Thursday, May 5, 2022

Unveiling the genes linked to the synthesis of many complex Human Milk Oligosaccharides (HMOs)

The complex carbohydrates in human milk (Human Milk Oligosaccharides or HMOs) are important to infant development. Studies supporting this claim continue to pile up, including a study led by UC San Diego researchers showing that one of the biggest killers of preterm infants, necrotising enterocolitis, is blocked by having enough of one complex sugar in particular.

There are hundreds of different molecular structures of these HMOs in human milk and several are being tied to neurodevelopment, immunity development, and modulation of the infant microbiome. One big challenge is that researchers don't know all the biochemical details of how HMOs are made in the mom. This makes it hard for researchers to understand why some moms make little or none of some important HMOs, or how we can metabolically engineer microbes to produce HMOs as nutraceutical additives or therapeutics in infants and people of all ages

In a study in Nature Communications published on May 4, 2022 entitled "Elucidating Human Milk Oligosaccharide biosynthetic genes through network-based multi-omics integration," a cross-disciplinary team led by UC San Diego researchers used a systems biology approach to integrate gene expression data and HMO composition data to discover the genes linked to the synthesis of many complex HMOs.

“In our study,” said UC San Diego professor Nathan Lewis, the corresponding author of this work, “we were able to decipher the details of the HMO biosynthetic pathway. This will help researchers link maternal genetics to differences in milk composition and guide metabolic engineering for HMO production in efforts to improve infant development and for further nutritional applications.” Lewis holds appointments in the Department of Pediatrics at UC San Diego Health and the Department of Bioengineering at the UC San Diego Jacobs School of Engineering. He is Co-Director of the CHO Systems Biology Center at the UC San Diego Jacobs School of Engineering and an alumnus of the bioengineering graduate program at UC San Diego. 

The paper includes authors from the Department of Pediatrics at UC San Diego Health; the Bioinformatics and Systems Biology Graduate Program at UC San Diego; the Department of Bioengineering at the UC San Diego Jacobs School of Engineering; the Larsson-Rosenquist Foundation Mother-Milk-Infant Center of Research Excellence (MOMI CORE), UC San Diego; the Complex Carbohydrate Research Center, University of Georgia, Athens; and the Department of Pediatrics, Children’s Nutrition Research Center, US Department of Agriculture/Agricultural Research Service, Baylor College of Medicine.

Screen shot of the paper title and author list from the May 4 2022 Nature Communications paper

Thursday, April 28, 2022

UC San Diego Space and Rocket Science Makes Strong Showing at Barrio Logan Event

Space science and rockets built by UC San Diego students were front and center at the Barrio Logan Science and Art Expo on April 16, 2022. 

The event is an inclusive, annual art, science and culture fair for families from southern San Diego, organized in partnership by the Barrio Logan Association, the San Diego Festival for Science and Engineering, UC San Diego and other community partners. 

This year, two student organizations joined Professor Boris Kramer from the Department of Mechanical and Aerospace Engineering to crew a booth themed "Space Research at UCSD."

"We got a lot of attention," said Boris Kramer, a professor in the department, who was also in attendance. "It is incredibly rewarding to take part in these outreach events." 

Kramer's research group, whose work is supported by the National Science Foundation, showed recent research in space weather forecasting. They also investigate how holes in the sun's corona and solar storms can cause disruptions to satellites and GPS as well as cause Earth-based power outages. 

SEDS@UC San Diego showed off Vulcan I, the world's first rocket powered by a 3D printed engine to be designed and launched by undergraduate students in 2016. The organization has also developed a testing set up for static firing, various rocket engines, a lander testbed and more. 

The Rocket Propulsion Laboratory showcased their Phoenix rocket, designed to reach up to 50,000 ft in altitude, as well as their Marginal Stability rocket, which is designed to reach the Von Karman line typically considered the edge of space, at 52 miles above the surface of the Earth. 


Wednesday, April 20, 2022

Tara Javidi awarded $1M NSF grant to make wireless networks more resilient

Tara Javidi, a professor of electrical and computer engineering at UC San Diego, has received a $1M award from the National Science Foundation’s Division of Computer and Network System as part of NSF’s new Resilient & Intelligent NextG Systems (RINGS) program.

Javidi, who is a founding co-director of the Center for Machine-Intelligence, Computing and Security (MICS) at UC San Diego, was awarded the grant to design a new generation of wireless networks that are resilient to unforeseen disruptive events, such as a weather event that can disable base station operations. The specific aim of the project is to design intelligent and actively vigilant networks that are in a constant state of preparedness, continually adapting their view of the world by actively sensing the environment, learning from the past, and counterfactually reasoning about the system’s future.

To bring intelligence and vigilance to these wireless networks, Javidi’s team will work on providing a novel active resiliency paradigm that senses both the internal system state and the external environment to learn and reason about anomalies. The inclusion of sensing into a future physical layer will be a cornerstone of realizing next generation wireless networks such as 6G. Joint sensing and communication will enable high performance allocation of limited resources and create the ability for the network to reason about itself and its environment.

Project title: LARA: Layering for Active Resiliency and Awareness in Next-generation in Wireless Networks

Wednesday, April 13, 2022

Rebecca Gow: using bioengineering to study movement and injury prevention in athletes

 By Kiran Kumar

Rebecca Gow as an undergraduate
rugby player. Now, she's using
bioengineering tools to prevent
injury in athletes.

UC San Diego bioengineering graduate student Rebecca Gow is currently working on a project to study movement competency in athletes, specifically female soccer players. Movement competency refers to how a certain movement or physical task is performed, and how it can correlate to injury. Gow, a student in bioengineering Professor Andrew McCulloch’s Cardiac Mechanics Research Laboratory, was particularly excited to contribute to this research since she’s been an athlete her whole life.

“I played softball for about 12 years, all the way up through high school, and then played rugby in college,” said Gow. “I was very much interested in conducting research with athletes.”

After receiving Institutional Review Board approval, Gow and researchers in McCulloch’s lab will work directly with athletes to study movement competency using a novel screening approach. These movement screen tests are crucial for training and injury prevention; however, most existing screening tools are visual assessments, and can miss minor functional deficits when observing movement competency and identifying asymmetries and postural deficiencies in athletes.

“Movement quality is currently assessed visually so this can be subjective and affected by how well trained the reviewer is,” said Gow.

Instead, Gow will use Inertial Measurement Units (IMUs) to provide a less subjective, mathematical alternative to the existing visual screen tests.  IMUs are small devices used to determine the orientation of, for example, a body segment. Athletes will wear them while performing a set sequence of actions and the data will be used to calculate joint angles. With a physics based analysis, this data will help explain the link between movement patterns and incidence of injury.

Another benefit of using IMUs is that these movement tests could then be done in a natural athletic setting, instead of having athletes come into a lab for a traditional motional analysis screening.

Ultimately, this new way to study movement could explain how different movement patterns lead to injury in the short and long term, helping prevent injury for athletes, as well as people performing everyday tasks.

Gow met McCulloch at a bioengineering department social, where she was also introduced to the Wu Tsai Human Performance Alliance, which this project is part of. The Alliance is a scientific collaboration among six universities including UC San Diego, that aims to transform human health on a global scale through the discovery and translation of the biological principles underlying human performance. For Gow, that means playing a role in injury prevention.

“I think that the Alliance is a great opportunity to make connections and collaborate with researchers all over the United States to do groundbreaking research,” said Gow. “It is an incredible group of people that I can learn more from.”

Tuesday, April 5, 2022

Help us reach our goal for Franklin Antonio Hall

 Maybe you’ve joined the virtual hard hat tours. Maybe you’ve read about the new construction. Maybe you've even seen it for yourself along Voigt Drive. But the big news is that Franklin Antonio Hall is nearly open and you can help support it. Franklin Antonio Hall is nearly 200,000 square feet of research, education, and creation space that is helping make bold possible at the Jacobs School. 

Alumni, corporations, and community members have truly stepped up to help make Franklin Antonio Hall a reality. We’ve raised over $59M toward our $60M goal for the new building. Thank you to all of our supporters. 

You can help, with a gift of your own. You can make a tax deductible gift online HERE. If interested, naming opportunities begin at $25,000 and can be paid over a five-year period. If interested, please contact (518) 331-1120 or 

Watch live as the Hall is being built: 

Thursday, March 31, 2022

Shaochen Chen receives NSF BRITE Award to develop 3D printed microscale human organs-on-a-chip

NSF Brite Fellow Shaochen Chen of the University of California San Diego will create a nanoscale biomanufacturing platform powered by artificial intelligence that can serve as a functional, three-dimensional model of human tissues, organs and systems. This “human-on-a-chip” could transform regenerative medicine and tools for disease modeling, drug screening, environmental studies, space exploration, and other applications. 

The National Science Foundation has awarded an engineering research grant to Shaochen Chen, professor and chair of nanoengineering at the University of California San Diego, to explore 3D printed microscale human organs-on-a-chip. 

Funded through the NSF Boosting Research Ideas for Transformative and Equitable Advances in Engineering (BRITE) program, the 5-year BRITE Fellow grants provide up to $1 million per project. The NSF BRITE program is funded by NSF Division of Civil, Mechanical and Manufacturing Innovation (CMMI) in the NSF Engineering Directorate. 

"NSF created the BRITE Fellows opportunity to support proven researchers who have a high-risk vision with the potential for high reward for the Nation," said CMMI Division Director Robert Stone. "We anticipate that the research of the BRITE Fellows will create new fields, challenge current paradigms, or present unconventional approaches to intractable problems."

With funding from the NSF Brite program, Chen will create a nanoscale biomanufacturing platform powered by artificial intelligence that can serve as a functional, three-dimensional model of human tissues, organs and systems. This "human-on-a-chip" could transform regenerative medicine and tools for disease modeling, drug discovery and screening, environmental toxicity studies, and other applications.

By powering his 3D bioprinting platform with artificial intelligence, Chen aims to minimize the trial-and-error associated with the process that often leads to waste of cells and time. "This is a critical issue for bioprinting since live cells are quite expensive, difficult to acquire (think of patient cells, for example), and do not survive well outside the incubator," he said. 

The ultimate goal of the project is to fabricate a human-on-a-chip in a microfluidic platform that integrates major human tissues including heart, liver, kidney, lung, and gut, and then study the chip's biomechanics and tissue functions. 

Wednesday, March 23, 2022

Jacobs School engineers named to Explorers Club 50 list

A Jacobs School of Engineering graduate student and a recent PhD alumna were among the 50 scientific explorers named to The Explorers Club 50 list of people changing the world who the world needs to know about. 

Founded in 1904 by a group of America's leading explorers, The Explorers Club is a multi-disciplinary professional society dedicated to the advancement of field research, scientific exploration, and the ideal that it is vital to preserve the instinct to explore. The club's mission is to encourage and promote scientific exploration of land, sea, air and space, with an emphasis on the physical and biological sciences. 

Vid Petrovic, computer science PhD student

UC San Diego computer science PhD student Vid Petrovic was named to the list for his work with the Cultural Heritage Engineering Initiative and the Drone Lab at the Qualcomm Institute at UC San Diego. His research interests span computer graphics, scientific visualization, machine learning and GIS, with a focus on the challenges of the accelerating collection and accumulation of site data in marine ecology, digital archaeology and cultural heritage. He is the principle developer of the Viscore platform, a software environment for integrating collected site data and performing virtual fieldwork, 

"I work to help make virtual exploration of remote sites practical and useful," said Petrovic. "Drawing on experience in digital documentation of archeological sites in Jordan and on digital augmented fieldwork in Florence, Italy, which is part of a search for a lost DaVinci wall painting, I have been developing tools and techniques for performing fieldwork digitally, especially on sites that are difficult to access.

"An underwater cave system such as the Sac Actun in the Yucatan is inaccessible except to highly skilled divers. Remote reefs such as the Palmyra Atoll do not require as much diving skill, but still present logistical barriers to a frequent, thorough study. In either case, opportunities for in-person exploration are constrained by the realities of underwater work. To get around this, we can use the limited time in the field to digitize the site through systematic imaging and surveying so that it can be explored virtually."

Jessica Sandoval, 2021 materials science PhD alumna

Jessica Sandoval, who earned her PhD in materials science and engineering in the Bioinspired Robotics and Design Lab at UC San Diego in 2021, is an avid ocean explorer, engineer and scientist. As a pilot of remotely operated vehicles (ROV), she works to advance technology in the fields of bioinspired robotics and deep-sea exploration by designing new adhesives and grippers for use in subsea manipulations. 

"As an ROV pilot, engineer and scientist, I strive to push boundaries and ultimately to transform the face of exploration. Working in the heavily male-dominated field of ROV piloting, I became one of a small handful of lead female pilots. With the support of the Ocean Exploration Trust, I have grown as a leader at sea. I have taken on additional roles on the ship, including working as a 15-ton certified crane operator during deck operations for launch and recovery of the vehicles. 

"Through my experiences, it became clear to me that representation and advocacy is crucial to broadening these fields to be more inclusive. I strive to encourage the participation of young women to join these fields. I frequently give guest lectures and presentations to young students and help to proctor workshops to encourage young women in STEM fields. I hope to lead by example and show that a Latina woman can push past barriers of representation and change the notion of what it means to be an explorer."