Expanded progenitor populations, vitreo-retinal abnormalities, and Müller glial reactivity in the zebrafish leprechaun/patched2 retina

Jonathan Bibliowicz and Jeffery M. Gross are with the Section of Molecular Cell and Developmental Biology, The University of Texas at Austin, Austin, TX, USA, and the Institute of Cell and Molecular Biology, The University of Texas at Austin, Austin, TX, USA -- Jeffery M. Gross is with the Institute for Neuroscience, The University of Texas at Austin, Austin, TX, USABackground: The roles of the Hedgehog (Hh) pathway in controlling vertebrate retinal development have been studied extensively; however, species- and context-dependent findings have provided differing conclusions. Hh signaling has been shown to control both population size and cell cycle kinetics of proliferating retinal progenitors, and to modulate differentiation within the retina by regulating the timing of cell cycle exit. While cell cycle exit has in turn been shown to control cell fate decisions within the retina, a direct role for the Hh pathway in retinal cell fate decisions has yet to be established in vivo. Results: To gain further insight into Hh pathway function in the retina, we have analyzed retinal development in leprechaun/patched2 mutant zebrafish. While lep/ptc2 mutants possessed more cells in their retinas, all cell types, except for Müller glia, were present at identical ratios as those observed in wild-type siblings. lep/ptc2 mutants possessed a localized upregulation of GFAP, a marker for 'reactive' glia, as well as morphological abnormalities at the vitreo-retinal interface, where Müller glial endfeet terminate. In addition, analysis of the over-proliferation phenotype at the ciliary marginal zone (CMZ) revealed that the number of proliferating progenitors, but not the rate of proliferation, was increased in lep/ptc2 mutants. Conclusion: Our results indicate that Patched2-dependent Hh signaling does not likely play an integral role in neuronal cell fate decisions in the zebrafish retina. ptc2 deficiency in zebrafish results in defects at the vitreo-retinal interface and Müller glial reactivity. These phenotypes are similar to the ocular abnormalities observed in human patients suffering from Basal Cell Naevus Syndrome (BCNS), a disorder that has been linked to mutations in the human PTCH gene (the orthologue of the zebrafish ptc2), and point to the utility of the lep/ptc2 mutant line as a model for the study of BCNS-related ocular pathologies. Our findings regarding CMZ progenitor proliferation suggest that, in the zebrafish retina, Hh pathway activity may not affect cell cycle kinetics; rather, it likely regulates the size of the retinal progenitor pool in the CMZ.Institute for Cellular and Molecular [email protected]

On the novelty, efficacy, and significance of weak measurements for quantum tomography

The use of weak measurements for performing quantum tomography is enjoying increased attention due to several recent proposals. The advertised merits of using weak measurements in this context are varied, but are generally represented by novelty, increased efficacy, and foundational significance. We critically evaluate two proposals that make such claims and find that weak measurements are not an essential ingredient for most of their advertised features.Comment: 12 pages, 10 figure

Bounded Search for de Novo Identification of Degenerate Cis-Regulatory Elements

The identification of statistically overrepresented sequences in the upstream regions of coregulated genes should theoretically permit the identification of potential cis-regulatory elements. However, in practice many cis-regulatory elements are highly degenerate, precluding the use of an exhaustive word-counting strategy for their identification. While numerous methods exist for inferring base distributions using a position weight matrix, recent studies suggest that the independence assumptions inherent in the model, as well as the inability to reach a global optimum, limit this approach

Higgs Mechanism in String Theory

In first-quantized string theory, spacetime symmetries are described by inner automorphisms of the underlying conformal field theory. In this paper we use this approach to illustrate the Higgs effect in string theory. We consider string propagation on M^{24,1} \times S^1, where the circle has radius R, and study SU(2) symmetry breaking as R moves away from its critical value. We find a gauge-covariant equation of motion for the broken-symmetry gauge bosons and the would-be Goldstone bosons. We show that the Goldstone bosons can be eliminated by an appropriate gauge transformation. In this unitary gauge, the Goldstone bosons become the longitudinal components of massive gauge bosons.Comment: 12 pages, Te

SCOPE: a web server for practical de novo motif discovery

SCOPE is a novel parameter-free method for the de novo identification of potential regulatory motifs in sets of coordinately regulated genes. The SCOPE algorithm combines the output of three component algorithms, each designed to identify a particular class of motifs. Using an ensemble learning approach, SCOPE identifies the best candidate motifs from its component algorithms. In tests on experimentally determined datasets, SCOPE identified motifs with a significantly higher level of accuracy than a number of other web-based motif finders run with their default parameters. Because SCOPE has no adjustable parameters, the web server has an intuitive interface, requiring only a set of gene names or FASTA sequences and a choice of species. The most significant motifs found by SCOPE are displayed graphically on the main results page with a table containing summary statistics for each motif. Detailed motif information, including the sequence logo, PWM, consensus sequence and specific matching sites can be viewed through a single click on a motif. SCOPE's efficient, parameter-free search strategy has enabled the development of a web server that is readily accessible to the practising biologist while providing results that compare favorably with those of other motif finders. The SCOPE web server is at <http://genie.dartmouth.edu/scope>

Pain Experiences and Their Relation to Opioid Misuse Risk and Emotion Dysregulation

Pain is a complex, multidimensional experience but often is measured as a unidimensional experience. This study aimed to separately assess the sensory and affective components of pain and identify their relations to important pain-related outcomes, particularly in terms of opioid misuse risk and emotion dysregulation among patients with chronic pain receiving treatment in Appalachia. Two hundred and twelve patients presenting to a multidisciplinary pain center completed the Difficulties in Emotion Regulation Scale (DERS-18), Screener and Opioid Assessment for Patients with Pain—Revised (SOAPP-R), and short-form McGill Pain Questionnaire (SF-MPQ). The sensory experience of pain was unrelated to emotion dysregulation (r = 0.06, p = 0.57) and weakly related to opioid misuse risk (r = 0.182, p \u3c 0.05). In contrast, the affective experience of pain was moderately related to emotion dysregulation (r = 0.217, p \u3c 0.05) and strongly related to opioid misuse risk (r = 0.37, p \u3c 0.01). In addition, emotion dysregulation predicted variance in opioid misuse risk above and beyond the affective and sensory experiences of pain ((b = 0.693, p \u3c 0.001). The results suggest patients with a strong affective experience versus sensory experience of pain and challenges with emotion regulation may require a more comprehensive intervention to address these underlying components in order to reduce their risk of misusing opioid medications

A Novel Ensemble Learning Method for de Novo Computational Identification of DNA Binding Sites

Despite the diversity of motif representations and search algorithms, the de novo computational identification of transcription factor binding sites remains constrained by the limited accuracy of existing algorithms and the need for user-specified input parameters that describe the motif being sought.ResultsWe present a novel ensemble learning method, SCOPE, that is based on the assumption that transcription factor binding sites belong to one of three broad classes of motifs: non-degenerate, degenerate and gapped motifs. SCOPE employs a unified scoring metric to combine the results from three motif finding algorithms each aimed at the discovery of one of these classes of motifs. We found that SCOPE\u27s performance on 78 experimentally characterized regulons from four species was a substantial and statistically significant improvement over that of its component algorithms. SCOPE outperformed a broad range of existing motif discovery algorithms on the same dataset by a statistically significant margin

A flexible organic reflectance oximeter array.

Transmission-mode pulse oximetry, the optical method for determining oxygen saturation in blood, is limited to only tissues that can be transilluminated, such as the earlobes and the fingers. The existing sensor configuration provides only single-point measurements, lacking 2D oxygenation mapping capability. Here, we demonstrate a flexible and printed sensor array composed of organic light-emitting diodes and organic photodiodes, which senses reflected light from tissue to determine the oxygen saturation. We use the reflectance oximeter array beyond the conventional sensing locations. The sensor is implemented to measure oxygen saturation on the forehead with 1.1% mean error and to create 2D oxygenation maps of adult forearms under pressure-cuff-induced ischemia. In addition, we present mathematical models to determine oxygenation in the presence and absence of a pulsatile arterial blood signal. The mechanical flexibility, 2D oxygenation mapping capability, and the ability to place the sensor in various locations make the reflectance oximeter array promising for medical sensing applications such as monitoring of real-time chronic medical conditions as well as postsurgery recovery management of tissues, organs, and wounds