iBiology Podcast

Microglia are the primary immune cells in the central nervous system. In the brain, they play central roles in proper development and function, as well as dysfunction and disease. In her first talk, Dr. Beth Stevens provides an overview of the many ways microglia cells operate, and how they can both harm and protect the brain. Fairly recent advances in the study of microglia through imaging have allowed researchers to identify different microglia states and study their dynamic roles at different stages of development.

Dr. Stevens dives deeper into the mechanisms that allow microglia to shape the network of connections between neurons in the brain. She provides an introduction to the role of microglia in synaptic pruning, the process of eliminating extra synapses in healthy developing brains. She then goes on to explain how the reactivation of this process affects aging and diseased brains.

Single cell sequencing, as the name implies, allows researchers to examine the genomic information for individual cells. This provides an opportunity to examine cell-to-cell differences and identify cell subtypes, which provides insight into how specific cells function within and respond to their environment. Dr. Eric Chow begins his talk with an overview of single cell sequencing with a focus on RNA. He then goes on to outline the predominant approaches, including plate-based, microfluidic-based, and combinatorial indexing methods. He finishes by addressing approaches to single cell analysis that don’t rely on RNA, including methods that use DNA, proteins, and antibodies. He also reviews some of the benefits and limitations of analysis at the level of individual cells.

The nucleosome is the central organizing structure of the eukaryotic genome. It consists of DNA wrapped around histone proteins. Dr. Karolin Luger shares her discovery of the three-dimensional structure of the nucleosome using X-ray crystallography, which provided a deeper understanding of chromatin organization.

In the past decade there has been an amazing change in the efficiency of DNA sequencing. Using traditional Sanger sequencing, the human genome project took 20 years and cost $3 billion. Current next generation sequencing methods allow a human genome to be sequenced for $1000, in 48 hours!  In this talk, Eric Chow explains the chemistry behind next generation sequencing, and describes how the next gen sequencers detect and display results. The most commonly used Illumina sequencers are image based and detect the addition of fluorescently labelled nucleotides. Chow also describes two different next generation sequencing technologies which provide benefits such as much longer reads but with downsides such as higher error rates. Chow finishes the talk with some insights into medical applications of next gen sequencing such as much less invasive prenatal testing or cancer detection.

Many of us are used to seeing cartoons of cells with organelles shown as static, isolated structures. The endoplasmic reticulum (ER) is often shown looking like a stack of pancakes pushed up against the nuclear envelope. In her first talk, Dr. Gia Voeltz explains that recent advances in light microscopy have given us a very different view of organelles and their interactions. The ER is, in fact, an expansive, and highly dynamic, network of tubules that spreads throughout the cell.  It interacts with other organelles such as the plasma membrane, endosomes, and mitochondria at points called membrane contact sites. Using beautiful fluorescent images and movies, Voeltz shows us that these ER membrane contact sites are important for many functions such as trafficking lipids and Ca2+ and determining where mitochondria divide and endosomes undergo fission. These exciting findings define a new cellular function for the ER.

Voeltz explains how her lab used a BioID strategy to identify some of the proteins found at membrane contact sites between the ER and endosomes; a difficult task given the transient nature of contact sites.  They were able to identify a number of proteins responsible for marking the timing and location of endosome fission and for recruiting the ER to the bud. Depleting these proteins blocked cargo sorting to the Golgi. Voeltz’ lab is now working to determine how much of this machinery is conserved in processes such as the mitochondrial 

Dr. Tom Rapoport explains that eukaryotic cells contain many membrane-bound organelles each of which has a characteristic shape and distinctive functions that are determined by specific proteins. Most proteins are made in the cytosol but must move to different cellular destinations.  Signal sequences on the proteins act as “zip codes” and direct protein sorting. Many proteins sort first to the endoplasmic reticulum (ER) before moving to other intracellular organelles or the plasma membrane. Rapoport explains that the Sec 61 channel in the ER membrane is key to protein sorting. Solving the structure of Sec 61 allowed Rapoport’s lab to understand how proteins are transported across the ER membrane and directed to their final destination.

The ER is a vast network that includes different domains with different functions. The rough ER is made of ribosome covered membrane sheets and is involved in protein translation.  The smooth ER consists of tubules and is important for lipid synthesis and Ca2+ transport. In his second talk, Rapoport explains how his lab identified several families of proteins needed to generate and maintain a tubular ER network. Using ultra-thin section microscopy, Rapoport and others also showed that stacked ER sheets are held together by helicoidal membrane connections that form a “parking-garage” like structure.

Dan Littman discusses the opposing roles of Th17 cells. They protect mucosal surfaces from infection with bacteria and fungi, but they can also cause autoimmune inflammation. Using a mouse model of autoimmunity called experimental autoimmune encephalomyelitis (EAE), Littman and his lab have shown that there are two types of Th17 cells. Non-pathogenic Th17 cells are induced by the microbiota and protect barrier surfaces, while pathogenic Th17 cells are induced by the presence of IL-23, likely the result of inflammation elsewhere in the body.  Both types Th17 cells secrete the cytokines IL-17A, IL-17F and IL-22, however, pathogenic Th17 cells also secrete interferon gamma (IFNγ) which induces further inflammation and autoimmune disease.  In the last 10 years, several classes of innate lymphoid cells have been found to share similar cytokine profiles to T helper cells and these cells appear to be another important layer in protecting surfaces in the gut and lung from infection.