Progress: November 2013

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Publications Citing Koch Institute Faculty Members

1. Microfluidic Platform for Combinatorial Synthesis and Optimization of Targeted Nanoparticles for Cancer Therapy. Valencia PM, Pridgen EM, Rhee M, Langer R, Farokhzad OC, Karnik R. ACS Nano. pubmed:24215426;  doi:10.1021/nn403370e

2. Biologically enhanced cathode design for improved capacity and cycle life for lithium-oxygen batteries. Oh D, Qi J, Lu YC, Zhang Y, Shao-Horn Y, Belcher AM. Nat Commun. pubmed:24220635;  doi:10.1038/ncomms3756

3. Nanotechnology: emerging tools for biology and medicine. Wong IY, Bhatia SN, Toner M. Genes Dev. pubmed:24240230;  doi:10.1101/gad.226837.113

4. Co-regulation of primary mouse hepatocyte viability and function by oxygen and matrix. Buck LD, Inman SW, Rusyn I, Griffith LG. Biotechnol Bioeng. pubmed:24222008;  doi:10.1002/bit.25152

5. 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

6. Hypoxia promotes liver stage malaria infection in primary human hepatocytes in vitro. Ng S, March S, Galstian A, Hanson K, Carvalho T, Mota MM, Bhatia SN. Dis Model Mech. pubmed:24291761;  doi:10.1242/dmm.013490

7. Network analysis of differential Ras isoform mutation effects on intestinal epithelial responses to TNF-alpha. Lau KS, Schrier SB, Gierut J, Lyons J, Lauffenburger DA, Haigis KM. Integr Biol (Camb). pubmed:24084984;  doi:10.1039/c3ib40062j

8. Transepithelial transport of fc-targeted nanoparticles by the neonatal fc receptor for oral delivery. Pridgen EM, Alexis F, Kuo TT, Levy-Nissenbaum E, Karnik R, Blumberg RS, Langer R, Farokhzad OC. Sci Transl Med. pubmed:24285486;  doi:10.1126/scitranslmed.3007049

9. 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

10. Immunogenicity of membrane-bound HIV-1 gp41 MPER segments is dominated by residue accessibility and modulated by stereochemistry. Kim M, Song L, Moon J, Sun ZY, Bershteyn A, Hanson M, Cain D, Goka S, Kelsoe G, Wagner G, Irvine D, Reinherz EL. J Biol Chem. pubmed:24047898;  doi:10.1074/jbc.M113.494609

11. 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

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

13. Genome-wide single-cell-level screen for protein abundance and localization changes in response to DNA damage in S cerevisiae. Mazumder A, Pesudo LQ, McRee S, Bathe M, Samson LD. Nucleic Acids Res. pubmed:23935119;  doi:10.1093/nar/gkt715

14. 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

15. 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

16. A catalytic independent function of the deubiquitinating enzyme USP14 regulates hippocampal short-term synaptic plasticity and vesicle number. Walters BJ, Hallengren JJ, Theile CS, Ploegh HL, Wilson SM, Dobrunz LE. J Physiol. pubmed:24218545;  doi:10.1113/jphysiol.2013.266015

17. 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

18. Global discovery of erythroid long non-coding RNAs reveals novel regulators of red cell maturation. Alvarez-Dominguez JR, Hu W, Yuan B, Shi J, Park SS, Gromatzky AA, van Oudenaarden A, Lodish HF. Blood. pubmed:24200680;  doi:10.1182/blood-2013-10-530683

19. Gene expression studies for the analysis of domoic acid production in the marine diatom Pseudo-nitzschia multiseries. Boissonneault KR, Henningsen BM, Bates SS, Robertson DL, Milton S, Pelletier J, Hogan DA, Housman DE. BMC Mol Biol. pubmed:24180290;  doi:10.1186/1471-2199-14-25

20. High-Resolution Mapping Reveals a Conserved, Widespread, Dynamic mRNA Methylation Program in Yeast Meiosis. Schwartz S, Agarwala SD, Mumbach MR, Jovanovic M, Mertins P, Shishkin A, Tabach Y, Mikkelsen TS, Satija R, Ruvkun G, Carr SA, Lander ES, Fink GR, Regev A. Cell. pubmed:24269006;  doi:10.1016/j.cell.2013.10.047

21. 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

22. Impaired Autophagy in the Lipid-Storage Disorder Niemann-Pick Type C1 Disease. Sarkar S, Carroll B, Buganim Y, Maetzel D, Ng AH, Cassady JP, Cohen MA, Chakraborty S, Wang H, Spooner E, Ploegh H, Gsponer J, Korolchuk VI, Jaenisch R. Cell Rep. pubmed:24290752;  doi:10.1016/j.celrep.2013.10.042

23. Type I Interferon Imposes a TSG101/ISG15 Checkpoint at the Golgi for Glycoprotein Trafficking during Influenza Virus Infection. Sanyal S, Ashour J, Maruyama T, Altenburg AF, Cragnolini JJ, Bilate A, Avalos AM, Kundrat L, Garcia-Sastre A, Ploegh HL. Cell Host Microbe. pubmed:24237697;  doi:10.1016/j.chom.2013.10.011

24. 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

25. Divergent transcription: a driving force for new gene origination?. Wu X, Sharp PA. Cell. pubmed:24267885;  doi:10.1016/j.cell.2013.10.048

26. 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

27. 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

28. 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

29. SIRT1 redresses tissue inhibitor of matrix metalloproteinase-1/matrix metalloproteinase-9 imbalance in the development of mouse emphysema and human COPD. Yao H, Hwang JW, Sundar IK, Friedman AE, McBurney MW, Guarente LP, Gu W, Kinnula VL, Rahman I. Am J Physiol Lung Cell Mol Physiol. pubmed:24039251;  doi:10.1152/ajplung.00249.2012

30. 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

31. 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

32. A Reversible Gene-Targeting Strategy Identifies Synthetic Lethal Interactions between MK2 and p53 in the DNA Damage Response In Vivo. Morandell S, Reinhardt HC, Cannell IG, Kim JS, Ruf DM, Mitra T, Couvillon AD, Jacks T, Yaffe MB. Cell Rep. pubmed:24239348;  doi:10.1016/j.celrep.2013.10.025

33. Tks5 and SHIP2 Regulate Invadopodium Maturation, but Not Initiation, in Breast Carcinoma Cells. Sharma VP, Eddy R, Entenberg D, Kai M, Gertler FB, Condeelis J. Curr Biol. pubmed:24206842;  doi:10.1016/j.cub.2013.08.044

34. Targeting Mitochondrial DNA with a Platinum-Based Anticancer Agent. Wisnovsky SP, Wilson JJ, Radford RJ, Pereira MP, Chan MR, Laposa RR, Lippard SJ, Kelley SO. Chem Biol. pubmed:24183971;  doi:10.1016/j.chembiol.2013.08.010

35. Synthetic Methods for the Preparation of Platinum Anticancer Complexes. Wilson JJ, Lippard SJ. Chem Rev. pubmed:24283498;  doi:10.1021/cr4004314

36. Monofunctional and Higher-Valent Platinum Anticancer Agents. Johnstone TC, Wilson JJ, Lippard SJ. Inorg Chem. pubmed:23738524;  doi:10.1021/ic400538c

37. The epigenetics of epithelial-mesenchymal plasticity in cancer. Tam WL, Weinberg RA. Nat Med. pubmed:24202396;  doi:10.1038/nm.3336

38. Characterization of a novel pyranopyridine inhibitor of the AcrAB efflux pump of Escherichia coli. Opperman TJ, Kwasny SM, Kim HS, Nguyen S, Houseweart C, D'Souza S, Walker GC, Peet NP, Nikaido H, Bowlin TL. Antimicrob Agents Chemother. pubmed:24247144;  doi:10.1128/AAC.01866-13

39. Enteric YaiW Is a Surface Exposed Outer Membrane Lipoprotein that Affects Sensitivity to an Antimicrobial Peptide. Arnold MF, Caro-Hernandez P, Tan K, Runti G, Wehmeier S, Scocchi M, Doerrler WT, Walker GC, Ferguson GP. J Bacteriol. pubmed:24214946;  doi:10.1128/JB.01179-13

40. Feedback Control of Gene Expression Variability in the Caenorhabditis elegans Wnt Pathway. Ji N, Middelkoop TC, Mentink RA, Betist MC, Tonegawa S, Mooijman D, Korswagen HC, van Oudenaarden A. Cell. pubmed:24209624;  doi:10.1016/j.cell.2013.09.060

41. 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

42. 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