2017 News

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.

Erin Bush Receives Award

Erin Bush with Department of Systems Biology Assistant Professor Peter Sims and College of Physicians & Sciences Dean Lee Goldman. (Photo: Amelia Panico)

The Department of Systems Biology is proud to congratulate Erin Bush on being selected for the Columbia University College of Physicians & Surgeons 2016 Officer of Research Award. The award is one of six given annually to recognize select staff members for their outstanding contributions in the workplace. Recipients of the 2016 were recognized in a ceremony that took place at Columbia University Medical Center on January 12, 2017.

Erin is a staff associate in the JP Sulzberger Columbia Genome Center and a sequencing specialist working in the laboratories of Peter Sims and Andrea Califano. She has been helping to develop new next-generation sequencing techniques, focusing on low input and single cell DNA and RNA library preparation and testing. As the CUMC Newsroom reports:

Harris WangHarris Wang

Harris Wang has been named a recipient of the prestigious Presidential Early Career Award for Scientists and Engineers (PECASE). Dr. Wang is among 102 researchers recognized today by President Barack Obama as the newest recipients of this honor.

The PECASE is considered the United States’ highest award for young scientists and engineers, conferred annually at the White House at the recommendation of participating federal agencies. The award celebrates young researchers at the beginning of their independent research careers who show exceptional promise to lead at the frontiers of twenty-first century science and technology.

Integrating data sources

Clinical and molecular data are currently stored in many different databases using different semantics and different formats. A new project called DeepLink aims to develop a framework that would make it possible to compare and analyze data across platforms not originally intended to intersect. (Image courtesy of Nicholas Tatonetti.)

Medical doctors and basic biological scientists tend to speak about human health in different languages. Whereas doctors in the clinic focus on phenomena such as symptoms, drug effects, and treatment outcomes, basic scientists often concentrate on activity at the molecular and cellular levels such as genetic alterations, gene expression changes, or protein profiles. Although these various layers are all related physiologically, there is no standard terminology or framework for storing and organizing the different kinds of data that describe them, making it difficult for scientists to systematically integrate and analyze data across different biological scales. Being able to do so, many investigators now believe, could provide a more efficient and comprehensive way to understand and fight disease.

A new project recently launched by Nicholas Tatonetti (Assistant Professor in the Columbia University Departments of Systems Biology and Biomedical Informatics) along with co-principal investigators Chunhua Weng (Department of Biomedical Informatics) and Michel Dumontier (Stanford University), aims to bridge this divide. With the support of a $1.1 million grant from the National Center for Advancing Translational Science (NCATS) the scientists have begun to develop a tool they call DeepLink, a data translator that will integrate health-related findings at multiple scales.

As Dr. Tatonetti explains, “We want to close what we call the interoperability gap, a fundamental difference in the language and semantics used to describe the models and knowledge between the clinical and molecular domains. Our goal is to develop a scalable electronic architecture for integrating the enormous multiscale knowledge that is now available.”