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April 2018

Molecular Biology and Genetics Archives

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

1. Breitkopf-Heinlein K, Meyer C, König C, Gaitantzi H, Addante A, Thomas M, Wiercinska E, Cai C, Li Q, Wan F, Hellerbrand C, Valous NA, Hahnel M, Ehlting C, Bode JG, Müller-Bohl S, Klingmüller U, Altenöder J, Ilkavets I, Goumans MJ, Hawinkels LJ, Lee SJ, Wieland M, Mogler C, Ebert MP, Herrera B, Augustin H, Sánchez A, Dooley S, Ten Dijke P. BMP-9 interferes with liver regeneration and promotes liver fibrosis. Gut. 2017 May;66(5):939-954.
Key words: cytokines; growth factors; hepatic fibrosis; hepatic stellate cell; hepatocyte

2. Guydosh NR, Green R. Translation of poly(A) tails leads to precise mRNA cleavage.
RNA. 2017 May;23(5):749-761.
Key words: Hbs1; PELO; cryptic polyadenylation; ribosome stalling; ski complex

3. Lambrus BG, Holland AJ. A New Mode of Mitotic Surveillance. Trends Cell Biol. 2017 May;27(5):314-321.
Key words: cell cycle arrest; centrosome; checkpoint; mitosis; surveillance

4. McClary B, Zinshteyn B, Meyer M, Jouanneau M, Pellegrino S, Yusupova G, Schuller A, Reyes JCP, Lu J, Guo Z, Ayinde S, Luo C, Dang Y, Romo D, Yusupov M, Green R, Liu JO. Inhibition of eukaryotic translation by the antitumor natural product agelastatin A. Cell Chem Biol. 2017 May 18;24(5):605-613.e5.
Key words: agelastatin A; brain cancer; chemical footprinting; drug design; marine alkaloid; molecular docking; peptidyl transferase center; rRNA seq; ribosome; translation elongation

1. Buskirk AR, Green R. Ribosome pausing, arrest and rescue in bacteria and eukaryotes. Philos Trans R Soc Lond B Biol Sci. 2017 Mar 19;372(1716).
Key words: Dom34/PELO, EFP, Hbs1/HBS1I; Rli1ABCE1, elF5A
PMID: 28138069

1. Bettridge J, Na CH, Pandey A, Desiderio S. H3K4me3 induces allosteric conformational changes in the DNA-binding and catalytic regions of the V(D)J recombinase. Proc Natl Acad Sci U S A. 2017 Feb 21;114(8):1904-1909. 10.1073/pnas.1615727114.
Key words: DNA recombination allosteric control epigenetic
PMID: 28174273

2. Chang H, Smallwood PM, Williams J, Nathans J. Intramembrane proteolysis of astrotactins. J Biol Chem.
2017 Feb 24;292(8):3506-3516.
Key words: Intramembrane proteolysis membrane protein transmembrane domain
PMID: 28100779

3. Dakhiya Y, Hussien D, Fridman E, Kiflawi M, Green R. Correlations between circadian rhythms and growth in challenging environments. Nat Commun. 2017 Mar;173(3):1724-1734.
Key words: Hypomorphic mutations, PolyA, translation, expression, elongation
PMID: 28153924

4. Guydosh NR, Green R. Translation of poly(A) tails leads to precise mRNA cleavage. RNA
2017 Feb 13. pii: rna.060418.116.
Key words: Translation, poly(A) tails, mRNA decay, ribosome profiling
PMID: 28193672

5. Mills EW, Green R, Ingolia NT. Slowed decay of mRNAs enhances platelet specific translation. Blood.
2017 Feb 17. pii: blood-2016-08-736108.
Key words: Ribosome profiling, human platelets, megakaryocyte, mRNA decay, PELO
PMID: 28213379

1. Arthur LL, Chung JJ, Jankirama P, Keefer KM, Kolotilin I, Pavlovic-Djuranovic S, Chalker DL, Grbic V, Green R, Menassa R, True HL, Skeath JB, Djuranovic S. Rapid generation of hypomorphic mutations. Nat Commun. 2017 Jan 20;8:14112.
Key words: Hypomorphic mutations polyA translation expression elongation
PMID: 28106166

2. Baker RP, Urban S. An inducible reconstitution system for the real-time kinetic analysis of protease activity and inhibition inside the membrane. Methods Enzymol.
Key words: Alzheimer's disease cancer cell signaling ER-association gamma-secretase
PMID: 28065265

3. Chung HK, Ryu D, Kim KS, Chang JY, Kim YK, Yi HS, Kang SG, Choi MJ, Lee SE, Jung SB, Ryu MJ, Kim SJ, Kweon GR, Kim H, Hwang JH, Lee CH, Lee SJ, Wall CE, Downes M, Evans RM, Auwerx J, Shong M. Growth differentiation factor 15 is a myomitokine governing systemic energy homeostasis. J Cel Biol. 2017 Jan 2;216(1):149-165.
Key words: GoF-15 TGF-ß muscle metabolism
PMID: 27986797

4. Eleftheriou NM, Sjölund J, Bocci M, Cortez E, Lee SJ, Cunha SI, Pietras K. Compound genetically engineered mouse models of cancer reveal dual targeting of ALK1 and endoglin as a synergistic opportunity to impinge on angiogenic TGF-? signaling. Oncotarget. 2016 Dec 20;7(51):84314-84325.
Key words: "ALK1 bmp9 angiogenesis endoglin"
PMID: 27741515

5. Housden BE, Muhar M, Gemberling M, Gersbach CA, Stainier DY, Seydoux G. Loss-of-function genetic tools for animal models: cross-species and cross-platform differences. Nat Rev Genet.
2017 Jan;18(1):24-40.
Key words: Caenorhabditis elegans loss-of-function genetic engineering
PMID: 27795562

6. Lambrus BG, Holland AJ. A new mode of mitotic surveillance. Trends Cell Biol. 2017 Feb 7. pii: S0962-8924(17)30014-4.
Key words: Centrosome mitosis cell cycle arrest
PMID: 28188027

7. Levine MS, Bakker B, Boeckx B, Moyett J, Lu J, Vitre B, Spierings DC, Lansdorp PM, Cleveland DW, Lambrechts D, Foijer F, Holland AJ. Centrosome Amplification is sufficient to promote spontaneous tumorigenesis in mammals. Dev Cell. 2017 Feb 6;40(3):313-322.e5.
Key words: Plk4 aneuploidy centriole centrosome amplification
PMID: 28132847

8. Muir AM, Massoudi D, Nguyen N, Keene DR, Lee SJ, Birk DE, Davidson JM, Marinkovich MP, Greenspan DS. BMP1-like proteinases are essential to the structure and wound healing of skin. Matrix Biol. 2016 Dec;56:114-131.
Key words: Biglycan bone morphogenetic protein mammalian
PMID: 27363389

9. Park BV, Freeman ZT, Ghasemzadeh A, Chattergoon MA, Rutebemberwa A, Steigner J, Winter ME, Huynh TV, Sebald SM, Lee SJ, Pan F, Pardoll DM, Cox AL. TGF?1-Mediated SMAD3 Enhances PD-1 Expression on Antigen-Specific T Cells in Cancer. Cancer Discov. 2016 Dec;6(12):1366-1381.
Key words: SMAD3 TGF-ß immune system

PMID: 27683557

10. Urban S. Snapshot: cartography of intramembrane proteolysis. Cell. ec 15;167(7):1898-1898.e1.
Key words: Intramembrane proteolysis membranes organelles regulation

PMID: 27984738

Smith J, Calidas D, Schmidt H, Lu T, Rasoloson D, Seydoux G. Spatial patterning of P granules by RNA-induced phase separation of the intrinsically-disordered protein MEG-3. eLife 2016;10.7554/eLife.21337.
Key words: RNA granule phase separation

1. Lambrus, BG, Daggubati V, Uetake Y, Scott PM, Clutario KM, Sluder G, Holland A.J. A USP28-53BP1-p53-p21 signaling axis arrests growth following centrosome loss or prolonged mitosis. Journal of Cell Biology. 2016 July; 214:143-153.
Key words: centrosome loss, mitosis, signaling pathway

1. Adler PN, Nathans J. The cellular compass. Sci Am. 2016 Mar;314(3):66-71.
Key words: cellular

2. Nathans J, Sterling P. How scientists can reduce their carbon footprint. Elife. 2016 Mar 31;5. pii: e15928. doi: 10.7554/eLife.15928.
Key words: carbon footprint, scientists, environment
PMID: 27029962

1. Cho SW, Dickey SW, Urban S. Crystal structures and inhibition kinetics reveal a two-stage catalytic mechanism with drug design implications for rhomboid proteolysis. Molecular Cell. 2016 Feb 4;61(3):329-40.
Key words: crystal structures, catalytic, rhomboid proteolysis
PMID: 26805573

1. Mohammad F, Woolstenhulme CJ, Green R, Buskirk AR. Clarifying the translational pausing landscape in bacteria by ribosome profiling. Cell Reports. 2016 S2211-1247(15)01529-6.
Key words: ribosome profiling, pausing, bacteria, Shine-Dalgarno

2. Chang H, Smallwood PM, Williams J, Nathans J. The spatio-temporal domains of Frizzled6 action in planar polarity control of hair follicle orientation. Dev Biol. 2016 Jan 1; 409(1):181-93.
Key words: Fz6; Merkel cell; Mouse development; Planar cell polarity; Skin; Tissue polarity; Vangl1; Vangl2

3. Zhou Y, Williams J, Smallwood PM, Nathans J. Sox7, Sox17, and Sox18 cooperatively regulate vascular development in the mouse retina. PLoS One. 2015 Dec 2; 10(12):e0143650.
Key words: mouse retina, vascular development, endothelial cells

1. Chang H, Cahill H, Smallwood PM, Wang Y, Nathans J. Identification of Astrotactin2 as a genetic modifier that regulates the global orientation of mammalian hair follicles. PLoS Genet. 2015 Sep 29;11(9):e1005532.
Key words: hair follicles, hair growth, Astrotactin2

2. Chang H, Smallwood PM, Williams J, Nathans J. The spatio-temporal domains of Frizzled6 action in planar polarity control of hair follicle orientation. Dev Biol. 2015 Nov 10. pii: S0012-1606(15)30192-5.
Key words: Frizzled6, hair follicle, hair growth

3. Koutmou KS, Radhakrishnan A, Green R. Synthesis at the speed of codons. Trends Biochem Sci. 2015 Dec;40(12):717-8.
Key words: ribosome profiling, codons

4. Hua ZL, Emiliani FE, Nathans J. Rac1 plays an essential role in axon growth and guidance and in neuronal survival in the central and peripheral nervous systems. Neural Dev. 2015 Sep 23;10(1):21.
Key words: axon growth, neuron, Rac1

5. Lee SS, Bohrson C, Pike AM, Wheelan SJ, Greider CW. ATM kinase is required for telomere elongation in mouse and human cells. Cell Reports. 2015 Nov 24;13(8):1623-32.
Key words: kinase, telomere

6. Zhou Y, Williams J, Smallwood PM, Nathans J. Sox7, Sox17, and Sox18 cooperatively regulate vascular development in the mouse retina. PLoS One. 2015 Dec 2;10(12):e0143650.
Key words: vascular development, mouse retina, transcription factors

1. Chang H, Cahill H, Smallwood PM, Wang Y, Nathans J. Identification of Astrotactin2 as a Genetic Modifier That Regulates the Global Orientation of Mammalian Hair Follicles. PLoS Genet. 2015 Sep 29;11(9):e1005532.
Key words: Astrotactin2, genetic modifier, mammalian hair follicles
PMID: 26418459

2. Chang H, Smallwood PM, Williams J, Nathans J. The spatio-temporal domains of Frizzled6 action in planar polarity control of hair follicle orientation. Dev. Biol. 2015 Oct 28. S0012-1606(15)30 192-5.
Key words: Key words: Fz6; Merkel cell; Mouse development; Planar cell polarity; Skin; Tissue polarity; Vangl1; Vangl2

3. Hua ZL, Emiliani FE, Nathans J. Rac1 plays an essential role in axon growth and guidance and in neuronal survival in the central and peripheral nervous systems. Neural Dev. 2015 Sep 23;10(1):21.
Key words: Rac1, axon growth, central nervous system, peripheral nervous system
PMID: 26395878

1. Holland AJ, Reis RM, Niessen S, Pereira C, Andres DA, Spielmann HP, Cleveland DW, Desai A, Gassmann R. Preventing farnesylation of the dynein adaptor Spindly contributes to the mitotic defects caused by farnesyltransferase inhibitors. Mol Biol Cell. 2015 May 15;26(10):1845-56.
Key words: farnesylation, dynein, mitotic defects, farnesyltransferase

2. Sun LO, Brady CM, Cahill H, Al-Khindi T, Sakuta H, Dhande OS, Noda M, Huberman AD, Nathans J, Kolodkin AL. Functional assembly of accessory optic system circuitry critical for compensatory
eye movements. Neuron. 2015 May 20;86(4):971-84.
Key words: neural circuitry; global visual field motion; eye movements
PMID: 25959730

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April 2018 articles:
Training Sessions: Relying on an External IRB (JHM IRB)
Fee Schedule Adjustment for Hospital Services Charged to Clinical Trial Budgets
Change in Federalwide Assurance [FWA] Numbers
Changes to NIH-funded Human Subjects Research
Free Resources for Longitudinal Clinical Research Studies
NIH requirement for Single IRB (sIRB)
JHM IRB Reliance Requests
Sharing Partnership for Innovative Research in Translation
Johns Hopkins Institute for Clinical and Translational Research
Johns Hopkins Research Network
Visit Animal Care and Use Committee Website
Current Classes
"Interinstitutional Assurance" Agreement
Health, Safety, and Environment (HSE) presents: Safety in Research Updates
Takeda Pharmaceutical Company Innovators in Science Award
Arnold and Mabel Beckman Foundation Scholars Program
Michael J. Fox Foundation (MJFF) Challenge
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
NIH Policy: Foreign Components Added to a Grant to a Domestic or Foreign Organization

This Month's Departmental Listings

Upcoming Deadlines for April, May and June

April Events at the Genetic Resources Core Facility


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