RESEARCH SUMMARY
Thesis Abstract: The role of Hox genes in crustacean development and appendage specialization

Crustaceans are among the most morphologically diverse organisms existing today.  Their body forms vary dramatically, and their appendages are often highly specialized to perform critical functions such as mating or defense.  One particularly interesting specialized appendage is the maxilliped, a thoracic appendage that has been modified such that it appears more like a mouthpart and functions in feeding rather than locomotion like its thoracic counterparts.  This thesis explores the possible genetic mechanisms by which the unique maxilliped morphology evolved.  Previous experiments in crustaceans illustrated a correlation between the expression boundary of a particular patterning gene, Ultrabithorax (Ubx), and maxilliped specification in diverse crustaceans (Averof and Patel, 1997).  Ubx is a member of a highly conserved family of genes, called Hox genes, which provide regional identity in animal body plans.  Additional Hox genes are expressed in the maxilliped appendages of diverse crustaceans during development, including Sex combs reduced (Scr) and Antennapedia (Antp), and may also play an important role in specifying their unique identity (Abzhanov and Kaufman, 1999, 2000).  

To further our understanding of how changes in Hox gene expression may lead to crustacean appendage specialization, this project examined the role of Scr, Antp, and Ubx in maxilliped specification during Parhyale hawaiensis development.  Parhyale hawaiensis is an amphipod crustacean raised in the lab that has become an incredibly useful system in which gene expression patterns, levels, and functions can be analyzed throughout development.  Parhyale Hox expression analysis suggested that Scr, Antp and Ubx are all involved in Parhyale maxilliped specification, and the results of gene functional analysis confirmed PhUbx is critical for maxilliped identity.  Reducing Parhyale Ubx function through injection of siRNAs resulted in transformation of some thoracic legs to a more maxilliped-like (mouthpart-like) identity.  Misexpression of Parhyale Ubx through the use of a Minos transposable element system had the opposite effect, as head appendages and segments gained a more walking leg-like identity.  Together, these experiments provide evidence that altering Hox gene expression was a potential mechanism by which the diversity of crustacean appendage morphology evolved.

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EDUCATION
Ph.D. Integrative Biology, University of California, Berkeley (2007)
M.S. Developmental Biology, University of Chicago, IL (2003)
B.Sc. (Honours Class I) Zoology, University of Queensland, Australia (2001)
B.S. Biology, minor Mathematics, Fairfield University, CT (2000)
Honors Program, Summa Cum Laude, Phi Beta Kappa, Alpha Sigma Nu, Pi Mu Epsilon

SCIENTIFIC RESEARCH
Graduate Student Researcher, University of Chicago and University of California, Berkeley (2001-2007)
* Completed independent project: The role of Hox genes in crustacean development and appendage specialization
* Invited to present my research for NOVA special on biodiversity/evolutionary developmental biology (airs 2009)
* Presented at conferences in Calgary (Canada), York (UK), Cancun (Mexico), San Francisco, San Diego, Orlando
* Developed protocols and drafted scientific manuscripts / abstracts
* Innovated novel techniques and the first knockdown protocol testing gene function in our laboratory organism
* Trained researchers on numerous techniques
* Invited to give seminars at the University of Nottingham (UK) and the University of Richmond
* Collected animals on Belize Barrier Reef
* Advisor: Nipam H. Patel

Fulbright Fellow, University of Queensland, Australia (2000-2001)
* Managed independent project: Analysis of gene expression in early development of a marine demosponge: identifying conserved developmental pathways
* Presented data (talk) at the Australian Marine Science Association Annual Meeting, in Townsville, Australia
* Collected sponges on the Great Barrier Reef (Heron Island) for molecular lab work
* Advisor: Bernard Degnan

Undergraduate Researcher, Fairfield University, CT (June-August 1998, June 1999-May2000)
* Project: Isolation and characterization of Hox-like genes in marine sponges
* Results were presented at the Pfizer Sunmer Undergraduate Research Fellows conference and in Fairfield University Honors thesis
* Advisor: April Hill 
 
UNIVERSITY TEACHING
Teaching Assistant, Topics in Biology: Evolution, Watson School of Biological Sciences, Cold Spring Harbor Labs, NY (2003, 2005, 2007)
* Lectured, led lab exercises, chose reference materials, facilitated discussion sessions, and wrote student evaluations with 2 additional teaching assistants and 3 faculty members for this graduate level one-week intensive course.  Ordered and organized all materials for a tree of life biodiversity exercise in which students determine relationships among living specimens based on techniques they learned during the course.

Teaching Assistant, Embryology, Marine Biological Laboratory, Woods Hole, MA (2006)
* Organized and taught the lab exercises associated with the arthropod section of this summer course for graduate students, post-doctoral researchers, and new faculty members from around the world.  Helped organize materials, developed material for the lab manual, provided technical instruction, and collected organisms for use in this one-week session.

Teaching Assistant, Developmental Biology, University of California, Berkeley (2005)
* Led a discussion section, wrote test questions, graded exams, held office hours, mentored students, wrote recommendation letters, for this undergraduate level course where I designed most of the teaching materials with the assistance of one other teaching assistant.  Coordinated with lectures given by 3 faculty members.

* Received Outstanding Graduate Student Instructor Award from the Department of Molecular and Cell Biology at UC Berkeley for my teaching efforts during this course (awarded in 2006 for 2005 teaching).

Teaching Assistant, Biodiversity, University of Chicago, IL (2002)
* Instructed students during a laboratory section of this undergraduate level course.  Attended lectures, held office hours, facilitated exercises in lab and in the field, organized lab materials, as well as graded exams.  Coordinated with 3 other teaching assistants and one faculty member while teaching this course. Wrote student support letters.

Teaching Assistant, General Biology, Fairfield University, CT (1999-2000)
* Worked alongside one faculty member to help teach a laboratory section of this undergraduate level course.  Tasks included organizing materials, answering questions, teaching lab techniques, and facilitating quizzes and exams. 

PUBLIC SCIENCE EDUCATION AND OUTREACH
Volunteer Teacher, Operation SMART Girls Inc., Oakland, CA (2005-2007)
* Facilitated learning in class of 12 3-5^th grade girls at an after school science program once a week alongside one instructor. Collaborated with a post-doctoral researcher and designed interactive biological science curriculum including “meet the arthropods” (with live organisms), “hooray for habitats” (drawing/matching), and “DNA messages” (genetic code writing) activities. Successfully assessed as having a positive impact by the program coordinator who was present while I taught two original lessons.

Teaching Module Author, Understanding Evolution, Berkeley, CA (2006-2007)
* Designed a web-based lesson at an upper high school level on eye diversity entitled “Why the Eye” for the Understanding Evolution project (University of California Museum of Paleontology Education Department). Developed content, organized images and wrote text to successfully communicate concepts of evolution to a general audience.  Published: http://evolution.berkeley.edu/evolibrary/article/0_0_0/eyes_01

Science Writer, Howard Hughes Medical Institute Ask A Scientist, Berkeley, CA (2006-2007)
* Engaged in online scientific consulting for a web-based program that communicates science to broader audiences. Participated as a scientist who creatively answered questions submitted by the public. Recognized for excellent writing for my answer to “Do identical twins have identical fingerprints?” by being published in the Howard Hughes Medical Institute Bulletin, May 2007. Published: http://www.hhmi.org/bulletin/may2007/pdf/ask_scientist.pdf

Science Education Opportunities Resource Author, University of California, Berkeley (2007)
* Established an online resource to identify outreach and science education opportunities in the Bay Area along with the help of another graduate student. Volunteer and paid teaching opportunities are listed, as well as career resources.  Published: http://ib.berkeley.edu/student/grad/fees/edopp.php

Marine Science Lead Instructor, Sally Ride Science Camp, Berkeley, CA (2006)
* Taught marine science/biology to a group of 11 6^th-8^thgrade girls for one week. Evaluated and improved content for science curriculum, introduced new lab exercises including one on biodiversity of living animals from the San Francisco Bay, led field trips to two labs on the Berkeley campus, as well as to the California Academy of Sciences. Facilitated small group presentations on different underwater habitats to the entire camp and their parents. Resulted in increased appreciation for marine organisms and interest in science careers.

ACADEMIC SERVICE AND LEADERSHIP POSITIONS
Academic Senate, Committee on University Extension, University of California, Berkeley (2005-2007)
* Represented the Graduate Assembly on the U.C. Extension Committee. Berkeley Extension is the branch of the University of California, Berkeley that focuses on adult and professional education as well as community outreach. This Senate group met approximately 3 times per semester to discuss issues ranging from program development to the relation of U.C. Extension with main campus activities.

Student Research Supervisor, Patel Lab, University of California, Berkeley (2004-2007)
* Trained, supervised, and developed research projects for undergraduates and graduate rotation students during academic years and summers in a developmental biology research laboratory.  Resulted in one student attending graduate school, another applying in the future.

Teaching Workshop Leader, University of California, Berkeley (2006)
* Instructed 40 new biological sciences graduate students on how to design new classroom exercises, provided information about resources on campus, highlighted skills/techniques to use while teaching, and led trouble shooting sessions for potential pitfalls/anxieties they may have about the upcoming semester. Received positive feedback in evaluations from students attending the workshop.

Conference Organizer, University of California, Berkeley (2006)
* Collaborated with a team of five graduate students to host the Integrating Evolution, Development, and Genomics conference with ­­­219 attendees June 2006 (http://evodevo.org) including 20 talks from invited speakers, additional talks from submitted abstracts, and a poster session. Organized a teaching workshop with staff from the University of California Museum of Paleontology, designed advertising materials, secured funding from sponsors on and off campus, managed a budget for the event, invited and communicated with speakers from around the world, led organizational meetings with the five graduate student leaders, as well as planned a strategy for deployment of and led a group of 15-20 volunteers throughout the meeting.

Evo-Devo Day Organizer, University of California, Berkeley (2005)
* United a 3-student team to organize a one-day symposium highlighting on-campus Evolution and Development research. Supervised volunteers at the event, initiated interaction among biological science departments, disseminated information about campus resources, and established an inviting and supportive atmosphere on campus in which we planned the future Integrating Evolution, Development and Genomics conference.

Graduate Student Representative at Faculty Meetings, University of California, Berkeley (2004)
* Represented the graduate students at the Department of Integrative Biology faculty meetings during the fall semester, 2004. Acquired insight into how the department functions, how new faculty members are recruited and hired, and how various departmental issues, ranging from facilities to budgeting, are resolved.

PRESENTATIONS AND SEMINARS
2008  University of Richmond, Richmond, VA
“These legs weren’t made for walkin’ and that’s not what they do!” (invited seminar)

2007  American Congress on Developmental Biology, Cancun, Mexico
“Hox genes and appendage identity in Parhyale hawaiensis” (poster)

2006  Integrating Evolution, Development, and Genomics, Inaugural Meeting, Berkeley, CA
“Analyzing the function of Hox genes in crustacean appendage diversity” (poster)

2006  British Society for Developmental Biology, Annual Meeting, York, England
“Analyzing the function of Hox genes in crustacean appendage diversity” (poster)
Presented this poster as an invited guest for winning the student poster competition at the Society for Developmental Biology meeting in San Francisco, 2005.

2006  Institute of Genetics, School of Biology, University of Nottingham, UK
“The role of Hox genes in crustacean appendage diversity” (invited seminar)

2006  Society for Integrative and Comparative Biology Annual Meeting, Orlando, FL
“Functional approaches to understanding the role of Hox genes during crustacean development” (poster)

2006  Evolution and Development Supergroup, University of California, Berkeley
“These legs weren’t made for walkin’ and that’s not what they do” (talk) 

2005  Society for Developmental Biology Annual Meeting, San Francisco, CA
“The role of Hox genes in crustacean appendage specialization” (poster)

2005  Society for Integrative and Comparative Biology Annual Meeting, San Diego, CA. 
“The role of Hox genes in crustacean appendage diversity” (talk)

2004  Society for Developmental Biology Annual Meeting, Calgary, Canada.
“The role of Ubx in crustacean development” (poster)

2001  Australian Marine Science Association Annual Meeting, Townsville, Australia.
“Analysis of gene expression in early development of a marine demosponge: identifying conserved developmental pathways.” (talk)

PRESENTATION AWARDS
* Best student poster presentation at the Society for Integrative and Comparative Biology Annual Meeting, Division of Evolutionary Developmental Biology, Orlando, FL (2006).

* Best student poster presentation at the Society for Developmental Biology Annual Meeting, San Francisco, CA (2005). Awarded the top prize, a full-paid trip to the British Society for Developmental Biology Annual Meeting, York, UK (2006).

* Crustacean Society best student oral presentation at the Society for Integrative and Comparative Biology Annual Meeting, San Diego, CA (2005).

* Ron Kenny Prize for 1 of 4 best student presentations (talk) at the Australian Marine Science Association Annual Meeting, Townsville, Australia (2001).

* Biology Department Award for Academic Excellence, Fairfield University, Fairfield, CT (2000)

RESEARCH AND TRAVEL GRANTS
* Graduate Division Travel Grant, University of California Berkeley (2007)  
* Society for Developmental Biology Student Travel Grant (2007)
* Doolittle Grant, University of Chicago (2003)
* National Science Foundation Graduate Student Research Fellowship (2001-2004)
* Fulbright Fellowship, Australian-American Fulbright Association (2000-2001)
* Council for Undergraduate Research Summer Fellowship (1999)
* Pfizer Summer Undergraduate Research Fellowship (1999)

PUBLICATIONS
Liubicich D, Serano J, Protas M, Tran K and Patel NH. Ultrabithorax knockdown phenotype supports the role of Hox genes in the evolution of crustacean appendage diversity (in prep).

Liubicich, D. (2007) “Why the Eye”, Understanding Evolution, UCMP.
http://evolution.berkeley.edu/evolibrary/article/0_0_0/eyes_01

Liubicich, D. (2007) “Do identical twins have identical fingerprints?” HHMI Bulletin, May 2007.

Larroux C, Fahey B, Liubicich D, Leys SP, Hinman VF, Gongora M, Woerheide G, and Degnan BM. (2006) Gene expression in sponge embryos and larvae: insights into the last common ancestor of all metazoans. Evol Dev.   8:150-173.

Hill A, Hill MS and DM Liubicich (2000) Insights into early animal evolution: developmental genes in sponges.  American Zoologist 40:1056-1057. (Abstract)