Student Engagement Blog

Here students relate material they discover outside of class back to the things they learn in the lab!

Chemical Shift based methods in NMR Structure determination

I read a research paper this week that talks about chemical shifts. Chemical shifts are highly sensitive probes used by NMR specialist and structural biologist as conformational parameters to characterize a range of biological molecules. It is a big diversifying ideal, as the development of new algorithms and expansion of curated databases has the potential to further improve the accuracy of the chemical shift based methods and to complement classical methods of NMR structure calculation. Since we used NMR to observe how the peptides TP3 and TP4 bind to membranes of bacterial cell mimics, I thought it would be cool to see how NMR can be used in different ways to obtain the same or even better results.

To read the full article, click here.


Planning Chemical Syntheses with Deep Neural Networks and Symbolic AI

Artificial Intelligence plays an increasingly important role in our daily life.
In 1960s, E.J. Corey formalized the concept of retrosynthetic analysis and was
awarded the Nobel Prize in 1990 for this. Retrosynthetic analysis is a technique for
solving problems in the planning of organic syntheses. This is achieved by transforming
a target molecule into simpler precursor structures without assumptions regarding
starting materials. Although scientists have used computer for aiding retrosynthesis
analysis over the years, the results were unsatisfactory.
This year a group of researchers from the University of Muenster in Germany has
demonstrated that the combination of Monte Carlo tree search and symbolic artificial
intelligence (AI) to discover retrosynthetic routes is working extremely well. This
discovery will contribute greatly to the research of new drug development.

Read the full article here!


Biologist Discover New Peptide that could be Anti-Cancer

I did this week’s topic on a new peptide (Discovered by MIT biologists) that can disrupt a key protein that many types of cancers, including some forms of lymphoma, leukemia, and breast cancer, need to survive, meaning this could be a future cancer solution. The new peptide targets a protein called Mcl-1, which helps cancer cells avoid the cell suicide that is usually induced by DNA damage. By blocking Mcl-1, the peptide can force cancer cells to undergo programmed cell death. It’s like how we have been manipulating T3 and T4 to see which one as more absorbency qualities and how we isolate certain molecules in them to see which could have the best anti-response systems. There’s a chance that the two peptides we manipulate can also produce anti-cancer qualities, just like this new peptide.


Read the full article here.

Stem Cell Research


I found the topic on production of stem cells through automation to be quite important because of all the things we could do with them. The Stem cell production can produce many stem cells within days, instead of months, which is time efficient. They can be used from a healthy donor to be given to someone with bone-marrow derived cells to replace their worn down-cells with brand news ones to help their immune system function better. Imagine an elderly person breaking a hip bone, they aren’t able to heal as quick as a 16-year-old for example, who broke the same bone, but because of the stem cell automation process, the elderly person can be given some new stem cells that can potentially heal their broken bones quicker!

To read more on this research, follow this link!


Two Bears Were Badly Burned in Wildfires, and Fish Skin Helped Heal Them

I found this article was highly related to our research. Two female bears were suffered from burns on their paw pads caused by the Southern California Thomas wildfire. Veterinarians at the University of California Davis treated them with tilapia fish skins as bondages on their wounds. The tilapia fish skins provided better treatments than usual care, from the perspectives of covering the burns and providing pain control.

The veterinarian came up this idea of using tilapia skin on burns from a story she had read about scientists in Brazil using sterilized tilapia skin on human burns successfully. While she rationalized that fish skin is moist and transfers collagen, which helps healing, I think it might be the peptide we are working on – piscidin 1 and piscidin 3 take the charge of helping healing. This makes me excited to see possible actual application of our research.


Read the article here!


Panda Tongues

This is an article from Science Magazine last week, talking about the immunity that panda’s tongues evolved to protect them from toxins. Pandas have gone vegetarian only a few million years ago. A study shows that compared to their carnivore relatives which have less or even no bitter taste receptor genes, pandas possess 16 intact bitter taste receptor genes. Although the number is still slightly less than most herbivores, it shows that pandas’ tongues have evolved the ability to detect and protect them from the toxins like cyanide, nicotine, and ricin synthesized by plants.


Read the article here!