TS Digest Issue | August 2024, Issue 1 | From Lab to Likes: Socializing Science Through Humor

Two ferrets look out of a rectangular hole in a wooden structure.

Article

Obesity Alters the Course of Influenza Infections

Researchers explored the effects of obesity on the lung microenvironment in ferrets, searching for new therapeutic targets to protect vulnerable populations.

Hannah Thomasy, PhD

Aug 1, 2024 | 2 min read

Image Credit:

Harald Schmidt

From aiding in the construction of Fermilab to serving as valuable models of cystic fibrosis, ferrets have been on the frontlines of many scientific endeavors. Now, researchers have turned to ferrets to investigate the impact of obesity on influenza dynamics, both within and between individuals. In a new study in Science Advances, researchers identified differences in symptom severity and lung gene expression between normal weight and obese ferrets, providing clues about the mechanisms by which body composition might influence antiviral responses.¹

Stacey Schultz-Cherry wears a white lab coat and stands in a laboratory full of research equipment.

Stacey Schultz-Cherry studies host-virus interactions with the aim of informing new strategies for protecting high-risk populations.

St. Jude Children’s Research Hospital

“We got interested in this because of the 2009 swine flu pandemic, where we saw for the first time, at least epidemiologically, that people who were overweight or obese were more likely to get severe disease,” said lead author Stacey Schultz-Cherry, who studies host-microbe interactions at St. Jude Children's Research Hospital.

Schultz-Cherry’s team found that, in accordance with increased H1N1 symptom severity, obese ferrets had significantly higher viral titers in their lungs than their normal weight counterparts. Even before infection, lung tissues from obese animals showed increased expression of genes related to cell death and inflammation. During infection, obese ferrets upregulated some inflammatory factors, including interleukin-1, while downregulating some genes associated with antiviral response and lung tissue repair.

Understanding how immune responses may be dysregulated in obesity is crucial for developing therapeutics to protect this high-risk group, said Schultz-Cherry. “I think it's very naive on our part to assume that people are just going lose weight… So how can we do science that is modern, that really reflects our current population?”

“This is a great study,” said Aubree Gordon, an influenza researcher at the University of Michigan who was not involved in the study. “Influenza in obese individuals is a substantial problem…having an obese ferret model is incredibly useful for understanding the mechanisms of what’s happening, and hopefully once we understand the mechanism we can get better treatments.”

Reference

Meliopoulos V, et al. Sci Adv. 2024;10(19):eadk9137.

Interview| Article

The Golden Pipette

Science plays the long game, but Adrian Liston celebrates the small achievements his team makes along the way.

Danielle Gerhard, PhD

Aug 1, 2024 | 2 min read

Image Credit:

Ntombizodwa Makuyana

Hanging on the wall of immunologist Adrian Liston’s laboratory at the University of Cambridge is a commemorative plaque. Engraved are the names of laboratory members who received the Golden Pipette Award, an annual honor that recognizes incremental advancements and team players. It may or may not grant the recipient the Midas Touch, but Liston reflected on how the tradition fosters a sense of community.

Photo of Amy Dashwood holding a golden multipipette and Adrian Liston holding an award plaque.

Adrian Liston (right) with Amy Dashwood (left), who won the eleventh Golden Pipette award for creating a genetic chimera system for analyzing microglia homeostasis and for being an outstanding mentor to undergraduate students.

Magda Ali

What is the Golden Pipette origin story?

In 2016, we had a special PhD candidate graduating from the lab. James Dooley had been a technician in my lab for several years prior to his graduation. To celebrate his achievements and the impact he had on the careers of others in the team, we painted one of his pipettes gold. The gesture was well received, so each year, we award the pipette to an individual who made a significant contribution to the team.

What does the Golden Pipette represent?

Science is tough. We work at the very limits of human knowledge, which means we constantly fail. The Golden Pipette tradition is one of the ways we create a positive culture and supportive environment. Big achievements, such as a paper, take a long time, so it’s important to celebrate the small successes: generating a transgenic mouse; developing a new protocol; the heroic effort that ends up as supplementary figure 12. It also signals our values and priorities: imagination, creativity, robust science, and team contributions.

How did your team respond to the Golden Pipette?

It seemed silly at first, but the tradition has outlasted everyone in the group. It serves as a visual reminder that we’re part of a greater project. In a recent hiring round, several people said that they look forward to the chance of winning the Golden Pipette.

This interview has been edited for length and clarity.

Share your unique lab traditions with us for a chance to be featured in an upcoming issue.

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Technology Highlight| Article

Navigating the Sea of Scientific Knowledge

Scientists seek more accessible educational content that bridges the gap between textbooks and single study journal articles.

Aug 1, 2024 | 2 min read

Image Credit:

For scientists, the quest for knowledge never ceases. Students new to research and established researchers must continually gain information to further their educations, enhance their careers, and foster fruitful collaborations. As novel scientific discoveries constantly add to the bulk of information on a topic, exploring a new scientific field, technique, or technology can seem daunting.

Image of three digital books: <em >Machine Learning in Chemistry, Cellular Agriculture</em>, and <em>Python for Chemists.</em>

ACS In Focus digital books provide scientists at any expertise level the opportunity to easily dive into a new topic area or technique.

ACS Publications

When exploring a new scientific topic, researchers are often faced with two options: digging through the basic material found within textbooks or piecing together information from niche scientific publications. Textbooks often provide overviews that are too broad for someone looking to meaningfully dive into a topic. Peer-reviewed journal articles deliver more up-to-date information, but focus on very narrow areas of research and are often overly technical. Many journal articles also do not provide a solid background for the topic at hand.

From brushing up on the basics of a scientific field to learning a new skillset for an interdisciplinary collaboration, scientists often need high-quality, accessible information in a convenient format. For example, ACS In Focus digital books are fitting primers for numerous scientific topics. More in depth than undergraduate textbooks but more approachable than scholarly articles, resources such as these get graduate students and seasoned scientists up to speed on emerging topics and techniques in a matter of hours. Scientists can access ACS In Focus digital books online or offline, utilizing convenient e-reader features for easy navigation and information-gathering, such as pop-up glossaries, expert video interviews, and related content links.

ACS In Focus digital books offer a solid middle ground, providing robust yet straightforward content for those seeking new knowledge for the sake of formal education, life-long learning, or to push their research into new avenues.

Learn more about researching new scientific topics using digital books.

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Two agar plates are shown. The one on the left shows black sporulating fungi, while the one on the right has white fungi reproducing without spores.

Article

Bacteria Sink in Their TALons to Control Their Host

Endosymbionts use effector proteins to hijack their fungal host’s ability to produce spores.

Shelby Bradford, PhD

Aug 1, 2024 | 2 min read

Image Credit:

Ingrid Richter

Endosymbiosis, a phenomenon in which one organism lives inside of another, exists across several species. “It’s basically the basis of life,” said Ingrid Richter, a microbiologist at the Leibniz Institute for Natural Product Research and Infection Biology. She and her team study the relationship between the plant and human pathogenic fungus, Rhizopus microsporus, and its endosymbiotic bacterium, Mycetohabitans rhizoxinica.

Fluorescent microscopy image of fungal walls labeled in blue with green-labeled bacteria inside.

Here, green M. rhizoxinica localized in the hyphae of R. microsporus (blue).

Ingrid Richter

In a paper published in mBio, the team showed that transcription activator-like effector (TAL) proteins from M. rhizoxinica controlled the sporulation of R. microsporus, which is advantageous to the fungi.¹ Understanding these endosymbiotic mechanisms could improve treatments against these fungal infections.

A photograph of a woman sitting at a computer in an office.

Ingrid Richter studies the endosymbiotic relationship between the bacteria M. rhizoxinica and the fungal pathogen R. microsporus.

Christine Poser

TAL in other plant pathogens promote their survival in the host, so the team investigated Mycetohabitans TAL (MTAL) as potential mediators that control R. microsporus sporulation.² They identified three of these proteins in the M. rhizoxinica genome and generated bacterial mutants, each with one MTAL deleted.

When the researchers replaced the endosymbiotic bacteria from the fungus with the mutant versions, they found significantly reduced sporulation compared to fungi with nonmutant M. rhizoxinica. “It’s basically hijacking the reproduction of the fungus,” Richter said. Confocal microscopy revealed that the bacteria resided primarily within the fungal hyphae, validating that MTAL mutations did not impact the bacteria’s infection abilities.

“This particular symbiotic association is very unusual because the fungal host is addicted to its bacterial endosymbionts for reproduction,” explained Teresa Pawlowska, a mycologist studying endosymbiosis at Cornell University who was not involved in the study. She found the study exciting because scientists don’t know the mechanisms of this manipulation. However, she pointed out that there are many MTAL in these endosymbionts beyond those studied in the paper. “It would be great to probe further and figure out what are the functionalities of these other TAL effectors,” she said.

References

Richter I, et al. mBio. 2023;14: e01824-23.
Verdier V, et al. New Phytol. 2012;196(4):1197-1207

A row of PCR tubes with clear liquid inside.

Technology Highlight| Article

Introducing More Flexibility to Automated Liquid Handling

The latest automated liquid handling robots are adaptable to numerous techniques for sample extraction, isolation, and purification.

Aug 1, 2024 | 2 min read

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Modern robotics allow automated pipetting to adapt to different workflows for sample purification, isolation, and extraction.

INTEGRA

Scientists working in the life sciences or disease research commonly have to isolate and extract specific components, such as nucleic acids or proteins, from heterogeneous samples. While researchers have derived several popular methods for doing this, such as magnetic bead purification or solid phase extraction, these processes typically remain labor intensive, requiring numerous liquid handling steps. They are also delicate, necessitating high levels of precision, as researchers must take care not to spoil the isolated fraction with external elements or unwanted aspects of the original sample. Finally, because isolation and extraction are usually the first steps within longer workflows, scientists often need to perform them in high volumes or at high throughputs.

Automation, especially in terms of liquid handling, has made scientists’ lives easier and their data more reproducible. However, integrating automated liquid handling into a multitude of different workflows without retaining a considerable amount of manual handling has historically been difficult. To that end, companies have been working to develop more flexible automation solutions. For example, INTEGRA’s ASSIST PLUS pipetting robot is compatible with electronic single, multichannel, and adjustable tip spacing pipettes, giving it the adaptability necessary to streamline a range of workflows, from sample preparation to magnetic bead-based PCR clean-ups and affinity purification. ASSIST PLUS is also instead of further compatible with 96 and 384 channel pipettes, enabling higher throughputs.

Learn more about how the latest robotic pipetting technology can help scientists ensure reproducible sample extraction and purification with increased throughputs.

What techniques in your laboratory require the most pipetting?

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A scientist in a laboratory looks surprised. She holds a tube in one hand.

Epic Fail| Article

A Miscalculated Step

As a graduate student, Tharin Blumenschein learned that too much sodium hydroxide breaks down more than just bacterial cells.

Mariella Bodemeier Loayza Careaga, PhD

Aug 1, 2024 | 2 min read

Image Credit:

modified from © istock.com, Rumi Fujishima, TopVectors, Nadezhda Ivanova; designed by Erin Lemieux

In the mid-1990s, I was a graduate student at the University of São Paulo working with EF-hand proteins, which are regulatory calcium and/or magnesium binding proteins characterized by two α-helices (E and F). I wanted to understand which amino acids in the protein’s binding site determine its affinity and specificity towards those ions.¹

A woman with wavy hair wears a blue shirt and glasses. She smiles at the camera.

In her laboratory at the University of East Anglia, biochemist Tharin Blumenschein studies the interactions that allow a protein from Chlamydia to modify the host cell cytoskeleton.

Rachel Smith

To explore this question, I transformed mutated EF-hand sequences into bacteria using plasmids to obtain larger plasmid amounts for my protein expression experiments.

One day, I was getting ready to purify the plasmids from the bacterial cultures. Since we did not have kits to isolate these circular bits of DNA back then, I had to prepare all the solutions in the protocol, including one that uses sodium hydroxide to break open the bacterial cells. After lysing the bacteria, I added cesium chloride (CsCl) and ethidium bromide (EtBr) to my bacterial lysates. CsCl creates a gradient that separates the plasmid DNA after high-speed centrifugation.

When my centrifugation time was up, I went to the equipment with syringes to collect the plasmid DNA from the tubes. Once I pulled the tubes out and looked for EtBr-stained DNA bands, I was surprised to see no bands.

Intrigued, I repeated the purification process, but it did not work. After confirming I didn’t miss any step in the protocol, I decided to redo my calculations for all the solutions. That’s when I realized that I had added ten times more sodium hydroxide to lyse my bacteria!

After overcoming my initial disappointment at making the mistake, I repeated the protocol with the new lysis solution and, lo and behold, I was able to obtain the plasmid DNA I needed.

This experience reinforced the importance of double-checking calculations before moving forward with an experiment. It also taught me an interesting property of sodium hydroxide, which can break down DNA molecules when used in excessive amounts.

This interview has been condensed and edited for clarity.

Share your Epic Fail story with us for a chance to be featured in an upcoming column.

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Reference

Blumenschein TM, Reinach FC. Biochemistry. 2000;39(13):3603-3610.

Image of a male researchers hands holding a phone displaying X (Twitter) while there is a research paper displayed on the computer in the background.

Interview| Article

From Lab to Likes: Socializing Science Through Humor

Oded Rechavi shares research and relatable science memes at the touch of his fingertips.

Laura Tran, PhD

Aug 1, 2024 | 2 min read

Image Credit:

Oded Rechavi, a molecular biologist at Tel Aviv University, studies the mysteries of memory in Caenorhabditis elegans. When he isn’t delving into the worm’s brain machinery, he taps into another kind of network: social media. With a flourish of keystrokes, Rechavi shares scientific research and jokes about academia with a global audience through social media (his preferred platform is X). By bringing much-needed levity to a serious field, he highlights the importance of humor and accessibility in science communication.

Oded Rechavi, a molecular biologist at Tel Aviv University, enjoys sharing new neuroscience research and memes about academia on social media.

Chen Gallili

What are the advantages of using social media as a researcher?

We want our science to be known, so we put ourselves out there on social media. Although it’s not conducive to proper scientific discussions, it’s still a very good way to explore science by reaching large groups of scientists from different fields and nonscientists. Even when we post a preprint, it can get traction. It’s impressive how far you can extend your reach. Most of my followers on social media are scientists, and the scientific community on X has been great. I have been lucky to see a few projects materialize through connections made on this platform.

What factors do you consider when posting on social media?

Social media is a platform where no one can hear you whisper. You have to shout. Like scientific conferences, social media complements sharing ideas and connecting with others. Normally, these interactions are confined to specific fields, but on X, you can't target a particular audience. You must be aware of other people and make sure your ideas are understood and hopefully, the work triggers their interest. I hope that something good will come out of sharing these posts, like new and unexpected ideas. Not only do I share new science and papers, but I also include jokes about academia when I come across a funny video or photo. These posts are meant to be lighthearted and offer a glimpse into the life of researchers and the publishing process.

This interview has been edited for length and clarity.

Science Snapshot| Article

Lighting Up the Neuronal Cytoskeleton

By combining microscopy techniques with genome engineering, scientists revealed the complexities of the presynaptic actin cytoskeleton.

Mariella Bodemeier Loayza Careaga, PhD

Aug 1, 2024 | 2 min read

Researchers used CRISPR-Cas9 to genetically edit two neurons (yellow) to express a tag in their endogenous actin. They labeled the remaining hippocampal neurons in culture to highlight the cell body and its ramifications (blue and purple), and the presynapses (green).

Christophe Leterrier

In the 1950s, advances in microscopy techniques allowed scientists to visualize synaptic communication between two brain cells for the first time.^1,2 However, many details beyond the general synapse structure, such as how the presynaptic and postsynaptic terminals are organized, remained elusive.

“If we want to understand how the synapse functions, we have to understand its organization,” said Christophe Leterrier, a neurobiologist at the Aix Marseille University.

To achieve this goal, Leterrier and his team decided to look at the actin cytoskeleton in the presynaptic terminal, a specialized region of the neurons’ axons where the organization of this network of protein filaments is poorly understood, according to Leterrier.

Imaging the actin cytoskeleton in presynapses is not easy as the abundance of the protein in the postsynaptic terminal often obscures its presence in the presynaptic one, Leterrier explained. Genome editing provided his team with an approach to circumvent this obstacle. Using a CRISPR-Cas9 system, they tagged endogenous actin to enhance its visibility in just a few cells of their hippocampal neuron cultures.³ They then labeled the cells with markers to highlight different neuronal components such as the axon, cell body, and presynapses, and imaged the cells using a fluorescence microscope.

The resulting image revealed how two CRISPR-edited neurons extend their actin-rich neuronal processes and make contacts with unedited neurons in the background. Along the blue neurons’ projections, tiny green dots mark the location of the presynapses, where the actin cytoskeleton forms distinct nanostructures that Leterrier’s team characterized using more advanced microscopy techniques.

“Now we've come up with a blueprint and we are categorizing actin in different types of structure,” Leterrier explained. “[This] provides a basis to explain how actin can shape and transform the synapse.”

References

De Robertis ED, Bennett HS. J Biophys Biochem Cytol. 1955;1(1):47-58.
Palay SL. J Biophys Biochem Cytol. 1956;2(4 Suppl):193-202.
Bingham D, et al. J Cell Biol. 2023;222(10):e202208110.