Author Archives: James Zheng

Well, here we are. In less than 48 hours, I’ll be boarding a plane headed home, signing off on a summer that has proven extremely toasty, challenging at times, and full of pleasant surprises.

Six weeks ago, if you had told me that I would be building tree objects in a setting outside of a computer science class, I probably would have retched a little on the inside, having completed my fair share of awful tree-building assignments in MIPS, Java, and C. My sleep-deprived and Zoom-fatigued brain would have called it quits even before almost screwing up a Western Blot on Week 3. Yet, here we are. 500+ lines of code and dozens of bugs crushed for some promising preliminary data. A forty-minute long, unscripted, lab meeting presentation that really should not have lasted more than twenty. Turns out presentations can be fun when you’re excited about what you’re talking about.

Through it all, I have greatly enjoyed the opportunity to pursue interesting questions, learn new things, and befriend many of my colleagues in the process. I’ve found what Bob Lefkowitz described as a “calling” in his faculty talk: a charge to prevent a major public health disaster like COVID-19 from ever happening again. While it’s not clear what the answer to that charge might look like, I know that it will be the challenge that gets me out of bed every morning. Maybe I’ll continue working on developing better antivirals, or pivot to something entirely different. All the same, I look forward to meeting new mentors, finding new opportunities, and continuing to discover my purpose.

In the words of Chadwick Boseman, “Purpose crosses disciplines. Purpose is an essential element of you. It is the reason you are on the planet at this particular time in history”.

James J Zheng¹
Mentors: John S Decker¹, Michael D Lynch, MD, PhD^1,2
Departments of Biomedical Engineering¹, Chemistry²

Lectins are naturally occurring proteins found in bacteria, plants, and algae that recognize specific carbohydrates found on many viral envelope proteins. This unique binding behavior allows these proteins to have broad-spectrum antiviral capabilities, neutralizing viruses such as HIV, influenza, Ebola, and SARS-CoV with varying degrees of activity. While multivalent binding between lectins and glycans has been shown to play a key role in viral neutralization beyond what can be explained by binding avidity alone, the mechanisms linking multivalency and neutralization are not well understood. We believe that lectin crosslinking between different envelope protein domains may inhibit cell-entry-associated conformational changes in viral envelope proteins, resulting in viral neutralization. Using rigid-body protein docking simulations between a subset of lectins and viral envelope proteins found on HIV-1 and H1N1, we compared predicted crosslinking to experimental data on neutralization potency and neutralization-modifying glycan deletions. Hopefully, this analysis will enable us to identify a key mechanism of lectin antiviral activity, providing a robust model for engineering improved broad-spectrum antivirals to counter emerging pandemic viruses such as SARS-CoV-2.

For those of us working on developing next-generation therapies, biotechnology, and pharmaceuticals, it’s easy to take the actual mechanism of drug delivery for granted. While the molecules we purify and test against pathogens and/or tumors may do perform quite well on a cell culture plate, ensuring that the actual administration and delivery of these drugs goes smoothly in live tissue is just as important. That’s what makes Camila’s work on pharmacokinetics at the Chilkoti lab so important.

Traditionally, when a drug is administered to the body, it has very little time to do what it needs to do before it gets excreted. This leads to multiple doses of highly-concentrated drug being used, which can yield additional negative side effects. A drug delivery mechanism that allows for more sustained, controlled release could substantially mitigate these challenges.

The Chilkoti group does a considerable amount of work on so-called elastin-like polypeptides, or ELPs. Derived from naturally-occurring elastin, these proteins undergo significant temperature-based solubility changes, becoming insoluble at body temperature and forming a slow-dissolving deposit within the target tissue. Any drugs attached to the ELP would then have much more time to act, resulting in sustained chemical release.

One of the biggest obstacles to the systematic usage of lectins like griffithsin as antivirals has been their high inherent toxicity in tissue. Given the strides being made by Camila and her colleagues in the Chilkoti lab, we may soon have the means to control just how much lectin gets released at one time, mitigating the adverse effects that would otherwise occur. I thoroughly enjoyed learning about her research and found her presentation of such a complex topic (just count the syllables in pharmacokinetics) super clear and interesting. Keep doing great things, Camila!

If there is one person in B-SURF that’s happy about living on East Campus again, it’s me. Unlike many of my colleagues, who undergo a daily commute to West Campus and back, I take a 15-minute walk through downtown Durham to get to my lab, strolling past many of the local businesses that are still mainstays of life at Duke during the school year. It’s been cool to see the gradual revival of pre-pandemic life during this small commute every day – restaurants and bars open for indoor dining, people walking around with the lower part of their face uncovered, signs posted on storefronts indicating that masks are now optional.

Originally a cigarette factory, the Chesterfield Building now houses many Duke facilities, including my lab on the fourth floor. Image: Bull City Rising

Days in the lab are highly variable, to say the least. I usually head in between noon and 1 PM and head out when the experiments we’re running are finished (anywhere from 6-8 PM), or when I feel I have made enough progress on my code. Sometimes, solutions need to be prepared and cells need to be grown too, but in the downtime when I’m not at the bench, I try my best to explore literature relevant to the project, using the skills we’ve been developing in our B-SURF journal clubs to dissect papers on a variety of cool topics such as viral entry mechanisms, lectin binding, and computational modeling of protein/ligand interactions. When I’m trying to debug and test code, you can also find me reading documentation for functions whose syntax I can never remember, scrolling through stack overflow posts. and crossing my fingers that the ridiculous amount of open tabs will not kill my laptop’s battery life.

I also have gotten the chance to participate in lab meetings on Fridays at 9 AM, learning about the other cool work happening in the lab and marveling at the (many) ingenious methods scientists have come up with to engineer enzymes, create scalable biosynthetic processes, and precisely regulate the metabolic pathways in E. coli to inhibit growth and maximize production of the molecule of interest. At the end of each meeting, Dr. Lynch always asks each person to offer one piece of positive feedback and one piece of constructive criticism to the presenter, and I often find myself having a very difficult time coming up with good critiques, or qualifying my feedback with the classic “I’m not super familiar with this field, but…” Hopefully, someday, I won’t feel the need to preface my statements with that phrase.

If you ever get the chance to meet Dr. Mike Lynch, you might be surprised to hear that he started off his career as an anthropology major at WUSTL,  only adding a second major in biomedical engineering after his parents expressed concern about there being no money in anthropology. This focus on applied science eventually led him into the MD/PhD program at the University of Colorado, Boulder, where he became interested in primary care and developed an interest in making synthetic biology tools applicable to the real world. By the end of his time in medical school, Lynch had set aside residency and founded his first start-up, OPX Biotechnologies, which used new methods to bring about large-scale production of more sustainable, bio-based alternatives to existing chemicals and fuels. In his own words, the company felt like a once in a lifetime opportunity.

It was this initial gig as an entrepreneur that eventually led Dr. Lynch to Duke. While he enjoyed the super collaborative nature and larger-scale design challenges faced in industry, he felt that academia offered him a great amount of flexibility, enabling him to tackle new questions, pursue the next start-up idea, and mentor the next generation of innovators and investigators, all at once.

Unsurprisingly, this journey from student to entrepreneur to principal investigator was not without its challenges. As an undergraduate working in a wet lab, Lynch was not particularly fond of his graduate student mentor, an experience which led him into the computational space by the time he did his master’s. He reverted back to the wet lab during his PhD, working in a protein lab before one unfortunate incident where one week’s worth of purified protein was lost to aggregation. This led Lynch to switch into a genetics lab, where he stayed for the remainder of his PhD. When I asked him what his advice would be to students who get stuck troubleshooting failed experiments, he recommends “going around the wall”, stepping back to see if there is an alternative pathway to answer the same scientific question.

Of all the esteemed faculty I have interacted with Duke, Dr. Lynch is one of the most down-to-earth and personable ones that I have met. To this day, you can still find him walking around lab, doing the hands-on work of growing E. coli and making LB while also making time to hang out with each of his students. I’ve greatly enjoyed seeing him around on a regular basis and look forward to the continued work ahead.

The last time I had to come up with a mechanism, it was on a (very tough) organic chemistry exam that I didn’t do very well on. Yet, whether it’s quantum mechanics or enzyme kinetics, asking how something works is one of the most fundamental questions in science.

Over the past couple of months, researchers have worked at remarkable speeds to figure out how the novel coronavirus (SARS-CoV-2) that has quarantined the world for 13+ months works. Particular attention has been paid to the all-too-familiar spike protein, which contains a particular region that can bind to a specific receptor (ACE2) on human cells. What makes this virus particularly infectious, however, is its ability to evade the immune system and pre-activate its spike proteins for cell membrane fusion. Thus, any effective treatment for SARS-CoV-2 would need to interfere with this process in which the virus can efficiently infiltrate human cells.

Griffithsin (abbreviated GRFT) is a red algae-derived protein that exhibits broad antiviral behavior against a wide variety of viruses, and scientists have most recently been interested in its ability to inhibit HIV cell entry. GRFT works by binding to various glycosylation sites (sugar scaffolding) present on all kinds of viral proteins, and has been shown to be effective against cousins of the current coronavirus, such as SARS-CoV and MERS. However, the detailed mechanism by which this protein inhibits coronavirus infection is not particularly well understood. This is especially true for SARS-CoV-2, a virus which remains every bit as mysterious as it is new.

Structural depiction of griffithsin (dimer form) (Xue et. al. 2012)

This summer, I’ll be figuring out how griffithsin blocks SARS-CoV-2 from entering cells, working to understand the complex interactions between GRFT and the coronavirus spike protein that allow for this unique behavior. Given my past history with figuring out mechanisms, it seems like a daunting task, but I have no doubt that I’ll learn a lot about experimental design along the way.

If there’s one thing COVID-19 has taught us, it’s to be amenable to change.

When I first came to Duke in August of 2019, I had three big goals in mind: to act in a play, to find a close group of friends, and to start working in a research lab in the spring. No part of my imagination would have thought that a far, far away virus in Wuhan would so fundamentally change my reality just eight months later.  I still remember getting a phone call from my parents in January,  informing me about how they had bought masks for family members in the mainland and telling me to be careful about Chinese New Year celebrations on campus.

At the time, I was meeting with some PIs across Duke who had been gracious enough to respond to my initial cold emails, selling myself as a slightly awkward germ nerd with no prior lab experience outside of being a complete klutz in organic chemistry lab. I learnt a great deal about the interesting work being done to understand the human microbiome, fight antibiotic resistance, and engineer microbes to synthesize useful products such as biofuels. Despite going into this search process anticipating a wet lab position, I ended up at Prof. Xiling Shen’s lab, working in the computational biology space to analyze 16S RNA sequences and put together a new analysis tool for microbiome data. Lucky for me, the pandemic did not put a stop on my work there, and I have learned a lot since.

One of my favorite things about Duke is the multitude of opportunities to explore, challenge, and build upon your research interests. This summer, I hope to ask many questions, learn from my (hopefully not too many) mistakes, and gain experience with many of the basic wet lab techniques used to address abstract scientific questions, and I am grateful to the Lynch Lab for  giving me the opportunity to continue growing as a student and scientist. I also want to gain some insight into the day-to-day life of an independent scientist (which will help inform some big career decisions in the near future), and hope that the experience will be a good complement to my computational background. Sure, it’ll take some time to get used to troubleshooting experimental set-ups as opposed to debugging Python code, but to borrow a quote from the late Chadwick Boseman, “the struggles along the way are only meant to shape you for your purpose”.