Monday, August 10, 2020

Evolutionary assimilation of foreign DNA in a new host

 

We know from decades of biological study that all living beings share many similar genes. We also know that these genes are subject to evolution, from mutations that change the DNA sequence of an organism’s offspring, or through horizontal gene transfer (HGT), the acquisition of DNA from a creature other than a parent, and even of a different species.

This got a team of bioengineers at UC San Diego wondering: could a human gene function in other organisms? And if it does function, what evolutionary changes are happening to the DNA to allow it to work properly in a new host species?

Bioengineers in Professor Bernhard Palsson’s Systems BiologyResearch Group used genetic engineering and laboratory evolution to test the functionality of DNA placed into a new species and study how it can mutate to become functional if given sufficient evolutionary time. They published their results on August 10 in Nature Ecology and Evolution.


Schematic of the experimental workflow. Native E. coli glycolytic isomerases pgi and tpiA were replaced with the coding sequence of foreign orthologues and subjected to laboratory evolution for improved exponential phase growth rate. Ma, million years ago.

The researchers used the bacteria E.coli to answer these questions. They took two common genes from the human genome involved in sugar metabolism, and used CRISPR to swap them into a commonly used laboratory strain of E. coli.

The two genes used—pgi and tpiA-- cripple E. coli when removed, causing the bacteria to grow about 5 times slower. Initially, following the gene swap, E. coli’s growth rate did drop, signaling that the genes weren’t functioning properly. But then, the researchers subjected the transformed E. coli strain to a laboratory “evolution machine”—a robotic system used to study how engineered bacteria adapt to changes. After thousands of generations of evolution, the new genes started to function properly. The human genes could serve just the same function in the bacterium as its own genes.

The automated evolution system enabled a large-scale study, generating hundreds of mutant strains evolved for more than 50,000 cumulative generations, something that would take decades rather than months if performed manually.

How was it possible that the human genes were fulfilling the same role in E.coli?  The researchers sequenced the genomes of the evolved strains to find out.

For every strain that successfully evolved, the critical factor was one or more mutations increasing gene expression level. Most of these mutations did not occur within the foreign gene, but rather in regions of E. coli’s DNA controlling regulation of the gene, with their nature depending sensitively on the gene’s specific DNA sequence and location in the chromosome. Some of these mutations occurred with shocking regularity, including one observed independently more than 20 times, demonstrating that evolutionary outcomes can be (probabilistically) predicted to the single DNA basepair.

“This result shows the importance of systems biology,” said Professor Bernhard Palsson, principal investigator of the study. “Namely, biological function, in this case, is not so much about the parts of the cell, but how they come together to function as a system.”

The original motivation for the study was to determine ’self’ versus ’non-self’ at the molecular biology level. The surprising answer is that even if human enzymes are foreign entities to the E. coli bacterium, they are not recognized as such, and the bacterium adopts their function by simply adjusting their abundance to achieve balanced phenotypic state.

This study establishes the influence of various DNA and protein features on cross-species genetic interchangeability and evolutionary outcomes, with implications for both natural horizontal gene transfer and strain design via genetic engineering.

Friday, July 24, 2020

NanoEngineer earns Dissertation Year Fellowship


Jacobs School of Engineering nanoengineering PhD student Qiaowan Chang has been awarded a Dissertation Year Fellowship funded by the Marye Anne Fox Endowed Fellowship Fund. This fellowship is awarded to students who demonstrate highly distinguished academic records, and provides recipients with a $22,000 stipend for their dissertation year, plus tuition and fees.

Qiaowan Chang
We spoke with Chang about her research, her accomplishments at UC San Diego, and her future goals.

Q: How did it feel to receive this award?
A: I feel very excited and lucky to receive this award. It's not only a recognition of my current research, but also encouragement for my future work. And thanks to my supervisor, Professor Zheng Chen, for the instruction, the help during my PhD studies, and for offering lots of opportunities to collaborate with other groups.

Q: Tell us about the research you’ve been conducting in Professor Zheng Chen's lab.
A: My research is mainly focused on designing electrocatalysts at atomic scale through fundamental understanding of their elementary processes in several key electrocatalytic applications and reactions, including decentralized hydrogen peroxide (H2O2) production (2-electron oxygen reduction reaction), direct liquid fuel cells (ethanol oxidation reaction), and carbon dioxide (CO2) conversion (carbon dioxide reduction reaction).

Q:  What are some of the applications of your research?
A: For the decentralized hydrogen peroxide (H2O2) production (2-electron oxygen reduction reaction), H2O2 is one of the most useful chemicals across the entire chemical industry. For the traditional production method, the transportation and storage of H2O2 are unresolved problems due to its chemical instability. Only a dilute H2O2 solution is needed for most applications. For example, 3% H2O2 solution is used as the disinfectant to fight the COVID-19 virus. My research is to develop a green and user-friendly method to produce H2O2 on-site from the two-electron oxygen reduction reaction.

For the direct ethanol fuel cells (ethanol oxidation reaction), it could be used in electric vehicles. In direct ethanol fuel cells, ethanol is oxidized by oxygen to generate electricity. Ethanol is a green and sustainable fuel that can be produced from agriculture feedstocks. Thus, direct ethanol fuel cells are environmentally-friendly techniques for powering vehicles.

For the carbon dioxide (CO2) conversion (carbon dioxide reduction reaction), electrochemical technology could reutilize and convert CO2 to other important chemicals to mitigate climate change and ocean acidification caused by the increased CO2 level. 

Q: Tell us about your dissertation topic.
A: My dissertation topic is to explore novel strategies to design electrocatalysts at atomic scale through fundamental understanding of their elementary processes in the above applications and reactions. The key to make such electrochemical reactions happen is the electrocatalysts. The thesis mainly discusses several strategies, including to tune the local chemical coordination between atomic catalyst clusters (metal) and their support materials (defect carbons) using a composite approach to achieve the synergistic effect of “1+1>2” (that is, Pd clusters deposited on the oxidized carbon nanotubes) for decentralized hydrogen peroxide (H2O2) production (2-electron oxygen reduction reaction), and to control the morphology and structure of the electrocatalyst (that is, the core-shell cubic-shaped electrocatalysts: 10 nm of platinum (Pt) nanocubes as a core and a ~0.2 nm thick of iridium (Ir) layer as a shell) in direct ethanol fuel cells (DEFCs).

Q: What are your future goals once you earn your PhD?
A: I will do a postdoc first to finish my remaining projects. Then, I will try to pursue a faculty position in academia, or a researcher/scientist position in industry.

Thursday, July 23, 2020

Using nanotechnology for more targeted, safer pesticide delivery


Nanoengineers at UC San Diego will develop more targeted ways to apply pesticides to food crops using plant virus nanocarriers, thanks to a $490,000 grant from the Department of Agriculture’s National Institute of Food and Agriculture. This could lead to a reduction in the amount of pesticide used, and therefore less chemical accumulation from pesticides in our food, drinking water and environment.

Engineers are using a plant virus as a nanocarrier
for more targeted pesticide delivery to protect crops
like tomatoes from root-eating nematodes. 
Pesticides are used extensively in food production to ensure crop health and yield. While these toxic chemicals can keep bugs, weeds, parasites, fungi and rodents from damaging crops, they also accumulate in the environment, in the crops themselves, and even in drinking water supplies, leading to adverse health effects for humans.

Nanoengineers led by Professor Nicole Steinmetz at the Jacobs School of Engineering plan to use a plant virus as a nanocarrier to more precisely deliver pesticide payloads when and where needed, resulting in less pesticide required, and less bioaccumulation. The team will study and use the tobacco mild green mosaic virus (TMGMV), which they’ve previously shown can carry cargo down to 30 centimeters below the soil surface, much deeper than traditional synthetic nanoparticles which travel 8 to 12 centimeters deep.

Their first target for these nanoparticles is a type of roundworm called a nematode, which eats plant roots, destroying the plant in the process. By being able to deliver the pesticide deeper into the plant’s root system, the researchers believe their plant virus nanoparticles will be more effective in stopping nematodes than synthetic pesticide delivery particles.

“In this project we focus on pesticides to target roundworms that infect the roots of crops, using our plant virus nanotechnology,” said Steinmetz.  “More specifically we will produce a library of nanoparticles derived from harmless plant viruses to answer how size, shape, and materials properties affect the nanocarriers interactions with soil and plants. Understanding these fundamental questions is expected to make an impact on next-generation pesticides, literally attacking the problem at its roots.”

Since plant viruses like TMGMV can be engineered to a custom size and certain physical properties, the researchers will study the effectiveness of plant virus nanocarriers of different sizes, shapes, and surface chemistries.  They’ll create a library of nanomaterials derived from TMGMV, detailing the nanocarriers’ pesticide delivery efficacy.

“We’ve seen that in medicine, changing the shape of a nanoparticle delivering a specific drug can lead to advantages such as enhanced diffusion and tissue penetration,” Steinmetz said. “We hypothesize that this is true for pesticide delivery as well, and will investigate the effect of nanocarrier size and shape on pesticide application effectiveness.”

The tobacco mild green mosaic virus is non-infectious to most plants, but the researchers will also create inactivation protocols to ensure it’s safe to use with any desired plant.  The virus is non-infectious in humans.

Steinmetz will collaborate with researchers Erin Rosskopf and Jason Hong at the USDA Agricultural Research Service, who will test candidate materials on nematode-infested crops.

Tuesday, July 21, 2020

Comic-Con@Home features UC San Diego scientists

Saura Naderi, outreach director at the Halıcıoğlu Data
Science Institute
Comic-Con 2020 may look a little different this year, coming to you from the comfort of your own home. The annual San Diego comic and pop culture convention is going virtual due to COVID-19, but the good news is more than 350 panels will be available for free online, no waiting overnight in line required.

Comic-Con@Home will feature seven UC San Diego speakers during the five-day virtual event running from July 22 to July 26.

Tune in on Thursday, July 23 from 3-4pm for The Science of Back to the Future, where the creative teams from "Back to the Future" and "Transformers" talk to local scientists about how they came up with their vision for each storyline and how science would play a part in these movies. UC San Diego panelists include engineer and roboticist Saura Naderi, the outreach director at the Halıcıoğlu Data Science Institute and an alumna of the Jacobs School of Engineering.

Marine biologist Ben Frable will speak on
the More Science in Your Fiction panel.
Up next is The League of Extraordinary Scientists and Engineers: More Science in Your Fiction on Thursday, July 23 from 6-7pm. Scientists and engineers will discuss how both comic books and science fiction push them to dive deeper into the unknown. UC San Diego panelists include Ben Frable, a marine biologist at Scripps Institution of Oceanography, and Angela Zoumplis, an extremophile explorer at Scripps Institution of Oceanography.

You can catch Sinless, Fearless, Ruthless - A look at science and social science in a YA sci-fi book Friday, July 25 at 4pm. Learn about the social sciences and the idea of morality behind Eye of the Beholder by author Sarah Tarkoff. UC San Diego panelists include Samantha Russman, a PhD student at the Jacobs School of Engineering.

Cognitive Science Professor Virgina De Sa
The Fleet Science Center Celebrates: Agents of S.H.I.E.L.D. - The Stories and Science of Androids, Space Travel and Aliens will air on Saturday, July 25 from 3-4pm. Celebrate the seven seasons of Marvel's Agents of S.H.I.E.L.D. and hear executive producers, actors, and writers discuss how accurate the science in the series was with local scientists. UC San Diego panelists include Virginia De Sa, a professor in the Cognitive Science Department and associate director of the Halıcıoğlu Data Science Institute ; Troy Sandberg, a bioengineering PhD alumnus; and Melissa Miller, a scientist and science writer at the Scripps Institution of Oceanography. 

To learn more about Comic-Con 2020 events, visit their website.

Monday, June 22, 2020

Olivia Graeve's team is "crystal clear" about quantifying crystallinity


UC San Diego engineering professor and materials science pioneer Olivia Graeve’s research team has a new paper out that reports on work that will be used to help materials scientists develop higher quality materials for use in many applications including super-durable solar cells, ultra-hard metals for space exploration, better infrared optical fibers for carrying digital information, and materials for new kinds of biomedical devices like self-expanding stents.

The paper was published by PLOS ONE on June 22, 2020.

A schematic representation of the team’s DSC-based methodology
 for determination of the change of crystallinity and 
crystallinity percentage as a function of temperature.
In this particular paper, the researchers present a new method for calculating the initial crystallinity, change of crystallinity and crystallinity percentage of amorphous metal alloys as a function of temperature. The first author on the paper is Arash Yazdani who is finishing his PhD at UC San Diego in Professor Graeve's lab.

"This is exciting materials science work that will have an impact in the field," said Graeve. “We all live in this world in which materials science plays a role in nearly everything we do. We all benefit from the materials science breakthroughs yet to be developed. If you think you're interested in this kind of work, pursue it. Don't leave it up to others to do the work. There is a place for everyone in materials science.”

The methods presented in this paper are particularly interesting because the behavior of amorphous materials for use in exciting applications often depends on the partial crystalline nature of the materials. Creating materials with properties such as ultra-hardness or super-resistance to corroding often depends on being able to characterize and control crystallinity, and that's what this research is working toward.

Paper info
"A Method to Quantify Crystallinity in Amorphous Metal Alloys:  A Differential Scanning Calorimetry Study," in PLOS.

Authors: Arash Yazdani (1), Günther W.H. Höhne (2), Scott T. Misture (3), Olivia A. Graeve (4)

1  Department of Mechanical and Aerospace Engineering
University of California, San Diego
9500 Gilman Drive – MC 0411
La Jolla, CA 92093-0411, USA

2  University of Ulm
Helmholtzstraße 16, 89081 Ulm, Germany

3  Kazuo Inamori School of Engineering
Alfred University
2 Pine Street, Alfred, NY 14802, USA

Thursday, May 28, 2020

Alumna combines engineering, medical expertise to alleviate PPE shortage


By Daniel Li


Dr. Aditi Sharma, a UC San Diego bioengineering alumna and resident physician at the UC Irvine dermatology department, is combining her engineering skills and medical expertise to solve one of the ongoing challenges of the COVID-19 pandemic: a shortage of protective masks for healthcare workers. 

Sharma and several colleagues developed a method to fabricate face masks out of discarded surgical tool sterilization wraps, and launched a project that aims to create 10,000 of these masks for healthcare workers. Their project was featured in the Los Angeles Times.

Their mask is made from recycled Halyard H600, a material used for surgical equipment sterilization, with straps made of recycled Gemini surgical wrap material. 

Their repurposed sterilization wrap mask has up to 86.5 percent filtration rate; this is lower than the 95 percent of N95 masks, but more than three times more effective than ordinary cloth masks, which many health care workers have been forced to use due to insufficient personal protective quipment (PPE). Their goal is to be able to reserve N95 masks for medical personnel working directly with known COVID-19 patients.

In just two months, Sharma and her team have made over 2,000 face masks, and are looking to expand the project to the entire state of California and hopefully the rest of the country. 

“We're hoping that ultimately not only will healthcare providers have the masks, but maybe even people in the community can have access to them as well,” Sharma said. “In terms of getting towards that 10,000 goal, I think probably in the next couple of weeks we should be there, between manufacturers in the local community who are willing to help us and volunteer groups who are willing to help.”

Sharma graduated from UC San Diego in 2009 with a degree in biomedical engineering, and then received her medical degree at the Medical College of Virginia. During her time at UC San Diego, Sharma had the opportunity to work at Pfizer as a research assistant and participate in the Amgen Scholars Program over the summer. These two experiences sparked her curiosity in immunology and inspired her to conduct research on biological warfare and bioterrorism under Dr. Anthony Fauci at the National Institutes of Health.
Sharma's masks, made from repurposed sterilization wrap.

After a one-year stint at the NIH, Sharma shifted gears and worked as an engineer at the World Health Organization to improve access to medical devices for low income individuals. She explained that her background in engineering has given her a unique approach to medicine. 

“I think something that is kind of fundamental to engineering is asking, “Is this the most efficient process and how can we improve it?” Sharma said. “I think sometimes in medicine, we accept what is told to us-- that this is how it is. And I find that that engineering side of me is constantly saying, ‘What can we do better?’”

When Sharma came back into the medical field, her main goal was to find a way to integrate the fields of public health, engineering, and medicine in her work; this project has allowed her to do so and help contribute to the fight against COVID-19. Sharma encourages students to take advantage of all the resources that UC San Diego offers and to dream big.  

“What I loved about UC San Diego is there are so many resources,” Sharma said. “I used to go to the Teaching and Learning Commons...and I remember really learning linear algebra very well because I had that extra support system. I am also grateful for applying for those job opportunities that I never thought I would get. I think it set me up for the rest of my career.”


Tuesday, May 12, 2020

Dispatches from a pandemic: graduate students create COVID virus simulations


By Daniel Li


As it became clear in late February that COVID-19 was not going anywhere, four UC San Diego graduate students were planning their final project for the Numerical Analysis for Multiscale Biology course, which uses math to simulate biological processes.

The mechanical engineering and bioengineering students—Parker Dow, Cathleen Nguyen, Clara Posner, and Patrick Wall—decided to put their skills to a new use, and build a predictive model analysis that could bridge from the molecular biology of the SARS-CoV-2 virus to the epidemiology of the spread of infection through the population. The team started the three-week project in early March.

“A lot of times, when working on basic cell biology research, it can seem kind of removed from the bigger picture of what’s happening in the world,” Posner said. “But working on this coronavirus project is a lot more motivating since it can help with this current crisis that’s affecting us all.”

The idea to focus the project on COVID-19 was first brought up by Dow. According to Dow, he had started to see new scientific literature related to the novel coronavirus come out and it became increasingly apparent that some of the data could be used for computer modeling.

“I floated the idea to the group because I’d seen in a paper that they got a new structure of the coronavirus binding protein,” Dow said. “Our group started to do a bit more research on it and discovered that the scientific community had been publishing things daily, so we all wanted to take a stab at it.”

Each student focused on a different level of the project: cellular, molecular, and population scale. Wall created an alveolus in the lung with the MCell modeling tool to figure out the virus's rate of spread. Dow analyzed viral binding kinetics using BrownDye software. Posner used Virtual Cell (VCell) to create a transforming growth factor (TGF)-beta signaling induced lung fibrosis model. Nguyen focused on creating a population infection model using Vcell at the population level.

Two of the tools—Browndye and MCell—that the team used to model their systems were developed in-house at UC San Diego. Several local scientists, including UC San Diego Project Scientist Gary Huber and Salk Institute Staff Scientist Tom Bartol, were actively involved and helped guide them through the project. 

“The course instructors went above and beyond,” Wall said. “It was really helpful to reach out to them and ask for their expert knowledge. They also were instrumental in getting our models to run properly.”

This hands-on course is one of seven lab courses offered by the Interfaces Graduate Training Program in Multi-scale Biology that involves students from 11 graduate programs at UC San Diego and is directed by Professor Andrew McCulloch from the Department of Bioengineering.

 “The scientific challenges of addressing the COVID-19 pandemic are so daunting because they span from the scale of the spike protein on the virus, to the cellular and pathophysiological responses of the infected human to the population of the globe. Problems like these require the kinds of novel multi-scale approaches and interdisciplinary teamwork that the Interfaces program was designed to teach and encourage.

According to Wall, one of the challenges when they first started was that the data surrounding COVID-19 was sparse. To tackle this, the team looked at similar viruses, such as SARS, and used data from that to generate initial models. 

“The 2002 SARS virus was also a coronavirus outbreak. These viruses are so similar,” Wall said, “we were able to use a lot of the data that was generated in the mid 2000s to early 2010s on the SARS coronavirus and extrapolate our modeling based off of that.”

Nguyen added that because the coronavirus was evolving in real time, there were a lot of unknowns and the team was forced to make assumptions throughout the project. 

“Everyday you’re receiving new information about the pandemic and want to apply it to the models,” Nguyen said. “You make a lot of assumptions and those assumptions are changing based on new information. You're changing your inputs, your process, and with every simplification you make, you lose some accuracy in the models.”

Nguyen enjoyed how she was able to work together with students of different engineering backgrounds.

“I’m more of a mechanical engineering background, but the rest of my team members have more of a bioengineering background,” Nguyen said. “And the novelty comes when you’re trying to work on a multiscale project with people who have different expertise and skills.”