Biosciences News

Engineering biological systems to specification–for example, designing a microbe to produce a cancer-fighting agent–requires a detailed mechanistic understanding of how all the parts of a cell work. Typically, this knowledge is acquired through years of painstaking work and a fair amount of trial and error. But Berkeley Lab scientists have created an Automated Recommendation Tool (ART) that adapts machine learning algorithms to the needs of synthetic biology to guide development systematically. With a limited set of training data, the algorithms are able to predict how changes in a cell’s DNA or biochemistry will affect its behavior, then make recommendations for the next engineering cycle along with probabilistic predictions for attaining the desired goal. The work was led by Hector Garcia Martin, a researcher in Berkeley Lab’s Biological Systems and Engineering (BSE) Division and Tijana Radivojevic, a BSE data scientist. In a pair of papers recently published in the journal Nature Communications, they presented the algorithm and demonstrated its capabilities.

Read more in the Berkeley Lab News Center.

The Aligning Science Across Parkinson’s (ASAP) initiative has awarded James Hurley, a faculty scientist in the Molecular Biophysics and Integrated Bioimaging (MBIB) Division, $7 million over three years to investigate the role of damaged mitochondria in the disease. The grant is among 21, totaling $161 million, announced by the ASAP initiative, which aims to fund basic research to close gaps in our understanding of the mechanisms of Alzheimer’s Disease and its progression.

Previous work on microbial mats had primarily relied on culturing virus and host pairs in the laboratory to study their interactions. In The ISME Journal, a team co-led by JGI postdoctoral researcher Mária Džunková used single-cell sequencing to sequence both a cell’s genome and detect accompanying viral sequences, which would suggest the virus had been infecting the cell. Read the full story on the JGI website.

Flowering plants abide by the concept, “the more the merrier,” with respect to their genomes. In their base state, they are diploids with two genome copies, one from each parent. Having three or more genome copies from additional parents or duplication, also known as “polyploidy,” is common amongst flowering plants. Crop breeders have harnessed polyploidy to increase fruit and flower size, and confer stress tolerance traits. In Nature Communications, a multi-institutional team led by researchers at Spain’s Universidad de Zaragoza and the DOE Joint Genome Institute (JGI) relied on a model grass system (Brachypodium) to learn more about the origins, evolution and development of plant polyploids. Read more on the JGI website.

For the past several months, teams of bioscientists have utilized Berkeley Lab’s world-class research facilities to contribute to the national response to COVID-19, resulting in a wide range of promising research. Four videos showcase researcher contributions from across the Biosciences Area, which aim to help address some of the many scientific challenges posed by the pandemic.