Center for Genome Regulation

A FONDAP Center of Excellence

"Exploring the Genomic Landscape of Chile"

2018 Publications

ISI Papers


1.     Marcoleta AE, Varas MA, Ortiz-Severín J, Vásquez L, Berríos-Pastén C, Sabag AV, Chávez FP, Allende ML, Santiviago CA, Monasterio O, Lagos R. 2018. Evaluating Different Virulence Traits of Klebsiella pneumoniae Using Dictyostelium discoideum and Zebrafish Larvae as Host Models. Frontiers in Cellular and Infection Microbiology. 8:30. DOI=10.3389/fcimb.2018.00030  


     2.     Contreras EG, Sierralta J, Glavic A. 2018. p53 is required for brain growth but is dispensable for resistance to nutrient restriction during Drosophila larval development. PLoS One 13(4):e0194344. doi: 10.1371/journal.pone.0194344.


     3.     Gutierrez-Urrutia I, Miossec MJ, Valenzuela SL, Meneses C, Dos Santos VAPM, Castro-Nallar E, Poblete-Castro I. 2018. Genome sequence of two members of the chloroaromatic-degrading MT community: Pseudomonas reinekei MT1 and Achromobacter xylosoxidans MT3. J Biotechnol. 275:13-16. doi: 10.1016/j.jbiotec.2018.03.019. 


     4.     Mandakovic D, Rojas C, Maldonado J, Latorre M, Travisany D, Delage E, Bihouée A, Jean G, Díaz FP, Fernández-Gómez B, Cabrera P, Gaete A, Latorre C, Gutiérrez RA, Maass A, Cambiazo V, Navarrete SA, Eveillard D & González M. 2018. Structure and co-occurrence patterns in microbial communities under acute environmental stress reveal ecological factors fostering resilience. Sci Rep. 8:5875. DOI:10.1038/s41598-018-23931-0


     5.     Cifuentes-Esquivel N, Celiz-Balboa J, Henriquez-Valencia C, Mitina I, Arraño-Salinas P, Moreno AA, Meneses C, Blanco-Herrera F, Orellana A. 2018. bZIP17 regulates the expression of genes related to seed storage and germination, reducing seed susceptibility to osmotic stress. J Cell Biochem. 119(8):6857-6868. doi: 10.1002/jcb.26882.


     6.     Nardocci G, Carrasco ME, Acevedo E, Hodar C, Meneses C, Montecino M. 2018. Identification of a novel long noncoding RNA that promotes osteoblast differentiation. J Cell Biochem. 2018 119(9):7657-7666. doi: 10.1002/jcb.27113.


     7.     Di Genova A, Ruz GA, Sagot MF, Maass A. 2018. Fast-SG: an alignment-free algorithm for hybrid assembly. Gigascience. 7(5). doi: 10.1093/gigascience/giy048


     8.     Aite M, Chevallier M, Frioux C, Trottier C, Got J, Cortés MP, Mendoza SN, Carrier G, Dameron O, Guillaudeux N, Latorre M, Loira N, Markov GV, Maass A, Siegel A.  2018. Traceability, reproducibility and wiki-exploration for "à-la-carte" reconstructions of genome-scale metabolic models. PLoS Comput Biol. 14(5):e1006146. doi: 10.1371/journal.pcbi.1006146.


     9.     Hodar C, Cambiazo V. 2018. The dorsoventral patterning of Musca domestica embryos: insights into BMP/Dpp evolution from the base of the lower cyclorraphan flies. Evodevo. 9:13. doi: 10.1186/s13227-018-0102-5.


     10.     Mandakovic D, Maldonado J, Pulgar R, Cabrera P, Gaete A, Urtuvia V, Seeger M, Cambiazo V, González M. 2018. Microbiome analysis and bacterial isolation from Lejía Lake soil in Atacama Desert. Extremophiles. 22(4):665-673. doi: 10.1007/s00792-018-1027-6.


     11.     Cabezas CE, Briones AC, Aguirre C, Pardo-Esté C, Castro-Severyn J, Salinas CR, Baquedano MS, Hidalgo AA, Fuentes JA, Morales EH, Meneses CA, Castro-Nallar E, Saavedra CP.  2018. The transcription factor SlyA from Salmonella Typhimurium regulates genes in response to hydrogen peroxide and sodium hypochlorite. Res Microbiol. 169(6):263-278. doi: 10.1016/j.resmic.2018.04.003.


     12.     Zúñiga A, Fuente F, Federici F, Lionne C, Bônnet J, de Lorenzo V, González B. 2018. An Engineered Device for Indoleacetic Acid Production under Quorum Sensing Signals Enables Cupriavidus pinatubonensis JMP134 To Stimulate Plant Growth. ACS Synth Biol. 7(6):1519-1527. doi: 10.1021/acssynbio.8b00002.


     13.     Araya HF, Sepulveda H, Lizama CO, Vega OA, Jerez S, Briceño PF, Thaler R, Riester SM, Antonelli M, Salazar-Onfray F, Rodríguez JP, Moreno RD, Montecino M, Charbonneau M, Dubois CM, Stein GS, van Wijnen AJ, Galindo MA.  2018. Expression of the ectodomain-releasing protease ADAM17 is directly regulated by the osteosarcoma and bone-related transcription factor RUNX2. J Cell Biochem.119(10):8204-8219. doi: 10.1002/jcb.26832.


     14.     González-Itier S, Contreras EG, Larraín J, Glavic Á, Faunes F. 2018. A role for Lin-28 in growth and metamorphosis in Drosophila melanogaster. Mech Dev. 154:107-115. doi: 10.1016/j.mod.2018.06.002.


     15.     Awan B, Turkov D, Schumacher C, Jacobo A, McEnerney A, Xu G,  Park D, Kalomoiris S, Nolta J, Jao L-E, Allende ML, Lebrilla C, Fierro FA. 2018. FGF2 induces migration of human bone marrow stromal cells by increasing core-fucosylations on N-glycans of integrins. Stem Cell Reports 11(2):325-333. doi: 10.1016/j.stemcr.2018.06.007.


     16.     Alvarez M, Chavez MN, Miranda M, Aedo G, Allende ML, Egaña JT. 2018. A Novel In Vivo Model to Study Impaired Tissue Regeneration Mediated by Cigarette Smoke. Sci Rep. 19;8(1):10926. doi: 10.1038/s41598-018-28687-1.


     17.     Pouchucq L, Undurraga CA, Fuentes R, Cornejo M, Allende ML, Monasterio A. 2018. γ-Tubulin small complex formation is essential for early zebrafish embryogenesis. Mech. Dev. 154:145-152. doi: 10.1016/j.mod.2018.06.006.


     18.     Latorre M, Quenti D, Travisany D, Singh KV, Murray BE, Maass A, Cambiazo V. 2018. The Role of Fur in the Transcriptional and Iron Homeostatic Response of Enterococcus faecalis. Front. Microbiol. 9:1580. doi: 10.3389/fmicb.2018.01580.


     19.     Narum SR, Di Genova A, Micheletti SJ, Maass A. 2018. Genomic variation underlying complex life-history traits revealed by genome sequencing in Chinook salmon. Proc. R. Soc. B 285: 20180935. doi: 10.1098/rspb.2018.0935.


     20.     Urra H, Henriquez DR, Cánovas J, Villarroel-Campos D, Carreras-Sureda A, Pulgar E, Molina E, Hazari YM, Limia CM, Alvarez-Rojas S, Figueroa R, Vidal RL, Rodriguez DA, Rivera CA, Court FA, Couve A, Qi L, Chevet E, Akai R, Iwawaki T, Concha ML, Glavic Á, Gonzalez-Billault C, Hetz C. 2018. IRE1α governs cytoskeleton remodelling and cell migration through a direct interaction with filamin A. Nat Cell Biol. 2018 20(10):1228. doi: 10.1038/s41556-018-0186-0.


     21.     Rojas A, Sepúlveda H, Henríquez B, Aguilar R, Opazo T, Nardocci G, Bustos F, Lian JB, Stein JL, Stein GS, van Zundert B, van Wijnen AJ, Allende ML, Montecino M. 2018. Mll-COMPASS complexes mediate H3K4me3 enrichment and transcription of the osteoblast master gene Runx2/p57 in osteoblasts. J. Cell. Physiol. 234(5):6244-6253. doi: 10.1002/jcp.27355.


     22.     Muñoz-Llanos M, García-Pérez MA, Xu X, Tejos-Bravo M, Vidal EA, Moyano TC, Gutiérrez RA, Aguayo FI, Pacheco A, García-Rojo G, Aliaga E, Rojas PS, Cidlowski JA, Fiedler JL. 2018. MicroRNA Profiling and Bioinformatics Target Analysis in Dorsal Hippocampus of Chronically Stressed Rats: Relevance to Depression Pathophysiology. Front Mol Neurosci. 11:251. doi: 10.3389/fnmol.2018.00251.


     23.     Parada M, Clatworthy A, Hagendorn EJ, Ernst C, Henninger JE, Riquelme R, Jijón H, Villablanca EJ, Zon LI, Hung D, Allende ML. 2018. Generation of Mouse-Zebrafish Hematopoietic Tissue Chimeric Embryos by Xenotransplantation. Dis. Model. Mech. 11: dmm034876. doi: 10.1242/dmm.034876.


     24.     Bermúdez L, Del Pozo T, Lira BS, de Godoy F, Boos I, Romanó C, Previtali V, Almeida J, Bréhélin C, Asis R, Quadrana L, Demarco D, Alseekh S, Salinas Gamboa R, Pérez-Flores L, Dominguez PG, Rothan C, Fernie AR, González M, Stocker A, Hemmerle A, Clausen MH, Carrari F, Rossi M. 2018. A Tomato Tocopherol Binding Protein Sheds Light on Intracellular α-tocopherol Metabolism in Plants. Plant Cell Physiol. 59(11):2188-2203. doi: 10.1093/pcp/pcy191.


     25.     Nilo-Poyanco R, Vizoso P, Sanhueza D, Balic I, Meneses C, Orellana A, Campos-Vargas R. 2018. A Prunus persica genome-wide RNA-seq approach uncovers major differences in the transcriptome among chilling injury sensitive and non-sensitive varieties. Physiol Plant. doi: 10.1111/ppl.12831.


     26.     Meacham KA, Cortés MP, Wiggins EM, Maass A, Latorre M, Ralle M, Burkhead JL. 2018. Altered zinc balance in the Atp7b-/- mouse reveals a mechanism of copper toxicity in Wilson disease. Metallomics. 10(11):1595-1606. doi: 10.1039/c8mt00199e.


     27.     Contreras EG, Palominos T, Glavic Á, Brand AH, Sierralta J, Oliva C. 2018. The transcription factor SoxD controls neuronal guidance in the Drosophila visual system. Sci Rep. 8(1):13332. doi: 10.1038/s41598-018-31654-5.


     28.     Edwards SS, Delgado MG, Nader GPF, Piel M, Bellaïche Y, Lennon-Duménil AM, Glavic Á. 2018. An in vitro method for studying subcellular rearrangements during cell polarization in Drosophila melanogaster hemocytes. Mech Dev. 154:277-286. doi: 10.1016/j.mod.2018.08.003. 


     29.     Kan A, Del Valle I, Rudge T, Federici F, Haseloff J. 2018. Intercellular adhesion promotes clonal mixing in growing bacterial populations. J R Soc Interface. 15(146). pii: 20180406. doi: 10.1098/rsif.2018.0406.


     30.     Zepeda B, Olmedo P, Ejsmentewicz T, Sepúlveda P, Balic I, Balladares C, Delgado-Rioseco J, Fuentealba C, Moreno AA, Defilippi BG, Meneses C, Pedreschi R, Campos-Vargas R. 2018. Cell wall and metabolite composition of berries of Vitis vinifera (L.) cv. Thompson Seedless with different firmness. Food Chem. 268:492-497. doi: 10.1016/j.foodchem.2018.06.065.


     31.     López C, Aguilar R, Nardocci G, Cereceda K, Vander Stelt K, Slebe JC, Montecino M, Concha II. 2018. Wnt/β-catenin signaling enhances transcription of the CX43 gene in murine Sertoli cells. J Cell Biochem. doi: 10.1002/jcb.27973.


     32.     Delgado R, Delgado MG, Bastin-Héline L, Glavic A, O'Day PM, Bacigalupo J. 2018. Light-Induced Opening of the TRP Channel in Isolated Membrane Patches Excised from Photosensitive Microvilli from Drosophila Photoreceptors. Neuroscience. 396:66-72. doi: 10.1016/j.neuroscience.2018.11.017. 


     33.     Pollak B, Cerda A, Delmans M, Álamos S, Moyano T, West A, Gutiérrez RA, Patron N, Federici F, Haseloff J. 2018. Loop assembly: a simple and open system for recursive fabrication of DNA circuits. New Phytol. doi: 10.1111/nph.15625. 


     34.     Wood JR, Díaz FP, Latorre C, Wilmshurst JM, Burge OR, Gutiérrez RA. 2018. Plant pathogen responses to Late Pleistocene and Holocene climate change in the central Atacama Desert, Chile. Sci Rep. 8(1):17208. doi: 10.1038/s41598-018-35299-2.


     35.     Fredes I, Moreno S, Díaz FP, Gutiérrez RA. 2018. Nitrate signaling and the control of Arabidopsis growth and development. Curr Opin Plant Biol. 47:112-118. doi: 10.1016/j.pbi.2018.10.004.


     36.     Rodríguez FE, Laporte D, González A, Mendez KN, Castro-Nallar E, Meneses C, Huidobro-Toro JP, Moenne A. 2018. Copper-induced increased expression of genes involved in photosynthesis, carotenoid synthesis and C assimilation in the marine alga Ulva compressa. BMC Genomics. 19(1):829. doi: 10.1186/s12864-018-5226-4.


     37.     Arraño-Salinas P, Domínguez-Figueroa J, Herrera-Vásquez A, Zavala D, Medina J, Vicente-Carbajosa J, Meneses C, Canessa P, Moreno AA, Blanco-Herrera F. 2018. WRKY7, -11 and -17 transcription factors are modulators of the bZIP28 branch of the unfolded protein response during PAMP-triggered immunity in Arabidopsis thaliana. Plant Sci. 277:242-250. doi: 10.1016/j.plantsci.2018.09.019. 


     38.     Paredes-Zúñiga S, Trost N, De la Paz J, Alcayaga J, Allende ML. 2018. Behavioral effects of triadimefon in zebrafish are associated with alterations of the dopaminergic and serotonergic pathways. Prog. Neuro-Psychopharmacol. Biol. Psychiatry. 92:118-126. doi: 10.1016/j.pnpbp.2018.12.012.


     39.     Vidal EA, Moyano TC, Bustos BI, Pérez-Palma E, Moraga C, Riveras E, Montecinos A, Azócar L, Soto DC, Vidal M, Di Genova A, Puschel K, Nuernberg P, Buch S, Hampe J, Allende ML, Cambiazo V, González M, Hodar C, Montecino M, Muñoz-Espinoza C, Orellana A, Reyes-Jara A, Travisany D, Vizoso P, Moraga M, Eyheramendy S, Maass A, De Ferrari GV, Miquel JF, Gutiérrez RA. 2018. Whole Genome Sequence, Variant Discovery and Annotation in Mapuche-Huilliche Native South Americans. Sci. Rep. (In Press). bioRxiv 252619; doi: https://doi.org/10.1101/252619.


     40.     López ME, Benestan L, Moore JS, Perrier C, Gilbey J, Di Genova A, Maass A, Diaz D, Lhorente JP, Correa K, Neira R, Bernatchez L, Yáñez JM. 2018. Comparing genomic signatures of domestication in two Atlantic salmon (Salmo salar L.) populations with different geographical origins. Evol Appl. 12(1):137-156. doi: 10.1111/eva.12689.


     41.     Figueroa M, Fernandez V, Arenas-Salinas M, Ahumada D, Muñoz-Villagrán C, Cornejo F, Vargas E, Latorre M, Morales E, Vásquez C, Arenas F.  2018. Synthesis and Antibacterial Activity of Metal(loid) Nanostructures by Environmental Multi-Metal(loid) Resistant Bacteria and Metal(loid)-Reducing Flavoproteins. Front Microbiol. 9:959. doi: 10.3389/fmicb.2018.00959.


     42.     Hart A, Cortés MP, Latorre M, Martinez S. 2018. Codon usage bias reveals genomic adaptations to environmental conditions in an acidophilic consortium. PLoS One. 13(5):e0195869. doi: 10.1371/journal.pone.0195869.


Non-ISI:


     43.     Mardones W, Di Genova A, Cortés MP, Travisany D, Maass A & Eyzaguirre J. 2018. The genome sequence of the soft-rot fungus Penicillium purpurogenum reveals a high gene dosage for lignocellulolytic enzymes. Mycology. 9(1):59-69. doi: 10.1080/21501203.2017.1419995.


     44.     Contreras-López O, Moyano TC, Soto DC, Gutiérrez RA. 2018. Step-by-Step Construction of Gene Co-expression Networks from High-Throughput Arabidopsis RNA Sequencing Data. Methods Mol Biol. 2018;1761:275-301. doi: 10.1007/978-1-4939-7747-5_21.