It’s Almost iGEM Season—Help Is On The Way!

The 2019 iGEM Competition is on the horizon and team registration opens this month. We’re excited to partner with the iGEM Foundation again this year and offer our support to the young scientists who participate. If you’re starting an iGEM project, there are going to be things you need along the way. We are pleased to share a number of different ways we can help your iGEM team from now until the Giant Jamboree.

Grant Sponsorship

Tell us about your iGEM project and your team could win a 2019 Promega iGEM Grant Sponsorship. Ten winning teams will each receive $2000 in free Promega products to use for their iGEM projects. Tell us about your project—What problem are you addressing? What is your proposed solution? What challenges does your team face? Last year’s winning teams selected from a wide range of reagents and supplies, including master mix, restriction enzymes, ligase, DNA purification kits, expression systems, DNA ladders and markers, buffers and agarose. Click here to apply! Continue reading “It’s Almost iGEM Season—Help Is On The Way!”

Extra extra: Read All About Tautonyms

If you’re active on #sciencetwitter, you may have seen a thread recently about tautonyms. “Tautonym” is a cool word for scientific names where the genus and species are the same word, For example, Vulpes vulpes is the scientific name for the red fox.

I have taken great delight in sharing these tautonyms with friends, colleagues, and random strangers on the bus. However, the problem that I keep having is that people want more details about something than the name. If you’ve had that problem, too, then this blog is for you. Continue reading “Extra extra: Read All About Tautonyms”

Goodbye to the Most Famous Bird in Maine

When Wisconsin plunged into a deep freeze during last week’s polar vortex, I built a roaring fire in my fireplace and settled into my armchair with a thick blanket and a video game controller. Except for the twenty minutes I spent driving to and from the office, I stayed warm and toasty.

Birds, however, don’t have it quite as easy. To survive freezing temperatures, non-migratory birds have developed many interesting adaptations. Many species grow extra down layers and huddle together for wind protection. Others, like the black-capped chickadee, use a process called regulated hypothermia to drop their resting body temperature by as much as 22°F to conserve energy. I’m particularly fascinated by the process of regional hypothermia—many species of ducks and gulls use a countercurrent heat exchange system to keep vital organs warm while letting temperatures fall in extremities.

Birds that aren’t accustomed to cold weather don’t have these adaptations, though. When a bird—or any animal—ends up far outside of its natural habitat, the consequences can be deadly.

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Meet Měnglà Virus: the newest cousin in the Ebola and Marburg virus family tree

Ebola virus (EBOV) and Marburg virus (MARV) are two closely-related viruses in the family Filoviridae. Filoviruses are often pathogenic, causing hemorrhagic fever disease in human hosts. The Ebola outbreak of 2014 caught the world by surprise by spreading so quickly and severely that public health organizations were unprepared. The devastating outcome was a total of over 11,000 deaths by the time the outbreak ended in 2016. Research that provides further understanding of filoviruses and their potential for transmission is important in preventing future outbreaks from occurring. But what if the outbreak comes from a virus we’ve never seen before?

fruit_bat
Měnglà virus was discovered among filoviruses isolated from Old World fruit bats (Rousettus)

All in the viral family

A recent study published in the journal Nature Microbiology provides evidence of a newly identified filovirus species. Using serum samples taken from bats, a well-known host for filoviruses, Yang et al. isolated and identified viral RNA for an unclassified viral genome sequence using next generation sequencing analysis. This new virus genome sequence was organized with the same open reading frames as other filoviruses, encoding for nucleoprotein (NP), viral protein 35 (VP35), VP40, glycoprotein (GP), VP30, VP24, and RNA-dependent RNA polymerase (L). This new genome sequence shared up to 54% of the nucleotide sequences for the filovirus species Lloviu virus (LLOV), EBOV and MARV, with MARV being the most similar. Their analysis suggested that this novel virus should be classified within the Filoviridae family tree as a separate genus, Dianlovirus, and was named Měnglà virus (MLAV).

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Twisted CRISPR: A Novel Activation Strategy to Treat Genetically Driven Obesity

Two Is Better Than One

Obese and normal mouse

Redundancy equips us to survive. We have more than one lung or one kidney for a reason—if one organ in a pair gets damaged, we can still manage if the other is functional. At the cellular level, we have two copies of each chromosome in every non-germline cell. Each copy was inherited originally from a single sperm and ovum, which are “haploid” cells. Consequently, there are two copies of any given gene in non-germline “diploid” cells. In many cases, should one copy of a gene be damaged, the cell can still survive with the other, functional copy of a gene. In plants, this redundancy is common, and many plants exhibit polyploidy. In an extreme example of polyploidy, the large (by bacterial standards) but otherwise unassuming species Epulopiscium contains tens of thousands of copies of its genome.

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Microsatellite Instability Symposium at Duke University

On January 23, doctors, scientists and researchers will gather for a symposium about Microsatellite Instability (MSI) at Duke University. During the one-day event, scientists from Duke University and The Ohio State University will share insight into their research on biomarkers, MSI status and GI cancer, Lynch Syndrome, and MSI and DNA mismatch repair deficiency (dMMR).

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Combatting Gun Violence with Synthetic Biology

Imagine you are a high school student living in a community devastated by gun violence and death. In the U.S., this could be one of many communities, but it happens to be Baltimore which had 301 deaths due to gun violence in 2017 (with a per capita rate well above other large cities). Then imagine you were part of an organization within that community that helped you, along with other students, gain knowledge and skills to come up with a viable solution to the problem using synthetic biology.

Baltimore Bio-Crew at the 2018 iGEM Giant Jamboree

This is exactly how the Baltimore Bio-Crew came up with their iGEM project, Coagulance Rx. The Baltimore Bio-Crew decided to tackle this community issue head-on. One team member, Mercedes Ferandes, reflected, “Living in Baltimore City, I have not only witnessed gun violence in front of me, but have had family members and friends die from it. I wanted to try to decrease the amount of deaths by gun violence using iGEM.”

After some research, they discovered that many of the gun deaths were due to blood loss and could have been prevented. The impoverished neighborhoods where this violence occurs lack the resources to provide timely emergency medical treatment. Many of these deaths can be attributed to delayed arrival of emergency response teams—wait times for an ambulance can be over an hour.

Although there were several contributing factors beyond their control, the team wanted to address this problem by focusing on blood clotting and how it could be helpful as a quick temporary treatment for open wounds. This solution could offer a reliable, cost efficient way to save lives by slowing or stopping blood loss until a victim could get medical attention. The team decided to pursue the use of snake venom after coming across some previous iGEM projects that had used it for clotting. Team member Henry Ryles pointed out that the need for snake venom powerful enough to clot blood quickly led them to choose the venom of the Russell’s Viper
(Daboia russelii).

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A Roadmap for PROTAC Development

PROTACs or Proteolysis-Targeting Chimeras are an emerging tool in protein degradation studies, potentially suited to any need involving the removal of a specific protein. These small-molecule chimeras are exciting due to: 1) their target specificity; and 2) their ability to enable target destruction versus target inhibition.

Destruction/Inhibition: Is There a Difference?
An analogy that microbiologists (and wrestlers or anyone that has ever spent time in a locker room shower) would understand, is fungicidal versus fungistatic compounds. A fungicidal compound kills fungus. A fungistatic compound just slows the fungus down a bit.

A small-molecule inhibitor attaches to its target protein, but for how long? What inhibitor testing must be done to determine how long the inhibition lasts?

On the other hand, a small-molecule agent that causes protein degradation first targets the protein of interest, then attaches ubiquitin to that target. Once a protein is marked with ubiquitin, it’s a dead man. E3 ligase must be involved, but if the ubiquitin is added by E3, the end is near. Next stop, Hades.

This ubiquitinated protein is headed to the proteasome and proteins that go there don’t come back. Ubiquitination was called the ‘molecular kiss of death’ when this discovery was awarded the Nobel prize in Chemistry in 2004.

PROTAC components: target protein ligand, E3 ligase and linker.

About PROTACs
PROTACs are degrader molecules composed of three parts: 1) a ligand that is specific for the target protein; 2) a ligand for E3 ligase; and 3) a linker molecule that connects the two ligands. The E3 ligase is one of three enzymes that can add ubiquitin to a cellular component, but only ubiquitins added by the E3 ligase cause targeting to the proteasome (Zoppi et al.).

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“We’re From NASA”: How Citizen Science Helped Find Ultima Thule

The science world is a-twitter with excitement lately, following the recent arrival of the New Horizons spacecraft at 2014 MU69, dubbed “Ultima Thule” by popular vote. The name means “beyond the borders of the known world”, signifying Ultima Thule’s status as the most distant object ever visited by Earthly spacecraft. Ultima Thule is a dark reddish rock in the Kuiper belt, a contact binary formed by two smaller rocks coming together in what was presumably a gentle fashion.

Do you wanna build a snowman? Credit: NASA/Johns Hopkins University Applied Physics Laboratory/Southwest Research Institute

Reaching this space snowman 6.5 billion kilometers away from Earth took brains, dedication, ingenuity and the help of an unnamed Argentinian man and his daughter.

To successfully intercept Ultima Thule, the New Horizons mission team needed to answer some questions, such as “What trajectory is Ultima Thule on?” and “Is there any space debris around Ultima Thule that will destroy our spacecraft?” Being so small (~30km diameter at its widest point), observing Ultima Thule directly from this far away would be too difficult, so the team relied on data gathered during stellar occultations, i.e., when Ultima Thule passed in front of a star.

One of these occultations occurred on July 17, 2017, in the Patagonia region of Argentina. The team had already struck out twice in trying to observe Ultima Thule passing over a star: once in South Africa, and again using the airborne telescope SOFIA over the Pacific Ocean, so tension was already running high.

On this particular night, it happened to be very windy where the observation team was, which is bad news when you’re trying to hold steady focus on a tiny object that’s really far away. The team found themselves needing help to shield the telescopes they had brought with them from wind vibrations, and get the data from the star “without it jiggling around all over the place”, as planetary scientist Anne Verbiscer puts it.

Where does one find volunteers for an astronomical observation? Well, apparently even in Argentina NASA is known and loved, and help can be found just by walking into the community. “If you just started out with ‘We’re from NASA,’ people started coming out of the woodwork,” said Dr. Verbiscer. And that is how one Argentinian man and his daughter ended up spending their evening blocking the wind from a telescope using a truck, a tarp and some plywood, allowing the NASA folks to collect the data they needed to send New Horizons to Ultima Thule.

Want to learn more about the search for Ultima Thule? Check out the episode of NOVA that inspired this blog!

2019: International Year of the Periodic Table

Periodic table of the elements

From the inside covers of elementary science textbooks to the walls of chemistry labs all around the world, the periodic table is one of the most pivotal and enduring tools of modern science. To honor the 150th anniversary of its discovery, the United Nations General Assembly and UNESCO have declared 2019 to be the International Year of the Periodic Table of Chemical Elements.

As with all scientific progress, Dmitri Mendeleev’s periodic table was the result of decades—centuries, even—of research performed by scientists all over the world. Aristotle first theorized the existence of basic building blocks of matter over 2,500 years ago, which later were believed to be earth, air, fire and water. Alchemist Hennig Brand is credited with discovering phosphorus in the late 17th century, sparking chemists to begin pursuing these basic atomic elements.

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