CBSD's 6th Annual CoBRE Research Symposium

Date: Sept. 8-9, 2017

Location: University of Montana, Missoula, MT 59812

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Agenda

All day open symposium, UC 326-327, unless otherwise noted.

8:30 – 10:45 a.m. Subproject Investigator Presentations

Moderator: Stephen Sprang

8:45 – 9:00 a.m. CBSD Director Stephen R. Sprang, opening remarks and introduction  |  UC 326-327

9:00 – 10:45 a.m.  UC 326-327 (20 minute presentation + questions)

  • Celine Beamer, New Developments in the Aryl Hydrocarbon Receptor Structure
  • Philippe Diaz, Potentiating the Activity of Endogenous Retinoic Acid A Neglected Therapeutic Strategy
  • Kasper Hansen, Investigations of Ligand Binding to NMDA Receptors
  • Andrea Stierle, Development of More Potent Inhibitors of Molecular Pathways Associated with Epithelial Mesenchymal Transition (EMT) and New Antibiotics from Cryptic Biosynthesis
  • Dong Wang, Catalytic Water Oxidation by a Bio-inspired Nickel Complex with Redox Active Ligand

10:45 – 11:00 a.m. BREAK

11:00 – 12:30 a.m. Pilot Project, Junior Investigator & Career Development Presentations  |  UC 326-327

Moderator: Bruce Bowler
  • Pilot Projects - 15 minute presentation + questions
    • J. Stephen Lodmell, RVFV Triggers Aberrant Splicing of Genes Essential for the Cellular Antiviral Response
    • Jack Nunberg, Arenavirus Envelope Glycoprotein Nanodiscs for CryoEM Structural Analysis
  • Junior Investigator and Career Development — (20 minute presentation + questions) 
    • Travis Wheeler, Searching for Similar Sequences, Obsessing on Speed and Sensitivity
    • Travis Hughes, Structure and Function Studies of the Transcription Factor PPAR Gamma
    • Patrick Secor, Entropically Driven Bacterial Aggregation Induces the SOS Response and Antibiotic Tolerance

12:30 – 1:45 p.m. Lunch

Lunch for participants will be served in the Meeting Room (MR) Foyer.


A private lunch for Vice President for Research and Creative Scholarship, CBSD Director, Associate Director, External Advisory Committee, & Internal Advisory Committee will be served in the Alumni Board Room (UC 329)

1:45 – 2:45 p.m. CBSD Fellowship Presentations (7 minute presentations) |  UC 326-327

Moderator: Cindee Yates-Hansen
  • Adam Drobish, Production of Poly-N-Acetylyglucosamine by the Spirochete Borrelia burdorferi
  • Miyuki Hayashi, Rift Valley Fever Virus Nucleocapsid Protein Binds to C/D Box Motifs of snoRNA
  • Yubin Kwon, Uncovering Late-Transition Metal-Oxo Species Beyond the Oxo-Wall
  • Daniel Olson, TRUCE: A Hidden Markov Model for Annotation of Tandem Repeats
  • Denis Shchepakin, A Photoswitchable Inhibitor of a Glutamate Transporter
  • Joachim Veit, Novel CYP26 Inhibitors Potentiate the Effects of All-Trans Retinoic Acid on Phenotype of Normal and Darier Disease Keratinocytes in Reconstructed Human Epidermis
  • Luke White, Rift Valley Fever Virus and Splicing: a Minigene Approach

2:45 – 3:00 p.m. BREAK

3:00 – 4:30 p.m.  Poster Presentation  |  UC 330-331

  • Dustin Becht, Residual Structure in the Denatured State of a Three-Helix Bundle Protein
  • Ian Chrisman, Examining the conformational ensemble in the peroxisome proliferation-activating receptor gamma (PPARγ) ligand binding domain
  • Nicholas Day, Dynein Light Chain 1 Participates in Post-Transcriptional Regulation of Germline mRNAs
  • Margaret Elmer-Dixon, Investigation of Membrane Curvature Dependency on Cytochrome c Binding to Cardiolipin
  • Miyuki Hayashi, Rift Valley Fever Virus Nucleocapsid Protein Binds to C/D Box Motifs of snoRNA
  • Katie Hornak, RVFV infection induced modification of host alternative splicing
  • Jake Johnston, Conformational changes of Gai1 nucleotide exchange catalyzed by Ric-8A
  • Yubin Kwon, Uncovering Late-Transition Metal-Oxo Species Beyond the Oxo-Wall
  • Moses Leavens, Denatured state conformational bias in a three-helix bundle
  • Haotian Lei, Effects of humanizing mutations on heme crevice loop of cytochrome c
  • Casey Massena, Delving into the Solution Dynamics of a Halogen Bonding Anion Triple Helicate
  • Levi McClelland, Kinetic insights into Ric-8A GEF activity
  • Michelle Nemetchek, Coregulators select conformational states from drug specific peroxisome proliferator-activated receptor gamma (PPARγ) conformational ensembles
  • Alex Nord, Splice-aware multiple sequence alignment improves protein alignment quality and supports alternative reading frame detection
  • Daniel Olson, TRUCE: A Hidden Markov Model for Annotation of Tandem Repeats
  • William Penny, Characterization of phospholipid and sphingomyelin bilayer solvation characteristics by nanodisc electrokinetic chromatography
  • James Rogan, Dimeric Human Cytochrome c Shows Increased Peroxidase Activity
  • Melissa Roseleip, Expression and Purification of Ric8B Delta9
  • Harmen Steele, Exploring the Stability and Cardiolipin Affinity of Cytochrome c’s Domain-Swapped Dimer Conformation
  • Sascha Stump, First crystal structure of the major quadruplex formed in the promoter region of the human c-MYC oncogene
  • Joachim Veit, Novel CYP26 Inhibitors Potentiate the Effects of All-Trans Retinoic Acid on Phenotype of Normal and Darier Disease Keratinocytes in Reconstructed Human Epidermis
  • Xiaobo Wang, Characterization of DLC-1 role in FBF-2 RNP assembly
  • Luke White, Rift Valley fever virus and splicing: a minigene approach
  • Ziquing Xie, Investigation of Membrane Curvature Dependency on Cytochrome c Binding to Cardiolipin
  • Feng Yi, Properties of triheteromeric NMDA receptors containing two distinct GluN1 isoforms
  • Baisen Zeng, A Structural Study on RIC-8A, a novel guanine-nucleotide exchange factor (GEF)
  • Le Zhang, Inter-strain variation in gH/gL complexes is influenced by both the expression-level, and the amino acid sequence of gO

4:30 – 5:00 p.m.  Graduate Student round table with EAC  |  UC 329 (Alumni Boardroom)

6:00 p.m. – Invitation only - Evening social

9:00 – 10:30 a.m. CBSD CoBRE Core Facility Presentations (20 minute presentations + questions) | UC 326

  • Biospectroscopy Core Research Laboratory (BCRL) - J.B. Alexander (Sandy) Ross

  • Macromolecular X-ray Diffraction Core Facility - Tung-Chung Mou

  • Molecular Computation Core Facility - David Holley

10:30 – 10:45 a.m. BREAK

10:45 – 11:30 a.m. CBSD Core Facility Round Table  |  UC 329 (Alumni Boardroom)

This is a round table for the CBSD Core Facility Directors, Managers, External Advisory Committee and Internal Advisory Committee Members.

  • BCRL (Sandy Ross; IAC: Ekaterina Voronina, Scott Wetzel)

  • MCCF (Nicholas Natale & David Holley; IAC: Xi Chu, Travis Hughes, Michael Kavanaugh)

  • MXDC (Stephen Sprang, Orion Berryman & T.C. Mou; IAC: Klara Briknarova, Bruce Bowler)

11:30 a.m. – 1:00 p.m. Lunch  |  UC 329 (Alumni Boardroom)

This is a private lunch for the CBSD Director, Associate Director and External Advisory Committee.

1:00 – 1:30 p.m. Break

1:30 – 2:30 p.m. Faculty Individual Meetings with External Advisory Mentor 

Escort from and back to UC 329 (Alumni Boardroom)

  • Travis Hughes and David Case
  • Dong Wang and Elizabeth Goldsmith
  • Philippe Diaz and Suzanne Scarlata
  • Patrick Secor and Elizabeth Goldsmith
  • Celine Beamer and Wesley Sundquist
  • Travis Wheeler and David Case

2:30 – 2:45 p.m. Break

2:45 – 4:00 p.m. External Advisory Committee Final Evaluation Meeting (private) |  UC 329 (Alumni Boardroom)

6:30 p.m. Dinner

A private dinner for CBSD Director, Associate Director and External Advisory Committee.

Abstracts

Exclusive access to these abstracts is granted to you directly by CBSD. No part of these abstracts may be used without the author(s) permission.

20 minute presentation + questions

  • Celine Beamer, New Developments in the Aryl Hydrocarbon Receptor Structure
    • Abstract not available.

 

  • Philippe Diaz, Potentiating the Activity of Endogenous Retinoic Acid A Neglected Therapeutic Strategy
    • Abstract not available.

 

  • Kasper Hansen, Investigations of Ligand Binding to NMDA Receptors
    • Abstract not available.

 

  • Andrea Stierle, Development of More Potent Inhibitors of Molecular Pathways Associated with Epithelial Mesenchymal Transition (EMT) and New Antibiotics from Cryptic Biosynthesis
For the past twenty years the Stierle research lab has studied the extremophilic fungi isolated from an acid mine waste lake. These Fungi have produced numerous compounds that target  pathways associated with several different types of pathologies including neurodegenerative diseases, stroke, cancer, and inflammation-associated disorders. A select group of these compounds will be described that have been assessed for their ability to inhibit cancer cell migration and invasion, two key processes associated with EMT and its role in carcinogenesis.
The Stierle lab is also studying the cryptic biosynthesis of new molecules produced by these fungi when grown as carefully time cocultures. The Berkeleylactones are a new class of antibiotic macrolide that targets Gram-positive bacteria, particularly erythromycin/methicillin-resistant strains of Staphylococcus aureus, with MIC values of 1 µg/mL. These compounds lack the sugar moieties usually associated with both the activity and induced resistance associated with other classes of macrolide antibiotics, and have a different mode of action. This presentation will also highlight the structural characterization, structure activity relationships and mode of action studies of these compounds.
  • Dong Wang, Catalytic Water Oxidation by a Bio-inspired Nickel Complex with Redox Active Ligand
    • Abstract not available.
  • Pilot Projects - 15 minute presentation + questions
J. Stephen Lodmell, RVFV Triggers Aberrant Splicing of Genes Essential for the Cellular Antiviral Response
Rift Valley fever virus is a mosquito-borne pathogen endemic to Africa and the Arabian Peninsula that causes significant human and livestock morbidity and mortality. Because the mosquito species that carries RVFV is present in the Western hemisphere, there is concern that RVFV outbreaks could occur in the Americas. Upon infection of mammalian cells by RVFV, the cell mounts an antiviral response to thwart the infection. However, RVFV, through the actions of the virally encoded N and NSs proteins, mitigates the expression of host antiviral factors. The role of N in triggering aberrant alternative splicing of cellular mRNAs will be discussed.
Jack Nunberg, Arenavirus Envelope Glycoprotein Nanodiscs for CryoEM Structural Analysis 
In contrast to the previously characterized Junín virus GPC, Lassa virus GPC purified from insect-cell membranes was found to fractionate as a broad peak on Superose 6 size-exclusion chromatography, ranging from the expected trimer (~220kDa) to presumed aggregates of >1000 kDa. The molecular size of the protein in the SEC fractions was stable to repeated chromatography and appeared to correlate with particle size determined by dynamic light scattering and negative-stain electron microscopy. Initial studies to form nanodiscs using the pooled material were unsuccessful. Efforts are now focused on stabilizing the LASV GPC trimer by varying extraction conditions and by mutation.
  • Junior Investigator and Career Development — (20 minute presentation + questions)
Travis Wheeler, Searching for Similar Sequences, Obsessing on Speed and Sensitivity
  • Abstract not available.

 

Travis Hughes, Structure and Function Studies of the Transcription Factor PPAR Gamma
  • Abstract not available.

 

Patrick Secor, Entropically Driven Bacterial Aggregation Induces the SOS Response and Antibiotic Tolerance
Bacteria causing chronic infections are generally observed to be living within cell aggregates, rather than as free-living individual cells, and bacterial phenotypes induced by aggregated growth are thought to be a key factor in infection persistence. Bacterial aggregation can occur as a consequence of active bacterial processes related to biofilm formation. However, particles within polymer suspensions (colloidal suspensions) can aggregate spontaneously by a mechanism called depletion aggregation. Depletion aggregation is an entropic force that operates between uncharged or like-charged polymers and particles in crowded, polymer-rich environments. When particles such as bacterial cells aggregate, more volume becomes available to the highly dynamic polymer coils, resulting in a net gain of entropy.

Because high concentrations of polymers are often present at sites of chronic infection, and both polymers and bacterial cells typically carry net-negative charges, we tested whether synthetic and disease relevant polymers caused aggregation of Pseudomonas aeruginosa via the depletion mechanism. We found that depletion aggregation operated on wild type bacteria, as well as biofilm-deficient and dead bacteria. Furthermore, depletion aggregation is a reversible mechanism; diluting the polymer-rich environment holding depletion aggregates together causes bacteria to disperse.

Aggregated growth is associated with antibiotic tolerance. Therefore, we tested the antibiotic tolerance of depletion aggregates. Depletion aggregates became tolerant to antibiotics after only minutes in the aggregated state. Control experiments showed that antibiotic tolerance was not due to inactivation of antibiotics by polymers. Because depletion aggregation promoted tolerance to multiple classes of antibiotics, we hypothesized that bacterial stress responses may be responsible for producing the tolerance phenotype. We began by testing the SOS stress response, which is known to promote antibiotic tolerance. Depletion aggregation activated a fluorescent SOS reporter and induced SOS-regulated genes. Furthermore, SOS inactivation reduced antibiotic tolerance of aggregates formed by the depletion mechanism. Together, these studies suggest that depletion aggregation induces genotoxic stress that induces the SOS response, resulting in antibiotic tolerance.

7 minute presentations

  • Adam Drobish, Production of Poly-N-Acetylyglucosamine by the Spirochete Borrelia burdorferi
Borrelia burgdorferi, the highly pathogenic bacterial agent of Lyme Disease, is the most commonly reported vector-borne disease in the United States. In nature, the bacteria cycle between hard ticks and mice throughout their lifetime. When the tick takes a blood meal from an infected mammal, the bacteria survive within the midgut under starvation conditions. Poly-N-¬acetylglucosamine (PNAG) is a known extracellular polysaccharide that allow certain bacteria to thrive in harsh environments. The role of PNAG production in Borrelia burgdorferi has been analyzed by immunofluorescence.
  • Miyuki Hayashi, Rift Valley Fever Virus Nucleocapsid Protein Binds to C/D Box Motifs of snoRNA
Nucleocapsid (N) protein in Rift Valley fever virus (RVFV) is an RNA binding protein and recognizes its binding target possibly by interacting with a secondary structure or specific sequence of RNA. Based on previous experiments, the N protein preferentially binds to RNAs that contain CUGA/UGA motifs. In this project, CLIP (cross-linking immunoprecipitation) sequencing data, which has been obtained by cross linking the N protein with human cellular RNA, was analyzed using a bioinformatics approach. The analysis has shown that N protein prefers binding to box C/D class small nucleolar RNA (snoRNA) over other classes of snoRNA.
  • Yubin Kwon, Uncovering Late-Transition Metal-Oxo Species Beyond the Oxo-Wall
Terminal-oxo species of transition metals are the key intermediates in many biological systems such as the mononuclear non-heme Fe oxygenases that utilize Fe(IV)-oxo intermediates to initiate oxidative transformations. The generation of stable high-valent metal-oxo complexes for late-transition metals is challenging synthetically. In this work we aim to study the reactivity of a nickel(II)-hydroxo complex with an O-transfer reagent iodosylbenzene by combined spectroscopic methods including UV-Vis, 1H NMR, FTIR, and X-ray crystallography. Our results indicate the formation of a new stable nickel species. Additionally, we have fine-tuned the nickel (II) complex by adding steric hinderance to observe the applied reaction.
  • Daniel Olson, TRUCE: A Hidden Markov Model for Annotation of Tandem Repeats
Short tandem repeats (STR) consist of tens to hundreds of residues in a repeating pattern, such as atgatgatgatgatg ('atg' repeated). STRs often decay so that the original pattern is obstructed. STRs cause false matches when searching for homologous sequences. To reduce false positives in sequences searches, STRs are masked by tandem repeat detectors such as TRF. Current generation software poorly detects insertions and deletions, leaving a large number of STRs entirely undetected and unmasked. We introduce a new STR detector called TRUCE (Tandem Repeat Unifying disCovErer) which uses hidden Markov models to detect even highly obstructed STRs.
  • Denis Shchepakin, A Photoswitchable Inhibitor of a Glutamate Transporter
Abstract not available.
  • Joachim Veit, Novel CYP26 Inhibitors Potentiate the Effects of All-Trans Retinoic Acid on Phenotype of Normal and Darier Disease Keratinocytes in Reconstructed Human Epidermis
Darier disease (DD) is a rare hereditary dominant human disorder characterized by warty papules and plaques in seborrheic areas of the skin. RA and its derivatives (retinoids) cause substantial clinical improvements in patients with DD. However, their use remains limited due to significant adverse effects. In this study, we investigated the effects of RA alone or in combination with these CYP26 inhibitors on gene expression and on epidermal barrier using transepithelial electrical resistance (TEER), in reconstructed human epidermis (RHE) made of primary keratinocytes from either normal or DD patients.
  • Luke White, Rift Valley Fever Virus and Splicing: a Minigene Approach
Rift Valley fever virus is an RNA virus endemic to Africa and the Arabian Peninsula that is devastating to both humans and livestock. The viral nucleocapsid protein, N, has been shown to not only protect viral RNA and aid in replication, but it also interacts with host transcripts. We hypothesize that N induces an alteration of host splicing patterns to subvert the host antiviral response. To understand how N affects splicing, we are taking a minigene approach using an intron-containing reporter gene to investigate N-induced alternative splicing.