Comprehensive Molecular Characterization of Human NODAL

Nodal and related ligands are highly conserved members of the TGF-beta superfamily with well-established and essential roles in the early embryonic development of vertebrates, and in cell fate decisions in human embryonic stem (hES) cells. Aberrant NODAL signaling also generally promotes pro-tumourigenic phenotypes and the progression of a wide array of human cancers. Despite being pursued as a potential therapeutic target, many aspects of NODAL’s molecular biology remain poorly understood. This thesis provides a comprehensive characterization of gene expression from the human NODAL locus at multiple levels. First, an intronic NODAL SNP known as rs2231947 was found to be functional in its modulation of a novel alternatively spliced exon. This exon contributed to a full-length processed NODAL variant transcript. The existence of this genetically regulated NODAL isoform suggests that NODAL biology is more complex than currently appreciated. At the protein level, the alternatively spliced NODAL variant differs in the C-terminal half of the NODAL mature peptide. The NODAL variant was preferentially secreted relative to constitutive NODAL, but displayed similar extracellular stability and processing. Differential N-glycosylation was partially responsible for this increased secretion, and for NODAL secretion in general. The NODAL variant protein is unlikely to adopt a constitutive NODAL-like structure, and did not induce expression of targets of canonical NODAL signaling in the zebrafish embryo. However, the NODAL variant did efficiently complex via inter-chain disulfide bonds, and induced pro-tumourigenic phenotypes to a limited extent relative to constitutive NODAL. In summary, this work demonstrates previously unknown complexity governing human NODAL gene expression and function. These molecular details will help broaden our understanding of NODAL function as well as aid in the continued development of potential targeted therapies to inhibit NODAL signaling in cancer

Structure retrieval at atomic resolution in the presence of multiple scattering of the electron probe

The projected electrostatic potential of a thick crystal is reconstructed at atomic-resolution from experimental scanning transmission electron microscopy data recorded using a new generation fast- readout electron camera. This practical and deterministic inversion of the equations encapsulating multiple scattering that were written down by Bethe in 1928 removes the restriction of established methods to ultrathin ($\lesssim 50$ {\AA}) samples. Instruments already coming on-line can overcome the remaining resolution-limiting effects in this method due to finite probe-forming aperture size, spatial incoherence and residual lens aberrations.Comment: 6 pages, 3 figure

Reconstructing the Scattering Matrix from Scanning Electron Diffraction Measurements Alone

Three-dimensional phase contrast imaging of multiply-scattering samples in X-ray and electron microscopy is extremely challenging, due to small numerical apertures, the unavailability of wavefront shaping optics, and the highly nonlinear inversion required from intensity-only measurements. In this work, we present a new algorithm using the scattering matrix formalism to solve the scattering from a non-crystalline medium from scanning diffraction measurements, and recover the illumination aberrations. Our method will enable 3D imaging and materials characterization at high resolution for a wide range of materials

The Effect of Dynamical Scattering on Single-plane Phase Retrieval in Electron Ptychography

Segmented and pixelated detectors on scanning transmission electron microscopes enable the complex specimen transmission function to be reconstructed. Imaging the transmission function is key to interpreting the electric and magnetic properties of the specimen, and as such four-dimensional scanning transmission electron microscopy (4D-STEM) imaging techniques are crucial for our understanding of functional materials. Many of the algorithms used in the reconstruction of the transmission function rely on the multiplicative approximation and the (weak) phase object approximation, which are not valid for many materials, particularly at high resolution. Herein, we study the breakdown of simple phase imaging in thicker samples. We demonstrate the behavior of integrated center of mass imaging, single-side band ptychography, and Wigner distribution deconvolution over a thickness series of simulated GaN 4D-STEM datasets. We further give guidance as to the optimal focal conditions for obtaining a more interpretable dataset using these algorithms

Herschel-ATLAS: VISTA VIKING near-IR counterparts in the Phase 1 GAMA 9h data

We identify near-infrared Ks band counterparts to Herschel-ATLAS sub-mm sources, using a preliminary object catalogue from the VISTA VIKING survey. The sub-mm sources are selected from the H-ATLAS Phase 1 catalogue of the GAMA 9h field, which includes all objects detected at 250, 350 or 500 um with the SPIRE instrument. We apply and discuss a likelihood ratio (LR) method for VIKING candidates within a search radius of 10" of the 22,000 SPIRE sources with a 5 sigma detection at 250 um. We find that 11,294(51%) of the SPIRE sources have a best VIKING counterpart with a reliability $R\ge 0.8$, and the false identification rate of these is estimated to be 4.2%. We expect to miss ~5% of true VIKING counterparts. There is evidence from Z-J and J-Ks colours that the reliable counterparts to SPIRE galaxies are marginally redder than the field population. We obtain photometric redshifts for ~68% of all (non-stellar) VIKING candidates with a median redshift of 0.405. Comparing to the results of the optical identifications supplied with the Phase I catalogue, we find that the use of medium-deep near-infrared data improves the identification rate of reliable counterparts from 36% to 51%.Comment: 20 pages, 20 figures, 3 tables, accepted by MNRA

An upper limit on the electron-neutrino flux from the HiRes detector

Air-fluorescence detectors such as the High Resolution Fly's Eye (HiRes) detector are very sensitive to upward-going, Earth-skimming ultrahigh energy electron-neutrino-induced showers. This is due to the relatively large interaction cross sections of these high-energy neutrinos and to the Landau-Pomeranchuk-Migdal (LPM) effect. The LPM effect causes a significant decrease in the cross sections for bremsstrahlung and pair production, allowing charged-current electron-neutrino-induced showers occurring deep in the Earth's crust to be detectable as they exit the Earth into the atmosphere. A search for upward-going neutrino-induced showers in the HiRes-II monocular dataset has yielded a null result. From an LPM calculation of the energy spectrum of charged particles as a function of primary energy and depth for electron-induced showers in rock, we calculate the shape of the resulting profile of these showers in air. We describe a full detector Monte Carlo simulation to determine the detector response to upward-going electron-neutrino-induced cascades and present an upper limit on the flux of electron-neutrinos.Comment: 13 pages, 3 figures. submitted to Astrophysical Journa

Opposition as victimhood in newspaper debates about same-sex marriage

In this paper, we take a queer linguistics approach to the analysis of data from British newspaper articles which discuss the introduction of same-sex marriage. Drawing on methods from CDA and corpus linguistics, we focus on the construction of agency in relation to the government extending marriage to same-sex couples, and those resisting this. We show that opponents to same-sex marriage are represented and represent themselves as victims whose moral values, traditions, and civil liberties are being threatened by the state. Specifically, we argue that victimhood is invoked in a way that both enables and permits discourses of implicit homophobia

The microstructure of non-polar a-plane (11 2 0) InGaN quantum wells

Atom probe tomography and quantitative scanning transmission electron microscopy are used to assess the composition of non-polar a-plane (11-20) InGaN quantum wells for applications in optoelectronics. The average quantum well composition measured by atom probe tomography and quantitative scanning transmission electron microscopy quantitatively agrees with measurements by X-ray diffraction. Atom probe tomography is further applied to study the distribution of indium atoms in non-polar a-plane (11-20) InGaN quantum wells. An inhomogeneous indium distribution is observed by frequency distribution analysis of the atom probe tomography measurements. The optical properties of non-polar (11-20) InGaN quantum wells with indium compositions varying from 7.9% to 20.6% are studied. In contrast to non-polar m-plane (1-100) InGaN quantum wells, the non-polar a-plane (11-20) InGaN quantum wells emit at longer emission wavelengths at the equivalent indium composition. The non-polar a-plane (11-20) quantum wells also show broader spectral linewidths. The longer emission wavelengths and broader spectral linewidths may be related to the observed inhomogeneous indium distribution.This work was carried out with the support of the United Kingdom Engineering and Physical Sciences Research Council under Grants Nos. EP\J001627\1, EP/I012591/1, and EP\J003603\1. The European Research Council has also provided financial support under the European Community's Seventh Framework Programme (FP7/2007-2013)/ERC Grant Agreement No. 279361 (MACONS). J. Etheridge and S. D. Findlay acknowledge funding from the Australian Research Council (ARC) (Project Nos. DP110104734 and DP110101570, respectively). The Titan3 80-300 TEM/STEM at the Monash Centre for Electron Microscopy was supported by the ARC Grant No. LE0454166.This is the final version of the article. It first appeared from the American Institute of Physics via http://dx.doi.org/10.1063/1.494829