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A visual year in review: 13 highlights from the Allen Institute in 2019

A look back on the year’s major moments in neuroscience, cell biology, immunology and the frontiers of bioscience

December 18, 2019

It's been an exciting year at the Allen Institute, with new discoveries, resources and award receipients throughout the year. Read on for a baker's dozen of some of our favorite moments of 2019 — and the inspiring images and photos that accompanied them.

1) First comprehensive view of human cell division

undefinedBy enabling a deeper understanding of how healthy human cells divide, a process known as mitosis, the model will further basic biology research as well as studies of cancer, a disease that often results from cell division gone awry.

Researchers at the Allen Institute for Cell Science debuted the Integrated Mitotic Stem Cell, a data-driven model and visualization tool that sheds new light on cell division, a critical process for human cells and a pivotal driver of cancer. The team is already using the tool to make new insights about cell division, also known as mitosis, with the potential for more on the horizon.

“These observations would not be possible without an integrated view of mitosis, but they’re also just the beginning of what can be uncovered,” said Susanne Rafelski, Ph.D., Director of Assay Development at the Allen Institute for Cell Science.

2) ‘Nature’s blueprint’

undefined"Snowflake yeast," a laboratory-generated version of the single-celled baker's yeast that could shed light on how larger creatures evolved. Image courtesy of Will Ratcliff, Ph.D.

From a tiny rod-shaped bacterium, to a tusked behemoth of an elephant, to a branching vine — what are the biological rules that underwrite life's intricate and beautifully varied forms? This spring, we hosted an international group of researchers for a symposium focused on how living creatures create and maintain their complicated shapes.

3) Out of Balance

undefinedMedical student Alyssa Clements bounced from doctor to doctor for her mysterious pain before she was finally diagnosed.

In May, we debuted a new story and video series for our newest division, the Allen Institute for Immunology. Out of Balance profiles people around the world living with immune-related diseases. One of our first stories featured medical student Alyssa Clements, who bounced from doctor to doctor for her mysterious pain before she was finally diagnosed with severe Crohn's disease. Researchers at the Allen Institute for Immunology are aiming to understand the immune mechanisms that drive the various stages of inflammatory bowel disorder, the group of conditions that includes Crohn's.

4) Sorting neurons by their shape and activity

undefinedAllen Institute for Brain Science researchers are working to develop a parts list, or “periodic table,” of cell types in the brain. Image by Benedicte Rossi.

In their quest to create a “periodic table” of brain cell types, Allen Institute for Brain Science researchers published a study in the journal Nature Neuroscience in June profiling mouse neurons by their 3D shape and electrical activity.

If you think of the classical periodic table, chemical elements can be described and sorted in a number of ways: their mass, their chemical properties, whether they are metal or not. Neuroscientists are faced with a similar challenge. A given neuron will have many different personality traits that distinguish it from other neuron types: its shape, its behavior, the unique set of genes it switches on, its location in the brain, the other types of cells it interacts with. To understand what a single cell type does, researchers need to explore all these attributes.

5) New tools for cell biologists

Classic approaches to rendering (left) remain useful for viewing volumetric data on slower computers or mobile devices. The cinematographic path-tracing approach offered in AGAVE (right) helps users grasp spatial relationships among objects in the volume more intuitively

Teams from the Allen Institute for Cell Science released new tools – AGAVE and the Allen Cell Structure Segmenter – to help researchers navigate and visualize 3D cells and their contents. AGAVE, a new 3D cell visualization tool, is built using path trace rendering, a method originally developed to make more realistic computer graphics. The Allen Cell Structure Segmenter uses both existing computer vision algorithms and a new machine learning approach to to identify structure boundaries in images of 3D cells.

6) Cell biology and brain science for the classroom

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In July, we debuted posters and lesson plans focused on cell division and neurons for high school and college science teachers to use in their classrooms. The customizable lesson plans introduce students to fundamental concepts in biology via guided experiments that use data from our ongoing research projects.

7) Simulations of life

undefinedMarkus Covert, Allen Discovery Center leader, presents his latest research at the Allen Institute.

In August, we welcomed researchers using modeling to ask and answer important scientific questions to the Allen Institute for a symposium on modeling in biology. The two-day event brought together researchers who use computational simulations to better understand living systems, from the tiny ruffling edge of a migrating immune cell to how a large group of cancer patients respond to an experimental therapy.

The speakers at the symposium, which was hosted by The Paul G. Allen Frontiers Group, all use computational models of the cells, organs or populations they study to help them answer questions in a way that’s not possible with laboratory experiments alone.

8) Brain discovery lays roadmap to better treatments

undefined Allen Institute for Brain Science researchers, Trygve Bakken, Ph.D., (left) and Rebecca Hodge, Ph.D., (right) working in the lab.

In a study published in August in the journal Nature, Allen Institute for Brain Science researchers found crucial differences between human and mouse brain cell types, a possible explanation for why many drugs that work in the lab don't work in us.

For example, they found that the proteins that allow our neurons to react to the brain chemical serotonin are used differently in mice and human neurons. This finding could explain why it’s been so difficult for clinical researchers to develop new therapies for depression and other disorders related to serotonin: A drug that acts on this chemical, which plays a starring role in mood, appetite and sleep, could affect a mouse very differently than it would us.

9) What it's like to donate your brain to science

undefined An x-ray image of Casey Schorr's skull after surgary to treat epilepsy. 

This summer, two epilepsy patients – Casey Schorr and Gary Williams – who donated part of their living brain tissue to neuroscience research at the Allen Institute shared their stories in profiles with us and the Seattle Times.

“I just wanted to help anyone who’s struggling with some sort of brain dysfunction that’s putting them behind and stopping them from being able to live their life,” Casey said. That is, anyone like him. 

10) Golden Birthday

On September 16, we celebrated our 16th anniversary — and our golden birthday. We even got a shout-out from a very special #16: the Seahawks’ Tyler Lockett. 

11) High-resolution map of how the brain is wired

undefinedAn artist’s rendering of cortical and thalamic connections in the mouse brain. Illustration by Benedicte Rossi.

A team from the Allen Institute for Brain Science traced thousands of connections between brain areas in a study published in October, laying the groundwork for researchers to better understand how brain circuitry might go awry in diseases and disorders such as Alzheimer’s disease and schizophrenia. The publicly available dataset resulting from approximately a thousand new experiments represents the most detailed map of connections in a mammalian brain to date. Sifting through the data, the researchers uncovered an underlying “org chart” of wiring among the different areas comprising these two structures, showing a defined order to the connections that are the underpinnings of what makes our brains tick.

12) First healthy volunteer samples arrive

undefinedAllen Institute for Immunology researchers recieving their first patient samples.

Allen Institute for Immunology researchers reached a new milestone: the first precious blood samples from local volunteers arrived on site, ready for analysis to study the dynamic balance of the healthy immune system. Together with research partners at Benaroya Research Institute at Virginia Mason, Allen Institute researchers are poised to study and define a healthy human immune system at a scale and precision never done before.

13) New Allen Distinguished Investigators

undefinedNew Allen Distinguished Investigator James Wells, Ph.D., will lead a team studying a rare type of intestinal cell known as enteroendocrine cells that sense nutrients from the food we eat and then control how nutrients are absorbed and stored. Image courtesy of Heather McCauley, Ph.D.

In November, we announced five newly selected Allen Distinguished Investigator awards to support research using human stem cells to model disease and new technology development to study tissues at the single-cell level.

“This award is enabling us to take a big risk in our arena by generating a completely new technology, one which will be useful to the scientific community. That’s really exciting for us,” said Samantha Morris, Ph.D., who is one of the newly selected Allen Distinguished Investigators and an Assistant Professor at Washington University in St. Louis.


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