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Pictured above, from left: Amy Herr (CZ Biohub Network VP), Daniel Wang (Chicago Group Leader), Shalin Mehta (SF Platform Leader), Csaba Forró (Chicago Group Leader), Rafael Gómez-Sjöberg (SF Chief Technology Officer), and Loïc Royer (SF Group Leader & Director of Imaging AI).

Last week CZ Biohub Chicago hosted the first-ever Chicago BioEngineering Conference – two packed days of learning, networking, and forging new connections with the life science research community in Chicagoland. Speaking to a sold-out crowd of 500 attendees, Biohub Chicago President Shana Kelley described the institute’s approach to engineering instrumented tissues. (Meet the team here, and learn more about their work here.) The Conference was also an opportunity for scientists across the Biohub Network to showcase their work. 

Investigator spotlight

In the news

The Scientist: Better living through algae biotechnology

Scientists are exploring the unique biological capabilities of microalgae — they are able to fix nitrogen, produce lipids and proteins, and treat wastewater — to address the planet’s sustainability issues. A feature in The Scientist describes a project by Stanford microbiologist Ellen Yeh, a CZ Biohub SF Investigator, to understand the endosymbiotic relationship between certain algae species and nitrogen-fixing bacteria. As her model system, Yeh uses a species that one of her graduate students collected from creek water while on a hike. Her lab hopes to leverage this natural process in algae to engineer nitrogen fixation in plants. Read more.

Gladstone Institutes: New technology could lead to alternative treatments for antibiotic-resistant bacteria

Viruses that attack bacteria — called bacteriophages — could prove a potent and precise weapon in the fight against antibiotic-resistant pathogens. Finding a naturally occurring virus that successfully targets a specific microbe, however, requires a time-consuming and labor-intensive search that may very well come up short. Instead, CZ Biohub SF Investigator Seth Shipman has developed a method to quickly tweak the genomes of bacteriophages and then screen the altered viruses for their potency against dangerous bacteria. The approach, which relies on components of the bacterial immune system called retrons, stands to speed up the discovery of effective viruses, while also giving researchers a better understanding of how specific genetic tweaks change virus behavior. Read more.

From Our Neurons to Yours: Unraveling Timothy syndrome

CZ Biohub SF Investigator Sergiu Pasca has pioneered techniques for growing human brain tissue in the lab to better understand brain development and disorders like autism and schizophrenia. His team uses organoids — tiny, lab-grown clusters of human brain cells that mimic aspects of real brain tissue, to study how genetic and environmental factors influence brain circuit formation. Pasca explains why rare disorders can serve as "Rosetta Stones" for understanding more common conditions and discusses how the ultra-rare Timothy syndrome — a genetic disorder that affects both the brain and heart — offers a unique opportunity to unravel the brain mechanisms of psychiatric disorders at the cellular level. Listen here.

Nanoscape: Nano solutions to black-box problems

Northwestern University professor of chemistry and biomedical engineering Shana Kelley is the president of CZ Biohub Chicago, launched last year with the mission of “engineering technologies to make precise, molecular-level measurements of biological processes within human tissues, with an ultimate goal of understanding and treating the inflammatory states that underlie many diseases.” In a new podcast from Northwestern’s International Institute for Nanotechnology, Kelley talks about how creating nanosensors that “match the size-scale of molecules” can allow researchers to make the kinds of precise measurements needed to look inside the “black-box” processes of immune function. She also shares details of how scientific leaders at the universities of Northwestern, Chicago, and Illinois Urbana-Champaign united to form the Chicago Biohub. Listen here.

What we're reading

Spatial Technologies of the Future

In a 2022 essay originally published as part of his Ph.D. thesis, Harvard postdoctoral scholar Zachary Chiang discusses how the combination of spatial and molecular technologies to study cells is fueling breakthroughs in biology today. Using the analogy of an aerial photo of San Francisco (standing in for a microscopy image) and a Wikipedia blurb about the city (standing in for DNA/RNA sequencing), Chiang discusses why we need both kinds of information to create informative “maps” of cellular processes. He then shares his perspectives about what the combination of microscopy and sequencing might look like in the future and how prioritizing those advances will get us closer to being able to visualize everything happening inside cells in real time. “Progress in microscopy and sequencing shows no signs of slowing in the near future,” he writes.

Recent publications

Cell Reports: Acute and persistent responses after H5N1 vaccination in humans

Richard Apps, Angélique Biancotto, Julián Candia, Yuri Kotliarov, Shira Perl, Foo Cheung, Rohit Farmer, Matthew P. Mulè, Nicholas Rachmaninoff, Jinguo Chen, Andrew J. Martins, Rongye Shi, Huizhi Zhou, Neha Bansal, Paula Schum, Matthew J. Olnes, Pedro Milanez-Almeida, Kyu Lee Han, Brian Sellers, Mario Cortese, Thomas Hagan, Nadine Rouphael, Bali Pulendran, Lisa King, Jody Manischewitz, Surender Khurana, Hana Golding, Robbert G. van der Most, Howard B. Dickler, Ronald N. Germain, Pamela L. Schwartzberg, John S. Tsang

Science: Single-cell chromatin accessibility reveals malignant regulatory programs in primary human cancers

Laksshman Sundaram, Arvind Kumar, Matthew Zatzman, Adriana Salcedo, Neal Ravindra, Shadi Shams, Bryan H. Louie, S. Tansu Bagdatli, Matthew A. Myers, Shahab Sarmashghi, Hyo Young Choi, Won-Young Choi, Kathryn E. Yost, Yanding Zhao, Jeffrey M. Granja, Toshinori Hinoue, D. Neil Hayes, Andrew Cherniack, Ina Felau, Hani Choudhry, Jean C. Zenklusen, Kyle Kai-How Farh, Andrew McPherson, Christina Curtis, Peter W. Laird, The Cancer Genome Atlas Analysis Network, M. Ryan Corces, Howard Y. Chang, William J. Greenleaf

Proceedings of the National Academy of Sciences (PNAS): Climate, demography, immunology, and virology combine to drive two decades of dengue virus dynamics in Cambodia

Cara E Brook, Carly Rozins, Jennifer A Bohl, Vida Ahyong, Sophana Chea, Liz Fahsbender, Rekol Huy, Sreyngim Lay, Rithea Leang, Yimei Li, Chanthap Lon, Somnang Man, Mengheng Oum, Graham R Northrup, Fabiano Oliveira, Andrea R Pacheco, Daniel M Parker, Katherine Young, Michael Boots, Cristina M Tato, Joseph L DeRisi, Christina Yek, Jessica E Manning

bioRxiv: Ultrack: Pushing the limits of cell tracking across biological scales

Jordão Bragantini, Ilan Theodoro, Xiang Zhao, Teun A.P.M. Huijben, Eduardo Hirata-Miyasaki, Shruthi VijayKumar, Akilandeswari Balasubramanian, Tiger Lao, Richa Agrawal, Sheng Xiao, Jan Lammerding, Shalin Mehta, Alexandre X. Falcão, Adrian Jacobo, Merlin Lange, Loïc A. Royer

MethodsX: Maximizing single cell dissociation protocol for individual zebrafish embryo

Shruthi VijayKumar, Michael Borja, Norma Neff, Loïc A. Royer, Merlin Lange 

bioRxiv: Genomic sequence analysis of the first mpox virus detected in Kenya 

Solomon K. Langat, Konongoi Limbaso, Samoel Khamadi, Albert Nyunja, Genay Pilarowski, Emmanuel Okunga, Victor Ofula, Paul Oluniyi, Hellen Koka, Edith Koskei, Samuel Owaka, Betty Chelangat, Francis Mulwa, James Mutisya, Edith Chepkorir, Joel Lutomiah, Daniel Langat, Patrick Amoth, Elijah Songok

bioRxiv: Spatial microenvironments tune immune response dynamics in the Drosophila larval fat body

Brandon H. Schlomann, Ting-Wei Pai, Jazmin Sandhu, Genesis Ferrer Imbert, Thomas G.W. Graham, Hernan G. Garcia

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