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News & Events

CBI alumnus Yadilette Rivera-Colon wins award!

We are proud to announce that Yadilette Rivera-Colon is one of nine winners of the Women of Color STEM Achievement Awards. See the full announcement here.

Yadilette completed her PhD in the Garman Lab in 2013, and is now an Assistant Professor of Biology at Bay Path University.

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Chalk Talk

Chalk Talk May 5, 2021 – CBI Trainees

Force-responsive Materials Utilizing Cryptic Crosslinking Sites
Adrian Lorenzana (Peyton Lab)

Establishing Adhesive Responses of Uropathogenic E. coli to Gels with Various Stiffnesses
Brandon Barajas (Schiffman Lab)

Metabolic Labeling as a Discovery Tool for Cell Wall Recycling
Rebecca Gordon (Siegrist Lab)

Chemical labeling of Mycobacteria for growth monitoring and detection
Kiserian Jackson (Siegrist Lab)

Please see our full dates for Fall 2020-Spring 2o21 and presenting labs here.

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Chalk Talk

Chalk Talk April 7, 2021 – Min Chen & Vince Rotello

Direct Cytosolic Delivery of GFP and the Awesome Power of Nuclear Fluorescence
David Luther (Rotello Lab)

Development of a Multiplex OmpG Biosensor
Josh Foster (M. Chen Lab)

Studying the conformational dynamics of Abl kinase in real time with a nanopore tweezer
Fanjun Li (M. Chen Lab)

Please see our full dates for Fall 2020-Spring 2o21 and presenting labs here.

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Chalk Talk

Chalk Talk March 3, 2021 – Yasu Morita and Dan Hebert

Polyprenol biosynthesis in the maintenance and regulation of mycobacterial membrane domain
Student Speaker -Malavika Prithviraj (Yasu Lab )

Understanding the selectivity of the UGGTs, key quality control sensors and gatekeepers of the mammalian secretory pathway
Student Speaker – Kevin Guay (Hebert Lab)

The identification and characterization of a putative ER adapter protein TTC17
Student Speaker – Nathan Canniff (Hebert Lab)

Please see our full dates for Fall 2020-Spring 2021 and presenting labs here.

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News & Events

CBI Students’ Publication: Ben Adams, Nathan Canniff and Kevin Guay reveal the specificity of key protein quality control sensors

UGGT1 and UGGT2 are key quality control factors that determine the fate of glycoproteins in the early mammalian secretory pathway. These two paralogues direct persistent molecular chaperone binding in the endoplasmic reticulum that helps with protein maturation and sorting. Persistent chaperone binding of terminally misfolded clients can target proteins for degradation by the proteasome, as well as lysosomal proteases. In our study, a quantitative glycoproteomics strategy was developed to identify cellular clients of UGGT1 and UGGT2. Interestingly, UGGT1 was found to preferentially recognize large membrane glycoproteins, while UGGT2 favored the modification of smaller soluble lysosomal proteins. This study opens the door to a detailed understanding of the recognition process for these important quality control factors and identifies targets whose folding trajectories may be altered in disease states. This work, recently published in eLife, blends chemical and cell biological approaches and was a collaborative effort by three CBI students in the lab, spearheaded by lead author Ben Adams. Ben recently started a postdoctoral position at Harvard Medical School. – Dan Hebert

“Our work identified native substrates of an essential protein quality control process and explored it’s role in glycoproteostasis.” – Ben Adams

“Novel substrates of the glucosyltransferases UGGT1 and UGGT2 have been identified and compared to an in silico N-glycoproteome” – Nathan Canniff

“Through a quantitative mass spectrometry approach we have determined endogenous substrates for UDP-glucose:glycoprotein glucosyltransferases (UGGT) 1 & 2, showing both are functional and preferentially target different substrates requiring folding assistance from calnexin and calreticulin” – Kevin Guay

Quantitative glycoproteomics reveals cellular substrate selectivity of the ER protein quality control sensors UGGT1 and UGGT2.Adams BM, Canniff NP, Guay KP, Larsen ISB, Hebert DN. Elife. 2020 Dec 15;9:e63997. doi: 10.7554/eLife.63997.PMID: 33320095. Free PMC article

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News & Events

Student Publication: Carey Dougan, “Cavitation in Soft Matter” 2020

Press release by Al Crosby, Professor of PSE

A type of damage in soft materials and tissue called cavitation is one of the least-studied phenomena in physics, materials science and biology, say expert observers. But strong evidence suggesting that cavitation occurs in the brain during sudden impact leading to traumatic brain injury (TBI) has accelerated interest recently, say materials scientist Alfred Crosby at the University of Massachusetts Amherst and his team.

Crosby is the senior author of a new “Perspectives” paper in Proceedings of the National Academy of Sciences. The researchers intend it to spark fresh discussion and drive collaboration among new communities of biologists, chemists, materials scientists, physicists and others to advance knowledge. They define high-priority goals and point out new opportunities in the field of how matter deforms and flows with cavitation.

Crosby says, “We’re breaking down barriers that separate different scientific fields to spur progress in understanding cavitation—how it causes difficult-to-diagnose injuries or unseen failure in soft materials.”

He and Ph.D. students Christopher Barney and Carey Dougan, co-first authors of the paper, worked with chemical engineer Shelly Peyton, mechanical engineer Jae-Hwang Lee and polymer scientist Greg Tew at UMass Amherst. Others on the “CAVITATE” team are chemical engineer Rob Riggleman at the University of Pennsylvania and mechanical engineer Shengqiang Cai at the University of California, San Diego. Support is from a $2.6 million grant from the U.S. Office of Naval Research.

“While the world of cavitation seems to be historically the realm of engineers and physicists, there are growing opportunities for synthetic chemistry to contribute to the field,” the authors state. “The chemistry community will significantly aid both the mechanics and biology communities in understanding the physical principles of cavitation as well as using them to advantage in chemical reactions.”

Studied mainly in fluids for many years, cavitation is the creation and collapse of bubbles in liquids, Crosby explains. When bubbles collapse they force liquid into a smaller area, causing a pressure wave and increased temperature, which lead to damage. In a pump, cavitation can erode metal parts over time, for example. Cavitation inside artificial heart valves can damage not only the parts but the blood, he says. Microcavitation in the brain as a result of high-impact blows or being near an explosion are factors in TBI.

Crosby says the team’s perspective paper explores how cavitation can be used not only for preventing damage but also how to use cavitation as a unique tool for understanding soft tissues. For example, new methods use cavitation to study how properties like strength evolve in tissues. Co-first author Barney says the researchers hope to spur new research and development in medicine, chemistry, biology, mechanics and to new uses.

Crosby invented a new experimental tool called cavitation rheology for measuring the local mechanical properties of soft matter. He says, “We hope this will lead to advances in medical devices for diagnosing disease, novel devices for protective gear and new sustainable approaches for cleaning materials.” 

Co-first author Dougan adds, “While cavitation is often thought of as something to be avoided, we aim to use it to benefit medicine and the development of new treatments.” For example, cavitation rheology can be used to measure the strength of interfaces within the brain, which is difficult to achieve with any other method, she notes. Specifically for TBI, the authors outline techniques for biologists to establish cavitation rheology as a tool for characterizing mechanical responses of soft biological tissues.

Barney, C. W., Dougan, C. E., Mcleod, K. R., Kazemi-moridani, A., & Zheng, Y. (2020). Cavitation in soft matter. Proceedings of the National Academy of Sciences of the United States of America, 117(17), 9157–9165.

https://doi.org/10.1073/pnas.1920168117
https://www.pnas.org/content/117/17/9157

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News & Events

Weiyue Xin – Graduate Research Student Seminar (GRASS) 3rd Place

CBI Trainee Weiyue Xin (Santore Lab) took third place in the Annual G.R.A.S.S. (Graduate Research Student Symposium) for her seminar on the interactions between solid domains in biomimetic membranes. Weiyue’s work is part of a larger DOE-sponsored collaboration between the Santore and Grason groups, aiming to understand new mechanisms occurring in membranes made from biomolecules, and how these interactions can be exploited in the creation of new materials.

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Chalk Talk

Chalk Talk Feb 3, 2021 – Lynmarie Thompson and Richard Vachet

“Investigating E. coli CheA Activation by Chemoreceptors using Hydrogen Deuterium Exchange Mass Spectrometry”
Student Speaker – Thomas Tran (Thompson Lab)

“DNA-Mediated Assembly of Functional Chemoreceptors: Using Structural DNA Nanotechnology to Advance Biophysical Research” Student Speaker – Tiernan Kenneday (Thompson Lab)

“Membrane Protein Structure and Binding Interactions Studied by Mass Spectrometry” Student Speaker – Xiao Pan (Vachet Lab)

Please see our full dates for Fall 2020-Spring 2021 and presenting labs here.

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Chalk Talk

Chalk Talk Dec 2, 2020 – S. Thai Thayumanavan and Patrick Flaherty Labs

Estimating Subclonal Populations from Structured DNA Sequencing Data
Student Speaker – Shai He (Flaherty Lab)

Antibody – Nanoparticle Conjugates for Targeted Delivery of Chemotherapeutics
Student Speaker – Khushboo Singh (Thayumanavan Lab)

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Chalk Talk

Chalk Talk Nov 4, 2020 – Eric Strieter and Mingxu You Labs

A Cryptic Site on the  Proteasome-Associated Deubiquitinase UCH37/UCHL5 is Required for Chain Editing and Degradation
Student Speaker – Jiale Du (Strieter Lab)

“Real-time Monitoring of Transient Lipid-Lipid Interactions in Live Cell Membranes using a DNA Prob
Student Speaker – Yousef Bagheri Zarringhabae (You Lab)

Multiplex Imaging in Living Cells with Fluorogenic RNAs
Student Speaker – Ru Zheng (You Lab)

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Chalk Talk

Chalk Talk Oct 7, 2020 – Jeanne Hardy and Amanda Woerman Labs

Studying allosteric sites on caspase-6 to aid the development of substrate-specific inhibitors
Student Speaker: Irina Sagarbarria and Andrew J. Smith (Hardy Lab)

Investigating alpha-synuclein aggregation using novel models of strain competition
Student Speaker: Sarah Holec (Woerman Lab)