Biosciences Area

Exploring Human Origins in the Uncharted Territory of Our Chromosomes

A group of geneticists from Berkeley Lab, UC Davis, UC Santa Cruz, and UC Berkeley are unraveling new details about human evolution by studying the uniquely regulated portion of our chromosomes that surround the centromeres. These stretches of DNA – termed centromere-proximal regions (CPRs) – are largely composed of highly repetitive, mostly non-gene-coding sequences that … Read more »

JGI Overhauls Perception of Inovirus Diversity

Inoviruses are filamentous viruses with small, single-stranded DNA genomes and a unique chronic infection cycle. In Nature Microbiology, a team led by DOE Joint Genome Institute (JGI) researchers applied machine learning to publicly available microbial genomes and metagenomes to search for inoviruses. The search tool combed through more than 70,000 microbial and metagenome datasets, ultimately identifying more than 10,000 inovirus-like sequences compared to the 56 previously known inovirus genomes. The results revealed inoviruses are in every major microbial habitat—including soil, water, and humans—around the world.

“We’re not sure why we systematically manage to miss them; maybe it’s due to the way we currently isolate and extract viruses,” said the study’s lead author Simon Roux, a JGI research scientist in the Environmental Genomics group. Click here to read the full story on the JGI site.

More Investment Needed for Machine Learning for Bioengineering

Machine Learning.In an opinion piece published July 19 in ACS Synthetic Biology, Hector Garcia Martin and Tijana Radivojevic of the Biosciences Area’s Biological Systems & Engineering Division collaborated with Pablo Carbonell of the Manchester Institute of Biotechnology’s SynBioChem Centre, to highlight the opportunities in a radical new approach to bioengineering that leverages the latest disruptive advances in machine learning.

JGI Helps Optimize Microbial Oil Production

Yarrowia lipolytica is a tantalizing microbial factory, capable of turning abundant biomass carbohydrates—glucose and xylose—into fatty acids that could be used for renewable fuel. In fact, lipids can make up more than 90 percent of the microbe’s dry weight.

In order to better harness these gobs of energy, a team of researchers sought to disrupt every gene in the genome with CRISPR-Cas9 in order to interrogate each one’s function. However, the team first needed to fix a defect in the approach: CRISPR-Cas9 relies on RNA with a short guiding sequence (20 bp) that directs the endonuclease where to cut, but these “single guide” RNAs (sgRNAs) can be faulty. Without a good sgRNA, Cas9 is ineffective and leaves the target gene intact: a false negative if the gene is actually essential.

Through the JGI’s Community Science Program, the scientists thus set out to identify which sgRNA sequences were reliable. Click here to read the science highlight on the JGI website.

Epic Research Endeavor Reveals Cause of Deadly Digestive Disease in Children

Berkeley Lab geneticist Len Pennacchio and his team helped a group of Israeli clinical researchers solve the mystery of a rare inherited disease that causes extreme, sometimes fatal, chronic diarrhea in children. The nearly decade-long investigation not only led to the discovery of a novel protein-coding gene that is critical for intestinal function, but also expanded our understanding of regulatory sequences in the human genome. The results were recently published in Nature.

Was this page useful?

Send
like not like
Follow us: