NCXT staff and collaborators have mapped the reorganization of genetic material that takes place when a stem cell matures into a nerve cell. Detailed 3-D visualizations show an unexpected connectivity in the genetic material in a cell’s nucleus, and provide a new understanding of a cell’s evolving architecture.
These unique 3-D reconstructions of mouse olfactory cells, which govern the sense of smell, were obtained using soft x-ray tomography. The results could help us understand how patterning and reorganization of DNA-containing material called chromatin in a cell’s nucleus relate to a cell’s specialized function as specific genes are activated or silenced.
LBL Press release
After a very successful tenure at the NCXT, we say goodbye to Myan Do and wish her well in graduate school at UCSD.
During mitochondrial fission, the mitochondrial outer membrane proteins Mff, MiD49 and MiD51 recruit Drp1 to execute organelle constriction. Intriguingly, recent studies indicate that endoplasmic reticulum (ER) tubules can wrap around mitochondria and mediate membrane constriction in a Drp1-independent manner, but it is still unclear whether other proteins are involved. To investigate whether MiD49 and MiD51 are linked to the role of the ER in mitochondrial fission, Kirstin Elgass and colleagues (p. 2795) used live-cell confocal imaging, correlative cryogenic fluorescence microscopy (CRM) and soft X-ray tomography (SXT) to render a 3D reconstruction of ER–mitochondria contact sites. They observed that MiD49 colocalised with Mff, and MiD51 colocalised with Mff and Drp1. Both MiD proteins formed dynamic foci that were found both within and outside of constriction sites, and within sites that underwent repeated constriction–expansion cycles. The authors then established that mitochondria–ER contact sites colocalise with MiD foci, but that only 40% of these contacts were at constriction sites. Using CRM-SXT they next reconstructed the 3D ER–mitochondria landscape, and found that the ER forms short extensions that contact the mitochondria at MiD foci, the length of which was under the limit of resolution for confocal microscopy. Therefore, besides showing that ER tubules contact mitochondria at MiD foci, this study also employs a novel imaging approach that could be extremely useful for high-resolution studies of intracellular structures.
J Cell Sci (2015) 128:2795-2804; Advance Online Article June 22, 2015
As part of the CSH Single Cell Analysis Course, the NCXT offered a multi-day workshop on soft x-ray tomography (SXT). Attendees had the opportunity to gain hands-on experience of working with SXT data, including sophisticated techniques, such as segmenting reconstructed cells. More details and photos of the team in action are here.
A warm welcome to Drs. Jian-Hua Chen and Andreas Walter, both of whom recently joined the NCXT as postdocs.
Associate Professor of Mathematics and Statistics Sam Isaacson has been awarded a CAREER Award in Mathematics by the National Science Foundation. It is a prestigious five-year grant, given annually to the top 20-30 tenure-track mathematicians nationally.
This award will fund the development of new numerical methods for simulating how proteins and mRNAs move about and interact within cells. These new methods are designed to allow the study of cellular processes, such as gene expression and signal transduction, in realistic three-dimensional models of the cellular space. An important feature of these models is the incorporation of explicit representations of cellular organelles and membrane surfaces, reconstructed from high resolution soft x-ray tomography data (courtesy C. Larabell at UCSF). The algorithms and computer programs made available by this research will enable more in depth studies of many pathways involved in cell signaling, growth, division, tissue development, and cancer proliferation.
The grant will also support the development of a more comprehensive mathematical biology program within the Department of Mathematics and Statistics. A new “Mathematical Biology on Clusters” course will be created to teach the process of computational model development for biological problems requiring the use of large datasets and large-scale computing resources. The new simulation tools we develop will be integrated into this course, enabling course projects in which students study models of specific cellular processes within their own cell (reconstructed from soft x-ray tomography data).
The award shows that there is substantial interest in developing new methods with which to model the spatial movement and interaction of proteins within cells. I’ve been interested in these questions for many years, but it is only recently that the needed computational resources, experimental data, and appropriate numerical methods to facilitate such modeling are becoming available. The planned research is one mathematical step in the long journey toward creating accurate, dynamic, three-dimensional in silico models of single cells from high-throughput and high resolution imaging data.
An abstract by NCXT staff and collaborators in the Panning Group (UCSF) was selected out of 4,500 other submissions as a Highlight of the 2014 Biophysical Society Meeting. Elizabeth Smith of the NCXT gave a talk entitled "The Topological Organization of the Inactive X Chromosome in its Native State". The talk was also accompanied by the Society Press release below (you can download a pdf version here).