Past MBTG Events

Monthly Student Seminar Series

2018-19 Speakers

Date Trainee Title of Talk
Oct 2, 2018 Hannah Rutledge Probing the role of a redox-switchable ligand in the nitrogenase P-cluster
Nov 6, 2018 John Gillies Lis1 promotes the formation of maximally activated dynein complexes
Dec 4, 2018 Kira Podolsky Peptide inhibitors for the membrane delocalization of KRAS4B
Jan 8, 2019 Sonjiala Hotchkiss Development of Allosteric Inhibitors of IKK2
Feb 5, 2019 Bryce Ackermann

Heterochromatin protein HP1α gelation dynamics revealed by solid-state NMR spectroscopy

Mar 5, 2019 Cyrus de Rozieres Investigating the NS1 mediated Translation Upregulation of Influenza Infection
Apr 2, 2019 Dominic McGrosso LAMPS: Ligand Activated Molecular Probes
May 7, 2019 Joshua Corpuz Structural studies of carrier protein specificity in antibiotic biosynthesis
Jun 4, 2019 Clara Posner Exploiting and Minimizing Fluorescence Fluctuations: New Methods for Superresolution Activity Imaging and Multiplexed FRET Imaging

2017-2018 Speakers

Date Speaker Topic
Oct 3, 2017 Noah Kopcho, Geoffrey Chang Lab “How the P-glycoprotein interacts with Amyloid beta”
Nov 7, 2017 Canceled
Dec 5, 2017 Evan Kobori, Susan Taylor Lab “Conformational States of PKA activation”
Jan 9, 2018 Kevin Sweeney, Ulrich Muller Lab "Lanthanides as cofactors for RNA world-relevant ribozymes"
Feb 6, 2018

Joshua Arriola, Ulrich Muller Lab

“Identification of the shortest catalytic motifs from hundreds of ribozymes”
Mar 6, 2018 Colin Deniston, Andres Leschziner Lab “Investigation into the structure of the Parkinson’s disease associated protein LRRK2 and its interaction with microtubules”
Apr 3, 2018 Adam Maloney, Simpson Joseph Lab “A Minimal Eukaryotic Translation System for Studies of FMRP”
May 1, 2018 Hetika Vora, Neal Devaraj Lab  "Targeted Depalmitoylation of N-Ras for Suppression of Oncogenic Signaling Pathways."
Jun 12, 2018 Bryce Timm, Kamil Godula Lab “Probing the Molecular Mechanisms of Human Sulfatase Specificity”

2016-2017 Speakers

Date Speaker Topic
Oct 4, 2016 Ben Jagger, Rommie Amaro/Andy McCammon Labs “Milestoning: Kinetic Rates for the 99%"
Nov 1, 2016 Charles Lin, Ross Walker Lab “Molecular Dynamics: Preparing AMBER for an Exoscale Future”
Dec 6, 2016 Riley Peacock, Elizabeth Komives Lab "Functional Dynamics of Thrombin"
Jan 10, 2017 Sarah Kochanek, Rommie Amaro/Andy McCammon Labs "Brownian Dynamics of Computationally Designed Proteins Against Influenza"
Feb 7, 2017

Please attend the Graduate Student Seminar in the Garren Auditorium (School of Medicine) at 4:00pm. 

William L. Jorgensen, PhD. Yale University

"Computationally Driven Discovery of Enzyme Inhibitors"

Mar 14, 2017 DeeAnn Asamoto, Judy Kim Lab "Investigation of Membrane Protein Folding in Nanodiscs"
Apr 11, 2017 Benjamin Dick, Seth Cohen Lab "Crystallographic Studies of Metalloenzyme Inhibitors"
May 9, 2017 Sam Kantonen, Mike Gilson Lab “Binding Thermodynamics Prediction and Measurement”
Jun 13, 2017 Jeff Mindrebo, Joe Noel/Mike Burkart Labs "Structure and Function of Secondary Metabolite Biosynthesis Enzymes"

Invited Seminar Series

Ahmet Yildiz

 

University of California, Berkeley

“The Mechanism of Dynein Motility
Feb 26, 2019 at 12:00pm - NSB Auditorium 1205
Hosted by Mounir Fizari

yildiz_ahmet.jpgMy laboratory studies the mechanism of cytoplasmic dynein, a AAA motor responsible for minus-end-directed motility along microtubules. Using single-molecule imaging and force spectroscopy in vitro, we showed that dynein has distinct features from kinesin and myosin motors. In my talk, I will present a robust mechanistic model of dynein motility, directionality and force generation. I will also show how adaptor proteins that recruit the dynein-dynactin complex to intracellular cargos regulate its motility and force generation.

 

Jon Clardy

Harvard Medical School

“Molecular Messages in the Human Gut Microbiome
Jan 30, 2019 at 12:00pm - Leichtag 107
Hosted by Hetika Vora

Jon Clardy

Numerous studies with varying degrees of statistical power have found correlations between the constitution of the human gut microbiome and disease states. But the molecules and mechanism(s) connecting a dysbiotic microbiome to a specific disease are not well known. In an attempt to address this gap, we undertook a series of screens to link bacterial metabolites with the regulation of pro- and anti-inflammatory cytokines. The talk will describe the screening logic of the approach, the selection of candidate bacterial producers, the discovery of the small molecule regulators of cytokine production and their biosynthesis, and speculations about mechanisms.

John Kuriyan

University of California, Berkeley 

“Deconstruction of the Ras switching cycle through saturation mutagenesis
Feb 12, 2018 at 12:00pm - Leichtag 107
Hosted by Adam Maloney

Stephen H. White

Department of Physiology and Biophysics, University of California at Irvine 

"Membrane Protein Folding: Biology Meets Thermodynamics"
May 30, 2017 at 12:00pm - NSB 1205
Hosted by Noah Kopcho

David E. Shaw

Columbia University and DE Shaw Research

“Long molecular dynamics simulations of proteins: Progress, promise, problems”
March 15th, 2016 at 2:00pm - NSB 1205
Hosted by Chris Lee

Marcus Covert

Stanford University

"Integrating Large-scale, Heterogeneous Measurements in a Single Cell"
May 9th, 2016 at 12:00pm - Leichtag 107
Hosted by Ryan Lannan

Thomas F. Miller, III

California Institute of Technology

"Multiscale Dynamics of Enzyme Catalysis and Sec-Facilitated Protein Translocation"
April 21, 2015 at 12:00pm - NSB 1205
Hosted by Jeff Wagner

Matthew Disney

The Scripps Research Institute

"Sequence-based design of selective small molecules targeting RNA"
February 20, 2015 at 12:00pm - NSB 1205
Hosted by Jessica Peters

Annual Retreat

2019 MBTG Annual Retreat

Friday, April 5th, 2019, 3:00pm - 7:00pm, Institute of the Americas

The 2019 MBTG Annual Retreat was held on Friday, April 5th at the Institute of the Americas. The program featured new MBTG faculty talks, alumni lightning talks, a trainee poster session, and dinner afterwards. MBTG Trainees, Alumni, Faculty Mentors, and interested PhD students all attended in support of the MBTG Program. 

The following new Chemistry Faculty gave talks on their research:

  • Tatiana Mishanina: RNA polymerase: Stop-and-go traffic on the DNA highway
  • Mark Herzik: Bringing Mitochondrial Transport into View Using Novel cryo-EM Methodologies

The 16 current MBTG trainees participated in a Poster Session, with the following trainees awarded:

poster-awards
  • 1st: Bryce Ackermann, Debelouchina Lab: "Heterochromatin protein HP1α gelation dynamics revealed by solid-state NMR spectroscopy"
  • 2nd: John Gillies, Reck Peterson Lab: "Lis1 promotes the formation of maximally activated dynein complexes"
  • 3rd: Hannah Rutledge, Tezcan Lab: "On the brink of lability: Stabilization of the nitrogenase P-cluster by a redox-switchable ligand"

  poster_session_1  mbtg-annual-retreat-2019_poster_session2-crop.jpg  poster_session3

Above, current MBTG Trainees participate in the poster session. 

audience  faculty-talk-tatiana-mishanina  faculty-talk-mark-herzik

Participants listen to faculty talks given by Dr. Tatiana Mishanina (center) and Dr. Mark Herzik (right).

rob-alberstein  deann-asamoto  colin-deniston

ben-jagger  evan-kobori  sarah-kochanek

noah-kopcho  chris-lee  ryan-lumpkin
jeff-mindrebo  sarah-ur

MBTG Alumni gave five-minute lightning talks on their research progress: Robert Alberstein (top left , DeeeAnn Asamoto, Colin Deniston, Benjamin Jagger, Evan Kobori, Sarah Kochanek, Noah Kopcho, Chirstropher Lee, Ryan Lumpkin, Jeffrey Mindrebo, & Sarah Ur (bottom right).

2019 MBTG Retreat Program Book & 2019 MBTG Retreat Schedule


2018 MBTG Annual Retreat

Friday, April 27th, 2018

MBTG Faculty and Trainees attended the MBTG Annual Retreat on Friday April 27th, 2018 at the Institute of the Americas’ Copley International Conference Center. The Retreat featured talks by the following emerging Chemistry faculty at UCSD:

  • Galia Debelouchina: “In cell structural biology of chromatin organization”
  • Colleen McHugh: “Identifying and targeting non-coding RNA and protein interactions”
  • Alexis Komor: “Investigating the Chemical Biology of DNA Damage and Repair”
  • Lalit Deshmukh: “Late stages of HIV-1 replication studied by solution NMR spectroscopy”

Three MBTG alumni gave quick lightning talks of five minutes each on their research:

  • Rob Alberstein, Tezcan Lab: "Engineering the Entropy-Driven Free-Energy Landscape of a Dynamic, Nanoporous Protein Assembly"
  • Christopher Fisher, Godula Lab: "Cell Surface Remodeling with Glycopolymers to examine Influenza A host recognition"
  • Kristen Ramsey, Komives Lab: "Prediction of the Presence of a Seventh Ankyrin Repeat in IκBε from Homology Modeling Combined with Hydrogen-Deuterium Exchange Mass Spectrometry (HDX-MS)"

Afterwards, MBTG trainees presented their research at a Poster Session held in the Arango Foyer. Congrats to the three poster award winners below!

  • Hannah Rutledge, Tezcan Lab: "Investigating the Role of an Oxygen Ligand to the P‐Cluster in Nitrogenase"
  • Noah Kopcho, Chang Lab: "ABC Transporter Dynamics: A New Perspective"
  • John Gillies, Reck-Peterson Lab: "Regulation of Human Dynein by Lis1"
Thanks to faculty, speakers, trainees, and alumni for their participation in making this event a great success! 
 Rob Alberstein  Chris Fisher  Kristen Ramsey
MBTG Alumni Rob Alberstein (l), Chris Fisher, and Kristen Ramsey (r) give Lightning talks. 
Sarah Ur, Betsy Komives  Ryan Lumpkin, Bryce Ackermann  Alexis Komor, Colin Deniston
MBTG Alum Sarah Ur presents her poster to Program PI Betsy Komives (l). MBTG Alumnus Ryan Lumpkin presents to graduate student Bryce Ackermann (center). Trainee Colin Deniston presents on his research to Alexis Komor (right).
Group dinner

2018 MBTG Retreat Program Book & 2018 MBTG Retreat Schedule

2017 MBTG Annual Retreat

Friday May 5th, 2017

 

MBTG Faculty and Trainees attended the MBTG Annual Retreat on Friday May 5th, 2017 at the Institute of the Americas’ Copley International Conference Center. The Retreat featured talks by young and emerging Faculty at UCSD. Elena Koslover of the Department of Physics gave a talk on "Emergent Physics of Intracellular Soft Matter, from DNA to Cytoplasm." Dmitry Lyumkis of the Salk Institute for Biological Studies followed with a talk describing his research on “Structural Insights into Retroviral Integration using Cryo-EM.”

Five MBTG alumni gave true “lightning” talks of five minutes each on their research to update the group on their progress since leaving the program. Afterwards, MBTG trainees presented their research at a Poster Session held in the Arango Foyer. PI Elizabeth Komives and the poster judges recognized Sarah Ur and Adam Maloney with poster awards for their research. Sarah's research was entitled: “The Msh4‐Msh5 complex’s role in meiotic crossover formation” and Adam's was "A Minimal In Vitro Translation for Structural Studies of FMRP." Congratulations Sarah and Adam!

Trainees and Faculty enjoyed a BBQ Dinner afterwards on the Friend Plaza to start off their weekend right. Thanks to faculty, speakers, trainees, and alumni for their participation in making this event a great success! 

2017 MBTG Retreat Program Book & 2017 MBTG Retreat Schedule

elena koslover talk    Bryan arias talk

Elena Koslover gives her presentation (l); MBTG Alumnus Bryan Arias gives a lightning talk (r).

Poster Session    Dinner

MBTG Trainee Benjamin Jagger presents his poster (l); attendees enjoy dinner after the program (r).

Annual Meeting in the Desert

2019 Annual MBTG Meeting in the Desert

Sat. May 18th - Sun. May 19th, 2019 Anza Borrego State Park

MBTG Trainees and Faculty participated in the second annual summer camping and hiking trip to Anza-Borrego State Park in CA. Students explored nearby Julian, hiked Hellhole Canyon as well as other trails, camped at Tamarisk Grove Campgrounds, and enjoyed stargazing at the park, which is recognized as an international Dark Sky Park. Join us next year for the next annual trip!

 

 

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Journal Club

2018-19 MBTG Journal Club

Third Tuesday of each month, 4:00 pm.
Date  Location Trainee Faculty Facilitator Paper Title 
Oct 16, 2018 Urey Room (2102 UH) Elizabeth Porto Simpson Joseph "Quantitative determination of ribosome nascent chain stability"
Jan 15, 2019 NSB 3211 Mounir Fizari Galia Debelouchina "Mapping Local and Global Liquid Phase Behavior in Living Cells Using Photo-Oligomerizable Seeds"
Feb 19, 2019 (Time change 5:15pm) NSB 3211 Joshua Arriola - "A “Clickable” Photoconvertible Small Fluorescent Molecule as a
Minimalist Probe for Tracking Individual Biomolecule Complexes"
Mar 19, 2019 NSB 3211 Douglas Zhang - "Ipa1 Is an RNA Polymerase II Elongation Factor that
Facilitates Termination by Maintaining Levels of the
Poly(A) Site Endonuclease Ysh1"
Apr 16, 2019 NSB 3211 Clara Posner Alexis Komor "Field-deployable viral diagnostics
using CRISPR-Cas13"
May 21, 2019 NSB 3211 Cyrus de Rozieres Patricia Jennings "Designed Mutations Alter the
Binding Pathways of an Intrinsically Disordered Protein"

2017-18 MBTG Journal Club

Third Tuesday of each month, 4:00 pm, NSB 3211
Date  Trainee Faculty Facilitator Paper Title 
Oct 17, 2017 Riley Peacock Neal Devaraj Development of a Microflow System for In-Cell Footprinting Coupled with Mass Spectrometry
Jan 16, 2018 Hannah Rutledge Ulrich Muller Crystal structure of a novel RNA motif that allows for precise positioning of a single metal ion
Feb 20, 2018 Hetika Vora TBD Light-activated chemical probing of nucleobase
solvent accessibility inside cells
Mar 20, 2018 Bryce Timm Akif Tezcan CRISPR-Cas12a target binding unleashes indiscriminate single-stranded DNase activity
Apr 17, 2018 Kira Podolsky Gourisankar Ghosh Precision glycocalyx editing as a strategy for cancer immunotherapy
May 15, 2018 John Gillies Elizabeth Komives

A biolayer interferometry-based enzyme-linked aptamer sorbent assay for real-time and highly sensitive detection of PDGF

2016-17 MBTG Journal Club

Third Tuesday of each month, 4:00 pm, NSB 3211
Date  Trainee Faculty Facilitator Paper Title 
Oct. 18, 2016 Ryan Lumpkin Kevin Corbett The Intrinsically Disordered Protein Atg13 Mediates Supramolecular Assembly of Autophagy Initiation Complexes.
Nov. 15, 2016 Jeff Mindrebo N/A The role of protein dynamics in the evolution of new enzyme function. 
Dec. 20, 2016 Sarah Ur Andreas Leschziner Assembly and activation of dynein–dynactin by the cargo adaptor protein Hook3
Jan. 17, 2017 Rob Alberstein Rommie Amaro Chemomechanical Coupling in Hexameric Protein−Protein Interfaces Harnesses Energy within V‑Type ATPases
Feb. 21, 2017 Colin Deniston N/A Interdomain Communication of the Chd1 Chromatin Remodeler across the DNA Gyres of the Nucleosome
Mar 21, 2017 Kevin Sweeney N/A

Structural Analysis of Human Argonaute‑2 Bound to a Modified siRNA Guide

Apr. 18, 2017 Sam Kantonen Patricia Jennings

A The heat released during catalytic turnover enhances the diffusion of an enzyme. 

May 16, 2017 Evan Kobori N/A

TIRR regulates 53BP1 by masking its histone methyl-lysine binding function.

Jun. 20, 2017 Adam Maloney N/A

Real-Time Imaging of Translation on Single mRNA Transcripts in Live Cells.

Special Seminars

Lorenzo Caselino 

UCSD

"How to make Beautiful Figures"
May 7, 2019 at 5:15pm - Leichtag, Room 107
Hosted by Betsy Komives 

Kevan Shokat

UCSF

"Chemical Tricks for Drugging the Undruggable"
Feb 28, 2019 at 2:00pm - Leichtag, Room 107
Hosted by Dr. Alexandra Newton

Stephen C. Harrison

Harvard Medical School

"Structure of Yeast Kinetochores"
Feb 21, 2019 at 4:00pm - Trustees Room at the Salk Institute
Hosted by Dr. Dmitry Lyumkis

"Mechanisms of viral cell entry"
Feb 22, 2019 at 11:00am - Fred Kavli Auditorium, Tata Hall
Hosted by Dr. Elizabeth Villa 

Mark Hall

Purdue University

“Phosphatase specificity in cell cycle control: the curious case of Cdc14”
Feb 21, 2019 at 12:00pm - Pacific Hall 4500
Hosted by Dr. Elizabeth Komives

Robert Lefkowitz

Nobel Laureate, Duke University

Part I: “A Brief History of G-Protein Coupled Receptors”
Feb 19, 2019 at 4:00pm - Health Sciences Education Auditorium
Hosted by Dr. Ed Dennis

Part II: "Molecular Basis for Biased and Allosteric Activation of GPCRs"
Feb 20, 2019 at 4:00pm - Health Sciences Education Auditorium
Hosted by Dr. Ed Dennis

Martin Högbom

Department of Biochemistry and Biophysics, Stockholm University

"Discovery of undescribed metal and radical-based enzymatic chemistry - small data, low throughput science"
Jan 25, 2019 at 11:00am - Pacific Hall 4500
Hosted by Dr. Akif Tezcan

Carsten Schultz

Department of Physiology and Pharmacology, OHSU

"Imaging disease-relevant events, a starting point for translational research"
May 24, 2018 at 12:00pm - Leichtag Building, Room 107
Hosted by Drs. Jin Zhang and Palmer Taylor

Joachim Frank

Nobel Laureate, Columbia University

"Single-Particle Cryo-EM: The Sky is the Limit"
Jan 25, 2018
Hosted by Dr. Susan Taylor

Antonina Roll-Mecak

NIH/NINDS 

"How cells read and write the tubulin code"
Jan 17, 2018 at 4:00pm - Marilyn G. Farquhar Seminar Room
Hosted by Sam Reck-Peterson

Welcome Lunch

2018 MBTG Fall Welcome Luncheon

Tuesday, September 25th, 2018, 12:00pm - 1:30pm, Faculty Club (Seuss Library Room).
Kick-off of the 2018-19 MBTG year, welcoming new trainees and their advisors.

2017 MBTG Fall Welcome Luncheon

Friday, October 20th, 2017, 12:00pm - 1:30pm, Faculty Club (Lounge).
Kick-off of the 2017-18 MBTG year, welcoming new trainees and their advisors.