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Golden Approach to High-speed DNA Reading

Schematic drawing of graphene nanopore with self-integrated
optical antenna (gold) that enhances the optical readout signal (red) of DNA as it passes through a graphene nanopore.

Berkeley researchers have created the world’s first graphene nanopores that feature integrated optical antennas. The antennas open the door to high-speed optical nanopore sequencing of DNA.

RCas9: A Programmable RNA Editing Tool

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A powerful scientific tool for editing the DNA instructions in a genome can now also be applied to RNA as Berkeley Lab researchers have demonstrated a means by which the CRISPR/Cas9 protein complex can be programmed to recognize and cleave RNA at sequence-specific target sites.

MaxBin: Automated Sorting Through Metagenomes

MaxBin, an automated software program for binning the genomes of individual microbial species from metagenomic sequences is available on-line through JBEI.

MaxBin is an automated software program for binning the genomes of individual microbial species from metagenomic sequences developed at the Joint BioEnergy Institute (JBEI).

Encyclopedia of How Genomes Function Gets Much Bigger

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A big step in understanding the mysteries of the human genome was unveiled today in the form of three analyses that provide the most detailed comparison yet of how the genomes of the fruit fly, roundworm, and human function. The analyses will likely offer insights into how the information in the human genome regulates development, and how it is responsible for diseases.

New Technique for Identifying Gene-Enhancers

Berkeley Lab researchers led the development of a new technique for identifying gene enhancers – sequences of DNA that act to amplify the expression of a specific gene – in the genomes of humans and other mammals. Called SIF-seq, this new technique complements existing genomic tools, such as ChIP-seq, and offers additional benefits.

Vast Gene-Expression Map Yields Neurological and Environmental Stress Insights

A consortium led by Berkeley Lab scientists has conducted the largest survey yet of how information encoded in an animal genome is processed in different organs, stages of development, and environmental conditions. Their findings, based on fruit fly research, paint a new picture of how genes function in the nervous system and in response to environmental stress.

New Insight into an Emerging Genome-Editing Tool

A collaboration led by Berkeley Lab’s Jennifer Doudna and Eva Nogales has produced the first detailed look at the 3D structure of the Cas9 enzyme and how it partners with guide RNA to interact with target DNA. The results should enhance Cas9’s value and versatility as a genome-editing tool.

Puzzling Question in Bacterial Immune System Answered

Berkeley researchers have answered a central question about Cas9, an enzyme that plays an essential role in the bacterial immune system and is fast becoming a valuable tool for genetic engineering: How is Cas9 able to precisely discriminate between non-self DNA that must be degraded and self DNA that may be almost identical within genomes that are millions to billions of base pairs long.

Microbial Who-Done-It For Biofuels

A multi-institutional collaboration led by researchers with the Joint BioEnergy Institute (JBEI) and Joint Genome Institute (JGI) has developed a promising technique for identifying microbial enzymes that can effectively deconstruct biomass into fuel sugars under refinery processing conditions.

Expressly Unfit for the Laboratory

A new Berkeley Lab study challenges the orthodoxy of microbiology, which holds that in response to environmental changes, bacterial genes will boost production of needed proteins and decrease production of those that aren’t. The study found that for bacteria in the laboratory there was little evidence of adaptive genetic response.