Cartilage stain, Xenopus


Birth defects are now the major cause of infant death in the US and Europe. Despite their tremendous impact, we know very little about the causes of most birth defects. Prior research has focused on environmental causes, especially nutrition (such as folate). However, recent evidence indicates that genetics is important too. Our goal is to analyze the gene sequences (“exome”) of birth defect patients in order to find a gene that might explain their disease. Deciphering the genes that cause birth defects is particularly difficult, however. In order to tackle this problem, we combine patient driven gene discovery with developmental mechanism discovery in disease model systems, especially the frog model, Xenopus. This model organism is particularly well-suited for studying birth defect genes because experiments are fast and easy to perform, and as a tetrapod, Xenopus has many similarities to human development. Once we have identified a candidate gene from our patient, we test it in frog to see if it also causes a similar phenotype. If it does, then we try to understand the underlying developmental mechanisms. We try to figure out “how” the gene directs embryonic development.

Congenital Malformations

Congenital Malformations - Ten Year Vision

Congenital malformation research will be transformed by the combination of 1) next generation human genomics and 2) functional analysis of candidate genes in model systems. In order to lead this revolution, we need to create a translational infrastructure that enrolls congenital malformations patients into genomics analyses, identifies candidate genes, and then tests those candidate genes in model systems for functional relevance. Once functional relevance is established, then deep mechanistic studies can discover the underlying developmental role. Go to the Congenital Malformations Research page to read about the long term aims of this research program.


composite RGB image of cilia

In our approach, we analyze genes from patients with birth defects in order to understand how they affect development. Then, in order to understand how the gene affects embryonic development, we need to see developmental events in action. In particular, we need to be able to watch the behavior of cells or subcellular organelles during development. Live imaging can be challenging but incredibly informative. In addition, we can label different parts of the cell or monitor dynamic cellular components (actin, calcium, etc) with new fluorophores in order to understand the processes that shape an embryo. In addition, microscopes continue to become more sensitive with greater resolution, allowing the visualization of things we could never see before. In addition to confocal microscopy, we are interested in lightsheet and super-resolution imaging methods to look into the embryo and see embryonic development in action. Go to the Imaging Research page.

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OTC Imaging

OTC imaging of embryonic heart valves in X. tropicalis - Engin Deniz

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Bead flow assay

Bead flow over embryo indicates epidermal ciliary function - Choma Lab



Cilia have diverse functions at the interface between the cell and the extracellular space. Cilia are large complex organelles composed of the ciliary axoneme surrounded by the ciliary membrane. The axoneme is comprised of 9 microtubule doublets and attached motor and transport proteins. Many cells have a single cilium that arises from the centriole (a monocilium). By displaying a variety of receptors, these “signaling” cilia are adapted to function as “cellular antennae”, reaching out beyond the cell surface to capture a variety of signals. Monocilia are created and resorbed in a cell-cycle dependent manner, predicting a central role in cell cycle regulation. Mechanisms that contribute to the biogenesis and resorption of cilia remain ill defined. Go to the Cilia Research page.


Notch signaling is essential for the balance of cilia type in the left-right Organizer (LRO). There are two types of cilia: motile and immotile. Activation of Notch leads to more immotile cilia.

The notch pathway plays an important role in cell fate decisions. In a patient with Heterotaxy, we identified an abnormality in galnt11, a glycosylation gene we showed alters LR patterning in Xenopus. Unexpectedly, loss of galnt11 also leads to an increase in the number of multicilitated cells on the epidermis of the frog embryo. The Kintner lab has elegantly shown this can be a Notch phenotype. In a series of experiments, we then showed galnt11 appears to activate the notch pathway, directly glycosylates Notch peptides, and interestingly, can enhance the cleavage of a Notch peptide spanning the juxtamembrane region of Notch. Proteolytic processing of Notch is critical for its signaling function. Finally, we demonstrated Notch is essential for specifying motile vs. immotile cilia in the Left-Right Organizer, and showed this specification is essential for establishing proper LR pattern. (Boskovski et al Nature 2013

Go to the Notch Research Page.

Nuclear localization of Beta catenin, stage 10, J. Griffin

The Wnt pathway is critical for many steps in embryonic patterning including dorsal ventral axis formation. We have found that patients with Heterotaxy fail to properly form the Left Right Organizer (LRO) which is a dorsal structure. Failure to properly form the LRO can lead to LR patterning defects. Go to the Wnt Signaling Research page.


Cartilage stain, Xenoput embryos

Many of the genes identified from patients with congenital malformations have no known role in embryonic development. In some cases, these genes are completely novel with nothing known about their function. Go to the Unknown Research page.