This year, the Biophysics Colloquium will be on Monday, September 30, from 9:30 a.m. to 5:00 p.m. at the Wisconsin Institutes for Discovery in the DeLuca Forum. Presenters will include faculty trainers in Biophysics and current Biophysics students. Biophysics Graduate students Ashley Heitt (Henzler-Wildman Lab) and Rhea Jakhwal (Chapman Lab) will emcee the event.
In addition, this year, we are partnering with the Biochemistry Colloquium Seminar Series and will have Professor Michael Stone from the University of California-Santa Cruz join us at the WID to give his talk (no registration required for this event).
RSVP and Call for Posters
Registration is open to students and trainers in the Biophysics program. We would also like to invite non-biophysics faculty, graduate students, postdocs, and scientists in the biophysics trainers’ labs to join (space permitting). Please feel free to share this email with your lab.
For those planning to attend just the talk by Michael Stone is open to anyone; no registration is required!
Please let us know if you have any questions! We are looking forward to seeing everyone at the colloquium!
Colloquium Schedule
Morning
9:30 – 10:00
- Coffee and Conversation with Peers
10:00 – 10:05
- Welcome – Professors Alessandro Senes and Silvia Cavagnero
10:10 – 10:30
- Katarzyna (Kasia) Radziwon, Biophysics PhD Student
- “Proteome-derived peptide library approach to study the specificity of protein phosphorylation erasers”
- Phosphorylation is a key post-translational modification that controls most cell signaling processes. While the specificity of kinases—enzymes responsible for adding phospho-marks—has been thoroughly studied, the other half of the story, the phospho-erasers, remains largely unexplored. These phospho-erasers include phosphatases, which catalyze reversible dephosphorylation, and phospholyases, which do it irreversibly. My research focuses on a phospholyase called OspF, and through this project, I’ve developed a method to study enzyme specificity that can be applied to the phospho-erasers. By understanding their specificity, we can deepen our understanding of cell signaling, and maybe even pave the way for developing new inhibitory drugs.
- “Proteome-derived peptide library approach to study the specificity of protein phosphorylation erasers”
10:35 – 11:05
- Andrea Putnam, Assistant Professor, Department of Biomolecular Chemistry
- “Granules, Foci, Clusters, Bodies: Membraneless compartments in development”
- The spatial and temporal organization of biomolecules is essential for driving developmental processes and environmental responses. While traditional cellular compartments are enclosed by lipid bilayers, many membraneless structures, known as condensates, form through liquid-liquid phase separation. This model for cellular organization requires a new investigative framework that incorporates the roles of multivalent, non-specific, and disordered interactions, alongside the biophysical properties of liquid droplets, such as surface tension and viscosity. In our research, we employ a combination of biochemical, biophysical, and biological techniques to demonstrate how these properties are dynamically regulated during C. elegans embryogenesis.
- “Granules, Foci, Clusters, Bodies: Membraneless compartments in development”
11:10 – 11:30
- Ye Liu, Biophysics PhD Student
- “How Does the Spliceosome Recognize Splice Sites?”
- A key step in eukaryotic gene expression is splicing, which removes introns from pre-mRNA and joins exons to form mature mRNA. The spliceosome recognizes splice sites (SS) (exon/intron boundaries) to determine which sequences to remove and which to keep. The 3′ SS is particularly challenging for the spliceosome to identify. We have studied how a key amino acid in the Prp8 splicing factor interacts with the 3′ SS and influences SS selection, particularly in controlling the preference for a pyrimidine within the YAG consensus motif. This work also provides insight into how the spliceosome searches for these sites.
- “How Does the Spliceosome Recognize Splice Sites?”
11:35 – 11:55
- Brendan Cullinane, Biophysics PhD Student
- “Watching Single Molecule Dynamics on the Microsecond Timescale”
- The observation time in solution-phase single-molecule spectroscopy is inherently limited by the Brownian motion of the molecule. While solution-phase techniques like Fluorescence Correlation Spectroscopy (FCS) and single-molecule FRET (smFRET) provide information on changes in conformation, they often require averaging over tens of thousands of molecules and can’t probe dynamics slower than diffusion. By using an Anti-Brownian Electrokinetic (ABEL) trap, we can observe solution-phase single molecules beyond the diffusion barrier up to several seconds. By combining the ABEL trap with smFRET and FCS we show the ability to look at the dynamics of individual DNA hairpins in solution over the microsecond to millisecond timescale.
- “Watching Single Molecule Dynamics on the Microsecond Timescale”
12:00 – 1:00: Lunch
Afternoon
1:05 – 1:35
- David Baum, Professor, Department of Botany
- “From chemistry to biology during life’s origin”
- The talk will summarize a new interdisciplinary approach to studying origins of life that entails diverse theoretical, computational, and laboratory research. This framework is shedding light on how systems capable of adaptive evolution can emerge from out-of-equilibrium chemistry and may guide the search for “life” across the universe and may ultimately enable the creation of new evolving chemical systems in the laboratory.
- “From chemistry to biology during life’s origin”
1:40 – 2:00
- Qixiang He, Biophysics PhD Student
- “Human CST sets the stage for Pol⍺-primase to jumpstart DNA replication at telomere overhang”
- Telomeres are protein-DNA structures at the end of eukaryotic chromosomes that are essential for genome integrity. Hence, the loss of telomere length maintenance leads to premature aging and cancer. Telomere maintenance is underpinned by a two-step telomeric DNA synthesis process: telomere G-overhang extension by telomerase and the complementary C-strand fill-in by DNA Polymerase alpha-primase (Polα-primase). Compared to the G-overhang extension by telomerase, the molecular mechanism underlying the human telomere C-strand fill-in process is poorly understood at multiple levels. My thesis research uses an interdisciplinary approach to investigate the structure-function relationship of the human telomere C-strand fill-in machinery. To achieve this goal, I utilize biochemical and structural biophysical techniques to study how Polα-primase and its telomeric accessory protein CTC1-STN1-TEN1 (CST) orchestrate de novo primer synthesis to fill in the telomeric C-strand at telomere overhangs.
- “Human CST sets the stage for Pol⍺-primase to jumpstart DNA replication at telomere overhang”
2:05 – 2:35
- Joshua Brockman, Assistant Professor, Department of Biomedical Engineering
- “Super-Resolution Imaging of the Magnitude and Distribution of Piconewton Receptor Forces via DNA-PAINT”
- Mechanical forces are critical in diverse biological processes, including coagulation, cancer metastasis, embryonic development, and immune function. Individual receptors exert forces at the piconewton scale, one trillionth the force required to lift an apple. Quantifying cellular forces and the structures that generate them remains a significant challenge. This talk will describe tension-points accumulation for imaging in nanoscale topography (tPAINT), a novel combination of the super-resolution microscopy technique DNA-PAINT with DNA-based molecular tension probes. In tPAINT, receptor forces transmitted to molecular tension probes reveal concealed DNA binding sites, enabling the transient binding of complementary fluorophore tagged DNA oligonucleotides to create single molecule fluorescence suitable for super-resolution imaging. tPAINT enables live cell super-resolution imaging of the location of receptor forces with up to 25nm spatial resolution. To date, tPAINT has been applied to quantify the magnitude and nanoscale distribution of integrin and T cell receptor forces. Importantly, multiplexed tPAINT analysis provides the ability to correlate receptor forces to the protein structures that produce them, promising insight into the mechanically active protein machinery of the cell.
- “Super-Resolution Imaging of the Magnitude and Distribution of Piconewton Receptor Forces via DNA-PAINT”
Coffee Break: 2:40 – 3:00
Biochemistry Colloquium Seminar Series Speaker
3:00 – 4:00 (registration is not required for this event)
- Michael Stone, UC Santa Cruz
- “Exploring the structure and function of telomeres and telomerase – one molecule at a time”
4:00 – 5:00: Poster Session
Kaitlyn Abe, Biochemistry, Biophysics PhD Student, Lim Lab
- “Small LEA proteins as an effective air-water interface protectant for fragile samples during cryo-EM grid plunge freezing”
Sourav Agrawal, Department of Biochemistry, Biophysics PhD Student, Lim Lab
- “Human Replication Protein A complex is a Telomerase Processivity Factor Essential for Telomere Maintenance”
Kaustubh Amritkar, Bacteriology, Biophysics PhD Student, Kaçar Lab
- “TBD”
Hareesh Ashok Kumar, Mechanical Engineering, Biophysics PhD Student, Notbohm Lab
- “Role of tractions and intercellular adhesion in cell jamming”
Samridhi Garg, Biochemistry (Senes lab), Research Assistant
- “What is the structure and function ftsQLB complex in cell division?”
Dhaval Ghone, Biophysics/Oncology, Biophysics PhD Student, Suzuki Lab
- “Visualizing the trafficking of HIV-1 genomic RNA by super-resolution microscopy”
Aviad Hai, Biomedical Engineering, Biophysics Faculty Trainer
- “Engineering electromagnetic neural interfaces at the microscale”
Benjamin Harding, Biochemistry, Biophysics PhD Student, Rienstra Lab
- “Objective Approaches to Acquire and Assess Multidimensional NMR Spectra of Biological Solids”
Ashley Hiett, Biochemistry, Biophysics PhD Student, Henzler-Wildman Lab
- “NMR structural studies of small multidrug resistance transporter EmrE reflect gated transport mechanism”
Nan Jiang, Biophysics, Biophysics PhD Student, Yin lab
- “Enhanced practices for detecting deletions in SARS-CoV-2 genomes from COVID-19 patients: elimination of false positives in multiplex-PCR sequencing data”
John Judge, Neuroscience, Biophysics PhD Student, Jackson Lab
- “Multi-barrel short-term depression in L4 excitatory subpopulations of barrel cortex”
Molly McCord, Mechanical Engineering, Biophysics PhD Student, Notbohm Lab
- “Energy injection through negative viscosity in an epithelial cell monolayer”
Moses Milchberg, Biochemistry, Biophysics PhD Student, Rienstra Lab,
- “TBD”
Shweta Mishra, Neuroscience, Biophysics PhD Student, Chapman Lab
- “Molecular mechanism of synaptotagmin 7 action in short-term synaptic plasticity”
Ummay Mahfuza Shapla, Chemistry, Biophysics PhD Student, Cavagnero Group
- “An L-tyrosine isotopolog bearing a quasi-isolated spin-pair leads to significant nuclear spin hyperpolarization via LC-photo-CIDNP”
Katherine Shreeve, Chemistry, Undergraduate Student, Cavagnero Group
- “A computational analysis of E. coli proteins with potential prion-like behavior”
Jonah Spencer, Mechanical Engineering, Biophysics PhD Student, Notbohm Lab
- “Biophysical Characterization of Increased Prostate Cancer Cell Survival in Muscle Tissue”
Dan Stevens, Biochemistry, Director of Biochemistry Core Facilities/Scientist III
- “The Biophysics Instrumentation Facility”
Perla Viera, Biochemistry, Biophysics PhD Student, Rienstra Lab
- “Intermediate Aggregation States of Glycosylated Polyene Macrolides”
Owen Warmuth, Biochemistry, Biophysics PhD Student, Rienstra
- “Structure of an Alpha-Synuclein Polymorph Solved by Integrating Cryo-EM and Solid-State NMR”
Kurt Weiss, Biochemistry, Director of the Biochemistry Optical Core/ Scientist I
- “The Biochemistry Optical Core”
Ziyang Xiao, Biochemistry, Biophysics PhD Student, Kirchdoerfer Lab
- “Structural and biochemical characterization of a new potential inhibitor toward SARS-CoV-2 polymerase”
