2013

Dr. Nicole Valenzuela

 

 
 

 


Current Lab Members

 


Dr. Nicole Valenzuela

I am an evolutionary biologist, and my research involves studies of:
  • Evolutionary and Ecological Genomics
  • Evolutionary Developmental Biology
  • Sex Determination
  • Population and Ecological Genetics
  • Life History Evolution
  • Herpetology
  • Tropical Biology
  • Conservation
Publications

Dr. Eugenia Elisabet Montiel, Postdoc

Eli is a postdoctoral fellow. Her PhD work focused on the evolutionary genetics of transposable elements in grasshoppers with different system of B chromosomes.

At the Valenzuela lab she is working on a phylogenomics project to study the repatterning of turtle genomes responsible for the co-evolution of diploid number and sex determination in turtles. This work is funded by another grant from the National Science Foundation (MCB 1244355 to N. Valenzuela).

Eli's Website

Valenzuela N, D Badenhorst, EE Montiel Jimenez, R. Literman. 2014. Molecular cytogenetic search for cryptic sex chromosomes in painted turtles Chrysemys picta. Cytogenetic and Genome Research 144: 39-46.


Robert Literman, PhD Candidate

    I am a PhD candidate in the Ecology and Evolutionary Biology program. I am interested in the evolution and functional basis of sex determination in reptiles. I am also a herp enthusiast, and have worked with reptiles in Costa Rica and New Zealand.

Bob’s Website

Literman R, Badenhorst D, Valenzuela N. 2014. QPCR-based molecular sexing by copy number variation in rRNA genes and its utility for sex identification in soft-shell turtles. Methods in Ecology and Evolution 5: 872-880.

Valenzuela N, D Badenhorst, EE Montiel Jimenez, R. Literman. 2014. Molecular cytogenetic search for cryptic sex chromosomes in painted turtles Chrysemys picta. Cytogenetic and Genome Research 144: 39-46.

Shaffer HB, P Minx, DE Warren, AM Shedlock, RC Thomson, N Valenzuela,....R. Literman et 40 altri. 2013. The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage. Genome Biology. doi:10.1186/gb-2013-14-3-r28

Valenzuela N., J. Neuwald, and R. Literman. 2013. Transcriptional evolution underlying vertebrate sexual development. Developmental Dynamics. 242:307–319.

Radhakrishnan, S, R. Literman, A. Severin, and N. Valenzuela. 2013. Comparative transcriptomic dynamics during embryonic gonadal development in turtles with genotypic and temperature-dependent sex determination. Plant & Animal Genome XXI Conference, San Diego, CA.


Srihari Radhakrishnan, PhD Candidate

 

I am a third year Ph.D. student in the Bioinformatics & Computational Biology program. I am interested in the transcriptomic analysis of gonadal development in turtles.

Shaffer HB, P Minx, DE Warren, AM Shedlock, RC Thomson, N Valenzuela,....S. Radhakrishnan et 40 altri. 2013. The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage. Genome Biology. doi:10.1186/gb-2013-14-3-r28

Radhakrishnan S, R. Literman, A. Severin, and N. Valenzuela. 2013. Comparative transcriptomic dynamics during embryonic gonadal development in turtles with genotypic and temperature-dependent sex determination. Plant & Animal Genome XXI Conference, San Diego, CA.


Ong Xiong, PhD Student

 

I am a PhD student in the Ecology and Evolutionary Biology program. I am interested in how genome organization, epigenetics, and population genetics influence phenotypic plasticity and diversification.


LingSze Lee, PhD Student

 

I am a PhD student in the Interdepartmenal Genetics program. For my Master's degree I studied human chromosome sequence variation. I am interested in chromosome and genome evolution in turtles.


Beatriz Mizoguchi, PhD Student

 

I am a PhD student in the Interdepartmenal Genetics program, and a Science Without Borders/LASPAU fellow from Brazil. I am interested in chromatin remodeling and the effect that it has on gene expression and phenotypic responses to environmental insult, such as exposure to toxins.


Former Graduate Students

 


Dr. Claudia Ceballos

I completed my Ph.D. in the EEB program at ISU in 2010. I am interested in understanding the causes and consequences of phenotypic evolution. My PhD work focused on phenotypic plasticity of body growth and its effect on the evolution of sexual size dimorphism in Podocnemis expansa and Chelydra serpentina and the evolution of Rensch's rule in turtles. My work was funded by the National Science Foundation (DEB 0808047) and the Turtle Conservation Fund, to N. Valenzuela (PI) and C Ceballos (CoPI).

I am now a faculty at the Veterinary Medicine Program of the University of Antioquia, Colombia.

Claudia’s Website

Ceballos, C. and Valenzuela, N. 2011. The role of sex-specific plasticity in shaping sexual dimorphism in a long-lived vertebrate, the snapping turtle Chelydra serpentina. Evolutionary Biology 38: 163-181.

Ceballos C.P, D.C. Adams, J.B. Iverson, y N. Valenzuela. 2013. Phylogenetic patterns of sexual size dimorphism in turtles and their implications for Rensch´s rule. Evolutionary Biology. 40: 194-208. DOI: 10.1007/s11692-012-9199-y.

Ceballos CP, OE Hernández and N Valenzuela. 2013. Divergent sex-specific plasticity in long-lived vertebrates with contrasting sexual dimorphism. Evolutionary Biology In press.


Dr. Jennifer Deitloff

Jenn completed my Ph.D. in the EEB program at ISU in 2008. Her work focused on the ecological processes responsible for species co-ocurrence patterns in two species of Plethodon salamanders. She was co-advised by Dr. Dean Adams. Jenn was a Postdoctoral Scholar in the Department of Biological Sciences at Auburn University, and a Postdoc in the Entomology Department at Iowa State University.

She is now an Assistant Professor at Lock Haven University.

Jenn's Website


Pedro Martinez, MSc

Pedro was a Ph.D. student in the Ecology and Evolutionary Biology Program (2006-2008) and the Genetics Program (2008-2009) at ISU. He worked on sex chromosome evolution in turtles, particularly in discovering a novel XX/XY system in the Australian chelid Emydura macquarii. He completed his PhD in Immunology in 2014 and is now a Postdoctoral Fellow at the Tisch Cancer Institute in the Icahn School of Medicine at Mount Sinai in New York.

Pedro's website

Martinez, P., Ezaz T., Valenzuela, N., Georges, A., and Graves J.A.M. 2008. An XX/XY heteromorphic sex chromosome system in the Australian chelid turtle Emydura macquarii, a new piece in the puzzle of sex chromosome evolution in turtles. Chromosome Research: 16(6): 815-825. DOI 10.1007/s10577-008-1228-4.


Former Graduate Rotation Students

 


Chris Chandler

Chris was a Ph.D. rotation student in the Ecology and Evolutionary Biology program. Chris is interested in the evolution of sex determination.

He is now an Assistant Professor at SUNY-Oswego.


Jeffrey Sander

Jeff was a Ph.D. rotation student from the Bioinformatics & Computational Biology program. He worked on sex ratio evolution models.


Jacqueline Farrel

Jacqueline was a MSc rotation student from the Interdepartmental Genetics program. she worked on the molecular evolution of genes involved in sex determination.


William Pett

Will was a Ph.D. rotation student from the Bioinformatics & Computational Biology program. He worked on the transcriptomic analysis of gonadal development in turtles.


Hanna Worral

Hanna was a Ph.D. rotation student from the Genetics program. She worked on gene expression of turtle gonad explants in vitro to test the effect of stochasticity on temperature-dependent sex determination.


Bri Vidrine

Bri was a Ph.D. rotation student from the Genetics program. She worked on gene expression of turtle gonad explants in vitro to test the effect of stochasticity on temperature-dependent sex determination.


Junmarie Soto

Junmarie was a Ph.D. rotation student from the Genetics program. She worked on the sex by temperature interaction effect on the transcriptional responses of Apalone spinifera turtles (GSD - ZZ/ZW) during gonadal development.


Laura Shultz

Laura was a Ph.D. rotation student from the Genetics program. She worked on the sex by temperature interaction effect on the transcriptional responses of Apalone spinifera turtles (GSD - ZZ/ZW) during gonadal development.


Garret Janzen

Garret was a Ph.D. rotation student from the Genetics program. He worked on the transcriptional responses to temperature of the endangered TSD tortoise Manouria emys phayrei during gonadal development.


Natalia Acevedo Luna

Natalia was a Ph.D. rotation student from the Bioinformatics and Computational Biology program. She worked on molecular evolution of genomic regions regulating turtle sex determination.


2010

 


Former Postdoctoral Associates

 


Dr. Daleen Badenhorst, Postdoc

Daleen is a postdoctoral fellow. Her PhD work focused on the Rattus complex and its role as a reservoir for human pathogens using a molecular cytogenetic, phylogenomic and gene expression approach.

At the Valenzuela lab she first worked on a phylogenomics project to study the evolution of sex chromosomes and sex-linked genes in turtles. This work was funded by the National Science Foundation (MCB 0815354 to N. Valenzuela and S.V. Edwards).

Daleen then worked on another phylogenomics project to study the repatterning of turtle genomes responsible for the co-evolution of diploid number and sex determination in turtles. This work is funded by another grant from the National Science Foundation (MCB 1244355 to N. Valenzuela).

Daleen's Website

Literman R, Badenhorst D, Valenzuela N. 2014. QPCR-based molecular sexing by copy number variation in rRNA genes and its utility for sex identification in soft-shell turtles. Methods in Ecology and Evolution 5: 872-880.

Valenzuela N, D Badenhorst, EE Montiel Jimenez, R. Literman. 2014. Molecular cytogenetic search for cryptic sex chromosomes in painted turtles Chrysemys picta. Cytogenetic and Genome Research 144: 39-46.

Shaffer HB, P Minx, DE Warren, AM Shedlock, RC Thomson, N Valenzuela,....D. Badenhorst et 40 altri. 2013. The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage. Genome Biology. doi:10.1186/gb-2013-14-3-r28

Badenhorst, D., R. Stanyon, T. Engstrom, and N. Valenzuela. 2013. A ZZ/ZW microchromosome system in the spiny softshell turtle, Apalone spinifera reveals an intriguing sex chromosome conservation in Trionychidae. Chromosome Research. 12(2): 137-147.


Dr. Jennifer Neuwald

Jennifer was a postdoctoral fellow. Her PhD work focused on the temporal changes in population genetic dynamics of the eastern collared lizard, Crotaphytus collaris collaris, in response to forest fire management.

At the Valenzuela lab she worked on an eco-genomics project to study the effect of fluctuating temperature on the expression of genes involved in gonadogenesis in TSD turtles.

Her work was funded by the National Science Foundation (IOS 0743284 to N. Valenzuela).

Jennifer is now a Research Associate at the Department of Fish and Wildlife Conservation Biology at Colorado State University.

Jennifer's Website

Neuwald J.L. and Valenzuela N. 2011. The Lesser Known Challenge of Climate Change: Thermal Variance and Sex-Reversal in Vertebrates with Temperature-Dependent Sex Determination. PloS ONE 6(3): e18117. doi:10.1371/journal.pone.0018117.

Valenzuela N., J. Neuwald, and R. Literman. 2013. Transcriptional evolution underlying vertebrate sexual development. Developmental Dynamics. 242:307–319.


Dr. Daniel Janes

Dan was a postdoctoral fellow. He is an evolutionary geneticist interested in the evolution of sex-determining mechanisms and sex chromosomes.

Dan's work was funded by the National Science Foundation (MCB 0815354 to N. Valenzuela and S.V. Edwards).

Dan now works for the National Institute of General Medical Sciences at the NIH.

Dan's Website

Shaffer HB, P Minx, DE Warren, AM Shedlock, RC Thomson, N Valenzuela,....DE Janes et 40 altri. 2013. The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage. Genome Biology. doi:10.1186/gb-2013-14-3-r28

Janes DE, Elsey RM, Langan EM, Moore B, Edwards SV and N Valenzuela. 2013. Sex-biased expression of sex-differentiating genes Foxl2 and Fgf9 in American alligators, Alligator mississippiensis. Sexual Development. 7: 253–260

Janes, D.E., Valenzuela N., Ezaz T., Amemiya C., and Edwards S.V. 2011. Sex chromosome evolution in Amniotes: applications for bacterial artificial chromosome libraries. Journal of Biomedicine and Biotechnology Vol 2011, doi:10.1155/2011/132975


Dr. Tibisay Escalona

I was an NSF postdoctoral fellow. I am very interested in the ecology, life history evolution and conservation of freshwater turtles in the Neotropics. I worked on the metapopulation genetic analysis of Podocnemis unifilis turtles in South America.

My work was funded by the National Science Foundation (DBI 0511958 to T. Excalona), and the Scott Neotropical Fund from the Cleveland Zoo (to N. Valenzuela [PI] and T. Escalona [CoPI]).

Tibisay’s Website

Escalona, T., Engstrom T.N., Hernandez O.E., Bock B.C., Vogt R.C. and Valenzuela N. 2009. Population genetics of the endangered South American freshwater turtle, Podocnemis unifilis, inferred from microsatellite DNA data. Conservation Genetics. DOI 10.1007/s10592-008-9746-3

Escalona, T., Adams, D.C., and Valenzuela, N. 2009. Nesting ecology in the freshwater turtle Podocnemis unifilis: spatiotemporal patterns and inferred explanations. Functional Ecology DOI 10.1111/j.1365-2435.2009.01562.x


Dr. Takahito Shikano

Postdoctoral associate. I worked on the molecular evolution of sex related genes across reptiles and other vertebrates that possess contrasting sex determining mechanisms, in order to shed light on the evolution of sex determination.

I am now a Postdoc in the Ecological Genetics Research Unit at the University of Helsinki.

Taka's Website

  • Valenzuela, N., LeClere A.R, and Shikano T. 2006. Comparative expression of steroidogenic factor 1 in Chrysemys picta and Apalone mutica turtles with environmental and genotypic sex determination. Evolution and Development 8 (5): 424-432.

  • Valenzuela, N. and Shikano T. 2007. Embryological ontogeny of Aromatase gene expression in Chrysemys picta and Apalone mutica turtles: comparative patterns within and across temperature-dependent and genotypic sex-determining mechanisms. Development, Genes and Evolution 217: 55-62.

Former Undergrads

 


Andrea R. LeClere

I graduated from the undergraduate Genetics program at ISU. For my honors thesis I worked during 2004-2005 on a project aimed to compare the expression profiles of sex genes (genes involved in sex differentiation) between turtles with temperature-dependent sex determination (Chrysemys picta) and turtles with genotypic sex determination (Apalone mutica) incubated under identical conditions. We were searching for key differences to understand the mechanics of both sex determining systems.

I am now a PhD student in the Molecular, Cellular and Structural Biology program at the University of Minnesota.

  • Valenzuela, N., LeClere A.R, and Shikano T. 2006. Comparative expression of steroidogenic factor 1 in Chrysemys picta and Apalone mutica turtles with environmental and genotypic sex determination. Evolution and Development 8 (5): 424-432.

  • LeClere A.R. and N. Valenzuela.2005. Comparative gene expression of multiple sex-determining genes in TSD and GSD turtles. Joint Meeting of the Society for the Study of Amphibians and Reptiles and the Herpetologists' League, Tampa, Florida.

Barbara Kagima

I was a Biology undergraduate at ISU, and during 2002-2005 I worked on population genetics of Podocnemis unifilis turtles from Colombia and Peru, and on maternal-effect genes related to sex differentiation in Chrysemys picta turtles from North America. I completed my Master’s in 2008 in the EEB program at ISU working on Wildlife Management with Dr. Sue Fairbanks. I completed my PhD at the University of Nebraska Lincoln.

I am now a Geospatial and Statistical Analyst for Concern Worldwide in Nairobi, Kenya.

Barbara's website

Kagima, B., Valenzuela, N., Engstrom, T., and Bock, B. 2004. Preliminary population genetic study of the yellow spotted Amazon river turtle (Podocnemis unifilis) using microsatellite DNA data. Annual Meeting of the Society of Integrative and Comparative Biology, New Orleans, Louisiana.

Kagima, B. and N. Valenzuela. 2005. Maternal effect genes for sex determination in painted turtles, Chrysemys picta. Joint Meeting of the Society for the Study of Amphibians and Reptiles and the Herpetologists' League, Tampa, Florida.


Sonia Morrone and Anthony Siegle

We were ITA interns at the Valenzuela Lab during 2008-2009, and were Biology majors at ISU. We worked on developmental biology and the effect of incubation temperature and posthatching environment on growth of snapping turtles, Chelydra serpentina.

Sonia is now a Biologist for the Louisiana Department of Wildlife and Fisheries.

Morrone S. and Siegle A. 2009. Effects of environment on growth. Iowa Academy of Sciences Annual Meeting,Des Moines, IA.


Katherine L. O'Shaughnessy

I was a summer intern with the ITA program at the Valenzuela Lab and the REU in Molecular Biotechnology and Genomics at ISU in 2009. I worked on developmental biology and expression profiling of genes involved in sex determination in turtles. I am now a Ph.D. student at the University of Florida where I am studying vetebrate EvoDevo.

O’Shaughnessy K, Valenzuela, N, Neuwald, N, Literman, R, Manternach, T, Harris, A. 2010. The genomics of temperature dependent sex determination in Chrysemys picta. Experimental Biology FASEB Annual Meeting, Anaheim, CA. Poster & Invited oral presentation - Winner of NSF travel grant for undergraduates - Winner of "ASBMB's Best Poster Theme" in the category of Systems Biology, Synthetic Biology, and Signal Transduction.

O'Shaughnessy K, Valenzuela, N, Neuwald, J, Literman, R, Manternach, T, Harris, A. 2010. The Genetic mechanism of temperature-dependent sex determination in the painted turtle. Capital University Research Symposium, Columbus, OH. Winner of Capital University's endowed "Bruning Award" for excellence in research.


Kevin Wenceslao

I was an ITA intern at the Valenzuela Lab during 2010-2011. I am a Biology major at ISU. I worked on developmental biology and the effect of incubation temperature on growth of painted turtles posthatching.

Wenceslao K, Literman R, Neuwald J, and Valenzuela N. 2011. The effect of temperautre on sex determination and fitness in painted turtles. Iowa Academy of Sciences Annual Meeting, Waverly, IA.


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