A Polymerase-chain-reaction Assay for the Specific Identification of Transcripts Encoded by Individual Carcinoembryonic Antigen (CEA)-gene-family Members

Carcinoembryonic antigen (CEA) is a tumor marker that belongs to a family of closely related molecules with variable expression patterns. We have developed sets of oligonucleotide primers for the specific amplification of transcripts from individual CEA-family members using the reverse transcriptase/ polymerase chain reaction (RT/PCR). Specific primer sets were designed for CEA, non-specific cross-reacting antigen (NCA), biliary glycoprotein (BGP), carcinoembryonic antigen gene-family members 1, 6 and 7 (CGMI, CGM6 and CGM7), and one set for all pregnancy-specific glycoprotein (PSG) transcripts. Primers were first tested for their specificity against individual cDNA clones and product-hybridization with internal, transcript-specific oligonucleotides. Total RNA from 12 brain and 63 gynecological tumors were then tested for expression of CEA-related transcripts. None were found in tumors located in the brain, including various mesenchymal and neuro-epithelial tumors. CEA and NCA transcripts were, however, present in an adenocarcinoma located in the nasal sinuses. In ovarian mucinous adenocarcinomas, we always found co-expression of CEA and NCA transcripts, and occasionally BGP mRNA. CEA-related transcripts were also found in some serous, endometrioid and clear-cell ovarian carcinomas. CEA, NCA and BGP transcripts were present in endometrial carcinomas of the uterus and cervical carcinomas, whereas uterine leiomyomas were completely negative. No transcripts were found from CGM 1, CGM6, CGM7 or from PSG genes in any of the tumors tested. The PCR data were compared with immunohistochemical investigations of ovarian tumors at the protein level using CEA (26/3/13)-, NCA-50/90 (9A6FR) and NCA-95 (80H3)-specific monoclonal antibodies

High-Resolution Sequencing and Modeling Identifies Distinct Dynamic RNA Regulatory Strategies

Cells control dynamic transitions in transcript levels by regulating transcription, processing, and/or degradation through an integrated regulatory strategy. Here, we combine RNA metabolic labeling, rRNA-depleted RNA-seq, and DRiLL, a novel computational framework, to quantify the level; editing sites; and transcription, processing, and degradation rates of each transcript at a splice junction resolution during the LPS response of mouse dendritic cells. Four key regulatory strategies, dominated by RNA transcription changes, generate most temporal gene expression patterns. Noncanonical strategies that also employ dynamic posttranscriptional regulation control only a minority of genes, but provide unique signal processing features. We validate Tristetraprolin (TTP) as a major regulator of RNA degradation in one noncanonical strategy. Applying DRiLL to the regulation of noncoding RNAs and to zebrafish embryogenesis demonstrates its broad utility. Our study provides a new quantitative approach to discover transcriptional and posttranscriptional events that control dynamic changes in transcript levels using RNA sequencing data.National Human Genome Research Institute (U.S.) (Centers for Excellence in Genomics Science 1P50HG006193-01)Howard Hughes Medical InstituteNational Institutes of Health (U.S.) (Pioneer Award)Massachusetts Institute of Technology. William Asbjornsen Albert Memorial FellowshipXerox Fellowship Progra

Laser writable high-K dielectric for van der Waals nano-electronics

This is the author accepted manuscript. The final version is available from American Association for the Advancement of Science via the DOI in this record.Like silicon-based semiconductor devices, van der Waals heterostructures will require integration with high-K oxides. This is needed to achieve suitable voltage scaling, improved performance as well as allowing for added functionalities. Unfortunately, commonly used high-k oxide deposition methods are not directly compatible with 2D materials. Here we demonstrate a method to embed a multi-functional few nm thick high-k oxide within van der Waals devices without degrading the properties of the neighbouring 2D materials. This is achieved by in-situ laser oxidation of embedded few layer HfS2 crystals. The resultant oxide is found to be in the amorphous phase with a dielectric constant of k~15 and break-down electric fields in the range of 0.5-0.6 V/nm. This transformation allows for the creation of a variety of fundamental nano-electronic and opto-electronic devices including, flexible Schottky barrier field effect transistors, dual gated graphene transistors as well as vertical light emitting and detecting tunnelling transistors. Furthermore, upon dielectric break-down, electrically conductive filaments are formed. This filamentation process can be used to electrically contact encapsulated conductive materials. Careful control of the filamentation process also allows for reversible switching between two resistance states. This allows for the creation of resistive switching random access memories (ReRAMs). We believe that this method of embedding a high-k oxide within complex van der Waals heterostructures could play an important role in future flexible multi-functional van der Waals devices.F.W acknowledges support from the Royal Academy of Engineering. J.D.M. acknowledges financial support from the Engineering and Physical Sciences Research Council (EPSRC) of the United Kingdom, via the EPSRC Centre for Doctoral Training in Metamaterials (Grant No. EP/L015331/1). S.R. and M.F.C. acknowledge financial support from EPSRC (Grant no. EP/K010050/1, EP/M001024/1, EP/M002438/1), from Royal Society international Exchanges Scheme 2016/R1, from The Leverhulme trust (grant title “Quantum Revolution” and "Quantum Drums"). A.P Rooney and S.J Haigh acknowledge support from the EPSRC postdoctoral fellowship and from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement ERC-2016-STG-EvoluTEM-715502) and the Defence Threat Reduction Agency (HDTRA1-12-1-0013). I.A. acknowledges financial support from The European Commission Marie Curie Individual Fellowships (Grant number 701704)

Improving the quality of toxicology and environmental health systematic reviews:What journal editors can do

Systematic reviews are fast increasing in prevalence in the toxicology and environmental health literature. However, how well these complex research projects are being conducted and reported is unclear. Since editors have an essential role in ensuring the scientific quality of manuscripts being published in their journals, a workshop was convened where editors, systematic review practitioners, and research quality control experts could discuss what editors can do to ensure the systematic reviews they publish are of sufficient scientific quality. Interventions were explored along four themes: setting standards; reviewing protocols; optimizing editorial workflows; and measuring the effectiveness of editorial interventions. In total, 58 editorial interventions were proposed. Of these, 26 were shortlisted for being potentially effective, and 5 were prioritized as short-term actions that editors could relatively easily take to improve the quality of published systematic reviews. Recent progress in improving systematic reviews is summarized, and outstanding challenges to further progress are highlighted

Blockade of T-cell activation by dithiocarbamates involves novel mechanisms of inhibition of nuclear factor of activated T cells.

Dithiocarbamates (DTCs) have recently been reported as powerful inhibitors of NF-kappaB activation in a number of cell types. Given the role of this transcription factor in the regulation of gene expression in the inflammatory response, NF-kappaB inhibitors have been suggested as potential therapeutic drugs for inflammatory diseases. We show here that DTCs inhibited both interleukin 2 (IL-2) synthesis and membrane expression of antigens which are induced during T-cell activation. This inhibition, which occurred with a parallel activation of c-Jun transactivating functions and expression, was reflected by transfection experiments at the IL-2 promoter level, and involved not only the inhibition of NF-kappaB-driven reporter activation but also that of nuclear factor of activated T cells (NFAT). Accordingly, electrophoretic mobility shift assays (EMSAs) indicated that pyrrolidine DTC (PDTC) prevented NF-kappaB, and NFAT DNA-binding activity in T cells stimulated with either phorbol myristate acetate plus ionophore or antibodies against the CD3-T-cell receptor complex and simultaneously activated the binding of AP-1. Furthermore, PDTC differentially targeted both NFATp and NFATc family members, inhibiting the transactivation functions of NFATp and mRNA induction of NFATc. Strikingly, Western blotting and immunocytochemical experiments indicated that PDTC promoted a transient and rapid shuttling of NFATp and NFATc, leading to their accelerated export from the nucleus of activated T cells. We propose that the activation of an NFAT kinase by PDTC could be responsible for the rapid shuttling of the NFAT, therefore transiently converting the sustained transactivation of this transcription factor that occurs during lymphocyte activation, and show that c-Jun NH2-terminal kinase (JNK) can act by directly phosphorylating NFATp. In addition, the combined inhibitory effects on NFAT and NF-KB support a potential use of DTCs as immunosuppressants

Chronic Oedema and the older person: The effects of ageing upon treatment outcomes

Chronic oedema (CO) and lymphoedema (LO) are long-term conditions that can become more complicated or are more likely to develop with age. The ageing process can involve alterations in the structures that support the normal function of the lymphatic system or put it at greater risk of damage. The main three components (skin care, exercise and compression therapy) within the management of CO/LO can become more difficult to apply with age. This is because of reduced healing rates, decreased cardiovascular capacity and deterioration in vascular and arterial structures. The impact of ageing and how this can affect patients and treatment outcomes requires careful consideration