Contemporary Authors

• A Crack in Creation: Gene Editing and the Unthinkable Power to Control Evolution - 2017 Houghton Mifflin Harcourt, Orlando, FL
• Molecular Biology: Principles and Practice 2nd Edition - 2015 W. H. Freeman, New York, NY
• Molecular Biology: Principles and Practice - 2011 W. H. Freeman, New York, NY

• Wikipedia -

  Jennifer Doudna
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  Jennifer Doudna

  Jennifer Doudna at the Royal Society admissions day in London in 2016
  Born
  Jennifer Anne Doudna
  February 19, 1964 (age 53)
  Nationality
  United States
  Alma mater
  Pomona College (BA)
  Harvard University (PhD)
  Known for
  RNA interference
  CRISPR[1]
  Spouse(s)
  Jamie Cate
  Awards
  Alan T. Waterman Award (2000)[2]
  Jacob Heskel Gabbay Award (2014)[3]
  Breakthrough Prize in Life Sciences (2015)[4]
  Japan Prize (2017)[5]
  See full list of awards and honors
  Website
  rna.berkeley.edu
  hhmi.org/scientists/jennifer-doudna
  Scientific career
  Fields
  Biochemistry
  Institutions
  University of California, Berkeley
  Yale University
  Thesis
  Towards the design of an RNA replicase (1989)
  Doctoral advisor
  Jack Szostak
  Other academic advisors
  Thomas Cech
  Jennifer Anne Doudna (born 19 February 1964)[6] is an American biochemist, Professor of Chemistry at the Department of Chemistry and Chemical Engineering, and Professor of Biochemistry and Molecular Biology at the Department of Molecular and Cell Biology at the University of California, Berkeley.[7] She has been an investigator with the Howard Hughes Medical Institute (HHMI) since 1997.[8][9][10] She is also the director of the joint UC Berkeley-UC San Francisco center Innovative Genomics Institute. She also holds Li Ka Shing Chancellor's Professorship in Biomedical and Health, and the chair of the Chancellor's Advisor Committee on Biology at UC Berkeley.[7]
  Doudna has been a leading figure in what is often referred to as the "CRISPR Revolution" for her early fundamental work and ongoing leadership in the development of CRISPR-mediated genome editing. In their seminal 2012 paper A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity, Doudna and Emmanuelle Charpentier were the first to propose that CRISPR/Cas9 could be used for programmable gene editing.[11] This discovery is considered as one of the most significant discoveries in the history of biology.[12] Their work has since been further developed by many research groups[13] for applications ranging from fundamental protein research to treatments for diseases including sickle cell anemia, cystic fibrosis, Huntington's disease, and HIV.
  Doudna has been widely acclaimed by the scientific community for her fundamental contributions to the fields of biochemistry and genetics, receiving many prestigious awards and fellowships. She was awarded the 2000 Alan T. Waterman Award for her research on ribozyme,[2] and 2015 Breakthrough Prize in Life Sciences for her contributions to CRISPR/Cas9 genome editing technology (with Charpentier).[4] She has also been a co-recipient of the Gruber Prize in Genetics (2015),[14] the Canada Gairdner International Award (2016)[15] and the Japan Prize (2017).[5] She has also been recognized outside the scientific community, being named one of the Time 100 most influential people in 2015 (with Charpentier)[16] and listed as a runner-up for Time Person of the Year in 2016 alongside other CRISPR researchers.[17]

  Contents [hide]
  1
  Early life and education
  1.1
  Early years
  1.2
  University education and post-doctoral years
  2
  Research and career
  2.1
  Szostak's lab, Cech's lab, and Yale University
  2.2
  University of California, Berkeley
  2.3
  CRISPR
  2.4
  Other work
  3
  Awards and honors
  4
  References
  5
  External links

  Early life and education[edit]
  Early years[edit]
  Jennifer Doudna was born in Washington, D.C.. Her father got his Ph.D. in English literature from the University of Michigan, and her mother, a stay-at-home parent, held a master's degree in education. When Doudna was seven years old, her father completed his thesis and moved his wife and three daughters from Michigan to Hawaii to teach American literature at the University of Hawaii at Hilo. Her mother earned a second master's degree in Asian history from the university, and taught history at a local community college.[14][18]
  Growing up in Hilo, Hawaii, she was fascinated by the environmental beauty of the island and its exotic plants and animals; they infused a sense of curiosity about how the nature works in her and she wanted to understand the underlying biological mechanisms. When she was in school, she developed interest in science and mathematics. Her father fostered a culture of intellectual pursuit in her home. He enjoyed reading about science and filled the home with plenty of books on popular science. When she was in the sixth grade, a copy of The Double Helix (a book by James Watson) was presented to her by her father. When she was in the high school, she was influenced by Miss Wong, a chemistry teacher.[18]
  University education and post-doctoral years[edit]
  Doudna entered Pomona College in Claremont, California to study biochemistry. During her sophomore year, while taking a course in general chemistry, she questioned her own ability to pursue a career in science, and considered switching her major to French. However, her French teacher suggested she to stick with science.[18] Fred Grieman and Corwin Hansch, both professors of chemistry at Pomona, had a major impact on her. She started her first scientific research in the lab of Sharon Panasenko.[9] She earned a Bachelor of Arts degree in Biochemistry from Pomona College in 1985. She went to Harvard Medical School for her doctoral study and earned a Ph.D. in Biological Chemistry and Molecular Pharmacology in 1989.[7] Her Ph.D. thesis was on engineering a self-replicating catalytic RNA[19] and was supervised by Jack W. Szostak.[20] From 1989 to 1991, she held research fellowships in molecular biology at the Massachusetts General Hospital and in genetics at Harvard Medical School. From 1991 to 1994, she was Lucille P. Markey Postdoctoral Scholar in Biomedical Science at the University of Colorado Boulder, where she worked with Thomas Cech.[7]
  Research and career[edit]
  Szostak's lab, Cech's lab, and Yale University[edit]
  Early in her scientific career, Doudna worked to uncover the structure and biological function of RNA enzymes or ribozymes. While in the Szostak lab, Doudna reengineered the self-splicing Group I catalytic intron into a true catalytic ribozyme that would copy RNA templates.[21] Her focus was on engineering ribozymes and understanding their underlaying mechanisms. However, she came to realize that not being able to see the molecular mechanisms of ribozymes was a major problem. She went to the lab of Thomas Cech at the University of Colorado Boulder to crystallize and determine the three-dimensional structure of ribozymes. She started this project in the Cech lab in 1991 and finished it at Yale University in 1996.[22] She joined Yale's Department of Molecular Biophysics and Biochemistry as an assistant professor in 1994.[7]
  At Yale, Doudna's group was able to crystallize and solve the three-dimensional structure of the Tetrahymena Group I ribozyme.[9] Initially, her group was able to grow high-quality crystals, but they struggled with the phase problem due to unspecific binding of the metal ions. One of her early graduate students and later her husband, Jamie Cate decided to soak the crystals in osmium hexamine to imitate magnesium. Using this strategy, they were able to solve the structure, the second solved folded RNA structure since tRNA.[23][24] The magnesium ions would cluster at the center of the ribozyme and would serve as a core for RNA folding similar to that of a hydrophobic core of a protein.[9] Her group has also crystallized other ribozymes,[22] including the HDV ribozyme.[9] This initial work to solve large RNA structures led to further structural studies on the IRES and protein-RNA complexes like the Signal recognition particle.[9]
  Doudna was promoted to the position of Henry Ford II Professor of Molecular Biophysics and Biochemistry at Yale in 2000.[7] In 2000-2001, she was Robert Burns Woodward Visiting Professor of Chemistry at Harvard University.[8]
  University of California, Berkeley[edit]

  Jennifer Doudna at the University of California, Berkeley.
  In 2002, she accepted a faculty position at University of California, Berkeley as a Professor of Biochemistry and Molecular Biology so that she would be closer to family and the synchrotron at Lawrence Berkeley National Laboratory. Her lab now focuses on obtaining a mechanistic understanding of biological processes involving RNA. This work is divided over three major areas, the CRISPR system, RNA interference, and translational control via MicroRNAs.[25]
  CRISPR[edit]
  In 2012, Doudna and her colleagues generated a new discovery that would reduce the time and work needed to edit genomic DNA. Their discovery relies on a protein named Cas9 found in the Streptococcus bacteria "CRISPR" immune system that works like scissors. The protein attacks its prey, the DNA of viruses, and slices it up.[26] In 2015, Doudna gave a TED Talk about the bioethics of using CRISPR.[27]
  Other work[edit]
  She has also discovered that the hepatitis C virus utilizes an uncommon strategy to synthesize viral proteins. This work could lead to new drugs to stop infections without causing harm to the tissues of the body.[22]
  Awards and honors[edit]
  Main article: List of awards and honors received by Jennifer Doudna
  Doudna was a Searle Scholar and received the 1996 Beckman Young Investigators Award.[28] In 2000, she was awarded the Alan T. Waterman Award, the National Science Foundation's highest honor that annually recognizes an outstanding researcher under the age of 35, for her earlier research on ribozyme.[2] In 2001, she received the Eli Lilly Award in Biological Chemistry of the American Chemical Society.[7]
  In 2015, together with Emmanuelle Charpentier, she received the Breakthrough Prize in Life Sciences for her contributions to CRISPR/Cas9 genome editing technology.[4] In 2016, together with Charpentier, Feng Zhang, Philippe Horvath and Rodolphe Barrangou, she received the Canada Gairdner International Award.[15] Also in 2016, she received the Heineken Prize for Biochemistry and Biophysics.[29] She has also been a co-recipient of the Gruber Prize in Genetics (2015),[14] the Tang Prize (2016),[30] the Japan Prize (2017)[5] and the Albany Medical Center Prize (2017).[31]
  She was elected to the National Academy of Sciences in 2002[9], the American Academy of Arts and Sciences in 2003, the National Academy of Medicine in 2010 and the National Academy of Inventors in 2014.[7] She was elected a Foreign Member of the Royal Society (ForMemRS) in 2016.[32]

• Howard Hughes Medical Institute Website - http://www.hhmi.org/scientists/jennifer-doudna

  Jennifer A. Doudna, PhD
  Investigator / 1997–Present

  Scientific Discipline
  Biochemistry, Structural Biology
  Related Links
  The Doudna Lab
  iBiology talk: Genome engineering with CRISPR-Cas9: Birth of a breakthrough technology
  CRISPR toolbox expanded by protein that cuts RNA in two distinct ways (9/26/16)

  Host Institution
  University of California, Berkeley
  Current Position
  Dr. Doudna is also a professor of molecular and cell biology and of chemistry at the University of California, Berkeley, where she holds the Li Ka Shing Chancellor's Chair in Biomedical and Health Sciences.

  In the genetic world, DNA often takes the spotlight while RNA works behind the scenes to carry out the complicated operations within a cell, like retrieving information from DNA and using it to build proteins. Increasingly, however, RNA is attracting more attention from scientists because it has proven far more versatile than DNA, despite their chemical similarities.
  Indeed, research has shown that RNA can also store genetic information, like DNA, and catalyze chemical reactions, like specialized proteins called enzymes. A growing number of scientists now believe that this biological diversity makes RNA an evolutionary precursor to both DNA and proteins, a theory that may be impossible to prove, acknowledges Jennifer A. Doudna, who specializes in the study of RNA. "I don't think we'll ever be able to prove how life began, but if we can demonstrate in a test tube the ways that RNA can carry out many of the reactions that are required for a living cell, that, in itself, would be a profound discovery," she explained.
  Doudna's research focuses on determining the molecular structures of RNA molecules as a basis for understanding their biological function. Her work lays the foundation for understanding the evolution of RNAs and their relationship to the molecules that played a role in early forms of life.
  Growing up in Hawaii, Doudna was always fascinated by the way things worked. In high school, she was drawn to chemistry because it allowed her to understand science on a fundamental level. A high school chemistry teacher encouraged this interest, and when Doudna graduated, she knew she wanted to go into chemistry.
  Later, her desire to understand biochemistry on a molecular level led Doudna to study catalytic RNAs called ribozymes, first as a graduate student in the laboratory of HHMI investigator Jack W. Szostak at Harvard University, and then as a postdoc in the laboratory of Thomas R. Cech at the University of Colorado at Boulder. It was Cech, former HHMI president, who discovered in 1982 that RNA can also have enzymatic properties—a finding for which he shared the 1989 Nobel Prize in Chemistry.
  In Szostak's laboratory, Doudna worked to create self-replicating ribozymes in a test tube, with the goal of observing how these enzymes may have evolved over time. While working on this project, however, Doudna came to realize that if she wanted to engineer ribozymes and understand how they work, she first needed to know what they looked like. So she headed to Tom Cech's lab to crystallize and determine the three-dimensional structure of a ribozyme, something that had never been accomplished before.
  This endeavor took far longer than Doudna could have anticipated. She began the work in Cech's lab in 1991 and completed the project at Yale in 1996, where she had moved to become an assistant professor. But the hard work paid off, and Doudna clearly remembers seeing the structure for the first time. "It was an incredible moment of discovery. My heart was racing, and I had chills down my spine," Doudna said.
  She has since crystallized other RNAs, including one from a virus that causes a rare form of hepatitis. Solving these structures is helping scientists answer important questions about how RNA molecules are organized and how they function as enzymes. In separate research, she and her colleagues have discovered that the hepatitis C virus, which causes 10,000 deaths each year in the United States, uses an unusual strategy to synthesize viral proteins—a line of research that could lead to new drugs to block the infection without harming body tissues.
  Doudna says she is most motivated by the "process of discovery—of having an idea about how something works and setting out to test it. I am intrigued by the many roles of RNA in biology. Understanding the chemical and biochemical basis for this, as well as the ways in which evolution has taken advantage of these properties to involve RNA at every level of gene expression and regulation in cells and viruses is a lifelong pursuit."

  Education
  BA, chemistry, Pomona College
  PhD, biochemistry, Harvard University

  Awards
  Breakthrough Prize in Life Sciences, 2015
  Dr. Paul Janssen Award for Biomedical Research
  Lurie Prize in Biomedical Sciences, Foundation for the National Institutes of Health
  Eli Lilly Award in Biological Chemistry, American Chemical Society
  Beckman Young Investigator Award, Arnold and Mabel Beckman Foundation
  David and Lucile Packard Foundation Fellowship for Science and Engineering
  National Academy of Sciences Award for Initiatives in Research
  Alan T. Waterman Award, National Science Foundation
  Japan Prize, Japan Prize Foundation

  Memberships
  National Academy of Sciences
  American Academy of Arts and Sciences
  National Academy of Medicine
  National Academy of Inventors
  American Association for the Advancement of Science, Fellow
  American Academy of Microbiology

  Mar 23 2016
  Research
  Doudna Receives Canada’s Gairdner Award for Research on CRISPR
  Summary
  In only the second time in history, all five Canada Gairdner International Awards are being given to one topic -- CRISPR-Cas technology.

  Ryan Anson / AP Images for HHMI
  The Gairdner Foundation announced today that Howard Hughes Medical Institute (HHMI) investigator Jennifer A. Doudna of the University of California, Berkeley is a recipient of the prestigious 2016 Canada Gairdner International Award in recognition of her contributions to medical science.
  The awards, which are presented annually, recognize scientists responsible for some of the world’s most significant medical discoveries. This year the awards center on two defining themes including the revolutionary Clustered regularly-interspaced short palindromic repeats (CRISPR) technique for gene editing and for work in the HIV/AIDS field within Canada and internationally.
  Doudna, who became an HHMI investigator in 1997, was honored for development of CRISPR-CAS as a genome-editing tool for eukaryotic cells. She was honored with scientists, Emmanuelle Charpentier of Umea University in Sweden, and Feng Zhang of the Broad Institute of MIT and Harvard. In addition, Rodolphe Barrangou of North Carolina State University, and DuPont Senior Scientist Dr. Philippe Horvath were honored for establishing and characterizing CRISPR-Cas bacterial immune defense system.
  The Foundation notes that this is only the second time in its history that all five Canada Gairdner International Awards are being given to one topic -- CRISPR-Cas technology.
  The 2016 John Dirks Canada Gairdner Global Health Award goes to Anthony S. Fauci of the National Institute of Allergy and Infectious Diseases. He is being highlighted for pioneering contributions to our understanding of HIV infections and his extraordinary leadership in bringing successful treatment to the developing world.
  The 2016 Canada Gairdner Wightman Award is awarded to Frank Plummer of the Public Health Agency of Canada and the University of Manitoba. He is being given this award for his groundbreaking research in Africa in understanding HIV transmission and his leadership at the Canadian National Microbiology Laboratory with pivotal roles in SARS, influenza and Ebola epidemics.
  The seven Gairdner laureates will be coming to Canada in October to visit 22 universities across the country to speak about their research with faculty, trainees, undergraduate and high school students.

  ennifer Doudna Shares Breakthrough Prize in Life Sciences
  Summary
  HHMI investigator Jennifer Doudna is among six scientists honored for transformative advances toward understanding living systems and extending human life.
  Highlights
  The Breakthrough Prizes recognize pioneering work in physics and genetics, cosmology, and neurology and mathematics.
  Doudna was honored with Emmanuelle Charpentier for harnessing an ancient mechanism of bacterial immunity into a powerful technology for editing genomes.

  Ryan Anson / AP Images for HHMI
  The Breakthrough Prize Foundation announced that Howard Hughes Medical Institute (HHMI) investigator Jennifer A. Doudna of the University of California, Berkeley is among six scientists awarded the Breakthrough Prizes in Life Sciences, which honor transformative advances toward understanding living systems and extending human life.
  The Breakthrough Prizes recognize pioneering work in physics and genetics, cosmology, and neurology and mathematics. Each prize carries an award of $3 million. Live streaming of the Breakthrough Prize in Life Sciences Symposium at Stanford University will begin at 9 a.m., PST, today.
  "The world faces many fundamental challenges today, and there are many amazing scientists, researchers and engineers helping us solve them,” said Mark Zuckerberg, a founder of the Breakthrough Prize Foundation and Facebook. “This year's Breakthrough Prize winners have made discoveries that will help cure disease and move the world forward. They deserve to be recognized as heroes."
  Doudna was honored with Emmanuelle Charpentier of the Helmholtz Center for Infection Research and Umeå University for harnessing an ancient mechanism of bacterial immunity into a powerful and general technology for editing genomes, with wide-ranging implications across biology and medicine.
  In the genetic world, DNA often takes the spotlight while RNA works behind the scenes to carry out the complicated operations within a cell, like retrieving information from DNA and using it to build proteins. Increasingly, however, RNA is attracting more attention from scientists because it has proven far more versatile than DNA, despite their chemical similarities.
  Doudna's research focuses on determining the molecular structures of RNA molecules as a basis for understanding their biological function. Her work lays the foundation for understanding the evolution of RNAs and their relationship to the molecules that played a role in early forms of life.
  Many bacteria have a CRISPR-based immune system that is used to recognize and destroy the genomes of invading viruses and plasmids. In 2012, the labs of Doudna and Charpentier showed that the protein Cas9 is a DNA-cutting enzyme guided by RNA. Cas9 relies on two short RNA guide sequences to find foreign DNA, and then cleaves the target sequences, thereby silencing the invaders' genes.

  An RNA-based complex guides the DNA-cutting enzyme Cas9 to specific sites in the genome. The natural RNA-programmed DNA cleavage system is shown on the left, with the engineered system on the right. Image: H. Adam Steinberg, artforscience.com
  The process is specific and efficient enough to fend off viral infections in bacteria, and those same qualities have made the CRISPR system a powerful research tool. Doudna's team adapted the system so that it can be guided by a single short RNA molecule. Researchers who use the system for genome editing can customize that RNA so that it directs Cas9 to cleave at a desired location in the genome.

  In addition to Doudna and Charpentier, the winners of the 2015 Breakthrough Prize in Life Sciences are:
  Alim Louis Benabid, Joseph Fourier University, for the discovery and pioneering work on the development of high-frequency deep brain stimulation (DBS), which has revolutionized the treatment of Parkinson’s disease.
  C. David Allis, The Rockefeller University, for the discovery of covalent modifications of histone proteins and their critical roles in the regulation of gene expression and chromatin organization, advancing the understanding of diseases ranging from birth defects to cancer.
  Victor Ambros, University of Massachusetts Medical School, and Gary Ruvkun, Massachusetts General Hospital and Harvard Medical School, for the discovery of a new world of genetic regulation by microRNAs, a class of tiny RNA molecules that inhibit translation or destabilize complementary mRNA targets. Each received a $3 million award.
  Prize recipients are invited to serve on the selection committee to select recipients of future prizes. Last year, HHMI investigators Richard P. Lifton of Yale University was awarded a Breakthrough Prize in the Life Sciences. The selection committee for the 2015 Breakthrough Prizes in Life Sciences included: James P. Allison, Cornelia I. Bargmann, David Botstein, Lewis C. Cantley, Hans Clevers, Titia de Lange, Mahlon R. DeLong, Napoleone Ferrara, Michael N. Hall, Eric S. Lander, Robert Langer, Richard P. Lifton, Charles L. Sawyers, Alexander Varshavsky, Bert Vogelstein, Robert A. Weinberg and Shinya Yamanaka.
  Founded in 2013, the Breakthrough Prize Foundation is a not-for-profit corporation dedicated to advancing breakthrough research, celebrating scientists and generating excitement about the pursuit of science as a career. The Foundation was founded by Sergey Brin and Anne Wojcicki, Mark Zuckerberg and Priscilla Chan, Jack Ma and Cathy Zhang, and Yuri and Julia Milner.

• Chemical & Engineering News - https://cen.acs.org/articles/95/i17/CRISPR-pioneer-Jennifer-Doudna-shares-her-outlook-for-the-groundbreaking-gene-editing-tool.html

  Volume 95 Issue 17 | pp. 28-29 | C&EN Talks With
  Issue Date: April 24, 2017 | Web Date: April 18, 2017

  CRISPR pioneer Jennifer Doudna shares her outlook for the groundbreaking gene-editing tool
  UC Berkeley biochemist discusses how CRISPR could affect chemistry in areas including drug discovery and agriculture
  By Melissa Pandika, special to C&EN
  [+]Enlarge

  Doudna
  Credit: Sam Willard Photography
  Vitals
  ▸ Hometown: Hilo, Hawaii
  ▸ Education: B.A., biochemistry, Pomona College, 1985; Ph.D., biological chemistry and molecular pharmacology, Harvard Medical School, 1989
  ▸ Current positions: professor, department of molecular and cell biology and department of chemistry at UC Berkeley; director, Innovative Genomics Initiative at UC Berkeley/UC San Francisco; investigator, Howard Hughes Medical Institute
  ▸ Inspiration for cracking the CRISPR code: My dad was not a scientist, but he loved solving puzzles. One of his favorites was cryptoquotes—quotes by famous people that are encrypted. The challenge is to break the code and solve the quote. They would come out in our local newspaper, and when my dad got stuck, he would often enlist help from family members, including me. It really taught me about the joy of finding things out. With cryptoquotes, it’s a bit like science; you have a hypothesis about what the code is, and you test it. That was my first exposure to the idea of setting up experiments.
  ▸ Favorite bacterium: Can I pick two? The first is Escherichia coli, the workhorse of molecular biology. The other is a group of bugs called the candidate phyla radiation, discovered by Jill Banfield, a biogeochemist and geomicrobiologist at UC Berkeley. These are tiny bacteria with only 50 ribosomes to make proteins [most bacteria contain tens of thousands of ribosomes] and super-small genomes. Yet some of them have CRISPRs. We’d like to understand why they do and what that might mean for the interesting properties that enable these bacteria to survive in groundwater, soil, and dairy farms.
  It’s been less than five years since University of California, Berkeley, biochemist Jennifer Doudna and colleagues unveiled the gene-editing tool CRISPR in Science (2012, DOI: 10.1126/science.1225829), but its use among researchers across the globe has already exploded.
  Last April, for example, Sichuan University scientists announced that they had used CRISPR to program T cells from the immune system of a person with lung cancer to kill tumor cells (Nature 2016, DOI: 10.1038/nature.2016.20988). And late last year, a UC Berkeley team reported harnessing the technology to correct the genetic mutation responsible for sickle cell anemia in stem cells from patients with the disease (Sci. Transl. Med. 2016, DOI: 10.1126/scitranslmed.aaf9336).
  Doudna didn’t set out to develop a far-reaching gene-editing tool years ago. Initially, her team wanted to uncover the role of CRISPRs—short for “clustered regularly interspaced short palindromic repeats”—which are repetitive sequences of RNA hidden in the genomes of many bacteria.
  Eventually, Doudna; Emmanuelle Charpentier, now the director of the Max Planck Institute for Infection Biology; and coworkers discovered that CRISPRs help bacteria fight viral infection. Bacteria snag bits of an invading virus’s RNA and tuck them into CRISPRs, the team found. If the virus strikes again, these modified CRISPRs bind to the pathogen’s DNA, signaling to the enzyme Cas9 to come and dice up the foreign genetic material. The researchers realized they could harness this machinery to cut and paste target DNA fragments at will, as long as they introduced the appropriate designer RNA sequences.
  What started as a small project “aimed at something seemingly unrelated … led to a very different direction,” Doudna said during the Kavli keynote address on April 3 at the ACS national meeting in San Francisco. C&EN caught up with Doudna at the meeting to discuss the importance of curiosity-driven basic research and her outlook for CRISPR.

  How do you think CRISPR will impact chemistry, including how chemists conduct research?
  The convergence of chemistry with other disciplines to tackle interesting problems in science is exciting. More and more, I see chemists using gene editing to make precise changes to molecules, such as proteins. That allows them to connect discoveries made using purified biomolecules outside cells—enzymes reacting in lab vessels, for instance—to what you would find in a living organism. That’s really amazing. With better chemical understanding of the way these enzymes operate, it will be possible to use them in ways that they don’t seem to be deploying in nature.
  The ability to make changes to the DNA of plant cells also opens up opportunities both in research and in solving problems in agriculture. That includes helping plants defend themselves against infection, drought, and other climate-change-related issues from a chemical perspective. With CRISPR, you understand the precise changes that you’re making to DNA—at the level of individual base pairs—rather than randomly introducing changes by exposing plant seeds to chemicals that cause DNA mutations.
  In drug discovery, one of the big challenges for chemists is determining the targets of small molecules. Now, you can potentially very rapidly figure out the targets by using CRISPR to query cells on a genomewide scale. You can disrupt certain genes and then ask if cells are still susceptible to the small molecules. I’m excited about that as an important research application but also as a practical way of doing drug discovery.

  Most CRISPR work has so far been carried out in the lab. What real-world applications of CRISPR can we expect to see first?
  We can do gene editing on cells ex vivo—meaning outside the organism—and the edited cells can then be reintroduced to the body, which gets around the challenge of drug delivery. For clinical use, we’ll probably see treatments like this that involve immune cells in the blood first, since they can be collected outside the body.
  In agriculture, we’ve already begun seeing products that have been created using precision gene editing. That brings up a bunch of regulatory challenges. The U.S. Department of Agriculture has decided that plant products created using CRISPR that don’t introduce foreign DNA are not considered genetically modified, which has led to lots of discussion. In other countries, the regulation of GMO plants is different, so I think people are being pushed to reevaluate how these are defined based on the opportunities we now have with CRISPR.
  What improvements would you like to see made to the technology?
  Where we’ll likely see advancements being made is in deploying CRISPR to do more specific kinds of things. One is using it not to cleave DNA directly but to make a direct chemical modification to DNA, whether it’s changing one nucleotide base into another one or adding a methyl group.

  What ethical issues will researchers need to consider in their applications of CRISPR?
  CRISPR has made possible genetic changes in individual organisms and even made it possible to pass along changes to offspring. This raises ethical concerns, particularly regarding human embryo or germ-line editing that might lead to permanent changes in the DNA that can be passed on to future generations. I’ve been actively involved in discussing these issues. As scientists, we need to explain what we’re doing and why we’re doing it, not dictating how these discoveries and technologies should be used. We need to participate in those conversations with the public. This is important, especially now, when there’s a lot of questioning about scientific knowledge, the value of facts, and how scientific data are used to help governments make decisions about regulations and funding.

  In February, the U.S. Patent & Trademark Office upheld patents awarded to the Broad Institute of Massachusetts Institute of Technology and Harvard University for the use of CRISPR in eukaryotic cells. About a month later, the European Patent Office announced plans to award a patent to the University of California that covers a wide range of CRISPR uses. How do you see the patent battle playing out in the years ahead?
  Patents around important technologies typically are complicated. It takes a while to sort them out, and CRISPR is no different. Honestly, I think it will take a while before the patent situation is resolved in different countries. The exciting thing for me is that we’re seeing rapid deployment of the CRISPR technology both in academic settings and in companies. That’s leading to real advances for various diseases. There are exciting uses in agriculture and in fundamental research. None of that is being hampered by the current patent situation.

  CORRECTION: This Q&A was updated on April 21, 2017, to correct the affiliation of the team that used CRISPR to fix the genetic mutation responsible for sickle cell anemia in patients’ stem cells. It is UC Berkeley, not Stanford.

  Melissa Pandika is a freelance science writer in Berkeley, Calif. This interview was edited for length and clarity.

• The Atlantic - https://www.theatlantic.com/science/archive/2017/06/how-crispr-yanked-jennifer-doudna-out-of-the-ivory-tower/531705/

  How CRISPR Yanked Jennifer Doudna Out of the Ivory Tower
  The pioneer biochemist feels a responsibility to weigh in on ethical debates about gene editing.

  Jennifer Doudna at a painting exhibition by children about the genome, in Oviedo, Spain, 2015
  Eloy Alonso / Reuters

  Ed Yong Jun 26, 2017 Science
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  Like ​The Atlantic? Subscribe to ​The Atlantic Daily​, our free weekday email newsletter.

  Jennifer Doudna remembers a moment when she realized how important CRIPSR—the gene-editing technique that she co-discovered—was going to be. It was in 2014, and a Silicon Valley entrepreneur had contacted Sam Sternberg, a biochemist who was then working in Doudna’s lab. Sternberg met with the entrepreneur in a Berkeley cafe, and she told him, with what he later described to Doudna as “a very bright look in her eye that was also a little scary,” that she wanted to start applying CRISPR to humans. She wanted to be the mother of the first baby whose genome had been edited with the technique. And she wanted to establish a business that would offer a menu of such edits to parents.
  Nothing of the kind could currently happen in the U.S., where editing the genomes of human embryos is still verboten. But the entrepreneur apparently had connections that would allow her to offer such services in other countries. “That’s a true story,” Doudna told a crowd at the Aspen Ideas Festival, which is co-hosted by the Aspen Institute and The Atlantic. “That blew my mind. It was a heads-up that people were already thinking about this—that at some point, someone might announce that they had the first CRISPR baby.”

  The possibility had always been there. Bacteria have been using CRISPR for billions of years to slice apart the genetic material of viruses that invade their cells. In 2012, Doudna and others showed how this system could be used to deliberately engineer the genomes of bacteria, cutting their DNA with exceptional precision. In quick succession, researchers found that they could do the same in mammalian cells, mice, plants, and—in early 2014—monkeys. “I had all of this at the back of my mind,” Doudna told me after her panel. But Sternberg’s story about his meeting “was the moment where I said I needed to get involved in this conversation. I’m not going to feel good about myself if I don’t talk about it publicly.”
  That has not been an easy journey. Doudna built her career on molecules and microbes. As few as five years ago, she was, by her own admission, working head-down in an ivory tower, with no plans of milking practical applications from her discoveries, and little engagement with the broader social impact of her work.
  But CRISPR forcefully yanked Doudna out of that closeted environment, and dumped her into the midst of intense ethical debates about whether it’s ever okay to change the DNA of human embryos, whether eradicating mosquitoes is a good idea, and whether “fixing” the genes behind inherited diseases is a blow to disabled communities. Now, she’s a spokesperson for a field, and an influencer of policy. She regularly makes appearances at conferences and panel discussions, which she often shares with not just scientists but also philosophers, ethicists, and policy-makers. With Sternberg, she is the author of a new book called A Crack in Creation, describing her role in the CRISPR story.
  “The worst thing we could do is to ignore it, and for scientists not to get involved.”
  All of this work consumes up to half of her time, taking her away from her lab of 25 people. “I find myself really struggling to maintain that balance,” she says. “But those are the cards I’ve been dealt and I feel an obligation to being involved in [the debates around CRISPR]. There aren’t that many people who know the technology deeply and willing to talk publicly about the societal and ethical issues. I have many science colleagues who don’t want to get involved. Yet it has to be done.”

  Her upbringing prepared her well for this newfound role. Her father was a professor of American literature at the University of Hawaii, who was fiercely intellectual and politically conservative but never dogmatic. Her family dinner table was a place where opposing views were shared openly and debated open-mindedly. It still is: Many of Doudna’s in-laws staunchly oppose any form of genetic modification, so her work is a point of contention, even among close family. “I spend a lot of time talking to people like me, and it’s a big challenge is to reach out those who aren’t,” she says. “It’s a paradigm for the challenges in our country right now.”
  With her increasing slate of talks, many of those unfamiliar opinions now seek her out. After a recent panel, a fellow speaker told her that her sister was born with a rare mutation that left her intellectually disabled and led to her dying in her 20s. “I want you to know,” the speaker said, “that if it were possible to use gene-editing to get rid of that mutation permanently, I would have no hesitation.” On the flipside, Doudna was recently interviewed by a journalist whose son has Down’s syndrome. “I want you to know,” the journalist said,” that I would never use CRISPR on him because he’s perfect just the way he is.”
  “I’m very respectful of both those points of view,” she tells me. “And I’ve learned a lot about myself in these last five years.”
  Much of the rhetoric around CRISPR is overblown. It is unlikely, for example, that CRISPR could ever be used to design babies to be smarter, taller, or free of conditions like obesity or schizophrenia, because such traits are the work of hundreds of genes, each with small effects. The threat of the technique can also be exaggerated in equal measure to its promise. One of Doudna’s colleagues recently attended a meeting at the Department of Energy, and was asked by a member of the Trump administration: “What about CRISPR? That’s dangerous. We need to get rid of it.”
  “Well you can’t,” Doudna says plainly. “We’re in the system we’re in, and we have to deal with the technology in that context. I’ve been encouraging an international discussion because the worst thing we could do is to ignore it, and for scientists not to get involved.”

• Proceedings of the National Academy of Sciences of the United States of America Website - http://www.pnas.org/content/101/49/16987.full

  Biography of Jennifer A. Doudna
  Melissa Marino , Freelance Science Writer

  In the central dogma of molecular biology, DNA is transcribed into RNA, which then is translated into protein. Although RNA may be considered simply an intermediary between these two important biological molecules, RNA is much more than just a recipe for making proteins. In the 1980s, researchers showed that certain RNA molecules function as enzymes, a role previously attributed solely to proteins. Jennifer A. Doudna, Ph.D., Professor of Molecular and Cell Biology and Chemistry at the University of California, Berkeley, has devoted her scientific career to revealing the secret life of RNA. Using structural biology and biochemistry, Doudna's work deciphering the molecular structure of RNA enzymes (ribozymes) and other functional RNAs has shown how these seemingly simple molecules can carry out the complex functions of proteins.
  In two landmark studies, Doudna and colleagues solved the crystal structures of two large RNAs, the P4-P6 domain of the Tetrahymena thermophila group I intron ribozyme (1) and the hepatitis delta virus (HDV) ribozyme (2). By determining their molecular structures, her work has advanced the understanding of RNA's biological function. In her Inaugural Article published in this issue of PNAS (3), Doudna describes how a special piece of hepatitis C viral RNA, called the internal ribosome entry site (IRES), hijacks the host cell's machinery and induces it to churn out viral proteins.

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  Figure 1
  Jennifer Doudna in the laboratory with postdoctoral associate Richard Spanggord.

  Among Doudna's numerous awards and accomplishments are the Searle Scholar Award (1996) and the National Academy of Sciences Award for Initiatives in Research (1999). She is also an investigator with the Howard Hughes Medical Institute and an American Academy of Arts and Sciences Fellow. In 2002, Doudna was elected to membership in the National Academy of Sciences for her contributions to the field of biochemistry.

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  Erupting Scientific Interests
  Doudna grew up in Hawaii amidst the volcanoes, lush tropical forests, and remote beaches of Hilo. These natural wonders instilled in her an awe and appreciation of nature. Although her immediate and extended family had no scientists, Doudna first became interested in science in high school when she took her first chemistry class and participated in a science seminar series highlighting the chemistry of biological systems. Her parents, both academics in the humanities with avid interests in astronomy, geology, and evolution, encouraged her interests. They provided Doudna with science books, museum visits, and her first “hands-on” science experience—a summer studying worms and mushrooms in the laboratory of professor and family friend Don Hemmes, at the University of Hawaii (Hilo). After reading The Double Helix, James Watson's account of his and Francis Crick's discovery of the structure of DNA, Doudna was hooked on science and desired to delve deeper into the mysteries of the life sciences.
  To indulge her scientific curiosity, Doudna studied chemistry at Pomona College (Claremont, CA) where she met several people who had a profound impact on her research career. These included chemistry professors Fred Grieman, whose passion for quantum mechanics was “infectious,” and Corwin Hansch, whose intensity and love for research was “inspirational.” Doudna began her first scientific research at Pomona, working in the laboratory of Sharon Panasenko, her undergraduate advisor. Panasenko was not only a superb scientist, said Doudna, but also led by example, showing that a woman could be successful in what some perceive as a male-dominated academic world. “It's a challenging job, especially for women,” says Doudna. “The further along I get in my career, the more I see how important it is for young women to have supportive female mentors.” Doudna feels fortunate to have had a strong female role model like Panasenko to help guide her early in her career.
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  RNA Exploration Begins
  After earning her bachelor's degree in chemistry from Pomona in 1985, Doudna went on to pursue her biochemistry doctorate with Jack Szostak at Harvard University (Cambridge, MA). During this time, Doudna's fascination with RNA began to blossom. “Up until the late 1980s, it was known that RNA was involved in protein synthesis, but the discovery that RNA could have catalytic activity really revolutionized the whole field,” recalls Doudna. This realization that RNA might have much greater functional activities than its role as messenger RNA (mRNA) or as part of the ribosome provided the impetus for Doudna's subsequent research career. With Szostak, Doudna made her first mark on the RNA field. Doudna and Szostak (1) reported the reengineering of an RNA self-splicing intron into a ribozyme, capable of copying an RNA template. “It was exciting for us because it suggested that RNA could function as a polymerase,” Doudna says.
  Graduating with her doctorate in 1989, Doudna remained in Szostak's laboratory as a postdoctoral fellow to continue her studies on self-replicating RNAs. “In the course of this work, I became curious about what the RNA structure might be that would allow it to have this kind of activity,” says Doudna.
  This curiosity eventually led Doudna to the University of Colorado (Boulder) and the laboratory of Thomas Cech, who received the 1989 Nobel Prize in chemistry for discovering the catalytic properties of RNA. As a research fellow in Cech's laboratory, Doudna began crystallizing RNA molecules in hopes of obtaining a molecular portrait of these unique structures. According to Doudna, Cech is a deeply insightful scientist who had assembled an outstanding laboratory research team. “The highlight of this time period was the late-night discussions with members of the lab and the occasional intense brainstorming sessions with Tom,” Doudna says.
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  Characterizing Ribozyme Structures
  In 1994, Doudna joined the faculty at Yale University (New Haven, CT) as an assistant professor. She rose rapidly through the ranks, becoming Henry Ford II Professor of Molecular Biophysics and Biochemistry in 2000. Early in her tenure at Yale, Doudna and Cech published the crystal structure of the P4-P6 domain of the Tetrahymena thermophila group I intron ribozyme (4). “That was the first time anyone had seen what a large structured RNA looked like other than tRNA,” Doudna says. This study directly revealed that RNA, rather than being a spaghetti-like molecule, could have a defined shape. “This P4-P6 domain structure showed us how RNA is able to pack helices together to form a three-dimensional shape,” she says, “which is much more reminiscent of what we see in proteins than anybody had previously been aware of for RNA.”
  In the studies that followed, Doudna, Jamie Cate, and Raven Hanna found that a core of five magnesium ions clustered in one region of the P4-P6 domain, forming a nucleus around which the rest of the structure could fold (5). “We presented that as analogous to what happens in proteins, where protein structures typically fold around a hydrophobic core,” she says. “Here the core is chemically different, but the principle of folding is similar.”
  Also in the P4-P6 crystal structure, Doudna observed several examples of a particular motif—abundant adenosines in unpaired regions of the RNA structure. By using various mutagenesis experiments, Doudna, along with Liz Doherty and Rob Batey, showed that this motif was the most critical interaction for allowing the RNA to form the structure that it does (6). Around the same time, her colleague at Yale, Thomas Steitz, reported the existence of an abundance of the same motif in the ribosome (7). “Even in a very large RNA, a motif that was observed in the P4-P6 domain turns out to be probably the most important motif, energetically, for folding the RNA,” says Doudna. Her work on the P4-P6 domain began to illustrate the structural similarities between ribozymes and protein enzymes.
  “Can we get enough information so that we can understand the chemical basis for RNA's many biological functions?”
  In a series of studies similar to the P4-P6 studies, Doudna examined a type of nonenzymatic RNA found within an RNA–protein complex called the signal recognition particle (SRP). SRP is a macromolecular machine that recognizes proteins leaving the ribosome and shunts them across the membrane of the cell or the endoplasmic reticulum. Doudna became “interested in [SRP] a few years ago because, as an RNA-focused lab, we wondered why this RNA is so important for protein recognition and why it had been so highly conserved in evolution.”
  Doudna and postdoctoral fellow Robert Batey went on to characterize the crystal structure of the signal-recognizing domain of SRP (8). In addition to the basic structure, Doudna, Batey, and Brian Rha conducted an in vivo experiment using a strain of bacteria in which portions of SRP sequence were manipulated. They found that only the most conserved part of the structure was necessary to support growth (9,10). “Analogous to what we had been able to do with the P4-P6 structure,” says Doudna, “we were able to use the crystal structure of the core of the SRP to direct biochemical studies to test what the most important interactions were energetically for holding that structure together.”
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  Investigating Viral RNA
  Although Doudna has a strong interest in the basic structure and function of RNA molecules, much of her current work involves viral RNAs. Determining how these RNAs function could lead to strategies to combat a host of viral diseases. Doudna's laboratory has determined how the small, self-cleaving RNA found in the hepatitis delta virus (HDV) is able to function. As a human pathogen, HDV is only coinfectious in patients who already have a hepatitis B virus infection; patients with HDV superinfection develop a more severe form of hepatitis.
  Doudna, Adrian Ferre-D'Amare, and Kaihong Zhou published the crystal structure of this viral RNA in 1998 (2). Based on this structure, they proposed that the HDV ribozyme uses a cytidine base in the RNA to shuttle protons during the reaction, a mechanism remarkably similar to protein ribonucleases. “The surprise was that RNA might be able to use a mechanism that is much more similar to proteins than had been appreciated before,” says Doudna. In 2004, Doudna, Zhou, and Ailong Ke published additional information on the functional characteristics of this viral RNA (11).
  Another focus of Doudna's laboratory involves a segment of viral RNA called the internal ribosome entry site (IRES). According to Doudna, IRES is a “pretty amazing structure that's basically able to grab the ribosomes of infected cells and hijack them for making viral proteins.” Her team is studying this in the hepatitis C virus (HCV), but the mechanism may be common to a number of viruses, including poliovirus. “I think this is the project in the lab that has the greatest potential to lead to something that might have an impact on human health,” Doudna says. In a series of experiments, Doudna and Jeff Kieft determined that HCV IRES RNA actually has a three-dimensional structure responsible for its activity (12, 13).
  In a collaboration with Joachim Frank at the State University of New York in Albany, Doudna characterized HCV IRES RNA interaction with the small subunit of the ribosome by using cryoelectron microscopy (EM) (14). The cryo-EM structures revealed that a mutant form of IRES was unable to induce a conformational change in the 40S ribosome that normally occurs when it binds to wild-type IRES RNA. This conformational change in the 40S subunit of the ribosome occurs in the region where the ribosome binds to the mRNA strand. “Based on the cryo-EM structures, the IRES RNA might actually be functioning like a C-clamp on the ribosome to physically clamp the ribosome onto the viral mRNA in the correct place to initiate translation,” says Doudna.
  Previous Section
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  CalifoRNiA
  In 2002, Doudna made another cross-country move to accept a faculty position at the University of California, Berkeley, as Professor of Biochemistry and Molecular Biology. Doudna, her husband, and their 2-year-old son, whom she calls “the biggest experiment I ever did,” are closer to their extended families and to a resource essential to both of their research—the synchrotron at the Lawrence Berkeley National Laboratory.
  At Berkeley, Doudna has continued to study IRES RNA. A curious aspect of IRES RNA is that it requires only a few of the initiation factors normally used to begin translation. In her Inaugural Article (3), Doudna, Ji Hong, and Chris Fraser extend previous findings to suggest a reason why mutant IRES RNA stalls at particular points in the assembly of active ribosomes. Using RNA-based affinity purification, they show that the IRES RNA is responsible for bringing two initiation factors, eIF3 and eIF2, together on the ribosome. Mutant IRES RNAs become trapped at intermediate stages along the pathway to active 80S ribosomes because one or both of these factors do not associate properly with the smaller (40S) ribosomal subunit.
  Although determining the structure and function of these RNA molecules may someday provide therapeutic targets against a number of viruses, Doudna's interest in them is more basic. “For me, the bigger question is, `Can we get enough information so that we can understand the chemical basis for RNA's many biological functions?”' she says. “It will be exciting to make meaningful comparisons between the chemistry of ribozyme reactions and what happens in protein enzymes that carry out similar reactions.”
  If RNA molecules show a breadth of structure and function similar to proteins, the findings may have major implications for one of the most fundamental scientific questions—the origin of life. Scientists have postulated that there might have been an ancient “RNA world,” where early forms of life were based almost entirely on RNA or an RNA-like molecule. “Obviously, until we build a time machine, we can't really go back and look at that,” says Doudna, “but what we might be able to do in the laboratory now is to find out, `Is it even plausible that RNA could catalyze a variety of different kinds of chemical reactions?”' Doudna continues, “If the answer is yes, then that makes it more likely that the `RNA World' hypothesis might actually be true,” although she says it is a hypothesis that can never truly be tested. Nevertheless, she says, “We hope that we can get information that will help us figure out whether that idea is likely to be true or not.”
  Doudna is excited about this possibility and continues to probe the mysteries of RNA in hopes that the results will provide a glimpse of early life on this planet: “I think the idea that RNA might have played a critical role in that process is very tantalizing.”

• New York Times - https://www.nytimes.com/2015/05/12/science/jennifer-doudna-crispr-cas9-genetic-engineering.html

  Jennifer Doudna, a Pioneer Who Helped Simplify Genome Editing
  Profiles in Science
  By ANDREW POLLACK MAY 11, 2015
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  Dr. Jennifer A. Doudna. Three years ago, she helped make one of the most monumental discoveries in biology.
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  Matt Edge for The New York Times
  BERKELEY, Calif. — As a child in Hilo, one of the less touristy parts of Hawaii, Jennifer A. Doudna felt out of place. She had blond hair and blue eyes, and she was taller than the other kids, who were mostly of Polynesian and Asian descent.
  “I think to them I looked like a freak,” she recently recalled. “And I felt like a freak.”
  Her isolation contributed to a kind of bookishness that propelled her toward science. Her upbringing “toughened her up,” said her husband, Jamie Cate. “She can handle a lot of pressure.”
  These days, that talent is being put to the test.
  Three years ago, Dr. Doudna, a biochemist at the University of California, Berkeley, helped make one of the most monumental discoveries in biology: a relatively easy way to alter any organism’s DNA, just as a computer user can edit a word in a document.
  The discovery has turned Dr. Doudna (the first syllable rhymes with loud) into a celebrity of sorts, the recipient of numerous accolades and prizes. The so-called Crispr-Cas9 genome editing technique is already widely used in laboratory studies, and scientists hope it may one day help rewrite flawed genes in people, opening tremendous new possibilities for treating, even curing, diseases.
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  But now Dr. Doudna, 51, is battling on two fronts to control what she helped create.
  While everyone welcomes Crispr-Cas9 as a strategy to treat disease, many scientists are worried that it could also be used to alter genes in human embryos, sperm or eggs in ways that can be passed from generation to generation. The prospect raises fears of a dystopian future in which scientists create an elite population of designer babies with enhanced intelligence, beauty or other traits.
  Scientists in China reported last month that they had already used the technique in an attempt to change genes in human embryos, though on defective embryos and without real success.
  Dr. Doudna has been organizing the scientific community to prevent this ethical line from being crossed. “The idea that you would affect evolution is a very profound thing,” she said.
  Photo

  Dr. Emmanuelle Charpentier and Dr. Doudna, center, with Dick Costolo, Twitter's chief executive, and the actress Cameron Diaz, in November. Each scientist won a $3 million Breakthrough Prize.
  Credit
  Kimberly White/Getty Images for Breakthrough Prize
  She is also fighting for control of what could be hugely lucrative intellectual property rights to the genome editing technique. To the surprise of many, the first sweeping patents for the technology were granted not to her, but to Feng Zhang, a scientist at the Broad Institute and M.I.T.
  The University of California is challenging the decision, and the nasty skirmish has cast a bit of a pall over the field.
  “I really want to see this technology used to help people,” Dr. Doudna said. “It would be a shame if the I.P. situation would block that.”
  The development of the Crispr-Cas9 technique is a story in which obscure basic biological research turned out to have huge practical implications. For Dr. Doudna, though, it is only one accomplishment in a stellar career.
  “She’s been a high-impact scientist from the time she was a graduate student,” said Thomas Cech, a Nobel laureate and professor of chemistry and biochemistry at the University of Colorado, for whom Dr. Doudna was a postdoctoral researcher. “New topics, new fields of science, but she just has a knack for discovery.”
  A ‘Dumbstruck’ Moment
  Dr. Doudna was 7 when she moved to Hilo, where her father taught literature at the University of Hawaii campus there, and her mother lectured on history at a community college. Their daughter loved exploring the rain forests and was fascinated by how things worked. She found her calling in high school after hearing a lecture by a scientist about her research into how normal cells became cancerous.
  “I was just dumbstruck,” Dr. Doudna recalled. “I wanted to be her.”
  After studying biochemistry at Pomona College in California, she went to Harvard for graduate school. There her adviser, the future Nobel laureate Jack Szostak, was doing research on RNA. Some scientists believe that RNA, not DNA, was the basis of early life, since the molecule can both store genetic information and catalyze chemical reactions.
  Dr. Doudna earned her doctoral degree by engineering a catalytic RNA that could self-replicate, adding evidence to that theory. But her inability to visualize this catalytic RNA hindered her work.
  So as a postdoctoral researcher in Colorado, she decided to try to determine the three-dimensional atomic structure of RNA using X-ray diffraction — and succeeded, though she had had no formal training in the technique. Structural and biochemical studies of RNA in action have been her forte ever since.
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  Breaking the Chain
  A complex immune system discovered in bacteria is already widely used in laboratory studies to modify the DNA of any organism.

  Snippet
  RNA
  Short, repeating
  block of DNA
  Cas9
  protein
  Cut
  Repair
  Edit
  Cut
  Spacer
  RNA
  Matching
  sequence
  of DNA
  RNA made
  from one
  spacer
  Disabled
  gene
  Double helix
  opened
  STORAGE Researchers in the 1980s noticed that bacteria had small blocks of palindromic DNA repeated many times, with nonrepeated spacers of DNA stored in between. This pattern is an immune system known by the acronym Crispr, for “clustered regularly interspaced short palindromic repeats.”
  RECOGNITION The spacers match pieces of DNA from viral invaders that bacteria or their ancestors have faced before. When needed, the DNA contained in the spacer is converted to RNA. A protein called Cas9 and a second piece of RNA latch on, forming a structure that will bind to strands of DNA that match the spacer’s sequence.
  CUTTING When a matching strand of DNA is found, the Cas9 protein opens the double helix and cuts both sides, breaking the strand and disabling the viral DNA. If a bacterium survives an attack by an unfamiliar virus, it will make and store a new spacer, which can be inherited by future generations.
  EDITING Researchers are learning how to use synthetic RNA sequences to control the cutting of any piece of DNA they choose. The cell will repair the cut, but an imperfect repair may disable the gene. Or a snippet of different DNA can be inserted to fill the gap, effectively editing the DNA sequence.
  Sources: Nature; Addgene

  By Jonathan Corum
  In 2000, while on the faculty at Yale, she won the Alan T. Waterman Award, given each year by the National Science Foundation to an exceptional young scientist. She moved to Berkeley in 2002.
  In 2005, Dr. Doudna was approached by Jillian Banfield, an environmental researcher at Berkeley who had been sequencing the DNA of unusual microbes that lived in a highly acidic abandoned mine. In the genomes of many of these microbes were unusual repeating sequences called “clustered regularly interspaced short palindromic repeats,” or Crispr.
  No one was quite sure what they did, though over the next few years scientists elsewhere established that these sequences were part of a bacterial immune system. Between the repeated sequences were stretches of DNA taken from viruses that had previously infected the bacteria — genetic most-wanted posters, so to speak.
  If the same virus invaded again, these stretches of DNA would permit the bacteria to recognize it and destroy it by slicing up its genetic material. Dr. Doudna was trying to figure out exactly how this happened.
  “I remember thinking this is probably the most obscure thing I ever worked on,” she said.
  It would prove to have wide use. At a conference in early 2011, she met Emmanuelle Charpentier, a French microbiologist at Umea University in Sweden, who had already made some fundamental discoveries about the relatively simple Crispr system in one bacterial species.
  The bacterial expert and the structural biologist decided to work together.
  “It was very enjoyable, because we were complementary,” said Dr. Charpentier, who recalled sitting in her office near the North Pole while Dr. Doudna regaled her with stories about Hawaii.
  Along with postdoctoral researchers Martin Jinek and Krzysztof Chylinski, the two scientists eventually figured out how two pieces of RNA join up with a protein made by the bacteria called Cas9 to cut DNA at a specific spot. The researchers also found that the two RNA pieces could be combined into one and still function.
  In a eureka moment, the scientists realized that this cellular defense system might be used to edit genomes, not just kill viruses.
  A specific sequence of guide RNA could be made to attach to a spot virtually anywhere on the genome, and the Cas9 protein would cleave the DNA at that spot. Then pieces of the DNA could be deleted or added, just as a film editor might cut a film and splice in new frames.
  More Reporting on Gene Editing

  Gene Drives Offer New Hope Against Diseases and Crop PestsDec. 22, 2015

  Scientists Seek Moratorium on Edits to Human Genome That Could Be InheritedDec. 04, 2015

  Open Season Is Seen in Gene Editing of AnimalsNov. 27, 2015

  Jennifer Doudna, a Pioneer Who Helped Simplify Genome EditingMay 12, 2015

  The researchers demonstrated this using DNA in a test tube. While there were other genome editing techniques, they found that Crispr-Cas9 was much simpler.
  The paper describing the technique, published by the journal Science in June 2012, set off a race to see if it would work in human, plant and animal cells.
  Dr. Doudna, whose expertise was in working with molecules, not cells, reported such a demonstration in human cells in January 2013. But her report came four weeks after two papers were published simultaneously, one by George Church at Harvard and the other by the Broad Institute’s Dr. Zhang.
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  The Patent Fight
  Now the University of California and the Broad Institute are arguing before the federal patent office over whether Dr. Doudna or Dr. Zhang, who last year received the Waterman Award for young scientists that Dr. Doudna had won years earlier, was the first to invent the genome editing technique. So far, the patents have gone to Dr. Zhang.
  The Broad Institute claims that the paper by Dr. Doudna and Dr. Charpentier in 2012 did not demonstrate how to alter DNA in cells with nuclei, including human cells, something requiring the inventive steps that Dr. Zhang took. His patent application included pages from a lab notebook he said demonstrated that he was doing Crispr genome editing even before the 2012 paper was published.
  The University of California says it filed for a patent months before Dr. Zhang did, though the Broad Institute says that initial application lacked necessary details. The university’s request to the patent office says that once the 2012 paper laid out the recipe, it was obvious how to use it in cells. The university also says Dr. Zhang’s notebook does not prove he could edit genomes before the 2012 paper.
  Patent disputes are often settled in time. In any event, Dr. Church of Harvard said, before Crispr-Cas9 could be used to treat disease, it would need important refinements from many other researchers.
  “It’s going to be hard to use Feng’s without Jennifer’s, and it would be hard to use either of them without further improvements,” he said.
  The scientists have formed competing companies with rights to their patents and pending patents. Dr. Doudna co-founded Caribou Biosciences to work on research uses of Crispr-Cas9, and more recently, Intellia Therapeutics to work on disease treatments.
  Photo

  Genetically altered twin cynomolgus monkeys were created in China using the Crispr-Cas9 genome editing technique.
  Credit
  Yuyu Niu, et al
  Dr. Church and Dr. Zhang are co-founders of Editas Medicine, which Dr. Doudna also helped start but then withdrew from. Dr. Charpentier, who is now at the Helmholtz Center for Infection Research in Germany, helped start Crispr Therapeutics. She and Dr. Doudna remain friends, but no longer collaborate on research.
  Even before the dust settles, researchers are moving ahead. While contending with the patents, Dr. Doudna began hearing reports that researchers were trying to use Crispr-Cas9 to make inheritable DNA changes in embryos. Genetically altered monkeys had already been created in China using the technique.
  “It’s very far afield from the kind of chemistry I think about and know about,” she said. Still, she felt it would be irresponsible to ignore the rumors.
  She organized a meeting of leading biologists in Napa, Calif., in January. In a subsequent commentary published in Science, the group called for a moratorium on attempts to create altered babies, though they said basic research on inheritable changes should still be done.
  Dr. Doudna said it was not practical to prohibit basic research. “You can’t really put a lid on it, even if you wanted to,” she said. She and others are trying to organize a bigger international meeting with participants from companies and governments as well as universities, possibly to set new guidelines.
  Learning to Live With Fame
  She is also trying to cope with her newfound quasi-celebrity status. She has been invited to hobnob with entrepreneurs in Silicon Valley, to speak to science fiction writers, to advise Hollywood on science-themed movies. The garden, her hobby, has had to wait.
  In November, Dr. Doudna and Dr. Charpentier were each awarded $3 million Breakthrough Prizes, endowed by leading Internet entrepreneurs. They accepted their awards at an Oscars-like black-tie affair attended by movie stars like Cameron Diaz and Benedict Cumberbatch. Recently Time magazine listed the two scientists among the 100 most influential people in the world.
  Dr. Doudna, who has a 12-year-old son, Andrew, also finds herself a role model for women in science. Her secret: “I have a great partner,” with whom she shares the chores.
  Her husband, Dr. Cate, is also a professor at Cal-Berkeley. The couple have adjacent offices, with views of the Golden Gate Bridge in the distance. Dr. Cate also studies RNA; there is some overlap, but mostly they do their own research. Andrew walks to their office from his middle school each afternoon and hangs out until his parents are ready to go home.
  “I don’t think of myself as a role model, but I can see that I am,” Dr. Doudna said. “I still think of myself as that person back in Hawaii.”
  A version of this article appears in print on May 12, 2015, on Page D1 of the New York edition with the headline: The Gene Editor. Order Reprints| Today's Paper|Subscribe
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• TED - https://www.ted.com/speakers/jennifer_doudna

  Jennifer Doudna
  Biologist
  rna.berkeley.edu

  TED Speaker
  Jennifer Doudna was part of inventing a potentially world-changing genetic technology: the gene editing technology CRISPR-Cas9.
  Why you should listen
  Together with her colleague Emmanuelle Charpentier of Umeå University in Sweden, Berkeley biologist Jennifer Doudna is at the center of one of today's most-discussed science discoveries: a technology called CRISPR-Cas9 that allows human genome editing by adding or removing genetic material at will. This enables fighting genetic diseases (cutting out HIV, altering cancer cells) as well as, potentially, opening the road to "engineered humans."
  Because some applications of genetic manipulation can be inherited, Doudna and numerous colleagues have called for prudent use of the technology until the ethics and safety have been properly considered.

• London Observer - https://www.theguardian.com/science/2017/jul/02/jennifer-doudna-crispr-i-have-to-be-true-to-who-i-am-as-a-scientist-interview-crack-in-creation

  Jennifer Doudna: ‘I have to be true to who I am as a scientist’

  Crispr inventor Jennifer Doudna talks about discovering the gene-editing tool, the split with her collaborator and the complex ethics of genetic manipulation

  Jennifer Doudna: ‘Experiments fail. To have people around that get along with each other is super important.’ Photograph: Bryan Derballa/Kintzing.com

  Hannah Devlin

  @hannahdev
  Sunday 2 July 2017 07.00 BST
  Last modified on Saturday 2 December 2017 14.36 GMT

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  Jennifer Doudna, 53, is an American biochemist based at the University of California, Berkeley. Together with the French microbiologist Emmanuelle Charpentier, she led the discovery of the revolutionary gene-editing tool, Crispr. The technology has the potential to eradicate previously incurable diseases, but also poses ethical questions about the possible unintended consequences of overwriting the human genome.
  Were you nerdy as a child? What got you hooked on science?
  Yes, I was nerdy. My father was a professor of American literature in Hawaii and he loved books. One day I came home from school and he had dropped a copy of The Double Helix on the bed, by Jim Watson. One rainy afternoon I read it and I was just stunned. I was blown away that you could do experiments about what a molecule looks like. I was probably 12 or 13. I think that was the beginning of starting to think, “Wow, that could be an amazing thing to work on.”
  You’ve spent most of your career uncovering the structure of RNA and never set out to create a tool to copy and paste human genes. How did you end up working on Crispr?
  I think you can put scientists into two buckets. One is the type who dives very deeply into one topic for their whole career and they know it better than anybody else in the world. Then there’s the other bucket, where I would put myself, where it’s like you’re at a buffet table and you see an interesting thing here and do it for a while, and that connects you to another interesting thing and you take a bit of that. That’s how I came to be working on Crispr – it was a total side-project.
  But when you first started your collaboration with Emmanuelle Charpentier, did you have a hunch you were on to something special?
  We met at a conference in San Juan, Puerto Rico, and took a walk around the old town together. She was so passionate, her excitement was very infectious. I still remember walking down this street with her and she said: “Well I’m really glad you want to work with us on the mysterious [Cas9 – the enzyme that snips DNA at the chosen location in the editing process].” It was this kind of electrifying moment. Even then I just had this gut feeling that this was something really interesting.

  I would have loved to continue working with Emmanuelle. I’m not blaming her: she had her reasons and I respect her

  How important is personal chemistry in science collaborations?
  It’s essential. Working in a lab is analogous to being in a high-school play: you’re rehearsing long hours, it’s crowded, there are stressful things that come up. It’s the same thing in science. Things never work as you think they will, experiments fail and so to have people around that really get along with each other is super important. Many collaborations don’t work out, usually just because people’s interests aren’t aligned or people don’t really like working together.
  The real frenzy around your work started in 2012, when you showed that Crispr-Cas9 could be used to slice up DNA at any site [of the DNA molecule] you wanted. Did you realise this was a big deal gradually or immediately?
  It wasn’t a gradual realisation, it was one of those OMG moments where you look at each other and say “holy moly”. This was something we hadn’t thought about before, but now we could see how it worked, we could see it would be such a fantastic way to do gene editing.
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  After you demonstrated Crispr could edit bacterial DNA, two rival labs (Harvard and the Broad Institute) got there first in human cells. How come they beat you to it?
  They were absolutely set up to do that kind of experiment. They had all the tools, the cells growing, everything was there. For us, they were hard experiments to do because it’s not the kind of science we do. What speaks to the ease of the system was that a lab like mine could even do it.
  The Broad Institute won the latest round of an ongoing legal battle over patent rights – they claim that it wasn’t obvious that Crispr could be used to edit human cells too. Where do you stand?
  People have asked me over and over again: “Did you know it was going to work?” But until you do an experiment you don’t know – that’s science. I’ve been lambasted for this in the media, but I have to be true to who I am as a scientist. We certainly had a hypothesis and it certainly seemed like a very good guess that it would.
  There’s the patent dispute and you and Emmanuelle Charpentier also ended up pursuing rival projects to commercialise the technology. Are you all still friends?
  If there’s a sadness to me about all of this – and a lot of it’s been wonderful and really exciting – it’s that I would’ve loved to continue working with Emmanuelle, scientifically. For multiple reasons that wasn’t desirable to her. I’m not blaming her at all – she had her reasons and I respect her a lot.
  The media loves to drive wedges, but we are very cordial. I was just with her in Spain and she was telling me about the challenges [of building her new lab in Berlin]. I hope on her side, certainly on my side, we respect each other’s work and in the end we’re all in it together.
  A Crack in Creation review – Jennifer Doudna, Crispr and a great scientific breakthrough
  This is an invaluable account, by Doudna and Samuel Sternberg, of their role in the revolution that is genome editing
  Read more

  In your book you describe a nightmare you had involving Hitler wearing a pig mask, asking to learn more about your “amazing technology”. Do you still have anxiety dreams about where Crispr might leave the human race?
  I had the Hitler dream and I’ve had a couple of other very scary dreams, almost like nightmares, which is quite unusual for an adult. Not so much lately, but in the first couple of years after I published my work, the field was moving so fast. I had this incredible feeling that the science was getting out way ahead of any considerations about ethics, societal implications and whether we should be worrying about random people in various parts of the world using this for nefarious purposes.
  In 2015, you called for a moratorium on the clinical use of gene editing. Where do you stand on using Crispr to edit embryos these days?
  It shouldn’t be used clinically today, but in the future possibly. That’s a big change for me. At first, I just thought why would you ever do it? Then I started to hear from people with genetic diseases in their family – this is now happening every day for me. A lot of them send me pictures of their children. There was one that I can’t stop thinking about, just sent to me in the last 10 days or so. A mother who told me that her infant son was diagnosed with a neurodegenerative disease, caused by a sporadic rare mutation. She sent me a picture of this little boy. He was this adorable little baby, he was bald, in his little carrier and so cute. I have a son and my heart just broke.
  What would you do as a mother? You see your child and he’s beautiful, he’s perfect and you know he’s going to suffer from this horrible disease and there’s nothing you can do about it. It’s horrible. Getting exposed to that, getting to know some of these people, it’s not abstract any more, it’s very personal. And you think, if there were a way to help these people, we should do it. It would be wrong not to.

  Are people going to start saying I want a child that’s 6ft 5in with blue eyes and so on? Do we really want to go there?

  What about the spectre of designer babies?
  A lot of it will come down to whether the technology is safe and effective, are there alternatives that would be equally effective that we should consider, and what are the broader societal implications of allowing gene editing? Are people going to start saying I want a child that’s 6ft 5in and has blue eyes and so on? Do we really want to go there? Would you do things that are not medically necessary but are just nice-to-haves, for some people? It’s a hard question. There are a lot of grey areas.
  Are you worried about cuts to science funding, including to the National Institutes of Health (NIH) budget?
  I am very concerned. Science funding is not a political football but in fact a down payment on discovery, the seed money to fund a critical step toward ending Alzheimer’s or curing cancer.
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  Researchers currently working on projects aimed at improving numerous aspects of our agriculture, environment and health may be forced to abandon their work. The outcome is that people will not receive the medical treatments they need, our struggle to feed our exploding population will deepen, and our efforts to manage climate change will collapse.
  Over the long term, the very role of fundamental science as a means to better our society may come into question. History and all evidence points to the fact that when we inspire and support our scientific community we advance our way of life and thrive.
  Were you disturbed when Trump tweeted, “If U.C. Berkeley does not allow free speech and practices violence on innocent people with a different point of view – NO FEDERAL FUNDS?” in response to a planned “alt-right” speaker being cancelled due to violent protests on campus?
  Yes. It was a confusing tweet since the university was clearly committed to ensuring that the event would proceed safely and first amendment rights were supported. Few expected the awful actions of a few to be met with a willingness from the highest office to deprive more than 38,000 students access to an education.
  You’ve spoken at Davos, shared the $3m 2015 Breakthrough prize, been listed among the 100 most influential people in the world by Time magazine. Are you still motivated about heading into the lab these days?
  Yesterday I was getting ready to go to a fancy dinner. I was in a cocktail gown and had my makeup on and my hair done, but I wanted to talk to a postdoc in my lab about an experiment he was doing, so I texted him saying can we Skype? It was 8am in California, I was over here [in the UK] in my full evening gown, talking about the experiment. That’s how nerdy I am.
  • A Crack in Creation: The New Power to Control Evolution by Jennifer Doudna and Sam Sternberg is published by The Bodley Head (£20). To order a copy for £17 go to bookshop.theguardian.com or call 0330 333 6846. Free UK p&p over £10, online orders only. Phone orders min p&p of £1.99

• A Crack in Creation Website - http://www.acrackincreation.com/

  Jennifer A. Doudna, Ph.D. is a professor in the Chemistry and the Molecular and Cell Biology Departments at the University of California, Berkeley, investigator with the Howard Hughes Medical Institute, and researcher in the Molecular Biophysics and Integrated Bioimaging Division at the Lawrence Berkeley National Laboratory. She is internationally recognized as a leading expert on RNA-protein biochemistry, CRISPR biology, and genome engineering. She lives in the Bay Area.

• Department of Molecular and Cell Biology, University of California, Berkeley Website - https://mcb.berkeley.edu/faculty/BMB/doudnaj.html

  Faculty Research Page

  Jennifer A. Doudna
  Howard Hughes Medical Institute Investigator, Li Ka Shing Chancellor's Chair in Biomedical and Health Sciences and Professor of Biochemistry, Biophysics and Structural Biology
  Lab Homepage: http://rna.berkeley.edu/
  Full Directory Information
  Research Interests
  RNA molecules are uniquely capable of encoding and controlling the expression of genetic information, often as a consequence of their three-dimensional structures. We are interested in understanding and harnessing RNA-mediated control of the genome, including CRISPR-Cas bacterial adaptive immunity and related systems.
  Current Projects
  The CRISPR bacterial adaptive immune system
  Prokaryotes have evolved a nucleic acid-based immune system that shares some functional similarities with RNA interference in eukaryotes. Central to this system are DNA repeats called CRISPRs (Clustered Regularly Interspaced Short Palindromic Repeats). CRISPRs are genetic elements containing direct repeats separated by unique spacers, many of which are identical to sequences found in phage and other foreign genetic elements. Recent work has demonstrated the role of CRISPRs in adaptive immunity and shown that small RNAs derived from CRISPRs (crRNAs) are implemented as homing oligos for the targeted interference of foreign DNA.
  Phylogenetic analysis of CRISPR-associated (Cas) proteins suggests there are at least seven distinct versions of this immune system. These systems can be extremely divergent mechanistically and provide a rich area to research RNA:protein interactions, including novel protein folds. To explore this diversity, we have determined the structures of diverse CRISPR-associated proteins, including the large E. coli CASCADE silencing complex. This seahorse-shaped assembly shows how the CRISPR RNA is cradled by six repeating subunits and presented for DNA inspection. Further, we have solved the structure of the CasA subunit by X-ray crystallography, which revealed that it is poised to have a role in discriminating between “nonself” (foreign DNA) or “self” (host DNA) prior to targeting. This step is critical, as reckless silencing could prove lethal to the host.
  RNA-guided DNA cleavage with the Type-II CRISPR enzyme Cas9
  Type II CRISPR-Cas systems use an RNA-guided DNA endonuclease, Cas9, to generate double-strand breaks in invasive DNA during an adaptive bacterial immune response. Cas9-mediated cleavage is strictly dependent on the presence of a protospacer adjacent motif (PAM) in the target DNA. The ability to program Cas9 for DNA cleavage at specific sites defined by guide RNAs has led to its adoption as a versatile platform for genome engineering and gene regulation. To compare the architectures and domain organization of diverse Cas9 proteins, we have solved the atomic structures of Cas9 from Streptococcus pyogenes (SpyCas9) and Actinomyces naeslundii (AnaCas9), revealing the structural core shared by all Cas9 family members, and the structurally divergent regions, including the PAM recognition loops, are likely responsible for distinct guide RNA and PAM specificities. Our EM analysis further shows that by triggering a conformational rearrangement in Cas9, the guide RNA acts as a critical determinant of target DNA binding (in collaboration with Eva Nogales, UC Berkeley, HHMI).
  Adaptive immunity in bacteria and the genome engineering technologies derived from it employ RNA-guided cleavage of double-stranded DNA targets using CRISPR (clustered regularly interspaced short palindromic repeats)-associated (Cas) proteins together with CRISPR transcripts. In Type II CRISPR-Cas systems, activation of Cas9 endonuclease for DNA recognition upon guide RNA binding occurs by an unknown mechanism. Crystal structures of Cas9 bound to an 85-nucleotide single-guide RNA reveal a conformation distinct from both the apo and DNA-bound forms of the protein, in which the 10-nucleotide RNA “seed” sequence required for initial DNA interrogation is pre-ordered in an A-form helical conformation. Biochemical experiments show this segment of the guide RNA to be essential for Cas9 to form a DNA recognition-competent structure that is poised to engage double-stranded DNA target sequences. Together, these results suggest convergent evolution of a “seed” mechanism reminiscent of that employed by Argonaute proteins during RNA interference in eukaryotes. Furthermore, our structural and biochemical data show that Cas9 is subject to multi-layered regulation during its activation. The pre-ordered RNA seed sequence and protein PAM-interacting cleft enable the Cas9-sgRNA complex to interact productively with potential DNA sequences for target sampling. The inactive conformation of apo Cas9, as well as the additional conformational changes required for the complex to reach its ultimate catalytically-active state, could help avoid spurious DNA cleavage within the host genome and hence minimize off-target effects in Cas9-based genome editing.
  RNA-guided RNA cleavage by the Csm complex
  In a collaboration with John van der Oost’s laboratory, we are studying the structure and function of the effector complex of the Type III-A CRISPR-Cas system of Thermus thermophilus: the Csm complex (TtCsm). Recently, we showed that multiple Cas proteins and a crRNA guide assemble to recognize and cleave invader RNAs at multiple sites. Our negative stain EM structure of the TtCsm complex exhibits the characteristic architecture of Type I and Type III CRISPR-associated ribonucleoprotein complexes, suggesting a model for cleavage of the target RNA at periodic intervals (in collaboration with Eva Nogales, UC Berkeley, HHMI).
  RNA-guided DNA cleavage with CASCADE
  Cascade is composed of Cse1, Cse2, Cas7, Cas5e, and Cas6e subunits and one crRNA, forming a structure that binds and unwinds dsDNA to form an R-loop in which the target strand of the DNA base pairs with the 32-nt crRNA guide sequence. Recently, we used single-particle electron microscopy reconstructions of dsDNA-bound Cascade with and without Cas3 to reveal that Cascade positions the PAM-proximal end of the DNA duplex at the Cse1 subunit and near the site of Cas3 association. The finding that the DNA target and Cas3 colocalize with Cse1 implicates this subunit in a key target-validation step during DNA interference. We show biochemically that base pairing of the PAM region is unnecessary for target binding but critical for Cas3-mediated degradation. In addition, the L1 loop of Cse1, previously implicated in PAM recognition, is essential for Cas3 activation following target binding by Cascade. Together, these data show that the Cse1 subunit of Cascade functions as an essential partner of Cas3 by recognizing DNA target sites and positioning Cas3 adjacent to the PAM to ensure cleavage (in collaboration with Eva Nogales, UC Berkeley).
  Tunable expression of the human transcriptome
  Eukaryotic cells exert control over gene expression at multiple layers. Control at the step of protein production, or translation, is frequently used to effect tight spatiotemporal regulation of gene expression. High-throughput methods such as ribosome profiling have revolutionized the study of translational control in cells. However, many eukaryotes frequently generate multiple transcript isoforms from a gene through the combined action of alternative transcription initiation, splicing, and polyadenylation, which are inaccessible to ribosome profiling. For example, in humans there is a median of five transcript isoforms per gene, each of which may have a distinct set of regulatory features. We developed a new method termed Transcript Isoforms in Polysomes sequencing, or TrIP-seq, to directly measure how well each individual human transcript isoform is translated in human cells. We found that thousands of human genes express multiple transcript isoforms that are differentially translated. Furthermore, we showed that regulatory regions from transcript isoforms are sufficient to control translation of an orthogonal gene in a manner predicted by TrIP-seq. Translational control conferred by transcript 5’ leader sequences is robust across cell types, while 3’ UTRs can exhibit cell-type specific expression. All told, our work has uncovered an underappreciated layer in gene regulation due to differential translation of transcript isoforms that broadly impacts human gene expression, and may be part of the reason mRNA and protein levels are poorly correlated.
  RNA-mediated signaling in eukaryotic innate immunity
  In collaboration with the Berger lab (Johns Hopkins Medical School) and Vance lab (UC-Berkeley), we are investigating a mammalian signaling network where small RNA oligonucleotide second messengers are enzymatically synthesized in response to pathogen infection. The human enzyme cyclic GMP–AMP synthase (cGAS) is responsible for detection of cytosolic DNA and synthesis of a cyclic GMP–AMP dinucleotide containing one canonical 3ʹ–5ʹ and one unique 2ʹ–5ʹ phosphodiester bond (2ʹ,3ʹ cGAMP). Previously, we determined the X-ray crystal structure of human cGAS revealing a bi-lobed enzyme that utilizes a zinc-ribbon modified cleft to couple DNA recognition and enzymatic activity. Through analysis of a distantly related bacterial enzyme encoded by Vibrio cholerae, we went on to delineate the molecular rules for mammalian-specific 2ʹ–5ʹ linkage formation and rationally reprogrammed human cGAS to produce an exclusively 3ʹ,3ʹ linked cGAMP product. These results reveal unexpected mechanistic homology between bacterial signaling and mammalian innate immunity, illustrating active site configurations that may underlie distinct 2ʹ,3ʹ and 3ʹ,3ʹ cGAMP signaling in the human population. Currently, we are using a paleo-biochemistry approach to investigate the unique potency of human 2ʹ,3ʹ cGAMP signaling.
  Selected Publications
  Generation of knock-in primary human T cells using Cas9 ribonucleoproteins. Schumann K, Lin S, Boyer E, Simeonov DR, Subramaniam M, Gate RE, Haliburton GE, Ye CJ, Bluestone JA, Doudna JA, Marson A Proc Natl Acad Sci U S A 2015 Jul 27
  A Cas9-guide RNA complex preorganized for target DNA recognition. Jiang F, Zhou K, Ma L, Gressel S, Doudna JA Science 2015 Jun 26;348(6242):1477-81
  Structures of the CRISPR-Cmr complex reveal mode of RNA target positioning. Taylor DW, Zhu Y, Staals RH, Kornfeld JE, Shinkai A, van der Oost J, Nogales E, Doudna JA Science 2015 May 1;348(6234):581-5
  Rational design of a split-Cas9 enzyme complex. Wright AV, Sternberg SH, Taylor DW, Staahl BT, Bardales JA, Kornfeld JE, Doudna JA Proc Natl Acad Sci U S A 2015 Mar 10;112(10):2984-9
  Integrase-mediated spacer acquisition during CRISPR-Cas adaptive immunity. Nuñez JK, Lee AS, Engelman A, Doudna JA Nature 2015 Mar 12;519(7542):193-8
  Dicer-TRBP complex formation ensures accurate mammalian microRNA biogenesis. Wilson RC, Tambe A, Kidwell MA, Noland CL, Schneider CP, Doudna JA Mol Cell 2015 Feb 5;57(3):397-407
  Enhanced homology-directed human genome engineering by controlled timing of CRISPR/Cas9 delivery. Lin S, Staahl BT, Alla RK, Doudna JA Elife 2014;3:e04766
  RNA targeting by the type III-A CRISPR-Cas Csm complex of Thermus thermophilus. Staals RH, Zhu Y, Taylor DW, Kornfeld JE, Sharma K, Barendregt A, Koehorst JJ, Vlot M, Neupane N, Varossieau K, Sakamoto K, Suzuki T, Dohmae N, Yokoyama S, Schaap PJ, Urlaub H, Heck AJ, Nogales E, Doudna JA, Shinkai A, van der Oost J Mol Cell 2014 Nov 20;56(4):518-30
  Programmable RNA recognition and cleavage by CRISPR/Cas9. O'Connell MR, Oakes BL, Sternberg SH, East-Seletsky A, Kaplan M, Doudna JA Nature 2014 Dec 11;516(7530):263-6
  RNA-guided assembly of Rev-RRE nuclear export complexes. Bai Y, Tambe A, Zhou K, Doudna JA Elife 2014;3:e03656
  Evolutionarily conserved roles of the dicer helicase domain in regulating RNA interference processing. Kidwell MA, Chan JM, Doudna JA J Biol Chem 2014 Oct 10;289(41):28352-62
  Structure-guided reprogramming of human cGAS dinucleotide linkage specificity. Kranzusch PJ, Lee AS, Wilson SC, Solovykh MS, Vance RE, Berger JM, Doudna JA Cell 2014 Aug 28;158(5):1011-21
  Insights into RNA structure and function from genome-wide studies. Mortimer SA, Kidwell MA, Doudna JA Nat Rev Genet 2014 Jul;15(7):469-79
  Cas1-Cas2 complex formation mediates spacer acquisition during CRISPR-Cas adaptive immunity. Nuñez JK, Kranzusch PJ, Noeske J, Wright AV, Davies CW, Doudna JA Nat Struct Mol Biol 2014 Jun;21(6):528-34
  CasA mediates Cas3-catalyzed target degradation during CRISPR RNA-guided interference. Hochstrasser ML, Taylor DW, Bhat P, Guegler CK, Sternberg SH, Nogales E, Doudna JA Proc Natl Acad Sci U S A 2014 May 6;111(18):6618-23
  DNA interrogation by the CRISPR RNA-guided endonuclease Cas9. Sternberg SH, Redding S, Jinek M, Greene EC, Doudna JA Nature 2014 Mar 6;507(7490):62-7
  Evolution of CRISPR RNA recognition and processing by Cas6 endonucleases. Niewoehner O, Jinek M, Doudna JA Nucleic Acids Res 2014 Jan;42(2):1341-53
  Photo credit: Keegan Houser.
  Last Updated 2015-09-17

  Jennifer A. Doudna

  Doudna Lab.

  Dr. Jennifer Doudna is a member of the departments of Molecular and Cell Biology and Chemistry at UC Berkeley, the Howard Hughes Medical Institute, and Lawrence Berkeley National Lab, along with the National Academy of Sciences, and the American Academy of Arts and Sciences.

  Biographical Highlights:
  Fellow, American Academy of Arts and Sciences (2003)
  Professor of Biochemistry and Molecular Biology, Department of Molecular and Cell Biology, the University of California, Berkeley (2003)
  Professor of Biochemistry and Molecular Biology, Department of Chemistry, the University of California, Berkeley (2003)
  Faculty, Biophysics Graduate Group, the University of California, Berkeley (2003)
  Faculty Scientist, Physical Biosciences Division, Lawerence Berkeley National Laboratory (2003)
  Member, National Academy of Sciences (2002)
  Member, Board of Trustees, Pomona College (2001)
  American Chemical Society Eli Lilly Award in Biological Chemistry (2001)
  R. B. Woodward Visiting Professor, Harvard University (2000-2001)
  Alan T. Waterman Award (2000)
  Investigator, Howard Hughes Medical Institute (1997)
  Searle Scholar, Kinship Foundation's Searle Scholars Program (1996)
  Henry Ford II Professor of Molecular Biophysics and Biochemistry, Center for Structural Biology, Department of Molecular Biophysics and Biochemistry, Yale University (1994-2002)
  Lucille P. Markey Scholar in Biomedical Science, University of Colorado (1991-1994, Dr. Thomas R. Cech)
  Postdoctoral Research Fellow, Molecular Biology, Massachusetts General Hospital and Harvard Medical School (1989-1991, Dr. Jack W. Szostak)
  Ph.D. Harvard University (1989, Dr. Jack W. Szostak)
  B.A. Pomona College (1985, Dr. Sharon M. Panasenko)

A Crack in Creation: Gene Editing and the Unthinkable Power to Control Evolution

Carl Coon
77.6 (November-December 2017): p42+.
Copyright: COPYRIGHT 2017 American Humanist Association
http://www.americanhumanist.org/
A Crack in Creation: Gene Editing and the Unthinkable Power to Control Evolution
by Jennifer Doudna and Samuel Sternberg
Houghton Mifflin Harcourt, 2017 304pp.; $28.00
CRISPR is the basis of a genome editing technology--the latest breakthrough in the grand tradition that began over 400 generations ago when we started to grow wheat and rice instead of just picking its wild cousins. We bred cattle for milk and meat, horses and oxen for labor, and dogs because they were useful, and anyway we liked them. We graduated from the banks of the Euphrates to Luther Burbank's 800+ strains and varieties of plants. We didn't understand the process but we did know enough to make a good thing better by selective breeding.
In the past couple of centuries our understanding of how our planet works has increased exponentially. We now face a vast jungle of detailed knowledge, more than any individual can understand in its entirety. We have specialists who can understand portions of it, and people who can relate those parts to the whole, and a lot of other people who don't understand nearly as much as they need to. Meanwhile there are many experts in well-funded labs addressing parts of big and complex problems.
One benefit from all this recent growth is that science has been able to probe the inner workings of many mysteries that had eluded individual geniuses in earlier times. We've graduated again, this time from Luther Burbank to molecular physics and the nature of life itself.
In this new environment, discovery has many parents. Jennifer Doudna, a professor of chemistry and of molecular and cell biology at UC Berkeley, came up through a rigorously selective process to work first in someone else's lab, then in one where she was the boss. She didn't discover CRISPR, nor does she say she did; she was just one of the people who led the charge.
The first half of her new book, written with Samuel Sternberg and titled, A Crack in Creation: Gene Editing and the Unthinkable Power to Control Evolution, describes the nature of that charge. It is too technical for the lay reader, at least this one. Just take the word CRISPR, an acronym, and spell it out: Clustered Regularly Interspaced Short Palindromic Repeats. See what I mean?

The book does try to explain why this isn't just gobbledygook, but Doudna's explanations require further explanations which you don't find until you look for them, and then those explanations often require further explanation. I gave up at one point and rattled off my own stream-of-consciousness translation, which I offer here as a substitute for those too lazy to opt for a more authentic explanation of why CRISPR is important. Here goes:
Think double helix, and DNA. Think a typewriter that lets you erase or replace or insert DNA's "letters" one at a time almost, or at least in small groups. The genome has many letters, so each one is small. The best we've been able to do so far, when we want to get rid of bad DNA, is delete chunks of the letters--ponds not droplets. That's okay if we don't care about the stuff in the rest of the pond that came out with what we wanted to delete, but some of that may also be for something, and are there unforeseen consequences? And what if we're inserting a chunk, not deleting, do we care what else in that chunk we are adding? Same thing. Yes, being accurate and specific and limited in what we change is important. And that, dear reader, is the point, the main point, about CRISPR. It's not only easy to use, it's about as precise as a typewriter, or will be once it's been perfected. We have a tool that is an automobile compared to the horse and buggy we used to have.
If that explanation doesn't satisfy you, tackle the first part of the book. You'll not only have the full monty by way of explanation, you'll also have a front row seat for what it means to be a class-A researcher with your own lab and all the personnel and other problems that entails. The rest of us can proceed to the second and final section, which also gets into some pretty complicated details but is focused more on the implications of this new tool, especially how we may decide to use it.
Doudna sets the stage for the "What Is It For" section with this:
CRISPR gives us the power to
radically and irreversibly alter
the biosphere that we inhabit by
providing a way to rewrite the very
molecules of life any way we wish ...
At the moment, I don't think there
is nearly enough discussion of the
possibilities it presents--for good,
but also for ill.
The key issue here is whether CRISPR should be used to alter the germline of human beings in ways that make the changes heritable. Are we going to alter the genetic code for our own species and create a population that will, for all time, be resistant to diseases that are otherwise incurable? Do we go on from there to "cure" features that we now consider undesirable? Make less intelligent people smarter?
We can use CRISPR to treat difficult diseases without making the immunity hereditary, of course, and a lot of that is already happening. To make the changes hereditary one has to make them in the embryo, before it completes the process of defining the code that will govern the formation of the new individual. If only one parent has a cell for Tay-Sachs, for example, and you knock it out, you eliminate the 50-percent possibility that the child will carry the disease. That would have been a sure thing in the unlikely event both parents have the same defective "letter" in their codes. And you can be pretty certain that that child, if it undergoes CRISPR, will never either have the disease, or carry it as a latent gene. As far as your bloodline is concerned, your action has eliminated the errant gene and rendered Tay-Sachs extinct.
No issue, you say, do it. But what if that recessive gene is valuable and you hope someday to produce a Wolfgang Amadeus Mozart or an Albert Einstein? Or, more likely, what if the world is arranged into two camps, with opposing views on this kind of issue? Who decides?
This question of who decides is going to surface from time to time over CRISPR-related issues. For the time being humanity may squeak by, by referring key decisions to some expert body, and that is probably the most we can accomplish until the world gets better at self-governance.
Another ethical issue might arise when some CRISPR-related action is proposed that either renders an existing species extinct or introduces a new one. There may be arguments based on specific gains or losses to human groups, but a larger issue might arise that could potentially affect all humanity. If we eliminate all mosquitoes wouldn't we all benefit? Or would we, by eliminating an important food source for other species, set up a chain reaction that could prove costly? Again, this problem shouldn't be resolved on a narrowly construed, cost-benefit basis but by a consensus including people with a broad understanding of the possible environmental consequences.
Doudna and Sternberg describe the use of animals in their laboratory and others. Mice are preferred to monkeys because they are more readily available, cheaper, and breed faster. Doudna wasn't concerned with possible animal rights, and whether they attached more to monkeys, but others could be. This is a possible issue for humanists in the broader CRISPR context.
The least sensitive issues are already in the hands of patent lawyers and merchandisers. Doudna gives some amusing examples, like the Chinese firm that developed a dwarf pig that proved so amusing it was sold not for sausages but as a pet. It follows that there are different kinds of CRISPR issues, and a one-size-fits-all solution for settling them won't suffice. A Crack in Creation gives plenty of examples.
Judging from Doudna and Sternberg's book (brand new as it was only released earlier this year), the question of "Who controls CRISPR?" is very much up for grabs. In 2015 Doudna and some colleagues met in the San Francisco Bay Area and produced a paper that was published in Science on March 19, 2015, titled "A Prudent Path Forward for Genomic Engineering and Germline Gene Modification." She lists four recommendations in the article, which strike me as a useful summation of where we stand at this moment on the whole CRISPR issue:
First, create forums to advise the public on both the scientific and the ethical issues involved;
Second, continue testing and developing the CRISPR model;
Third, convoke an international meeting to discuss relevant safety and ethical implications; and
Fourth, all scientists should refrain, for the time being, from "attempting to make heritable changes in the human genome."
The last was the key. Let's all hit the pause button on human germline changes until further notice. But will such a prohibition stick?
That's where we stand right now. Is this an issue that concerns humanists? Of course, we are centrally concerned about the future of humanity and this germline issue goes right to the heart thereof.
Doudna expresses concern about the gap in understanding between the scientific community and the public. I agree. Can we do more to close that gap? On this issue, perhaps. Let's try.
Predictably, the question of who controls CRISPR will soon be seen as a critical issue important to all humanity, comparable to climate change and the threat of nuclear war. Like the other two, it cannot, or at least will not, be settled by the United Nations as long as the UN remains subject to the vetoes of the more powerful states. Could this issue eventually provide the straw that breaks the camels back and persuades the big countries to surrender some of their precious sovereignty on the really big issues? Probably not, but it's too early to be certain.
Carl Coon, former US ambassador to Nepal, is the author of Culture Wars and the Global Village; One Planet, One People: Beyond "Us versus Them"; and A Short History of Evolution. In 2013 he received the Lifetime Achievement Award from the American Humanist Association.
Source Citation (MLA 8th Edition)
Coon, Carl. "A Crack in Creation: Gene Editing and the Unthinkable Power to Control Evolution." The Humanist, Nov.-Dec. 2017, p. 42+. General OneFile, http://link.galegroup.com/apps/doc/A515578944/ITOF?u=schlager&sid=ITOF&xid=66b7e51d. Accessed 10 Dec. 2017.

Gale Document Number: GALE|A515578944

Doudna, Jennifer A.: A CRACK IN CREATION

(Apr. 1, 2017):
Copyright: COPYRIGHT 2017 Kirkus Media LLC
http://www.kirkusreviews.com/
Doudna, Jennifer A. A CRACK IN CREATION Houghton Mifflin Harcourt (Adult Nonfiction) $28.00 6, 13 ISBN: 978-0-544-71694-0
A pair of biochemists offer a fresh examination of the "newest and arguably most effective genetic-engineering tool."Biological spectaculars--e.g., genetic engineering, cloned sheep, in vitro fertilization--have produced headlines and bestsellers but flopped where it counts: they don't save many lives. CRISPR (clustered regularly interspaced short palindromic repeats) is changing that, write Doudna (Chemistry and Molecular Biology/Univ. of California; co-author: Molecular Biology: Principles and Practice, 2011, etc.) and Sternberg in this enthusiastic and definitely not dumbed-down account of gene manipulation that, unlike earlier methods, is precise and easy. In the first half of the book, "The Tool," the authors summarize a century of research but focus on the discovery, in the early 2000s, that bacteria possess an ingenious immune system that destroys invading viruses by cutting their DNA into pieces. Within the past decade, researchers converted this into an ingenious technique for literally debugging DNA: putting in good genes in the place of bad. "Because CRISPR allows precise and relatively straightforward DNA editing," write the authors, "it has transformed every genetic disease--at least, every disease for which we know the underlying mutation--into a potentially treatable target." The second half, "The Task," describes the miraculous powers of CRISPR to cure disease and control evolution--but not yet. Replacing a single defective gene cures muscular dystrophy in mice; clinical trials in humans for this and similar disorders (sickle-cell, hemophilia, cystic fibrosis) are in the works. CRISPR can't yet cure cancer, prevent AIDS, wipe out malaria, revive the wooly mammoth, or regenerate a limb, but an avalanche of startups (Doudna's included) is betting billions that it eventually will. An important book about a major scientific advance but not for the faint of heart. Readers not up to speed on high school biology should prepare themselves with a good popular primer on DNA, such as Matthew Cobb's Life's Greatest Secret (2015).
Source Citation (MLA 8th Edition)
"Doudna, Jennifer A.: A CRACK IN CREATION." Kirkus Reviews, 1 Apr. 2017. General OneFile, http://link.galegroup.com/apps/doc/A487668584/ITOF?u=schlager&sid=ITOF&xid=c25322c9. Accessed 10 Dec. 2017.

Gale Document Number: GALE|A487668584

A Crack in Creation: Gene Editing and the Unthinkable Power to Control Evolution

264.15 (Apr. 10, 2017): p62+.
Copyright: COPYRIGHT 2017 PWxyz, LLC
http://www.publishersweekly.com/
A Crack in Creation:
Gene Editing and the Unthinkable
Power to Control Evolution
Jennifer A. Doudna and Samuel H. Sternberg. HMH, $28 (320p) ISBN 978-0-544-71694-0
Doudna, professor of biology at UC-Berkeley, and Sternberg, her former graduate student and current collaborator, explain the basics of the potentially revolutionary CRISPR technology, the events leading up to Doudna's discovery of that technology, and the ethical dilemmas posed by the newfound ability to alter any living being's genetic composition. The authors describe the biological mechanisms in a way that nonspecialists can appreciate, though the simplistic diagrams scattered throughout add little to the text. They also enthusiastically survey many of the uses to which CRISPR technology has already been applied, noting the great interest by venture capitalists who have already invested well over $1 billion in this technology. Doudna and Sternberg make a clear distinction between manipulating reproductive and non-reproductive cells, since the former can cause permanent evolutionary shifts. The second half of the book delves into the ethical implications arising from this difference, thoughtfully covering effects on both human and non-human species. Though the authors note that science involves both "competition and collaboration," they avoid discussion of the myriad conflicts that exist in this exciting new field---an absence that makes the rosy picture presented in this otherwise excellent book just a bit too unbelievable. Illus. Agent: Max Brockman, Brockman Inc. (June)
Source Citation (MLA 8th Edition)
"A Crack in Creation: Gene Editing and the Unthinkable Power to Control Evolution." Publishers Weekly, 10 Apr. 2017, p. 62+. General OneFile, http://link.galegroup.com/apps/doc/A490319293/ITOF?u=schlager&sid=ITOF&xid=f594d7cc. Accessed 10 Dec. 2017.

Gale Document Number: GALE|A490319293

Book World: New gene editing tool could cure disease. Or customize kids. Or aid bioterrorism

Jerry A. Coyne
(June 29, 2017): News:
Copyright: COPYRIGHT 2017 The Washington Post
http://www.washingtonpost.com/
Byline: Jerry A. Coyne
A Crack in Creation: Gene Editing and the Unthinkable Power to Control Evolution
By Jennifer A. Doudna and Samuel H. Sternberg
Houghton Mifflin Harcourt. 281 pp. $28
---
Some of the greatest benefactors of our species are not the recognized do-gooders but those paid to satisfy their curiosity: the scientists. Such pure and unsullied inquiry has yielded thousands of valuable byproducts, including antibiotics, vaccinations, X-rays and insulin therapy.
Jennifer Doudna and Samuel Sternberg's "A Crack in Creation" describes another fortuitous discovery, a method that promises to revolutionize biotechnology by allowing us to change nearly any gene in any way in any species. The method is called CRISPR, pronounced like the useless compartment in your fridge. In terms of scientific impact, CRISPR is right up there beside the double helix (1953); the ability, developed in the 1970s, to determine the sequence of DNA segments; and the polymerase chain reaction, a 1980s invention that allows us to amplify specified sections of DNA. All three achievements were recognized with Nobel Prizes. CRISPR - developed largely by Doudna and her French colleague Emmanuelle Charpentier - also has a strong whiff of Nobel about it, for its medical and practical implications are immense.
The story of CRISPR is told with refreshing first-person directness in this book. (Sternberg was Doudna's student, but the book uses Doudna's voice.) It is not often in science writing that the actual discoverer puts pen to paper - rather, the story is usually told by a science writer or colleague - so this insider account is especially engaging.
CRISPR, an acronym for "clustered regularly interspaced short palindromic repeats,"is a way to edit DNA. With CRISPR, we can change a sequence from ATTGGCG to ATTGGGG or to CCCCCCC, or to anything else. There are other recently developed ways to do this, but they are uniformly unwieldy, time-consuming and inefficient. The joy of CRISPR is that it allows us to edit genes painlessly: It is easily applied and seems to work well in whatever species or cell type we choose.
The history of CRISPR is a prime example of the unexpected benefits of pure research, for it began with a handful of curious scientists not intent on changing the world. In the late 1980s, scientists observed a bizarre section of DNA in some bacteria, consisting of short, identical and repeated "palindromic" sequences that read the same way backward and forward (e.g., CATGTTGTAC). The repeated palindromes were separated by 20-letter segments of unique DNA, segments eventually found to come from viruses that infect bacteria. People soon realized that the CRISPR region was the bacterium's immune system against dangerous viruses.
CRISPR helps bacteria "remember" previous viral attacks and thus prepares them for future attacks by the same virus. This is analogous to our immune system, which also "remembers" intruders: If you have had measles once, you won't get it again because the first exposure preps the immune system for subsequent exposures. The way bacteria do this is by storing a segment of the virus's DNA from the first attack. When the same kind of virus strikes again, the bacterium recognizes that the alien DNA segment has reappeared by matching the stored segment to the intruder DNA. Having identified the intruder as a bad guy, the bacterium can snip up, i.e. destroy, the intruder's DNA, guided by the same stored-DNA/intruder-DNA match.
Doudna and Charpentier realized that it was possible to subvert the CRISPR system: Instead of viral intruder DNA, we can use the DNA sequence we're interested in (say, one causing a genetic disease), with the result that CRISPR snips up any and all DNA molecules with the target sequence. Once DNA is snipped up, there are ways to repair it using a different sequence, including a version of the gene that does not produce disease. Presto: gene editing and a path to designer genes.
Rewriting genes has the potential to cure many genetic illnesses. People suffering from sickle-cell disease, for instance, have just a single mutated "letter" in the DNA coding for their hemoglobin. It shouldn't be hard for CRISPR to replace that letter in embryos or bone marrow, curing the millions who suffer from this devastating malady.
But that's just one of myriad possible edits. CRISPR can in principle cure any disease caused by one or a few mutations: not just sickle-cell but Huntington's disease, cystic fibrosis, muscular dystrophy or color blindness. We could cure AIDS patients by editing out the HIV viruses that hide in their DNA. By editing early embryos, we could reduce the incidence of genetically influenced diseases such as Alzheimer's and some types of breast cancer. We could make cosmetic changes in our children, altering their hair and eye color or even, in principle, their height, weight, body shape and intelligence. None of this has been tried in people, but since CRISPR works well in human cell cultures, it seems just a matter of time.
Turning to other species, we could genetically engineer either pigs or people so we could transplant pig organs into humans without activating our immune response. We've used CRISPR to make virus-resistant farm animals, and we can now engineer insecticide-making genes into the DNA of crops, eliminating the need for dangerous sprays. As the book title implies, CRISPR allows us to bypass or undo evolution without relying on the hit-or-miss methods of selective breeding.
But of course DNA editing also raises ethical issues, and these occupy the final quarter of the book. Doudna worries about the return of Nazi-style eugenics and even had a dream about Hitler asking her for CRISPR technology. Should we engage only in "somatic" gene editing: changing genes in affected tissues where they can't be passed on to the next generation? Or should we also do "germline" editing, changing early embryos in a way that could be transmitted to future generations? While that conjures up the bad old days of eugenics, it is in fact the only way to repair most "disease genes." But if we do that, should we stick to fixing genes that would debilitate the offspring, as with sickle-cell disease, or should we also change genes that merely raise the possibility of illness: those that could produce high cholesterol or heart disease?
Things get even more slippery. Should we edit the embryos of deaf parents to produce deaf offspring, so that their children can participate in "deaf culture"? And - the ultimate taboo - genetic enhancement: Should we give our children a leg up in looks or intelligence? That, after all, will provide genetic advantages only to those who can afford the technology.
Finally, how do we keep the technology out of the hands of bioterrorists? Cheap and simple CRISPR kits are now sold on the Internet, allowing anyone to edit the genes of bacteria. The nightmarish prospect of engineered diseases looms. While it's good to consider all these questions before the technology is widely available, Doudna and Sternberg come to few conclusions, and their extended vacillating is the book's sole flaw.
Alongside the ethical quandaries come commercial ones. There is a great deal of money to be made through the licensing of CRISPR technology. We have already seen a protracted patent battle between Doudna's employer, the University of California, and Harvard/MIT's Broad Institute, home to Feng Zhang, who was largely responsible for converting CRISPR from a device for editing bacterial genes into a lab-friendly tool that works in human cells. There is a lot at stake.
And this brings us an issue conspicuously missing from the book. Much of the research on CRISPR, including Doudna's and Zhang's, was funded by the federal government - the American taxpayer. Yet both scientists have started biotechnology companies that have the potential to make them and their universities fabulously wealthy from licensing CRISPR for use in medicine and beyond. So if we value ethics, transparency and the democratization of CRISPR technology, as do Doudna and Sternberg, let us also consider the ethics of scientists enriching themselves on the taxpayer's dime. The fight over patents and credit impedes the free exchange among scientists that promotes progress, and companies created from taxpayer-funded research make us pay twice to use their products.
Finally, let us remember that it was not so long ago that university scientists refused to enrich themselves in this way, freely giving discoveries such as X-rays, the polio vaccine and the Internet to the public. The satisfaction of scientific curiosity should be its primary reward.
---
Coyne is professor emeritus in the department of ecology and evolution at the University of Chicago. He is the author of "Why Evolution Is True" and "Faith vs. Fact: Why Science and Religion Are Incompatible."
Source Citation (MLA 8th Edition)
Coyne, Jerry A. "Book World: New gene editing tool could cure disease. Or customize kids. Or aid bioterrorism." Washington Post, 29 June 2017. General OneFile, http://link.galegroup.com/apps/doc/A497356286/ITOF?u=schlager&sid=ITOF&xid=91ac0c14. Accessed 10 Dec. 2017.

Gale Document Number: GALE|A497356286

Coon, Carl. "A Crack in Creation: Gene Editing and the Unthinkable Power to Control Evolution." The Humanist, Nov.-Dec. 2017, p. 42+. General OneFile, http://link.galegroup.com/apps/doc/A515578944/ITOF?u=schlager&sid=ITOF&xid=66b7e51d. Accessed 10 Dec. 2017. "Doudna, Jennifer A.: A CRACK IN CREATION." Kirkus Reviews, 1 Apr. 2017. General OneFile, http://link.galegroup.com/apps/doc/A487668584/ITOF?u=schlager&sid=ITOF&xid=c25322c9. Accessed 10 Dec. 2017. "A Crack in Creation: Gene Editing and the Unthinkable Power to Control Evolution." Publishers Weekly, 10 Apr. 2017, p. 62+. General OneFile, http://link.galegroup.com/apps/doc/A490319293/ITOF?u=schlager&sid=ITOF&xid=f594d7cc. Accessed 10 Dec. 2017. Coyne, Jerry A. "Book World: New gene editing tool could cure disease. Or customize kids. Or aid bioterrorism." Washington Post, 29 June 2017. General OneFile, http://link.galegroup.com/apps/doc/A497356286/ITOF?u=schlager&sid=ITOF&xid=91ac0c14. Accessed 10 Dec. 2017.

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