MBIB News

Both plants and animals are targeted by rapidly evolving pathogens, including viruses, bacteria and fungi. Thanks to highly adaptive immune receptors, humans can mount a new antibody response towards infection or a vaccine over the course of a week. Plant immune receptors, however, do not typically change over the lifetime of an individual. Berkeley Lab scientist Daniil Prigozhin collaborated with Ksenia Krasileva from University of California, Berkeley to study plant immune receptors using pan-genome sequencing, a technique which allows them to scan all genomes for every strain in a species within a particular branch on the tree of life. Their pan-genome analysis, published recently in The Plant Cell, showed that some plant immune receptors show a surprising degree of diversity within species. In addition, it allowed them to study how innate immunity evolves, where new receptor specificities come from, and the costs associated with making new receptors, such as the potential for autoimmunity.

The multi-protein structure polycomb repressive complex 2 (PRC2) is involved in “silencing” genes so that they are not “read” by the cellular machinery that decodes genetic information, effectively keeping the genetic information in the “off” state. PRC2 silences genes by chemically depositing tri-methylation marks on histone H3 at lysine 27. Failure to regulate the activity of PRC2 not only impairs the process of development, but also contributes to the reversal of cell differentiation and the uncontrolled cell growth that are the hallmarks of cancer.

A team of scientists at Berkeley Lab and UC Berkeley have uncovered the molecular basis for the recruitment of PRC2 to certain locations of the genome and for the regulation of its activity. In a study published January 22 in Science, the researchers describe the structure of PRC2 while bound to a biologically relevant chromatin target. Using cryo-electron microscopy (cryo-EM), they uncovered crucial structural and functional information about this key regulator of cell differentiation and identity.

The diffraction limit is a fundamental property of light that has long prevented optical microscopes from bringing into focus anything smaller than half the wavelength of visible light (~200 nanometers), which is at least an order of magnitude larger than the tiny protein machines that keep cells, and us, running. A team of researchers co-led scientists in Berkeley Lab’s Molecular Foundry and Columbia University’s school of engineering developed a new class of crystalline material that, when used as a microscopic probe, overcomes the diffraction limit without heavy computation or a super-resolution microscope. The amazing new material, called avalanching nanoparticles (ANPs), will advance high-resolution, real-time bio-imaging of a cell’s organelles and proteins, as well as the development of ultrasensitive optical sensors and neuromorphic computing that mimics the neural structure of the human brain, among other applications. The work was reported in a cover article in the journal Nature.

A team of UC Berkeley and Berkeley Lab researchers used X-ray crystallography performed at the Advanced Light Source (ALS) to determine the atomic structure of ORF8, a protein secreted by the SARS-CoV-2 virus that is thought to help the pathogen evade and dampen response from human immune cells.

A team based at Berkeley Lab’s Advanced Light Source is making waves with its new approach for whole-cell visualization, using the world’s first soft X-ray tomography (SXT) microscope built for biological and biomedical research. In its latest study, published in Science Advances, the team used its platform to reveal never-before-seen details about insulin secretion in pancreatic cells taken from rats. This work was done in collaboration with a consortium of researchers dedicated to whole-cell modeling, called the Pancreatic β-Cell Consortium.