Developmental Biology

An ancient manual for the assembly of creatures from Planet Earth*

How does the genome of an egg control cell division, cell movement, and cellular differentiation to produce a multicellular organism? How does evolution manipulate this program so that a better adapted life form is produced?

For the answers to these questions and more, students should consider taking Introduction to Dev Biol. If you have taken Genetics you can also take one of the advanced courses Dev Genetics or Developmental Biology. If you are a grad student, you should also consider our Molecular Biology Journal Club.

To do research in Developmental Biology, prospective grad students and undergrads are encouraged to apply to work in our lab. We are interested in understanding how cell lineage and cell movement control cell fate during early development. Vignettes from some of our projects and some techniques we use are below.

*Tools not required.


How do cells move to produce the elegant changes in morphology seen in the early embryo? In this project we are trying to figure out how the blastoderm thins during a morphogenetic process termed epiboly. We found that the molecule E-cadherin is mutated in half baked mutants, and this molecule is necessary for the process of radial intercalation, shown above.

This figure is from our Kane 2005 paper.


blood lineage

Blood Lineage

How do stem stems divide to produce one daughter cell that becomes differentiated but another daughter that remains a stem cell, like its mother cell? In a new project spearheaded by Rachel Warga, we have been examining the early lineages of the primitive blood, using clonal analysis to establish relationships amongst the blood cells. The above figure summarizes some of our new findings showing the early lineage relationship between red and white blood cells, and their origins in the gastrula stage embryo.

Our Warga 2009 paper was in Dev Cell.


harpy mut

Early Cell Cycle Control

How is the early cell cycle controlled? In the zebrafish mutant screen in Tübingen, we identified genes that, when mutant, produced the Early Arrest Phenotypes. Almost all of these have turned out to be cell cycle genes. One example is shown above, harpy, a phenotype caused by a mutation in the gene emi1 that is necessary for mitosis. In this mutant, mitosis is bypassed and cells enter the next cycle, going through S-phase. As they continue to bypass mitosis, the nuclei ultimately accumulate 4 to 8 times the normal amount of DNA!

Read more in our Riley 2010 paper and in our newer Warga 2016 paper.



The Cell Cycle in vivo

How we monitor the cell cycle in vivo? We follow cells with the Dual FUCCI transgene from David Kimelman's lab. This transgene is transcribed in every cell of the embryo and encodes two florescent proteins that are targeted for destruction in different phases of the cell cycle. Nuclei appear red in early G1; pink (red + blue) in late G1; blue in S, G2 and early M; and colorless in mitosis. In the confocal time lapse above, three lineages of dividing skin cells are shown; consider lineage 2. At time 0:05 cell 2 is in S/G2 (blue). At time 0:35, the nucleus of the cell disappears as it enters mitosis. At time 1:05, the nuclei 2a and 2b reappear in late G1 (pink), apparently skipping early G1, and then at 1:30, the cells enter S (blue).

Using FUCCI to look at segmentation.




How do we knockout genes that we wish to study? Recent advances in technology allow us to make targeted double strand breaks in the the DNA encoding specific genes using the CRISPR/Cas9 system. What with no homologous template nearby, these breaks are repaired imprefectly and a mutation results. We have done that in the case of two genes we work on in the laboratory, specter and zombie. Now we are trying new methods where we include a homologous repair template, so we can modify a specific locus so that we can directly and predictably control the activity of the endogeneous gene. Brave new world stuff (except that they were doing it in mouse 20 years ago).

A nice summary by Heidi Ledford in Nature.



Making Fish Transgenes

How do we insert modified genes into zebrafish? Design a plasmid construct inside a Tol2 transposon. First we add our favorite gene under the control of some promoter, usually a heat shock promoter. This gene is tethered to a some color reporter. Normally we include a (second) color reporter that is driven by an ubiquitous promoter so we know which cells (or embryos) contain the transgene. We use these constructs in two ways. Usually we inject the transgene (with transposase) at the one cell stage and look at the transient expression of the gene in clones of cells that have inherited the construct. Or, we can try to get the gene into the germline and start a line of transgenic fish. That's fun, making colored zebrafish!

Very nice review from Koichi Kawakami...and another one of his here.