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: serano[at]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: serano[at]berkeley.edu
Research Summary
Few developmental gene families have been studied as extensively as the Hox genes, which encode homeodomain-containing transcription factors that determine regional identity along the anterior/posterior (AP) axis in bilaterian animals. Hox genes are typically organized within the genome in conserved clusters that display colinearity—that is, their position along the chromosome correlates with the positions of their expression domains along the AP axis. Misexpression, knockdown, and gain- and loss-of-function mutations in Hox genes are associated with homeotic transformations, where body parts in one region of an animal are transformed to resemble those of another region. Given their importance in establishing regional and segmental identity, it is not surprising that several lines of molecular, genetic and developmental evidence have implicated changes in Hox genes expression in the generation of morphological diversity in evolution.
I am interested in using the amphipod crustacean Parhyale hawaiensis as a system to study Hox gene evolution within the phylum Arthropoda. Since crustaceans are the closest relatives to insects, it is possible for us to design comparative studies using the vast developmental and genetic data available for Drosophila combined with our knowledge of morphological and developmental diversity in other insects and crustaceans. Parhyale also provide a tractable system to study embryogenesis and is amenable to numerous molecular and functional techniques (e.g., genetic transformation, misexpression, RNAi, in situ hybridization and immunocytochemistry).
Using a degenerate PCR strategy, I isolated homeodomain sequence fragments corresponding to each of canonical Hox genes (with the exception of fushi tarazu, for which no ortholog was found) and the ParaHox gene caudal. Along with my collaborator Danielle Liubicich (who has focused on primarily on Scr, Antp and Ubx), I used RACE and other PCR strategies to isolate full-length cDNAs for each Hox gene. We then carried out in situ hybridization to determine Hox expression domains. In general, Parhyale Hox genes demonstrate not only spatial, but temporal colinearity in their expression patterns. In addition, for most Hox genes, transcripts accumulate in the parasegmental precursor cells or their immediate progeny, thus it appears that segmental identity is already established at the time when individual parasegments are just single rows of cells. This early expression significantly precedes visible differences in segment identity (e.g., appendage morphology).
To determine whether Parhyale Hox genes are organized into clusters, I screened a Parhyale BAC library using probes specific for each Hox gene. Inverse PCR was used to isolate sequences at the ends of each positive BAC clone, and these sequences were then used as probes to both re-screen the BAC library and to map individual BACs in relation to one another. One collection of BACs that together span four linked Hox genes (5’-Ubx, Antp, Scr, Dfd-3’) and second that spans two linked Hox genes (5’-pb, lab-3’) were found. In both cases, the Hox genes are oriented in a linear fashion consistent with what has been reported for vertebrate and other Hox clusters. BAC clones corresponding to the three remaining Hox genes (Abd-B, abd-A and Hox3) were also isolated, but I have not yet been able to determine whether they are located near or adjacent to each other and/or the aforementioned Hox miniclusters.
Representative BAC clones for all of the Hox genes, plus a BAC containing the Distalless-early (Dll-e) gene, are currently being sequenced by the Stanford Human Genome Center. The results will help formulate future experiments investigating Hox gene regulation and their role in regulating the expression of potential downstream genes (e.g., Dll-e). Functional experiments aimed at knocking down or misexpressing Hox genes in Parhyale embryos are currently in process.
Publications
Serano, J. and Rubin, G. M. (2003). The Drosophila synaptotagmin-like protein bitesize is required for growth and has mRNA localization sequences within its open reading frame. Proc. Natl. Acad. Sci. USA 100, 13368-13373. [PDF] click for article
Page-McCaw, A., Serano, J., Santé, J. and Rubin, G.M. (2003) Drosophila Matrix Metalloproteinases are required for tissue remodeling but not embryonic development. Developmental Cell 4, 95-106. [PDF] click for article
Littleton, J. T.*, Serano, T. L.*, Rubin, G. M., Ganetzky, B. and Chapman, E. R. (1999). Synaptic function modulated by changes in the ratio of Synaptotagmin I and IV. Nature 400, 757-760.
* these authors contributed equally to this work
Kopczynski, C. C., Noodermeer, J. N., Serano, T. L., Chen, W.-Y., Pendleton, J. D., Lewis, S., Goodman, C. S. and Rubin, G. M. (1998). A high throughput screen to identify secreted and transmembrane proteins involved in Drosophila embryogenesis. Proc. Natl. Acad. Sci. USA 95, 9973-9978.
Karlin-McGinness, M., Serano, T. L. and Cohen, R. S. (1996). Comparative analysis of the kinetics and dynamics of K10, bicoid, and oskar mRNA localization in the Drosophila oocyte. Dev. Genet. 19, 238-248.
Serano, T. L. and Cohen, R. S. (1995). A small predicted stem-loop structure mediates oocyte localization of Drosophila K10 mRNA. Development 121, 3809-3818.
Serano, T. L. and Cohen, R. S. (1995). Gratuitous mRNA localization in the Drosophila oocyte. Development 121, 3013-3021.
Serano, T. L., Karlin-McGinness, M. and Cohen, R. S. (1995). The role of fs(1)K10 in the localization of the mRNA of the TGFalpha homolog gurken within the Drosophila oocyte. Mech. of Dev. 51, 183-192.
Cohen, R. S. and Serano, T. L. (1995). mRNA localization and function of the Drosophila fs(1)K10 gene. In Localized RNAs (ed. H. D. Lipshitz), pp. 99-112. Austin: R. G. Landes.
Serano, T. L., Cheung, H.-K., Frank, L. H. and Cohen, R. S. (1994). P element transformation vectors for studying Drosophila melanogaster oogenesis and early embryogenesis. Gene 138, 181-186.
Cheung, H.-K., Serano, T. L. and Cohen, R. S. (1992). Evidence for a highly selective RNA transport system and its role in establishing the dorsoventral axis of the Drosophila egg. Development 114, 653-661.
Education
Ph.D. in Biochemistry and Molecular Biophysics
Columbia University, New York, New York
Thesis Advisor: Robert Cohen
1989-1995
1985-1989
Philadelphia University, Philadelphia, Pennsylvania
B. A. in Life Science
Additional Research Experience
Research Specialist, University of California, Berkeley
Principal Investigator: Nipam H. Patel, Ph.D.
2003-present
• Cloning and functional characterization of Hox genes in the crustacean Parhyale hawaiensis: degenerate PCR, cloning of full-length cDNAs, BAC library screening and analysis, determination of RNA expression, stealth RNAi, misexpression of genes in Parhyale and/or Drosophila, and characterization of phenotypes.
Post-doctoral Fellow, University of California, Berkeley
Principal Investigator: Gerald M. Rubin, Ph.D.
1995 - 2003
• Collaborated on a high throughput expression-based screen to identify novel membrane and secreted proteins in Drosophila: supervision of the DNA sequencing technician, coordinating sequence homology (BLAST) searches with the bioinformatics group, determination of whether newly identified genes encoded membrane-targeted proteins based on these homologies.
• Identification and characterization of 16 genes expressed during Drosophila development: cloning of full-length cDNAs, determination of mRNA expression, gene structure and predicted function, construction of misexpression and gene-fusion constructs for functional analyses in vivo. This work resulted in publications on three genes: synaptotagmin IV, bitesize, and matrix metalloproteinase-2.
• Characterization of the Drosophila synaptotagmin-like protein bitesize: generation of loss-of-function mutants, genetic and mosaic analyses implicating the gene in growth signaling, generation of truncation/deletion variants and epitope-tagged proteins, immunocytochemistry to determine protein subcellular localization, isolation of cis-acting sequences required for apical mRNA localization.
• Genetic interaction screen for genes involved in Rho GTPase signaling in Drosophila: development of a phenotypic assay system suitable for the screen, carrying out mutagenesis, complementation analysis and mapping.
Honors and Awards
The Leukemia and Lymphoma Society Special Fellow Award, 2000-2003.
Tobacco-Related Disease Research Program Postdoctoral Fellowship (awarded in 2000, but declined).
The Jane Coffin Childs Memorial Fund for Medical Research Postdoctoral Fellowship, 1996-1999.
National Eye Institute Training Grant, 1989-1992.
Full Academic Scholarship, Philadelphia University, 1985-1989.
Few developmental gene families have been studied as extensively as the Hox genes, which encode homeodomain-containing transcription factors that determine regional identity along the anterior/posterior (AP) axis in bilaterian animals. Hox genes are typically organized within the genome in conserved clusters that display colinearity—that is, their position along the chromosome correlates with the positions of their expression domains along the AP axis. Misexpression, knockdown, and gain- and loss-of-function mutations in Hox genes are associated with homeotic transformations, where body parts in one region of an animal are transformed to resemble those of another region. Given their importance in establishing regional and segmental identity, it is not surprising that several lines of molecular, genetic and developmental evidence have implicated changes in Hox genes expression in the generation of morphological diversity in evolution.
I am interested in using the amphipod crustacean Parhyale hawaiensis as a system to study Hox gene evolution within the phylum Arthropoda. Since crustaceans are the closest relatives to insects, it is possible for us to design comparative studies using the vast developmental and genetic data available for Drosophila combined with our knowledge of morphological and developmental diversity in other insects and crustaceans. Parhyale also provide a tractable system to study embryogenesis and is amenable to numerous molecular and functional techniques (e.g., genetic transformation, misexpression, RNAi, in situ hybridization and immunocytochemistry).
Using a degenerate PCR strategy, I isolated homeodomain sequence fragments corresponding to each of canonical Hox genes (with the exception of fushi tarazu, for which no ortholog was found) and the ParaHox gene caudal. Along with my collaborator Danielle Liubicich (who has focused on primarily on Scr, Antp and Ubx), I used RACE and other PCR strategies to isolate full-length cDNAs for each Hox gene. We then carried out in situ hybridization to determine Hox expression domains. In general, Parhyale Hox genes demonstrate not only spatial, but temporal colinearity in their expression patterns. In addition, for most Hox genes, transcripts accumulate in the parasegmental precursor cells or their immediate progeny, thus it appears that segmental identity is already established at the time when individual parasegments are just single rows of cells. This early expression significantly precedes visible differences in segment identity (e.g., appendage morphology).
To determine whether Parhyale Hox genes are organized into clusters, I screened a Parhyale BAC library using probes specific for each Hox gene. Inverse PCR was used to isolate sequences at the ends of each positive BAC clone, and these sequences were then used as probes to both re-screen the BAC library and to map individual BACs in relation to one another. One collection of BACs that together span four linked Hox genes (5’-Ubx, Antp, Scr, Dfd-3’) and second that spans two linked Hox genes (5’-pb, lab-3’) were found. In both cases, the Hox genes are oriented in a linear fashion consistent with what has been reported for vertebrate and other Hox clusters. BAC clones corresponding to the three remaining Hox genes (Abd-B, abd-A and Hox3) were also isolated, but I have not yet been able to determine whether they are located near or adjacent to each other and/or the aforementioned Hox miniclusters.
Representative BAC clones for all of the Hox genes, plus a BAC containing the Distalless-early (Dll-e) gene, are currently being sequenced by the Stanford Human Genome Center. The results will help formulate future experiments investigating Hox gene regulation and their role in regulating the expression of potential downstream genes (e.g., Dll-e). Functional experiments aimed at knocking down or misexpressing Hox genes in Parhyale embryos are currently in process.
Publications
Serano, J. and Rubin, G. M. (2003). The Drosophila synaptotagmin-like protein bitesize is required for growth and has mRNA localization sequences within its open reading frame. Proc. Natl. Acad. Sci. USA 100, 13368-13373. [PDF] click for article
Page-McCaw, A., Serano, J., Santé, J. and Rubin, G.M. (2003) Drosophila Matrix Metalloproteinases are required for tissue remodeling but not embryonic development. Developmental Cell 4, 95-106. [PDF] click for article
Littleton, J. T.*, Serano, T. L.*, Rubin, G. M., Ganetzky, B. and Chapman, E. R. (1999). Synaptic function modulated by changes in the ratio of Synaptotagmin I and IV. Nature 400, 757-760.
* these authors contributed equally to this work
Kopczynski, C. C., Noodermeer, J. N., Serano, T. L., Chen, W.-Y., Pendleton, J. D., Lewis, S., Goodman, C. S. and Rubin, G. M. (1998). A high throughput screen to identify secreted and transmembrane proteins involved in Drosophila embryogenesis. Proc. Natl. Acad. Sci. USA 95, 9973-9978.
Karlin-McGinness, M., Serano, T. L. and Cohen, R. S. (1996). Comparative analysis of the kinetics and dynamics of K10, bicoid, and oskar mRNA localization in the Drosophila oocyte. Dev. Genet. 19, 238-248.
Serano, T. L. and Cohen, R. S. (1995). A small predicted stem-loop structure mediates oocyte localization of Drosophila K10 mRNA. Development 121, 3809-3818.
Serano, T. L. and Cohen, R. S. (1995). Gratuitous mRNA localization in the Drosophila oocyte. Development 121, 3013-3021.
Serano, T. L., Karlin-McGinness, M. and Cohen, R. S. (1995). The role of fs(1)K10 in the localization of the mRNA of the TGFalpha homolog gurken within the Drosophila oocyte. Mech. of Dev. 51, 183-192.
Cohen, R. S. and Serano, T. L. (1995). mRNA localization and function of the Drosophila fs(1)K10 gene. In Localized RNAs (ed. H. D. Lipshitz), pp. 99-112. Austin: R. G. Landes.
Serano, T. L., Cheung, H.-K., Frank, L. H. and Cohen, R. S. (1994). P element transformation vectors for studying Drosophila melanogaster oogenesis and early embryogenesis. Gene 138, 181-186.
Cheung, H.-K., Serano, T. L. and Cohen, R. S. (1992). Evidence for a highly selective RNA transport system and its role in establishing the dorsoventral axis of the Drosophila egg. Development 114, 653-661.
Education
Ph.D. in Biochemistry and Molecular Biophysics
Columbia University, New York, New York
Thesis Advisor: Robert Cohen
1989-1995
1985-1989
Philadelphia University, Philadelphia, Pennsylvania
B. A. in Life Science
Additional Research Experience
Research Specialist, University of California, Berkeley
Principal Investigator: Nipam H. Patel, Ph.D.
2003-present
• Cloning and functional characterization of Hox genes in the crustacean Parhyale hawaiensis: degenerate PCR, cloning of full-length cDNAs, BAC library screening and analysis, determination of RNA expression, stealth RNAi, misexpression of genes in Parhyale and/or Drosophila, and characterization of phenotypes.
Post-doctoral Fellow, University of California, Berkeley
Principal Investigator: Gerald M. Rubin, Ph.D.
1995 - 2003
• Collaborated on a high throughput expression-based screen to identify novel membrane and secreted proteins in Drosophila: supervision of the DNA sequencing technician, coordinating sequence homology (BLAST) searches with the bioinformatics group, determination of whether newly identified genes encoded membrane-targeted proteins based on these homologies.
• Identification and characterization of 16 genes expressed during Drosophila development: cloning of full-length cDNAs, determination of mRNA expression, gene structure and predicted function, construction of misexpression and gene-fusion constructs for functional analyses in vivo. This work resulted in publications on three genes: synaptotagmin IV, bitesize, and matrix metalloproteinase-2.
• Characterization of the Drosophila synaptotagmin-like protein bitesize: generation of loss-of-function mutants, genetic and mosaic analyses implicating the gene in growth signaling, generation of truncation/deletion variants and epitope-tagged proteins, immunocytochemistry to determine protein subcellular localization, isolation of cis-acting sequences required for apical mRNA localization.
• Genetic interaction screen for genes involved in Rho GTPase signaling in Drosophila: development of a phenotypic assay system suitable for the screen, carrying out mutagenesis, complementation analysis and mapping.
Honors and Awards
The Leukemia and Lymphoma Society Special Fellow Award, 2000-2003.
Tobacco-Related Disease Research Program Postdoctoral Fellowship (awarded in 2000, but declined).
The Jane Coffin Childs Memorial Fund for Medical Research Postdoctoral Fellowship, 1996-1999.
National Eye Institute Training Grant, 1989-1992.
Full Academic Scholarship, Philadelphia University, 1985-1989.
Parhyale stage 21 embryo after in situ hybridization with probes for the Hox genes Dfd (red) and Scr (yellow).
NIPAM H. PATEL
PHOTO ON LEFT:
DfdEmbryogenesis
Deformed gene expression in red, co-stained with either labial (lab), engrailed-1 (en1) or Sex combs reduced (Scr) in yellow, during different stages of Parhyale embroygenesis (Dapi staining in blue).
DfdEmbryogenesis
Deformed gene expression in red, co-stained with either labial (lab), engrailed-1 (en1) or Sex combs reduced (Scr) in yellow, during different stages of Parhyale embroygenesis (Dapi staining in blue).
PHOTO ON LEFT:
Hox-en1-doubles
Parhyale Hox gene expression (in red) precedes engrailed-1 expression (in yellow) and the formation of four-row wide parasegments as shown for A) Sex combs reduced, B) Ultrabithorax, C) abdominal-A, and D) Abdominal-B (Dapi staining in blue).
Hox-en1-doubles
Parhyale Hox gene expression (in red) precedes engrailed-1 expression (in yellow) and the formation of four-row wide parasegments as shown for A) Sex combs reduced, B) Ultrabithorax, C) abdominal-A, and D) Abdominal-B (Dapi staining in blue).
PHOTO ON LEFT:
ParhyaleHoxFig
Parhyale Hox gene expression in late stage embryos (Dapi staining in blue, Hox expression in red).
ParhyaleHoxFig
Parhyale Hox gene expression in late stage embryos (Dapi staining in blue, Hox expression in red).