All-Star Scientific Team Seeks to Edit Entire Microbiomes with CRISPR
Berkeley Lab scientists vital to UC Berkeley-led work on microbial “community editing”

---Adapted from a UC Berkeley news release

To date, CRISPR enzymes have been used to edit the genomes of one type of cell at a time: They cut, delete, or add genes to a specific kind of cell within a tissue or organ, for example, or to one kind of microbe growing in isolation in a test tube.

Now, a team led by Jennifer Doudna and Jillian Banfield – the UC Berkeley scientists who invented the CRISPR-Cas9 genome editing technology and pioneered metagenomics, respectively – has found a way to add or modify specific genes within a microbial community of many different species simultaneously, opening the door to what could be called “community editing.” The technique is described in Nature Microbiology.

While this technology is still exclusively applied in lab settings, it could be used both to edit and to track edited microbes within a natural community, such as in the gut or on the roots of a plant, where thousands of different microbes congregate. Such tracking becomes necessary as scientists talk about genetically altering microbial populations: inserting genes into microbes in the gut to fix digestive problems, for example, or altering the microbial environment of crops to make them more resilient to pests or drought.

“Eventually, we may be able to eliminate genes that cause sickness in your gut bacteria or make plants more efficient by engineering their microbial partners,” said co-first author Brady Cress, a postdoctoral researcher in Jennifer Doudna’s lab. “But likely, before we do that, this approach will give us a better understanding of how microbes function within a community.”

Berkeley Lab scientists Adam Deutschbauer and Trenton Owens, both authors on the new paper, helped the UC Berkeley team develop an approach to determine which microbes in a community are actually susceptible to gene editing, an important first step toward the goal of community editing. 

The new approach greatly extends the capabilities of a technique called random-barcode transposon site sequencing, or RB-TnSeq, which randomly makes mutations in a single bacterium’s genome and uses sequencing to determine which mutations confer a competitive advantage or disadvantage. RB-TnSeq was previously developed by Deutschbauer and Adam Arkin, who are both in the lab’s Environmental Genomics and Systems Biology Division. 

“The new microbial community editing approach leverages CRISPR technology and enables the genetic modification of a specific gene within a specific bacterium,” said Deutschbauer.     

Banfield, Doudna, and Deutschbauer are principal investigators on the Department of Energy-funded Microbial Community Analysis and Functional Evaluation in Soils Scientific Focus Area (m-CAFEs), which supported the development of this new technique. m-CAFEs is developing the tools and knowledge necessary to understand microbial interactions in the soil environment surrounding plant roots. 

“This really opens the door to investigating the roles of specific bacteria and their genes in mediating interactions with each other and with plants, including for microbes that we cannot currently cultivate in isolation in the laboratory,” said Deutschbauer. 

This research was also supported by the National Institutes of Health.

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New Technique Visualizes Every Pigment Cell of Zebrafish in 3D 
X-ray study could help scientists understand melanin’s role in human skin pigmentation and skin cancer

---By Theresa Duque

Researchers have developed a new technique that images every pigment cell of a whole zebrafish in 3D. The work, recently reported in the journal eLife, could help scientists understand the role of melanin in skin cancer. 

Melanin is a natural pigment that gives color to the skin, hair, and eyes in humans and animals. Melanin also has implications in melanin-containing cancers, or melanomas, which are typically staged by the depth of penetration in skin.    

But studying melanin directly with a conventional microscope is challenging because the pigment blocks light. So Keith C. Cheng, a distinguished professor of pathology, pharmacology and biochemistry, and molecular biology at Penn State College of Medicine, turned to X-ray imaging, which can pass through optically opaque matter like melanin.

To perform the imaging, Cheng partnered with Dula Parkinson, a staff scientist at Berkeley Lab’s Advanced Light Source (ALS), to image two sets of zebrafish samples – one with the normal pigmentation associated with the zebrafish’s characteristic black stripes, and another from a mutant zebrafish line with lighter stripes called golden. Over 15 years ago, Cheng and his lab discovered a key gene implicated in human skin color by studying golden zebrafish. That discovery highlighted the zebrafish’s utility as an animal model of human pigmentation in skin disorders such as albinism or melanoma skin cancer.

To visualize the melanin, lead author Spencer R. Katz developed a staining technique using silver, which binds to the pigment and blocks X-rays. Using the ALS and an X-ray detector system developed by the Cheng lab, the researchers visualized every melanocyte – a cell containing melanin – of whole wild-type and golden zebrafish larvae about 1.5 mm long. The researchers then mapped the cells in 3D through a technique called micro-computed tomography (micro-CT).

Micro-CT, which is like a human CT scan but on a much smaller scale, reconstructs a 3D representation of the original object by capturing a series of X-ray images from different angles. The technique combines the Cheng lab’s new detector system with high X-ray flux from the ALS to achieve a resolution that is 2,000-fold higher than conventional CT.

The researchers say that their silver-staining technique could be used to learn more about the 3D architecture of melanoma tumors and potentially guide treatment decisions.

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New Techno-Economic Model Optimizes Waste-Heat Conversion Technologies
Berkeley Lab researchers identify minimum temperature to cost-effectively generate electricity from waste heat

---By Kiran Julin

Every year, 50% of the energy produced worldwide from coal, oil, natural gas, nuclear, and renewable energy sources is lost as heat. This untapped resource could be a promising additional source of useful energy, and for decades, scientists have worked to develop efficient systems to convert waste heat to electric power.  

In a recent study published in Joule, Berkeley Lab researchers developed a techno-economic model to predict the economic viability of different waste-heat conversion technologies. Their model will help guide future research by steering scientists toward novel designs and technologies that are more likely to enable cost-effective and efficient waste-heat conversion. 

Up until now, most of the research centered around waste-heat conversion technologies has been focused on the physics behind waste-heat conversion engines, such as thermoelectric generators that recover exhaust heat in internal combustion engines. Berkeley Lab’s techno-economic model enables researchers to have a more system-wide approach, which focuses on technological requirements for commercial viability, such as the temperature of the waste heat source, the cost of heat exchangers, or the minimum capacity factor – the fraction of the time the waste heat source is available.  

“Although more than 60% of the waste heat is available below 100 degrees Celsius, our analysis shows the waste heat conversion is only economical above 150 degrees Celsius,” said Ravi Prasher, associate lab director at Berkeley Lab. “This finding is very important in prioritizing research and development for waste heat conversion heat engines.” 

The techno-economic model from this study enables researchers to better predict which sectors and circumstances will be more ideally suited to waste-heat conversion technologies.

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Nature Microbiology; eLife; Joule

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