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May 2016
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Molecular Biology and Genetics Archives

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
http://www.sciencedirect.com/science/article/pii/S1097276515009788
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
http://www.ncbi.nlm.nih.gov/pubmed/26776510

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
http://www.ncbi.nlm.nih.gov/pubmed/26517967

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
http://www.ncbi.nlm.nih.gov/pubmed/26630461

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
http://www.ncbi.nlm.nih.gov/pubmed/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 Nov 10. pii: S0012-1606(15)30192-5.
Key words: Frizzled6, hair follicle, hair growth
http://www.ncbi.nlm.nih.gov/pubmed/26517967

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
http://www.ncbi.nlm.nih.gov/pubmed/26526516

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
http://www.ncbi.nlm.nih.gov/pubmed/26395878

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
http://www.ncbi.nlm.nih.gov/pubmed/26586427

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
http://www.ncbi.nlm.nih.gov/pubmed/26630461

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
http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1005532
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
http://www.ncbi.nlm.nih.gov/pubmed/26517967

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
http://www.neuraldevelopment.com/content/10/1/21
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
http://www.molbiolcell.org/content/26/10/1845.long
PMID:25808490

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
http://www.sciencedirect.com/science/article/pii/S0896627315002883
PMID: 25959730

1. Paix A, Wang Y, Smith HE, Lee CY, Calidas D, Lu T, Smith J, Schmidt H, Krause MW, Seydoux G. Scalable and versatile genome editing using linear DNAs with microhomology to Cas9 Sites in Caenorhabditis elegans. Genetics. 2014 Dec;198(4):1347-56.
Key words: genome, microhomology, C. elegans
http://www.ncbi.nlm.nih.gov/pubmed/25249454

2. Wang JT, Smith J, Chen BC, Schmidt H, Rasoloson D, Paix A, Lambrus BG, Calidas D, Betzig E, Seydoux G. Regulation of RNA granule dynamics by phosphorylation of serine-rich, intrinsically disordered proteins in C. elegans. Elife. 2014 Dec 23;4. doi: 10.7554/eLife.04591.
Key words: RNA, proteins, phosphorylation, C. elegans
http://www.ncbi.nlm.nih.gov/pubmed/25535836

3. Zhang G, Li C, Li Q, Li B, Larkin DM, Lee C, Storz JF, Antunes A, Greenwold MJ, Meredith RW, Ödeen A, Cui J, Zhou Q, Xu L, Pan H, Wang Z, Jin L, Zhang P, Hu H, Yang W, Hu J, Xiao J, Yang Z, Liu Y, Xie Q, Yu H, Lian J, Wen P, Zhang F, Li H, Zeng Y, Xiong Z, Liu S, Zhou L, Huang Z, An N, Wang J, Zheng Q, Xiong Y, Wang G, Wang B, Wang J, Fan Y, da Fonseca RR, Alfaro-Núñez A, Schubert M, Orlando L, Mourier T, Howard JT, Ganapathy G, Pfenning A, Whitney O, Rivas MV, Hara E, Smith J, Farré M, Narayan J, Slavov G, Romanov MN, Borges R, Machado JP, Khan I, Springer MS, Gatesy J, Hoffmann FG, Opazo JC, Håstad O, Sawyer RH, Kim H, Kim KW, Kim HJ, Cho S, Li N, Huang Y, Bruford MW, Zhan X, Dixon A, Bertelsen MF, Derryberry E, Warren W, Wilson RK, Li S, Ray DA, Green RE, O'Brien SJ, Griffin D, Johnson WE, Haussler D, Ryder OA, Willerslev E, Graves GR, Alström P, Fjeldså J, Mindell DP, Edwards SV, Braun EL, Rahbek C, Burt DW, Houde P, Zhang Y, Yang H, Wang J; Avian Genome Consortium, Jarvis ED, Gilbert MT, Wang J. Comparative genomics reveals insights into avian genome evolution and adaptation. Science. 2014 Dec 12;346(6215):1311-20.
Key words: genomics, avian genome, evolution
http://www.ncbi.nlm.nih.gov/pubmed/25504712

1. Rattner A, Wang Y, Zhou Y, Williams J, Nathans J. The role of the hypoxia response in shaping retinal vascular development in the absence of norrin/frizzled4 signaling. Invest Ophthalmol Vis Sci. 2014 Nov 20;55(12):8614-25.
Key words: hypoxia, retina, norrin/fizzled4 signaling
http://www.ncbi.nlm.nih.gov/pubmed/25414188

2. Lu C, Ward A, Bettridge J, Liu Y, Desiderio S. An autoregulatory mechanism imposes allosteric control on the V(D)J recombinase by histone H3 methylation. Cell Rep. 2015 Jan 6;10(1):29-38.
http://www.sciencedirect.com/science/article/pii/S2211124714010122
PMID: 2554314

1. Hua ZL, Chang H, Wang Y, Smallwood PM, Nathans J. Partial interchangeability of Fz3 and Fz6 in tissue polarity signaling for epithelial orientation and axon growth and guidance. Development. 2014 Oct;141(20):3944-54.
Key words: Fz3, Fz6, tissue polarity, epithelial
http://dev.biologists.org/content/141/20/3944.long
PMID: 25294940

2. Zhou Y, Wang Y, Tischfield M, Williams J, Smallwood PM, Rattner A, Taketo MM, Nathans J. Canonical WNT signaling components in vascular development and barrier formation. J Clin Invest. 2014 Sep 2;124(9):3825-46.
Key words: WNT signaling, vascular development
http://www.ncbi.nlm.nih.gov/pubmed/25083995

3. Zhou Y, Nathans J. Gpr124 controls CNS angiogenesis and blood-brain barrier integrity by promoting ligand-specific canonical wnt signaling. Dev Cell. 2014 Oct 27;31(2):248-56.
Key words: CNS angiogenesis, blood-brain barrier. Ligand, WNT signaling http://www.sciencedirect.com/science/article/pii/S1534580714005486#
PMID: 25373781

1. Hickman AB, Ewis HE, Li X, Knapp JA, Laver T, Doss AL, Tolun G, Steven AC, Grishaev A, Bax A, Atkinson PW, Craig NL, Dyda F. Structural basis of hAT transposon end recognition by Hermes, an octameric DNA transposase from Musca domestica. Cell. 2014 Jul 17;158(2):353-67. doi: 10.1016/j.cell.2014.05.037.
Key words: transposon, DNA transposase
http://www.ncbi.nlm.nih.gov/pubmed/25036632

2. Choi KY, Spencer JM, Craig NL. The Tn7 transposition regulator TnsC interacts with the transposase subunit TnsB and target selector TnsD. Proc Natl Acad Sci U S A. 2014 Jul 15;111(28):E2858-65. doi: 10.1073/pnas.1409869111.
Key words: Tn7, transposition, transposase
http://www.ncbi.nlm.nih.gov/pubmed/24982178

3. Preis A, Heuer A, Barrio-Garcia C, Hauser A, Eyler DE, Berninghausen O, Green R, Becker T, Beckmann R. Cryoelectron microscopic structures of eukaryotic translation termination complexes containing eRF1-eRF3 or eRF1-ABCE1. Cell Rep. 2014 Jul 10;8(1):59-65. doi: 10.1016/j.celrep.2014.04.058.
Key words: cryoelectron microscope, eukaryotic translation
http://www.sciencedirect.com/science/article/pii/S2211124714004884
PMID:25001285

4. Brunelle JL, Green R. Coomassie blue staining. Methods Enzymol. 2014;541:161-7. doi: 10.1016/B978-0-12-420119-4.00013-6.
Key words: Coomassie blue
http://www.sciencedirect.com/science/article/pii/B9780124201194000136
PMID: 24674070

5. Brunelle JL, Green R. One-dimensional SDS-polyacrylamide gel electrophoresis (1D SDS-PAGE). Methods Enzymol. 2014;541:151-9. doi: 10.1016/B978-0-12-420119-4.00012-4.
Key words: SDS-polyacrylamide gel, electrophoresis
http://www.sciencedirect.com/science/article/pii/B9780124201194000124
PMID: 24674069

6. Wang JT, Seydoux G. P granules. Curr Biol. 2014 Jul 21;24(14):R637-8. doi: 10.1016/j.cub.2014.06.018.
Key words: P. granules
http://www.sciencedirect.com/science/article/pii/S0960982214007325
PMID: 25050955

1. Chang H, Wang Y, Wu H, Nathans J. Flat mount imaging of mouse skin and its application to the analysis of hair follicle patterning and sensory axon morphology. J Vis Exp. 2014 Jun 25;(88). doi: 10.3791/51749.
Key words: hair follicle, sensory axon, morphology, imaging, mouse
http://www.jove.com/video/51749/flat-mount-imaging-mouse-skin-its-application-to-analysis-hair
PMID: 24999071

2. Hua ZL, Jeon S, Caterina MJ, Nathans J. Frizzled3 is required for the development of multiple axon tracts in the mouse central nervous system. Proc Natl Acad Sci U S A. 2014 Jul 22;111(29):E3005-14
Key words: frizzled3, axons, mouse, central nervous system
http://www.pnas.org/content/111/29/E3005.long
PMID: 24799694

3. Wu H, Williams J, Nathans J. Complete morphologies of basal forebrain cholinergic neurons in the mouse. Elife (Cambridge). 2014 May 7;3:e02444. doi: 10.7554/eLife.02444.
Key words: forebrain, cholinergic neurons
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4038840/
PMID: 24894464

4. Zhou Y, Wang Y, Tischfield M, Williams J, Smallwood PM, Rattner A, Taketo MM, Nathans J. Canonical WNT signaling components in vascular development and barrier formation. J Clin Invest. 2014 Aug 1. pii: 76431. doi: 10.1172/JCI76431.
Key words: WNT, vascular development, barrier formation
http://www.jci.org/articles/view/76431
PMID:25083995

1. Guo Y, Park JM, Cui B, Humes E, Gangadharan S, Hung S, FitzGerald PC, Hoe K-L, Grewal SIS, Craig NL, Levin HL. Integration profiling of gene function with dense maps of transposon integration. Genetics 2013 Oct; 195(2):599-609.
Key words: Hermes, Schizosaccharomyces pombe, Transposon, integration profile
http://www.genetics.org/content/195/2/599.full.pdf+html
PMID:23893486

2. Wright JA, Smith RC, Li X, Craig NL, Atkinson PW. IPB7 transposase behavior in Drosophila melanogaster and Aedes aegypti. Insect Biochemistry and Molecular Biology 2013; 43:899-906.
Key words: piggyBac, Transposable element, Hyperactive, Drosophila, Aedes http://www.sciencedirect.com/science/article/pii/S096517481300115X
PMID:23835045

1. Rattner A, Yu H, Williams J, Smallwood PM, Nathans J. Endothelin-2 signaling in the neural retina promotes the endothelial tip cell state and inhibits angiogenesis. Proc Natl Acad Sci USA. 2013 Oct 1;110(40)
Key words: endothelin-2, neural retina, angiogenesis
http://www.pnas.org/content/110/40/E3830.long
PMID: 24043815

1. Halper-Stromberg E, Steranka J, Giraldo-Castillo N, Fuller T, Desiderio S, Burns KH. Fine mapping of V(D)J recombinase mediated rearrangements in human lymphoid malignancies. BMC Genomics. 2013 Aug 19;14(1):565 [Epub ahead of print]
Key words: Lymphocytes, antigen, PCR amplification
http://www.biomedcentral.com/1471-2164/14/565/abstract
PMID: 23957733

2. Lee J, Baldwin WM 3rd, Lee Cy, Desiderio S. Stat3? mitigates development of atherosclerosis in apolipoprotein E-deficient mice. J Mol Med (Berl). 2013 Aug; 91(8):965-76.
Key words: transcription factor, Stat3, pathologic sequelae
http://link.springer.com/article/10.1007%2Fs00109-013-1013-5
PMID: 23619910

1. Choi KY, Li Y, Sarnovsky R, Craig NL. Direction interaction between the TnsA and TnsB subunits controls the heteromeric Tn7 transposase. Proc. Nat'l Acad. Sci. U.S.A. 2013 May 28;110(22):E2038-45.
Key words: protein-protein interaction, transposition, protein-DNA interaction, asymmetric transposon ends
http://www.pnas.org/content/110/22/E2038.long
PMID: 23674682

2. Li X, Burnight ER, Cooney AL, Malani N, Brady T, Sander JD, Staber J, Wheelan S, Joung JK, McCray PB Jr, Bushman FD, Sinn PL, Craig NL. piggyBac transposase tools for genome engineering. Proc. Nat'l Acad. Sci. U.S.A. 2013 Jun 18;110(25):E2279-87.
Key words: GULOP, ROSA26, induced pluripotent stem cell production, protein-DNA interaction
http://www.pnas.org/content/110/25/E2279.long
PMID: 23723351; PMCID: PMC3690869

3. O'Donnell KA, An W, Schrum, CT, Wheelan SJ, Boeke JD. Controlled Insertional mutagenesis using a LINE-1 (ORFeus) gene-trap mouse model. 2013 Jul 16;110(29):E2706-13.
Key words: L1 retrotransposon; mud musculus; tet-promoter; white-spotted phenotype; LINE-1
http://www.ncbi.nlm.nih.gov/pubmed/23818630

4. Rybanska-Spaeder I, Reynolds TL, Chou J, Prakash M, Jefferson T, Husso DL, Desiderio S, Franco S. 53BP1 is limiting for nonhomologous end-joining in ATM-deficient cells subjected to oncogenic stress or radiation. Mol Cancer Res. 2013 Jul 15 (Epub ahead of print)
Key words: Oncogneric translocations, T lineage lymphomas, NHEJ defect, double mutants http://www.ncbi.nlm.nih.gov/pubmed/23858098

1. Huang L, Rattner A, Liu H, Nathans J. How to draw the line in biomedical research. Elife. 2013;2:e00638. doi: 10.7554/eLife.00638
Key words: biomedical research, scatter plot
http://www.ncbi.nlm.nih.gov/pubmed/23538852

2. Lee J, Baldwin WM 3rd, Lee CY, Desiderio S. Stat3? mitigates development of atherosclerosis in apolipoprotein E-deficient mice J Mol Med (Berl). 2013 Apr 26. Epub ahead of print
Key words: transcription factor Stat3, dimerization, DNA binding
http://link.springer.com/article/10.1007%2Fs00109-013-1013-5
PMID: 236119910

3. Newman RH, Hu J, Rho HS, Xie Z, Woodard C, Neiswinger J, Cooper C, Shirley M, Clark HM, Hu S, Hwang W, Seop Jeong J, Wu G, Lin J, Gao X, Ni Q, Goel R, Xia S, Ji H, Dalby KN, Birnbaum MJ, Cole PA, Knapp S, Ryazanov AG, Zack DJ, Blackshaw S, Pawson T, Gingras AC, Desiderio S, Pandey A, Turk BE, Zhang J, Zhu H, Qian J. Construction of human activity-based phosphorylation networks. Mol Syst Biol. 2013 Apr 2:9:655 doi.10.1038/msb.201312.
Key words: human phosphorylation networks, vivo phosphorylated residues, kinase-substrate relationships, CEASAR
http://www.nature.com/msb/journal/v9/n1/full/msb201312.html
PMID: 23549483

4. Shilagardi, K., Li, S., Luo, F., Marikar, F, Duan R., Jin, P., Kim, J., Murnen, K., and Chen, E.H. Actin-propelled invasive membrane protrusions promote fusogenic protein engagement during cell-cell fusion. Science. 2013 Apr 19;340(6130):359-363.
Key words: cell-cell fusion, actin polymerization, invasive membrane protrusion
http://www.sciencemag.org/content/340/6130/359.long
PMID: 23623557

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