Center for Genome Regulation

A FONDAP Center of Excellence

"Exploring the Genomic Landscape of Chile"

2017 Publications

1.     Garrido V, Mendoza-Torres E, Riquelme J, Diaz A, Pizarro M, Bustamante M, Chávez MN, Ocaranza MP, Mellado R, Corbalan R, Allende ML, Lavandero S. 2017. Novel Therapies Targeting Cardioprotection and Regeneration. Curr Pharm Design 23(18):2592-2615.

     2.     Saez-Aguayo, S.,  Rautengarten,  C., Temple, H., Sanhueza, D., Ejsmentewicz,  T., Sandoval-Ibañez, O., Doñas,  D., Parra-Rojas, JP., Ebert, B., Lehner, A., Mollet, J-C., Dupree, P., Scheller, H., , Heazlewood, J., Reyes, F. and Orellana, A. 2016. UUAT1 Is a Golgi-Localized UDP-Uronic Acid Transporter that Modulates the Polysaccharide Composition of Arabidopsis Seed Mucilage. Plant Cell 29(1):129-143.

     3.     Paredes-Zúñiga S, Morales RA, Muñoz-Sánchez S, Muñoz-Montecinos C, Parada M, Tapia K, Rubilar C, Allende ML* , Peña OA*. 2017. CXCL12a/CXCR4b acts to retain neutrophils in caudal hematopoietic tissue and to antagonize recruitment to an injury site in the zebrafish larva. Immunogenetics 69(5):341-349.

     4.     Varas MA, Fariña A, Díaz-Pascual F, Ortíz-Severín J, Marcoleta AE, Allende ML, Santiviago CA, Chávez FP. 2017. Live cell imaging of Salmonella Typhimurium interaction with zebrafish larvae after injection and immersion delivery methods. J Microbiol Methods 135:20-25.

     5.     Hefzi H, Ang KS, Hanscho M, Bordbar A, Ruckerbauer D, Lakshmanan M, Orellana CA, Baycin-Hizal D, Huang Y, Ley D, Martinez VS, Kyriakopoulos S, Jiménez NE, Zielinski DC, Quek LE, Wulff T, Arnsdorf J, Li S, Lee JS, Paglia G, Loira N, Spahn PN, Pedersen LE, Gutierrez JM, King ZA, Lund AM, Nagarajan H, Thomas A, Abdel-Haleem AM, Zanghellini J, Kildegaard HF, Voldborg BG, Gerdtzen ZP, Betenbaugh MJ, Palsson BO, Andersen MR, Nielsen LK, Borth N, Lee DY, Lewis NE.A Consensus Genome-scale Reconstruction of Chinese Hamster Ovary Cell Metabolism. 2016. Cell Syst. 3(5):434-443.e8. doi: 10.1 2016. 016/j.cels.2016.10.020.

     6.     Bustos FJ, Jury N, Martinez P, Ampuero E, Campos M, Abarzúa S, Jaramillo K, Ibing S, Mardones MD, Haensgen H, Kzhyshkowska J, Tevy MF, Neve R, Sanhueza M, Varela-Nallar L, Montecino M, van Zundert B. 2017. NMDA Receptor Subunit Composition Controls Dendritogenesis of Hippocampal Neurons through CAMKII, CREB-P and H3K27ac. J Cell Physiol. 232: 3677-3692.

     7.     Dudakovic A, Gluscevic M, Paradise CR, Dudakovic H, Khani F, Thaler R, Ahmed FS, Li X, Dietz AB, Stein GS, Montecino MA, Deyle DR, Westendorf JJ, van Wijnen AJ. 2017. Profiling of human epigenetic regulators using a semi-automated real-time qPCR platform validated by next generation sequencing. Gene. 609:28-37.

     8.     Undurraga SF, Ibarra-Henríquez C, Fredes I, Álvarez JM, Gutiérrez RA. 2017. Nitrate signaling and early responses in Arabidopsis roots. J Exp Bot. 2017 Mar 28. doi: 10.1093/jxb/erx041.

     9.     Nuñez IN, Matute TF, Del Valle ID, Kan A, Choksi A, Endy D, Haseloff J, Rudge TJ, Federici F. 2017. Artificial Symmetry-Breaking for Morphogenetic Engineering Bacterial Colonies. ACS Synth Biol. 6:256-265.

     10.     De la Paz J, Beiza N, Paredes-Zúñiga S, Hoare M, Allende ML. 2017. Triazole fungicides inhibit zebrafish hatching by blocking the secretory function of hatching gland cells. Int J Mol Sci 18:710.

     11.     Pastenes L, Valdivieso C, Di Genova A, Travisany D, Montecino M, Orellana A, González M, Gutiérrez RA, Allende ML, Maass A, Méndez MA. 2017. Transcriptome analysis provides insight on local temperature adaptation to geothermal streams in larvae of the Andean toad Rhinella spinulosa (Anura, Bufonidae). Sci Rep 16;7(1):1966.

     12.     Varas MA, Ortíz-Severín J, Marcoleta AE, Díaz-Pascual F, Allende ML, Santiviago CA, Chávez FP. 2017. Salmonella Typhimurium induce cloacitis-like symptoms in zebrafish larvae. Microb Pathog 107:317-320.

     13.     Naour S, Espinoza BM, Aedo JE, Zuloaga R, Maldonado J, Bastias-Molina M, Silva H, Meneses C, Gallardo-Escarate C, Molina A, Valdés JA. 2017. Transcriptomic analysis of the hepatic response to stress in the red cusk-eel (Genypterus chilensis): Insights into lipid metabolism, oxidative stress and liver steatosis. PLoS One. 12(4):e0176447.

     14.     Rautengarten C, Birdseye D, Pattathil S, McFarlane HE, Saez-Aguayo S, Orellana A, Persson S, Hahn MG, Scheller HV, Heazlewood JL, Ebert B. 2017. The elaborate route for UDP-arabinose delivery into the Golgi of plants. Proc Natl Acad Sci U S A. 114(16):4261-4266.

     15.     Ibar C, Glavic Á. 2017. Drosophila p115 is required for Cdk1 activation and G2/M cell cycle transition. Mech Dev. 2017 Apr 8. pii: S0925-4773(17)30078-3. doi: 10.1016/j.mod.2017.04.001.

     16.     Castillo K, Rojas-Rivera D, Lisbona F, Caballero B, Nassif M, Court FA, Schuck S, Ibar C, Walter P, Sierralta J, Glavic A, Hetz C. 2017. BAX inhibitor-1 regulates autophagy by controlling the IRE1α branch of the unfolded protein response. EMBO J. 2017 Jun 1;36(11):1640.

     17.     Macqueen DJ, Primmer CR, Houston RD, Nowak BF, Bernatchez L, Bergseth S, Davidson WS, Gallardo-Escárate C, Goldammer T, Guiguen Y, Iturra P, Kijas JW, Koop BF, Lien S, Maass A, Martin SAM, McGinnity P, Montecino M, Naish KA, Nichols KM, Ólafsson K, Omholt SW, Palti Y, Plastow GS, Rexroad CE Rd, Rise ML, Ritchie RJ, Sandve SR, Schulte PM, Tello A, Vidal R, Vik JO, Wargelius A, Yáñez JM; FAASG Consortium. 2017. Functional Annotation of All Salmonid Genomes (FAASG): an international initiative supporting future salmonid research, conservation and aquaculture. BMC Genomics. 18(1):484.

     18.     Díaz-Pascual F, Ortíz-Severín J, Varas MA, Allende ML, Chávez FP. 2017. In vivo Host-Pathogen Interaction as Revealed by Global Proteomic Profiling of Zebrafish Larvae. Front Cell Infect Microbiol. 7:334.

     19.     Díaz-Jiménez D, Núñez L, De la Fuente M, Dubois-Camacho K, Sepúlveda H, Montecino M, Torres-Riquelme A, García-González P, Chnaiderman J, Vossenkamper A, MacDonald TT, Simian D, González MJ, Cidlowski JA, Quera R, Hermoso MA. 2017. A functional IL1RL1 variant regulates corticosteroid-induced sST2 expression in ulcerative colitis. Sci Rep. 7:10180.

     20.     Sepulveda H, Villagra A, Montecino M. 2017. Tet-mediated DNA demethylation is required for SWI/SNF-dependent chromatin remodeling and histone modifying activities that trigger expression of the Sp7 osteoblast master gene during mesenchymal lineage commitment. Mol Cell Biol. doi: 10.1128/MCB.00177-17.

     21.     Canales J, Contreras-López O, Álvarez JM, Gutiérrez RA. 2017. Nitrate induction of root hair density is mediated by TGA1/TGA4 and CPC transcription factors in Arabidopsis thaliana. Plant J. doi: 10.1111/tpj.13656.

     22.     Armijo G, Gutiérrez RA. 2017. Emerging Players in the Nitrate Signaling Pathway. Mol Plant. 10:1019-1022.

     23.     Loira N, Mendoza S, Paz Cortés M, Rojas N, Travisany D, Genova AD, Gajardo N, Ehrenfeld N, Maass A. 2017. Reconstruction of the microalga Nannochloropsis salina genome-scale metabolic model with applications to lipid production. BMC Syst Biol. 11:66. 

     24.     Alberti A, Poulain J, Engelen S, Labadie K, Romac S, Ferrera I, Albini G, Aury JM, Belser C, Bertrand A, Cruaud C, Da Silva C, Dossat C, Gavory F, Gas S, Guy J, Haquelle M, Jacoby E, Jaillon O, Lemainque A, Pelletier E, Samson G, Wessner M; Genoscope Technical Team, Acinas SG, Royo-Llonch M, Cornejo-Castillo FM, Logares R, Fernández-Gómez B, Bowler C, Cochrane G, Amid C, Hoopen PT, De Vargas C, Grimsley N, Desgranges E, Kandels-Lewis S, Ogata H, Poulton N, Sieracki ME, Stepanauskas R, Sullivan MB, Brum JR, Duhaime MB, Poulos BT, Hurwitz BL; Tara Oceans Consortium Coordinators, Pesant S, Karsenti E, Wincker P. 2017. Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition. Sci Data. 4:170093. doi: 10.1038/sdata.2017.93.

     25.     Sepulveda H, Aguilar R, Prieto CP, Bustos F, Aedo S, Lattus J, van Zundert B, Palma V, Montecino M. 2017. Epigenetic Signatures at the RUNX2-P1 and Sp7 Gene Promoters Control Osteogenic Lineage Commitment of Umbilical Cord-Derived Mesenchymal Stem Cells. J Cell Physiol. 232:2519-2527. 

     26.     Bustos F, Sepúlveda H, Prieto CP, Carrasco M, Díaz L, Palma J, Lattus J, Montecino M, Palma V. 2017. Runt-Related Transcription Factor 2 Induction During Differentiation of Wharton's Jelly Mesenchymal Stem Cells to Osteoblasts Is Regulated by Jumonji AT-Rich Interactive Domain 1B Histone Demethylase. Stem Cells. 2017 Sep 12. doi: 10.1002/stem.2704. 

     27.     Acuña M, Castro-Fernández V, Latorre M, Castro J, Schuchman EH, Guixé V, González M, Zanlungo S. 2017. Structural and functional analysis of the ASM p.Ala359Asp mutant that causes acid sphingomyelinase deficiency. Biochem Biophys Res Commun. 2016 Oct 21;479(3):496-501.

     28.     Aballai V, Aedo JE, Maldonado J, Bastias-Molina M, Silva H, Meneses C, Boltaña S, Reyes A, Molina A, Valdés JA. 2017. RNA-seq analysis of the head-kidney transcriptome response to handling-stress in the red cusk-eel (Genypterus chilensis). Comp Biochem Physiol Part D Genomics Proteomics. 24:111-117.

     29.     Bustos FJ, Ampuero E, Jury N, Aguilar R, Falahi F, Toledo J, Ahumada J, Lata J, Cubillos P, Henríquez B, Guerra MV, Stehberg J, Neve RL, Inestrosa NC, Wyneken U, Fuenzalida M, Härtel S, Sena-Esteves M, Varela-Nallar L, Rots MG, Montecino M, van Zundert B. 2017. Epigenetic editing of the Dlg4/PSD95 gene improves cognition in aged and Alzheimer's disease mice. Brain. 140(12):3252-3268. doi: 10.1093/brain/awx272. 

     30.     Cortés MP, Mendoza SN, Travisany D, Gaete A, Siegel A, Cambiazo V and Maass A. 2017. Analysis of Piscirickettsia salmonis Metabolism Using Genome-Scale Reconstruction, Modeling, and Testing. Front. Microbiol. 8:2462. doi: 10.3389/fmicb.2017.02462.

     31.     Nuñez-Badinez P, Sepúlveda H, Diaz E, Greffrath W, Treede RD, Stehberg J, Montecino M, van Zundert B. 2017. Variable transcriptional responsiveness of the P2 × 3 receptor gene during CFA-induced inflammatory hyperalgesia. J Cell Biochem. 2017 Dec 8. doi: 10.1002/jcb.26534. 

     32.     Friesner J, Assmann SM, Bastow R, Bailey-Serres J, Beynon J, Brendel V, Buell CR, Bucksch A, Busch W, Demura T, Dinneny JR, Doherty CJ, Eveland AL, Falter-Braun P, Gehan MA, Gonzales M, Grotewold E, Gutierrez R, Kramer U, Krouk G, Ma S, Markelz RJC, Megraw M, Meyers BC, Murray JAH, Provart NJ, Rhee S, Smith R, Spalding EP, Taylor C, Teal TK, Torii KU, Town C, Vaughn M, Vierstra R, Ware D, Wilkins O, Williams C, Brady SM. 2017. The Next Generation of Training for Arabidopsis Researchers: Bioinformatics and Quantitative Biology. Plant Physiol. 2017 Dec;175(4):1499-1509. doi: 10.1104/pp.17.01490. 

     33.     Nuñez I, Matute T, Herrera R, Keymer J, Marzullo T, Rudge T, Federici F. 2017. Low cost and open source multi-fluorescence imaging system for teaching and research in biology and bioengineering. PLoS One. 2017 Nov 15;12(11):e0187163. doi: 10.1371/journal.pone.0187163.

     34.     Thomas F, Bordron P, Eveillard D, Michel G. 2017. Gene Expression Analysis of Zobellia galactanivorans during the Degradation of Algal Polysaccharides Reveals both Substrate-Specific and Shared Transcriptome-Wide Responses. Front Microbiol. 2017 Sep 21;8:1808. doi: 10.3389/fmicb.2017.01808. 

     35.     Correa K, Lhorente JP, Bassini L, López ME, Di Genova A, Maass A, Davidson WS, Yáñez JM. 2017. Genome wide association study for resistance to Caligus rogercresseyi in Atlantic salmon (Salmo salar L.) using a 50K SNP genotyping array. Aquaculture, 472: 61-65. https://doi.org/10.1016/j.aquaculture.2016.04.008.

     36.     Gras DE, Vidal EA, Undurraga SF, Riveras E, Moreno S, Domínguez-Figueroa J, Alabadi D, Blázquez M, Medina J, and Gutiérrez RA (2017). SMZ/SNZ and gibberellin signaling are required for nitrate-elicited delay of flowering time in Arabidopsis thaliana. J Exp Bot, erx423, https://doi.org/10.1093/jxb/erx423.


NON ISI



     37.     Rojas-Benítez D, Eggers C, Glavic A. 2017. Modulation of the Proteostasis Machinery to Overcome Stress Caused by Diminished Levels of  t6A-Modified tRNAs in Drosophila. Biomolecules. 7(1).