Progress: October 2013

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Publications Citing Koch Institute Faculty Members

1. Fully Biodegradable Airway Stents Using Amino Alcohol-Based Poly(ester amide) Elastomers. Wang J, Boutin KG, Abdulhadi O, Personnat LD, Shazly T, Langer R, Channick CL, Borenstein JT. Adv Healthc Mater. pubmed:23526787;  doi:10.1002/adhm.201200348

2. Single Step Reconstitution of Multifunctional High-Density Lipoprotein-Derived Nanomaterials Using Microfluidics. Kim Y, Fay F, Cormode DP, Sanchez-Gaytan BL, Tang J, Hennessy EJ, Ma M, Moore K, Farokhzad OC, Fisher EA, Mulder WJ, Langer R, Fayad ZA. ACS Nano. pubmed:24079940;  doi:10.1021/nn4039063

3. Inhibition of vein graft stenosis with a c-jun targeting DNAzyme in a cationic liposomal formulation containing 1,2-dioleoyl-3-trimethylammonium propane (DOTAP)/1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (DOPE). Li Y, Bhindi R, Deng ZJ, Morton SW, Hammond PT, Khachigian LM. Int J Cardiol. pubmed:23886527;  doi:10.1016/j.ijcard.2013.05.092

4. Human (alpha2-->6) and avian (alpha2-->3) sialylated receptors of influenza A virus show distinct conformations and dynamics in solution. Sassaki GL, Elli S, Rudd TR, Macchi E, Yates EA, Naggi A, Shriver Z, Raman R, Sasisekharan R, Torri G, Guerrini M. Biochemistry. pubmed:24015903;  doi:10.1021/bi400677n

5. Synthesis of Highly Stable Sub-8 nm TiO Nanoparticles and Their Multilayer Electrodes of TiO/MWNT for Electrochemical Applications. Hyder MN, Gallant BM, Shah NJ, Shao-Horn Y, Hammond PT. Nano Lett. pubmed:24003950;  doi:10.1021/nl401387s

6. Drug Delivery Interfaces in the 21st Century: From Science Fiction Ideas to Viable Technologies. Chertok B, Webber MJ, Succi MD, Langer R. Mol Pharm. pubmed:23915375;  doi:10.1021/mp4003283

7. High concentrations of drug in target tissues following local controlled release are utilized for both drug distribution and biologic effect: An example with epicardial inotropic drug delivery. Maslov MY, Edelman ER, Wei AE, Pezone MJ, Lovich MA. J Control Release. pubmed:23872515;  doi:10.1016/j.jconrel.2013.06.038

8. Nanoparticles That Sense Thrombin Activity As Synthetic Urinary Biomarkers of Thrombosis. Lin KY, Kwong GA, Warren AD, Wood DK, Bhatia SN. ACS Nano. pubmed:24015809;  doi:10.1021/nn403550c

9. Synthesis and in vitro evaluation of a multifunctional and surface-switchable nanoemulsion platform. Gianella A, Mieszawska AJ, Hoeben FJ, Janssen HM, Jarzyna PA, Cormode DP, Costa KD, Rao S, Farokhzad OC, Langer R, Fayad ZA, Mulder WJ. Chem Commun (Camb). pubmed:23877789;  doi:10.1039/c3cc43618g

10. Receptor specificity does not affect replication or virulence of the 2009 pandemic H1N1 influenza virus in mice and ferrets. Lakdawala SS, Shih AR, Jayaraman A, Lamirande EW, Moore I, Paskel M, Sasisekharan R, Subbarao K. Virology. pubmed:24074599;  doi:10.1016/j.virol.2013.08.011

11. Addressing polyspecificity of antibodies selected from an in vitro yeast presentation system: a FACS-based, high-throughput selection and analytical tool. Xu Y, Roach W, Sun T, Jain T, Prinz B, Yu TY, Torrey J, Thomas J, Bobrowicz P, Vasquez M, Wittrup KD, Krauland E. Protein Eng Des Sel. pubmed:24046438;  doi:10.1093/protein/gzt047

12. Rational Design of a Biomimetic Cell Penetrating Peptide Library. Karagiannis ED, Urbanska AM, Sahay G, Pelet JM, Jhunjhunwala S, Langer R, Anderson DG. ACS Nano. pubmed:24047542;  doi:10.1021/nn4027382

13. Stretchable Polymeric Multielectrode Array for Conformal Neural Interfacing. Guo L, Ma M, Zhang N, Langer R, Anderson DG. Adv Mater. pubmed:24150828;  doi:10.1002/adma.201304140

14. Osteotropic Therapy via Targeted Layer-by-Layer Nanoparticles. Morton SW, Shah NJ, Quadir MA, Deng ZJ, Poon Z, Hammond PT. Adv Healthc Mater. pubmed:24124132;  doi:10.1002/adhm.201300465

15. HIV-1 infection induces strong production of IP-10 through TLR7/9-dependent pathways. Simmons RP, Scully EP, Groden EE, Arnold KB, Chang JJ, Lane K, Lifson J, Rosenberg E, Lauffenburger DA, Altfeld M. AIDS. pubmed:24096630;  doi:10.1097/01.aids.0000432455.06476.bc

16. Crystal Structure of an HSA/FcRn Complex Reveals Recycling by Competitive Mimicry of HSA Ligands at a pH-Dependent Hydrophobic Interface. Schmidt MM, Townson SA, Andreucci AJ, King BM, Schirmer EB, Murillo AJ, Dombrowski C, Tisdale AW, Lowden PA, Masci AL, Kovalchin JT, Erbe DV, Wittrup KD, Furfine ES, Barnes TM. Structure. pubmed:24120761;  doi:10.1016/j.str.2013.08.022

17. Synergistic effect of local endothelial shear stress and systemic hypercholesterolemia on coronary atherosclerotic plaque progression and composition in pigs. Koskinas KC, Chatzizisis YS, Papafaklis MI, Coskun AU, Baker AB, Jarolim P, Antoniadis A, Edelman ER, Stone PH, Feldman CL. Int J Cardiol. pubmed:24148915;  doi:10.1016/j.ijcard.2013.10.021

18. Layer-by-Layer Nanoparticles for Systemic Codelivery of an Anticancer Drug and siRNA for Potential Triple-Negative Breast Cancer Treatment. Deng ZJ, Morton SW, Ben-Akiva E, Dreaden EC, Shopsowitz KE, Hammond PT. ACS Nano. pubmed:24144228;  doi:10.1021/nn4047925

19. A developmentally regulated translational control pathway establishes the meiotic chromosome segregation pattern. Berchowitz LE, Gajadhar AS, van Werven FJ, De Rosa AA, Samoylova ML, Brar GA, Xu Y, Xiao C, Futcher B, Weissman JS, White FM, Amon A. Genes Dev. pubmed:24115771;  doi:10.1101/gad.224253.113

20. Engineering synthetic vaccines using cues from natural immunity. Irvine DJ, Swartz MA, Szeto GL. Nat Mater. pubmed:24150416;  doi:10.1038/nmat3775

21. Enhancing tumor cell response to chemotherapy through nanoparticle-mediated codelivery of siRNA and cisplatin prodrug. Xu X, Xie K, Zhang XQ, Pridgen EM, Park GY, Cui DS, Shi J, Wu J, Kantoff PW, Lippard SJ, Langer R, Walker GC, Farokhzad OC. Proc Natl Acad Sci U S A. pubmed:24167294;  doi:10.1073/pnas.1303958110

22. Translating materials design to the clinic. Hubbell JA, Langer R. Nat Mater. pubmed:24150414;  doi:10.1038/nmat3788

23. Delivery materials for siRNA therapeutics. Kanasty R, Dorkin JR, Vegas A, Anderson D. Nat Mater. pubmed:24150415;  doi:10.1038/nmat3765

24. 3' UTR-isoform choice has limited influence on the stability and translational efficiency of most mRNAs in mouse fibroblasts. Spies N, Burge CB, Bartel DP. Genome Res. pubmed:24072873;  doi:10.1101/gr.156919.113

25. Global analyses of UPF1 binding and function reveals expanded scope of nonsense-mediated mRNA decay. Hurt JA, Robertson AD, Burge CB. Genome Res. pubmed:23766421;  doi:10.1101/gr.157354.113

26. The Somatic Genomic Landscape of Glioblastoma. Brennan CW, Verhaak RG, McKenna A, Campos B, Noushmehr H, Salama SR, Zheng S, Chakravarty D, Sanborn JZ, Berman SH, Beroukhim R, Bernard B, Wu CJ, Genovese G, Shmulevich I, Barnholtz-Sloan J, Zou L, Vegesna R, Shukla SA, Ciriello G, Yung WK, Zhang W, Sougnez C, Mikkelsen T, Aldape K, Bigner DD, Van Meir EG, Prados M, Sloan A, Black KL, Eschbacher J, Finocchiaro G, Friedman W, Andrews DW, Guha A, Iacocca M, O'Neill BP, Foltz G, Myers J, Weisenberger DJ, Penny R, Kucherlapati R, Perou CM, Hayes DN, Gibbs R, Marra M, Mills GB, Lander E, Spellman P, Wilson R, Sander C, Weinstein J, Meyerson M, Gabriel S, Laird PW, Haussler D, Getz G, Chin L. Cell. pubmed:24120142;  doi:10.1016/j.cell.2013.09.034

27. Genomic analysis identifies targets of convergent positive selection in drug-resistant Mycobacterium tuberculosis. Farhat MR, Shapiro BJ, Kieser KJ, Sultana R, Jacobson KR, Victor TC, Warren RM, Streicher EM, Calver A, Sloutsky A, Kaur D, Posey JE, Plikaytis B, Oggioni MR, Gardy JL, Johnston JC, Rodrigues M, Tang PK, Kato-Maeda M, Borowsky ML, Muddukrishna B, Kreiswirth BN, Kurepina N, Galagan J, Gagneux S, Birren B, Rubin EJ, Lander ES, Sabeti PC, Murray M. Nat Genet. pubmed:23995135;  doi:10.1038/ng.2747

28. Inhibition of Megakaryocyte Development in the Bone Marrow Underlies Dengue Virus-Induced Thrombocytopenia in Humanized Mice. Sridharan A, Chen Q, Tang KF, Ooi EE, Hibberd ML, Chen J. J Virol. pubmed:23966397;  doi:10.1128/JVI.01156-13

29. Criteria for the use of omics-based predictors in clinical trials. McShane LM, Cavenagh MM, Lively TG, Eberhard DA, Bigbee WL, Williams PM, Mesirov JP, Polley MY, Kim KY, Tricoli JV, Taylor JM, Shuman DJ, Simon RM, Doroshow JH, Conley BA. Nature. pubmed:24132288;  doi:10.1038/nature12564

30. A set of genes critical to development is epigenetically poised in mouse germ cells from fetal stages through completion of meiosis. Lesch BJ, Dokshin GA, Young RA, McCarrey JR, Page DC. Proc Natl Acad Sci U S A. pubmed:24043772;  doi:10.1073/pnas.1315204110

31. The Role of miRNAs in Regulating Gene Expression Networks. Gurtan AM, Sharp PA. J Mol Biol. pubmed:23500488;  doi:10.1016/j.jmb.2013.03.007

32. Antigen-specific B-cell receptor sensitizes B cells to infection by influenza virus. Dougan SK, Ashour J, Karssemeijer RA, Popp MW, Avalos AM, Barisa M, Altenburg AF, Ingram JR, Cragnolini JJ, Guo C, Alt FW, Jaenisch R, Ploegh HL. Nature. pubmed:24141948;  doi:10.1038/nature12637

33. Multiplexed activation of endogenous genes by CRISPR-on, an RNA-guided transcriptional activator system. Cheng AW, Wang H, Yang H, Shi L, Katz Y, Theunissen TW, Rangarajan S, Shivalila CS, Dadon DB, Jaenisch R. Cell Res. pubmed:23979020;  doi:10.1038/cr.2013.122

34. Gene signatures related to B-cell proliferation predict influenza vaccine-induced antibody response. Tan Y, Tamayo P, Nakaya H, Pulendran B, Mesirov JP, Haining WN. Eur J Immunol. pubmed:24136404;  doi:10.1002/eji.201343657

35. Integrative radiogenomic profiling of squamous cell lung cancer. Abazeed ME, Adams DJ, Hurov KE, Tamayo P, Creighton CJ, Sonkin D, Giacomelli AO, Du C, Fries DF, Wong KK, Mesirov JP, Loeffler JS, Schreiber SL, Hammerman PS, Meyerson M. Cancer Res. pubmed:23980093;  doi:10.1158/0008-5472.CAN-13-1616

36. Intrachromosomal homologous recombination between inverted amplicons on opposing Y-chromosome arms. Lange J, Noordam MJ, van Daalen SK, Skaletsky H, Clark BA, Macville MV, Page DC, Repping S. Genomics. pubmed:23643616;  doi:10.1016/j.ygeno.2013.04.018

37. Super-Enhancers in the Control of Cell Identity and Disease. Hnisz D, Abraham BJ, Lee TI, Lau A, Saint-Andre V, Sigova AA, Hoke HA, Young RA. Cell. pubmed:24119843;  doi:10.1016/j.cell.2013.09.053

38. Identification and Rescue of alpha-Synuclein Toxicity in Parkinson Patient-Derived Neurons. Chung CY, Khurana V, Auluck PK, Tardiff DF, Mazzulli JR, Soldner F, Baru V, Lou Y, Freyzon Y, Cho S, Mungenast AE, Muffat J, Mitalipova M, Pluth MD, Jui NT, Schule B, Lippard SJ, Tsai LH, Krainc D, Buchwald SL, Jaenisch R, Lindquist S. Science. pubmed:24158904;  doi:10.1126/science.1245296

39. Global Transcriptional and Translational Repression in Human-Embryonic-Stem-Cell-Derived Rett Syndrome Neurons. Li Y, Wang H, Muffat J, Cheng AW, Orlando DA, Loven J, Kwok SM, Feldman DA, Bateup HS, Gao Q, Hockemeyer D, Mitalipova M, Lewis CA, Vander Heiden MG, Sur M, Young RA, Jaenisch R. Cell Stem Cell. pubmed:24094325;  doi:10.1016/j.stem.2013.09.001

40. Sequential Reassortments Underlie Diverse Influenza H7N9 Genotypes in China. Wu A, Su C, Wang D, Peng Y, Liu M, Hua S, Li T, Gao GF, Tang H, Chen J, Liu X, Shu Y, Peng D, Jiang T. Cell Host Microbe. pubmed:24055604;  doi:10.1016/j.chom.2013.09.001

41. Evidence for Scgb1a1 Cells in the Generation of p63 Cells in the Damaged Lung Parenchyma. Zheng D, Yin L, Chen J. Am J Respir Cell Mol Biol. pubmed:24134540;  doi:10.1165/rcmb.2013-0327OC

42. No bull: Upholding community standards in public sharing of biological datasets. Hughes JF, Skaletsky H, Bellott DW, Chowdhary BP, Warren WC, Worley KC, Wilson RK, Gibbs RA, Page DC. Proc Natl Acad Sci U S A. pubmed:24173037;  doi:10.1073/pnas.1315122110

43. Renal tubular Sirt1 attenuates diabetic albuminuria by epigenetically suppressing Claudin-1 overexpression in podocytes. Hasegawa K, Wakino S, Simic P, Sakamaki Y, Minakuchi H, Fujimura K, Hosoya K, Komatsu M, Kaneko Y, Kanda T, Kubota E, Tokuyama H, Hayashi K, Guarente L, Itoh H. Nat Med. pubmed:24141423;  doi:10.1038/nm.3363

44. Mapping differential interactomes by affinity purification coupled with data-independent mass spectrometry acquisition. Lambert JP, Ivosev G, Couzens AL, Larsen B, Taipale M, Lin ZY, Zhong Q, Lindquist S, Vidal M, Aebersold R, Pawson T, Bonner R, Tate S, Gingras AC. Nat Methods. pubmed:24162924;  doi:10.1038/nmeth.2702

45. Calorie restriction and sirtuins revisited. Guarente L. Genes Dev. pubmed:24115767;  doi:10.1101/gad.227439.113

46. The many sides of CIN. Knouse KA, Amon A. Nat Rev Mol Cell Biol. pubmed:24061225;  doi:10.1038/nrm3666

47. Yeast Reveal a "Druggable" Rsp5/Nedd4 Network that Ameliorates alpha-Synuclein Toxicity in Neurons. Tardiff DF, Jui NT, Khurana V, Tambe MA, Thompson ML, Chung CY, Kamadurai HB, Kim HT, Lancaster AK, Caldwell KA, Caldwell GA, Rochet JC, Buchwald SL, Lindquist S. Science. pubmed:24158909;  doi:10.1126/science.1245321

48. The Folliculin Tumor Suppressor Is a GAP for the RagC/D GTPases That Signal Amino Acid Levels to mTORC1. Tsun ZY, Bar-Peled L, Chantranupong L, Zoncu R, Wang T, Kim C, Spooner E, Sabatini DM. Mol Cell. pubmed:24095279;  doi:10.1016/j.molcel.2013.09.016

49. A Central Role for mTOR in Lipid Homeostasis. Lamming DW, Sabatini DM. Cell Metab. pubmed:23973332;  doi:10.1016/j.cmet.2013.08.002

50. PKM2 Isoform-Specific Deletion Reveals a Differential Requirement for Pyruvate Kinase in Tumor Cells. Israelsen WJ, Dayton TL, Davidson SM, Fiske BP, Hosios AM, Bellinger G, Li J, Yu Y, Sasaki M, Horner JW, Burga LN, Xie J, Jurczak MJ, Depinho RA, Clish CB, Jacks T, Kibbey RG, Wulf GM, Di Vizio D, Mills GB, Cantley LC, Vander Heiden MG. Cell. pubmed:24120138;  doi:10.1016/j.cell.2013.09.025

51. Small-Molecule Allosteric Activators of Sirtuins. Sinclair DA, Guarente L. Annu Rev Pharmacol Toxicol. pubmed:24160699;  doi:10.1146/annurev-pharmtox-010611-134657

52. The DivJ, CbrA and PleC system controls DivK phosphorylation and symbiosis in Sinorhizobium meliloti. Pini F, Frage B, Ferri L, De Nisco NJ, Mohapatra SS, Taddei L, Fioravanti A, Dewitte F, Galardini M, Brilli M, Villeret V, Bazzicalupo M, Mengoni A, Walker GC, Becker A, Biondi EG. Mol Microbiol. pubmed:23909720;  doi:10.1111/mmi.12347

53. Synthesis and Characterization of Pt(IV) Fluorescein Conjugates to Investigate Pt(IV) Intracellular Transformations. Song Y, Suntharalingam K, Yeung J, Royzen M, Lippard SJ. Bioconjug Chem. pubmed:23957697;  doi:10.1021/bc400281a

54. Analysis of In Vitro Insulin-Resistance Models and Their Physiological Relevance to In Vivo Diet-Induced Adipose Insulin Resistance. Lo KA, Labadorf A, Kennedy NJ, Han MS, Yap YS, Matthews B, Xin X, Sun L, Davis RJ, Lodish HF, Fraenkel E. Cell Rep. pubmed:24095730;  doi:10.1016/j.celrep.2013.08.039

55. An Integrin-Linked Machinery of Cytoskeletal Regulation that Enables Experimental Tumor Initiation and Metastatic Colonization. Shibue T, Brooks MW, Weinberg RA. Cancer Cell. pubmed:24035453;  doi:10.1016/j.ccr.2013.08.012

56. Peptide-Based Inhibitors of Plk1 Polo-box Domain Containing Mono-anionic Phosphothreonine Esters and Their Pivaloyloxymethyl Prodrugs. Qian WJ, Park JE, Lim D, Park SY, Lee KW, Yaffe MB, Lee KS, Burke TRJr. Chem Biol. pubmed:24120332;  doi:10.1016/j.chembiol.2013.09.005

57. Structure of the Toxoplasma gondii ROP18 kinase domain reveals a second ligand binding pocket required for acute virulence. Lim D, Gold DA, Julien L, Rosowski EE, Niedelman W, Yaffe MB, Saeij JP. J Biol Chem. pubmed:24129568;  doi:10.1074/jbc.M113.523266

58. Dampening of expression oscillations by synchronous regulation of a microRNA and its target. Kim DH, Grun D, van Oudenaarden A. Nat Genet. pubmed:24036951;  doi:10.1038/ng.2763

59. Highly expressed loci are vulnerable to misleading ChIP localization of multiple unrelated proteins. Teytelman L, Thurtle DM, Rine J, van Oudenaarden A. Proc Natl Acad Sci U S A. pubmed:24173036;  doi:10.1073/pnas.1316064110