Problem-solving algorithm created by Cole Williams contributes to more inclusive science

Since fifth grade, Cole Williams knew he had an interest in genetics and the relationship between biology, math and probability after first learning about Punnett squares. Williams, a class of 2019 genetics and genomics major, was able to further these interests at UC Davis through his classes and through his work in the lab of Associate Anthropology Professor Brenna Henn. He was recently named the 2019 Undergraduate of the Year by the UC Davis College of Biological Sciences.

“Not many schools offer genetics as a major, where you can focus solely on genetics,” Williams said. “UC Davis had so many classes that interested me, so it was a great place to study this.” 

After working at another lab, Williams wanted to perform research more closely related to genetics and genomics and, at the start of the Winter Quarter of his third year, Williams began working at Dr. Henn’s lab, where he could do just that. Here, he was able to write an algorithm that allowed researchers to distinguish between complex familial relationships in genetic datasets of Africans. 

In Dr. Henn’s lab, researchers study populations from southern Africa and neighboring countries to solve questions about human evolution and disease. According to Williams, these populations are some of the most genetically diverse in the world, yet some of the least studied. 

“The lab uses genetics to study the genetics of complex traits, like skin color, disease susceptibility, tuberculosis … and demographic history of the region,” Williams said. 

Limited genetic information is known about non-European individuals, as the majority of knowledge about human diseases comes from data sets with large proportions of European individuals. Seventy-eight percent of individuals in “genome-wide association studies” are of European descent, according to an article published in Cell, however, according to the U.N., Europeans make up only about 10% of the world’s population.

“Not a lot is known about non-European populations and there is a tremendous amount of information we can learn from these populations,” Williams said. 

In Williams’ project, he worked with a dataset from the Himba population of Northern Namibia and was tasked with constructing pedigrees using genetic data alone. His goal was to study tuberculosis susceptibility and the inheritance of traits in a family context, as well as understand family structure and mating practices in the population. 

The Himba population has unique attributes including a complex mating system where both men and women have partners outside of their marriage. This results in complicated family trees of multiple half relatives. Additionally, mating between first cousins in this population is preferable, resulting in an inbred population, according to Williams. These factors made constructing the pedigrees difficult for Williams because most algorithms have been designed and developed using outbred northern European datasets, which are incapable of factoring in the Himba database’s complexities. 

Previously used algorithms cannot decipher between relationships where individuals share a quarter of the same DNA, such as grandparent-grandchildren, half-siblings and avuncular relationships — those between uncles and aunts and their nieces and nephews — without external information. According to Williams, this is because algorithms review the genome in terms of the proportion of the genome that is identical by descent. 

“I tested these algorithms, and they didn’t work at all because of these problems, so I decided to write my own algorithm that dealt with these populations better,” Williams said. 

Williams’ algorithm looks at identical by descent segments instead of proportions since they are more informative. Through this algorithm, Williams can decipher between the differences in segments between different familial relationships. Through this discovery, he was able to create a pedigree for the Himba population. 

“Being able to distinguish the relations, that’s been a problem in genetics for a really long time,” Williams said. “My algorithm solves that problem. The way the future is going, it is important that we can build these family trees so we can study disease in the context of families and not as the population as a whole, so we can better understand how these traits and diseases work.”

Williams’ academic performance, in addition to his volunteer work as a counselor at Camp Kesem, a student run organization for children with parents affected by cancer, was taken into consideration in his selection as 2019 Undergraduate of the Year by the College of Biological Sciences.

“Camp Kesem was a really huge part of my time at UC Davis,” Williams said. 

Currently, Williams works as a research assistant at the Colorado Center for Personalized Medicine at the University of Colorado Anschutz Medical School. He is working to rewrite and improve his algorithm in order to be able to apply it to more outbred populations and larger datasets. 

“I’m continuing what I was doing and learning more about disease in non-European individuals,” Williams said. 

Written by: Margo Rosenbaum — science@theaggie.org 

30-second TV inserts might help children become more empathetic

The high saturation of messages from television shows is nothing new, but the influence of these messages on children might have previously been overlooked. Recent research conducted by Drew Cingel, an assistant professor of communication at UC Davis, along with professors at other universities, however, demonstrates that with further explanation, these messages can help children develop more prosocial behaviors.

“Media and technology use is a dominant activity of childhood and adolescence, not just in the United States, but around the world, and I don’t think it’s going anywhere,” Cingel said. “So I would like to spend my time as a researcher trying to understand for whom and under which conditions we can leverage these really powerful and far-reaching technologies to benefit kids in some particular way.”

For this particular field of research, Cingel was interested in how TV can be designed to promote or impede learning. Whether we are aware of it or not, children are learning both positive and negative lessons from media, explained Marina Krcmar, an associate chair and professor of communication at Wake Forest University. 

Krcmar said she was curious how children extract moral lessons from media and how media influences not only short-term behavior, but also “their more complicated processes like developing a sense of right and wrong.”

In the study, two groups of children were shown an episode of the TV show “Sofia the First.” One group watched a 30-second insert before the episode started that gave a general overview of the episode while the other group watched a 30-second insert that explicitly explained the lesson of the episode before it began, Cingel explained.

After watching the show, the children from each group were met with puppets used by researchers to measure whether their intentions to behave prosocially had increased. Since the episodes showed to the children concerned lessons around inclusivity, the researchers, via the puppets, asked questions such as, “How nice do you think this child is?” or “Would you like to be friends with this person?” 

Cingel and his team found that children who had a low theory of mind — meaning children who struggle to conceptualize other people’s thoughts — who had watched the episode including the insert explicitly explaining the lesson had an increase in prosocial intentions. Since it only takes 30 seconds to see this change in behavior, Cingel explained that production companies would be able to add these explanatory inserts in with little impact on advertising time. In addition, these inserts are cost-effective, since they don’t require a high level of production. The researchers were able to see results even though the inserts were not professionally made.

“I’d like people to see that well-designed, developmentally appropriate media can have a positive impact in the lives of kids and that there are things that we can do as content producers, as parents, as supportive adults in the lives of at least a child,” Cingel said. “There are relatively small things that we can do to help a child learn something that can be really important. Learning to be more prosocial and more stigmatizing is going to have a profound impact on many dimensions of that child’s life.”

Krcmar advises parents to be selective with the media they let their children consume to mitigate its negative effects while also being active consumers with their children in order to enforce the positive messages. 

“Television influences kids not in terms of their behavior, but [in] more subtle ways including things that we hope that we’re doing well which is improving their sense of moral reasoning,” Krcmar said. “If we could teach children to take the perspective of others, hopefully we can create a population that is more ethical — essentially better human beings.”

Written by: Michelle Wong — science@theaggie.org

Some believe negligence is to blame

Seven infant primates died while under the watch of scientists at the California National Primate Research Center. Dedicated to improving the health of both animals and people, The California National Primate Research Center is located on the outskirts of the UC Davis Campus, between West Village and Putah Creek. 

“The center carries out research that benefits human health, for example on HIV/AIDs, Zika virus and other infectious disease, respiratory disease, reproductive health, Alzheimer’s disease and aging,” said Andy Fell, a spokesperson for the primate center.

The animals died due to a suspected cause of negligence in 2018. However, this news was not announced until just last month. 

The university said the infant primates died from an allergic reaction to dye passed on to them by their mothers, but Michael Budkie of Stop Animal Exploitation NOW says this is not likely. 

“It seems to me that UC Davis is attempting a cover-up,” Budkie wrote in a complaint filed with the U.S. Department of Agriculture. 

According to federal documents, the baby primates died from untreated sepsis and bronchopneumonia. There is no evidence of veterinary care given to these animals, according to Budkie. 

“The records indicate that five of the infant monkeys likely had an anaphylactic reaction. But the other two had severe infections. Things like this do not develop overnight. UC Davis clearly failed to provide adequate veterinary care and their negligence in that regard killed two of these infants,” Budkie said. 

Fell said animals at the center receive “the utmost care.”

In an attempt to improve this animal rights issue, SAEN filed a complaint with the USDA asking for a $10,000 fine to be imposed on The California National Primate Research Center for the death of each primate.

Written by: Ellen Caminiti — science@theaggie.org

UC Davis, Carnegie Mellon engineers bring together synthetic biology and soft robotics

Robots are often thought of as metallic, manufactured and artificial. Yet recent research conducted by engineers at both UC Davis and Carnegie Mellon University (CMU) has opened up a branch of science in which robots and nature collide.

Carmel Majidi, an associate professor of mechanical engineering and director of the Soft Machines Lab at CMU, expressed interest in the relationship between biology and machinery.

“I’ve always been interested in how natural organisms and biological materials

can inspire new types of machines and materials technologies,” Majidi said.

Cheemeng Tan, an associate professor in biomedical engineering at UC Davis, began collaborating with Majidi when he was a post-doctorate at CMU. They both wondered if combining synthetic bacteria with a soft robot could create a new function for the robot.

The term “soft robot” is due to the robot’s gripper function — the fingers are made soft in order to grab and adapt to the shape of the object, according to Tan. Majidi explained that these rubbery fingers are embedded with sensors composed of genetically modified E. coli bacteria that are able to create fluorescent proteins when in contact with a certain chemical and a flexible circuit. The fluorescence is then converted into an electrical signal that directs the robot’s fingers.

“We chose E. coli because of the versatility with which we can turn it into an artificial cell with properties that we can engineer,” Majidi said. “Through genetic modifications, we can ‘program’ the E. coli bacteria so that it responds to chemical stimulation in a way that we can measure with on-board electronics.”

Tan discussed two primary challenges that arose when designing the robot: creating an environment within the soft robot where the bacteria could function and engineering an interface where the bacteria could communicate with the robot. The solution was to house the bacteria in an artificial growth chamber and design a tube to detect the optical signal from the bacteria and instruct the robot.

“We had a challenge for awhile with the membrane system, but we didn’t know it for awhile,” said Phillip LeDuc, a professor of mechanical engineering, biomedical engineering, computational biology and biological sciences at CMU. “It was through patience and persistence that this was solved!”

Since the communication aspect of the robot was one of the most challenging parts of the design — because of how small the signal being detected was in comparison to the environment — it took two years to finetune this function. The original idea for this collaboration was conceived in 2013, and its first prototype was developed around three to four years later.

“The next steps are to literally design the robot so that it can start taking steps,” Majidi said. “The current robot is a gripper that is mounted to a robotic arm. The next robot would be like an octopus or starfish that could move around and collect chemical samples at different locations. Another future goal is to use advancements in synthetic biology to be able to measure a wider range of chemicals or environmental conditions.”

Majidi hopes that from their research people will realize it is indeed possible to combine synthetic biology and soft robots in the same material architecture. She believes that the continuation of this field of study could lead to the development of soft biohybrid robots that use artificial cells to achieve new adaptive functions. 

“In terms of science, I’d like people to learn about how we could combine living cells and materials in a new way to create new hybrid systems that can do new things that existing organisms or existing materials cannot do,” Tan said. “In terms of just general approach, I’d like people to know more about interdisciplinary science and how one can work with people with different expertise and then combine the expertise to really create a new area.”

Written by: Michelle Wong — science@theaggie.org