Models and career-makers

Even outside the pantheon of classic models, there’s career-making

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For this month’s Technology Feature in Nature Methods, I spoke to researchers working on organisms not considered the classic model organisms, such as human, mouse, rat, corn, Arabidopsis, fruit fly, zebrafish, yeast and E.coli. Perhaps, notes Howard Hughes Medical Institute investigator Alejandro Sánchez Alvarado, who is also the executive director and chief scientific officer of the Stowers Institute for Medical Research, it’s time to retire the term model organism. In Developmental Biology, he writes:

“The time has come to dispose of the terms “model” and “non-model” systems and adopt instead the more accurate term “research organism. Our remarkable advances in genome editing, imaging, bioinformatics, high throughput assays and automation demands it. Adopting the term research organism allows us to bring our technological armamentarium to explore the wealth of Life on Earth and expand the boundaries of biological knowledge in the decades ahead.”

This strikes me as important and noble. But, I wondered, given that there are many fewer labs working on these ‘other’ research organisms, it could mean it's a challenge to grow a community.

Qiang Tu helped me with some data analysis on this subject. And you can see more on that further down on this page. He is a researcher at the Institute of Genetics and Developmental Biology, which is part of the Chinese Academy of Sciences in Beijing. He works on zebrafish but mainly on the ‘other’ model organism/fish, namely medaka. There are fewer labs working medaka than on zebrafish. And this trends holds true for other organisms in this story.

I wondered how researchers entice junior scientists, graduate students and post-docs to join in their small community and encourage them to take the path of the less well-known organism?

Maybe those junior scientists say after hearing a talk about this alternate path: “Yes agreed! Elegant talk!” Then over a cup of tea or a glass of wine: “Yes, but [PhD student looks at the floor] it’s easier to get grants if we use C. elegans….”

Or : [post-doc twists hand into worn-out sweat-shirt] “But my PI Dr. Important uses zebrafish, so who am I to say another might be better. He thinks medaka are useless.”

Or: [graduate student, eyes sparkling] “I love organism x, but [sparkle dims] in grad school I keep hearing I need to switch to something sexy and hot.”

Here is what some scientists told me on the subject of careers with the ‘other’ research organisms.

Ashbya

Ashbya gossypii

(Gladfelter lab, T. Gerbich, G. McLaughlin/UNC Chapel Hill.)

Amy Gladfelter, a researcher at University of North Carolina, Chapel Hill studies the filamentous fungus Ashbya gossypii. During her training, Gladfelter jumped at the chance to do a postdoctoral fellowship in Switzerland. “I’ll play with this organism for a while,” she says. “Maybe I’ll end up making my life’s work out of it, or maybe I’ll do another postdoc.” 

The flatworm Schmidtea mediterranea is one of the research organisms Sánchez Alvarado works with. He says that all living organisms on the planet are a model of something, each one chiseled by evolution through millions of years not only using essential the same clay such as DNA, RNA, proteins, lipids, metabolites and “the same tools” as the deep conservation of all genomic sequence thus far demonstrates.

He calls studying regeneration, as he does in planarians, “the last wild frontier of developmental biology.” It’s appealing to researchers, he says. “This thirst for the unknown appeals to the best in us as scientists, and for some it will become a calling,” he says. In his view, that is more than enough brick and mortar to build a community with.

 When Sánchez Alvarado talks about disposing of the term model organism and using research organism instead, people react variably, “usually along a career divide, but not always,” he says.  “Generally, the earlier you are in your career the more attractive this idea becomes.” Still, it takes courage, as the perception exists that getting funding to study a non-traditional organism is harder than if you were studying already established systems. “This is the wrong way to go about this issue. We are not studying an organism. We are studying a problem. All living organisms in our planet are a model of something,” he says.

Amphiura filiformis

(Oliveri lab, UCL)

At University College London, Paola Oliveri studies echinoderms.

Her thinking was shaped by her time as a postdoctoral fellow in the lab of developmental biologist Eric Davidson at California Institute of Technology. When she arrived after her PhD, she found his enthusiasm for research and science contagious. Working with him was a fantastic experience, she says and she learned from him the love for doing research, how to mentor people, how to walk “a path that nobody has ever walked before,” she says. And to not be afraid to do so.

For junior scientists in cancer research eager to solve human disease, some experience in echinoderms might be a passing interest, says Oliveri. One of her students was focused on human genetics and had been assigned to her lab for a project on regeneration in echinoderms. At first the student “was a bit disappointed,” she says. 

But she stayed through her master’s and then did PhD research with Oliveri, too. “We worked together,” she says, they collected animals at a marine station in the summers--brittlestars--extracted DNA, sequenced their genomes, look at the transcriptome and studied how much of the developmental processes are used or reused in regeneration. It became clear to this student interested in human genetics how much one can advance basic questions in biology by looking at echinoderms.

Mouse lemur

Microcebus murinus

(D. Huber, U. of Geneva.)

Daniel Huber at the University of Geneva works with mouse lemurs. He wishes funding agencies and institutions provided more support and incentives to explore alternative ‘research organisms’ and thus push for more ‘comparative’ research. “That would have advantages over the eternal ‘translational’ approach based on a handful of highly convenient ‘model species,’” he says. 

Huber is glad he has a close collaboration with a CNRS lab at Musée National d’Histoire Naturelle in Paris, a lab that studies behavior, metabolism and evolution in mouse lemurs.

Every few years there are mouse lemur meetings, he says, that include neuroscientists who do cognitive or behavioral neuroscience, also people from zoos, and scientists from Madagaskar, mouse lemur’s native home. “It’s a tiny community, but it’s a fun mix of people,” says Huber. But it is indeed hard to build a research community.

Daniel Kronauer at Rockefeller University works on ants, clonal raider ants in particular. He says when it comes to recruiting graduate students and post-docs, “it’s a bit like the Wild West – it’s hard because you have to build and develop everything yourself, but there’s also much less competition and a lot of open experimental and intellectual space. Pretty much anything you do is new and has the potential to lead to exciting discoveries.”

He feels lucky that there are enough people looking for exactly that kind of challenge and he has had many “amazing students and postdocs” ever since he decided to set out for the clonal raider ant frontier. “Some of them are already leading their own labs and continue to work on the species,“ he says.

Medaka

(Tu lab, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences)

The Chinese name for medaka, a freshwater fish native to East Asia, sounds a little like channel catfish, says Qiang Tu. General conversations about his model of choice therefore might depart from talking about a dish of grilled catfish.

In that kind of conversation about dinner plate, Tu then launches into the advantages of medaka--or Oryzias latipes--such as the fact that it's much smaller size than catfish. He works with zebrafish but his main model organism of choice is medaka.

It’s not easy to recruit junior researchers to an area that involves research with a less well-known model organism, he says. Beyond the obvious question a junior scientist must consider issues such as ‘will a given principal investigator be a good mentor for training’, ‘is his or her lab doing good research.’ It is in his view, perhaps not as critical to consider which model a lab is using. “The bad point of using minor organisms is, when you go out for a conference, it might be a little difficult to find common topics in the conversation with new friends, unless you can make jokes about catfish,” he says.

On a more serious note, Tu took a quick look at resources and the number of labs working on major and some of the less well known organisms.

Behind the scenes of this dataviz with Qiang Tu:

In the National Center for Biotechnology Information (NCBI) gene expression omnibus (GEO) there are data about 5,035 organisms.

(Tu lab, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences)

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GEO presents a tally of sample numbers for the organisms, which refers to data sets such as DNA and RNA data. Some organisms are mentioned for which there are fewer than 10 samples available in GEO, so Tu removed those from a quick analysis. That leaves 2,248 organism.

For the research organism that Tu mainly studies medaka--Oryzias latipes--the NCBI's GEO holdings offer information about 584 samples. For, the zebrafish--Danio rerio--there are 27,481 samples

(V. Marx; Danio rerio: Peter Kutsnetsov, Pixabay; Oryzias latipes; Tu lab, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences)

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Using PubMed Tu queried for keywords, limited his search to the most recent five years, January 1, 2016 – December 31, 2020. That yielded the number of papers published in each field. He then extracted the last author and calculated the count table.

He selected the authors with more than one paper published and called those labs "active labs.” As positive controls, one can consider C. elegans labs of which there are around 1400.

Human and mouse papers are too numerous to include. So it's perhaps best to compare the less well-known models to zebrafish. In that comparison, compared to zebrafish, both medaka and sea urchin have about 6% labs and published 6% papers, but they have only 2% of the 'omics samples. Perhaps, he says, this means that the zebrafish community has more genomics resources, and that it likes to work with 'omics methods. 

  Organism     Papers - 5 years     Number of labs   Number of active labs 
Danio rerio

      16,943

       7,457            2,751
Caenorhabditis   elegans         9,022        4,329            1,405
Schmidtea mediterranea         3,723        3,723            1,071
Oryzias latipes             942           493               169
Microcebus murinus             146             87                 24
Pristionchus pacificus               81             32                   6 
Ashbya gossypii               39             21                   6
Ooceraea biroi                 6               2                   1

(Tu lab, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences)

When Tu was a post-doctoral fellow working on sea urchin, he profiled its transcriptome and built gene models. Then, as a PI working with medaka, his first project was to expand the profiling to three assays, which he calls the “the minimum ENCODE toolbox.” He built gene models for medaka with the data. For those starting out with less-known organisms this approach has great value, he says.

Ralf Sommer, a researcher at the Max Planck Institute for Developmental Biology, has worked on C. elegans but mainly works on another model, the nematode Pristionchus pacificus. His lab is quite inter-disciplinary, he says. There are naturalists, geneticists, biochemists, bioinformaticians and ecologists. “I am very fortunate to have a great group of students and postdocs,” who often arrive at the lab with a C. elegans background. But he stays on the lookout for new members.

“Given the unique research we have, I am getting very good applicants,” says Sommer. “Crime sells….”

--

Coast Redwood.

M. Shoys  Save the Redwoods League.

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David Neale, professor emeritus of the University of California, Davis, always knew he wanted to work with trees. He studies, for example redwood trees, which can live for thousands of years. These trees “have a lot to offer in terms of discovery of basic knowledge related to adaptation and longevity,” he says. Neale is in the midst of switching gears from the role of a principal investigator to taking on an advisory role on forest-related research projects. He is currently working on a grant to sequence the bristlecone pine.

“I’m just enjoying trying to essentially empower the next generation,”  says Neale.

Neale is passionate about trees and about ways to empower the next generation of scientists, too. The genomic resources being built for redwoods and other trees will help to power that next research. “There’s plenty of work to be done, for sure.”


 

Llamas

(Pezibear, Pixabay)

Camelids are not model organisms in the traditional use of the term, says Jason McLellan, a structural biologist at the University of Texans at Austin. Those classic organisms such as the fruit fly, zebrafish, and the nematode C. elegans are used for example to study development and behavior.

With camelids, McLellan and others exploit “a unique molecule that these animals produce,” he says. Camelid antibodies are nanobodies and receive increased attention in the context of COVID-19. Some labs, including his, try to engineer neutralizing nanobodies against the SARS-CoV-2 virus that causes COVID-19.

One alpaca (Vicugna pacos) and one llama  (Lama glama) played an important role in the work of a team at the University of Bonn in Germany, along with colleagues at Karolinska Institutet, Scripps Research Institute and the University of Illinois at Urbana-Champaign. The scientists study the virus that causes COVID-19, severe acute respiratory syndrome coronavirus 2 (SARS COV-2).

In addition to vaccines, labs seek neutralizing antibodies to better understand SARS-Cov-2 and to explore ways to treat people infected with SARS-CoV-2 such as people with compromised immune systems who cannot be vaccinated or children.

In their Science paper, the team points out that once traditional neutralizing antibodies are discovered, they cannot be easily and economically produced for a population-wide use and it’s hard, certainly expensive, to modify them to include multiple specificities. The alternative is to work with nanobodies, which are the variable domains of the heavy-chain only antibodies in camelids such as llamas. Nanobodies are small and could, in principle, latch on to the receptor binding domain of the virus’s spike protein through which it infects cells.

One issue is the RBDs can have an ‘up’ and a ‘down’ conformation. In the ‘up’ conformation, the virus can latch onto the ACE-2 protein on cells, for example in the lung. And this is what a neutralizing nanobody would have to stop. 

The team immunized the animals with the receptor binding domain (RBD) of the SARS CoV-2 spike and an inactivated SARS-CoV-2.  Using phage display, they identified nanobodies the animals produced that seemed promising nanobodies and assessed how well they neutralized the virus. 

They applied techniques such as x-ray crystallography and cryo-electron microscopy to characterize the spike-nanobody complexes and engineered four multivalent nanobodies that target the SARS-COV-2 RBD based on these candidates. In testing, they found that these candidates enhance the neutralizing potential of these nanobodies. They highlight that nanobodies can be produced in prokaryotic expression systems and are stable at various temperatures.

We engineered improved multivalent nanobodies neutralizing SARS-CoV-2 on the basis of two principles: (i) detailed structural information of their epitopes and binding modes to the viral spike protein and (ii) mechanistic insights into viral fusion with cellular membranes catalyzed by the spike.

“Llamas and other camelids have been great friends to scientists since the early 1990s when researchers discovered that these animals can produce a heavy-chain only antibody that is smaller than conventional antibodies,” says McLellan. Since then, scientists have pursued the clinical development of camelid antibodies in many areas including cancer and infectious diseases. “Our work builds on the decades of previous research from these great scientists,” he says.

McLellan and his team along with the lab of Xavier Saelens at Ghent University, colleagues in Germany and at NIH, worked with llama nanobodies and published results in the journal Cell. These are heavy-chain-only nanobodies that the animal produced against the spike glycoprotein of coronaviruses that decorate the surface of coronaviruses such as MERS-CoV-1, SARS-CoV-1.

They sequenced the antibodies, then used phage display and panning to tease out the ones with the greatest specificity against these proteins. In this process bacteria are transformed with antibody genes, and the antibodies are then ‘displayed’ on the surface of bacteriophages.

The scientists leveraged the crystal structures of these nanobodies bound to the targets of the virus and aligned them with cryo-EM structures also of SARS-CoV-2, which causes COVID-19. They wanted to assess how well the nanobodies neutralize the virus in a test-tube to see which one is most likely to disrupt the virus in vivo.

Parts of the viral spike protein, the receptor binding domains (RBDs) of the virus, can be in an ‘up’ conformation in which the RBDs jut out from the rest of the spike protein. This position seems to ease the further steps the virus undertakes to latch onto the angiotensin converting enzyme-2 on the surface of, say, lung cells in a person. To neutralize, the virus a nanobody needs to trap the RBD in that ‘up’ conformation.

What’s helpful about nanobodies is that they are thermostable and chemostable. They could potentially be delivered as an inhaled spray, which would get them to the infection site-the lung—fast, as a potential therapeutic or perhaps as a potential preventative treatment.

The scientists isolated nanobodies that “potently neutralized” MERS-CoV and some that potently neutralized SARS-CoV-1. One of the nanobodies that neutralizes SARS-CoV-1 can also neutralize SARS-CoV-2. “This nanobody binds to a small region on the receptor-binding domain that is well conserved among SARS-like coronaviruses,” says McLellan.

Because nanobodies are small, they can recognize surfaces and recessed cavities that larger conventional antibodies cannot, says McLellan. Their small size makes it easier and cheaper to produce them in E.coli and yeast. 

To make the SARS-directed nanobody a more effective potential therapeutic, says Daniel Wrapp, a PhD student in the McLellean lab, “we engineered a bivalent molecule that exhibited more favorable characteristics.” Single-domain antibodies, nanobodies, are attractive because they are more stable, for example, than other types. Unmodified, single-domain antibodies can potentially be lyophilized and administered as an inhalable spray as treatment for respiratory pathogens. 

 

Vivien Marx

Journalist , Nature Portfolio

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