Juan Pablo Crdenas

Bsc. Biochemistry
Phone: 56-2-28502236
Birth date: July 13th, 1982
Birthplace: Puente Alto, Santiago, Chile
E-mail: jpcardenas_alpha@yahoo.com
Web: https://www.researchgate.net/profile/Juan_Cardenas2

Current status
Doctoral Candidate: Biotechnology PhD Program, Universidad Andres Bello (UNAB) and
Fundacion Ciencia & Vida (FCV); Santiago, Chile

About my work
My doctoral thesis is focused on how acidophilic microorganisms respond to oxidative
stress, considering that their way of life can potentially expose them to unusually high levels of
dangerous radicals. For example, their environment often has high concentrations of iron and
many have very high rates of oxygen consumption rendering them particularly exposed to
products of the Fenton reaction. They are also exposed to high concentrations of toxic metals. I
have been addressing these issues from a comparative genomics perspective, using also other
bioinformatic tools (i.e. metabolic reconstruction, phylogenetic analysis, regulon prediction, etc)
to suggest molecular machinery and mechanisms involved in stress adaptation.

I am also

interested in trying to understand the evolution of stress responses.

Keywords
Comparative

Genomics,

Bioinformatics,

Acidophiles,

Phylogeny, Oxidative Stress, Microbiology, Ecophysiology.

Bioleaching,

Metabolism,

Working experience
April 2010 Current
Associated PhD student in Basal project PFB-16, FCV (Chile)
June 2008 March 2010
Research assistant in INNOVA project 08CM01-03, FCV (Chile)
April 2013 Current
Collaborator in the Peruvian Genomics Studies Center (CEGENP, Peru)
January December 2013
External assistance in Bioinformatics; CONCYTEC-PROCYT project Reg. #20426
(Peru)

Scholarships, Grants and Fellowships

March 2010 March 2014
CONICYT Scholarship for Doctoral Studies (Chile)
November 2013
III Escuela Latinoamericana de Evolucin (3rd LatinAmerican Evolution School)
fellowship (Argentina)
October 2013
UNU-BIOLAC Tutorial Fellowship, 4rd SoiBio Conference (Argentina)
January December 2012
UNAB Initiation grant DI-116-12/I (Chile)
September 2011
First

Class

Accommodation

Symposium (China)

Fellowship,

19th

International

Biohydrometallurgy

Academic background
Undergraduate studies
BSc: Biochemistry; University of Santiago of Chile (USACH), 2001-2008
Undergraduate thesis
Anlisis bioinformtico y experimental del metabolismo central de carbn en
Acidithiobacillus ferrooxidans (Experimental and bioinformatic analysis of central
carbon metabolism in Acidithiobacillus ferrooxidans). Faculty of Chemistry and
Biology, University of Santiago of Chile, 2008. Status: approved, grade 7 where 7 is the
best grade.

ISI publications
1. Crdenas JP, Ortiz R, Norris PR, Watkin E, Holmes DS. Reclassification of Thiobacillus
prosperus (Huber and Stetter 1989) as Acidihalobacter prosperus sp. nov., gen. nov., a
member

of

Ectothiorhodospiraceae.

Int

Syst

Evol

Microbiol.

2015;

doi:

10.1099/ijsem.0.000468.
2. Nuez H, Loyola D, Crdenas JP, Holmes DS, Johnson DB, Quatrini R. Multi Locus
Sequence

Typing

scheme

for

Acidithiobacillus

caldus

strain

evaluation

and

differentiation. Res Microbiol. 2014; 165(9):735-42. doi: 10.1016/j.resmic.2014.07.014.

3. Gonzlez C, Yanquepe M, Cardenas JP, Valdes J, Quatrini R, Holmes DS, Dopson M.
Genetic variability of psychrotolerant Acidithiobacillus ferrivorans revealed by
(meta)genomic

analysis.

Res

Microbiol.

2014;

165(9):726-34.

doi:

10.1016/j.resmic.2014.08.005.
4. Acua LG, Crdenas JP, Covarrubias PC, Haristoy JJ, Flores R, Nuez H, Riadi G,
Shmaryahu A, Valds J, Dopson M, Rawlings DE, Banfield JF, Holmes DS, Quatrini R.
Architecture and gene repertoire of the flexible genome of the extreme acidophile
Acidithiobacillus

caldus.

PLoS

One.,

2013;

8(11):e78237.

doi:

10.1371/journal.pone.0078237.
5. Crdenas JP, Moya F, Covarrubias P, Shmaryahu A, Levicn G, Holmes DS, Quatrini R.
Comparative genomics of the oxidative stress response in bioleaching microorganisms.
Hydrometallurgy, 2012; 127128:162-167. http://dx.doi.org/10.1016/j.hydromet.2012.07.014.

6. Norambuena J, Flores R, Crdenas JP, Quatrini R, Chvez R, Levicn G. Thiol/Disulfide

system plays a crucial role in redox protection in the acidophilic iron-oxidizing
bacterium

Leptospirillum

ferriphilum.

PLoS

One.

2012;

7(9):

e44576.

doi:

10.1371/journal.pone.0044576.
7. Crdenas JP, Valds J, Quatrini R, Duarte F, Holmes DS. Lessons from the genomes of
extremely acidophilic bacteria and archaea with special emphasis on bioleaching
microorganisms. Appl Microbiol Biotechnol. 2010; 88(3):605-20. doi: 10.1007/s00253-0102795-9.
8. Valds J, Crdenas JP, Quatrini R, Esparza M, Osorio H, Duarte F, Lefimil C, Sepulveda R,
Jedlicki E, Holmes DS. Comparative genomics begins to unravel the ecophysiology of
bioleaching. Hydrometallurgy, 2010; 104:471-476. doi:10.1016/j.hydromet.2010.03.028.
9. Esparza M, Crdenas JP, Bowien B, Jedlicki E, Holmes DS. Genes and pathways for CO2
fixation in the obligate, chemolithoautotrophic acidophile, Acidithiobacillus ferrooxidans.
BMC Microbiol., 2010; 10:229. doi: 10.1186/1471-2180-10-229.
10. Appia-Ayme C, Quatrini R, Denis Y, Denizot F, Silver S, Roberto F, Veloso F, Valds J,
Crdenas JP, Esparza M, Orellana O, Jedlicki E, Bonnefoy V, Holmes DS. Microarray and
bioinformatic analyses suggest models for carbon metabolism in the autotroph
Acidithiobacillus

ferrooxidans.

Hydrometallurgy,

2006;

83:273-280.

http://dx.doi.org/10.1016/j.hydromet.2006.03.02

Non-ISI publications
1. Crdenas JP, Quatrini R, Holmes DS. Progress in acidophile genomics. In: Quatrini R,
Johnson DB (eds). The Acidophiles. Horizon Scientific Press, 2015; accepted.
2. Crdenas JP, Lazcano M, Ossandon FJ, Corbett M, Holmes DS, Watkin E. Draft Genome
Sequence of the Iron-Oxidizing Acidophile Leptospirillum ferriphilum Type Strain DSM
14647. Genome Announc. 2014; 2(6). pii: e01153-14. doi: 10.1128/genomeA.01153-14.
3. Ossandon FJ, Crdenas JP, Corbett M, Quatrini R, Holmes DS, Watkin E. Draft Genome
Sequence of the Iron-Oxidizing, Acidophilic, and Halotolerant "Thiobacillus prosperus"
Type Strain DSM 5130. Genome Announc. 2014; 2(5). pii: e01042-14. doi:
10.1128/genomeA.01042-14.

4. Moya-Beltrn A, Crdenas JP, Covarrubias PC, Issotta F, Ossandon FJ, Grail BM, Holmes
DS, Quatrini R, Johnson DB. Draft Genome Sequence of the Nominated Type Strain of
"Ferrovum myxofaciens," an Acidophilic, Iron-Oxidizing Betaproteobacterium. Genome
Announc. 2014;2(4). pii: e00834-14. doi: 10.1128/genomeA.00834-14.
5. Crdenas JP, Martnez V, Covarrubias P, Holmes DS, Quatrini R. Predicted CO/CO2
fixation in Ferroplasma spp. via a novel chimaeric pathway. Advanced Materials Research
2009; 71-73:219-222.
6. Osorio H, Crdenas JP, Valds J, Holmes DS. Prediction of FNR regulated genes and
metabolic pathways potentially involved in anaerobic growth of Acidithiobacillus
ferrooxidans. Advanced Materials Research 2009; 71-73: 195-198.

Oral communications
1. Crdenas J, Ossandon FJ, Ortiz R, Watkin E, Holmes DS. Genomic and evolutionary
insights into adaptation of "Thiobacillus prosperus" (Acidihalobacillus prosperus sp. nov)
to saline and acidic environments. XXXVI Congreso Chileno de Microbiologa, La Serena,
Chile. December 2nd 5th, 2014.
2. Crdenas JP, Quatrini R, Holmes DS. La vida en ambientes cidos: de la microbiologa a la
genmica (y ms all) (Life in acidic environments: from microbiology to genomics (and
beyond)). Primer Congreso Internacional de Innovacin e Investigacin en Ingeniera
aplicada a Biotecnologa, Arequipa, Peru, December 17th 19th, 2014.
3. Crdenas JP. Aplicaciones de la genmica al estudio de microorganismos (Applications of
Genomics in Microbiology Research). II Conferencia en Bioinformtica, Universidad
Nacional Federico Villarreal (UNFV), Lima, Peru, April 15th, 2013.
4. Crdenas JP. La vida en ambientes acdicos: Desde la Microbiologa a la (Meta)Genmica
(Life in acidic environments: from Microbiology to (Meta)genomics). Instituto Peruano de
Energa Nuclear (IPEN), Lima, Peru, April 12th, 2013.
5. Crdenas JP, Holmes DS, Quatrini R. Genmica comparativa de la respuesta a estrs
oxidativo en organismos acidfilos (Comparative genomics of the oxidative stress response
in acidophilic microorganisms). XII Congreso Nacional de Estudiantes de Biologa.
Lambayeque, Peru, November 27th - December 2nd. 2011.

6. Crdenas JP, Covarrubias P, Shmaryahu A, Demergasso C, Levicn G, Holmes DS, Quatrini

R.

Comparative

genomics

of

the

oxidative

stress

response

in

bioleaching

microorganisms. 19th International Biohydrometallurgy Symposium, Changsha, China,

September 18th-22th, 2011.
7. Crdenas JP, Arenas M, Demergasso C, Galleguillos P, Acosta M, Holmes DS, Levicn G,
Quatrini R. Genmica comparativa de la respuesta a estrs oxidativo en organismos acidfilos
(Comparative genomics of the oxidative stress response in acidophilic microorganisms).
XXXII Congreso Chileno de Microbiologa, Antofagasta, Chile. November 30th December
3th, 2010.

Congress posters
1. Garca-Gonzlez R, Crdenas JP, Holmes DS. Anlisis filogenmico del complejo
heterodislfuro reductasa (HdrABC) en genomas microbianos (Phylogenomic analysis of
Heterodisulfide Reductase complex (HdrABC) in microbial genomes). XXXV Congreso
Chileno de Microbiologa, Hotel Marbella, Chile. November 26th 29th, 2013.
2. Crdenas JP, Holmes DS, Quatrini R. Oxidative stress response in acidophilic bacteria: the
role of Fur and PerR regulators. 4to. Congreso Argentino de Bioinformtica y Biologa
Computacional (4CAB2C) y 4ta. Conferencia Internacional de la Sociedad Iberoamericana de
Bioinformtica (SolBio). Rosario, Argentina, October 29th-31th, 2013.
3. Crdenas JP, Arenas M, Quatrini R and Holmes DS. Niche specific oxidative stress response
in extreme acidophiles. 9th International Congress On Extremophiles, Sevilla, Spain,
September 10th-13th, 2012.
4. Crdenas JP, Levicn G, Holmes DS, Quatrini R. Comparative genomics of the oxidative
stress response in acidophilic microorganisms. International Society for Computational
Biology (ISCB) Latin America Conference, Santiago, Chile, March 17th-21th, 2012.
5. Garcs K, Nez H, Crdenas JP, Covarrubias P, Shmaryahu A, Demergasso C, Holmes DS,
Quatrini R. Biofilm Formation Capabilities in the Bioleaching Microbial Consortium: A
Comparative Genomics Approach. 19th International Biohydrometallurgy Symposium,
Changsha, China, September 18th-22th, 2011.
6. Crdenas JP, Esparza M, Valds J, Quatrini R. & Holmes DS. Genmica comparativa de
bacterias auttrofas facultativas y obligadas: diferencias clave para la regulacin del ciclo de

Calvin y otros aspectos de la autotrofa (Comparative genomics of facultative and obligate

autotrophic bacteria: key differences in Calvin cycle regulation and other aspects of
autotrophy). XXXI Congreso Sociedad de Microbiologa de Chile. Santa Cruz, Chile
December 1st-4th, 2009.
7. Crdenas JP, Martnez V, Covarrubias P, Holmes DS, Quatrini R. Predicted CO/CO2
fixation in Ferroplasma spp. via a novel chimaeric pathway. 18th. International
Biohydrometallurgy Symposium, Bariloche, Argentina, September 13th-17th, 2009.
8. Osorio H, Crdenas JP, Valds J, DS Holmes. Prediction and Experimental Validation of
Genes and Metabolic Pathways involved in Anaerobic Growth of Acidithiobacillus
ferrooxidans. 18th. International Biohydrometallurgy Symposium, Bariloche, Argentina,
September 13th-17th, 2009.
9. Crdenas JP, Martnez V, Holmes DS, Quatrini R. Metabolic reconstruction predicts a
novel CO/CO2 fixation pathway in Ferroplasma spp. (Reconstruccin metablica predice
una nueva ruta de fijacin de CO/CO2 en Ferroplasma spp.). XXX Congreso Chileno de
Microbiologa, Concepcin, Chile, December 4th-6th, 2008.
10. Crdenas JP, Valdes J, Jedlicki E, Holmes DS. Prediccin de sitios de unin de RpoN en el
genoma de Acidithiobacillus ferrooxidans muestra un modelo inicial del sigmuln RpoN
(RpoN-binding site prediction in Acidithiobacillus ferrooxidans genome shows a
preliminary model of RpoN sigmulon). XXIX Congreso Chileno de Microbiologa, Via del
Mar, Chile, December 3rd-5th, 2007.

Teaching experiences
Short course organization or collaboration

Genmica comparativa de microorganismos, Lambayeque, Peru, April 3th 5th, 2013

III Curso Internacional de Bioinformtica: Genmica Comparativa y Filogenias

Moleculares y su aplicacin e investigacin en Biotecnologa y Biodiversidad. Lambayeque,
Peru, November 23th 26th, 2011.

Genmica mdica: la bioinformtica en medicina y en la fisiologa de los microorganismos

patgenos. Lima, Peru, August 4th-7th, 2010.

Genmica y Protemica del Virus de la Influenza (AH1N1) y de la bacteria Bartonella

bacilliformis de la Enfermedad de Carrin. Lima, Peru, August 10th-15th, 2009.

Teaching assistance

Doctoral Course BIO502: Bioinformatics and Genome Biology. Andres Bello University,
Santiago, Chile. September November 2013; November 2014

CV updated to July 22th, 2015