TS Digest Issue | December 2023 | Mean, Green, Antibody-producing Machines

Frozen laboratory test tubes in box container in a research lab.

From the Editor| Article

Save the Sample

Researchers must plan for the future of their lab materials long before they decide to move on.

Meenakshi Prabhune, PhD

Dec 1, 2023 | 2 min read

Image Credit:

When I was wrapping up my graduate studies, questions about the future of my project loomed large in my mind. The uncertainty around the fate of my oligonucleotide tubes felt like a cliffhanger moment in the season finale of a beloved series that has yet to be renewed for the following season. I recall the relief when a colleague took over my project, and I was spared the horror of having to pull the plug on the samples that I invested so much time and effort in.

Even though I had spent only four years on the project, it warmed my heart to know that my tubes would retain their spot in the freezer a few years longer. So, when a retiring academic recently posted on social media about the impending doom of their freezer boxes with the end of their flourishing career, I could imagine the utter disappointment of losing a lifelong work. Scrolling through the comments from other researchers, I realized that this was sadly a common occurrence.

In this age of automation and digitization, one might expect better alternatives for handling biological materials. Options such as storing them in a repository or shipping them to collaborators exist, but these solutions often require planning ahead—a luxury that not many can afford. Between helping their students graduate and wrapping up other pending projects, by the time researchers think of their samples, it is often too late. Even for the early planners, the options might be limited depending on the type of sample, particularly for those working in a niche field. Lastly, sample storage may require immaculate record keeping, and let’s face it, some researchers’ Da-Vinci-Code-level-hard-to-crack lab notebooks might not be adequate.

Perhaps with improved electronic record keeping and growing bio-storage solutions, we might not need to take up the #SavetheSample cause in the future. Until then, we would love to hear from all of you about your recommended solutions for keeping years of work from going down the drain (sometimes literally).

Suggest an Idea

A scientist not in frame is holding a plant leave with forceps in one hand and a petri dish with more leaves in the other.

Article

Mean, Green, Antibody-producing Machines

A plant-based monoclonal antibody goes head-to-head with its commercial counterpart to target tumors in mice.

Shelby Bradford, PhD

Dec 1, 2023 | 2 min read

Image Credit:

Plants are incredible organisms that may soon have a new function: producing monoclonal antibodies. Plant-made antibodies against viral diseases generated immunity in mice and nonhuman primates.^1-3 While some researchers showed the tumor targeting potential of these antibodies in cancer models, few demonstrated their antitumor activity in vivo.^4,5

Waranyoo Phoolcharoen, a plant molecular biologist at Chulalongkorn University, and her team set out to do just that. In a recent paper in Scientific Reports, the team reported in vivo tumor growth inhibition from plant-produced atezolizumab, an immune checkpoint inhibitor that binds programmed death ligand 1 (PD-L1) on cancer cells to block their immune suppressive activity.⁶

"Many groups of researchers try to…study the structures of the antibodies. That's one thing, but [to] confirm that it can reduce tumors in animals, that’s the big thing,” said Phoolcharoen.

To test the activity of plant-produced atezolizumab, the group expressed the monoclonal antibody in an Australian tobacco plant, isolated it, and compared it to its commercial counterpart. The two antibodies were comparable in their size, glycosylation patterns, and binding to human PD-L1 in vitro.

Mice implanted with tumors and treated with either antibody gained weight and reduced tumor size similarly and did so significantly more than nontreated mice.

“Such data are often difficult to come by,” said Johannes Buyler, a bioprocess engineer at the University of Natural Resources and Life Sciences who wasn’t involved in the study. He emphasized that the findings bridge an important gap since comparative studies have been lacking in the field.

Next, Phoolcharoen wants to study the distribution, clearance, and toxicity of plant-produced atezolizumab to eventually take it to clinical trials.

References

Hurtado J, et al. Plant Biotechnol. J. 2020;18(1):266-273
Lai H, et al. Proc Natl Acad Sci. 2010;107(6):2419-2424
Olinger Jr GG, et al. Proc Natl Acad Sci 2012;109(44):18030-18035
Dent M, et al. Plant Biotechnol J. 2022;20(11):2217-2230
Ludwig DL, et al. Hum Antibodies. 2004;13(3):81-90
Rattanapisit A, et al. Sci Rep.2023;13(1):14146

Infographic

Engineered RNA Export From Living Cells

A nondestructive approach for packaging, exporting, and delivering RNA provides a glimpse into the dynamic lives of cells.

Danielle Gerhard, PhD

Dec 1, 2023 | 1 min read

Inspired by viral delivery systems, Michael Elowitz’s team developed a system for the nondestructive export of RNA from living cells called Controlled Output and Uptake of RNA for Interrogation, Expression, and Regulation (COURIER). The researchers used this platform to monitor changes in cell states and for cell-to-cell RNA delivery.

Photographic rendering of Woolly Mammoth and elephant with background elements merging together

Article

Measuring Mammoth Mutations

Comparing mammoth and elephant genomes revealed genetic mutations that may have helped mammoths survive in the Arctic.

Hannah Thomasy, PhD

Dec 1, 2023 | 2 min read

Image Credit:

Modified from © shutterstock.com, QuangTrungArt; © istock.com, Wirestock

For more than 500 thousand years, woolly mammoths ruled the cold steppe tundra across the northern part of the globe. Fascinated by the adaptations that allowed these majestic beasts to thrive in harsh conditions, David Díez del Molino, a geneticist at the Center for Palaeogenetics, and his colleagues compared mammoth and modern day elephant genomes to determine the underlying genetic secrets. Their findings published in Current Biology help scientists piece together the evolutionary history of mammoths. ¹

“This is probably the largest study thus far on mammoth genomics,” said Alfred Roca, an animal geneticist at the University of Illinois at Urbana-Champaign who was not involved in the research. “It’s a very impressive study.”

Paleogeneticist David Díez del Molino holds the molar of a woolly mammoth.

David Díez del Molino

By delving into 23 mammoth genomes and 28 modern elephant genomes, the researchers identified several mutations in genes related to hair development that may be responsible for the mammoth’s eponymous woolly coat. Relative to elephants, woolly mammoths also had unique mutations in fat storage and metabolism genes, which may have helped them survive long winters with little food. Altered thermosensation may also be an important trait for thriving in the cold. Woolly mammoths carried mutations in multiple genes related to temperature sensing, including SCN10A, which enables animals to perceive intense cold as painful.

Researchers also compared the genome of one of the earliest mammoths—a 700-thousand-year-old specimen—with animals that lived 50,000 to 4,000 years ago.

“What we found was quite exciting,” said Díez del Molino. “Many of the characteristics of woolly mammoths—furry hair, the size of the ears, fat deposits—kept evolving throughout the lifespan of the species, all the way up until they went extinct four thousand years ago. It really shows that species are not stable in terms of their adaptations.”

Reference

Díez-Del-Molino D et al. Curr Biol. 2023;33(9):1753-1764.e4.

Interview| Article

To Boldly Go Where No Squid Has Gone Before

Jamie Foster’s space-faring squid and its symbiotic bacteria illuminate host-microbe communication.

Hannah Thomasy, PhD

Dec 1, 2023 | 2 min read

Image Credit:

Jamie Foster, an astrobiologist at the University of Florida, always wanted to be an astronaut. While she hasn’t yet been to space, she has sent the tiny bobtail squid in her stead. Foster explores how stresses such as microgravity alter the biomolecular communication between the squid and its symbiotic bacteria, Vibrio fischeri. Ultimately, this could help scientists gain insights about the impact of space flights on the partnership between astronauts and their microbiomes.

Jamie Foster wears a black shirt and smiles

Astrobiologist Jamie Foster studies host-microbe interactions in microgravity.

Scot Lerner

Why is the bobtail squid a good model for studying host-microbe communication?

The squid has a special symbiotic organ called the light organ, which is colonized by one species of bacteria. These bacteria give the squid the power to glow in the dark, which the animal uses as an antipredator defense mechanism. This simple system makes it easier for us to identify and manipulate the molecular signals from the bacteria and determine the effects they have on the host. This is very different from the human body, where there are thousands of different microbial taxa interacting with one another and with our cells.

What have you learned so far?

We measured how the squid responded to microgravity with or without their microbes. In microgravity, the squid initially turned on many different stress response genes. While they stayed stressed in the first few hours after we gave them the bacteria, after about ten hours, they turned off the stress response. When we didn’t give the animal the right microbe, it stayed stressed. So, having the right microbes seems essential for dealing with the stress of microgravity for the squid.

Even with the right microbes though, the immune system didn’t respond exactly how it should. We have seen inhibitors of the innate immune response get upregulated within a few hours of exposure to microgravity, which may delay the proper activation of the immune system. If spaceflight dysregulates astronauts’ immune systems as well, it will be really important to keep track of what microbes we bring with us to space.

This interview has been condensed and edited for clarity.

Article

Fighting Cancer: Lessons from the Naked Mole-rat

Mice live longer, healthier lives thanks to a gene from their glabrous subterranean cousins.

Hannah Thomasy, PhD

Dec 1, 2023 | 2 min read

Image Credit:

In the quest to improve human healthspan, researchers seek to borrow tricks from animal super agers. “Probably the most striking thing about naked mole-rats is their longevity and health,” said Vera Gorbunova, who studies the biology of aging at the University of Rochester. Naked mole-rats can live for more than 40 years—about ten times as long as the maximum lifespan of a mouse—and are resistant to many age-related diseases, including cancer.¹

Vera Gorbunova studies the biological mechanisms of aging in a variety of species.

ANDREI SELUANOV

In a recent Nature study, Gorbunova and her colleagues showed that some of these remarkable health features could be genetically transferred to another species, raising hopes that they could one day be applied to improve human healthspan as well.²

In a previous study, the researchers found that high-molecular-mass hyaluronic acid (HMM-HA) produced by the hyaluronan synthase 2 (HAS2) gene mediates cancer resistance in naked mole-rats.³ To investigate if HMM-HA prevents cancer in other species and to explore its role in aging-related processes, scientists created transgenic mice that overexpressed the naked mole-rat HAS2 gene. These genetically-upgraded mice were less likely to develop both spontaneous and chemically-induced cancers. The naked mole-rat HAS2 gene also reduced inflammation, which is a major driver of many age-related diseases. Ultimately, the median survival of the transgenic mice increased by 4.4 percent.

“This was a really convincing paper using a comprehensive group of assays,” said Matthew Pamenter, who studies naked mole-rat biology at the University of Ottawa and who was not involved in the study. “It really captures the potential of studying these comparative species, like naked mole-rats, to learn lessons from nature and try to reverse engineer what nature has taught us.”

Gorbunova said that her team is currently developing drugs to inhibit HMM-HA-degrading enzymes. “That may be a path to clinical applications,” she said. “That way, we wouldn’t need to do gene therapy on people; we could just slow the degradation process using small molecule inhibitors.”

References

Oka K, et al. Annu Rev Anim Biosci. 2023;11:207-226.
Zhang Z, et al. Nature. 2023;621(7977):196-205.
Tian X, et al. Nature. 2013;499(7458):346-349.

Cartoon illustration of John Gonzalez eating food and questioning if it is chicken

Just Curious| Article

Why Does Everything Taste Like Chicken?

With an appetite for answers, scientists get to the meat of why some unusual foods taste like our favorite fowl.

Laura Tran, PhD

Dec 1, 2023 | 2 min read

Image Credit:

modified from © istock.com, MariaGisina; designed by erin lemieux

Frogs and alligators bear no similarities in their appearances to chickens. But when some people taste these unique meats for the first time, their review commonly ends up being, “It tastes like chicken.” So, what exactly makes these meats taste fowl?

John Gonzalez, an animal and meat scientist at the University of Georgia, studies muscle growth and function.

University of Georgia

Scientists have served up different possibilities of evolutionary roots, with chickens and modern reptiles descending from the diapsids group, linking them as relatives and connecting some physiological traits. However, food scientists primarily attribute this phenomenon to biochemical composition.

“Ultimately, [flavor] comes down to the fat composition and the muscle profile, while the amount of sugar plays a minor role,” said John Gonzalez, an animal and meat scientist at the University of Georgia.

According to Gonzalez, the flavor of meat derives from the complex combination of these molecules. During cooking, lipids in the meat undergo thermal degradation, and the Maillard reaction, a nonenzymatic browning reaction, breaks down protein and sugar.¹

Muscle physiology also plays a significant role in flavor. Chicken is considered a white meat due to its relatively low myoglobin content, which gives the meat a lighter color and milder flavor than red meats like beef or lamb. Comprised of white muscle fibers, chicken breast and wings rely more on glycogen than myoglobin since they are specialized for more sporadic and brief energy demands.

Likewise, unique meats such as frogs and alligators are also considered white meat. They boast a leaner meat profile, a palatable flavor, and a chicken-like texture. “[By having comparable muscle profiles], it is most likely going to contribute a similar meat flavor component,” said Gonzalez. This commonality bridges the culinary experience of these distinct meats. That’s food for thought!

What makes you curious? Submit a question for us to answer in future “Just Curious” columns.

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Reference

Jayasena DD, et al. Asian-Australas J Anim Sci. 2013;26(5):732-742.

A white brain with clock hands rests in the middle of two scenes of two different times of day, nighttime, indicated by stars on a blue background, is on the left and day, indicated by light blue clouds, on the right.

Article

Sleep Rhythms Prompt Long-term Memories

A bridge between neurons triggers longer, deeper sleep and memory formation in fly larvae.

Shelby Bradford, PhD

Dec 1, 2023 | 2 min read

Image Credit:

Sleep-wake patterns in most adult animals are controlled by the circadian rhythm, a network of genes and proteins that act like an internal clock, but these patterns cycle independently of this clock in early life in many of these species.^1,2How sleep comes under circadian control and its advantages remains poorly understood. Matthew Kayser, a sleep scientist at the University of Pennsylvania, uses fly larvae to explore the relationships between behavioral patterns, the circadian rhythm, and development in early life.

In a recent article, Kayser and his team identified the time that sleep synchronized to this circadian clock in larvae and showed that this prompted long-term memory formation in the animals.³

A confocal microscopy image of a larval fly brain lobes shows that arousal neurons, labeled in green, are concentrated at the top of the lobe and clock neurons, labeled in red, extend down the far side of the lobe away from the center and arousal neurons.

Researchers in the Kayser lab studied arousal neurons (green) and clock neurons (red) in stage three larval brains to explore when sleep synchronized to the circadian rhythm.

Amy Poe

The researchers quantified sleep duration and frequency in mid to late larval stages by visualizing neurons and assessing their connections during development. They found that neurons responsible for arousal acted independently of clock signals until late in the last developmental stage when they physically connected to clock neurons.

“As soon as that happens, then suddenly that arousal cue that's unchecked comes under control of our timing mechanisms,” Kayser said.

Circadian-controlled sleep allowed for deeper sleep, which promotes memory formation in adult flies, so the team investigated if circadian-controlled sleep influenced this in larvae.⁴ Using an odor conditioning assay, the team found that only larvae in the last developmental stage formed a long-term memory after training.

“The level and quantity of evidence they brought to really tracing that circuit—it's so definitive,” said Michael Antle, a chronobiologist who studies circadian rhythms in rodents at the University of Calgary and was not involved in the study.

Kayser’s team next intends to study the trigger that promotes the connection between arousal and clock neurons.

References

Vitaterna MH, et al. Alcohol Res Health 2001;25(2):85-93
Wager-Smith K, Kay SA. Nat Genet. 2000;26(1): 23-27
Poe AR, et al. Sci Adv.2023; 9(36)eadh2301
Dag U, et al. Neuroscience. 2019;8:e42786

Image of Christmas tree made up of beakers

Epic Fail| Article

The Christmas Mix-up

In a rush to wrap up an experiment before the holidays, a slip of the hand almost ruined the festive mood for Cleo Parisi.

Danielle Gerhard, PhD

Dec 1, 2023 | 2 min read

Image Credit:

Ten years ago, I was a graduate student in Evi Lianidou’s laboratory at the University of Athens working on the molecular characterization of circulating tumor cells in breast cancer. In my third year, I had an exciting opportunity to pursue a year-long research exchange program at the University Hospital of Montpellier. With the holidays and my impending trip around the corner, I had just under two weeks to wrap things up. An important pending task was optimizing my experiments so that a colleague could continue the project in my absence.

Cleo Parisi is a research engineer at the Centre of Biological Resources, Biobank Lariboisière, AP-HP.

Cleo Parisi

When I slightly tweaked the experiment and ran my fluorescence intensity measurement assay, I was utterly confused. There was nothing! Panicked, I adjusted the experiment every day for the next few days in search of clues. Then one day, while rummaging through the freezer, which was filled to the brim with boxes and ice build-up, it dawned on me. In a whirlwind of haste, I had grabbed the wrong box.

I had mistakenly used 25 mM MgCl₂ when we needed 50 mM MgCl₂to optimally boost DNA amplification. With just two days to spare, I ran the experiment again using the appropriate concentration and voilà! The fluorescence emerged, shining as bright as the festive lights adorning Athens. I finished optimizing the experiment just in time for the holidays. It was a Christmas miracle!

The project progressed nicely while I was away, and we eventually published the results, which formed the bedrock of my thesis defense.¹ In the end, it was a lesson learned and shared. My professor incorporated my graph with the striking drop off in fluorescence in her course as an example to teach students the importance of MgCl₂concentration in a PCR protocol.

This interview has been edited for length and clarity.

Reference

Parisi CP, et al. Clin Chim Acta. 2016;461:156-164.

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Science Snapshot| Article

Pancreatic Organoids Take the Stage

Meritxell Huch tackled her pipedream of growing three-dimensional pancreatic tissue in a dish.

Laura Tran, PhD

Dec 1, 2023 | 2 min read

NIKITAS GEORGAKOPOULOS, UNIVERSITY OF CAMBRIDGE

The early days of stem cell culture set the stage for organoid research by spotlighting highly proliferative tissues such as the small intestine, stomach, and liver. Excited by the potential specificity for disease modeling, Meritxell Huch, now a stem cell biologist at the Max Planck Institute of Molecular Cell Biology and Genetics, stepped into the organoid scene during her time as a postdoctoral researcher in Hans Clever’s laboratory at the Hubrecht Institute.

Huch first succeeded at culturing stomach and liver organoids; then she decided to translate the technique to the pancreas, which was notoriously challenging for its low proliferative capacity.

On a Friday evening in 2010, Huch isolated pancreas cells from surplus lab mice, placed the cells into a culture plate, and incubated them. The next morning, she apprehensively imaged the sample. When she peered into the eyepiece, she was thrilled to see the cells expanding in a three-dimensional manner. She had created the first pancreatic organoids.¹

“It was obvious from the very first experiment that it was going to be possible,” said Huch. “It became evident that [these organoids] were going to be important as tools to understand concepts we couldn’t study before.”

Over the next year, Huch iterated on her protocol to grow and visualize organoid morphology effectively. In the image shown here, she tagged pancreatic ductal cells with fluorescent dyes to mark the nuclei in blue, actin cytoskeleton in red, and a stem cell marker in green. These markers allowed her to visualize the organoids in 3D. This preliminary work provided useful insights into the pancreatic organoids' architecture.

Huch further validated organoids using other cell markers, which set the stage for her work on pancreatic cancer organoid models.² These models transformed Huch’s work on disease modeling and became an emergent platform for precision medicine in pancreatic research.

References

Huch M, et al. EMBO J. 2013;32:2708–2721.
Boj SF, et al. Cell. 2015;160(1-2):324-338.

Save the Sample

Researchers must plan for the future of their lab materials long before they decide to move on.

Mean, Green, Antibody-producing Machines

A plant-based monoclonal antibody goes head-to-head with its commercial counterpart to target tumors in mice.

Engineered RNA Export From Living Cells

A nondestructive approach for packaging, exporting, and delivering RNA provides a glimpse into the dynamic lives of cells.

Measuring Mammoth Mutations

Comparing mammoth and elephant genomes revealed genetic mutations that may have helped mammoths survive in the Arctic.

To Boldly Go Where No Squid Has Gone Before

Jamie Foster’s space-faring squid and its symbiotic bacteria illuminate host-microbe communication.

Why is the bobtail squid a good model for studying host-microbe communication?

What have you learned so far?

Fighting Cancer: Lessons from the Naked Mole-rat

Mice live longer, healthier lives thanks to a gene from their glabrous subterranean cousins.

Why Does Everything Taste Like Chicken?

With an appetite for answers, scientists get to the meat of why some unusual foods taste like our favorite fowl.

Sleep Rhythms Prompt Long-term Memories

A bridge between neurons triggers longer, deeper sleep and memory formation in fly larvae.

The Christmas Mix-up

In a rush to wrap up an experiment before the holidays, a slip of the hand almost ruined the festive mood for Cleo Parisi.

Pancreatic Organoids Take the Stage

p.p1 {margin: 0.0px 0.0px 0.0px 0.0px; font: 13.8px Helvetica; color: #000000}Meritxell Huch tackled her pipedream of growing three-dimensional pancreatic tissue in a dish.

Meritxell Huch tackled her pipedream of growing three-dimensional pancreatic tissue in a dish.