Proteins associated with pancreatic cancer survival in patients with resectable pancreatic ductal adenocarcinoma.

Pancreatic ductal adenocarcinoma (PDAC) is a highly lethal disease with a dismal prognosis. However, while most patients die within the first year of diagnosis, very rarely, a few patients can survive for >10 years. Better understanding the molecular characteristics of the pancreatic adenocarcinomas from these very-long-term survivors (VLTS) may provide clues for personalized medicine and improve current pancreatic cancer treatment. To extend our previous investigation, we examined the proteomes of individual pancreas tumor tissues from a group of VLTS patients (survival ≥10 years) and short-term survival patients (STS, survival <14 months). With a given analytical sensitivity, the protein profile of each pancreatic tumor tissue was compared to reveal the proteome alterations that may be associated with pancreatic cancer survival. Pathway analysis of the differential proteins identified suggested that MYC, IGF1R and p53 were the top three upstream regulators for the STS-associated proteins, and VEGFA, APOE and TGFβ-1 were the top three upstream regulators for the VLTS-associated proteins. Immunohistochemistry analysis using an independent cohort of 145 PDAC confirmed that the higher abundance of ribosomal protein S8 (RPS8) and prolargin (PRELP) were correlated with STS and VLTS, respectively. Multivariate Cox analysis indicated that 'High-RPS8 and Low-PRELP' was significantly associated with shorter survival time (HR=2.69, 95% CI 1.46-4.92, P=0.001). In addition, galectin-1, a previously identified protein with its abundance aversely associated with pancreatic cancer survival, was further evaluated for its significance in cancer-associated fibroblasts. Knockdown of galectin-1 in pancreatic cancer-associated fibroblasts dramatically reduced cell migration and invasion. The results from our study suggested that PRELP, LGALS1 and RPS8 might be significant prognostic factors, and RPS8 and LGALS1 could be potential therapeutic targets to improve pancreatic cancer survival if further validated

Structural Plasticity of the Semliki Forest Virus Glycome upon Interspecies Transmission

Cross-species viral transmission subjects parent and progeny alphaviruses to differential post-translational processing of viral envelope glycoproteins. Alphavirus biogenesis has been extensively studied, and the Semliki Forest virus E1 and E2 glycoproteins have been shown to exhibit differing degrees of processing of N-linked glycans. However the composition of these glycans, including that arising from different host cells, has not been determined. Here we determined the chemical composition of the glycans from the prototypic alphavirus, Semliki Forest virus, propagated in both arthropod and rodent cell lines, by using ion-mobility mass spectrometry and collision-induced dissociation analysis. We observe that both the membrane-proximal E1 fusion glycoprotein and the protruding E2 attachment glycoprotein display heterogeneous glycosylation that contains N-linked glycans exhibiting both limited and extensive processing. However, E1 contained predominantly highly processed glycans dependent on the host cell, with rodent and mosquito-derived E1 exhibiting complex-type and paucimannose-type glycosylation, respectively. In contrast, the protruding E2 attachment glycoprotein primarily contained conserved under-processed oligomannose-type structures when produced in both rodent and mosquito cell lines. It is likely that glycan processing of E2 is structurally restricted by steric-hindrance imposed by local viral protein structure. This contrasts E1, which presents glycans characteristic of the host cell and is accessible to enzymes. We integrated our findings with previous cryo-electron microscopy and crystallographic analyses to produce a detailed model of the glycosylated mature virion surface. Taken together, these data reveal the degree to which virally encoded protein structure and cellular processing enzymes shape the virion glycome during interspecies transmission of Semliki Forest virus

A human embryonic kidney 293T cell line mutated at the Golgi -mannosidase II locus

Disruption of Golgi -mannosidase II activity can result in type II congenital dyserythropoietic anemia and can induce lupus-like autoimmunity in mice. Here, we isolate a mutant human embryonic kidney (HEK) 293T cell line, called Lec36, that displays sensitivity to ricin that lies between the parental HEK 293T cells, whose secreted and membrane-expressed proteins are dominated by complex-type glycosylation, and 293S Lec1 cells, which only produce oligomannose-type N-linked glycans. The stem cell marker, 19A, was transiently expressed in the HEK 293T Lec36 cells, and in parental HEK 293T cells with and without the potent Golgi -mannosidase II inhibitor, swainsonine. Negative-ion nano-electrospray ionization mass spectra of the 19A N-linked glycans from HEK 293T Lec36 and swainsonine-treated HEK 293T cells were qualitatively indistinguishable and, as shown by collision-induced dissociation spectra, dominated by hybrid-type glycosylation. Nucleotide sequencing revealed mutations in each allele of MAN2A1, the gene encoding Golgi -mannosidase II: a point mutation in one allele mapping to the active site and an in-frame deletion of twelve-nucleotides in the other. Expression of wild-type but not the mutant MAN2A1 alleles in Lec36 cells restored processing of the 19A reporter glycoprotein to complex-type glycosylation. The Lec36 cell line will be useful for expressing therapeutic glycoproteins with hybrid-type glycans and provides a sensitive host for detecting mutations in human MAN2A1 causing type II congenital dyserythropoietic anemia

InGaAs spin light emitting diodes measured in the Faraday and oblique Hanle geometries

InGaAs quantum well light emitting diodes (LED) with spin-injecting, epitaxial Fe contacts were fabricated using an in situ wafer transfer process where the semiconductor wafer was transferred under ultrahigh vacuum (UHV) conditions to a metals growth chamber to achieve a high quality interface between the two materials. The spin LED devices were measured optically with applied magnetic fields in either the Faraday or the oblique Hanle geometries in two experimental set-ups. Optical polarizations efficiencies of 4.5% in the Faraday geometry and 1.5% in the Hanle geometry are shown to be equivalent. The polarization efficiency of the electroluminescence is seen to decay as the temperature increases although the spin lifetime remains constant due to the influence of the D'yakonov–Perel' spin scattering mechanism in the quantum well.RM would like to acknowledge support from the EPSRC.This is the final version of the article. It first appeared from the Institute of Physics via https://doi.org/10.1088/0022-3727/49/16/16510

Long-range electronic reconstruction to a dxz,yz-dominated Fermi surface below the LaAlO3/SrTiO3 interface

Low dimensionality, broken symmetry and easily-modulated carrier concentrations provoke novel electronic phase emergence at oxide interfaces. However, the spatial extent of such reconstructions - i.e. the interfacial ‘‘depth’’ - remains unclear. Examining LaAlO3/SrTiO3 heterostructures at previously unexplored carrier densities n2D 14 cm-2 , we observe a Shubnikov-de Haas effect for small in-plane fields, characteristic of an anisotropic 3D Fermi surface with preferential dxz,yz orbital occupancy extending over at least 100 nm perpendicular to the interface. Quantum oscillations from the 3D Fermi surface of bulk doped SrTiO3 emerge simultaneously at higher n2D. We distinguish three areas in doped perovskite heterostructures: narrow (nm) 2D interfaces housing superconductivity and/or other emergent phases, electronically isotropic regions far (\u3e120 nm) from the interface and new intermediate zones where interfacial proximity renormalises the electronic structure relative to the bulk

Bat trait, genetic and pathogen data from large-scale investigations of African fruit bats, Eidolon helvum.

Bats, including African straw-coloured fruit bats (Eidolon helvum), have been highlighted as reservoirs of many recently emerged zoonotic viruses. This common, widespread and ecologically important species was the focus of longitudinal and continent-wide studies of the epidemiological and ecology of Lagos bat virus, henipaviruses and Achimota viruses. Here we present a spatial, morphological, demographic, genetic and serological dataset encompassing 2827 bats from nine countries over an 8-year period. Genetic data comprises cytochrome b mitochondrial sequences (n=608) and microsatellite genotypes from 18 loci (n=544). Tooth-cementum analyses (n=316) allowed derivation of rare age-specific serologic data for a lyssavirus, a henipavirus and two rubulaviruses. This dataset contributes a substantial volume of data on the ecology of E. helvum and its viruses and will be valuable for a wide range of studies, including viral transmission dynamic modelling in age-structured populations, investigation of seasonal reproductive asynchrony in wide-ranging species, ecological niche modelling, inference of island colonisation history, exploration of relationships between island and body size, and various spatial analyses of demographic, morphometric or serological data.This is the final version of the article. It first appeared from Nature Publishing Group via http://dx.doi.org/10.1038/sdata.2016.4

Systematic Study of Ferromagnetism in CrxSb2-xTe3 Topological Insulator Thin Films using Electrical and Optical Techniques.

Ferromagnetic ordering in a topological insulator can break time-reversal symmetry, realizing dissipationless electronic states in the absence of a magnetic field. The control of the magnetic state is of great importance for future device applications. We provide a detailed systematic study of the magnetic state in highly doped CrxSb2-xTe3 thin films using electrical transport, magneto-optic Kerr effect measurements and terahertz time domain spectroscopy, and also report an efficient electric gating of ferromagnetic order using the electrolyte ionic liquid [DEME][TFSI]. Upon increasing the Cr concentration from x = 0.15 to 0.76, the Curie temperature (Tc) was observed to increase by ~5 times to 176 K. In addition, it was possible to modify the magnetic moment by up to 50% with a gate bias variation of just ±3 V, which corresponds to an increase in carrier density by 50%. Further analysis on a sample with x = 0.76 exhibits a clear insulator-metal transition at Tc, indicating the consistency between the electrical and optical measurements. The direct correlation obtained between the carrier density and ferromagnetism - in both electrostatic and chemical doping - using optical and electrical means strongly suggests a carrier-mediated Ruderman-Kittel-Kasuya-Yoshida (RKKY) coupling scenario. Our low-voltage means of manipulating ferromagnetism, and consistency in optical and electrical measurements provides a way to realize exotic quantum states for spintronic and low energy magneto-electronic device applications

Crystal structure and carbohydrate analysis of Nipah virus attachment glycoprotein:a template for antiviral and vaccine design

Two members of the paramyxovirus family, Nipah virus (NiV) and Hendra virus (HeV), are recent additions to a growing number of agents of emergent diseases which use bats as a natural host. Identification of ephrin-B2 and ephrin-B3 as cellular receptors for these viruses has enabled the development of immunotherapeutic reagents which prevent virus attachment and subsequent fusion. Here we present the structural analysis of the protein and carbohydrate components of the unbound viral attachment glycoprotein of NiV glycoprotein (NiV-G) at a 2.2-A resolution. Comparison with its ephrin-B2-bound form reveals that conformational changes within the envelope glycoprotein are required to achieve viral attachment. Structural differences are particularly pronounced in the 579-590 loop, a major component of the ephrin binding surface. In addition, the 236-245 loop is rather disordered in the unbound structure. We extend our structural characterization of NiV-G with mass spectrometric analysis of the carbohydrate moieties. We demonstrate that NiV-G is largely devoid of the oligomannose-type glycans that in viruses such as human immunodeficiency virus type 1 and Ebola virus influence viral tropism and the host immune response. Nevertheless, we find putative ligands for the endothelial cell lectin, LSECtin. Finally, by mapping structural conservation and glycosylation site positions from other members of the paramyxovirus family, we suggest the molecular surface involved in oligomerization. These results suggest possible pathways of virus-host interaction and strategies for the optimization of recombinant vaccines

Topological states and phase transitions in Sb2Te3-GeTe multilayers

Topological insulators (TIs) are bulk insulators with exotic ‘topologically protected’ surface conducting modes. It has recently been pointed out that when stacked together, interactions between surface modes can induce diverse phases including the TI, Dirac semimetal, and Weyl semimetal. However, currently a full experimental understanding of the conditions under which topological modes interact is lacking. Here, working with multilayers of the TI Sb2Te3 and the band insulator GeTe, we provide experimental evidence of multiple topological modes in a single Sb2Te3-GeTe-Sb2Te3 structure. Furthermore, we show that reducing the thickness of the GeTe layer induces a phase transition from a Dirac-like phase to a gapped phase. By comparing different multilayer structures we demonstrate that this transition occurs due to the hybridisation of states associated with different TI films. Our results demonstrate that the Sb2Te3-GeTe system offers strong potential towards manipulating topological states as well as towards controlledly inducing various topological phases

On the alleged simplicity of impure proof

Roughly, a proof of a theorem, is “pure” if it draws only on what is “close” or “intrinsic” to that theorem. Mathematicians employ a variety of terms to identify pure proofs, saying that a pure proof is one that avoids what is “extrinsic,” “extraneous,” “distant,” “remote,” “alien,” or “foreign” to the problem or theorem under investigation. In the background of these attributions is the view that there is a distance measure (or a variety of such measures) between mathematical statements and proofs. Mathematicians have paid little attention to specifying such distance measures precisely because in practice certain methods of proof have seemed self- evidently impure by design: think for instance of analytic geometry and analytic number theory. By contrast, mathematicians have paid considerable attention to whether such impurities are a good thing or to be avoided, and some have claimed that they are valuable because generally impure proofs are simpler than pure proofs. This article is an investigation of this claim, formulated more precisely by proof- theoretic means. After assembling evidence from proof theory that may be thought to support this claim, we will argue that on the contrary this evidence does not support the claim