Course Description
Discussion of pertinent articles from current literature. Credit/no-credit only.
Spring 2019 Schedule
Coordinator: Mike Guttman
The theme for this quarter will be: Tutorials and Research Practicals
Date | Topic | Supplemental Information |
---|---|---|
Apr 8 | Making figures, illustrator examples | Making Effective Scientific Figures |
Apr 15 | Publication insights & quick tutorial on PyMOL | Publication Notes PyMOL Basics |
Apr 22 | 3D printers & material compatibility | Material Combatibility 3D Printers |
Apr 29 | Modern approaches to cloning and DNA sequencing | Cloning Overview |
May 6 | Linux and DOS basics | Operating Systems MSDOS |
May 13 | Model selection and fitting Excel Example |
Model Selection and Fitting Data Fitting Using Excel |
May 20 | Rotation talks (20 min each) | |
May 27 | No meeting (Memorial day) | |
Jun 3 | Practical aspects and best practices with light spectroscopy |
Winter 2019 Schedule
Coordinator: Libin Xu
The theme for this quarter will be: Focus on grant writing.
Presenter should write a short proposal and present it (white board preferred,
powerpoint and/or handouts allowed). Three students serve as primary peer reviewers,
but all will have a chance to provide feedback in class.
Please send PDF versions of your papers to Sarah on the Wednesday before MNM.
Date | Presenter | Paper (Click title to download PDF) |
Supplemental Information |
---|---|---|---|
Jan 7 | No Meeting | ||
Jan 14 | Libin Xu | NIH Grant Writing and Peer Review | Peer Review Form |
Jan 21 | No Meeting | MLK Holiday | |
Jan 28 | Ben Maldonato (Totah) | Maldonato Proposal on Canvas site | |
Feb 4 | Mark Benhaim (Lee) | Benhaim Proposal on Canvas site | |
Feb 11 | John Kowalski (Rettie) | Kowalski Proposal on Canvas site | |
Feb 18 | No Meeting | President's Day Holiday | |
Feb 25 | Amy Li (Xu) | Li Proposal on Canvas site | |
Mar 4 | Eddie Hodge (Lee) | Hodge Proposal on Canvas site | |
Mar 11 | Mike Watson (Guttman) | Watson Proposal will be posted on Canvas site |
Autumn 2018 Schedule
Coordinator: Rheem Totah
Please send PDF versions of your papers to Sarah on the Wednesday before MNM.
Spring 2018 Schedule
Coordinator: Bill Atkins
Please send PDF versions of your papers to Sarah on the Wednesday before MNM.
The theme for this quarter will be: Papers that changed the way you think about your project other than methodology.
Date | Student Moderator | Faculty Moderator | Paper (Click title to download PDF) |
Supplemental Information |
---|---|---|---|---|
Apr 9 | Li | Atkins | Cholesterol-mediated Degradation of 7-Dehydrocholesterol Reductase Switches the Balance from Cholesterol to Vitamin D Synthesis | |
Apr 16 | Hodge | Atkins | The Tetrameric Plant Lectin BanLec Neutralizes HIV through Bidentate Binding to Specific Viral Glycans | |
Apr 23 | Watson | Atkins | Molecular Basis of Assembly and Activation of Complement Component C1 in Complex with Immunoglobulin G1 and Antigen | Supplemental Info |
Apr 30 | Paco | Atkins | Selective Mechanism-Based Inactivation of CYP3A4 by CYP3cide (PF-04981517) and Its Utility as an In Vitro Tool for Delineating the Relative Roles of CYP3A4 versus CYP3A5 in the Metabolism of Drugs | |
May 7 | Murphree/Shen | Atkins | rotation talks | |
May 14 | Do/Cho | Atkins | rotation talks | |
May 21 | Vorauer/Larsen | Atkins | rotation talks | |
May 28 | No Meeting | Memorial Day Holiday |
Winter 2018 Schedule
Coordinator: Abhinav Nath
The theme for this quarter will be:
Papers that overnturned a
pre-existing paradigm in their field.
Date | Student Moderator | Faculty Moderator(s) | Paper (Click title to download PDF) |
Supplemental Information |
---|---|---|---|---|
Jan 8 | No Meeting | |||
Jan 15 | No Meeting | MLK Holiday | ||
Jan 22 | Evangelista | Nath | Efficient Hypoxic Activation of the Anticancer Agent AQ4N by CYP2S1 and CYP2W1 | |
Jan 29 | Ross | Nath | Structural basis of Smoothened regulation by its extracellular domains | |
Feb 5 | Aliwarga | Nath | Dual inhibition of cyclooxygenase-2 and soluble epoxide hydrolase synergistically suppresses primary tumor growth and metastasis | |
Feb 12 | Baughman | Nath | Amyloid-β peptide protects against microbial infection in mouse and worm models of Alzheimer’s disease | |
Feb 19 | No Meeting | President's Day Holiday | ||
Feb 26 | Redhair | Nath | Cytochrome P450 Compound I: Capture, Characterization, and C-H Bond Activation Kinetics; | |
Mar 5 | Williams | Nath | Antibody-Dependent Enhancement of Dengue Virus Infection in Primary Human Macrophages; Balancing Higher Fusion against Antiviral Responses |
Autumn 2017 Schedule
Coordinator: Kent Kunze
The theme for this quarter will be:
Reproducibility and Science and Scientific Literature
Spring 2017 Schedule
Coordinator: Mike Guttman
The theme for this quarter will be: CRISPR & PCSK9 Inhibitors
Please continue to follow all of the guidelines below. Papers must be made available online by the Thursday before MNM so send PDF versions of your papers to Sarah on Wednesdays.
Follow these guidelines for your presentation, no exceptions:
- Papers should cover either:
1) CRISPR: Therapeutic uses or new applications
or
2) PCSK9 Inhibitors - No articles from before 2009, reviews, or articles with your PI listed as an author. You may, however, provide any of these as supplemental material.
- The week before your presentation, papers must be sent to Sarah Lenti on Wednesday for posting on Thursday.
- Prepare talking points as before: one page maximum, at least 12 point font + 1” margins, preferably double-spaced. Do not copy/paste text from the article. Bring enough copies for the group, or distribute them by e-mail the Friday before meeting.
- You may also prepare up to 3 powerpoint slides. These should be uncluttered and easily readable from the back of the room. Save text for talking points.
Date | Student Moderator | Faculty | Paper |
Supplemental Information |
---|---|---|---|---|
Mar 27 | No Meeting | |||
Apr 3 |
Rob | Libin & Mike | Multiplex Genome Editing to Generate Universal CAR T Cells Resistant to PD1 Inhibition | CAR T Cells - Supplemental |
Apr 10 | Mark | Rheem & Libin | Multi-input CRISPR/Cas genetic circuits that interface host regulatory networks | |
Apr 17 | James | Kent & Abhi | Engineering Complex Synthetic Transciptional Programs with CRISPR RNA Scaffolds | |
Apr 24 | Lorela | Kent & Rheem | Nucleic acid detection with CRISPR-Cas13a/C2c2 | Supplemental Materials |
May 1 | Michelle | Abhi & Kelly | Identification of a Small Peptide That Inhibits PCSK9 Protein Binding to the Low Density Lipoprotein Receptor | |
May 8 | Dylan | Mike & Bill | In vivo genome editing using Staphylococcus aureusCas9 | |
May 15 | Amy and Mike | Rotation Talks | ||
May 22 | Eddie | Rotation Talks | ||
May 29 | No Meeting - Memorial Day |
Winter 2017 Schedule
Coordinators: Eri Nakatani-Webster (Kelly Lee)
The theme for this quarter will be: “What can structure tell us and what can’t it tell us about biological and enzymatic function?”
Please continue to follow all of the guidelines below. Papers must be made available online by the Thursday before MNM so send PDF versions of your papers to Sarah on Wednesdays, but they do not need to be submitted to Eri for review first.
Follow these guidelines for your presentation, no exceptions:
- No articles from before 2009, reviews, or articles with your PI listed as an author. You may, however, provide any of these as supplemental material.
- The week before your presentation, papers must be sent to Sarah Lenti on Wednesday for posting on Thursday.
- Prepare talking points as before: one page maximum, at least 12 point font + 1” margins, preferably double-spaced. Do not copy/paste text from the article. Bring enough copies for the group, or distribute them by e-mail the Friday before meeting.
- You may also prepare up to 3 powerpoint slides. These should be uncluttered and easily readable from the back of the room. Save text for talking points.
Additionally, Ben and Ryan have volunteered to present a 1-2 page writing sample to be workshopped. The samples will be available under Supplemental Information, along with a feedback form to be completed by the readers. Please be prepared to hand it in on the day of the workshop.
Date | Student Moderator | Faculty | Paper |
Supplemental Information |
---|---|---|---|---|
Jan 2 | No Meeting | |||
Jan 9 | Dennis | Mike, Libin | Competition for FcRn-mediated transport gives rise to short half-life of human IgG3 and offers therapeutic potential | Supplemental Information |
Jan 16 | MLK Day – No Meeting | |||
Jan 23 | John | Abhi, Rheem | Mechanism of Inactivation of Neuronaal Nitric Oxide Synthase by (S)-2-Amino-5-(2-(methylthio)acetemidamido)pentanoic Acid | |
Jan 30 | Ben | Rheem | Ben's Workshop (feedback form) | |
Feb 6 | David | Libin, Mike | Remarkably Fast Coupled Folding and Binding of the Intriniscally Disordered Transactivation Domain of CMyb to CBP KIX | Supplemental Information |
Feb 13 | Eric | Kelly, Kent | Structures of Human Steroidogenic Cytochrome P450 17A1 with Substrates | |
Feb 20 | Presidents Day – No Meeting | |||
Feb 27 | Rob | Kelly, Abhi | TBA | |
Mar 6 | Ryan | Kent | Ryan's Workshop (feedback form) | Writing Sample |
Autumn 2016 Schedule
Coordinator: Eri Nakatani-Webster (Allan Rettie)
This quarter, select a paper that nicely showcases the technique of your choosing. It can be one you are already familiar with, or something you have been interested in learning more about. Please come prepared to thoroughly explain this technique to your peers.
We will be returning to the newer MNM format. Please e-mail papers to Sarah Lenti to be posted to the website after they are approved.
Follow the guidelines below for your presentation, no exceptions:
- No articles from before 2009, reviews, or articles with your PI listed as an author. You may, however, provide any of these as supplemental material.
- The week before your presentation, papers must be sent to Eri for review by 11:59 PM on Tuesday, and sent out for posting by 5:00 PM on Thursday.
- Prepare talking points as before- one page maximum, at least 12 point font + 1” margins, preferably double-spaced. Do not copy/paste text from the article. Bring enough copies for the group, or distribute them by e-mail the Friday before meeting.
- You may also prepare up to 3 powerpoint slides. These should be uncluttered and easily readable from the back of the room. Save text for talking points.
Feel free to contact Eri Nakatani-Webster with any questions or concerns.
Date | Student Moderator | Faculty Moderator(s) | Paper (Click title to download PDF) |
Supplemental Information |
---|---|---|---|---|
Oct 3 | No Meeting | |||
Oct 10 | Mark Benhaim | Rheem, Mike | Folding of a Large Protein at High Structural Resolution | |
Oct 17 | James Williams | Abhi, Mike | Native structure of a retroviral envelope protein and its conformational change upon interaction with the target cell | |
Oct 24 | Kelly Hines (Postdoc) | Libin | Research Presentation: HILIC-IM-MS Reveals Altered Bacterial Lipidome in Antimicrobial Resistance | |
Oct 31 | Lorela Paço | Kelly, Kent | Visualizing the kinetic power stroke that drives proton-coupled zinc(II) transport | Supplemental Information |
Nov 7 | Mavis Li | Rheem, Libin | The uncoupled ATPase activity of the ABC transporter BtuC2D2 leads to a hysteretic conformational change, conformational memory, and improved activity | |
Nov 14 | Eri Nakatani-Webster (Postdoc) | Abhi | Building mechanistic models from kinetic data: adventures in amyloid formation | |
Nov 21 | Michelle Redhair | Allan, Kelly | Revisiting the Metabolism of Ketoconazole Using Accurate Mass | |
Nov 28 | No Meeting - Thanksgiving | |||
Dec 5 | Dylan Ross | Allan, Kent | Travelling-wave ion mobility mass spectrometry and negative ion fragmentation of hybrid and complex N-glycans |
Spring 2016 Schedule
Coordinator: Wendel Nelson
Winter 2016 Schedule
Coordinator: Libin Xu
Autumn 2015 Schedule
Coordinator: Eri Nakatani-Webster (Rheem Totah)
This quarter, we ask that you present a paper that is central to your research, and one you refer back to often -- perhaps a critical study that helped form the basis of your project, or one that is focused around a technique or system that is of great importance to your work. The idea is to play to your own strengths -- choosing a paper you are familiar with will help ensure it is a quality publication, while giving the new students a chance to acquaint themselves with everyone's projects and areas of expertise.
We encourage you to present newer papers, but if you can make a good case for one that is over 20 years old, we are open to discuss it. Please refrain from presenting review articles and publications coming from your own lab.
We will be trying a radically different, PowerPoint-free format for Monday Night Meeting this quarter. Rather than a presentation, please prepare a number of talking points you'd like to discuss with the group. More details will come during the October 5 discussion.
Spring 2015 Schedule
Coordinator: Kent Kunze
Date | Speaker | Paper (Click title to download PDF) | Supplemental Information |
---|---|---|---|
Apr 13 | Ryan Seguin | Carbon Radicals in the Metablism of Alkyl Hydrazines | |
Apr 20 | James Williams | Virus Capsid Expansion Driven by the Capture of Mobile Surface Loops | |
Apr 27 | Wynton McClary | Metabolic Switching in Cytochrome P-450cam: Deuterium Isotope Effects on Regiospecificity and the Monooxygenase/Oxidase Ratio | |
May 4 | Hannah Baughman David Baggett |
The Conformational Ensembles of α-Synuclein and Tau: Combining Single-Molecule FRET and Simulations | Supplemental information |
May 11 | Ben Maldonato | ||
May 18 | Mark Behnaim | ||
May 25 | HOLIDAY | NO MNM | |
Jun 1 | John Kowalski | TBD |
Winter 2015 Schedule
Coordinator: Abhinav Nath
Guidelines for choosing a paper: Your paper should describe at least one conceptual or technical breakthrough. You should be prepared to discuss exactly what elevates your choice over a routine paper in the field. We're looking for good papers that challenge us and teach us something new, rather than for run-of-the-mill papers that may be easier to tear down. They don't necessarily have to be recent - if you have a classic paper that you'd like to share, bring it on.
I suggest taking the time to explain how any non-routine techniques or assays work. A common theme in many of the survey responses is that unfamiliarity with techniques is an obstacle to appreciating papers that are out of one's comfort zone.
Date | Speaker | Paper (Click title to download PDF) | Supplemental Information |
---|---|---|---|
Jan 5 | NO MNM | ||
Jan 12 | All | Open discussion about the peer review process | Slides and useful links |
Jan 19 | HOLIDAY | NO MNM | |
Jan 26 | Natalie Garcia | Amphipols Outperform Dodecylmaltoside Micelles in Stabilizing Membrane Protein Structure in the Gas Phase | |
Feb 2 | Lucas Monkkonen | The Orbitrap: a new mass spectrometer | |
Feb 9 | David Baggett | A new antibiotic kills pathogens without detectable resistance | Supplemental information |
Feb 16 | HOLIDAY | NO MNM | |
Feb 23 | Eric Evangelista | A rationally designed monomeric peptide triagonist corrects obesity and diabetes in rodents | Supplemental information |
Mar 2 | Dennis Goulet | Generation of bispecific lgG antibodies by structure-based design of an orthogonal Fab interface | Supplemental information |
Mar 9 | Amanda Johnson | AAV-expressed eCD4-Ig provides durable protection from multiple SHIV challenges |
Autumn 2014 Schedule
Coordinator: Carlos Catalano
Spring 2014 Schedule
Coordinator: William Atkins
Date | Speaker | Paper (Click title to download PDF) | Supplemental Information |
---|---|---|---|
Apr 7 | NO MNM | NO MNM | |
Apr 14 | Grant Barker | 1-Aminobenzotriazole Coincubated with (S)-Warfarin Results in Potent Inactivation of CYP2C9 | |
Apr 21 | Amanda Johnson | Menadione (Vitamin K3) is a Catabolic Product of Oral Phylloquinone (Vitamin K1) in the Intestine and a Circulating Precursor of Tissue Menaquinone-4 (Vitamin K2) in Rats | |
Apr 28 | Natalie Garcia | pH-Controlled Two-Step Uncoating of Influenza Virus | Supplemental Information |
May 5 | Lucas Monkkonen | Use of the interior cavity of the P22 capsid for site-specific initiation of atom-transfer radical polymerization with high-density cargo loading | Supplemental Information |
May 12 | Dennis Goulet | ||
May 19 | David Baggett | ||
June 2 | Eric Evangelista |
Autumn 2013 Schedule
Coordinator: Allan Rettie
Spring 2013 Schedule
Coordinator: Wendel Nelson
Date | Speaker | Paper (Click title to download PDF) | Supplemental Information |
---|---|---|---|
Apr 15 | Amanda Johnson | Formation, Reactivity, and Antiplatelet Activity of Mixed Disulfide Conjugates of Clopidogrel | Supplemental Information |
Apr 22 | Wynton McClary | Detection of Drug Bioactivation in Vivo: Mechanism of Nevirapine-Albumin Conjugate Formation in Patients | Supplemental Information |
Apr 29 | Ryan Seguin | Quinone-Induced Activation of Keap1/Nrf2 Signaling by Aspirin Prodrugs Masquerading as Nitric Oxide | Supplemental Information |
May 6 | Shannon Kruse | Selective Estrogen Receptor Modulator (SERM) Lasofoxifene Forms Reactive Quinones Simmilar to Estradiol | |
May 13 | Aaron Teitelbaum | Thiolactone Sulfoxides as New Reactive Metabolites Acting as Bis-Electrophiles: Implication in Clopidogrel and Prasugrel Bioactivation | |
May 20 | NO MNM | NO MNM | |
May 27 | HOLIDAY | NO MNM | |
Jun 3 | Rotation Talks | NOTE: Begins at 3:30 p.m. |
Winter 2013 Schedule
Coordinator: Rheem Totah