CRISPR

Curiosity killed the cat, but it may help you get the Nobel prize

Anonymous — Fri, 17 Mar 2017 06:00:00 +0000

Curiosity killed the cat, but it may help you get the Nobel prize Anonymous (not verified) Fri, 03/17/2017 - 00:00

BioFrontiers Institute

I don't feel frightened by not knowing things, by being lost in a mysterious universe without having any purpose - which is the way it really is so far as I can tell - it does not frighten me.

–Richard Feynman, The Pleasure of Finding Things Out

Doctoral students have a lot of time on their hands. It may appear otherwise, but the unstructured nature of a graduate student’s life lends itself to exploring seemingly endless plains of fascinating information. I am a Materials Science and Engineering Ph.D. student working on developing molecular tools like CRISPR (Clustered Regularly-Interspaced Short Palindromic Repeats used for editing DNA) to make microorganisms that can convert sugar into plastics. And somehow, on a snowy day in early January, I found myself going down a rabbit hole of attention-grabbing references that led from CRISPR to molybdenum.

Here are just a few fascinating facts I learned from this search: Did you know that molybdenum, occupying position 42 in the periodic table, has the sixth-highest melting point of any element? And that one of the world’s largest molybdenum mines – the Henderson Mine – is located near Leadville, Colorado, and adjoins a 10-mile railroad tunnel that goes under the Continental Divide? Or that molybdenum is an essential cofactor for nitrogen fixation in plants and arsenic detoxification in the liver? That there are species of archaea – some of the most ancient organisms on our planet – that can survive at pH < 0 (think battery acid) and reproduce at 250° F? And that some archaea have flat square-shaped cells? Oh, and that thing that initially began my search? There are now over 16 different subtypes of CRISPR systems.

So, how did I get from CRISPR to molybdenum mining? Mere curiosity. It may appear like a form of procrastination, but I prefer to think of it as an “idea treasure hunt.” In the process of mental exploration, one thought leads to another through association. Sometimes they flow in a linear pattern, other times they branch, splay and explode into thousands of new connections, forming intricate webs of facts and concepts in our brains. Occasionally an idea might wormhole its way to a distant node in the network, generating a surprising product – or even a revolutionary discovery. The mind theorists call this process the “promiscuous combination of ideas,” and it has led many scientists to come up with new theories and unexpected solutions.

Richard Feynman had the spark for his Nobel Prize-winning idea when he saw a student throw a plate across the cafeteria. Initially, he set out to solve a classical mechanics problem, but ended up in the quantum physics realm: the calculations of the wobbling speed and rotation of the plate transformed into a theory of how electron orbits move in relativity. Of course, that flying dish alone did not inspire the Nobel Prize theory. It involved connecting the dots from a giant constellation of concepts and theories in his mind. In the words of Feynman, “then there's the Dirac equation in electrodynamics. And then quantum electrodynamics. And before I knew it…the whole business that I got the Nobel Prize for came from that piddling around with the wobbling plate.”

One could argue that it was his deep understanding of physical principles and intense concentration that led Feynman to formulate the theory. I bet at least part of it was that Feynman was a man with insatiable curiosity; he was curious about how dreams work, how smart ants are, Japanese culture, or whether jelly can set at a low temperature if continuously stirred. When something grabbed his attention – like the wobbling plate – he chased after it, regardless of whether it was an elusive physics problem or something trivial he simply wanted to know more about. On his curiosity-fueled hunt for interesting things, he acquired a wealth of information and the ability to effectively process it, which enables one to draw surprising connections between distant ideas.

The information age has created a kind of “meta-mind” where people can easily share their ideas and together contribute to solving advanced problems. Most of the scientific discoveries today come not from individual researchers, but from the combined efforts of many people working in a field. For example, initial observations of the effects of CRISPR occurred in the dairy industry, where deliberate exposure to bacterial viruses (phages) was used to protect bacterial cultures against future phage infections¹. A computer search for similar sequences found fragments of phage DNA in the curious spacer-repeat CRISPR patterns, so it was proposed to be the bacterial “immune system”. Later, other researchers realized that CRISPRs could be expressed in different organisms and harnessed to target specified DNA sequences. Thus, CRISPR editing technology emerged from the combined efforts of many different labs and is now being proposed for applications like modifying human embryos – a prospect almost as far removed from its original use for making yogurt as it is from molybdenum mining.

I doubt that any scientist could have single-handedly figured out the application of CRISPR technology for gene editing purposes. Advancements like that take the combinatorial powers of the collective scientific mind. However, smaller discoveries are happening in labs every day, and they also require connecting the dots between quite distant concepts. So, next time you catch yourself procrastinating by reading seemingly unrelated articles on the internet, or by watching ants going about their business, or throwing a Frisbee (while trying to calculate its rotation speed in the air) – don’t be so hard on yourself. After all, you may just stumble upon your Nobel Prize idea.

¹If you are curious, this source provides a great timeline of CRISPR discovery and development.

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BioFrontiers postdoctoral fellow first Coloradan to receive prestigious award

Anonymous — Thu, 12 Jan 2017 15:00:50 +0000

BioFrontiers postdoctoral fellow first Coloradan to receive prestigious award Anonymous (not verified) Thu, 01/12/2017 - 08:00

CUBT - CU Boulder Today

If an anti-aging regimen that involves telomeres – part of the human chromosome – sounds too good to be true, it probably is, says Jens Schmidt, a postdoctoral fellow in the Cech Lab at CU Boulder’s BioFrontiers Institute.

“There are all these products out there that say ‘hypercharge your telomeres!’ But if you do that in cells that are predisposed to turn into cancer cells you might be in trouble,” says Schmidt, who was just named the first Coloradan to win the prestigious Damon Runyan-Dale Frey Breakthrough Award for cancer research.

Telomeres are elongated caps at the ends of each of our 46 chromosomes which, like the tips of shoelaces, serve to protect our precious DNA from fraying. As telomeres shorten, cells wither and die, and we age. Consequently, telomere preservation – via everything from gene therapy to dietary supplements – has been broadly viewed as the modern-day Fountain of Youth. But Schmidt sees telomeres in a darker light. When preserved via a naturally-occurring enzyme called telomerase, they can also immortalize some cells that are meant to stop dividing and die. Left to proliferate, those cells can lead to cancer.

“Telomere maintenance is one of the few key things cancer needs to survive,” says Schmidt.

With a brand new baby at home, the 33-year-old, Berlin-born scientist aims to use the $100,000 award to further his groundbreaking research exploring precisely how the telomerase enzyme finds, attaches itself to and replenishes telomeres. Ultimately, he and others envision a new generation of targeted cancer drugs which would work by inhibiting that cell-preserving process in cancer cells, while sparing healthy ones (thus avoiding the hair loss and other side effects that cancer drugs can bring).

“Jens has made a significant contribution to the field of understanding telomerase, which has big potential to impact cancer treatment,” says Yung Lie, chief scientific officer for the Damon Runyan Cancer AV��ʪ Foundation. “He has a developed a very unique way of looking at this in a way that was not technologically possible before.”

To understand just how a telomerase enzyme replenishes a fraying chromosomal end, Schmidt first set out to learn how the two find each other in the relatively vast open space inside the cell. “It’s like if you have 10 buddies and you all go to a Broncos game and you scatter at the stadium,” he explains. “How are you going to find each other without cell phones? What are the chances you’ll just bump into each other? And if you do, how do you keep holding hands to make sure you don’t lose each other again?”

In August, Schmidt and his mentor Nobel laureate Thomas Cech coauthored a paper in the journal Cell which shed significant light on the process.

Schmidt developed a method using the CRISPR genome editing tool to attach fluorescent tags to telomerase enzymes and telomeres. Then he used a high-powered microscope to spy on their movements inside the nuclei of living human cancer cells. A resulting video shows telomerase zipping around the nuclei at a frenzied pace, bumping into telomere after telomere thousands of times before settling in on some, resting there for up to 8 minutes, then zipping away. Schmidt suspects the telomerase is adding DNA sequences as it rests there, elongating the telomere. With his next study, he hopes to find out for sure. “I want to understand this whole process in gory detail.”

Originally from Germany, Schmidt attended the Freie Universitat in Berlin before earning a doctorate in biology from the Massachusetts Institute of Technology and coming to CU Boulder to study with Cech under a postdoctoral fellowship sponsored by the Damon Runyon Cancer AV��ʪ Foundation. Of 27 fellows who applied for the Breakthrough Award, he was one of three recipients.

He notes that in some cases, as with the stem cells that yield skin and hair, telomere preservation is indeed beneficial. But when it comes to dietary supplements that aim to promote longevity by enhancing the process, he warns: Buyer beware. None have been approved by the Food and Drug Administration and whether they do anything to truly influence telomeres remains uncertain.

And if they do? “You might look younger,” he says. “But you also might be boosting your cancer risk.”

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Live Cells reveal cancer process

Anonymous — Thu, 11 Aug 2016 06:00:00 +0000

Live Cells reveal cancer process Anonymous (not verified) Thu, 08/11/2016 - 00:00

BioFrontiers

A deep look inside the live cells reveals a key cancer process

Telomerase, a powerful enzyme found at the ends of chromosomes, can keep humans healthy, or promote cancer growth. AV��ʪers at the University of Colorado in Boulder used a process called single-molecule imaging to look into the complicated processes that this enzyme uses to attach itself to the ends of chromosomes. This new understanding could help researchers develop better diagnostics and drugs for treating cancer and other diseases.

The findings, which were recently published in the journal Cell, show that telomerase has a small window of opportunity, lasting only minutes, to connect to the telomeres at the ends of chromosomes. The team was surprised to find that telomerase may probe each telomere thousands of times, rarely forming a stable connection, in order to be successful at connecting to the chromosomes. AV��ʪers believe that inhibiting telomerase from attaching to cancer cells is a target for better treatment of the disease.

Telomeres have been studied since the 1970’s for their role in cancer. They are constructed of repetitive nucleotide sequences that sit at the ends of our chromosomes like the ribbon tails on a bow. This extra material protects the ends of the chromosomes from deteriorating, or fusing, with neighboring chromosome ends. Telomeres are consumed during cell division and, over time, will become shorter and provide less cover for the chromosomes they are protecting. The enzyme, telomerase, replenishes telomeres throughout their lifecycles.

Telomerase is the enzyme that keeps cells young. From stem cells to germ cells, telomerase helps cells continue to live and multiply. Too little telomerase produces diseases of bone marrow, lungs and skin. Too much telomerase results in cells that over proliferate and may become “immortal.” As these immortal cells continue to divide and replenish, they build cancerous tumors. Scientists estimate that telomerase activation is a contributor in up to 90 percent of human cancers.

“This discovery changes the way we look at how telomerase recruitment works in general,” says University of Colorado Boulder Distinguished Professor and Nobel laureate Thomas Cech, who is director of CU’s BioFrontiers Institute and the lead author on the study. “It’s exciting to see this in living cells as it happens. Single-molecule imaging freezes the process, allowing us to study it. We are the only ones who have done this type of imaging of telomerase.”

The research team included coauthors, Jens Schmidt (pictured, left), a postdoctoral fellow and staff scientist, Arthur Zaug. They used the CRISPR genome editing and single molecule imaging to track telomerase’s movements in the nuclei of living human cancer cells. CRISPR, or Clustered Regularly Interspaced Short Palindromic Repeats, uses segments of DNA that contain short copies of base sequences. The team used single-molecule imaging, attaching fluorescent protein tags to human cancer cells so that the enzymatic process was visible under a powerful microscope.

“At the end of the day, the goal is to target telomerase as an approach to treat cancer,” say Schmidt. “You can inhibit telomerase across the board, but the challenge is isolating the telomerase in cancer cells from the telomerase participating in the normal processes of healthy cells. This research brings us closer to understanding these processes.”

CU Boulder Wins Silver at 2014 iGEM

Anonymous — Thu, 29 Jan 2015 07:00:00 +0000

CU Boulder Wins Silver at 2014 iGEM Anonymous (not verified) Thu, 01/29/2015 - 00:00

BioFrontiers

CU-Boulder Student Team Wins Silver at Premiere Biology Competition

The International Genetically Engineered Machine (iGEM) event is the top synthetic biology competition in the world and the CU-Boulder team wanted to make an impact at this year’s competition in Boston. Last year’s 2013 Buffs iGEM team was successful, winning a North American Regional award for best new BioBrick and publishing their research in ACS Synthetic Biology. The 2014 Buffs iGEM team was confident they could compete at the international level. Unlike previous years, this year the iGEM competition (called a Jamboree) had no regional qualifying round, creating formidable competition: 2,500 undergraduate and graduate synthetic biology researchers from 245 universities across 32 countries. In the end, the CU scientists came home with a Silver medal and an interlab study distinction.

“Hard to believe I had never heard of iGEM until earlier this year,” says Leighla Tayefeh, a CU senior with a double major in MCD biology and neuroscience. “But the idea of synthetic biology’s vast potential to benefit society enticed me to join the team. We wanted to stand out and work with new technology, so this led us straight to the endogenous CRISPR-Cas9 system and the clinical need for an alternative to antibiotics.”

The CU iGEM team wanted to tackle the serious problem of antibiotic-resistant bacterial infections, like MRSA and tuberculosis, in a way that didn’t damage the body’s healthful bacteria colonies at the same time. They focused on phage therapy, which is a virus that uses bacteria’s cellular resources to reproduce until the host bacteria’s cell is eventually destroyed. CRISPR-Cas9 is a phage system that is able to more specifically target the DNA of a bacterial infection, resulting in cell death. What made the CU-Boulder team’s efforts even more valuable was their development of a delivery system for the phage therapy. The result is that the CRISPR-Cas9 phage binds to part of the DNA in the cell and cuts the DNA strand, killing the bacteria cell.

iGEM promotes educational outreach as part of their team projects. The CU team used the opportunity over the summer to host a camp from Heritage High School in Littleton, Colo. to teach them DNA basics. The high school students extracted their own DNA from saliva and examined differences between pathogenic and healthy DNA fragments. The CU team also collaborated with Colorado State University’s iGEM team to validate some of their findings during the project.

“The 2014 CU iGEM team was successful at making progress on a difficult scientific problem, namely alternatives to fight antibiotic resistance, but also at impacting the local community. The high school students who came to visit have written raving about their experiences,” says Assistant Professor of Molecular, Cellular and Developmental Biology and BioFrontiers faculty member, Robin Dowell who served as the CU iGEM mentor for the last two years.

iGEM, which began in 2003, provides each team with a kit of biological parts -- like promoters that respond to particular stimuli, genes, or regulators -- at the beginning of each summer. Students then use these parts, or parts of their own design, in their projects. The iGEM Giant Jamboree was held at the Hynes Convention Center in Boston, October 30 through November 3.