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Peter Sims Lab Wins CZI Award

Assistant Professor Peter Sims and postdoctoral research scientist Jinzhou Yuan displaying their platform for automated single-cell RNA sequencing. (Photo: Lynn Saville)

Assistant Professor Peter Sims, PhD , has been awarded an inaugural Chan Zuckerberg Initiative (CZI) award for gene sequencing research that will help advance the Human Cell Atlas project. Launched in 2016 by a cohort of world-leading scientists, the Human Cell Atlas is a high-profile endeavor whose goal is to identify and define every cell type of the human body and create a collection of maps that will describe the cellular basis of health and disease.

With the support of CZI, founded by Facebook CEO Mark Zuckerberg and his wife, Priscilla Chan, Dr. Sims and his group in the Department of Systems Biology will receive grant funding to pilot a revolutionary technique for high throughput single-cell sequencing. Called SCOPE-Seq, the novel, economical method conducts RNA sequencing coupled with live imaging of the same individual cell on a large scale.

Poster winners with Department Chair Andrea Califano (far right), left to right: Sebastien Weyn-Vanhentenryck, Yun Hao and Jinzhou Yuan

Research diversity and innovation were the key themes at the Department of Systems Biology’s annual retreat. Held Sept. 18 in Tarrytown, N.Y., the retreat was attended by 145 guests and included a mix of faculty, students, post-docs, research scientists and department guests. A series of presentations showcased the collaborative projects underway in the Center for Cancer Systems Therapeutics (CaST), along with sessions by faculty about their ongoing research, for example, in the areas of computational genetics, complex predictive methods and cancer-related genomics. The all-day event also included a poster session and competition, highlighting the department’s pool of talented students and researchers.

Department chair Andrea Califano said his hope is that the annual retreat gives everyone a chance to “reflect on the various different studies and diverse approaches currently going on in the department.” 

Faculty judges named three winners of the poster competition, recognizing the work of students Yun Hao and Sebastien Weyn-Vanhentenryck and post-doctoral research scientist, Jinzhou Yuan.

Sway Chen, a PhD student in the Harris Wang Lab,  won the Best Poster Award at one of the premiere international conferences, the 2017 Synthetic Biology: Engineering, Evolution & Design (SEED) in Vancouver, British Columbia, Canada on June 23rd. Sway’s poster was titled “In Situ Metagenomic Perturbation of Mammalian Gut Microbiomes Through Engineered Horizontal Gene Transfer”.  Carlotta Ronda, a postdoc in the Wang Lab, and Vitor Cabral, a former postdoc in the Wang Lab, contributed to Sway’s project as well. 

‘SEED 2017 is focused on advances in the science and technology emerging from the field of synthetic biology. This is broadly defined as technologies that accelerate the process of genetic engineering. The conference highlighted new tool development, as well as the application of these tools to diverse problems in biotechnology, including therapeutics, industrial chemicals and fuels, natural products, and agriculture. This year's theme is "building foundations of synthetic biology, scaling it up, and applying it to critical problems.”’  

Congratulations, Sway! 

Researchers at Columbia University Medical Center have created a new tool to describe the many possible ways in which a cell may develop. Rooted in the mathematical field of topology, the tool provides a roadmap that offers detailed insight into how stem cells give rise to specialized cells. 

The study was published May 1st in Nature Biotechnology. 

Every organism begins with one cell. As that cell divides, its copies branch off to become specialized cells—such as heart, bone, or brain cells—in a process known as differentiation. To understand the internal and external cues that move cells along this path, scientists can sequence their RNA—the molecular messenger that translates DNA into proteins and other products. 

Sequencing RNA from a batch of cells is not ideal, however, because the cells are usually in different states of development. To address this problem, scientists have developed single-cell RNA sequencing. “It’s like a new microscope, giving us the ability to study many biological phenomena at once,” said Raul Rabadan, PhD, associate professor of systems biology and biomedical informatics at Columbia and co-author of the paper. “However, researchers are still left with the problem of understanding the relationships between different cell states, which drive the process of development.” 

Sexual reproduction may have never become possible if organisms hadn’t evolved a way to restrain the immune system during fertilization, according to a new study from the lab of Sagi Shapira, PhD, assistant professor of systems biology.

The study, published today in Immunity, took an in-depth look at how vertebrate eggs are fertilized.

To fight invading pathogens, all organisms (including vertebrate cells) are programmed to detect and attack any DNA and foreign RNA found outside of the nucleus in the cell’s cytoplasm. It’s usually a safe bet that any DNA found in the cytoplasm is from a foreign microbe, because the cell’s own DNA is safely sequestered in the nucleus. But during fertilization, DNA and RNA from sperm may be briefly exposed to the cytoplasm of an egg—and to the danger of being recognized and attacked.

For fertilization to succeed, Dr. Shapira reasoned that something must prevent the immune system from attacking DNA during fertilization and searched for candidates in the genome.

The search revealed a gene called NLRP14, which encodes a protein that Dr. Shapira’s laboratory demonstrated to play a role in the innate immune system. Without NLRP14, the immune system induces a strong inflammatory response to DNA and RNA found in the cytoplasm, and the fertilization process comes to a halt.