EXECUTIVE SUMMARY
SCIENCE SNAPSHOTS a quick summary of 10 genetics and biotech stories
Now more than ever, there is a critical need to communi- cate the meaning of these scientific findings – using under- standable language that doesn’t stray beyond the boundar- ies of what the data can tell us. Around the world, science educators have stepped into this gap, going beyond the headlines to separate fact from fear. That same goal drove the creation of HudsonAlpha’s Shareable Science Beyond the Blog: a continuously updated library of short videos explaining recent COVID-19 results. These straightforward mini-lessons are at hudsonalpha.org/beyond-the-blog. In spite of the pandemic, scientific research continues to break new ground in agriculture, human health and other bioscience fields. This year’s guidebook brings together 45 of those discoveries, ranging from the production of dairy-identical proteins through fermentation to a gene editing breakthrough that treats thalassemia and sickle cell anemia. An infographic on pandemics rounds out the content. Each story includes a link to the original research article or data source, to give learners first-hand access to the science. For additional background and context, look to our online Biotech Basics series at hudsonalpha.org/biotech-basics . Twenty-four foundational topics provide an introduction to key genomic and bioscience concepts and technologies. For educators, we’ve also included the Alabama Course of Study Alignment Guide , linking the foundational stories to high school life science and career and technical education coursework.
The laboratories of HudsonAlpha faculty researchers Jane Grimwood, PhD, and Jeremy Schmutz contributed to this work. The genome of Cryphonectria parasitica , the fungus that causes chestnut blight, was recently sequenced. Researchers hope to identify key clues within the genome to uncover the mechanisms that allow this pathogen to destroy chestnut trees. 1. First identified in 1903, chestnut blight resulted in the destruction of an estimated four billion mature American chestnut trees over the following half century.
6. The All of Us research initiative seeks to build a diverse human database with more than 1 million Americans.
chestnuts
The laboratory of HudsonAlpha faculty researcher Shawn Levy, PhD, is testing technologies associated with long-read sequencing for the All of Us initiative. from their electronic medical records and donating samples for genetic testing. Half of the participants are from racial or ethnic minority groups. The initial set of data are available for study through the All of Us Researcher Workbench , currently in beta testing. More than 350,000 have enrolled since the program began in mid 2018 — completing surveys, sharing data
2. Scientists have created a comprehensive catalog of all the known genomes of bacteria living inside our digestive system. The freely accessible Unified Human Gastrointestinal Genome Collection includes over 200,000 genomes frommore than 4,600 bacterial species. The research team developed a companion catalog of over 170 million proteins produced by these bacteria. The specific activity of more than 70% of the gut bacteria in this collection remains unknown. 3. CAR T therapy genetically engineers a subset of a patient’s T cells (a specialized immune cell) to recognize a protein on the surface of cancer cells and coordinate their destruc- tion. This form of immunotherapy has experimentally treated a number of different cancers, but has been less effective in treating glioblastoma, an aggressive 4. While there are over 2,000 known mutations in the CFTR gene that are associated with cystic fibrosis, the most common is F508del which deletes the genetic code for the amino acid phenylala- nine at the 508th position in the protein. At least 90% of patients with cystic fibrosis carry one or more F508del mutations. The U.S. Food and Drug Administration recently approved Trikafta ® , a combination of three drugs that target faulty CFTR proteins caused by mutations like F508del. Trikafta helps the damaged protein fold correctly. It also increases the flow of chloride molecules through the protein channel. The protein operates more effectively, improving lung function for patients. The drug is priced at $311,000 per year, but is covered by some insurers. form of brain cancer. A recent tweak to the process incorporates a protein found in scorpion venom. This allows the engineered T-cells to lock on to more glioblastoma cells without attacking the surrounding normal cells. Clinical trials are now underway. 5. Forensic genetic genealogy is a popular new tool to uncover clues in criminal cold cases as well as more recent crimes. The approach scans public databases to identify families with a potential connection to DNA samples recovered from crime scenes. The branches of those family trees are then searched in hopes of finding a suspect. The U.S. Department of Justice has developed an interim policy for genetic genealogy in response to privacy concerns raised among ethicists and legal experts. The approach is limited to violent crimes or unidentified human remains where no match is found in the existing FBI genetic database. The policy went into effect in November 2019 with final guidance to follow.
7. The Encyclopedia of DNA Elements (ENCODE) Project is a worldwide effort to understand how the human genome functions. For nearly two decades, researchers have been developing a map of the millions of DNA switches that regulate when and where genes are turned on and off. Findings from the most recent phase of ENCODE were described in over a dozen papers coordinated for simultane- ous publication. Six thousand additional datasets were generated from 500 cell and tissue samples. Nearly one million new regulatory regions were identified in the human genome, along with nearly 340,000 similar regions in mice.
Neil Lamb, PhD
It’s a supreme understatement to say that 2020 has been eventful. In particular, the COVID-19 pandemic has taken a staggering economic, educational and emotional toll. Activities that traditionally brought people together became potential pathways for infection. Seemingly overnight, physical distancing and learning from home became the standard for millions of households. Around the globe, the pandemic quickly mobilized the scientific and technological workforce in new directions, diving deeper into the fields of biology, immunology and in- fectious disease. Researchers, clinicians and data analysts set aside their usual responsibilities and dedicated them- selves to learning as much as possible about COVID-19 and the SARS-CoV-2 virus. Entrepreneurs, innovators and manufacturers applied those findings to developing tools for improved testing, treatment and prevention. The process of scientific discovery has been on full display. Students are discovering that “The Scientific Method” is nothing like those six easy steps listed in their textbook. The data is messy, contradictory at times, and certainly not resolved by a single experiment.
The laboratory of HudsonAlpha faculty researcher Richard M. Myers, PhD, contributed to this research.
8. Historically, researchers have developed and utilized a single “reference genome” for an individ- ual species, e.g., the Human Genome Project. While beneficial, these references are limited in their ability to capture the variety of DNA sequences present within a population. Scientists have begun developing a multi- genome human reference that is as universal and complete as possible, representing 350 human genomes and known as a “pan-genome.” They estimate that a full human pan-genome may include as many as forty million bases of DNA missing from the current reference. 9. Approximately 10% of the human population is left handed. Prior studies have suggested there is a genetic component to hand- edness, but the specific genes have remained elusive. Analyzing the genomes of approximately 400,000 individuals, including 38,332 “lefties,” identified four DNA regions associated
Neil E. Lamb, PhD Vice President for
Educational Outreach HudsonAlpha Institute for Biotechnology email: nlamb @ hudsonalpha.org twitter: @ neillamb
with left-handedness. The strongest association is located in a gene associated with brain development and patterning. 10. An epigenetics study on aging throws doubt on the saying that one year of a dog’s life is equivalent to seven human years. Patterns of DNA methylation
were compared between 104 Labradors and 320 humans across a range of ages. Changes in DNA
This year’s Guidebook would not have been possible without the dedicated efforts of my colleagues at HudsonAlpha. This includes science writer Sarah Sharman as well as layout and design expert Cathleen Shaw. Special thanks go to April Reis, Jennifer Carden, Jennifer Hutchison, Madelene Loftin and Dasi Price, who served as advisors and reviewers throughout the Guidebook ’s development. I’m humbled and grateful to work with such a talented group of individuals.
methylation occur predictably over time and are one way to measure aging. Dogs and humans showed changes in similar sets of developmental genes. Compared to humans, the process occurs more quickly in young dogs but slows as they get older.
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SCIENCE FOR LIFE
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