Mailing Address:
University of California, Berkeley
Dept. of Integrative Biology
3060 VLSB #3140
Berkeley, CA 94720-3140
Lab phone: 510/643-4201
Fax: 510/643-5022
Email: paulooin@berkeley.edu
University of California, Berkeley
Dept. of Integrative Biology
3060 VLSB #3140
Berkeley, CA 94720-3140
Lab phone: 510/643-4201
Fax: 510/643-5022
Email: paulooin@berkeley.edu
Research Interests
I am broadly interested in the evolution of developmental mechanisms (“evo-devo”) and how they contribute to the diversity of organism form. Given the particular aims of evo-devo, the philosophical framework of our field is somewhat different from both traditional evolution and developmental biology. Of the many brands of evo-devo, the approach I have taken is largely comparative and example-driven, where I compare extant taxa in order to deduce the ancestral state. This allows us to first rebuild the past and then to create plausible scenarios of developmental change during the course of a taxa’s evolution. Ultimately, we can reconstruct the history of life to explain the present and at the same time, derive the general principles driving the evolution of development.
The Conundrum
It is intuitive that divergent developmental trajectories will yield different morphological outcomes, but it is much less obvious that the opposite is can also be true. Surprisingly, conserved developmental outcomes are products of very different developmental pathways. For my postdoctoral work, I am studying two such examples, one in the crustacean, Parhyale hawaiensis, and the other in the insect, Oncopeltus fasciatus.
Parhyale Neurogenesis
The early architecture of the malacostracan crustacean and insect CNS show many similarities, with neuroblasts (the neural stem cells) arranged in fundamentally the same pattern. However, early neurogenic events leading up to this conserved architecture are surprisingly different between insects and malacostracans. For example in some malacostracans, no apparent proneural cluster is formed before neuroblast differentiation. Interestingly, it has also been observed that once these neuroblasts are formed, they are able to switch between neural and ectodermal divisions—implying that neural stem cell fate may be more plastic than assumed from work in Drosophila.
To explore these differences, I am performing experiments to explore neuroblast selection and their subsequent behavior in the malacostracan crustacean, Parhyale hawaiensis. The apparent lack of proneural clusters implies that a lateral inhibition mechanism may not be used during early neurogenesis in Parhyale. To determine if this is the case, I will examine the expression and function (via siRNA inhibition) of genes of the Notch signaling pathway. In order to further characterize neuroblasts that are undergoing the ectodermal division, neuroblasts will be assayed for asymmetric Prospero localization, mitotic spindle orientation, and expression of the neuroblast temporal identity genes. Eventually, I aim to elucidate the mechanism controlling this division pattern and the subsequent differentiation of neuroblasts versus and ectodermal cells.
Oncopeltus Segmentation
The adult insect body plan is very well conserved, yet the developmental processes of segmentation leading up to this conserved output are surprisingly varied across species. Long germ insects, such as Drosophila, form all their body segments simultaneously—their entire future body plan can be proportionally mapped on the early blastoderm. In contrast, short and intermediate germ insects specify only their anterior segments during the blastoderm stage. The remaining segments are formed sequentially in an anterior to posterior direction from a terminal “growth zone”. Given that long germ insects evolved from short or intermediate germ insects, what, how, and when did changes in segmentation occur? What aspects of segmentation are common to both modes and which are specific to only one?
In order to gain insight into these questions, I am continuing my work on understanding segmentation in the intermediate germ insect, Oncopeltus fasciatus. I am currently studying the genetic interactions between the gap genes and the pair-rule genes with the ultimate aim of building the segmentation gene network within Oncopeltus.
Education and Training
2005-present
Howard Hughes Medical Institute, UC Berkeley. Department of Integrative Biology
Damon Runyon Cancer Research Foundation Postdoctoral Fellow
Advisor: Nipam H. Patel
1997-2005
Indiana University, Bloomington. Department of Biology.
PhDNSF IGERT Graduate Trainee, NIH Graduate Genetics Trainee Major in Genetics, minor in EvolutionAdvisors: Thomas C. Kaufman and Rudolf Raff
1995-1997
UC Berkeley. Department of Molecular and Cell Biology.
Staff Research Associate
Supervisor: Barbara J. Meyer
1991-1995
UC Berkeley. Department of Molecular and Cell Biology BA
Emphasis in Genetics
1994-1995
UC Berkeley. Department of Plant and Microbial Biology
Undergraduate Researcher (volunteer position)
Supervisor: Michael Freeling
Teaching and Mentoring
2007-present
Supervised undergraduate researcher, Andrew Maxwell.
May 2007
Coordinated and set up lab activity for graduate Evolution and Development course. Collected marine and terrestrial organisms representing diverse taxa.
Spring 2004
Supervised visiting scholar Kristen Panfilio, Cambridge University, UK. Resulted in publication in Developmental Biology.
Spring 2004
Associate Instructor, Indiana University. Biology L112, Biological Mechanisms. Planned discussion section activities, coordinated undergraduate instructors, created and graded exams.
Spring 2003
Supervised visiting scholar Dr. Carlo Brena, Padua University, Italy. Resulted in publication in Evolution and Development.
2001- 2002
Supervised two undergraduate researchers, Jana Hewitt and Gretchen Fair.
Fall 2000
Associate Instructor, Indiana University. Biology L112, Biological Mechanisms. Planned discussion section activities, coordinated undergraduate instructors, created and graded exams.
Publications
K. A. Panfilio, P. Z. Liu, M. Akam, and T. C. Kaufman (2006). Oncopeltus fasciatus zen is essential for serosal tissue function in katatrepsis. Developmental Biology 292:226-243.
P. Z. Liu and T. C. Kaufman (2005). Short and long germ segmentation: unanswered questions in the evolution of a developmental mode. Evolution and Development.[PDF]
D. Angelini, P. Z. Liu, C. L. Hughes, and T. C. Kaufman (2005). Hox gene functions and interactions in the milkweed bug Oncopeltus fasciatus (Heteroptera). Developmental Biology.[PDF]
P. Z. Liu and T. C. Kaufman (2005). even-skipped expression and function in the large milkweed bug, Oncopeltus fasciatus, an intermediate germband insect. Development 132:2081-2092. LINK: http://dev.biologists.org/cgi/content/full/132/9/2081
C. Brena, P. Z. Liu, A. Mineli, and T. C. Kaufman (2005). Abd-B expression in Porcellio scaber Latreille, 1804 (Isopoda, Crustacea): conserved pattern vs. novel roles in development and evolution. Evolution and Development 7:42-50. LINK: http://www.blackwell-synergy.com/doi/abs/10.1111/j.1525-142X.2005.05005.x?cookieSet=1
C. L. Hughes, P. Z. Liu, and T. C. Kaufman (2004). Expression patterns of the rogue Hox genes Hox3/zen and fushi tarazu in the apterygote insect Thermobia domestica. Evolution and Development 6:393-401.LINK: http://www.blackwell-synergy.com/doi/abs/10.1111/j.1525-142X.2004.04048.x
P. Z. Liu and T. C. Kaufman (2004) Krüppel is a gap gene in the intermediate germband insect Oncopeltus fasciatus and is required for development of both blastoderm and germband-derived segments. Development 131:4567-4579. LINK: http://dev.biologists.org/cgi/content/full/131/18/4567
P. Z. Liu and T. C. Kaufman (2004) hunchback is required to suppress abdominal identity and for proper germband growth and segmentation in the intermediate germband insect Oncopeltus fasciatus. Development 131:1515-1527. LINK: http://dev.biologists.org/cgi/content/full/131/7/1515
Extramural Oral Presentations
October 2007
Kewalo Marine Laboratory, Honolulu, HI
December 2004
New York University, NY.
October 2003
Developmental Basis of Evolutionary Change IIIUniversity of Chicago, IL
October 2003
Midwest Drosophila ConferenceRobert Allerton Park, Monticello, IL
October 2002
Midwest Drosophila ConferenceRobert Allerton Park, Monticello, IL
September 2002
Understanding Mechanisms of EvolutionWood’s Hole, MA
Funding and Grants
2005-present
Damon Runyon Postdoctoral Fellowship (UC Berkeley)
2005
NIH NRSA Postdoctoral Fellowship (UC Berkeley). Declined in favor of Damon Runyon.
Summer 2004
Summer Dissertation Fellowship (Indiana University)
2001-2003
IGERT Fellowship in Evolution and Development (Indiana University)
1997-2001
NIH Genetics Training Grant (Indiana University)
Service
Fall, 2007
Ad hoc grant reviewer, NSF
2003-2005
Campus representative, Science’s Next Wave (now ScienceCareers.org), AAAS
2002-2003
Graduate student representative, faculty job search in evolution and development,
Department of Biology, Indiana University
I am broadly interested in the evolution of developmental mechanisms (“evo-devo”) and how they contribute to the diversity of organism form. Given the particular aims of evo-devo, the philosophical framework of our field is somewhat different from both traditional evolution and developmental biology. Of the many brands of evo-devo, the approach I have taken is largely comparative and example-driven, where I compare extant taxa in order to deduce the ancestral state. This allows us to first rebuild the past and then to create plausible scenarios of developmental change during the course of a taxa’s evolution. Ultimately, we can reconstruct the history of life to explain the present and at the same time, derive the general principles driving the evolution of development.
The Conundrum
It is intuitive that divergent developmental trajectories will yield different morphological outcomes, but it is much less obvious that the opposite is can also be true. Surprisingly, conserved developmental outcomes are products of very different developmental pathways. For my postdoctoral work, I am studying two such examples, one in the crustacean, Parhyale hawaiensis, and the other in the insect, Oncopeltus fasciatus.
Parhyale Neurogenesis
The early architecture of the malacostracan crustacean and insect CNS show many similarities, with neuroblasts (the neural stem cells) arranged in fundamentally the same pattern. However, early neurogenic events leading up to this conserved architecture are surprisingly different between insects and malacostracans. For example in some malacostracans, no apparent proneural cluster is formed before neuroblast differentiation. Interestingly, it has also been observed that once these neuroblasts are formed, they are able to switch between neural and ectodermal divisions—implying that neural stem cell fate may be more plastic than assumed from work in Drosophila.
To explore these differences, I am performing experiments to explore neuroblast selection and their subsequent behavior in the malacostracan crustacean, Parhyale hawaiensis. The apparent lack of proneural clusters implies that a lateral inhibition mechanism may not be used during early neurogenesis in Parhyale. To determine if this is the case, I will examine the expression and function (via siRNA inhibition) of genes of the Notch signaling pathway. In order to further characterize neuroblasts that are undergoing the ectodermal division, neuroblasts will be assayed for asymmetric Prospero localization, mitotic spindle orientation, and expression of the neuroblast temporal identity genes. Eventually, I aim to elucidate the mechanism controlling this division pattern and the subsequent differentiation of neuroblasts versus and ectodermal cells.
Oncopeltus Segmentation
The adult insect body plan is very well conserved, yet the developmental processes of segmentation leading up to this conserved output are surprisingly varied across species. Long germ insects, such as Drosophila, form all their body segments simultaneously—their entire future body plan can be proportionally mapped on the early blastoderm. In contrast, short and intermediate germ insects specify only their anterior segments during the blastoderm stage. The remaining segments are formed sequentially in an anterior to posterior direction from a terminal “growth zone”. Given that long germ insects evolved from short or intermediate germ insects, what, how, and when did changes in segmentation occur? What aspects of segmentation are common to both modes and which are specific to only one?
In order to gain insight into these questions, I am continuing my work on understanding segmentation in the intermediate germ insect, Oncopeltus fasciatus. I am currently studying the genetic interactions between the gap genes and the pair-rule genes with the ultimate aim of building the segmentation gene network within Oncopeltus.
Education and Training
2005-present
Howard Hughes Medical Institute, UC Berkeley. Department of Integrative Biology
Damon Runyon Cancer Research Foundation Postdoctoral Fellow
Advisor: Nipam H. Patel
1997-2005
Indiana University, Bloomington. Department of Biology.
PhDNSF IGERT Graduate Trainee, NIH Graduate Genetics Trainee Major in Genetics, minor in EvolutionAdvisors: Thomas C. Kaufman and Rudolf Raff
1995-1997
UC Berkeley. Department of Molecular and Cell Biology.
Staff Research Associate
Supervisor: Barbara J. Meyer
1991-1995
UC Berkeley. Department of Molecular and Cell Biology BA
Emphasis in Genetics
1994-1995
UC Berkeley. Department of Plant and Microbial Biology
Undergraduate Researcher (volunteer position)
Supervisor: Michael Freeling
Teaching and Mentoring
2007-present
Supervised undergraduate researcher, Andrew Maxwell.
May 2007
Coordinated and set up lab activity for graduate Evolution and Development course. Collected marine and terrestrial organisms representing diverse taxa.
Spring 2004
Supervised visiting scholar Kristen Panfilio, Cambridge University, UK. Resulted in publication in Developmental Biology.
Spring 2004
Associate Instructor, Indiana University. Biology L112, Biological Mechanisms. Planned discussion section activities, coordinated undergraduate instructors, created and graded exams.
Spring 2003
Supervised visiting scholar Dr. Carlo Brena, Padua University, Italy. Resulted in publication in Evolution and Development.
2001- 2002
Supervised two undergraduate researchers, Jana Hewitt and Gretchen Fair.
Fall 2000
Associate Instructor, Indiana University. Biology L112, Biological Mechanisms. Planned discussion section activities, coordinated undergraduate instructors, created and graded exams.
Publications
K. A. Panfilio, P. Z. Liu, M. Akam, and T. C. Kaufman (2006). Oncopeltus fasciatus zen is essential for serosal tissue function in katatrepsis. Developmental Biology 292:226-243.
P. Z. Liu and T. C. Kaufman (2005). Short and long germ segmentation: unanswered questions in the evolution of a developmental mode. Evolution and Development.[PDF]
D. Angelini, P. Z. Liu, C. L. Hughes, and T. C. Kaufman (2005). Hox gene functions and interactions in the milkweed bug Oncopeltus fasciatus (Heteroptera). Developmental Biology.[PDF]
P. Z. Liu and T. C. Kaufman (2005). even-skipped expression and function in the large milkweed bug, Oncopeltus fasciatus, an intermediate germband insect. Development 132:2081-2092. LINK: http://dev.biologists.org/cgi/content/full/132/9/2081
C. Brena, P. Z. Liu, A. Mineli, and T. C. Kaufman (2005). Abd-B expression in Porcellio scaber Latreille, 1804 (Isopoda, Crustacea): conserved pattern vs. novel roles in development and evolution. Evolution and Development 7:42-50. LINK: http://www.blackwell-synergy.com/doi/abs/10.1111/j.1525-142X.2005.05005.x?cookieSet=1
C. L. Hughes, P. Z. Liu, and T. C. Kaufman (2004). Expression patterns of the rogue Hox genes Hox3/zen and fushi tarazu in the apterygote insect Thermobia domestica. Evolution and Development 6:393-401.LINK: http://www.blackwell-synergy.com/doi/abs/10.1111/j.1525-142X.2004.04048.x
P. Z. Liu and T. C. Kaufman (2004) Krüppel is a gap gene in the intermediate germband insect Oncopeltus fasciatus and is required for development of both blastoderm and germband-derived segments. Development 131:4567-4579. LINK: http://dev.biologists.org/cgi/content/full/131/18/4567
P. Z. Liu and T. C. Kaufman (2004) hunchback is required to suppress abdominal identity and for proper germband growth and segmentation in the intermediate germband insect Oncopeltus fasciatus. Development 131:1515-1527. LINK: http://dev.biologists.org/cgi/content/full/131/7/1515
Extramural Oral Presentations
October 2007
Kewalo Marine Laboratory, Honolulu, HI
December 2004
New York University, NY.
October 2003
Developmental Basis of Evolutionary Change IIIUniversity of Chicago, IL
October 2003
Midwest Drosophila ConferenceRobert Allerton Park, Monticello, IL
October 2002
Midwest Drosophila ConferenceRobert Allerton Park, Monticello, IL
September 2002
Understanding Mechanisms of EvolutionWood’s Hole, MA
Funding and Grants
2005-present
Damon Runyon Postdoctoral Fellowship (UC Berkeley)
2005
NIH NRSA Postdoctoral Fellowship (UC Berkeley). Declined in favor of Damon Runyon.
Summer 2004
Summer Dissertation Fellowship (Indiana University)
2001-2003
IGERT Fellowship in Evolution and Development (Indiana University)
1997-2001
NIH Genetics Training Grant (Indiana University)
Service
Fall, 2007
Ad hoc grant reviewer, NSF
2003-2005
Campus representative, Science’s Next Wave (now ScienceCareers.org), AAAS
2002-2003
Graduate student representative, faculty job search in evolution and development,
Department of Biology, Indiana University
Above Left: Paul Liu in the lab. Above Right: Two Parhyale neuroblasts stained with an antibody recognizing Prospero (red) and an antibody recognizing b-catenin (green).
NIPAM H. PATEL
ABOVE, LEFT:
A Parhyale embryo stained for Prospero (red) and DNA (blue). Prospero expression initiates in the d1h cell lineage just after the first differential division. This is the homologous neuroblast that in Diastylis has been observed to give rise to both neural and ectodermally fated cells.
A Parhyale embryo stained for Prospero (red) and DNA (blue). Prospero expression initiates in the d1h cell lineage just after the first differential division. This is the homologous neuroblast that in Diastylis has been observed to give rise to both neural and ectodermally fated cells.
ABOVE, RIGHT:
Two Parhyale neuroblasts stained with an antibody recognizing Prospero (red) and an antibody recognizing b-catenin (green).
Two Parhyale neuroblasts stained with an antibody recognizing Prospero (red) and an antibody recognizing b-catenin (green).
PHOTO ON LEFT:
A Parhyale embryo expressing a membrane-localized GFP. The cells of the early germband can be easily seen.
A Parhyale embryo expressing a membrane-localized GFP. The cells of the early germband can be easily seen.