June 9, 2020
by Carol Lynn Alpert
QSTORM on the eve of #ShutDownSTEM
Participating: Jessica, Carol Lynn, Peter (top row); Thomas, Elizabeth, Abhijit (2nd row).
Shout out to Thomas who graduated with the class of 2020!
It was great to see each other. The labs are starting to open up over the next couple of weeks, while opening the Museum to the public will take much longer. We decided to give ourselves two months until our next meeting, hoping that there will be at least a month’s worth of data to report and discuss. We discussed #ShutDownSTEM https://www.shutdownstem.com, occurring tomorrow, June 10, but it is not having a big impact on the two university campuses, since they’re not open anyway. The Museum is observing the day and though shut, is urging all employees to explore resources provided about racism and anti-racism.
Optics Team – Georgia
Abhijit reported that UGA is opening next week, and labs are expected to maintain a minimum of 250 square feet per person. He is working on the “Localization Precision with SIDH” paper, exploring the minimum boundaries of localization precision, using the Cramer-Rao Lower Bound technique. The results show indicate they are reaching the lower bound (4.4-5.0 nm) in the x and y dimensions, but stuck at 40 nm in z. Is this the best they can do? Abhijit is going to tackle refinements to the algorithm, but basically they need better photon emitters to minimize the effect of background noise. He was intrigued by a recently published Nature Methods article on using “A 6-nm ultra-photostable DNA FluoroCube for fluorescence imaging.” The authors report that these 6 nm-sized, non-blinking fluorophores achieved a 54-fold longer lifetime and a 43-fold increase in photon emission over single organic dyes and could be used to track single motor proteins for more than 800 steps with nanometer precision. Abhijit shared the paper with all of us. https://doi.org/10.1038/s41592-020-0782-3
QDot Team – Ohio
In Columbus, 1 person at a time will be allowed in the lab until June 22, when 3 people will be allowed at the same time. They will work in shifts. Elizabeth joined us from the lab, as she was in today to check supplies of hand sanitizer and so forth. Elizabeth briefed us on the paper she’s preparing on DNA cages and walked us through her binding studies. The first figure from the paper shows how specifically-designed interlocking DNA oligomers come to form hexagonal DNA cages around the surface of the green sphere.
The green sphere represents the micelle that will contain the fluorophores. The targeting ssDNA (shown in lighter green) is designed to bind the micelle to a molecule of the structure to be imaged in the cell. The interlock is temperature dependent and this allows the lab to control whether the cages stay intact or disintegrate, releasing a portion of the fluorophores to drift or be washed away. As this occurs, it becomes possible to apply sub-diffraction-limit point localization to the scattered micelles remaining bound to the target. The Winter lab has been able to demonstrate an even better technique for "erasing" a portion of the fluorophore-containing micelles. They call it "strand invasion." In this approach, a longer, more complementary DNA substitutes for and thus erases from the target the shorter, less complementary strands binding the micelles. Said Jessica, “We can use DNA as a means of erase, which may enable STORM imaging.” Current tests show that even with low efficiency the reactions are working as planned. This could turn out to be useful for STORM, and Jessica told Peter that she’d probably be able to get him the materials to try out with a simple flow cell in the microscope, perhaps within a few months. She and Elizabeth want to improve the antibody conjugation first.
Communications Team – Boston
The Museum is observing #ShutDownSTEM on June 10, and the CEO has asked all staff to make use of resources on racism and anti-racism. The Museum remains closed and surveys show that science museums are not high on the list of places people will want to venture when reopening begins. We do not know yet when we will return to our offices.
We did make a fun 8 minute film about how our research partners at CIQM are getting through being “Locked out of the Lab.” It’s at https://www.youtube.com/watch?v=SxXYJzsmJwk
In other news, we concluded our participation in the NSF-OSTP project to establish a set of Key Concepts for Future QIS (Quantum Information Science) Learners. The concepts are published at https://qis-learners.research.illinois.edu.
Next Meeting: Our next Zoom meeting will be Wednesday August 5 at 11 am. Blog posts due August 3.
Fare well, all.