Web notes  

June 2020
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Molecular Biology and Genetics Archives

1. Lee C-YS, Putnam A, Lu T, He S, Ouyang JPT, Seydoux, G. Recruitment of mRNAs to P granules by condensation with intrinsically-disordered proteins. Elife. 2020 Jan 24;9. pii: e52896. doi: 10.7554/eLife.52896. [Epub ahead of print]
Key words: C. elegans; MEG-3; RNA granules; cell biology; developmental biology; germ granules; germ line; intrinsically-disordered proteins; phase transition

https://www.ncbi.nlm.nih.gov/pubmed/31975687

2. Culbertson EM, Khan AA, Muchenditsi A, Lutsenko S, Sullivan DJ, Petris MJ, Cormack BP, Culotta VC. Changes in mammalian copper homeostasis during microbial infection. Metallomics. 2020 Jan 24. doi: 10.1039/c9mt00294d. [Epub ahead of print]
Key words: copper homeostasis, microbial infection
https://www.ncbi.nlm.nih.gov/pubmed/31976503

3. Heng JS, Hackett SF, Stein-O'Brien GL, Winer BL, Williams J, Goff LA, Nathans J. Comprehensive analysis of a mouse model of spontaneous uveoretinitis using single-cell RNA sequencing. Proc Natl Acad Sci U S A. 2019 Dec 16. pii: 201915571. doi: 10.1073/pnas.1915571116. [Epub ahead of print]
Key words: Aire knockout; autoimmune uveitis; mouse model; ocular immunology; single-cell RNAseq
https://www.ncbi.nlm.nih.gov/pubmed/31843893

4. Martín-Expósito M, Gas ME, Mohamad N, Nuño-Cabanes C, Tejada-Colón A, Pascual-García P, de la Fuente L, Chaves-Arquero B, Merran J, Corden J, Conesa A, Pérez-Cañadillas JM, Bravo J, Rodríguez-Navarro S. Mip6 binds directly to the Mex67 UBA domain to maintain low levels of Msn2/4 stress-dependent mRNAs. EMBO Rep. 2019 Dec 5;20(12):e47964. doi: 10.15252/embr.201947964.
Key words: Mex67; Mip6; Msn2/4; RNA-binding protein; mRNA export

https://www.ncbi.nlm.nih.gov/pubmed/31680439

5. Paix A, Rasoloson D, Folkmann A, Seydoux G. Rapid tagging of human proteins with fluorescent reporters by genome engineering using double-stranded DNA donors. Curr Protoc Mol Biol. 2019 Dec;129(1):e102. doi: 10.1002/cpmb.102.
Key words: CRISPR; Cas9; double-stranded DNA donors; fluorescent protein; genome engineering; homology-directed repair; tissue culture cells
https://www.ncbi.nlm.nih.gov/pubmed/31710422

6. Park EM, Scott PM, Clutario K, Cassidy KB, Zhan K, Gerber SA, Holland AJ. WBP11 is required for splicing the TUBGCP6 pre-mRNA to promote centriole duplication. J Cell Biol. 2020 Jan 6;219(1). pii: e201904203. doi: 10.1083/jcb.201904203.
Key words: WBP11, mRNA, centriole
https://www.ncbi.nlm.nih.gov/pubmed/31874114

7. Sabbagh MF, Nathans J. A genome-wide view of the de-differentiation of central nervous system endothelial cells in culture. Elife. 2020 Jan 8;9. pii: e51276. doi: 10.7554/eLife.51276.
Key words: Wnt; beta-catenin; blood-brain barrier; cell culture; chromatin; endothelial; genetics; genomics; mouse; neuroscience

https://www.ncbi.nlm.nih.gov/pubmed/31913116

8. Schatzman SS, Peterson RL, Teka M, He B, Cabelli DE, Cormack BP, Culotta VC. Copper-only superoxide dismutase enzymes and iron starvation stress in Candida fungal pathogens. J Biol Chem. 2020 Jan 10;295(2):570-583. doi: 10.1074/jbc.RA119.011084. Epub 2019 Dec 5.
Key words: Candida albicans; Candida auris; Candida tropicalis; SOD4; copper; oxidative stress; reactive oxygen species (ROS); superoxide dismutase (SOD); superoxide ion; virulence factor
https://www.ncbi.nlm.nih.gov/pubmed/31806705

9. Tesina P, Lessen LN, Buschauer R, Cheng J, Wu CC, Berninghausen O, Buskirk AR, Becker T, Beckmann R, Green R. Molecular mechanism of translational stalling by inhibitory codon combinations and poly(A) tracts. EMBO J. 2019 Dec 20:e103365. doi: 10.15252/embj.2019103365. [Epub ahead of print]
Key words: disome; frameshift; ribosome collision; stalling; translation

https://www.ncbi.nlm.nih.gov/pubmed/31858614

10. Veltri AJ, D'Orazio KN, Green R. Make or break: the ribosome as a regulator of mRNA decay. Cell Res. 2020 Jan 8. doi: 10.1038/s41422-019-0271-3. [Epub ahead of print]
Key words: ribosome, mRNA
https://www.ncbi.nlm.nih.gov/pubmed/31913358

11. Wangen JR, Green R. Stop codon context influences genome-wide stimulation of termination codon readthrough by aminoglycosides. Elife. 2020 Jan 23;9. pii: e52611. doi: 10.7554/eLife.52611. [Epub ahead of print]
Key words: chromosomes; gene expression; human

https://www.ncbi.nlm.nih.gov/pubmed/31971508

1. Keener R, Connelly CJ, Greider CW. Tel1 activation by the MRX complex is sufficient for telomere length regulation but not for the DNA damage response in Saccharomyces cerevisiae. Genetics. 2019 Oct 23. pii: genetics.302713.2019. doi: 10.1534/genetics.119.302713. [Epub ahead of print]
Key words: DNA damage response; MRX complex; Tel1; epistasis; telomere

https://www.ncbi.nlm.nih.gov/pubmed/31645360

2. Ouyang JPT, Folkmann A, Bernard L, Lee CY, Seroussi U, Charlesworth AG, Claycomb JM, Seydoux G. P Granules Protect RNA Interference Genes from Silencing by piRNAs. Dev Cell. 2019 Sep 23;50(6):716-728.e6. doi: 10.1016/j.devcel.2019.07.026. Epub 2019 Aug 8.
Key words: Argonautes; P granules; RNA-mediated interference; epigenetic silencing; piRNAs
https://www.ncbi.nlm.nih.gov/pubmed/31402283

3. Perez-Gonzalez NA, Rochman ND, Yao K, Tao J, Le MT, Flanary S, Sablich L, Toler B, Crentsil E, Takaesu F, Lambrus B, Huang J, Fu V, Chengappa P, Jones TM, Holland AJ, An S, Wirtz D, Petrie RJ, Guan KL, Sun SX. YAP and TAZ regulate cell volume. J Cell Biol. 2019 Oct 7;218(10):3472-3488. doi: 10.1083/jcb.201902067. Epub 2019 Sep 3.
Key words: cell volume, YAP, TAZ, cell cycle progression
https://www.ncbi.nlm.nih.gov/pubmed/31481532

4. Pike AM, Strong MA, Ouyang JPT, Greider CW. TIN2 functions with TPP1/POT1 to stimulate telomerase processivity. Mol Cell Biol. 2019 Oct 11;39(21). pii: e00593-18. doi: 10.1128/MCB.00593-18. Print 2019 Nov 1.
Key words: POT1; TIN2; TPP1; alternative splicing; processivity; shelterin; telomerase; telomere
https://www.ncbi.nlm.nih.gov/pubmed/31383750

5. Rattner A, Williams J, Nathans J. Roles of HIFs and VEGF in angiogenesis in the retina and brain.
J Clin Invest. 2019 Aug 12;130:3807-3820. doi: 10.1172/JCI126655. eCollection 2019 Aug 12. Roles of HIFs and VEGF in angiogenesis in the retina and brain.
https://www.ncbi.nlm.nih.gov/pubmed/31403471
Key words: Development; Vascular Biology; endothelial cells

1. Breslow DK, Holland AJ . Mechanism and regulation of centriole and cilium biogenesis. Annu Rev Biochem. 2019 Jun 20;88:691-724. doi: 10.1146/annurev-biochem-013118-111153. Epub 2019 Jan 11.
Key words: cell cycle; centriole; centrosome; cilia; ciliopathy; mitosis
https://www.ncbi.nlm.nih.gov/pubmed/30601682

2. Cable J, Brangwynne C, Seydoux G, Cowburn D, Pappu RV, Castañeda CA, Berchowitz LE, Chen Z, Jonikas M, Dernburg A, Mittag T, Fawzi NL. Phase separation in biology and disease-a symposium report. Ann N Y Acad Sci. 2019 Jun 14. doi: 10.1111/nyas.14126. [Epub ahead of print]
Key words: biomolecular condensates; granules; membraneless organelles; phase diagram; phase separation; protein disorder
https://www.ncbi.nlm.nih.gov/pubmed/31199001

3. Cho C, Wang Y, Smallwood PM, Williams J, Nathans J. Molecular determinants in Frizzled, Reck, and Wnt7a for ligand-specific signaling in neurovascular development. Elife. 2019 Jun 21;8. pii: e47300. doi: 10.7554/eLife.47300.
Key words: CNS angiogenesis; Gpr124; Reck; Wnt7; blood-brain barrier; canonical Wnt signaling; developmental biology; mouse; neuroscience
https://www.ncbi.nlm.nih.gov/pubmed/31225798

4. Muszkieta L, Fontaine T, Beau R, Mouyna I, Vogt MS, Trow J, Cormack BP, Essen LO, Jouvion G, Latgé JP. The glycosylphosphatidylinositol-anchored DFG family is essential for the insertion of galactomannan into the ?-(1,3)-glucan-chitin core of the cell wall of Aspergillus fumigatus. mSphere. 2019 Jul 31;4(4). pii: e00397-19. doi: 10.1128/mSphere.00397-19.
Key words: Aspergillus fumigatus ; cell wall; glycobiology
https://www.ncbi.nlm.nih.gov/pubmed/31366710

5. Peng X, Williams J, Smallwood PM, Nathans J. Defining the binding interface of amyloid precursor protein (APP) and contactin3 (CNTN3) by site-directed mutagenesis. PLoS One. 2019 Jul 18;14(7):e0219384. doi: 10.1371/journal.pone.0219384. eCollection 2019.
Key words: amyloid precursor protein, contactin3, mutagenesis
https://www.ncbi.nlm.nih.gov/pubmed/31318883

1. Cho C, Wang Y, Smallwood PM, Williams J, Nathans J. Dlg1 activates beta-catenin signaling to regulate retinal angiogenesis and the blood-retina and bloodbrain barriers. Elife. 2019 May 8;8. pii: e45542. doi: 10.7554/eLife.45542.
Key words: blood-brain barrier; blood-retina barrier; canonical Wnt signaling; developmental biology; genetics; genomics; mouse; mouse genetics; retinal angiogenesis; vascular endothelial cells
http://www.ncbi.nlm.nih.gov/pubmed/31066677

2. DeFelice MM, Clark HR, Hughey JJ, Maayan I, Kudo T, Gutschow MV, Covert MW, Regot S. NF-?B signaling dynamics is controlled by a dose-sensing autoregulatory loop. Sci Signal. 2019 Apr 30;12(579). pii: eaau3568. doi: 10.1126/scisignal.aau3568.
Key words: NF-?B, signaling dynamics
http://www.ncbi.nlm.nih.gov/pubmed/31040261

3. Heng JS, Rattner A, Stein-O'Brien GL, Winer BL, Jones BW, Vernon HJ, Goff LA, Nathans J. Hypoxia tolerance in the Norrin-deficient retina and the chronically hypoxic brain studied at single-cell resolution. Proc Natl Acad Sci U S A. 2019 Apr 30;116(18):9103-9114. doi: 10.1073/pnas.1821122116. Epub 2019 Apr 15.
Key words: Norrie disease; familial exudative vitreoretinopathy; metabolomics; serine synthesis; singlecell RNA-seq
http://www.ncbi.nlm.nih.gov/pubmed/30988181

4. Kearse MG, Goldman DH, Choi J, Nwaezeapu C, Liang D, Green KM, Goldstrohm AC, Todd PK, Green R, Wilusz JE. Ribosome queuing enables non-AUG translation to be resistant to multiple protein synthesis inhibitors. Genes Dev. 2019 Jun 6. doi: 10.1101/gad.324715.119. [Epub ahead of print]
Key words: RAN translation; cycloheximide; near-cognate; start codon; translation initiation; translational control
http://www.ncbi.nlm.nih.gov/pubmed/31171704

5. LoMastro GM, Holland AJ. The emerging link between centrosome aberrations and metastasis. Dev Cell. 2019 May 6;49(3):325-331. doi: 10.1016/j.devcel.2019.04.002. Review.
Key words: aneuploidy; cancer; centrosomes; metastasis
http://www.ncbi.nlm.nih.gov/pubmed/31063752

6. Moyer TC, Holland AJ. PLK4 promotes centriole duplication by phosphorylating STIL to link the procentriole cartwheel to the microtubule wall. Elife. 2019 May 22;8. pii: e46054. doi: 10.7554/eLife.46054. [Epub ahead of print]
Key words: cell biology; human
http://www.ncbi.nlm.nih.gov/pubmed/31115335

7. Valotteau C, Prystopiuk V, Cormack BP, Dufrêne YF. Atomic force microscopy demonstrates that candida glabrata uses three Epa proteins to mediate adhesion to abiotic surfaces. mSphere. 2019 May 1;4(3). pii: e00277-19. doi: 10.1128/mSphere.00277-19.
Key words: AFM; Candida glabrata ; EPA ; adhesion
http://www.ncbi.nlm.nih.gov/pubmed/31043520

8. Wang Y, Sabbagh MF, Gu X, Rattner A, Williams J, Nathans J. Beta-catenin signaling regulates barrier-specific gene expression in circumventricular organ and ocular vasculatures. Elife. 2019 Apr 1;8. pii: e43257. doi: 10.7554/eLife.43257.
Key words: Wnt; beta-catenin; blood-brain barrier; circumventricular organ; developmental biology; endothelial; mouse; neuroscience; vascular
http://www.ncbi.nlm.nih.gov/pubmed/30932813

9. Wang Y, Liu S, Sun L, Xu N, Shan S, Wu F, Liang X, Huang Y, Luk E, Wu C, Zhou Z. Structural insights into histone chaperone Chz1-mediated H2A.Z recognition and histone replacement. PLoS Biol. 2019 May 20;17(5):e3000277. doi: 10.1371/journal.pbio.3000277. eCollection 2019 May.
Key words: histone, Chz1
http://www.ncbi.nlm.nih.gov/pubmed/31107867

1. Bowler M, Kong D, Sun S, Nanjundappa R, Evans L, Farner V, Holland A, Mahjoub MR, Sui H, Loncarek J. Highresolution characterization of centriole distal appendage morphology and dynamics by correlative STORM and electron microscopy. Nat Commun. 2019 Mar 1;10(1):993.
Key words: centrioles, CCDC, appendage protein, DAs, SDAs
https://www.ncbi.nlm.nih.gov/pubmed/30824690

2. Kreutzberger AJB, Ji M, Aaron J, Mihaljevic L, Urban S. Rhomboid distorts lipids to break the viscosity-imposed speed limit of membrane diffusion. Science. 2019 Feb 1;363(6426). pii: eaao0076.
Key words: Rhomboid, membrane viscosity, enzyme diffusion, substrate molecules, Drosophila
https://www.ncbi.nlm.nih.gov/pubmed/30705155

3. Lee CY, Seydoux G. Dynamics of mRNA entry into stress granules. Nat Cell Biol. 2019;10.1038/s41556-019-0278-5. Key Words: Stress granules, SGs, mRNAs, Ras-GAP SH3 PMID: 30664788 Folkmann AW, Seydoux G. Spatial regulation of the polarity kinase PAR-1 by parallel inhibitory mechanisms. Development. 2019 Mar 25;146(6). pii: dev171116.
Key words: Kinase, MEX-6, P granules, PAR proteins, PAR-3, Polarity

https://www.ncbi.nlm.nih.gov/pubmed/30814118

4. Mohammad F, Green R, Buskirk AR. A systematically-revised ribosome profiling method for bacteria reveals pauses at single-codon resolution. Elife. 2019 Feb 6;8. pii: e42591.
Key words: E. coli, bacteria, biochemistry, chemical biology, ribosome profiling
https://www.ncbi.nlm.nih.gov/pubmed/30724162

5. Putnam A, Cassani M, Smith J, Seydoux G. A gel phase promotes condensation of liquid P granules in Caenorhabditis elegans embryos. Nat Struct Mol Biol. 2019 Mar;26(3):220-226.
Key words: RNA granules, Caenorhabditis, elegans, embryos
https://www.ncbi.nlm.nih.gov/pubmed/30833787

6. Wu CC, Zinshteyn B, Wehner KA, Green R. High-Resolution ribosome profiling defines discrete ribosome elongation states and translational regulation during cellular stress. Mol Cell. 2019 Mar 7;73(5):959-970.e5.
Key words: eEF2 phosphorylation, ribosome functional states, ribosome profiling, translation elongation
https://www.ncbi.nlm.nih.gov/pubmed/30686592

1. Bowler M, Kong D, Sun S, Nanjundappa R, Evans L, Farner V, Holland A, Mahjoub MR, Sui H, Loncarek J. Highresolution characterization of centriole distal appendage morphology and dynamics by correlative STORM and electron microscopy. Nat Commun. 2019 Mar 1;10(1):993.
Key words: centrioles, CCDC, appendage protein, DAs, SDAs
https://www.ncbi.nlm.nih.gov/pubmed/30824690

2. Breslow DK, Holland AJ. Mechanism and regulation of centriole and cilium biogenesis. Annu Rev Biochem. 2019 Jan;10.1146/annurev-biochem-013118-111153. [Epub ahead of print].
Key words: Centriole, centrosome, cilia, ciliopathy, cell cycle, mitosis
https://www.ncbi.nlm.nih.gov/pubmed/30601682

3. Corden JL. An arginine nexus in the RNA Polymerase II CTD. Mol Cell. 2019 Jan 3;73(1):3-4.
Key words: C-Termination domain, CTD, RNA polymerase II, arginine deiminase, citrulline
https://www.ncbi.nlm.nih.gov/pubmed/30609390

4. Folkmann AW, Seydoux G. Spatial regulation of the polarity kinase PAR-1 by parallel inhibitory mechanisms. Development. 2019 Mar 25;146(6). pii: dev171116. [Epub ahead of print].
Key words: Kinase, MEX-6, P granules, PAR proteins, PAR-3, Polarity
https://www.ncbi.nlm.nih.gov/pubmed/30814118

5. Kreutzberger AJB, Ji M, Aaron J, Mihaljevic L, Urban S. Rhomboid distorts lipids to break the viscosity-imposed speed limit of membrane diffusion. Science. 2019 Feb 1;363(6426).
Key words: Rhomboid, membrane viscosity, enzyme diffusion, substrate molecules, Drosophila
https://www.ncbi.nlm.nih.gov/pubmed/30705155

6. Lee CY, Seydoux G. Dynamics of mRNA entry into stress granules. Nat Cell Biol. 2019 Feb;21(2):116-117.
Key words: Stress granules, SGs, mRNAs, Ras-GAP SH3
https://www.ncbi.nlm.nih.gov/pubmed/30664788

7. Mohammad F, Green R, Buskirk AR. A systematically-revised ribosome profiling method for bacteria reveals pauses at single-codon resolution. Elife. Feb 6;8. pii: e42591.
Key words: E. coli, bacteria, biochemistry, chemical biology, ribosome profiling
https://www.ncbi.nlm.nih.gov/pubmed/30724162

8. Putnam A, Cassani M, Smith J, Seydoux G. A gel phase promotes condensation of liquid P granules in Caenorhabditis elegans embryos. Nat Struct Mol Biol. 2019 Mar;26(3):220-226.
Key words: RNA granules, Caenorhabditis, elegans, embryos https://www.ncbi.nlm.nih.gov/pubmed/30833787

9. Wu CC, Zinshteyn B, Wehner KA, Green R. High-Resolution ribosome profiling defines discrete ribosome elongation states and translational regulation during cellular stress. Mol Cell. Mar 7;73(5):959-970.e5.
Key words: eEF2 phosphorylation, ribosome functional states, ribosome profiling, translation elongation
https://www.ncbi.nlm.nih.gov/pubmed/30686592

10. Zinshteyn B, Chan D, England W, Feng C, Green R, Spitale RC. Assaying RNA structure with LASER-Seq. Nucleic Acids Res. 2019 Jan 10;47(1):43-55.
Key words: RNA molecules, LASER, SHAPE, Watson-Crick, LASER-seq https://www.ncbi.nlm.nih.gov/pubmed/30476193

1. Wang Y, Cho C, Williams J, Smallwood PM, Zhang C, Junge HJ, Nathans J. Interplay of the Norrin and Wnt7a/Wnt7b signaling systems in blood-brain barrier and blood-retina barrier development and maintenance. Proc Natl Acad Sci USA. 2018 Dec 11;115(50):E11827-E11836.
Key words: Central nervous system, mouse genetics, vascular endothelial cells, ?-catenin signaling
https://www.ncbi.nlm.nih.gov/pubmed/30478038

2. Zinshteyn B, Chan D, England W, Feng C, Green R, Spitale RC. Assaying RNA structure with LASER-Seq. Nucleic Acids Res. 2018 Nov 22. doi: 10.1093/nar/gky1172. [Epub ahead of print]
Key words: RNA-protein complexes, LASER-Seq, LASER, C8 position, RT-stop, mutational profiling (MaP)
https://www.ncbi.nlm.nih.gov/pubmed/30476193

1. Folkmann AW, Seydoux G. Single-molecule study reveals the frenetic lives of proteins in gradients. Proc Natl Acad Sci U S A. 2018 Sep 18;115(38):9336-9338.
Key words: Caenorhabditis elegans zygotes, Drosophila embryos, Bicoid protein
https://www.ncbi.nlm.nih.gov/pubmed/30181287

2. Forman-Kay JD, Kriwacki RW, Seydoux G. Phase separation in biology and disease. J Mol Biol. 2018 Nov 2;430(23):4603-4606.
Key words: Cytoplasm, star fish, membrane-less organelles, RGG/RG motif-containing proteins
https://www.ncbi.nlm.nih.gov/pubmed/30213727

3. Kreutzberger AJB, Urban S. Single-molecule analyses reveal rhomboid proteins are strict and functional monomers in the membrane. Biophys J. 2018 Oct 2. pii: S0006-3495(18)31105-6.
Key words: Rhomboid Proteins; hydrolyze peptide; intramembrane proteases; photobleaching; monomeric; oligomeric
https://www.ncbi.nlm.nih.gov/pubmed/30342748

4. Leda M, Holland AJ, Goryachev AB. Autoamplification and competition drive symmetry breaking: initiation of centriole duplication by the PLK4-STIL network. iScience. 2018 Oct 26;8:222-235.
Key words: Biological Sciences; Developmental Biology; In Silico Biology
https://www.ncbi.nlm.nih.gov/pubmed/30340068

5. Luo J, Sun X, Cormack BP, Boeke. Karyotype engineering by chromosome fusion leads to reproductive isolation in yeast. 2018 Aug;560(7718):392-396.
Key words: karyotype, CRISPER-Cas9-mediated, yeast sporulation
https://www.ncbi.nlm.nih.gov/pubmed/30069047

6. Peng X, Emiliani F, Smallwood PM, Rattner A, Lei H, Sabbagh MF, Nathans J. Affinity capture of polyribosomes followed by RNAseq (ACAPseq), a discovery platform for proteinprotein interactions. Elife. 2018 Oct 22;7. pii: e40982. doi: 10.7554/eLife.40982.
Key words: RNAseq; biochemistry; chemical biology; extracellular interactome; protocadherin
https://www.ncbi.nlm.nih.gov/pubmed/30345971

7. Sabbagh MF, Heng JS, Luo C, Castanon RG, Nery JR, Rattner A, Goff LA, Ecker JR, Nathans J. Transcriptional and epigenomic landscapes of CNS and non-CNS vascular endothelial cells. eLife. 2018 Sep 6;7. pii: e36187.
Key words: DNA methylation, Wnt, accessible chromatin, blood-brain barrier, vascular endothelial cell
https://www.ncbi.nlm.nih.gov/pubmed/30188322

8. Seydoux G. The P Granules of C. elegans: A genetic model for the study of RNA-protein condensates. J Mol Biol. 2018 Nov 2;430(23):4702-4710.
Key words: C. elegans, Germline condensates, P granules, RNA granules
https://www.ncbi.nlm.nih.gov/pubmed/30096346

9. Shaytan AK, Xiao H, Armeev GA, Gaykalova DA, Komarova GA, Wu C Studitsky VM, Landsman D, Panchenko AR. Structural interpretation of DNA-protein hydroxyl-radical footprinting experiments with high resolution using HYDROID. Nat Protoc. 2018 Nov;13(11):2535-2556.
Key words: HYDROID; hydroxyl-radical footprinting (HRF); DNAse I; DNA cleavage frequency
https://www.ncbi.nlm.nih.gov/pubmed/30341436

1. Levine MS, Holland AJ. The impact of mitotic errors on cell proliferation and tumorigenesis. Genes Dev. 2018 May 1;32(9-10):620-638.
Key words: aneuploidy, chromosomal instability, mitosis
https://www.ncbi.nlm.nih.gov/pubmed/29802124

1. Alder JK, Hanumanthu VS, Strong MA, DeZem AE, Stanley SE, Takemoto CM, Danilova L, Applegate CD, Bolton SG, Mohr DW, Brodsky RA, Casella JF, Greider CW, Jackson JB, Armanios M. Diagnostic utility of telomere length testing in a hospital-based setting. Proc Natl Acad Sci U S A. 2018 Mar 6;115(10):E2358-E2365.
Key words: aplastic anemia; interstitial lung disease; liver disease; precision medicine
https://www.ncbi.nlm.nih.gov/pubmed/29463756

2. Heerma van Voss MR, Kammers K, Vesuna F, Brilliant J, Bergman Y, Tantravedi S, Wu X, Cole RN, Holland A, van Diest PJ, Raman V. Global effects of DDX3 inhibition on cell cycle regulation identified by a combined phosphoproteomics and single cell tracking approach. Transl Oncol. 2018 Jun;11(3):755-763.
Key words: DDX3, RK-33, DEAD box RNA, ATPase dependent
https://www.ncbi.nlm.nih.gov/pubmed/29684792

3. Schuller AP, Green R. Roadblocks and resolutions in eukaryotic translation. Nat Rev Mol Cell Biol. 2018 May 14. doi: 10.1038/s41580-018-0011-4. [Epub ahead of print]
Key words: aminoacyl-tRNAs, ribosome rescue, hypusine
https://www.ncbi.nlm.nih.gov/pubmed/29760421

4. Ward A, Kumari G, Sen R, Desiderio S. The RAG-2 inhibitory domain gates accessibility of the V(D)J recombinase to chromatin. Mol Cell Biol. 2018 May 14. pii: MCB.00159-18.
Key words: Gating of chromatin, RAG-2, of H3K4me3, spontaneous V(D)J
https://www.ncbi.nlm.nih.gov/pubmed/29760281

1. Dever TE, Dinman JD, Green R. Translation elongation and recoding in eukaryotes. Cold Spring Harb Perspect Biol. 2018 April 2;10.1101/xahpweapwxr.032649 [Epub ahead of print]
Key words: eIF5A eukaryotes ribosomal frameshifting elongation
https://www.ncbi.nlm.nih.gov/pubmed/29610120

2. Evans LT, Holland AJ. Pushed out of a tough crowd: centrosome aberrations promote invasiveness. EMBO J. 2018 April 5;10.15252/embj.201899422. [Epub ahead of print]
Key words: Centrosome non-cell-autonomous aberrations
https://www.ncbi.nlm.nih.gov/pubmed/29622546

3. Liakath-Ali K, Mills EW, Sequeira I, Lichtenberger BM, Pisco AO, Sipila KH, Mishra A, Yoshikawa H, Wu CC, Ly T, Lamond Al, Adham IM, Green R, Watt FM. An evolutionarily conserved ribosome-rescue pathway maintains epidermal homeostasis. Nature. 2018 April; 556(7701):376-380.
Key words: mRNA epidermal homeostasis evolutionarily ribosome-rescue
https://www.ncbi.nlm.nih.gov/pubmed/29643507

4. Nigg EA, Holland AJ. Once and only once: mechanisms of centriole duplication and their deregulation disease. Nat Rev Mol Cell Biol. 2018 May; 19(5):297-312.
Key words: Centrioles cilia flagella organelles
https://www.ncbi.nlm.nih.gov/pubmed/29363672

1. Kudo T, Jeknic S, Macklin DN, Akhter S, Hughey JJ, Regot S, Covert MW. Live-cell measurements of kinase activity in single cells using translocation reporters. Nat Protoc. 2018 Jan. 13(1):155-169. Doi: 10.1038/nprot.2017.128. Epub 2017 Dec 21
Key words: Image processing, kinases, protein translocation
https://www.ncbi.nlm.nih.gov/pubmed/29266096

2. Schuller AP, Zinshteyn B, Enam SU, Green R. Directed hydroxyl radical probing reveals Upf1 binding to the 80S ribosomal E site rRNA at the L1 stalk. Nucleic Acids Res. 2017 Dec. doi 10.1093/nar/gkx1263. [Epub ahead of print]
Key words: Upf1 RNA protein complexes ribosome
https://www.ncbi.nlm.nih.gov/pubmed/29253221

1. Besold AN, Gilston BA, Radin JN, Ramsoomair C, Culbertson EM, Li CX, Cormack BP, Chazin WJ, Kehl-Fie TE, Culotta VC. The role of calprotectin in withholding zinc and copper from Candida albicans. Infect Immun. 2017 Nov 13. pii: IAI.00779-17. doi: 10.1128/IAI.00779-17. [Epub ahead of print]
Key words: calprotectin, zinc, copper, Candida albicans
https://www.ncbi.nlm.nih.gov/pubmed/29133349

2. Cook JD, Ng SY, Lloyd M, Eddington S, Sun H, Nathans J, Bok D, Radu RA, Travis GH. Peropsin modulates transit of vitamin A from retina to retinal pigment epithelium. J Biol Chem. 2017 Nov 6. pii: jbc.M117.812701. doi: 10.1074/jbc.M117.812701. [Epub ahead of print]
Key words: G protein-coupled receptor (GPCR); gene knockout; membrane; photoreceptor; retina; retinal metabolism; retinoid-binding protein; retinol; vitamin A
https://www.ncbi.nlm.nih.gov/pubmed/29109151

3. Lee CS, Lu T, Seydoux G. Nanos promotes epigenetic reprograming of the germline by down-regulation of the THAP transcription factor LIN-15B. Elife. 2017 Nov 7;6. pii: e30201. doi: 10.7554/eLife.30201. [Epub ahead of print].
Key words: C. elegans; cell biology; developmental biology; stem cells
https://www.ncbi.nlm.nih.gov/pubmed/29111977

4. Levine M, Holland A. Cell cycle proteins moonlight in multiciliogenesis. Science. 2017 Nov 10;358(6364):716-718. doi: 10.1126/science.aaq0770.
Key words: cell cycle, proteins, multiciliogenesis
https://www.ncbi.nlm.nih.gov/pubmed/29123048

5. Lu W, Dordai D, Huso D, Desiderio S. Smoothened signaling in the mouse osteoblastoid lineage is required for efficient B lymphopoiesis. Blood. 2017 Nov 22. pii: blood-2017-06-793539. doi: 10.1182/blood-2017-06-793539. [Epub ahead of print]
Key words: mouse, osteoblastoid, B lymphopoiesis
https://www.ncbi.nlm.nih.gov/pubmed/29167177

6. Mills EW, Green R. Ribosomopathies: There's strength in numbers. Science. 2017 Nov 3;358(6363). pii: eaan2755. doi: 10.1126/science.aan2755.
Key words: ribosomopathies, ribosomal protein haploinsufficiency, homeostasis, Diamond-Blackfan anemia
https://www.ncbi.nlm.nih.gov/pubmed/29097519

7. Paix A, Folkmann A, Goldman DH, Kulaga H, Grzelak MJ, Rasoloson D, Paidemarry S, Green R, Reed RR, Seydoux G. Precision genome editing using synthesis-dependent repair of Cas9-induced DNA breaks. Proc Natl Acad Sci U S A. 2017 Dec 12;114(50):E10745-E10754. doi: 10.1073/pnas.1711979114.
Key words: CRISPR; HDR; PCR repair template; SDSA; short homology arms
https://www.ncbi.nlm.nih.gov/pubmed/29183983

8. Rossi DCP, Gleason JE, Sanchez H, Schatzman SS, Culbertson EM, Johnson CJ, McNees CA, Coelho C, Nett JE, Andes DR, Cormack BP, Culotta VC. Candida albicans FRE8 encodes a member of the NADPH oxidase family that produces a burst of ROS during fungal morphogenesis. PLoS Pathog. 2017 Dec 1;13(12):e1006763. doi: 10.1371/journal.ppat.1006763. eCollection 2017 Dec.
Key words: Candida albicans, NADPH oxidase, fungal morphogenesis
https://www.ncbi.nlm.nih.gov/pubmed/29194441

9. Xiao H, Wang F, Wisniewski J, Shaytan AK, Ghirlando R, FitzGerald PC, Huang Y, Wei D, Li S, Landsman D, Panchenko AR, Wu C. Genes Dev. Molecular basis of CENP-C association with the CENP-A nucleosome at yeast centromeres. 2017 Oct 1;31(19):1958-1972. doi: 10.1101/gad.304782.117. Epub 2017 Oct 26.
Key words: AT-rich DNA; Cse4/CENP-A; Mif2/CENP-C; budding yeast; centromere; nucleosome
https://www.ncbi.nlm.nih.gov/pubmed/29074736

10. Yoon KJ, Ringeling FR, Vissers C, Jacob F, Pokrass M, Jimenez-Cyrus D, Su Y, Kim NS, Zhu Y, Zheng L, Kim S, Wang X, Doré LC, Jin P, Regot S, Zhuang X, Canzar S, He C, Ming GL, Song H. Temporal control of mammalian cortical neurogenesis by m6A methylation. Cell. 2017 Nov 2;171(4):877-889.e17. doi: 10.1016/j.cell.2017.09.003. Epub 2017 Sep 28.
Key words: Mettl14; RNA methylation; autism; epitranscriptomics; human organoid; m(6)A; neurogenesis; radial glia cell; schizophrenia; transcriptional prepatterning
https://www.ncbi.nlm.nih.gov/pubmed/28965759

1. Guydosh NR, Kimmig P, Walter P, Green R. Regulated Ire1-dependent mRNA decay requires no-go mRNA degradation to maintain endoplasmic reticulum homeostasis in S. pombe. Elife. 2017 Sep 25;6. pii: e29216. doi: 10.7554/eLife.29216. [Epub ahead of print].
Key words: S. pombe; cell biology
https://www.ncbi.nlm.nih.gov/pubmed/28945192

2. Mok CA, Au V, Thompson OA, Edgley ML, Gevirtzman L, Yochem J, Lowry J, Memar N, Wallenfang MR, Rasoloson D, Bowerman B, Schnabel R, Seydoux G, Moerman DG, Waterston RH. MIP-MAP: High-throughput mapping of Caenorhabditis elegans temperature-sensitive mutants via molecular inversion probes. Genetics. 2017 Oct;207(2):447-463. doi: 10.1534/genetics.117.300179. Epub 2017 Aug 21.
Key words: Caenorhabditis elegans; genetic mapping; massively multiplex sequencing; molecular inversion probes; temperature-sensitive mutations
https://www.ncbi.nlm.nih.gov/pubmed/28827289

3. Tischfield MA, Robson CD, Gilette NM, Chim SM, Sofela FA, DeLisle MM, Gelber A, Barry BJ, MacKinnon S, Dagi LR, Nathans J, Engle EC. Cerebral vein malformations result from loss of Twist1 expression and BMP signaling from skull progenitor cells and dura. Dev Cell. 2017 Sep 11;42(5):445-461.e5. doi: 10.1016/j.devcel.2017.07.027. Epub 2017 Aug 30.
Key words: BMP2; BMP4; ICP; Twist1; cerebral veins; coronal suture; craniosynostosis; osteoblast; skull; venous angiogenesis
https://www.ncbi.nlm.nih.gov/pubmed/28844842

4. Wang S, Pike AM, Lee SS, Strong MA, Connelly CJ, Greider CW. BRD4 inhibitors block telomere elongation. Nucleic Acids Research. 2017 Aug 21;45(14):8403-8410.
Key words: phosphotransferases telomerase telomere mice telomere shortening
https://www.ncbi.nlm.nih.gov/pubmed/28854735

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June 2020 articles:
Essential Information for Human Subjects Research Teams Related to COVID-19
Coronavirus Research Billing Notices and FAQ
Research Billing Buzz eNewsletter
Managing Investigational Product Returns from Research Participants
Update to Organization Policy on Registration of Clinical Trials
Changes in HSR Recertification
Update on Insurance and Research Participant Financial Responsibility Information Sheet: Signature No Longer Required
Change in JHM IRB Review Fees for Commercially-Funded Studies
Data and Safety Monitoring Board Training Manual Now Available
Good Clinical Practice (GCP) Fundamentals: Understanding and Applying GCP to Human Subject Research
Fee Schedule Adjustment for Hospital Services Charged to Clinical Trial Budgets
Changes to NIH-funded Human Subjects Research
Free Resources for Longitudinal Clinical Research Studies
JHM IRB Reliance Requests
Sharing Partnership for Innovative Research in Translation
Johns Hopkins Institute for Clinical and Translational Research
Johns Hopkins Clinical Research Network
 
Visit Animal Care and Use Committee Website
Current Classes
"Interinstitutional Assurance" Agreement
Health, Safety, and Environment (HSE) presents: Safety in Research Updates
COVID-19 Funding Opportunities
National Science Foundation (NSF) Partnerships for Innovation (PFI) Program
1907 Trailblazer Award
Michael J. Fox Foundation (MJFF) Challenge
Updated Guidance from NIH on COVID-19 Flexibilities for Applicants and Recipients
COVID-19 and Research Updates
Townhall Thursdays - Providing a Pulse on What's Happening in Research at JHU
New System to Request Outgoing Subawards
Point of Contact for NIH Loan Repayment Program
JHU SOM Update on NIH Policy on Foreign Involvement
Disclosure of Payments from Foreign Educational Institutions and Government Agencies
Institutional Letter of Support Required for Institutional Training Grant Applications
Notice to the Johns Hopkins Community Regarding the National Science Foundation Grant Reporting Requirement for Harassment Findings and Actions
Prohibited Mention of Prior Review for New Replacement Applications
NIH Policy on Foreign Component Involvement
NIH Policy: Foreign Components Added to a Grant to a Domestic or Foreign Organization
Why Project Outcomes Matter in your Interim and Final Research Performance Progress Report (RPPR)
NIH Matchmaker, A Tool For Finding Similar NIH Projects
NIH Video Tutorials on How to Apply for Grants

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