance of native forests through pollination and seed dispersal. Bats also host a wide diversity of coronaviruses globally, including several viral species that are closely related to SARS-CoV-2 and other emergent human respiratory coronaviruses. Although there are hundreds of studies of bat coronaviruses globally, there are only three studies of bat coronaviruses in Australian bat species, and no systematic studies of drivers of shedding. These limited studies have identified two betacoronaviruses and seven alphacoronaviruses, but less than half of Australian species are included in these studies and further research is therefore needed. There is no current evidence of spillover of coronaviruses from bats to humans in Australia, either directly or indirectly via intermediate hosts. The limited available data are inadequate to determine whether this lack of evidence indicates that spillover does not occur or occurs but is undetected. Conversely, multiple international agencies have flagged the potential transmission of human coronaviruses (including SARS CoV-2) from humans to bats, and the consequent threat to bat conservation and human health. Australia has a long history of bat research across a broad range of ecological and associated disciplines, as well as expertise in viral spillover from bats. This strong foundation is an ideal platform for developing integrative approaches to understanding bat health and sustainable protection of human health

Damping mechanisms for oscillations in solar prominences

Small amplitude oscillations are a commonly observed feature in prominences/filaments. These oscillations appear to be of local nature, are associated to the fine structure of prominence plasmas, and simultaneous flows and counterflows are also present. The existing observational evidence reveals that small amplitude oscillations, after excited, are damped in short spatial and temporal scales by some as yet not well determined physical mechanism(s). Commonly, these oscillations have been interpreted in terms of linear magnetohydrodynamic (MHD) waves, and this paper reviews the theoretical damping mechanisms that have been recently put forward in order to explain the observed attenuation scales. These mechanisms include thermal effects, through non-adiabatic processes, mass flows, resonant damping in non-uniform media, and partial ionization effects. The relevance of each mechanism is assessed by comparing the spatial and time scales produced by each of them with those obtained from observations. Also, the application of the latest theoretical results to perform prominence seismology is discussed, aiming to determine physical parameters in prominence plasmas that are difficult to measure by direct means.Comment: 36 pages, 16 figures, Space Science Reviews (accepted

Neonatal intervention

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/68335/2/10.1177_027112148300300105.pd

Varying numbers of players in small-sided soccer games modifies action opportunities during training

This study examined the effects of the numbers of players involved in small-sided team games (underloading and overloading) on opportunities for maintaining ball possession, shooting at goal and passing to teammates during training. These practice constraint manipulations were assumed to alter values of key performance variables identified in previous research, such as interpersonal distances between players and time to intercept shots and passes. Fifteen male soccer players (age: 19.60±1.99 years) were grouped into three teams and played against each other in different versions of small-sided soccer games, in which the number of players was manipulated in three different conditions: 5 vs. 5, 5 vs. 4 and 5 vs. 3. Dependent variables were the values of interpersonal distance between an outfield attacker and nearest defender (ID), and the relative distance of a defender needed to intercept the trajectory of a shot (RDishot) or pass (RDipass). Statistical analyses revealed that mean ID values were significantly lower in 5 vs. 5 than in 5 vs. 4 and 5 vs. 3 conditions, and significantly lower in 5 vs. 4 than 5 vs. 3. They also revealed that mean values of RDishot were significantly higher in 5 vs. 3 than in 5 vs. 5 conditions. Finally, results showed that the mean values of RDipass were significantly higher in 5 vs. 3 than in 5 vs. 5. Findings revealed how task constraints in SSGs can be manipulated to vary values of key spatial and temporal performance variables (interpersonal distance and time to intercept) to influence the nature of interpersonal interactions between competing players during practice. We observed that these manipulations tended to decrease opportunities for maintaining ball possession during training when equal numbers of attackers and defenders existed in SSGs, and led to more shots and passes emerging when the number of defenders was decreased relative to attackers

Coping with the effects of fear of failure in young elite athletes

Coping with stress is an important element in effective functioning at the elite level in sports, and fear of failure (FF) is an example of a stressor that athletes experience. Three issues underpin the present preliminary study. First, the prevalence of problems attributed to FF in achievement settings. Second, sport is a popular and significant achievement domain for children and adolescents. Third, there is a lack of research on FF in sport among this population. Therefore, the objectives of the study were to examine the effects of FF on young athletes and to find out their coping responses to the effects of FF. Interviews were conducted individually with nine young elite ath­letes (5 males, 4 females; ages 14-17 years). It was inferred from the data that FF affected the athletes' well-being, interpersonal behavior, sport performance, and schoolwork. The athletes employed a combination of problem-focused, emotion-fo­cused, and avoidance-focused coping strategies, with avoidance strategies being the most frequently reported

Dynamics of coupled cell networks: synchrony, heteroclinic cycles and inflation

Copyright © 2011 Springer. The final publication is available at www.springerlink.comWe consider the dynamics of small networks of coupled cells. We usually assume asymmetric inputs and no global or local symmetries in the network and consider equivalence of networks in this setting; that is, when two networks with different architectures give rise to the same set of possible dynamics. Focussing on transitive (strongly connected) networks that have only one type of cell (identical cell networks) we address three questions relating the network structure to dynamics. The first question is how the structure of the network may force the existence of invariant subspaces (synchrony subspaces). The second question is how these invariant subspaces can support robust heteroclinic attractors. Finally, we investigate how the dynamics of coupled cell networks with different structures and numbers of cells can be related; in particular we consider the sets of possible “inflations” of a coupled cell network that are obtained by replacing one cell by many of the same type, in such a way that the original network dynamics is still present within a synchrony subspace. We illustrate the results with a number of examples of networks of up to six cells

Comparison of deep inelastic electron-photon scattering data with the HERWIG and PHOJET Monte Carlo models

Deep inelastic electron-photon scattering is studied in the $Q^2$ range from 1.2 to 30 GeV$^2$ using the LEP1 data taken with the ALEPH, L3 and OPAL detectors at centre-of-mass energies close to the mass of the Z boson. Distributions of the measured hadronic final state are corrected to the hadron level and compared to the predictions of the HERWIG and PHOJET Monte Carlo models. For large regions in most of the distributions studied the results of the different experiments agree with one another. However, significant differences are found between the data and the models. Therefore the combined LEP data serve as an important input to improve on the Monte Carlo models.Deep inelastic electron-photon scattering is studied in the Q**2 range from 1.2 to 30 GeV**2 using the LEP1 data taken with the ALEPH, L3 and OPAL detectors at centre-of-mass energies close to the mass of the Z boson. Distributions of the measured hadronic final state are corrected to the hadron level and compared to the predictions of the HERWIG and PHOJET Monte Carlo models. For large regions in most of the distributions studied the results of the different experiments agree with one another. However, significant differences are found between the data and the models. Therefore the combined LEP data serve as an important input to improve on the Monte Carlo models

A Two-Dimensional Electron Gas as a Sensitive Detector for Time-Resolved Tunneling Measurements on Self-Assembled Quantum Dots

A two-dimensional electron gas (2DEG) situated nearby a single layer of self-assembled quantum dots (QDs) in an inverted high electron mobility transistor (HEMT) structure is used as a detector for time-resolved tunneling measurements. We demonstrate a strong influence of charged QDs on the conductance of the 2DEG which allows us to probe the tunneling dynamics between the 2DEG and the QDs time resolved. Measurements of hysteresis curves with different sweep times and real-time conductance measurements in combination with an boxcar-like evaluation method enables us to unambiguously identify the transients as tunneling events between the s- and p-electron QD states and the 2DEG and rule out defect-related transients

Atomic X-ray Spectroscopy of Accreting Black Holes

Current astrophysical research suggests that the most persistently luminous objects in the Universe are powered by the flow of matter through accretion disks onto black holes. Accretion disk systems are observed to emit copious radiation across the electromagnetic spectrum, each energy band providing access to rather distinct regimes of physical conditions and geometric scale. X-ray emission probes the innermost regions of the accretion disk, where relativistic effects prevail. While this has been known for decades, it also has been acknowledged that inferring physical conditions in the relativistic regime from the behavior of the X-ray continuum is problematic and not satisfactorily constraining. With the discovery in the 1990s of iron X-ray lines bearing signatures of relativistic distortion came the hope that such emission would more firmly constrain models of disk accretion near black holes, as well as provide observational criteria by which to test general relativity in the strong field limit. Here we provide an introduction to this phenomenon. While the presentation is intended to be primarily tutorial in nature, we aim also to acquaint the reader with trends in current research. To achieve these ends, we present the basic applications of general relativity that pertain to X-ray spectroscopic observations of black hole accretion disk systems, focusing on the Schwarzschild and Kerr solutions to the Einstein field equations. To this we add treatments of the fundamental concepts associated with the theoretical and modeling aspects of accretion disks, as well as relevant topics from observational and theoretical X-ray spectroscopy.Comment: 63 pages, 21 figures, Einstein Centennial Review Article, Canadian Journal of Physics, in pres