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October 2017
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Molecular Biology and Genetics Archives

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
https://www.ncbi.nlm.nih.gov/pubmed/28336518

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
https://www.ncbi.nlm.nih.gov/pubmed/28193672

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
https://www.ncbi.nlm.nih.gov/pubmed/28188027

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
https://www.ncbi.nlm.nih.gov/pubmed/28457705

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
http://rstb.royalsocietypublishing.org/content/372/1716/20160183
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
http://www.pnas.org/content/114/8/1904
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
http://www.jbc.org/content/292/8/3506
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
http://www.nature.com/articles/ncomms14705
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
http://rnajournal.cshlp.org/content/early/2017/02/13/rna.060418.116
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
http://www.bloodjournal.org/content/early/2017/02/17/blood-2016-08-736108?sso-checked=true
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
http://www.nature.com/ncomms/2017/170120/
ncomms14112/full/ncomms14112.html
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.
2017;584:229-253.
Key words: Alzheimer's disease cancer cell signaling ER-association gamma-secretase
http://dx.doi.org/10.1016/bs.mie.2016.10.025
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
http://jcb.rupress.org/content/216/1/149
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"
http://dx.doi.org/10.18632/oncotarget.12604
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
http://www.nature.com/nrg/journal/v18/n1/full/nrg.2016.118.html
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
http://www.sciencedirect.com/science/article/pii/S0962892417300144
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
http://www.sciencedirect.com/science/article/pii/S1534580716309170
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
http://dx.doi.org/10.1016/j.matbio.2016.06.004
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
http://cancerdiscovery.aacrjournals.org/search/Mediated%
252BSMAD3%252BEnhances%252BPD-1

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

http://www.sciencedirect.com/science/article/pii/S0092867416316531
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
https://elifesciences.org/content/5/e21337
PMID:27914198

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
http://www.ncbi.nlm.nih.gov/pubmed/27432896

1. Adler PN, Nathans J. The cellular compass. Sci Am. 2016 Mar;314(3):66-71.
Key words: cellular
http://www.ncbi.nlm.nih.gov/pubmed/27066647

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
https://elifesciences.org/content/5/e15928
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
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

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October 2017 articles:
Changes to NIH-funded Human Subjects Research
Free Resources for Longitudinal Clinical Research Studies
New Fee Schedule for Commercially Funded Studies
NIH requirement for Single IRB (sIRB)
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Sharing Partnership for Innovative Research in Translation
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Understanding, Preventing, and Managing Immunotherapy-related Adverse Events (irAEs) Associated with Checkpoint Inhibition for Melanoma and Other Cancers
AHA Institute for Precision Cardiovascular Medicine
National Science Foundation (NSF) Major Research Instrumentation Program (MRI) Instrument Acquisition or Development
Camille Dreyfus Teacher-Scholar Award
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NIH Policy: Foreign Components Added to a Grant to a Domestic or Foreign Organization

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