Spotlight publications

1. EPIGENETICS: RNA processing

In this study, Broccoli fluorescent RNA aptamer was used as a reporter to visualize its expression within a gel fluorescence assay. The fluorescent signals of 3,5-difluoro-4-hydroxybenzylidene imidazolinone (DFHBI) bound to Broccoli in gel were detected and visualized by an Amersham Typhoon 5 biomolecular imager. The total RNA was stained with ethidium bromide or SYBR™ Gold and then imaged on an Amersham Imager 600 followed by analysis using ImageQuant TL software. Radioisotope-labeled Northern blotting was performed and the images were captured by the phosphor imaging mode on an Amersham Typhoon system with a storage phosphor screen.

Schmidt CA, Giusto JD, Bao A, et al. Molecular determinants of metazoan tricRNA biogenesis. Nucleic Acids Res. 2019;47(12):6452-6465. https://doi.org/10.1093/nar/gkz311

Reference list ID number: 2

2. CELL BIOLOGY: Stem cell

In this study, red fluorescent tdTomato (tdTom) reporter expression was detected in colon whole-mounts using an Amersham Typhoon 5 biomolecular imager at a 10 µm resolution. With this whole-mount approach, over a 2 × 2 mm area of tissue with tdTom-positive colon crypts was clearly visualized and presented. This reporter system was used to visualize the transcription factor Atoh1 in Atoh1-expressing cells and to elucidate the contribution of these cells to epithelial regeneration.

Tomic G, Morrissey E, Kozar S, et al. Phospho-regulation of ATOH1 Is Required for Plasticity of Secretory Progenitors and Tissue Regeneration. Cell Stem Cell. 2018;23(3):436-443.e7. https://doi.org/10.1016/j.stem.2018.07.002

Reference list ID number: 7

3. GENETIC ENGNEERING: Plants

In this study, expression of the yellow fluorescent protein (YFP) reporter and chlorophyll in transplastomic Arabidopsis thaliana plants were visualized with an Amersham Typhoon RBG biomolecular imager. The transplastomic seedlings were growing in Petri dishes. The YFP and chlorophyll fluorescence signals were co-detected using 488 nm and 635 nm excitations, respectively. The entire Petri dishes with sample were scanned and images captured. A high level of reporter protein expression and chlorophyll in the entire seedlings of genetically modified A. thaliana was confirmed.

Ruf, S., Forner, J., Hasse, C. et al. High-efficiency generation of fertile transplastomic Arabidopsis plants. Nat. Plants 5, 282–289 (2019). https://doi.org/10.1038/s41477-019-0359-2

Reference list ID number: 19

4. CELL BIOLOGY: Yeast

In this study, a fluorescent Western blot with Cy5-conjugated secondary antibody was carried out on cell membrane fractions from yeast. The blotted membrane image was captured by an Amersham Typhoon scanner. With this Western blot, authors showed the expression levels of enzymes for phospholipid synthesis. Phospholipid characterizations was then performed using thin-layer chromatography separation. Phospholipids were labeled with a radioisotope and the image was captured using a storage phosphor screen and the Amersham Typhoon 5 model.

Kudo S, Shiino H, Furuta S, Tamura Y. Yeast transformation stress, together with loss of Pah1, phosphatidic acid phosphatase, leads to Ty1 retrotransposon insertion into the INO4 gene. FASEB J. 2020;34(3):4749-4763. https://doi.org/10.1096/fj.201901811RR

Reference list ID number: 29

5. PET IMAGING: New PET ligand development

In this study, in vitro autoradiography of a newly developed PET ligand (18F-labeled potent antagonist to Nmethyl-D-aspartate receptors [NMDARs] in rat and nonhuman primate [NHP] brain sections) was carried out using a storage phosphor screen and the Amersham Typhoon 5 phosphor imaging mode. Localization of the new PET ligand was identified in brain cryosections from rats and NHPs after incubation with the 18F-labeled PET ligand.

Fu H, Tang W, Chen Z, et al. Synthesis and Preliminary Evaluations of a Triazole-Cored Antagonist as a PET Imaging Probe ([18F]N2B-0518) for GluN2B Subunit in the Brain. ACS Chem Neurosci. 2019;10(5):2263-2275. https://doi.org/10.1021/acschemneuro.8b00591

Reference list ID number: 11

Publications and presentations

  1. Siddiquey MNA, Zhang H, Nguyen CC, et al. The Human Cytomegalovirus Endoplasmic Reticulum-Resident Glycoprotein UL148 Activates the Unfolded Protein Response. J Virol. 2018;92(20):e00896-18. Published 2018 Sep 26. https://doi.org/10.1128/JVI.00896-18
  2. Holder JP, Izumi N, Beach M, et al. On the system stability and calibration of the image plate/scanner system for plasma diagnosis at the National Ignition Facility. Rev Sci Instrum. 2018;89(10):10F123. https://doi.org/10.1063/1.5039363
  3. Tombak EM, Männik A, Burk RD, et al. The molecular biology and HPV drug responsiveness of cynomolgus macaque papillomaviruses support their use in the development of a relevant in vivo model for antiviral drug testing. PLoS One. 2019;14(1):e0211235. Published 2019 Jan 25. https://doi.org/10.1371/journal.pone.0211235

  1. Ueda E, Tamura Y, Sakaue H, et al. Myristoyl group-aided protein import into the mitochondrial intermembrane space. Sci Rep. 2019;9:1185. https://doi.org/10.1038/s41598-018-38016-1
  2. Tomic G, Morrissey E, Kozar S, et al. Phospho-regulation of ATOH1 Is Required for Plasticity of Secretory Progenitors and Tissue Regeneration. Cell Stem Cell. 2018;23(3):436-443.e7. https://doi.org/10.1016/j.stem.2018.07.002
  3. Ruf, S., Forner, J., Hasse, C. et al. High-efficiency generation of fertile transplastomic Arabidopsis plants. Nat. Plants 5, 282–289 (2019). https://doi.org/10.1038/s41477-019-0359-2
  4. Fechter P. Mapping Changes in Cell Surface Protein Expression Through Selective Labeling of Live Cells. Methods Mol Biol. 2018;1737:119-127. https://doi.org/10.1007/978-1-4939-7634-8_8

  1. Lyon SE, Chen TH, Wallace AJ, Adib K, Gopalan V. An RNase P-Based Assay for Accurate Determination of the 5'-Deoxy-5'-azidoguanosine-Modified Fraction of in Vitro-Transcribed RNAs. Chembiochem. 2018;19(22):2353-2359. https://doi.org/10.1002/cbic.201800447
  2. Schmidt CA, Giusto JD, Bao A, et al. Molecular determinants of metazoan tricRNA biogenesis. Nucleic Acids Res. 2019;47(12):6452-6465. https://doi.org/10.1093/nar/gkz311
  3. Saha R, Verbanic S, Chen IA. Lipid vesicles chaperone an encapsulated RNA aptamer. Nat Commun. 2018;9(1):2313. Published 2018 Jun 13. https://doi.org/10.1038/s41467-018-04783-8
  4. Beránek V, Reinkemeier CD, Zhang MS, Liang AD, Kym G, Chin JW. Genetically Encoded Protein Phosphorylation in Mammalian Cells. Cell Chem Biol. 2018;25(9):1067-1074.e5. https://doi.org/10.1016/j.chembiol.2018.05.013
  5. Matera AG, Raimer AC, Schmidt CA, et al. Composition of the Survival Motor Neuron (SMN) Complex in Drosophila melanogaster. G3 (Bethesda). 2019;9(2):491-503. Published 2019 Feb 7. https://doi.org/10.1534/g3.118.200874
  6. Vještica A, Merlini L, Nkosi PJ, Martin SG. Gamete fusion triggers bipartite transcription factor assembly to block re-fertilization. Nature. 2018;560(7718):397-400. https://doi.org/10.1038/s41586-018-0407-5
  7. Klein HL, Ang KKH, Arkin MR, et al. Guidelines for DNA recombination and repair studies: Mechanistic assays of DNA repair processes. Microb Cell. 2019;6(1):65-101. Published 2019 Jan 7. https://doi.org/10.15698/mic2019.01.665
  8. Elbarbary RA, Maquat LE. Evaluating the susceptibility of AGO2-loaded microRNAs to degradation by nucleases in vitro. Methods. 2019;152:18-22. https://doi.org/10.1016/j.ymeth.2018.05.010
  9. Knutson SD, Arthur RA, Johnston HR, et al. Selective Enrichment of A-to-I Edited Transcripts from Cellular RNA Using Endonuclease V. J Am Chem Soc. 2020;142(11):5241-5251. https://doi.org/10.1021/jacs.9b13406
  10. Derbis M, Konieczny P, Walczak A, et al. Quantitative Evaluation of Toxic Polyglycine Biosynthesis and Aggregation in Cell Models Expressing Expanded CGG Repeats. Front Genet. 2018;9:216. Published 2018 Jun 19. https://doi.org/10.3389/fgene.2018.00216
  11. Walton T, Pazienza L, Szostak JW. Template-Directed Catalysis of a Multistep Reaction Pathway for Nonenzymatic RNA Primer Extension. Biochemistry. 2019;58(6):755-762. https://doi.org/10.1021/acs.biochem.8b01156
  12. Taylor K, Sznajder LJ, Cywoniuk P, et al. MBNL splicing activity depends on RNA binding site structural context. Nucleic Acids Res. 2018;46(17):9119-9133. https://doi.org/10.1093/nar/gky565
  13. Kroupova A, Ivascu A, Reimão-Pinto MM, Ameres SL, Jinek M. Structural basis for acceptor RNA substrate selectivity of the 3' terminal uridylyl transferase Tailor. Nucleic Acids Res. 2019;47(2):1030-1042. https://doi.org/10.1093/nar/gky1164
  14. Iwasaki S, Iwasaki W, Takahashi M, et al. The Translation Inhibitor Rocaglamide Targets a Bimolecular Cavity between eIF4A and Polypurine RNA. Mol Cell. 2019;73(4):738-748.e9. https://doi.org/10.1016/j.molcel.2018.11.026
  15. Ruszkowska A, Ruszkowski M, Dauter Z, et al. Structural insights into the RNA methyltransferase domain of METTL16. Sci Rep. 2018;8(1):5311. Published 2018 Mar 28. https://doi.org/10.1038/s41598-018-23608-8

  1. Fu H, Tang W, Chen Z, et al. Synthesis and Preliminary Evaluations of a Triazole-Cored Antagonist as a PET Imaging Probe ([18F]N2B-0518) for GluN2B Subunit in the Brain. ACS Chem Neurosci. 2019;10(5):2263-2275. https://doi.org/10.1021/acschemneuro.8b00591
  2. ULindemann M, Hinz S, Deuther-Conrad W, et al. Radiosynthesis and in vivo evaluation of a fluorine-18 labeled pyrazine based radioligand for PET imaging of the adenosine A2B receptor. Bioorg Med Chem. 2018;26(16):4650-4663. https://doi.org/10.1016/j.bmc.2018.07.045

  1. Zemella A, Thoring L, Hoffmeister C, et al. Cell-free protein synthesis as a novel tool for directed glycoengineering of active erythropoietin. Sci Rep. 2018;8(1):8514. Published 2018 Jun 4. https://doi.org/10.1038/s41598-018-26936-x
  2. Ordureau A, Paulo JA, Zhang W, et al. Dynamics of PARKIN-Dependent Mitochondrial Ubiquitylation in Induced Neurons and Model Systems Revealed by Digital Snapshot Proteomics. Mol Cell. 2018;70(2):211-227.e8. https://doi.org/10.1016/j.molcel.2018.03.012

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