Microscopy and Microanalysis
Milwaukee, Wisconsin
Katsuaki presented the group’s cryogenic atom probe work, which sets out to image mineralized collagen while it is still frozen and hydrated.
A sea urchin embryo grows two single crystals that curve, branch, and mirror one another. A single-celled acantharean in the open ocean sifts strontium out of seawater where calcium outnumbers it a hundred to one. Ameloblasts build enamel and then die, leaving a tissue that can last a lifetime with no living cell to maintain it.
We work out the mechanisms: how these tissues are built, how function emerges from them, how they record their environment, and what happens when things go awry. Once we understand the principles evolution landed on, the applications follow, whether that is predicting the course of tooth decay or pulling radioactive strontium-90 out of nuclear waste.
Derk Joester, Professor of Materials Science and Engineering
McCormick School of Engineering, Northwestern University
Evanston, Illinois, USA
Five projects, spanning marine organisms, human tissue, and synthetic model systems. Each has its own page.
Dental enamel is the hardest, most wear-resistant tissue our bodies make. Yet once it is damaged or lost, our options for restoring it remain surprisingly limited. To change this, we study its structure, composition, and degradation from single atoms on up.
Read more →To build their skeletons, single-celled acanthareans pick strontium out of seawater in which calcium is a hundred times more abundant. We are working out how, so that one day we can pull radioactive strontium-90 out of nuclear waste and the environment.
Read more →Crystal growth is a fundamentally enabling technology in materials science. We study the sea urchin embryo to learn how it controls the elongation and branching of single crystals along specific crystallographic directions.
Read more →Sea urchins tunnel into rock far harder than their own teeth. We want to know how they control the magnesium content of the calcite lattice, driving it far past the equilibrium solubility limit in some parts of the tooth and not others.
Read more →Phase transformations in biology are often controlled at cellular length scales. We use liposomes and microfluidic droplet reactors to measure how confinement and additives change the kinetics of nucleation and crystal growth.
Page in preparationChęciny, Poland
17 to 20 September 2026. Derk will talk about dental enamel, and what its structure, composition and transport processes look like from single atoms up to the whole tissue.
Milwaukee, Wisconsin
Katsuaki presented the group’s cryogenic atom probe work, which sets out to image mineralized collagen while it is still frozen and hydrated.
Il Ciocco, Lucca, Italy
Michaela gave a short talk and a poster on the acantharean project, on what these single-celled organisms carry in their transcriptomes that lets them sift strontium out of seawater. Derk presented on dental enamel.
Northwestern University, Evanston
Michael Angelo presented work on the enamel project, teaching neural networks to find enamel in micro-CT scans of mouse molars.
Virtual
Derk sat on the panel, on what a shed baby tooth records about the environment the child grew up in.
Dresden, Germany
Derk presented on dental enamel, and on the fast paths that ions take through a tissue that looks dense.
Northwestern University, Evanston
Olivia presented on the sea urchin tooth, on how the plumula mineralizes and takes shape.
Deerfield, Illinois
Katsuaki presented the cryogenic atom probe work, which looks at the interface between mineral and matrix without letting the water go.
Paris, France
Ethan presented on the enamel project, on measuring mouse teeth in bulk from their three-dimensional reconstructions. Derk presented on how ions move through enamel.
Northwestern University, Evanston
Melanie presented on the enamel project, on the order in which enamel densifies as it matures.
Boston, Massachusetts
Derk presented on nucleation in confinement, and on how fast amorphous carbonates crystallize when there is very little room.
Deerfield, Illinois
Derk presented on dental enamel, from single atoms up to the whole tissue.
Northwestern University, Evanston
Michaela presented on bioengineering single crystal growth, and on what cryogenic electron tomography shows of a sea urchin spicule as it grows.
Organisms control phase transformations with a precision that laboratory synthesis cannot yet reach, building anatomy that ranges from single-crystalline skeletal elements that curve and branch to hierarchically structured teeth that survive a lifetime of chewing.
Time matters as much as space. These materials are built over days or years, serve for decades, and can still be read tens of millions of years later — development, aging, disease, environment and fossilization each leave something behind.
Three questions run through our work:
Depending on the question we work with preserved tissue, animal models, cell culture, or entirely in vitro, combining materials characterization and synthesis with biochemistry, cell biology, and computational modeling.
Dental enamel is the hardest, most wear-resistant tissue our bodies make. Yet once it is damaged or lost, our options for restoring it remain surprisingly limited. To change this, we study its structure, composition, and degradation from single atoms on up.
Read more →To build their skeletons, single-celled acanthareans pick strontium out of seawater in which calcium is a hundred times more abundant. We are working out how, so that one day we can pull radioactive strontium-90 out of nuclear waste and the environment.
Read more →Crystal growth is a fundamentally enabling technology in materials science. We study the sea urchin embryo to learn how it controls the elongation and branching of single crystals along specific crystallographic directions.
Read more →Sea urchins tunnel into rock far harder than their own teeth. We want to know how they control the magnesium content of the calcite lattice, driving it far past the equilibrium solubility limit in some parts of the tooth and not others.
Read more →Phase transformations in biology are often controlled at cellular length scales. We use liposomes and microfluidic droplet reactors to measure how confinement and additives change the kinetics of nucleation and crystal growth.
Page in preparationOnce enamel is deposited on the surface of our teeth, the cells that built it die. After eruption it can survive a century or more of the conditions inside the mouth: hundreds of millions of chewing cycles, acidic and abrasive foods, repeated swings in temperature. It is considered the most durable of biological materials, and in fossils it preserves usable information for more than 40 million years.
Things can go awry during development, as in the rare inherited disorder amelogenesis imperfecta, or the far more common molar hypomineralization — "chalky teeth". They can also go wrong after eruption, when enamel is the first tissue damaged by erosive wear and by tooth decay. These conditions are rarely life-threatening, but their burden on patients and on society is enormous. Dental expenditure in the United States is approaching $200 billion a year, and around three billion people worldwide have untreated caries.
What makes enamel both fascinating and hard to understand is that its properties arise from a hierarchical architecture spanning many length scales. It is built from highly elongated crystallites only tens of nanometers across, each like a strand of uncooked spaghetti. Tens of thousands of these are bundled into rods, and the rods are woven together to form the enamel layer. As we and others have learned over the past decade, the hierarchy continues below the crystallite itself. Crystallites are joined by a vanishingly thin amorphous inorganic glue; their composition differs between core and shell; and even neighboring structural domains such as rod and interrod enamel are chemically and crystallographically distinct. These differences amount to only a few atomic percent, yet they strongly influence how enamel dissolves, wears, and resists damage.
A human premolar, and a section through its crown. The pale outer layer is enamel; the yellow interior is dentin. Everything that follows happens inside that outer couple of millimetres.
Light micrographs. DEJ marks the dentin–enamel junction, EES the enamel exterior surface. Scale bars 1 cm and 1 mm.
Step 1 of 8 · 1 cm
Enamel is built from rods — bundles a few micrometres across that weave past one another. The traced line follows the edge of a single rod.
Scanning electron micrograph of a polished and etched surface. Each rod bundles thousands of crystallites of shared orientation; the weave is what resists cracks.
Step 2 of 8 · 5 µm
Within each rod are the crystallites themselves — long, thin ribbons of mineral packed almost parallel.
SEM of a fractured surface showing crystallite ends and long axes.
Step 3 of 8 · 250 nm
Cut across, the crystallites are flattened hexagons. The dark spaces between them turn out to matter as much as the crystals do.
SEM of crystallite cross-sections; the dashed outline marks one crystallite. The intergranular space hosts a chemically distinct phase.
Step 4 of 8 · 100 nm
A crystallite is not chemically uniform. It has a core with a different composition from its shell — a gradient inside an object 50 nanometres wide.
STEM image; arrows mark core, shell and intergranular phase. Reported in DeRocher et al., Nature 583, 66 (2020).
Chemical gradients in human enamel crystallites · Nature 2020
Step 5 of 8 · 50 nm
At this magnification the regular planes of atoms show up as fine stripes running through the crystal.
High-resolution TEM. Crystallographic directions [001], ⟨010⟩ and ⟨100⟩ are indicated.
Step 6 of 8 · 10 nm
Each bright spot is a column of atoms seen end-on, in the hexagonal arrangement of the mineral hydroxylapatite.
HRTEM with FFT inset; (002) and (100) reflections indexed. Inset scale 5 nm⁻¹.
Step 7 of 8 · 1 nm
And finally the unit that repeats to build all of it — drawn over the image of the real thing, nine orders of magnitude below where we started.
Hydroxylapatite unit cell model overlaid on the lattice image.
Step 8 of 8 · 1 nm
We use imaging, microanalytical, and spectroscopic techniques to map the structure and composition of enamel across nine orders of magnitude in length scale and throughout its development, from an entire tooth down to individual atoms, and from the first deposition of the enamel matrix to fully mature enamel. We are now folding these measurements into computational models that aim to predict how enamel forms, matures, and dissolves under physiological conditions. This work frequently involves collaborators across the United States and around the world and contributes to a shared enamel atlas rather than remaining in a single laboratory’s drawer. Ultimately, we hope that understanding how enamel is built and deteriorates across scales will help us learn how to better protect, repair, and perhaps one day replace it.
Human enamel is remarkable: once it is formed, the cells that built it disappear, yet it can survive decades of mechanical and chemical challenges. At the same time, enamel cannot meaningfully regenerate after eruption. Our long-term goal is to understand how enamel acquires its extraordinary durability, how its structure and composition change during disease and aging, and how those changes influence dissolution and failure. Ultimately, we hope these insights will guide improved prevention, diagnostics, and future approaches to enamel repair or replacement.
One of our major current efforts is the development of predictive models of enamel dissolution across length scales. With Peter Voorhees, James Rondinelli, and Stuart Stock (Northwestern), Lara Estroff (Cornell), and Michel Koo (Penn), we are combining atomistic approaches — DFT, molecular dynamics, and AI-assisted simulation — with continuum phase-field models to understand how enamel responds to clinically relevant chemical challenges. On the experimental side this is supported by systematic mapping of enamel structure and composition across individuals, developmental stages, and disease states.
Using high-throughput imaging, spectroscopy, and machine learning, we are building the Biophysical Enamel Atlas: a framework for comparing enamel across developmental stages, genetic backgrounds, and disease models. The effort relies on genetically engineered mouse models from Ophir Klein (Cedars-Sinai/UCSF), Tom Diekwisch (Rochester), Michael Paine and Janet Moradian-Oldak (USC), and Jan Hu and Jim Simmer (Michigan), and on automated pipelines for segmenting the large three-dimensional datasets that SMCT, laboratory microCT, and FIB/SEM tomography produce.
With Tilman Grünewald (Aix-Marseille Université, CNRS, Institut Fresnel) and Manfred Burghammer (ESRF, Grenoble), we are using texture tomography (TexTom) to determine how enamel crystallites are oriented in space — letting us test long-standing models of enamel architecture rigorously, and follow how orientation changes during development, across species, and in disease.
Using APT, ToF-SIMS, XPS, and STEM we study how ions move through and are retained within enamel and dentin. How does fluoride become incorporated into dental tissues, and what limits its effectiveness? How do treatments such as silver fluoride and nanozyme-based therapies alter tissue chemistry? How do environmental and physiological exposures accumulate over a lifetime? With Michel Koo (Penn), and Mikako Hayashi and Katsuaki Naito (Osaka University).
Using atom probe tomography, we found that rodent enamel crystallites are joined by an ultrathin amorphous inorganic interphase rather than fused directly to one another. This previously unknown component helps control the mechanical behavior of enamel and changed how the field thinks about its structure.
Gordon et al., Science, 2015We showed that human enamel crystallites are chemically heterogeneous: each contains a core and a shell of slightly different composition. The difference amounts to only a few atomic percent, yet it strongly influences solubility and mechanical behavior.
DeRocher et al., Nature, 2020We demonstrated that enamel architecture varies systematically between rod and interrod enamel. These structural and compositional gradients give a new framework for understanding how enamel balances strength, toughness, and controlled dissolution.
Free et al., PNAS, 2022SEM · FIB/SEM tomography · STEM · Atom probe tomography (APT) · ToF-SIMS
Synchrotron micro-computed tomography (SMCT) · X-ray fluorescence microscopy (XFM)
Micro-XRD · Texture tomography (TexTom) · Total scattering
X-ray photoelectron spectroscopy (XPS) · X-ray absorption spectroscopy (XANES, EXAFS)
DFT · Molecular dynamics · AI/ML-assisted simulation · Phase-field modeling · ML image segmentation
NIH-NIDCR · National Science Foundation · Nakano Foundation · Nakao Foundation · Graduate research fellowships and training grants
Ethan Suwandi · Julia Dreher-Threlkeld · Katsuaki Naito · Derk Joester
We come from materials science, chemistry, biology, physics and engineering. What unites us is curiosity about the natural world.
We have been fortunate to work with a remarkably diverse group of people over the years. They are listed here, most recent departures first. We try to keep tabs on everyone, but each entry records only the last position we knew of — if yours is out of date, drop us a line and we will fix it.
| Name | Role | Degree or major | Where they are now |
|---|---|---|---|
| Litzy Gorostieta | Undergraduate → Post-baccalaureate researcher2025–2026 | Biology | unknown |
| Maddox Clarke | Undergraduate2026 | Biology | Dental Intern, Domino Dental, Brooklyn, NY |
| Ana Colliton | Undergraduate2025–2026 | — | PhD Student, Northwestern University |
| Michael Angelo San Juan | Undergraduate2025–2026 | — | unknown |
| Xingchen Zhao | Postdoctoral fellow2022–2025 | — | UPenn |
| Sarah Boyer | PhD student | PhD (MSE) 2025 | Argonne National Laboratory |
| Mel Andrade-Muñoz | Undergraduate2024–2025 | Neuroscience/Computer Science | unknown |
| Siya Brown | Undergraduate2024–2025 | Biol Sci/pre-dental | Dental Assistant, Evanston Dental Center |
| Erin Meyer | Postdoctoral fellow2022–2024 | — | University of North Caroline Wilmington |
| Lauren Jingles | Undergraduate2024 | Biology | unknown |
| Danielle Duggins | PhD student → Postdoctoral fellow2022–2023 | PhD (MSE) 2022 | Data Analysis Manager, University of Manchester (Harwell Science Campus, UK) |
| Victoria Cooley | PhD student | PhD (MSE) 2023 | Northwestern University, then ANL/APS |
| Yvette Calvillo | MS student | MS (MBP) 2023 | UIC (Dental School) |
| Xiangyu Gu | MS student | MS (MBP) 2023 | Biogen Inc, Boston, MA |
| Nilofar Khanbhai | MS student | MS (MBP) 2023 | Chicago Venture Fellow |
| Guanying Li | MS student | MS (MSE) 2023 | PhD student in Mechanical Engineering, Northwestern University |
| Youssef Aboukoura | Undergraduate2022–2023 | Biology | unknown |
| Ava Conyer | Undergraduate2023 | Chemical Engineering | MS student in Industrial Engineering, New York University |
| Jacob Cox | Undergraduate2023 | CBE | unknown |
| Layla Johnson | Undergraduate2023 | Chemistry | unknown |
| Genesis Kang | Undergraduate2022–2023 | MSE | unknown |
| Bradley Moreno | PhD student | PhD (MSE) 2022 | Intel Corporation, Portland, OR |
| Jaron Ma | MS student | MS (MSE) 2022 | Celadyne Technologies |
| Wenle Xu | MS student | MS (MSE) 2022 | Texas A&M University, College Station, TX. |
| Yiheng Du | Undergraduate2022 | MSE | unknown |
| Maya Kompella | Undergraduate2019–2022 | BME | Student Success Coach at City Year Chicago |
| Dylan McAfee | Undergraduate2021–2022 | Physics | unknown |
| Allessandra Dicorato | PhD student | PhD (MSE) 2021 | Broad Institute, Boston, MA. |
| Bisma Ajaz | MS student | MS (MBP) 2021 | Solid Bioscience, Cambridge, MA. |
| Maxine Faas | MS student | MS (MBP) 2021 | Exicure, Chicago, IL. |
| Samiha Syed | Undergraduate2021 | Chemistry | student at Benedictine University |
| Tarek Zaki | Undergraduate2019–2021 | MSE | Gateway to Graduate School Postbaccalaureate Research Internship & Mentoring (PRISM) Program, Novartis Institutes for Biomedical Research (NIBR). |
| Jessica Walker | Postdoctoral fellow2018–2020 | — | Diamond Light Source, UK |
| Karen DeRocher | PhD student | PhD (MSE) 2020 | NIST Gaithersburg, MD. |
| Robert Free | PhD student | PhD (MSE) 2020 | unknown |
| Sho Harisawa | MS student | MS (MSE) 2020 | Intel Corporation, Hillsboro, OR. |
| Yanfang Song | MS student | MS (MBP) 2020 | Catalent Pharma Solutions, Bloomington, IN. |
| Dante Montoto | Undergraduate2019–2020 | MSE | Mattiq, Skokie, IL. |
| Noah Metoki | Postdoctoral fellow2017–2019 | — | Sibel Health |
| Paul Smeets | Postdoctoral fellow2016–2019 | — | Northwestern University (NUANCE) |
| Linus Stegbauer | Postdoctoral fellow2016–2019 | — | University Stuttgart, Germany |
| Ning Han | MS student | MS (MBP) 2019 | WuXi Biologics, Cambridge, MA. |
| Utthara Rameshbabu | MS student | MS (MSE) 2019 | Impossible Foods, Redwood City, CA. |
| Vivian Merk | Postdoctoral fellow2017–2018 | — | Florida Atlantic University |
| Alp Alptekin | Undergraduate2017–2018 | MSE | unknown |
| Brian Lee | Undergraduate2018 | Biology | unknown |
| Michael Whittaker | PhD student | PhD (MSE) 2017 | LBNL/UC Berkeley. |
| Emilie Campbell | MS student | MS (MSE) 2017 | Razorfish Health, Chicago, IL. |
| Irene Yin-Ting Chang | Postdoctoral fellow2012–2016 | — | Merck & Co. |
| Robert (Jack) Cavanaugh | MS student2013–2016 | BS/MS 2016 | Ginkgo Bioworks, Inc., Boston, MA. |
| David Cadena | Undergraduate2016 | Physics | Accenture Federal Services, San Antonio, TX. |
| Jonathan Huang | Undergraduate2015–2016 | MSE | Apple, San Francisco, CA. |
| Kayla Moeller | Undergraduate2016 | Biology | Columbia University School of Dental Medicine |
| Victoria Nelson | Undergraduate2016 | MSE | unknown |
| Barghava Marisa | Undergraduate2015 | MSE | unknown |
| Regina Knapp | Postdoctoral fellow2010–2014 | — | PerkinElmer, Munich, Germany |
| Lyle Gordon | PhD student | PhD (MSE) 2014 | Nano Precision Medical, CA. |
| Michael Cohen | MS student | MS (MSE) 2014 | CVS/Aetna, New York, NY. |
| Huey-Ming Mak | MS student | MS (MBP) 2014 | Ginkgo Bioworks, Inc., Boston, MA. |
| Darcie Patterson | MS student | MS (MBP) 2014 | Alexion Pharmaceuticals, Inc., Glenview, IL. |
| Leanne Friedrich | Undergraduate2013–2014 | MSE | NIST Gaithersburg, MD. |
| Alexandra Rindone | Undergraduate2014 | BME | PhD student, Johns Hopkins University |
| Keara Saud | Undergraduate2014 | MSE | PhD student, U. Michigan Ann Arbor |
| Chantel Tester | PhD student | PhD (MSE) 2013 | Johnson & Johnson, NJ. |
| Ching-Hsuan Wu | PhD student | PhD (MSE) 2013 | unknown |
| David Goetsch | Undergraduate2013 | MSE | USC, Pasadena, CA. |
| Huang Vickie | Undergraduate2013 | MSE | unknown |
| Minna Pace (née Krejci) | PhD student | PhD (MSE) 2012 | Astellas Pharma, Northbrook, IL. |
| Fei Yin Luk | MS student2010–2012 | MS 2012 | US Department of Justice |
| Kimberly Blake | Undergraduate2011–2012 | African American Studies | Deputy Counsel - ICC International Court of Arbitration, New York, NY |
| Wisaruth Maethasith | Undergraduate2010–2012 | MSE | unknown |
| Kellen Mobilia | Undergraduate2010–2012 | ChBE | Berkeley Lights, Inc., San Francisco, CA. |
| Yuchen Yang | Undergraduate2011–2012 | Biology | Northwestern University |
| Elina Zaonegina | Undergraduate2011–2012 | Biology | NICE Ltd, Chicago, IL. |
| Evan Zaruba | Undergraduate2012 | BME | unknown |
| Christopher Carhart | Undergraduate2011 | ME | Boeing, Seattle, WA. |
| Laura Mueller | Undergraduate2009–2011 | BME | Philips Healthcare |
| Alexander Park | Undergraduate2008–2011 | MSE | Google, Chicago, IL. |
| Lawrence Tran | Undergraduate2010–2011 | MSE | Facebook, San Francisco, CA |
| Kathryn West (Halpern) | Intern → Undergraduate2010 | Biology | ECHO-Chicago, University of Chicago, IL. |
| Rose Gruenhagen | Undergraduate2009–2010 | BME | Medtronic, Minneapolis-St Paul, MN. |
| Janesh Lakhoo | Undergraduate2007–2010 | BME | Vanderbilt U. Medical Center, Nashville, TN. |
| Piotr Maniak | Undergraduate2007–2010 | BME | Baxter Healthcare, Evanston, IL. |
| Fangzheng Qian | Undergraduate2009–2010 | MSE | unknown |
| Jonathan Brickey | Undergraduate2008–2009 | MSE | Colorado Department of Public Health and Environment, Englewood, CO. |
| Jan Brueckner | Undergraduate2009 | Chemistry | Tesla, Grünheide, Brandenburg, Germany. |
| Pongkarn Chakthranont | Undergraduate2009 | ChBE | National Nanotechnology Center of Thailand, Bangkok City, Thailand. |
| Boping Lu | Undergraduate2009 | MSE | unknown |
| Brian Wasserman | Undergraduate2008–2009 | MSE | MD student, University of Miami |
| Ryan Brock | Undergraduate2008 | MSE | Exponent, Menlo Park, CA. |
| Steve Fitzgerald | Undergraduate2007–2008 | MSE | unknown |
| Mackenzie Marshall | Undergraduate | — | unknown |
| Xinjie (Jack) Wu | Undergraduate | — | unknown |
| Rhiannon Flanagan-Rosario | Intern | — | Barge Design Solutions, Inc., Atlanta, GA. |
| Laura McGinn | Intern | — | unknown |
| Haley Sproull | Intern | — | Creative Artists Agency, Los Angeles, CA. |
Mineralized tissues are organic–inorganic composites that provide mechanical strength to an organism, helping it feed, move, defend itself, and even sense its environment. Their hierarchical architectures tolerate damage, resist fatigue, and can regenerate, remodel, or repair themselves. And they are made in water, near ambient temperature and pressure, from abundant ingredients, a route inherently more sustainable than the high-temperature processing we use to make ceramics.
The sea urchin embryo is an excellent model system for studying how an organism controls phase transformations. Its skeleton is two mirror-symmetric spicules of calcite (CaCO3, as in limestone or chalk). Each spicule is a single crystal that curves and branches at closely controlled times and in precise crystallographic directions. Spicules from different species have distinct shapes, which suggests their growth is under genetic control. Each one is deposited by a small number of primary mesenchyme cells (PMCs) working so closely together that they fuse into a syncytium, sharing a single plasma membrane. The ability to shape the crystal may depend on the calcium carbonate arriving as a transient amorphous phase rather than crystallizing directly from solution.
In the embryo, primary mesenchyme cells (PMCs) build two spicules that serve as a skeleton. The PMCs are descendants of the micromeres that form in the 4th cleavage of the sea urchin embryo, about 6.5 hours after the egg is fertilized (hpf = hours post fertilization).
Schematic drawing, lateral view. The animal pole of the embryo is on top, the vegetal pole on the bottom. Micromeres are colored red.
Panel 1 of 12
Subsequent divisions give rise to 32 (or 64, depending on the species) descendants at the vegetal pole of the early blastula.
Schematic cutaway drawing, lateral view. The blastocoel is the fluid-filled cavity surrounded by a monolayer of cells. The descendants of the micromeres are rendered in dark red.
Panel 2 of 12
This marks an epithelial-to-mesenchymal transition, where tightly bound cells become loosely organized, migratory cells. This stage is also called the mesenchyme blastula. At this point, the endoderm (green) starts to differentiate from the ectoderm (yellow) and begins to invaginate.
Schematic cutaway drawing, lateral view. The blastocoel is the fluid-filled cavity surrounded by a monolayer of cells. The descendants of the micromeres are rendered in dark red.
Panel 3 of 12
As the endoderm continues to invaginate, PMCs migrate to form two ventrolateral clusters (VLC), a ring around the endoderm, and two strands towards the animal pole. Fusion of PMCs results in two syncytial masses. Each syncytium contains 16 (or 32) nuclei and is surrounded by a shared plasma membrane.
Schematic cutaway drawing, lateral view. PMCs (red), ectoderm (yellow), endoderm (green).
Panel 4 of 12
Biomineralization commences with the formation of a single crystalline calcite granule within each of the VLCs. The granule grows into the three-fold symmetric triradiate rudiment.
Schematic cutaway drawing, showing the vegetal half of the embryo seen along the animal–vegetal axis. PMCs (red), ectoderm (yellow), endoderm (green), granule and triradiate rudiment (black).
Panel 5 of 12
Biomineralization commences with the formation of a single crystalline calcite granule within each of the VLCs. The granule grows into the three-fold symmetric triradiate rudiment.
Brightfield image of a S. purpuratus embryo at 31 hpf. Both a granule (asterisk, and inset on bottom right) and an early triradiate rudiment (tr, inset on top right) are present.
Panel 6 of 12
Biomineralization commences with the formation of a single crystalline calcite granule within each of the VLCs. The granule grows into the three-fold symmetric triradiate rudiment.
Brightfield image of a S. purpuratus embryo at 35 hpf. Two triradiate rudiments (red arrowheads) are present.
Panel 7 of 12
The three arms of the triradiate rudiment grow in the crystallographic a-directions of the hexagonal calcite structure.
Schematic drawing of the triradiate rudiment (black) and the basal plane (001) of the calcite lattice (yellow). The crystallographic a- and c-directions are indicated.
Panel 8 of 12
On the way between the late gastrula and the prism stage of embryo development, one of the three radii changes growth direction by 90 degrees and turns into the body rod. The antero-lateral rod branches off the body rod. A little later, the second radius also changes growth direction by 90 degrees and turns into the post-oral rod.
Polarized light image of a S. purpuratus embryo at 51 hpf. br: body rod; al: antero-lateral rod; po: post-oral rod.
Panel 9 of 12
On the way between the late gastrula and the prism stage of embryo development, one of the three radii changes growth direction by 90 degrees and turns into the body rod. The antero-lateral rod branches off the body rod. A little later, the second radius also changes growth direction by 90 degrees and turns into the post-oral rod.
Schematic drawing of one prism-stage spicule (black and gray) and the basal plane (001) of the calcite lattice (yellow). The crystallographic a- and c-directions are indicated.
Panel 10 of 12
From the prism to the pluteus stage, the second radius completes its change of direction and, as the post-oral rod, elongates along the c-axis direction. The antero-lateral and body rods also elongate, the latter thickens at the distal end. Note that the two spicules are mirror images.
Polarized light image of a S. purpuratus pluteus at 71 hpf. br: body rod; al: antero-lateral rod; po: post-oral rod; mv: mid-ventral rod.
Panel 11 of 12
From the prism to the pluteus stage, the second radius completes its change of direction and, as the post-oral rod, elongates along the c-axis direction. The antero-lateral and body rods also elongate, the latter thickens at the distal end. Note that the two spicules are mirror images.
Schematic drawing of a pluteus stage embryo with two mirror-symmetric spicules (gray). The location of the original triradiate is indicated for one of the spicules (black).
Panel 12 of 12
What sets this system apart is that the PMCs keep working outside the embryo. That is rare enough among mineralizing cells to be worth a project in its own right. It means we can manipulate the process by genetic engineering or by providing molecular cues to the cells, and observe both cellular behavior and crystal growth in real time. This is what makes the long-term goal plausible: putting PMCs, or the molecules they depend on, to work making materials.
We use a broad range of techniques to get there. Cryo-electron tomography, STEM, and FIB/SEM tomography show us the cellular structures and the crystals themselves. Transcriptomics, proteomics, and recombinant antibodies tell us which molecules are present and where. Cell culture and in vitro experiments let us test what those molecules actually do. What we want to know is how specific proteins are assembled and patterned in the spicule matrix, and how that patterning sets nucleation kinetics and the direction the crystal grows. That is the first step towards porting the key players into a system that can be engineered and scaled using the tools of synthetic biology.
Sea urchins make masterful use of calcite throughout their lives. The embryo’s skeleton is only two single crystals; the adult’s test, spines, and teeth are orders of magnitude larger in volume and more complex in microstructure, composition, and function. We expect the design principles and the molecular toolkit to be shared. The embryo is where they are simplest to study, and what we learn there should show how skeletal elements arise from cellular processes across length scales, and how those processes shape crystal growth. That is a first step towards connecting developmental biology to the materials genome. The knowledge could reach areas as far apart as the programmed synthesis of bone grafts and the large-scale sequestration of carbon dioxide.
We are re-assessing the spicule proteome using modern proteomics and transcriptomics, with the goal of extending the analysis of functional roles beyond the known set of occluded proteins, SM50 and SM30. We are also mapping how spicule matrix proteins are distributed within the spicule.
Using in vitro experiments in microfluidic droplets and in vivo knock-down experiments, we are analyzing how native and recombinant spicule matrix proteins affect nucleation, polymorph selection, and crystal growth.
Imaging and tomography let us study interfacial processes at the spicule growth front. We are also working to elucidate the ultrastructure of the spicule elongation apparatus: the machinery that we hypothesize allows the PMCs to elongate the spicule in specific crystallographic directions.
Building on prior work by Okazaki, Wilt, and others, we used micro-contact printing in an in vitro culture system of sea urchin embryo primary mesenchyme cells (PMCs) to control the deposition of endoskeletal spicules made from single-crystalline calcite (CaCO3).
Wu, Park & Joester, Journal of the American Chemical Society, 2011Again using an in vitro culture system, we discovered that recombinant vascular endothelial growth factor (rVEGF) can be used to control the shape and crystallographic growth direction of spicules.
Knapp, Wu, Mobilia & Joester, Journal of the American Chemical Society, 2012We published our optimized PMC isolation and culture protocols as part of a two-volume series of invited contributions on echinoderm biology.
Moreno et al., Methods in Cell Biology, 2019More recently, transcriptional profiling using RNAseq has given us deep insight into the molecular players that may be involved. Together with the culture system, that gives us an unusual opportunity: to investigate the mechanism behind this example of biological control over crystal growth in a well-characterized in vitro system.
Polarized light · Fluorescence · DIC · Live-cell microscopy · Confocal microscopy · µ-Raman
SEM · VolumeScope · TEM · STEM · Cryo-SEM · Cryo-ET · (Cryo-)FIB/SEM tomography
X-ray absorption spectroscopy (XANES, EXAFS)
X-ray fluorescence microscopy (XFM)
Nano-XRD
Transcriptomics (RNAseq) · Proteomics
National Science Foundation · Graduate research fellowships and training grants
Acanthareans are marine, single-celled organisms that build an endoskeleton of celestine (SrSO4). Three things about them are worth the attention. They grow their spicules as single crystals with shapes that are very different from those observed in lab-grown crystals, and those shapes are specific to the species. They remodel the skeleton, and even dissolve it, at defined points in the life cycle. And they select Sr2+ out of seawater in which Ca2+ is a hundred times more abundant.
Each individual has either ten diametral or twenty radial spicules. Shape, connectivity, and the architecture of the central junction that joins them differ markedly among the roughly 150 known species. Spicules are faceted in some, smoothly curving in others, and can carry barbs, wings, or branches that anastomose into regular lattices and porous plates. Aspect ratios reach twenty, where synthetic celestine grows as faceted tablets. In the few species examined so far, the long axis of the spicule runs parallel to the crystallographic a-axis. Form this consistent, and this specific to a species, is strong evidence that the process is under genetic control.
The form is not fixed within a single life either. Spicules grow more elaborate as an individual matures, and in some clades the endoskeleton is remodelled into a mineralized cyst before hundreds or thousands of flagellated swarmer cells are released. So the organism can reshape its crystals at different points in its development and dissolve them in a controlled way, which suggests genetic regulation here too, perhaps through overlapping or life-stage-specific sets of genes.
Seawater holds 88 µM Sr2+ against 10.5 mM Ca2+, and it is undersaturated with respect to celestine. Sulfate, at 28.9 mM, is not limiting. Because their ionic radii are similar, Ca2+ and Sr2+ are usually transported more or less indiscriminately by calcium channels and pumps, so most biominerals take up strontium at close to the ambient ratio. Acanthareans do not. How they manage it is unknown: the answer could lie in selective channels or pumps, or in holding the local sulfate concentration in the narrow range that precipitates celestine but none of the calcium sulfates.
The organic and inorganic biochemistry and physiology of acanthareans is largely unexplored. Our long-term goals are to identify the design principles used by acanthareans and apply them in bio-inspired materials and bio-enabled routes to capture Sr2+ in the presence of chemically similar ions. That ability matters directly for the efficient removal of 90Sr, a highly active radioisotope present in nuclear fallout, in spent fuel rods, and in the high-level nuclear waste held at federal facilities. 90Sr is dangerous precisely because nothing distinguishes it from calcium: a similar ionic radius and similar chemistry mean transport proteins take it up indiscriminately, so it accumulates in bone and teeth, where its beta decay, with a half-life of about 29 years, goes on delivering a dose for decades.
We are profiling acantharean transcriptomes to find the genes expressed during skeleton formation and the proteins they encode.
We are identifying the Sr2+ and SO42− transporters and characterizing what they do, to work out how the ions reach the site of mineralization. In parallel, we use elemental mapping to determine uptake routes and the incorporation of elements into the biomineral.
Polarized light · Fluorescence · DIC · Live-cell microscopy · Confocal microscopy
SEM · TEM · STEM · FIB/SEM
X-ray fluorescence microscopy (XFM)
Nano-XRD
Transcriptomics (RNAseq) · Proteomics
National Science Foundation · Army Research Office
Many sea urchins graze on rocky reefs, frequently occupying pits they excavate themselves. They erode not only soft lime- and mudstone (Mohs 2 to 3) but substantially harder substrates, including sandstone and granite (Mohs 6 to 7). Their teeth, however, are composed largely of calcite (Mohs 3), softer than much of the substrate they cut. Sea urchins compensate through a strongly hierarchical, compositionally and functionally graded architecture, and through continuous growth.
Continuous growth means that every stage of tooth development is present in a single tooth at any one time. Odontoblasts arise in the plumula attached to the cervical end and fuse into a syncytium that deposits magnesian calcite (Ca1-xMgxCO3). As the maturing tissue advances towards the incisal end, the syncytium withdraws, connecting the crystalline elements with widening mineral columns and ultimately yielding an acellular tissue. In effect, the bricks go down first and the mortar is filled in afterwards.
The tooth combines fibrous and platy elements that in combination confer wear resistance, toughness, and self-sharpening. These microstructural elements differ markedly in Mg content. Primary and secondary plates, among others, consist of high magnesian calcite (HMC), with up to 13 at% Mg on Ca lattice sites. The columns that connect the plates reach 35 at% Mg, far beyond the nominal solubility limit of Mg in calcite; we refer to this phase as very high magnesian calcite (VHMC).
Many sea urchins graze on rocky reefs, occupying pits they excavate themselves. The five teeth that do the cutting are carried in Aristotle’s lantern.
Volume rendering of Strongylocentrotus purpuratus Aristotle’s lantern, oblique view.
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Each tooth in Aristotle’s lantern is held by an independently controlled jaw apparatus that also advances it as it grows.
Volume rendering of S. purpuratus lantern, oral view.
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Only the self-sharpening tip meets the substrate the sea urchin grazes on. The rest of the tooth is a reserve, still maturing, that will be pushed forward to replace what is worn away.
Cutaway view of S. purpuratus lantern, the section plane slicing the tooth on the left along its center line.
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In this transverse section, the five-fold symmetry of the lantern is on display.
Cutaway view of S. purpuratus lantern, the section plane normal to the lantern’s axis.
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In this mature tooth, the keel (vertical) is well developed and topped by a broad flange.
Cross section of a mature Lytechinus variegatus tooth.
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At increasing magnification, the intricate microstructure of the tooth emerges.
Cross section of a mature L. variegatus tooth.
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Primary plates (pp) and secondary plates (sp) are laid down first, then connected by columns.
Cross section of a mature L. variegatus tooth.
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As the syncytium of odontoblasts withdraws, the columns grow laterally until they fill space.
Cross section of a mature L. variegatus tooth.
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It lies roughly along the center line of the flange and appears darker in BSE images. As the hardest part of the tooth, it forms the cutting edge.
Cross section of a mature L. variegatus tooth.
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In this closeup, the continuity of primary and secondary plates in the lateral parts of the flange is apparent.
Cross section of a mature L. variegatus tooth.
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In this closeup, the very fine needles that reinforce the composite become apparent.
Cross section of a mature L. variegatus tooth.
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Elemental mapping reveals the high Mg content in the stone.
Mg/(Mg+Ca) ratio map of the previous panel.
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In this closeup, the primary plates, secondary plates, and needles appear brighter; the columns appear darker due to their high Mg content.
Cross section of a mature L. variegatus tooth.
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Primary and secondary plates are high magnesian calcite, with up to 13 at% Mg on Ca lattice sites. The columns that connect them reach 35 at%, far beyond the nominal solubility limit of Mg in calcite.
Mg/(Mg+Ca) ratio map of the previous panel.
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Immunohistochemical imaging (IHC) using a fluorescently labeled secondary antibody reveals the distribution of a member of a family of proline-alanine-rich phosphoproteins (PARPs).
Tissue section, flange right, stained with anti-PARP.
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Both HMC and VHMC are thermodynamically unstable under ambient conditions, and no ambient synthesis of VHMC is known. The strongly hydrated Mg2+ ion poisons calcite growth, so large single crystals of HMC or VHMC are difficult to obtain under mild solution conditions. Synthetic routes rely on elevated temperature and pressure and yield polycrystalline material with small grain sizes. Given the substantial increase in hardness on Mg substitution, and evidence of precipitation hardening in Mg-substituted calcites, there is considerable interest in how organisms achieve it. For this reason we are working to understand the mechanism by which sea urchins control Mg content far from equilibrium. Candidates are already in hand: comparing the proteome of the sea urchin tooth, which contains VHMC, with those of mineralized tissues that contain only HMC, Keith Alvares and co-workers identified a family of proline-alanine-rich phosphoproteins (PARPs).
Developmental, cellular, and physicochemical processes are inextricably linked in the biosynthesis of mineralized tissues, and biological control over phase transformations is an integral part of it. Properties and performance depend strongly on microstructure: the arrangement of inorganic and organic components, and the compositional gradients running through them. Understanding how cells pattern and maintain a privileged environment for mineral deposition, how they transport and modulate precursor concentrations, and what cellular machinery they use to control crystal growth across length scales is a prerequisite for intervening when developmental processes go awry, for engineering strategies to regrow and replace damaged tissue, and for designing bio-enabled and bio-inspired materials and processes. No hierarchical, functionally graded tissue of this kind is yet understood at that level. The availability of transgenic adult sea urchins now makes the tooth a tractable system in which to bring developmental and structural biology, biochemistry, and materials science to bear together.
We are testing how PARPs affect Mg incorporation and mechanical properties, both in vivo and in vitro.
We are using transcriptomics and proteomics to identify additional candidate proteins.
SEM · SEM-EDS · SEM-EBSD · STEM · FIB/SEM
X-ray fluorescence microscopy (XFM)
Transcriptomics (RNAseq) · Proteomics
Loss-of-function and gain-of-function mutants
Magnesian calcite growth assays
National Science Foundation
Data and code the group has published for others to use.
Our enamel data on FaceBase, the NIDCR-funded repository for craniofacial research.
Analysis code and processing pipelines from the group.
Last updated September 2026
An NIH- and NSF-funded effort with James Rondinelli and Peter Voorhees. Open to postdocs, PhD students and MS students in three thrusts:
NSF-funded. Open to PhD and MS students. We ask how the primary mesenchyme cells of the sea urchin embryo control the branching of a single crystal of calcium carbonate in precise crystallographic directions, using a wide range of techniques from materials science and the life sciences. Primary mentor: Derk Joester
PhD students who bring their own fellowship support are welcome in any of our active research areas, as are MS students. See the five current projects.
Welcome in any of our active research areas. Derk is glad to discuss projects for submission to funding agencies or foundations.
We prefer that you join a project in Fall or Winter, so that we get to know you and you get to know us before the summer. We look for students who are open to full-time, paid work over the summer.
How to apply is under Routes in, just below.
Our research is transdisciplinary, drawing on materials science and engineering, chemistry, and the life sciences. Whichever of those you trained in, you will pick up skills from the others. The work runs from experiments at the bench, in core facilities at Northwestern and at our Chicagoland partners, and at national user facilities — the Advanced Photon Source, the Advanced Light Source, the Midwest Center for Cryo-Electron Tomography — through demanding data analysis and visualization to computational modeling. No single project needs all of it. Wherever possible, you will learn to run even the most sophisticated instruments yourself rather than hand samples to someone else.
Postdocs should write directly with a CV and a letter covering what you have worked on, what you want to work on here, and why.
PhD students apply through the Materials Science and Engineering PhD program at Northwestern. The department receives more than 600 applications each cycle, and every one is vetted by the graduate admissions committee. Individual professors are much easier to reach once the committee has offered you a place in the department. When you do write, Derk generally replies only to inquiries that make clear why our field, and this lab in particular, appeal to you.
MS students also apply through Materials Science and Engineering. Once you are admitted, write to Derk to discuss projects for MSE 499 Independent Study or for the thesis-track MS.
Northwestern and Chicagoland undergraduates from any science or engineering background are welcome to write and ask about research opportunities.
Undergraduates at other US and international institutions should come through one of the Northwestern-run summer programs: the MRSEC REU, the IIN REU, SROP, or MICRO. We cannot host students from outside the US except through these or equivalent programs. Note that the MRSEC and IIN REU programs require US citizenship or permanent residency.
Interns from Chicagoland schools are welcome to write and ask what is currently available.
Where to write. Derk Joester, Northwestern University · d-joester@northwestern.edu
Maddox characterized the microstructure of the continuously growing teeth of the sea urchin Lytechinus pictus. Shown here is a ground and polished cross section using backscattered electron contrast in SEM (left), and a false-colored map of the cation ratio for Mg (right).
Summary to come from the mentor.
Eugene analyzed diffraction patterns of ice crystals formed in fruit fly larvae that express a putative antifreeze protein. Shown here are a 2D WAXS pattern (left), 1D diffraction data recorded at different temperatures (top right), and the a lattice parameter in wild-type and CaAFP-expressing larvae at 245 K (bottom right).
Summary to come from the mentor.
Summary to come from the mentor.
Michael evaluated how convolutional neural networks (CNNs) of different architectures perform when trained to segment mineralized tissues in synchrotron µCT reconstructions. Shown here are three tomographic slices of a murine hemimandible (left), the architectures compared (middle), and the same three slices after segmentation (right).