A cryo-electron tomography image of an ultra-small bacteria similar to the ones found to have small, compact CRISPR-Cas systems potentially suitable for laboratory gene-editing. The bacteria is less than 200 nanometers across (bar is 100 nanometers). The three objects near the bacteria are viruses, or phages, that attack bacteria. (Banfield lab image)
UC Berkeley scientists have discovered simple CRISPR systems similar to CRISPR-Cas9 — a gene-editing tool that has revolutionized biology — in previously unexplored bacteria that have eluded efforts to grow them in the laboratory.
The new systems are highly compact, befitting their presence in some of the smallest life forms on the planet. If these systems can be re-engineered like CRISPR-Cas9, their small size could make them easier to insert into cells to edit DNA, expanding the gene-editing toolbox available to researchers and physicians.
“These are particularly interesting because the key protein in these CRISPR systems is approximately the same as Cas9, but is not Cas9. It is part of a minimal system that has obvious potential for gene editing,” said Jill Banfield, a UC Berkeley professor of earth and planetary sciences and of environmental science, policy and management.
In CRISPR-Cas systems, the Cas protein is the scissors. When targeted to a specific sequence of DNA, the Cas protein binds and severs double-stranded DNA. The new discovery nearly doubles the number of simple and compact CRISPR-Cas systems potentially useful as laboratory and biomedical tools.
“The important thing here is that we found some of these CRISPR systems in a major branch of the bacterial tree, opening the door to a whole new world of microbes that are not cultured in the lab, so we don’t really know what they are and what their habits are,” said co-author Jennifer Doudna, a UC Berkeley professor of molecular and cell biology and of chemistry and a Howard Hughes Medical Institute investigator. Both Doudna and Banfield are faculty scientists at Lawrence Berkeley National Laboratory.
The team also found the first CRISPR-Cas9 system in some of the world’s smallest microbes: a nano-scale member of the archaea, which is a sister group to the bacteria.
The variety of uncultivable bacteria has only recently been recognized, in large part due to Banfield and her lab colleagues, who use metagenomic analysis to explore microbial diversity in exotic environments, from toxic pools in abandoned mines to the soil in Superfund contamination cleanup sites and the guts of premature infants. The majority of all bacterial life on the planet is basically unknown because these organisms cannot be cultivated in lab dishes, probably because they are symbionts and rely upon other microbes for nutrients needed to survive.
One of the new CRISPR proteins, dubbed CasY, was discovered in a massive group of recently recognized bacteria — what Banfield calls candidate phyla radiation (CPR) and which may contain half of all bacterial diversity — that live in geysers and in soil several feet underground. Another new one, CasX, was found in bacteria from known phyla living in groundwater and sediment. The two groups of nanoarchaea found to contain CRISPR-Cas9 were first described by Banfield from acid mine drainage.
Banfield, Doudna and their colleagues reported the findings today in the journal Nature.Thursday, December 22, 2016 - 09:45byline: Robert Sanders, UC Berkeley Media RelationsLegacy: section header item: Date: Thursday, December 22, 2016 - 09:45headline_position: Top Leftheadline_color_style: Normalheadline_width: Longcaption_color_style: Normalcaption_position: Bottom Left
MCB's Professor Jennifer Doudna, in collaboration with Professor Jill Banfield (of earth & planetary sciences and of ESPM), have "discovered simple CRISPR systems similar to CRISPR-Cas9 — a gene-editing tool that has revolutionized biology — in previously unexplored bacteria that have eluded efforts to grow them in the laboratory."
Professor Jennifer Doudna will be given a Luminary Award at the Precision Medicine World Conference on January 23rd-25th, 2017. Doudna will also be one of the key speakers at the conference -- read a recent PMWC Q&A with Professor Doudna.
Are you interested in attending the conference? PMWC has created a discount code for UC Berkeley attendees -- It is "berkeley_discount_pmwc2017" (expires on January 11, 2017). Or register here and have the code applied automatically.
MCB Professor Nicole King, her graduate student, Arielle Woznica and collaborators have found the first demonstration that bacteria can drive sexual mating in eukaroyotes. "Researchers seeking the evolutionary roots of the animal kingdom have discovered a bacterium, Vibrio fischeri, that acts as an aphrodisiac on a species of protozoan choanoflagellates, the closest living relatives of animals, by releasing an enzyme that sends Salpinogoeca rosetta, into a full mating frenzy."
Evolutionary Biology Workshop in the Alps (The previous posting contained a typo in an invited professor’s name, for which we apologize.) The 2017 edition of the Evolutionary Biology Workshop in the Alps will take place on 17-23 June 2017 in Riederfurka, Switzerland. Target participants are PhD students in early stages of PhD and advanced Master students.
Metabolic disorders are complex health problems, and with that complexity comes a necessity for dynamic models to study their causes and effects.
UC Berkeley researchers have designed an in vivo imaging system that can help them better study one metabolic disorder—fatty liver disease—in a real-time, non-invasive fashion. In vivo methods are those that can be performed in a living organism. While there have been ways to image fat uptake by other areas in the body, such as brown fat or the intestine, the location of the liver near many other fat-utilizing tissues has long posed a challenge.
When we eat a meal our blood gets an increase in fatty acids, the energy-rich molecules that are the building blocks of fats. Those fatty acids travel through the body’s circulation to many different tissues, including the liver, where they can be broken down and used for energy to perform the organ’s functions. However, when taken in at excessive levels, fatty acids can form deposits among the healthy tissue in the liver. This causes a condition called hepatosteatosis, or fatty liver disease.
In order to better understand hepatosteatosis, it is important to have a method for studying the fundamental mechanisms underlying lipid metabolism in the liver. In vivo imaging plays a major role in achieving that goal.
The imaging protocol is described in an article that appeared in the journal Gastroenterology in October. It builds on a method for fatty acid imaging already in use, but with several important alterations that heighten the clarity and accuracy of liver-specific images.
For these studies, laboratory mice are injected with a synthetic fat that is tagged with a molecule called luciferin. When these luciferin-fatty acid probes enter cells they release the luciferin, which in turn can produce light with the help of an enzyme from fireflies termed luciferase.
The innovation of first author Hyo Min Park, then a Ph.D. student in nutritional sciences and toxicology at UC Berkeley, came with breeding a new strain of mice that produce luciferase only in liver tissue. This adjustment ensures that the luminescence depicted in the images correlates to fat uptake solely by the liver.
“This system allows us a totally different approach for fatty acid flux studies,” said Hyo Min Park, who is now working for a biotech startup company he founded following graduation. He explains that current methods require sacrificing the animal in order to extract the liver and measure the amount of tagged fatty acids. For this reason, they are of limited value when studying a trend that requires monitoring across multiple time points in the same organism.
However, say that a group of researchers wants to measure the effect of a potential treatment over the course of one month. With Park’s method, they can measure fatty acid uptake every five or ten days in the same animals and track the effects during the entire period. The information garnered by continuous monitoring helps construct a more robust and detailed picture of cause and effect, one that is crucial during pre-clinical trials.
The article describes several findings made by Park and his colleagues using the new in vivo imaging method. In one 10-day trial, ingestion of fenofibrate, a medication currently used to treat high cholesterol and hyperlipidemia, resulted in a 40% increase in liver fatty acid uptake compared to control mice.
Now, that may seem counterproductive for shrinking the size of fat deposits in the liver - and that is because it is. Although fenofibrate has been known to increase the rate of fatty acid breakdown in the liver, the gross anatomy of the diseased livers would continue to appear pockmarked by fat deposits. The results from this trial indicate that this discrepancy could be partly explained by the observation that the drug itself causes increased fatty acid uptake to begin with.
“Previous studies demonstrated that fenofibrate increases beta oxidation and [fatty acid transporter] expression in the liver. But no one showed the effect of fenofibrate on hepatic fatty acid uptake increase in vivo,” Park explained. “After this experiment, I feel like I found a missing puzzle piece.”
In another trial performed by post-doctoral fellow Kim Russo and Lance Kriegsfeld, professor and vice chair of the UC Berkeley Department of Psychology, the in vivo system was used to monitor fatty acid uptake every hour for a 24-hr period. The results indicated that fatty acid uptake by the liver is altered across the day and night, suggesting a strong diurnal rhythm.
In addition to Park, Russo, and Kriegsfeld, study authors included Andreas Stahl, professor and chair of the Department of Nutritional Sciences and Toxicology. Michael Park, undergraduate student in Microbial Biology, aided with experiments. Luminescent fatty acid probes were produced by Grigory Karateev and Elena Dubikovskaya from the Swiss Federal Institute of Technology of Lausanne. This work was supported in part by the National Institutes of Health.Image: Date: Monday, December 12, 2016 - 09:45byline: By Liza Raffi Legacy: section header item: Date: Monday, December 12, 2016 - 09:45headline_position: Top Leftheadline_color_style: Normalheadline_width: Longcaption_color_style: Normalcaption_position: Bottom Left
Professor Michael Freeling
UC Berkeley geneticist Michael Freeling has been awarded the McClintock Prize for Plant Genetics and Genome Studies for his fundamental contributions to the understanding of gene and genome biology in plants.
The prize, which recognizes scientific accomplishment over the course of a career, is awarded annually by the Maize Genetics Executive Committee, a professional organization for scientists and researchers working in the field of maize genetics. It is named in honor of Barbara McClintock, a distinguished geneticist and winner of the 1983 Nobel Prize in Physiology or Medicine.
“The MGEC is excited to award the McClintock prize to Professor Freeling,” said Shawn Kaeppler, chair of the committee and a professor of agronomy at the University of Wisconsin-Madison. “He has been a leader in the maize genetics community throughout his career. His groundbreaking research on conserved non-coding sequences found in genomes across species, and fundamental work on gene content following genome duplication, has provided important insights into genome evolution and gene function. These discoveries are important in utilizing genome information to discover new biological mechanisms and to develop applied solutions important to the agricultural enterprise. His work on genome evolution and sequence conservation across species exemplifies the basic discoveries that we seek to recognize with the McClintock award.”
Freeling is a professor in the Department of Plant and Microbial Biology in the College of Natural Resources at Berkeley. He will receive this prize and deliver a scientific presentation at the Annual Maize Genetics Conference, March 9-12, 2017, in St. Louis, Missouri.
“I have the highest respect for the past recipients of this prize, and just having my name on the same page as McClintock’s is an honor,” Freeling said.
Freeling earned his Ph.D. in 1973 at Indiana University and immediately became a professor at Berkeley. In addition to teaching graduate and postdoctoral students, he taught “Genetics for Poets” to large classes for decades. He has mentored 25 doctoral students and 42 postdoctoral scholars. Freeling was also named a Guggenheim Fellow in 1980, and was elected to the U.S. National Academy of Sciences in 1994.
Freeling’s early work focused on gene regulation, anaerobic genes and transposons, but his research focus eventually pivoted to developmental genetics. By 2003 he had switched his efforts to plant comparative genomics and understanding evolutionary trends.
Learn more about the research at the Freeling Lab website.Image: Date: Thursday, December 8, 2016 - 10:45byline: Brett Israel, UC Berkeley Media relationsLegacy: section header item: Date: Thursday, December 8, 2016 - 10:45headline_position: Top Leftheadline_color_style: Normalheadline_width: Longcaption_color_style: Normalcaption_position: Bottom Left