Morris Lab Research

This site is under reconstruction. Please come back to see the updates. 
Current publications list available on CV.

Dr. Bob:   email: 
telephone: 508-286-3953
    twitter, instagram: @drbobmorris
office: Mars Science Center 1137

Our research focus and recent data
Lab members and their projects
Lab protocols and recipes
Lab reading list
Links related to our research


Our research focus:

Research in the Morris Lab is centered on understanding the roles of cell movement in animal development.  Cells are complex and dynamic machines which can generate force along their own skeletons to move and to divide. My students and I are investigating how movement is generated within cells, and how these movements are involved in cell growth and differentiation.

In particular, my lab is currently focused on the process of ciliogenesis - the formation of new cilia.  Cilia are long cellular appendages that beat like paddles to move fluid over a cell or stand straight like antennae to receive signals from the outside world.  Healthy cilia help embryos grow and lungs clear, eyes see and ears hear.  By revealing how cilia grow and change to perform different functions in different tissues, our research helps explain the birth defects and diseases that arise from problems with these universal and versatile organelles.

One group of proteins we study in cilia are the kinesins, a superfamily of microtubule-based motor proteins that are involved in delivering materials to the ciliary tip for assembly.  We study these processes in sea urchin embryos because these embryos are easy to create, easy to culture, beautiful to look at, amenable to experimentation, similar to human cells in fundamental ways, and because studying sea creatures takes us to the coast. We employ basic techniques for studying cell development including genomics, light and fluorescence microscopy, microinjection, digital imaging, and digital image analysis.

We welcome comments and suggestions on our projects and webpages. - Dr. Bob


Some of our recent work:

The genome of the sea urchin Strongylocentrotus purpuratus

Sea Urchin Genome Sequencing Consortium:  Sodergren E, Weinstock GM, Davidson EH, Cameron RA, Gibbs RA, Angerer RC, Angerer LM, Arnone MI, Burgess DR, Burke RD, Coffman JA, Dean M, Elphick MR, Ettensohn CA, Foltz KR, Hamdoun A, Hynes RO, Klein WH, Marzluff W, McClay DR, Morris RL, Mushegian A, Rast JP, Smith LC, Thorndyke MC, Vacquier VD, Wessel GM, Wray G, Zhang L, Elsik CG, Ermolaeva O, Hlavina W, Hofmann G, Kitts P, Landrum MJ, Mackey AJ, Maglott D, Panopoulou G, Poustka AJ, Pruitt K, Sapojnikov V, Song X, Souvorov A, Solovyev V, Wei Z, Whittaker CA, Worley K, Durbin KJ, Shen Y, Fedrigo O, Garfield D, Haygood R, Primus A, Satija R, Severson T, Gonzalez-Garay ML, Jackson AR, Milosavljevic A, Tong M, Killian CE, Livingston BT, Wilt FH, Adams N, Bellé R, Carbonneau S, Cheung R, Cormier P, Cosson B, Croce J, Fernandez-Guerra A, Genevičre AM, Goel M, Kelkar H, Morales J, Mulner-Lorillon O, Robertson AJ, Goldstone JV, Cole B, Epel D, Gold B, Hahn ME, Howard-Ashby M, Scally M, Stegeman JJ, Allgood EL, Cool J, Judkins KM, McCafferty SS, Musante AM, Obar RA, Rawson AP, Rossetti BJ, Gibbons IR, Hoffman MP, Leone A, Istrail S, Materna SC, Samanta MP, Stolc V, Tongprasit W, Tu Q, Bergeron KF, Brandhorst BP, Whittle J, Berney K, Bottjer DJ, Calestani C, Peterson K, Chow E, Yuan QA, Elhaik E, Graur D, Reese JT, Bosdet I, Heesun S, Marra MA, Schein J, Anderson MK, Brockton V, Buckley KM, Cohen AH, Fugmann SD, Hibino T, Loza-Coll M, Majeske AJ, Messier C, Nair SV, Pancer Z, Terwilliger DP, Agca C, Arboleda E, Chen N, Churcher AM, Hallböök F, Humphrey GW, Idris MM, Kiyama T, Liang S, Mellott D, Mu X, Murray G, Olinski RP, Raible F, Rowe M, Taylor JS, Tessmar-Raible K, Wang D, Wilson KH, Yaguchi S, Gaasterland T, Galindo BE, Gunaratne HJ, Juliano C, Kinukawa M, Moy GW, Neill AT, Nomura M, Raisch M, Reade A, Roux MM, Song JL, Su YH, Townley IK, Voronina E, Wong JL, Amore G, Branno M, Brown ER, Cavalieri V, Duboc V, Duloquin L, Flytzanis C, Gache C, Lapraz F, Lepage T, Locascio A, Martinez P, Matassi G, Matranga V, Range R, Rizzo F, Röttinger E, Beane W, Bradham C, Byrum C, Glenn T, Hussain S, Manning G, Miranda E, Thomason R, Walton K, Wikramanayke A, Wu SY, Xu R, Brown CT, Chen L, Gray RF, Lee PY, Nam J, Oliveri P, Smith J, Muzny D, Bell S, Chacko J, Cree A, Curry S, Davis C, Dinh H, Dugan-Rocha S, Fowler J, Gill R, Hamilton C, Hernandez J, Hines S, Hume J, Jackson L, Jolivet A, Kovar C, Lee S, Lewis L, Miner G, Morgan M, Nazareth LV, Okwuonu G, Parker D, Pu LL, Thorn R, Wright R.

Science. 314(5801):941-52.  2006.

Link to Sea Urchin Sequencing Consortium paper (2006) in Science through Pubmed

We report the sequence and analysis of the 814-megabase genome of the sea urchin Strongylocentrotus purpuratus, a model for developmental and systems biology. The sequencing strategy combined whole-genome shotgun and bacterial artificial chromosome (BAC) sequences. This use of BAC clones, aided by a pooling strategy, overcame difficulties associated with high heterozygosity of the genome. The genome encodes about 23,300 genes, including many previously thought to be vertebrate innovations or known only outside the deuterostomes. This echinoderm genome provides an evolutionary outgroup for the chordates and yields insights into the evolution of deuterostomes.

Analysis of Cytoskeletal and Motility Proteins in the
Sea Urchin Genome Assembly

R.L. Morris 1,  M.P. Hoffman 2,  R.A. Obar 3,  S.S. McCafferty 1,  I.R. Gibbons 4A.D. Leone 2, J. Cool 1,  E.L. Allgood 1,  A.M. Musante 1,  K.M. Judkins 1, 
B.J. Rossetti
1,  A.P. Rawson 1D.R. Burgess 2.

Developmental Biology.  300(1):219-37.  2006. 

1Department of Biology, Wheaton College, Norton, Massachusetts 02766
2Department of Biology, Boston College, Chestnut Hill, MA 0246
3Tethys Research, LLC, 53 Downing Road, Bangor, Maine 04401; Present
Address: Massachusetts General Hospital Cancer Center, Charlestown, MA
4Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720

Link to R.L. Morris et al, 2006 through PubMed

The sea urchin embryo is a classical model system for studying the role of the cytoskeleton in such events as fertilization, mitosis, cleavage, cell migration and gastrulation.  We have conducted an analysis of gene models derived from the Strongylocentrotus purpuratus genome assembly and have gathered strong evidence for the existence of multiple gene families encoding cytoskeletal proteins and their regulators in sea urchin.  While many cytoskeletal genes have been cloned from sea urchin with sequences already existing in public databases, genome analysis reveals a significantly higher degree of diversity within certain gene families.  Furthermore, genes are described corresponding to homologs of cytoskeletal proteins not previously documented in sea urchins.  To illustrate the varying degree of sequence diversity that exists within cytoskeletal gene families, we conducted an analysis of genes encoding actins, specific actin-binding proteins, myosins, tubulins, kinesins, dyneins, specific microtubule-associated proteins, and intermediate filaments.  We conducted ontological analysis of select genes to better understand the relatedness of urchin cytoskeletal genes to those of other deuterostomes.  We analyzed developmental expression (EST) data to confirm the existence of select gene models and to understand their differential expression during various stages of early development.

Redistribution of the kinesin-II subunit KAP from cilia to nuclei during the mitotic and ciliogenic cycles in sea urchin embryos

R.L. Morris 1,  C.N. English 1,  J.E. Lou 1F.J. Dufort 1J.J. Nordberg 1M. Terasaki 2,  B. Hinkle 2.

Developmental Biology 274:56-69.  2004.

1Wheaton College, Norton, MA;  2University of Connecticut Health Center, Farmington CT

Link to R.L. Morris et al, 2004 through PubMed

KAP is the non-motor subunit of the heteromeric plus-end directed microtubule (MT) motor protein kinesin-II essential for normal cilia formation.   Studies in Chlamydomonas have demonstrated that kinesin-II drives the anterograde intraflagellar transport (IFT) of protein complexes along ciliary axonemes.  We used a green fluorescent protein (GFP) chimera of KAP, KAP-GFP, to monitor movements of this kinesin-II subunit in cells of sea urchin blastulae where cilia are retracted and rebuilt with each mitosis.  As expected if involved in IFT, KAP-GFP localized to apical cytoplasm, basal bodies, and cilia, and became concentrated on basal bodies of newly forming cilia. Surprisingly, after ciliary retraction early in mitosis, KAP-GFP moved into nuclei before nuclear envelope breakdown, was again present in nuclei after nuclear envelope reformation, and only decreased in nuclei as ciliogenesis reinitiated.  Nuclear transport of KAP-GFP could be due to a putative nuclear localization signal and nuclear export signals identified in the sea urchin KAP primary sequence.  Our observation of a protein involved in IFT being imported into the nucleus after ciliary retraction and again after nuclear envelope reformation suggests KAP115 may serve as a signal to the nucleus to reinitiate cilia formation during sea urchin development.

Honors Thesis presented by Jonah Cool

Wheaton College, May 22, 2004

Identification of Candidate Regulatory Sequences for Ciliary Genes

A gene battery is a collection of related genes that are expressed in unison. When a gene battery is responsible for regulating a group of genes, the genes share spatial and temporal expression patterns. Empirical evidence suggests that cilia are candidates for coordinate regulation and could be subject to control by a gene battery based upon temporal expression of necessary proteins. A gene battery regulates sets of genes through consensus sequences upstream of every gene included. We hypothesize that consensus sequences have been evolutionarily conserved upstream of genes coding for unique ciliary proteins and are responsible for the regulation of ciliary gene battery. To test this hypothesis, we performed comparative sequence analysis, in Chlamydomonas, upstream of twelve candidate ciliary genes from the dynein heavy chain and radial spoke protein families. Sequence analysis revealed five different motifs upstream of all twelve candidate ciliary genes. Of the five motifs, three stood out as putative binding elements. Based upon this data, we can conclude that consensus sequences exist upstream of ciliary genes and could coordinate regulation of a gene battery comprised of unique ciliary genes.


Figure 1.2a.  A possible ciliary gene battery.
The red arrow, in the top left, shows a transcription factor produced during the cell cycle. Transcription of the gene regulated by “Cell Cycle Control” produces the ciliogenesis launcher transcription protein. The ciliogenesis launcher transcription protein is a binding factor (shown as a red arrow) that regulates twelve ciliary genes. This figure visualizes the ability of a single factor to coordinately regulate alarge sub-set of ciliary genes. Each downward red arrow indicates a protein factor being able to influence regulation of the gene to whose upstream region it is directed.  (figure based on Erwin and Davidson, 2002, Development 129:3021-32.)


 Lab Members and their projects

Current and Recent student research projects in the Morris lab:

Students in the Morris lab work on a variety of projects related to the lab research focus. Research is ongoing year-round and includes time spent at Wheaton and Woods Hole.

Blair Rossetti '09, Ashlan Musante '07,
Kyle Judkins '07, and Amanda Rawson '09
"Analysis of ciliary and flagellar genes in the sea urchin genome."  poster for the American Society of Cell Biology meeting, San Diego CA, December 2006.
 Danielle Erkoboni '05 "Restructuring of the cytoskeleton during the mitotic and ciliogeneic cycles in sea urchin embryos."  poster presented at National Conference for Undergraduate Research (NCUR), Lexington VA, April 2005.
 Jonah Cool '04 "Genomic analysis of genes involved in ciliogenesis."  Senior Honor's Thesis, May 2004
Chris English '03  "Molecular localization signals in the motor protein kinesin-II"
poster presented at the Wheaton College Academic Festival, April 2002.
Cate Hunt '03,
Stephen Benz '05, and
Danielle Erkoboni '05
 "Subcellular movements of the motor protein kinesin-II".
poster presented at the Wheaton College Academic Festival, April 2002.
Julia Lou '01 "Analysis of the motor protein kinesin-II in early sea urchin embryos" Senior Honors Thesis presented May 2001
Chris English '03   "Microscopic analysis of cytoskeletal dynamics in developing sea urchin embryos."  presented at Wheaton's Academic Festival, April 2001
Fay Dufort '00  "Investigation of kinesin-II in ciliogenesis of sea urchin embryos"
Senior Honors Thesis presented May 2000
Josh Nordberg '00 "Evidence that ciliogenesis in sea urchin embryos occurs in discrete steps" Senior Honors Thesis presented May 2000


Here on a research trip to our collaborator Mark Terasaki's laboratory at the Marine Biological Laboratory at Woods Hole, the Morris Lab of summer 2000 spends an incubation period contemplating the clearly harsh lifestyle that summers of research entail.  
(L to R, Amy Manning '01, Julia Lou '01, Dr. Bob).


Lab Protocols and Recipes

Check back soon for PBS, Fixation Buffers, Artificial Sea Water, and other family recipes.


Lab Reading List

Selected primary literature articles on kinesin-II and ciliogenesis.


Links related to our research  Mark Terasaki and colleagues' productions from Room 2 at the MBL. See how the masters do it.

Dr. Bob (

) created this page. Please direct any comments or suggestions to him at


Image of Dr. Bob, surgeon and chief cut-up on "Vetrinarian's Hospital," courtesy of Miranda Galadriel Capra and Miranda's Muppet Pictures

Picture of Morris Lab taken at Woods Hole by Mark Terasaki during research trip, summer 2000.

Webpage author and designer Bob Morris (email:

Last updated: 04/2009