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Items: 44

1.

Origin, genomic diversity and microevolution of the Clostridium difficile B1/NAP1/RT027/ST01 strain in Costa Rica, Chile, Honduras and Mexico.

Guerrero-Araya E, Meneses C, Castro-Nallar E, Guzmán D AM, Álvarez-Lobos M, Quesada-Gómez C, Paredes-Sabja D, Rodríguez C.

Microb Genom. 2020 Mar 16. doi: 10.1099/mgen.0.000355. [Epub ahead of print]

2.

Copper-induced concomitant increases in photosynthesis, respiration, and C, N and S assimilation revealed by transcriptomic analyses in Ulva compressa (Chlorophyta).

Laporte D, Rodríguez F, González A, Zúñiga A, Castro-Nallar E, Sáez CA, Moenne A.

BMC Plant Biol. 2020 Jan 15;20(1):25. doi: 10.1186/s12870-019-2229-5.

3.

In infants with severe bronchiolitis: dual-transcriptomic profiling of nasopharyngeal microbiome and host response.

Fujiogi M, Camargo CA Jr, Bernot JP, Freishtat RJ, Harmon B, Mansbach JM, Castro-Nallar E, Perez-Losada M, Hasegawa K.

Pediatr Res. 2020 Jan 6. doi: 10.1038/s41390-019-0742-8. [Epub ahead of print] No abstract available.

PMID:
31905367
4.

The Transcription Factor ArcA Modulates Salmonella's Metabolism in Response to Neutrophil Hypochlorous Acid-Mediated Stress.

Pardo-Esté C, Castro-Severyn J, Krüger GI, Cabezas CE, Briones AC, Aguirre C, Morales N, Baquedano MS, Sulbaran YN, Hidalgo AA, Meneses C, Poblete-Castro I, Castro-Nallar E, Valvano MA, Saavedra CP.

Front Microbiol. 2019 Dec 5;10:2754. doi: 10.3389/fmicb.2019.02754. eCollection 2019.

5.

Altered Middle Ear Microbiome in Children With Chronic Otitis Media With Effusion and Respiratory Illnesses.

Kolbe AR, Castro-Nallar E, Preciado D, Pérez-Losada M.

Front Cell Infect Microbiol. 2019 Oct 4;9:339. doi: 10.3389/fcimb.2019.00339. eCollection 2019.

6.

Arsenic Response of Three Altiplanic Exiguobacterium Strains With Different Tolerance Levels Against the Metalloid Species: A Proteomics Study.

Castro-Severyn J, Pardo-Esté C, Sulbaran Y, Cabezas C, Gariazzo V, Briones A, Morales N, Séveno M, Decourcelle M, Salvetat N, Remonsellez F, Castro-Nallar E, Molina F, Molina L, Saavedra CP.

Front Microbiol. 2019 Sep 26;10:2161. doi: 10.3389/fmicb.2019.02161. eCollection 2019.

7.

Variability in Genomic and Virulent Properties of Porphyromonas gingivalis Strains Isolated From Healthy and Severe Chronic Periodontitis Individuals.

Mendez KN, Hoare A, Soto C, Bugueño I, Olivera M, Meneses C, Pérez-Donoso JM, Castro-Nallar E, Bravo D.

Front Cell Infect Microbiol. 2019 Jul 10;9:246. doi: 10.3389/fcimb.2019.00246. eCollection 2019.

8.

In-Depth Genomic and Phenotypic Characterization of the Antarctic Psychrotolerant Strain Pseudomonas sp. MPC6 Reveals Unique Metabolic Features, Plasticity, and Biotechnological Potential.

Orellana-Saez M, Pacheco N, Costa JI, Mendez KN, Miossec MJ, Meneses C, Castro-Nallar E, Marcoleta AE, Poblete-Castro I.

Front Microbiol. 2019 May 24;10:1154. doi: 10.3389/fmicb.2019.01154. eCollection 2019.

9.

Genomic and Physiological Traits of the Marine Bacterium Alcaligenes aquatilis QD168 Isolated From Quintero Bay, Central Chile, Reveal a Robust Adaptive Response to Environmental Stressors.

Durán RE, Méndez V, Rodríguez-Castro L, Barra-Sanhueza B, Salvà-Serra F, Moore ERB, Castro-Nallar E, Seeger M.

Front Microbiol. 2019 Apr 5;10:528. doi: 10.3389/fmicb.2019.00528. eCollection 2019.

10.

Copper-induced increased expression of genes involved in photosynthesis, carotenoid synthesis and C assimilation in the marine alga Ulva compressa.

Rodríguez FE, Laporte D, González A, Mendez KN, Castro-Nallar E, Meneses C, Huidobro-Toro JP, Moenne A.

BMC Genomics. 2018 Nov 20;19(1):829. doi: 10.1186/s12864-018-5226-4.

11.

Genomic Analysis of 48 Paenibacillus larvae Bacteriophages.

Stamereilers C, Fajardo CP, Walker JK, Mendez KN, Castro-Nallar E, Grose JH, Hope S, Tsourkas PK.

Viruses. 2018 Jul 19;10(7). pii: E377. doi: 10.3390/v10070377.

12.

The transcription factor SlyA from Salmonella Typhimurium regulates genes in response to hydrogen peroxide and sodium hypochlorite.

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.

Res Microbiol. 2018 Jul - Aug;169(6):263-278. doi: 10.1016/j.resmic.2018.04.003. Epub 2018 May 29.

13.

Genome sequence of two members of the chloroaromatic-degrading MT community: Pseudomonas reinekei MT1 and Achromobacter xylosoxidans MT3.

Gutierrez-Urrutia I, Miossec MJ, Valenzuela SL, Meneses C, Dos Santos VAPM, Castro-Nallar E, Poblete-Castro I.

J Biotechnol. 2018 Jun 10;275:13-16. doi: 10.1016/j.jbiotec.2018.03.019. Epub 2018 Mar 29.

PMID:
29605637
14.

Comparative genomic analysis of a new tellurite-resistant Psychrobacter strain isolated from the Antarctic Peninsula.

Muñoz-Villagrán CM, Mendez KN, Cornejo F, Figueroa M, Undabarrena A, Morales EH, Arenas-Salinas M, Arenas FA, Castro-Nallar E, Vásquez CC.

PeerJ. 2018 Feb 19;6:e4402. doi: 10.7717/peerj.4402. eCollection 2018.

15.

Tracheal Microbiota in Patients With a Tracheostomy Before, During and After an Acute Respiratory Infection.

Pérez-Losada M, Graham RJ, Coquillette M, Jafarey A, Castro-Nallar E, Aira M, Hoptay C, Freishtat RJ, Mansbach JM.

Pediatr Infect Dis J. 2018 Nov;37(11):e269-e271. doi: 10.1097/INF.0000000000001952.

16.

Cyclic AMP Regulates Bacterial Persistence through Repression of the Oxidative Stress Response and SOS-Dependent DNA Repair in Uropathogenic Escherichia coli.

Molina-Quiroz RC, Silva-Valenzuela C, Brewster J, Castro-Nallar E, Levy SB, Camilli A.

mBio. 2018 Jan 9;9(1). pii: e02144-17. doi: 10.1128/mBio.02144-17.

17.

Computational Methods for Human Microbiome Analysis.

Miossec MJ, Valenzuela SL, Mendez KN, Castro-Nallar E.

Curr Protoc Microbiol. 2017 Nov 9;47:1E.14.1-1E.14.17. doi: 10.1002/cpmc.41.

PMID:
29120486
18.

Mutation and recombination in pathogen evolution: Relevance, methods and controversies.

Arenas M, Araujo NM, Branco C, Castelhano N, Castro-Nallar E, Pérez-Losada M.

Infect Genet Evol. 2018 Sep;63:295-306. doi: 10.1016/j.meegid.2017.09.029. Epub 2017 Sep 22. Review.

PMID:
28951202
19.

Microbial sequence typing in the genomic era.

Pérez-Losada M, Arenas M, Castro-Nallar E.

Infect Genet Evol. 2018 Sep;63:346-359. doi: 10.1016/j.meegid.2017.09.022. Epub 2017 Sep 21. Review.

20.

The temporal dynamics of the tracheal microbiome in tracheostomised patients with and without lower respiratory infections.

Pérez-Losada M, Graham RJ, Coquillette M, Jafarey A, Castro-Nallar E, Aira M, Freishtat RJ, Mansbach JM.

PLoS One. 2017 Aug 10;12(8):e0182520. doi: 10.1371/journal.pone.0182520. eCollection 2017.

21.

Draft Genome Sequences of Five Enterococcus Species Isolated from the Gut of Patients with Suspected Clostridium difficile Infection.

Castro-Nallar E, Valenzuela SL, Baquedano S, Sánchez C, Fernández F, Trombert AN.

Genome Announc. 2017 May 18;5(20). pii: e00379-17. doi: 10.1128/genomeA.00379-17.

22.

DNA Barcoding analysis of seafood accuracy in Washington, D.C. restaurants.

Stern DB, Castro Nallar E, Rathod J, Crandall KA.

PeerJ. 2017 Apr 25;5:e3234. doi: 10.7717/peerj.3234. eCollection 2017.

23.

Comparative Genomics Analysis of a New Exiguobacterium Strain from Salar de Huasco Reveals a Repertoire of Stress-Related Genes and Arsenic Resistance.

Castro-Severyn J, Remonsellez F, Valenzuela SL, Salinas C, Fortt J, Aguilar P, Pardo-Esté C, Dorador C, Quatrini R, Molina F, Aguayo D, Castro-Nallar E, Saavedra CP.

Front Microbiol. 2017 Mar 21;8:456. doi: 10.3389/fmicb.2017.00456. eCollection 2017.

24.

Genome Sequence of Streptomyces sp. H-KF8, a Marine Actinobacterium Isolated from a Northern Chilean Patagonian Fjord.

Undabarrena A, Ugalde JA, Castro-Nallar E, Seeger M, Cámara B.

Genome Announc. 2017 Feb 9;5(6). pii: e01645-16. doi: 10.1128/genomeA.01645-16.

25.

Draft Genome Sequence of a Multi-Metal Resistant Bacterium Pseudomonas putida ATH-43 Isolated from Greenwich Island, Antarctica.

Rodríguez-Rojas F, Tapia P, Castro-Nallar E, Undabarrena A, Muñoz-Díaz P, Arenas-Salinas M, Díaz-Vásquez W, Valdés J, Vásquez C.

Front Microbiol. 2016 Nov 8;7:1777. eCollection 2016. No abstract available.

26.

Genome Sequence of Clostridium paraputrificum 373-A1 Isolated in Chile from a Patient Infected with Clostridium difficile.

Guerrero-Araya E, Plaza-Garrido A, Díaz-Yañez F, Pizaro-Guajardo M, Valenzuela SL, Meneses C, Gil F, Castro-Nallar E, Paredes-Sabja D.

Genome Announc. 2016 Nov 3;4(6). pii: e01178-16. doi: 10.1128/genomeA.01178-16.

27.

Metataxonomic and Metagenomic Approaches vs. Culture-Based Techniques for Clinical Pathology.

Hilton SK, Castro-Nallar E, Pérez-Losada M, Toma I, McCaffrey TA, Hoffman EP, Siegel MO, Simon GL, Johnson WE, Crandall KA.

Front Microbiol. 2016 Apr 7;7:484. doi: 10.3389/fmicb.2016.00484. eCollection 2016.

28.

Redefining Healthy Urine: A Cross-Sectional Exploratory Metagenomic Study of People With and Without Bladder Dysfunction.

Groah SL, Pérez-Losada M, Caldovic L, Ljungberg IH, Sprague BM, Castro-Nallar E, Chandel NJ, Hsieh MH, Pohl HG.

J Urol. 2016 Aug;196(2):579-87. doi: 10.1016/j.juro.2016.01.088. Epub 2016 Jan 22.

PMID:
26807926
29.

Composition, taxonomy and functional diversity of the oropharynx microbiome in individuals with schizophrenia and controls.

Castro-Nallar E, Bendall ML, Pérez-Losada M, Sabuncyan S, Severance EG, Dickerson FB, Schroeder JR, Yolken RH, Crandall KA.

PeerJ. 2015 Aug 25;3:e1140. doi: 10.7717/peerj.1140. eCollection 2015.

30.

Integrating microbial and host transcriptomics to characterize asthma-associated microbial communities.

Castro-Nallar E, Shen Y, Freishtat RJ, Pérez-Losada M, Manimaran S, Liu G, Johnson WE, Crandall KA.

BMC Med Genomics. 2015 Aug 16;8:50. doi: 10.1186/s12920-015-0121-1.

31.

Dual Transcriptomic Profiling of Host and Microbiota during Health and Disease in Pediatric Asthma.

Pérez-Losada M, Castro-Nallar E, Bendall ML, Freishtat RJ, Crandall KA.

PLoS One. 2015 Jun 30;10(6):e0131819. doi: 10.1371/journal.pone.0131819. eCollection 2015.

32.

Concordance and discordance of sequence survey methods for molecular epidemiology.

Castro-Nallar E, Hasan NA, Cebula TA, Colwell RR, Robison RA, Johnson WE, Crandall KA.

PeerJ. 2015 Feb 17;3:e761. doi: 10.7717/peerj.761. eCollection 2015.

33.

PathoScope 2.0: a complete computational framework for strain identification in environmental or clinical sequencing samples.

Hong C, Manimaran S, Shen Y, Perez-Rogers JF, Byrd AL, Castro-Nallar E, Crandall KA, Johnson WE.

Microbiome. 2014 Sep 5;2:33. doi: 10.1186/2049-2618-2-33. eCollection 2014.

34.

Single-molecule long-read 16S sequencing to characterize the lung microbiome from mechanically ventilated patients with suspected pneumonia.

Toma I, Siegel MO, Keiser J, Yakovleva A, Kim A, Davenport L, Devaney J, Hoffman EP, Alsubail R, Crandall KA, Castro-Nallar E, Pérez-Losada M, Hilton SK, Chawla LS, McCaffrey TA, Simon GL.

J Clin Microbiol. 2014 Nov;52(11):3913-21. doi: 10.1128/JCM.01678-14. Epub 2014 Aug 20.

35.

Clinical PathoScope: rapid alignment and filtration for accurate pathogen identification in clinical samples using unassembled sequencing data.

Byrd AL, Perez-Rogers JF, Manimaran S, Castro-Nallar E, Toma I, McCaffrey T, Siegel M, Benson G, Crandall KA, Johnson WE.

BMC Bioinformatics. 2014 Aug 4;15:262. doi: 10.1186/1471-2105-15-262.

36.

Whole genome single-nucleotide variation profile-based phylogenetic tree building methods for analysis of viral, bacterial and human genomes.

Faison WJ, Rostovtsev A, Castro-Nallar E, Crandall KA, Chumakov K, Simonyan V, Mazumder R.

Genomics. 2014 Jul;104(1):1-7. doi: 10.1016/j.ygeno.2014.06.001. Epub 2014 Jun 12.

37.

Pathoscope: species identification and strain attribution with unassembled sequencing data.

Francis OE, Bendall M, Manimaran S, Hong C, Clement NL, Castro-Nallar E, Snell Q, Schaalje GB, Clement MJ, Crandall KA, Johnson WE.

Genome Res. 2013 Oct;23(10):1721-9. doi: 10.1101/gr.150151.112. Epub 2013 Jul 10.

38.

Phage cluster relationships identified through single gene analysis.

Smith KC, Castro-Nallar E, Fisher JN, Breakwell DP, Grose JH, Burnett SH.

BMC Genomics. 2013 Jun 19;14:410. doi: 10.1186/1471-2164-14-410.

39.

tat Exon 1 exhibits functional diversity during HIV-1 subtype C primary infection.

Rossenkhan R, MacLeod IJ, Sebunya TK, Castro-Nallar E, McLane MF, Musonda R, Gashe BA, Novitsky V, Essex M.

J Virol. 2013 May;87(10):5732-45. doi: 10.1128/JVI.03297-12. Epub 2013 Mar 13.

40.

Pathogen typing in the genomics era: MLST and the future of molecular epidemiology.

Pérez-Losada M, Cabezas P, Castro-Nallar E, Crandall KA.

Infect Genet Evol. 2013 Jun;16:38-53. doi: 10.1016/j.meegid.2013.01.009. Epub 2013 Jan 26. Review.

PMID:
23357583
41.

Population genomics and phylogeography of an Australian dairy factory derived lytic bacteriophage.

Castro-Nallar E, Chen H, Gladman S, Moore SC, Seemann T, Powell IB, Hillier A, Crandall KA, Chandry PS.

Genome Biol Evol. 2012;4(3):382-93. doi: 10.1093/gbe/evs017. Epub 2012 Feb 21.

42.

The evolution of HIV: inferences using phylogenetics.

Castro-Nallar E, Pérez-Losada M, Burton GF, Crandall KA.

Mol Phylogenet Evol. 2012 Feb;62(2):777-92. doi: 10.1016/j.ympev.2011.11.019. Epub 2011 Nov 27. Review.

43.

Molecular phylodynamics and protein modeling of infectious salmon anemia virus (ISAV).

Castro-Nallar E, Cortez-San Martín M, Mascayano C, Molina C, Crandall KA.

BMC Evol Biol. 2011 Dec 2;11:349. doi: 10.1186/1471-2148-11-349.

44.

Androgen receptor gene CAG and GGN repeat polymorphisms in Chilean men with primary severe spermatogenic failure.

Castro-Nallar E, Bacallao K, Parada-Bustamante A, Lardone MC, López PV, Madariaga M, Valdevenito R, Piottante A, Ebensperger M, Castro A.

J Androl. 2010 Nov-Dec;31(6):552-9. doi: 10.2164/jandrol.109.008821. Epub 2010 Apr 8.

PMID:
20378930

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