PI: Schwartz, Samantha Lynne Title: Regulation of 2'-5'-oligoadenylate synthetase 1 (OAS1) by dsRNA 

Received: 12/08/2016 FOA: PA16-309 Council: 05/2017 

Competition ID: FORMS-D FOA Title: RUTH L. KIRSCHSTEIN NATIONAL RESEARCH SERVICE AWARD 

(NRSA) INDIVIDUAL PREDOCTORAL FELLOWSHIP (PARENT F31) 

1 F31 AI133950-01 Dual: Accession Number: 4001165 

IPF: 2384501 Organization: EMORY UNIVERSITY 

Former Number: Department: GRS: GDBBS BCDB 

IRG/SRG: ZRG1 F13-C (20)L AIDS: N Expedited: N 

Subtotal Direct Costs 

(excludes consortium F&A) 

Animals: N 

Humans: N 

Clinical Trial: N 

Current HS Code: 10 

HESC: N 

New Investigator: N 

Early Stage Investigator: N 

Senior/Key Personnel: Organization: Role Category: 

Samantha Schwartz Emory University PD/PI 

Graeme Conn Emory University Other (Specify)-Sponsor 

Anice Lowen Emory University Other (Specify)-Co-sponsor 

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OMB Number: 4040-0001 

Expiration Date: 06/30/2016 

APPLICATION FOR FEDERAL ASSISTANCE 

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Regulation of 2'-5'-oligoadenylate synthetase 1 (OAS1) by dsRNA 

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Funding Opportunity Number: PA-16-309 . Received Date: Tracking Number: GRANT12302947 2016-12-08T16:40:52.000-05:00 Page 1 
 

 

 

 

 

 

 

 

 

 

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SF 424 (R&R) APPLICATION FOR FEDERAL ASSISTANCE Page 2 

14. PROJECT DIRECTOR/PRINCIPAL INVESTIGATOR CONTACT INFORMATION 

Prefix: First Name*: Samantha Middle Name: Last Name*: Schwartz Suffix: 

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424 R&R and PHS-398 Specific 

Table Of Contents 

SF 424 R&R Cover Page. ...............................................................................................................1 

Table of Contents .................................................................................................................3 

Performance Sites. .........................................................................................................................4 

Research & Related Other Project Information ...........................................................................5 

Project Summary/Abstract(Description)............................................................................6 

Project Narrative...................................................................................................................7 

Bibliography & References Cited........................................................................................8 

Facilities & Other Resources. .......................................................................................... 11 

Equipment. ......................................................................................................................... 13 

Research & Related Senior/Key Person.................................................................................... 15 

PHS Fellowship Supplemental................................................................................................... 31 

Applicant's Background and Goals for Fellowship Training .........................................35 

Specific Aims..................................................................................................................... 39 

Research Strategy............................................................................................................. 40 

Respective Contributions................................................................................................. 46 

Selection of Sponsor and Institution............................................................................... 47 

Training in the Responsible Conduct of Research .........................................................48 

Sponsor and Co-Sponsor Statements ............................................................................ 49 

Letters of Support from Collaborators, Contributors, and Consultants.......................55 

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Resource Sharing Plan ..................................................................................................... 60 

Table of Contents Page 3 
 

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OMB Number: 4040-0001 

Expiration Date: 06/30/2016 

RESEARCH & RELATED Other ProjectInformation 

1. Are Human Subjects Involved?* ❍ Yes ● No 

1.a. If YES to Human Subjects 

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collaborators?* 

❍ Yes ● No 

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Filename 

7. Project Summary/Abstract* Project_Summary_Schwartz1032089604.pdf 

8. Project Narrative* Project_Narrative_Schwartz1032089601.pdf 

9. Bibliography & References Cited References_Schwartz1032089677.pdf 

10. Facilities & Other Resources Facilities_and_Other_Resources_Schwartz1032089597.pdf 

11. Equipment Key_Equipment_Schwartz1032089598.pdf 

Page 5 

Tracking Number: GRANT12302947 Funding Opportunity Number: PA-16-309. Received Date:

2016-12-08T16:40:52.000-05:00 
Contact PD/PI: Schwartz, Samantha 

PROJECT SUMMARY 

The innate immune system is a broad set of critical intracellular and extracellular processes that limit viral 

infectivity. In order to provide its essential first line of defenses against pathogens, the innate immune system 

must be able to accurately distinguish “self” from foreign molecules. Misregulation of the innate immune 

system can cause increased persistence and susceptibility to viral infection and human diseases, such as 

interferonopathies. The 2’-5’-oligoadenylate synthetase (OAS) family of enzymes are important innate immune 

sensors of cytosolic double-stranded RNA (dsRNA). Attesting to the importance of the OAS/RNase L pathway, 

viruses have developed ways to evade OAS. Previous structural studies have revealed that dsRNA binding 

allosterically induces structural changes in OAS1 that reorganize the catalytic site to drive synthesis of 2’-5’-

oligoadenylates from ATP. These 2’-5’-oligoadenylate secondary messengers activate a single known target, 

the latent ribonuclease (RNase L). Active RNase L in turn degrades viral and cellular RNA to halt viral 

replication. Although X-ray crystal structures have given some insight into how OAS1 is activated by dsRNA, 

we still understand very little about how specific features of the dsRNA contribute to the level of OAS1 

activation. To address which specific features of dsRNA are required for potent OAS1 activation, we designed 

dsRNA hairpin variants, based on the RNA duplex used in the structural studies. Remarkably, while a single 

point mutation on one strand resulted in complete loss of OAS1 activity, the equivalent mutation on the 

opposite strand led to increased OAS1 activity. Despite these stark differences in ability to activate OAS1, both 

variants appear to bind OAS1 with similar affinity. Given these preliminary findings, I hypothesize that 

dsRNAs may contain competing OAS1 binding sites with remarkably different capacities to activate the 

protein in a context dependent manner. However, the molecular signatures defining these sites as activating 

and non-activating are unknown. The goal of this project is to determine how specific sequences in dsRNA, 

and their context, control regulation of OAS1 in the following two Specific Aims. Aim 1. To use complementary 

assays of OAS1 activity in vitro and in human cells to determine the features of dsRNA that lead to potent 

activation of OAS1. Aim 2. To use biochemical, biophysical, and structural approaches to define the molecular 

mechanism(s) by which the dsRNA hairpin variants differ in their effects upon OAS1 activation. These 

experiments will reveal new insights into the regulation of OAS1 by dsRNA. In doing so, I will enhance our 

understanding of host-pathogen interactions, such as how viruses might circumvent the OAS1/RNase L 

pathway by masking activating motifs to evade detection. My results will furthermore provide new insights into 

cellular translational control in the context of infection and potentially strengthen the foundations necessary to 

design effective treatments for viral infection. 

Project Summary/Abstract Page 6 
 

 

 

Contact PD/PI: Schwartz, Samantha 

PROJECT NARRATIVE 

The innate immune system is our cell’s front line defense against infecting pathogens. This project will 

investigate how one important RNA-sensing component of the innate immune system is regulated by specific 

molecular signatures within double-stranded RNA molecules. Such studies are essential to understand how 

the innate immune system is controlled, how its effects can be circumvented by infecting viruses, and as a 

potential platform to design effective antiviral treatments. 

Project Narrative Page 7 
 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Contact PD/PI: Schwartz, Samantha 

REFERENCES 

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20. Wreschner DH, James TC, Silverman RH, Kerr IM. (1981) Ribosomal RNA cleavage, nuclease 

activation and 2-5A(ppp(A2'p)nA) in interferon-treated cells. Nucleic Acids Res, 9(7):1571-81. PMCID: 

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38. Liu R, Moss B. (2016) Opposing Roles of Double-Stranded RNA Effector Pathways and Viral Defense 

Proteins Revealed with CRISPR-Cas9 Knockout Cell Lines and Vaccinia Virus Mutants. J Virol, 

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central domain structure reveals minimum requirements for RNA-mediated inhibition of PKR. J Biol 

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References Cited Page 10 
 

 

 

 

 

 

 

 

 

 

 

 

 

Contact PD/PI: Schwartz, Samantha 

FACILITIES AND OTHER RESOURCES 

INTELLECTUAL ENVIRONMENT: 

I am well positioned to take advantage of the many outstanding intellectual resources Emory has to offer. In 

the Conn and Lowen labs, I will work directly alongside graduate students from several programs (including 

BCDB, Immunology and Molecular Pathogenesis (IMP), and Microbiology and Molecular Genetics (MMG)) 

as well as postdocs and other lab personnel with diverse backgrounds. Lab meetings, BCDB programsponsored events, research group meetings (e.g. Structural Biology and Emory RNA Club), and other 

Emory or local symposia will afford me many opportunities to seek important critical feedback on my work 

and enrich my intellectual and professional development. 

PHYSICAL RESOURCES: 

As described below, my Sponsor’s and Co-sponsor’s labs have the physical resources necessary for me to 

complete my proposed research (please also see Equipment for description of Conn and Lowen lab 

equipment, as well as Departmental shared equipment and Emory core facilities). Additionally, both labs 

have sufficient funding to provide me with any additional reagents/small equipment I will need. 

Laboratory: 

Dr. Conn’s research group occupies ~1250 sq. ft. of laboratory space on the fourth floor of the Rollins 

Research Center on the Emory University School of Medicine Clifton Road campus. I have designated 

bench space, complete with ample storage, and my own set of four pipetman and small equipment 

(microfuge, vortex, etc.). The laboratory is divided into four main rooms for organizational and containment 

purposes: the larger main lab space (where each lab member has their own bench), and three small labs for 

microbiology work (bacterial culture for protein expression, etc.), a hot lab for all radioisotope work, and 

crystallography area, including a stereo microscope and storage space for crystallization screens (three 

dedicated crystallization incubators). The laboratory is equipped with standard wet benches, certified fume 

hood, sinks, utilities, deionized water, etc. for experimental biochemistry, biophysics, and molecular and 

structural biology research. The Conn laboratory is approved for Biosafety Level 2 (BSL-2) work and has 

currently approved biosafety and radioisotope protocols. I also have completed all of the required safety 

training established by the Environmental Health and Safety Office, including research laboratory safety, 

biosafety, and radiation safety. Adjacent shared laboratory space is also available in common laboratories, 

computer rooms, darkrooms, temperature-controlled environments (-20, 4, 30 and 37  ̊C), libraries, and

meeting areas. The Conn laboratory has (or has immediate access to) all of the essential equipment 

required for the proposed work (see Equipment for further details). 

Dr. Lowen’s research group occupies 850 sq. ft. of recently renovated laboratory space on the third floor of 

the Rollins Research Center. The laboratory is equipped with standard wet benches, a certified fume hood, 

sink, utilities, deionized water, etc. and includes an adjoining room dedicated for cell culture. Additionally, 

Dr. Lowen has 50% use of a 100 sq. ft. cold room and 10% use of a freezer room. All equipment required is 

housed within the laboratory. The Lowen laboratory is approved for Biosafety Level 2 (BSL-2) work with 

current biosafety approvals. 

Clinical: 

N/A 

Animal: 

N/A 

Computer: 

I have an Apple MacBook Pro loaded with the Microsoft Office suite, GraphPad Prism, Adobe Illustrator and 

Photoshop, Endnote, and Findings electronic notebook software. I have wireless Internet access throughout 

the lab and office spaces, as well as access to a departmental server with a backup system. The laboratory 

and office are each supplied with networked computers and printers. In addition to my personal computer, a 

shared facility on the ground floor of the Rollins Research Center building adjacent to the X-ray laboratory 

Facilities & Other Resources Page 11 
 

 

 

 

 

X-ray Crystallographic Facilities. The Department of Biochemistry maintains an ~150 sq. ft. state-of-theart automated crystallization and ‘in-house’ X-ray data collection facility to support the research programs of 

four structural biology groups (see Equipment for details). 

 

 

Contact PD/PI: Schwartz, Samantha 

has an extensive molecular graphics area in which the Conn Laboratory has dedicated space for their 

existing computer workstations (2 x Apple Mac OSX) for data processing, model building, and refinement. 

Office: 

I have access to ~200 sq. ft. of shared office space for Conn lab postdocs, students, and staff. Drs. Conn 

and Lowen each have ~200 sq. ft. of office space with enough room to meet with students and staff located 

adjacent to their respective labs. 

INSTITUTIONAL SUPPORT: 

Synchrotron (Advanced Photon Source, APS): Emory is a member of SER-CAT (Southeast Regional 

Collaborative Access Team) at the Advanced Photon Source (APS), providing 12 days ID (undulator 

insertion device) beamtime and 12 days of BM (bending magnet) beamtime per year to the Biochemistry Xray crystallography groups. Further details are provided in the Equipment section. 

Emory Core Facilities. This proposal will use facilities within several Emory centers and core facilities: (1) 

The Emory Chemical Biology Discovery Center (http://www.pharm.emory.edu/ECBDC/capabilities.html) 

houses ‘hands-on’ equipment for quantifying molecular interactions using label-free methods, including a 

FortéBIO OctetRED384 bio-layer interferometry instrument (see attached letters). The ECBDC is located on 

the fourth floor of the Whitehead Research building, which is connected directly by internal bridge walkway 

on each floor to the Rollins Research Center (<1 minute walk from our lab). (2) The Emory Integrated 

Genomics Core (EIGC, http://cores.emory.edu/eigc/) houses instrumentation we will use for analysis of 

extracted ribosomal RNA to assess RNase L activity in transfected and/ or virus infected cells. The EIGC is 

located in a Clinical Laboratory Improvement Amendments (CLIA) certified (CLIA ID:11D1086150) 

laboratory located on the seventh floor of the Woodruff Memorial Research Building on the Clifton Road 

campus (about a 5 minute walk from our lab in the Rollins Research Center), with 2400 sq. ft. of dedicated 

wet-lab space. The EIGC’s laboratory areas include dedicated pre- and post-PCR spaces. (3) HDX-MS is 

available on campus through a new core facility established by Dr. Renhao Li in the Department of 

Pediatrics at Emory (see attached letter and Equipment for further details on the facility). The facility is 

housed in ~250 sq. ft. of newly renovated space adjacent to Dr. Li’s lab in the Emory Childrens’ Center on 

the Clifton Road campus (about a 10 minute walk from our lab in the Rollins Research Center). (4) the 

Emory Comprehensive Glycomics Core (ECGC; http://www.cores.emory.edu/ecgc/) houses additional 

‘hand-on’ instrumentation for quantifying molecular interactions using label-free methods (BiaCore X100 

surface plasmon resonance and a Malvern/ MicroCal Auto-iTC200 isothermal titration calorimetry instrument) 

in a 250 sq. ft. laboratory on the fourth floor of the Rollins ResearchCenter. 

Facilities & Other Resources Page 12 
 

 

 

 

 

 

 

 

 

 

 

 

 

 

Contact PD/PI: Schwartz, Samantha 

EQUIPMENT 

As described in the sections below, collectively the Sponsor and Co-sponsor laboratories, the Departments of 

Biochemistry and Microbiology & Immunology as well as the Emory core facilities can provide me with access 

to all of the equipment I will need to complete my proposed research. 

Conn Laboratory: All necessary equipment for RNA in vitro transcription and protein synthesis, purification, 

analysis, and crystallization is already available in the Conn laboratory on the fourth floor of the Rollins 

Research Center. We have Infors Multitron dual and Ecotron orbital shaker incubators (both with cooling 

module for low temperature expression) for bacterial culture for protein expression; a Beckman Allegra 25R 

table top centrifuge with swinging bucket and fixed angle rotors; two ÄKTA Purifier10 (FPLC) systems each 

housed in a dedicated 4  ̊C chromatography refrigerator and equipped with column selection kit for protein and

protein-RNA complex purification; a BioTek Synergy 4 multimode (absorbance, luminescence, fluorescence) 

plate reader on which we have optimized our 96-well plate chromogenic assay of OAS activation; a Cary400 

UV/Vis spectrophotomer with 6x6 cell multichanger (used for RNA UV thermal melting analysis); a Nanodrop 

2000 UV/Vis spectrophotomer; three incubators for macromolecular crystallization and Leica optical 

microscope with digital camera for viewing and recording crystallization experiments; electrophoresis 

equipment for horizontal agarose, vertical mini/ preparative PAGE (the latter custom designed for large scale 

purification of in vitro transcribed RNA), three BioRad Sequi-Gen GT sequencing gel systems, and power 

supplies; all other essential small equipment, e.g. pH meter, balances, PCR thermocycler, microcentrifuges; 

and, low temperature storage units, e.g. chiller cabinets and refrigerator (4  ̊C) and freezers (-20 and -80 ̊C).

Lowen Laboratory: Dr. Lowen’s laboratory is located on the third floor of the Rollins Research Center and is 

fully equipped for molecular and cellular biology experiments. Major equipment includes two laminar flow 

hoods, CO2 incubators, an inverted phase contract microscope, microcentrifuges, a table-top centrifuge, 

several electrophoresis systems, water baths, a bacterial culture shaker/incubator, liquid nitrogen tank, and a -

80  ̊C freezer. Additionally, a BioRad ChemiDoc imager, two DNA thermal cyclers, two BioRad real-time PCR 

instruments with 384-well capability, and a new droplet digital PCR instrument (BioRad QX200) are located in 

Dr. Lowen’s laboratory. BioRad GenePulser Xcell and Lonza Nucleofector devices for electroporation of cells 

are available in an adjacent lab. A Zeiss fluorescent microscope with digital recording system is available in the 

department, and the lab has full access to a Becton Dickenson FACS Calibur flow cytometer that is located 

down the hall. An ultracentrifuge and darkroom facilities are located within 100 feet of thelab. 

Departmental Shared Equipment: To support X-ray crystallographic studies, the Biochemistry Department 

provides a state-of-the-art facility for automated crystallization and ‘in-house’ X-ray data collection to support 

the research programs of three structural biology groups (led by Drs. Conn, Eric Ortlund, and Christine 

Dunham). This equipment is housed in dedicated laboratory space within the Rollins Research Center and 

includes a Phoenix nanoliter dispensing crystallization robot (Art Robbins Instruments), a Formulator liquid 

handling robot (Formulatrix) for crystal optimization, and a Rigaku MicroMax007HF generator with an ACTOR 

automated crystal mounting robot, Varimax-HF optics, a Saturn 944+ CCD detector, and Oxford Cryosystem XStream system. Adjacent to these facilities is an extensive molecular graphics area with dedicated space for 

computers for X-ray data processing, model building, and refinement. Emory is also a member of SER-CAT 

(Southeast Regional Collaborative Access Team) at the Advanced Photon Source (APS), providing 12 days ID 

(undulator insertion device) beamtime and 12 days of BM (bending magnet) beamtime per year to the 

Biochemistry X-ray crystallography groups. 

For recording and quantitation of OAS assays using 32P or fluorescently labeled RNAs, we have access to two 

imaging systems: a GE Typhoon FLA9000 (for 32P only) in the Department of Biochemistry and a GE 

Typhoon Trio variable mode imager system (32P and multi-color fluorescence) located in the Department of 

Microbiology and Immunology on the third floor of the Rollins Research Center building (adjacent to Dr. 

Lowen’s laboratory). 

Additional shared laboratory areas immediately adjacent to the Conn Lab house equipment available as 

needed for this project, including preparative and ultracentrifuges, autoclaves, DNA/protein gel-imaging 

system, scintillation counter, and X-ray film developer. Another shared gel imaging system, scintillation 

counter, and X-ray developer are available as in the Department, adjacent to the X-ray crystallography suite on 

the ground floor of the Rollins Research Center building. 

Equipment Page 13 
Emory Core Facilities: 

Contact PD/PI: Schwartz, Samantha 

The following core facilities house equipment that I will use during the course of my project: 

Emory Chemical Biology Discovery Center (ECBDC): For analysis of OAS1 interaction with dsRNAs, we 

have access to a high-throughput bio-layer interferometry (BLI) instrument, the FortéBIO OctetRED384 . The 

ECBDC is located in the adjacent building to the Rollins Research Center (<1 minute walk via an internal 

connecting bridge). Further info: http://www.pharm.emory.edu/ECBDC/. 

Emory HDX-MS Core: This newly established HDX-MS facility is located in the Department of Pediatrics in 

the Emory Childrens’ Center (~5 minute walk from the Rollins Research Center) on the Emory Clifton Road 

Campus. The instrument consists of an ACQUITY UPLC System with HDX Manager and automatic sampler 

paired with a Waters Q-TOF Premier mass spectrometer capable of a maximum resolution of 1/17,500 Da. 

Masslynx 4.1, ProteinLynx Global SERVERTM (PLGS 3.0), and Dynamix 3.2 software packages control the 

instrument and HDX-MS analysis. The instrument collects an H/D exchange data profile after each sample 

injection, with as many as 50 sequential injections setup in one experiment using the autosampler program. 

Emory Integrated Genomics Core (EIGC): For analysis of RNase L activation in cell assays the Agilent 

2100 Bioanalyzer on a chip platform is available through the EIGC. This system allows for rapid quantification 

of nucleic samples (here, ribosomal RNA using the RNA nano chip) and information about the size distribution 

of the fragments. Further info: http://cores.emory.edu/eigc/. 

Emory Comprehensive Glycomics Core (ECGC): The ECGC houses additional equipment potentially 

relevant to this proposal in a dedicated laboratory in the same hall as the Conn lab on the fourth floor of the 

Rollins Research Center building. Specifically, for measurement of molecular interactions, we have available a 

shared a GE Biacore X-100 surface plasmon resonance (SPR) instrument and also an automated small cell 

isothermal titration calorimeter (Malvern/ MicroCal Auto-iTC200). These instruments are maintained under 

service agreements by the ECGC to ensure instrument availability. 

Further info: http://www.cores.emory.edu/ecgc/. 

Equipment Page 14 
 

 

 

 

Contact PD/PI: Schwartz, Samantha OMB Number: 4040-0001 

Expiration Date: 06/30/2016 

RESEARCH & RELATED Senior/Key Person Profile(Expanded) 

PROFILE - Project Director/Principal Investigator 

Prefix: First Name*: Samantha Middle Name Last Name*: Schwartz Suffix: 

Position/Title*: Research Fellow/Trainee 

Organization Name*: Emory University 

Department: 

Division: 

Street1*: 

Street2: 

City*: 

County: 

State*: 

Province: 

Country*: 

Zip / Postal Code*: 

Phone Number*: Fax Number: 

E-Mail*: 

Credential, e.g., agency login: 

Project Role*: PD/PI Other Project Role Category: 

Degree Type: Degree Year: 

Attach Biographical Sketch*: File Name: NIH_Biosketch_Schwartz_12_20161032089585.pdf 

Attach Current & Pending Support: File Name: 

Page 15 

Funding Opportunity Number: PA-16-309 . Received Date: Tracking Number: GRANT12302947 2016-12-08T16:40:52.000-05:00 
 

 

 

 

 

 

 

 

 

Contact PD/PI: Schwartz, Samantha 

PROFILE - Senior/Key Person 

Prefix: First Name*: Graeme Middle Name Leslie Last Name*: Conn Suffix: 

Position/Title*: Asc Professor 

Organization Name*: Emory University 

Department: Biochemistry 

Division: 

Street1*: 

Street2: 

City*: 

County: 

State*: 

Province: 

Country*: 

Zip / Postal Code*: 

Phone Number*: Fax Number: 

E-Mail*: 

Credential, e.g., agency login: 

Project Role*: Other (Specify) Other Project Role Category: Sponsor 

Degree Type: PHD, Chemistry Degree Year: 1996 

Attach Biographical Sketch*: File Name: NIH_Biosketch_Conn_12_20161032089586.pdf 

Attach Current & Pending Support: File Name: 

PROFILE - Senior/Key Person 

Prefix: First Name*: Anice Middle Name Carmen Last Name*: Lowen 

Position/Title*: Assistant Professor 

Organization Name*: Emory University 

Department: Microbiology & Immunology 

Division: 

Street1*: 

Street2: 

City*: 

County: 

State*: 

Province: 

Country*: 

Zip / Postal Code*: 

Suffix: 

Phone Number*: Fax Number: 

E-Mail*: 

Credential, e.g., agency login: 

Project Role*: Other (Specify) Other Project Role Category: Co-sponsor 

Degree Type: PhD Degree Year: 2005 

Attach Biographical Sketch*: File Name: NIH_Biosketch_Lowen_12_5_161032089587.pdf 

Attach Current & Pending Support: File Name: 

Page 16 

Funding Opportunity Number: PA-16-309 . Received Date: Tracking Number: GRANT12302947 2016-12-08T16:40:52.000-05:00 
 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Contact PD/PI: Schwartz, Samantha 

OMB No. 0925-0001 and 0925-0002 (Rev. 10/15 Approved Through 10/31/2018) 

BIOGRAPHICAL SKETCH 

Provide the following information for the Senior/key personnel and other significant contributors. 

Follow this format for each person. DO NOT EXCEED FIVE PAGES. 

NAME: Schwartz, Samantha Lynne 

eRA COMMONS USER NAME: 

POSITION TITLE: Graduate Student 

EDUCATION/TRAINING 

INSTITUTION AND LOCATION DEGREE 

(if applicable) 

Start Date 

MM/YYYY 

Completion Date 

MM/YYYY FIELD OF STUDY 

Armstrong State University, 

Savannah, GA 

Emory University, Atlanta, GA 

B.S. 

Ph.D. 

08/2007 

08/2015 

05/2012 

In progress 

Biology 

Biochemistry, 

Structural Biology 

A. Personal Statement 

The goal of this proposal is to obtain extramural funding to support my Ph.D. thesis research. This independent 

funding will enhance my technical and professional training experience through my project investigating the 

molecular mechanisms of RNA-mediated regulation of innate immune system proteins. I hope that securing 

this fellowship award will be an important step on the path to a career as an independent researcher. 

Being a first-generation college student was not without its challenges. At the beginning of my 

sophomore year I received my first and only ‘F’ grade in organic chemistry. This result initially shook my 

confidence but also made me realize that I had a lot of growing to do. Recognizing that this might not be my 

last setback, I used this renewed motivation to work harder and to not be intimidated by obstacles. Determined 

to show (mainly to myself) that I could overcome such obstacles, I later repeated organic chemistry and earned 

the ‘A’ I knew I was always capable of achieving. Although my confidence in my own ability and potential has 

grown considerably since those early days in college, the determination to overcome such setbacks and to 

continue to learn and improve as I work towards my career goals has stuck with me. My persistent-nature has 

been an asset and I think a valuable quality to have in the field of scientificresearch. 

Later in my undergraduate career, I pursued a research opportunity with one of my professors, Dr. 

Jennifer Brofft, investigating microbes that cause sea turtle eggs’ failed development. After undergrad, I knew I 

wanted to pursue graduate school, but I wanted to make a more informed decision prior to making a 

commitment. To gain this additional experience, I became a research technician at Emory University where I 

worked on the double-stranded RNA (dsRNA)-activated protein kinase (PKR). My thesis project will not only 

allow me to gain new technical skills (as well as perfect existing ones), but to also use this opportunity to 

develop as an independent scientist. I plan to seek opportunities that will aid in my professional development, 

such as attending conferences, giving poster presentations and talks, as well as writing primary literature to 

improve the way I communicate science. It is important to me to have both the technical and professional skills 

necessary to be successful as I will require these skill sets to secure a position as a postdoctoral fellow and 

ultimately lead an independent research team. 

B. Positions and Honors 

ACTIVITY/ 

OCCUPATION 

START 

DATE 

(mm/yy) 

END 

DATE 

(mm/yy) 

FIELD INSTITUTION/ 

COMPANY 

SUPERVISOR/ 

EMPLOYER 

Undergraduate 

Researcher 01/2011 05/2012 Microbiology Armstrong State University Jennifer Brofft, Ph.D. 

Biosketches Page 17 
 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Contact PD/PI: Schwartz, Samantha 

ACTIVITY/ 

OCCUPATION 

START 

DATE 

(mm/yy) 

END 

DATE 

(mm/yy) 

FIELD INSTITUTION/ 

COMPANY 

SUPERVISOR/ 

EMPLOYER 

Tutor, Writing Center 

Research Specialist 

08/2011 

06/2012 

05/2012 

08/2015 

Communication, 

Writing 

Biochemistry 

Armstrong State 

University 

Emory University 

Deborah Reese, Ph.D. 

Graeme Conn, Ph.D. 

Academic and Professional Honors 

2007-2012 HOPE Scholarship, Armstrong State University: Merit-based award available to Georgia 

residents who have demonstrated academic achievement. Must graduate from high school with 

a minimum 3.0 grade point average and maintain a minimum 3.0 cumulative post-secondary 

grade point average to remain eligible. 

2009-2012 Dean’s List, Armstrong State University: Must be enrolled full-time and earn a grade point 

average of at least 3.6 per semester. 

2010-2012 Tri-Beta National Biological Honor Society, Armstrong State University: Must maintain a 

grade point average of at least 3.0 in all biology major courses. 

2011-2012 National Science Foundation STEM Talent Expansion Program, Armstrong State University: 

Bridging the Gap: Using Research and Learning Communities to Increase STEM Majors 

(0856593). 

2011-2012 Biology Faculty Recognition Award, Armstrong State University: Faculty nominate and award 

a student who demonstrates outstanding leadership abilities, excels in undergraduate research, 

and achieves other notable academic distinctions. 

2012 Phi Kappa Phi Honor Society, Armstrong State University: By invitation only. Must be a senior 

in the top 10 percent of their class. 

2012 Magna Cum Laude, Armstrong State University: Must graduate with a grade point average of 

3.50-3.79. 

2016-present National Institutes of Health Training Grant (T32), Emory University: Training Program in 

Biochemistry, Cell, and Developmental Biology (5T32GM008367-27). 

C. Contributions to Science 

1. Regulation of 2’-5’-oligoadenylate synthetase 1 (OAS1) by double-stranded RNA. 

My thesis project in Dr. Graeme Conn’s lab involves elucidating the mechanisms underlying OAS1 regulation 

by RNA. This work will provide novel insights into cellular translational control as well as the foundations 

necessary to design effective treatments for viral infection. I am currently working to develop bio-layer 

interferometry and cell-based assays as outlined in this proposal. My preliminary data will also be presented at 

the 14th Annual DSAC Student Research Symposium (ref. a) sponsored by the Laney Graduate School of 

Emory University. 

a) Schwartz, S.L., Conn, G.L. Differential regulation of 2’-5’-oligoadenylate synthetase 1 (OAS1) by small 

double-stranded RNAs. 14th Annual DSAC Student Research Symposium. Atlanta, GA. 19 January 2017. 

[Poster] 

2. Droplet digital PCR: A novel method for detection of influenza virus defective interfering particles. 

During my ten-week rotation in Dr. Anice Lowen’s lab, I developed a method based on reverse transcription 

droplet digital PCR. To apply droplet digital PCR technology for the measurement of defective interfering (DI) 

genomes, I designed primers targeting: i) nucleotides 50–150 of each gene segment, a region typically present 

in both DI and standard segments, and ii) an internal site lacking in all DI segments described to date. The 

ratio of internal to terminal copies/μl for a given segment was used to indicate what proportion of the total

copies was full-length. All segments were analyzed for three stocks of influenza A/Panama/2007/99 (H3N2) 

Biosketches Page 18 
 

 

 

 

 

 

 

 

 

 

Contact PD/PI: Schwartz, Samantha 

virus of differing passage histories. Evidence of DI particles was seen in each stock, but their abundance 

differed substantially and as expected based on passage history. I performed and analyzed the results of all 

experiments, designed figures, and wrote the manuscript (ref. a and b) with insight from Dr. Lowen. 

a) Schwartz, S.L., Lowen, A.C. (2016). Droplet digital PCR: A novel method for detection of influenza virus 

defective interfering particles. J. Virol. Meth. 237, 159-165 (PMCID: PMC5056858). 

b) Schwartz, S.L., Lowen, A.C. Droplet digital PCR assay for quantification of defective interfering influenza A 

viruses. 9th Annual NIAID Centers of Excellence for Influenza Research and Surveillance Network Meeting. 

Memphis, TN. 26-29 June 2016. [Poster] 

3. Developed and applied a high throughput assay to measure PKR activity. 

During my time as a research specialist in Dr. Graeme Conn’s lab, I developed a high-throughput radiometric 

assay used to measure PKR activity. The activity assays allowed the discovery of novel findings: the 

interdomain linker appeared to be unexpectedly unnecessary for regulation of PKR (activation or inhibition), 

domain swapping showed that both the double-stranded RNA-binding domain (dsRBD) and kinase domain are 

important for inhibition, and the general scheme of inhibition seemed to be the same for different inhibitory 

RNAs. The PKR activity assay became the key feature of two of my publications (ref. a and b) and has 

become the standard assay still used by others in the lab today. I was also invited to my undergraduate 

institute, Armstrong State University, to give a lecture (ref. c) on these published works (ref. a and b) with the 

goal of sharing my experiences and inspiring undergraduates with the knowledge I have garnered through my 

time both as a research specialist working at the bench full-time and as a current graduatestudent. 

a) Wilson J.L.*, Vachon V.K.*, Sunita S., Schwartz S.L., Conn, G.L. (2014). Dissection of the adenoviral VA 

RNAI central domain structure reveals minimal requirements for RNA-mediated inhibition of PKR. J. Biol. 

Chem. 289(33), 23233-23245 (PCMID: PMC4132820). [*Co-first author] 

b) Sunita, S.*, Schwartz, S.L.*, and Conn, G.L. (2015). The regulatory and kinase domains but not the 

interdomain linker determine human double-stranded RNA-activated kinase (PKR) sensitivity to inhibition by 

viral non-coding RNAs. J. Biol. Chem. 290(47), 28156-28165 (PCMID: PMC4653674). [*Co-firstauthor] 

c) Schwartz, S.L. (2016). Human double-stranded RNA-activated kinase (PKR) inhibition by viral RNA 

requires both structured domains. Armstrong State University, Savannah. 3 November 2016. Lecture. 

<https://www.armstrong.edu/academic-departments/biology-spring-seminar-series>. 

PUBLICATIONS 

https://www.ncbi.nlm.nih.gov/sites/myncbi/1XQwdr7tzrPQ1/bibliography/51319590/public 

D. Scholastic Performance 

ARMSTRONG STATE UNIVERSITY (UNDERGRADUATE)

GPA: 3.60 

YEAR SCIENCE COURSE TITLE GRADE 

2007 Principles of Chemistry I A 

2008 Principles of Chemistry II C 

2008 Principles of Biology I A 

2008 Principles of Biology II A 

2008 Organic Chemistry I F 

2008 Organic Chemistry I Lab A 

2009 Microbiology B 

2009 Zoology A 

2009 Introductory Physics I A 

2009 Introductory Physics I Lab A 

2009 Introductory Physics II A 

YEAR OTHER COURSE TITLE GRADE 

2007 Composition I A 

2007 Civilization I B 

2007 Pre-calculus Mathematics B 

2008 Composition II A 

2008 Calculus I B 

2008 Ethics/Morals in Science A 

2008 Beginning Weight Training A 

2008 Introduction to Psychology A 

2009 Elementary Statistics A 

2009 Aerobic Dance A 

2009 Introductory Sociology A 

Biosketches Page 19 
Yoga for Beginners 

EMORY UNIVERSITY (GRADUATE)

GPA: 3.90 

 

 

 

 

 

 

 

 

 

Contact PD/PI: Schwartz, Samantha 

YEAR SCIENCE COURSE TITLE GRADE YEAR OTHER COURSE TITLE GRADE 

2009 Introductory Physics II Lab A 2009 Elementary French I A 

2009 Principles of Modern Biology B 2009 Elementary French II A 

2010 Cell Biology A Political History of America and 

Georgia 2009 B 

2010 Histological Technique A 2009 A 

2010 Survey of Kingdoms Plantae and 

Fungi 

C 2010 Literature and Humanities A 

2010 Mammalian Physiology B 2010 Cultural Geography B 

2010 Virology B 2010 Shakespeare A 

2011 Natural History of Vertebrate 

Animals 

A 2011 Popular Literature A 

2011 Applied Microbiology A 2012 Art History I A 

2011 Organic Chemistry I A 

2011 Tropical Field Biology A 

2011 General Ecology B 

2011 Senior Seminar (General Biology) S 

2011 Organic Chemistry II B 

2011 Organic Chemistry II Lab B 

2012 Genetics A 

2012 Cell and Molecular Biology Lab A 

2012 Biochemistry I B 

YEAR SCIENCE COURSE TITLE GRADE YEAR OTHER COURSE TITLE GRADE 

2015 Foundations in BCDB I A 

2015 Introductory Graduate Seminar A2015 Laboratory Rotations A 

2016 Foundations in BCDB II A2016 Introductory Graduate Seminar A 

2016 Laboratory Rotations A 

2016 Advanced Graduate Research A 

2016 Hypothesis Design and Scientific A 

Writing 

2016 Advanced Graduate Seminar S 

2016 Advanced Graduate Research A 

2015 Jones Program in Ethics S 

2016 Jones Program in Ethics: Workshop S 

2016 

Graduate School Teaching Assistant 

Workshop S 

For letter grades: A = 90-100%, A- = 90-92%, B = 80-89%, C = 70-79% (grades with +/- distinction only apply 

to Emory University). Attendance and/or participation were used to grade Satisfactory (S) or Unsatisfactory (U) 

courses. 

Biosketches Page 20 
 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Contact PD/PI: Schwartz, Samantha 

OMB No. 0925-0001 and 0925-0002 (Rev. 11/16 Approved Through 10/31/2018) 

BIOGRAPHICAL SKETCH 

Provide the following information for the Senior/key personnel and other significant contributors. 

Follow this format for each person. DO NOT EXCEED FIVE PAGES. 

NAME: Conn, Graeme Leslie 

eRA COMMONS USER NAME (credential, e.g., agency login): 

POSITION TITLE: Associate Professor 

EDUCATION/TRAINING 

INSTITUTION AND LOCATION DEGREE 

(if applicable) 

Completion Date 

MM/YYYY FIELD OF STUDY 

University of Edinburgh, UK 

University of Edinburgh, UK 

Johns Hopkins University 

B.Sc. 

Ph.D. 

Postdoc 

05/1993 

10/1996 

12/1999 

Chemistry 

Structural Biology 

Structural Biology 

A. Personal Statement 

My role as the Sponsor of this Ruth L. Kirschstein National Research Service Award (NRSA) F31 Pre-doctoral 

fellowship application by Ms. Samantha (Sam) Schwartz will be to provide a research environment dedicated 

to Sam’s mentorship, training, and scientific development. As her graduate thesis research advisor, I am 

committed to overseeing Sam’s technical training and development of laboratory and analytical skills through 

the execution of the project she has devised. Further, supported by the outstanding resources and facilities of 

the Biochemistry, Cell and Developmental Biology (BCDB) graduate program, the Laney Graduate School, and 

Emory University, I am also committed to Sam’s broader professional development to support her goal of a 

future independent research career in the area of innate immunity and molecularvirology. 

I have been actively involved in mentoring and training graduate students and other junior trainees 

throughout my independent research career over the last ~17 years (at two different institutes, the University of 

Manchester, United Kingdom, 2000-2008, and Emory University, 2008-present). Since I arrived at Emory in 

2008, I have been an active training faculty member of two graduate programs, BCDB (Sam’s program) and 

the Microbiology and Molecular Genetics (MMG) program. I have twice served on the BCDB Executive 

Committee (EC; 2009-2012 and 2014-present) and currently serve as the Program’s Director of Graduate 

Studies. I also serve on the MMG EC through my role on the Program’s student recruitment committee, and on 

the EC of a cross-program NIH T32 Antimicrobial Resistance and Therapeutic Discovery Program (ARTDTP) 

(PI: William Shafer, PhD). I also contribute extensively to graduate education in these programs, including the 

BCDB Year 1 BCDB-501 Foundations in BCDB I (a 2-week minicourse on macromolecular structure), BCDB/ 

MMG Year 2 IBS-522r Hypothesis Design and Scientific Writing, and ARTDTP IBS-568 Principles of AntiInfectives. The development, design and delivery of the BCDB IBS-522r course was the subject of an article I 

recently coauthored (see ref. a, below). Finally, in addition to being the direct advisor and mentor in my lab to 5 

Emory graduate students (2 graduated and 3 current, including Sam), I have served on the thesis committees 

of 17 Emory graduate students (9 present). In total, 8 PhD students have successfully graduated from my lab 

(6 Manchester and 2 Emory) and these former pre-doctoral trainees have gone on to the successful positions 

in academia and industry they desired. My current trainees are involved in projects investigating ribosomal 

RNA methyltransferase enzymes that confer bacterial resistance to antibiotics, or viral/ cellular non-coding 

RNA structure and activity against proteins of the human host cell antiviral response. Sam’s project represents 

an important new contribution in the latter area. 

Sam joined my lab as a BCDB graduate student in Summer 2016 and has developed a new project 

focused on understanding the regulation of activation of the innate immune system double-stranded RNA 

(dsRNA) sensor oligoadenylate synthetase 1 (OAS1). As Sam describes elsewhere in her application, her 

project is based on an initial observation by a former graduate student (Dr. Ginny Vachon) that minor changes 

to a model dsRNA containing two OAS1 activation consensus sequences had dramatically different impacts on 

the RNA’s ability to activate OAS1. From that starting point, with my help Sam has developed a plan to define 

the molecular basis for this unexpected phenomenon and assess its impact on the OAS/RNase L pathway in 

cells. Sam’s project will deliver broad experimental training that exploits both the strengths of my lab in 

biochemistry, structural and other biophysical methods, molecular biology and microbiology, as well as other 

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resources and expertise across campus (such as the HDX-MS core). Additionally, Sam will have Co-sponsor 

Dr. Anice Lowen as a co-mentor and advisor. Dr. Lowen is an expert in the cell-based assays and models of 

viral infection that will extend and enhance the impact of Sam’s in vitro analyses of OAS1 regulation by RNA. 

Dr. Lowen is a colleague at Emory in the Department of Microbiology and Immunology, one floor down from us 

in the same building. Sam and Dr. Lowen have already established an excellent rapport through the BCDB 

program’s Year 1 rotations and Sam’s project will further build on established interactions between our groups 

In summary, I have a demonstrated record of successful mentorship and engagement in graduate 

training in my lab and programs at Emory. Together with Dr. Lowen, I am committed to providing Sam with a 

research environment that offers outstanding breadth of technical training, professional and transferable skills 

development, mentorship and the career guidance needed to promote her development as an independent 

researcher of outstanding promise. 

a. Kahn, R.A., Conn, G.L., Pavlath, G.K. and Corbett, A.H. (2016). Use of a grant writing class in training Ph.D. 

students. Traffic. 17(7), 803-814. 

B. Positions and Honors 

Positions and Employment 

1996–1999 Wellcome Trust Postdoctoral Fellow, Johns Hopkins University, Baltimore, MD. 

1999–2000 Wellcome Trust Postdoctoral Fellow, Dept. of Biomolecular Sciences, UMIST, UK. 

2000–2004 Wellcome Trust Independent Research Career Development Fellow, Departmentof

Biomolecular Sciences, UMIST, UK. 

2000–2004 Lecturer (equivalent to Assistant Professor, tenure track), Department ofBiomolecular 

Sciences, UMIST, UK. 

2004–2007 Lecturer (equivalent to Assistant Professor, with tenure). Faculty of Life Sciences, University 

of Manchester, UK. 

2007–2008 Senior Lecturer (equivalent to Associate Professor), Faculty of Life Sciences,Universityof

Manchester, UK. 

2008– Associate Professor, Department of Biochemistry, Emory University School ofMedicine,

Atlanta, GA. 

Other Experience, Service and Professional Memberships

2000-present Biochemical Society UK (2003-2007), Association for Chemoreception Sciences (since 2003), 

American Society for Microbiology (ASM; since 2008), American Association for the 

Advancement of Science (AAAS; since 2009), American Crystallographic Society (ACA; since 

2010) and The American Society for Biochemistry and Molecular Biology (ASBMB; since 

2011). 

2001-present Ad hoc grant reviewer/ study section: The Wellcome Trust, BBSRC (UK), American Cancer 

Society, NIH/CSR (IMST-G 30 (S10 Shared Equipment review), ZRG1 BCMB-R 02 M, ZDC1 

SRB-K17 (R03 review) and DP5 Director’s Early Independence Award), American Heart 

Association and the Canadian Council for the Arts (Killam ResearchFellowship). 

2001-present Manuscript reviewer: Nature Methods, Nature Protocols, PNAS, J.Mol. Biol., Nucleic Acids 

Res., J. Biol. Chem., BioTechniques, Biochemistry, Cell. Mol. Life Sci., Chem. Senses,Biol. 

Cell., J. Biotechnology, Current Biology, Molecular Microbiology, FEMS Letters and PLoSONE, ChemBioChem. 

2012 ‘Recombinant and in vitro RNA synthesis: Methods and Protocols’ (Editor), Methods in 

Molecular Biology series (Walker, J.M., series Editor), Humana Press. 

2012 Co-chair, Proteins and Crystallography Committee 2, American HeartAssociation. 

2013-2014 Chair, Proteins and Crystallography Committee 2, American HeartAssociation. 

2014-present Frontiers in Molecular Biosciences, Reviewing Editor (Structural Biology) 

2015 NIH/CSR ZRG1 F13-C 20 L, Fellowships: Infectious Diseases and Microbiology (twice). 

2016 NIH/CSR ZRG1 F13-C 20 L, Fellowships: Infectious Diseases and Microbiology(twice). 

Awards/Honors

1990–1993 Faculty of Science and Engineering Bursary, University of Edinburgh, UK. 

1990–1994 1st, 3rd and 4th Year Class Prize, Department of Chemistry, University of Edinburgh, UK. 

1993–1996 Royal Society of Edinburgh Caledonian Trust Scholarship (PhD). 

1996–2000 Wellcome Trust International Traveling Prize Fellowship (Postdoctoral). 

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2000–2004 Wellcome Trust Independent Research Career Development Fellowship. 

C. Contribution to Science 

Complete List of Published Work in My NCBI (61 total publications): My Bibliography-Conn, G.L. 

[http://www.ncbi.nlm.nih.gov/sites/myncbi/graeme.conn.1/bibliography/40548662/public/?sort=date&direction=descending] 

Trainees (in my lab only) are highlighted as follows in the references in the following sections: 

undergraduate†

/ graduate students (bolded and underlined) and postdoctoral researchers (italicized and 

underlined); additionally, students from underrepresented minorities are noted¶

. 

1. Non-coding RNA structure and regulation of the innate immune protein PKR. My lab has long-standing 

interests in the structure and activity of viral non-coding RNAs, such as Adenovirus VA RNAI – an essential, 

pro-viral RNA best known for inhibition of the double-stranded (ds)RNA-activated protein kinase (PKR). Our 

early work defined the stabilities and roles of the conserved domains within VA RNAI (e.g. refs a,b), including 

the remarkable finding that the entire Terminal Stem could be deleted without loss of activity (whereas smaller 

deletions were detrimental). Our finding complemented the discovery that VA RNAI is similarly processed in the 

cell by Dicer, offering the prospect (still to be fully explored) that Adenovirus may exploit Dicer activity to tune 

the activity of VA RNAI appropriately to the stage of viral replication. More recent work has defined the minimal 

requirements for PKR inhibition by VA RNAI, offering a satisfying explanation for why VA RNAs from different 

serotypes are equally effective despite their wide variation in sequence and length (ref. c). Finally, we recently

demonstrated that both the N-terminal dsRNA binding domain and the C-terminal kinase domain of human

PKR, but not the interdomain linker, contain important determinants for inhibition by human viral non-coding 

RNAs (ref. d). 

a. Wahid, A.M., Coventry, V.K. and Conn, G.L. (2008). Systematic deletion of the adenovirus-associated 

RNAI terminal stem reveals a surprisingly active RNA inhibitor of double-stranded RNA-activated protein 

kinase. J. Biol. Chem. 283(25), 17485–17493. [PMCID: PMC2427366] 

b. Wahid, A.M., Coventry, V.K. and Conn, G.L. (2009). The PKR-binding domain of adenovirus VA RNAIexists 

as a mixture of two functionally non-equivalent structures. Nucleic Acids Res. 37(17), 5830-5837. [PMCID: 

PMC2761268] 

c. Wilson*, J.L, Vachon*, V.K., Sunita, S., Schwartz, S.L. and Conn, G.L. (2014). Dissection of the adenoviral 

VA RNAI Central Domain structure reveals minimal requirements for RNA-mediated inhibition of PKR. J. 

Biol. Chem. 289(33), 23233-23245. (*Co-first author) [PMCID: PMC4132820] 

d. Sunita S., Schwartz SL, Conn GL. (2015) The Regulatory and kiinase domains but not the Interdomain 

linker determine human double-stranded RNA-activated kinase (PKR) sensitivity to inhibition by viral noncoding RNAs. J. Biol. Chem. 290(47):28156-28165. (*Co-first author) [PMCID: PMC4653674] 

2. Molecular mechanisms of RNA-mediated regulation of OAS1. In response to dsRNA, 2’-5’ 

oligoadenylate synthetase (OAS) proteins produce 2’-5’-linked oligoadenylate second messengers for which 

the only known target is the latent ribonuclease, RNase L. Activation of the OAS/RNase L pathway triggers a 

program of cellular and viral RNA degradation designed to halt protein synthesis in the infected cell. We 

reported the discovery of a novel single-stranded RNA motif (termed 3’-ssPy, or “three prime spy”) that strongly 

potentiates OAS1 activation by a short model dsRNA duplex as well as structured viral and cellular non-coding 

RNAs (ref. a). Our current studies have revealed that even for “simple” model dsRNAs there is a potentially 

complex interplay of RNA features that controls whether OAS1 becomes activated. We next aim to extend 

these initial finding to define the “rules” that govern potent OAS1 activation by dsRNA and the impacts of motifs 

like 3’-ssPy or a novel tertiary structure within the cellular non-coding RNA 886 (nc886) in non the activation of 

the OAS/RNase L pathway both in vitro and in the context of cellular infection. Sam’s project will be a critical 

component of this long-term goal. Finally, in unpublished work, we have recently cloned and expressed human 

OAS3 in E. coli and will extend our studies to this additional component of the OAS/ RNase L pathway. For 

example, we will test whether similar rules about OAS-activating RNA features apply to this RNA or if OAS3 

has evolved as a more general sensor longer dsRNAs. 

a. Vachon, V.K., Calderon, B.M.¶ and Conn, G.L. (2015). A novel RNA molecular signature for activation of 

2'-5' oligoadenylate synthetase-1. Nucleic Acids Res. 43(1), 544-552. [PMCID: PMC4288181] 

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Contact PD/PI: Schwartz, Samantha 

3. Molecular basis for aminoglycoside-resistance arising from 16S rRNA methylation. Aminoglycoside 

antibiotics typically act by binding and inducing specific conformational changes in the ribosome “decoding 

center” that result in aberrant protein synthesis. Aminoglycosides have retained potent activity, leading to a 

reevaluation of their potential utility in the clinic in the face of increasing resistance to many first line drugs. 

Clinical aminoglycoside resistance typically arises through the action of aminoglycoside modifying enzymes, 

while drug-producing bacteria invariably use 16S rRNA methyltransferase enzymes to modify the ribosomal 

drug binding site, either at the N7 position of G1405 (m7

G1405) or the N1 position of A1408 (m1A1408). Now, a 

serious threat to the potential clinical usefulness of aminoglycosides has arisen from the acquisition and 

spread among human bacterial pathogens of these rRNA methyltransferases. rRNA modification confers 

exceptionally high level resistance and, combined, these modifications are capable of blocking the effects of all 

clinically useful aminoglycosides including the latest generation drugs. Determining the structures of these 

enzymes and defining the features which govern their interactions with cosubstrate S-adenosyl-L-methionine 

(SAM) and 30S substrate, have been a major contribution from my lab. Our early work defined critical features 

for SAM binding and 30S recognition by Sgm (a drug producer m7

G1405 enzyme), and expanded in a later 

study which experimentally determined the methylation target for a representative group of putative m7

G1405 

enzymes. Subsequently, we determined the first structures of m1

A1408 enzymes with cosubstrate, KamB from 

the aminoglycoside-producer S. tenebrarius, and NpmA which was identified as the source of treatment failure 

in a clinical infection (ref. a). More recently, we presented a major breakthrough in the field with the 

determination of a first structure of a resistance methyltransferase (NpmA) bound to its 30S substrate (ref. b). 

This structure revealed the basis for the requirement of mature 30S as substrate, and the molecular details 

underpinning specific target recognition, including flipping of the target A1408 base into the NpmA active site. 

Our on-going studies include efforts to obtain complementary structure-function insights for members of the 

m7

G1405 family, and investigating the molecular mechanisms of action of enzymes from both families (e.g. 

see ref. c,d). Our long term goal is to exploit the understanding we develop of the enzymes and their target 

recognition mechanisms to facilitate development of specific inhibitors of these resistancedeterminants. 

a. Macmaster, R., Zelinskaya, N., Savic, M., Rankin, C.R. and Conn, G.L. (2010). Structural insights intothe 

function of aminoglycoside-resistance A1408 16S rRNA methyltransferases from antibiotic-producing and 

human pathogenic bacteria. Nucleic Acids Res. 38(21), 7791-7799. [PMCID: PMC2995053] 

b. Dunkle, J.A., Vinal, K., Desai, P.M., Zelinskaya, N., Savic, M., West, D.M., *Conn, G.L. and *Dunham, C.M. 

(2014). Molecular recognition and modification of the 30S ribosome by theaminoglycosideresistance methyltransferase NpmA. Proc. Natl. Acad. Sci. U.S.A. 111(17), 6275-6280. (*Co-corresponding 

author) [PMCID: PMC4035980] 

c. Savic, M., Sunita, S., Zelinskaya, N., Desai, P.M., Macmaster, R., Vinal, K. and Conn, G.L. (2015). 30S 

subunit-dependent activation of the S. cellulosum So ce56 aminoglycoside-resistance 16S rRNA 

methyltransferase Kmr. Antimicrob. Agents Chemother. 59(5), 2807-2816. [PMCID:PMC4394793] 

d. Witek, M.A. and Conn, G.L. (2016). Functional dichotomy in the 16S rRNA (m1

A1408) methyltransferase 

family and control of catalytic activity via a novel tryptophan mediated loop reorganization. Nucleic Acids 

Res. 44(1), 342-353 [PMCID: PMC4705659] 

4. Mentorship of Trainees. As described in my Personal Statement (see section A, above), I have a strong 

track record of mentorship of junior trainees in my lab. My former lab members have gone on to successful 

graduate/ medical school training, postdoctoral positions, and science-related careers in academia and 

industry. To date, my lab has graduated 8 PhD students, and contributed to the training of three current 

graduate students, 8 postdoctoral scientists, 12 graduate rotation students (at Emory only, 2008-present), and 

>30 undergraduates or high school students during summer and other research experiences. The publications 

below are the most recent from my current or past trainees that are not included in the specific Contribution 

sections above. 

a. Kuiper, E.G. and Conn, G.L. (2014). Binding induced RNA conformational changes control substrate 

recognition and catalysis by the thiostrepton-resistance methyltransferase (Tsr). J.Biol.Chem. 289(38), 

26189-26200 [PMCID: PMC4176221] 

b. Myers, C.L., Kuiper, E.G., Grant, P.C., Hernandez, J.¶†, Conn, G.L. and Honek, J.F. (2015). Co-substrate 

binding and enzyme catalysis by the thiostrepton resistance RNA methyltransferase (Tsr) from 

Streptomyces cyaneus, FEBS Lett. 589(21), 3263-3270. [PMCID: PMC4661090] 

c. Vachon, V.K. and Conn, G.L. (2016). Adenovirus VA RNA: An essential pro-viral non-coding RNA. Virus 

Res. 212, 39-52. 

d. Owings, J.P.*, Kuiper, E.G.*, Prezioso, S.M., Meisner, J., Varga, J.J., Zelinskaya, N., Dammer,

E.B., Duong, 

D.M., Seyfried, N.T., Albertí, S., Conn, G.L. and Goldberg, J.B. (2016). Pseudomonas aeruginosa EftMisa 

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Contact PD/PI: Schwartz, Samantha 

thermoregulated methyltransferase. J. Biol. Chem. 291(7), 3280-90 (*Co-first authors) [PMCID: 

PMC4751374] 

D. Research Support 

Ongoing Research Support 

R01 AI088025 (Conn, PI) 05/01/2010 – 04/30/2020 

NIH/NIAID 

RNA modification and antibiotic resistance. 

This project will investigate 16S ribosomal RNA methyltransferase enzymes that confer resistance to 

aminoglycoside antibiotics. The goals are to determine methyltransferase and methyltransferase-30S substrate 

complex X-ray crystal structures and to define the molecular mechanisms which underpin target (30S 

ribosome) recognition by these resistance enzymes. Role: PI. 

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OMB No. 0925-0001 and 0925-0002 (Rev. 11/16 Approved Through 10/31/2018) 

BIOGRAPHICAL SKETCH 

Provide the following information for the Senior/key personnel and other significant contributors. 

Follow this format for each person. DO NOT EXCEED FIVE PAGES. 

NAME: Lowen, Anice C 

eRA COMMONS USER NAME: 

POSITION TITLE: Assistant Professor of Microbiology and Immunology 

EDUCATION/TRAINING 

INSTITUTION AND LOCATION DEGREE 

Completion 

Date 

MM/YYYY 

FIELD OF STUDY 

University of Alberta, Edmonton, Canada B.Sc. 2001 Biochemistry 

University of Glasgow, Scotland Ph.D. 2005 Virology 

Mount Sinai School of Medicine, New York, NY Postdoc 2005-2009 Virology 

A. Personal Statement 

My role in this proposal as Co-sponsor will be to provide Ms. Samantha Schwartz (Sam) with mentorship and 

technical guidance for her proposed experiments to correlate OAS1 activity in vitro with that in human lung 

carcinoma (A549) cells (Aim 1.2). I am an Assistant Professor in Microbiology and Immunology at Emory 

University, having joined this Department in 2011. Effective mentoring of graduate students is one of my 

highest priorities in the lab. I have taken on four students for their dissertation work to date; two of these 

students have obtained their PhDs and both are now employed in related fields. I also serve on the committees 

of a number of graduate students and participate actively in annual recruiting, teaching and seminar series 

associated with the Microbiology and Molecular Genetics (MMG) and Immunology and Molecular 

Pathogenesis (IMP) graduate programs. Along with Sam’s mentor and Sponsor on this application, I am 

currently a member of the MMG Program Executive Committee and Graduate Recruitment Committee. I have 

studied the biology of influenza viruses for the past 11 years, working in animal models and cell-based culture 

systems. As a post-doctoral fellow working with Peter Palese, I gained a firm grounding in molecular virology 

and virus-host interactions, including innate antiviral responses to infection. I have continued this work as an 

independent researcher, with a current focus on mechanisms of influenza A virus evolution. My lab is therefore 

well equipped for the experiments Sam describes in her proposal, including cell-based experiments involving 

delivery of specific RNA molecules to the cytoplasm, assessment of OAS activation and impact on viral 

infection. By combining biochemical and virological approaches, Sam’s project promises to reveal novel 

insights into the molecular mechanisms by which viral pathogen-associated molecular patterns (PAMPS) are 

sensed and responded to within infected cells. In carrying out this project, she will furthermore receive valuable 

training in biochemistry and virology, two highly complementary disciplines. Sam had a very productive rotation 

in my lab during the first year of her graduate studies and we have an excellent relationship. Based on this 

foundation, the established ties between my lab and Dr. Conn’s, my track-record of mentorship, and relevant 

research expertise, I am well-placed to provide Sam with technical and professional training that will support 

her career goal of becoming an independent researcher further exploring the field of innateimmunity. 

B. Positions and Honors 

Positions 

2009-2010 Assistant Professor, research track, Department of Microbiology, Mount Sinai Schoolof 

Medicine 

2011-present Assistant Professor, tenure track, Department of Microbiology and Immunology, Emory 

University School of Medicine 

Other experience and professional memberships 

2005-present Member, American Society for Virology 

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2008-present Editorial board, Journal of Virology 

2011-present Member, American Society for Microbiology 

2013-2015 Ad hoc reviewer for Virology B study section 

2015-present Editor, mSphere 

Honors 

2002 Wellcome Trust Studentship of the Wellcome Trust 

2002-2004 Overseas Research Student Award of the Universities, UK 

2003 Joel M. Dalrymple award from the American Society for Virology 

2007-2010 Parker B Francis Fellow in Pulmonary Research 

2013 Member of “The Emory 1%” awarded in recognition of perfect score on NIH grant application 

2013 One of the top 25 peer reviewers for the Journal of Virology (see JVI 87:13087) 

2015 Ann C. Palmenberg Award for Junior Investigators from the American Society forVirology 

2015 One of the top 25 peer reviewers for the Journal of Virology (see JVI 89:12233) 

2016 Finalist for Burroughs Wellcome Fund Investigators in the Pathogenesis of Infectious 

Disease award 

C. Contribution to Science 

1. A system for the study of influenza virus reassortment. Since starting my own laboratory I have 

developed novel system that, for the first time, allows influenza virus reassortment to be studied directly. The 

system relies on a matched pair of parental viruses that differ only by a handful of silent mutations and offers 

an important advantage over traditional approaches: all 256 progeny genotypes emerging from mixed infection 

are of equivalent fitness. For this reason, reassortment efficiency can be measured in an unbiased fashion. 

Already, we have made strides in understanding reassortment at intracellular and organismal levels. We have 

shown that genome mixing and therefore reassortment are efficient in co-infected cells and that reassortment 

occurs routinely in an animal host. Our recent data indicate that semi-infectious influenza virus particles, which 

fail to deliver one or more gene segments to the site of replication, are important determinants of the high 

efficiency of reassortment. Together, our results suggest that, rather than being an episodic event that occurs 

when conditions permit (as was thought previously), reassortment is a routine feature of influenza virus 

infections that contributes to viral evolution on a continual basis. 

a. Marshall N, Priyamvada L, Ende Z, Steel J and Lowen AC. 2013. Influenza virus reassortment occurs 

with high frequency in the absence of segment mismatch. PLOS Pathogens. 9(6):e1003421. 

PMC3681746 

b. Tao H, Steel J and Lowen AC. 2014. Intra-host dynamics of influenza virus reassortment. Journal of 

Virology. 88(13):7485-7492. PMC4054463 

c. Tao H, Li L, White MC, Steel J and Lowen AC. 2015. Influenza A virus co-infection through 

transmission can support high levels of reassortment. Journal of Virology. 89(16):8453-61. 

PMC4524221 

d. Fonville JM, Marshall NM, Tao H, Steel J and Lowen AC. Influenza virus reassortment is enhanced by 

semi-infectious particles but can be suppressed by defective interfering particles. PLOS Pathogens. 

11(10): e1005204. PMCID: PMC4595279 

2. Guinea pig model of influenza virus transmission. As a post-doctoral fellow with Dr. Peter Palese, I 

developed the guinea pig as a model for the study of influenza virus transmission, providing a valuable 

alternative to the well-established ferret model. The utility of the model is evidenced by the fact that a number 

of laboratories have adopted its use and generated important new knowledge on influenza virus transmission. 

a. Lowen AC, Mubareka S, Tumpey TM, García-Sastre A, and Palese P. 2006. The guinea pig as a 

transmission model for human influenza viruses. Proceedings of the National Academy of Sciences. 

103(26):9988-9992. PMC1502566 

b. Bouvier N, Lowen AC. 2010. Animal Models for Influenza Virus Pathogenesis and Transmission. 

Viruses. 2(8):1530-1563. PMC3063653 

c. Lowen AC, Bouvier N, Steel J, 2014. Transmission in the guinea pig model. Current Topics in 

Microbiology and Immunology. 385: 157-183. PMID: 25001209 

3. An explanation for winter-time seasonality of influenza. The guinea pig system allowed my colleagues 

and I to address a long-standing question in the influenza field - that of the underlying basis for winter-time 

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seasonality. We found that influenza virus transmission was strongly favored by low temperature and low 

humidity, suggesting that environmental conditions account for the seasonality of epidemics. This work offered 

the first experimental evidence supporting a role for climatic factors in determining the seasonality of influenza 

and has reinvigorated the influenza field with respect to understanding the timing with which epidemics occur 

and what factors drive that timing. Our article in PLOS Pathogens was featured by several news outlets, 

including on the front page of the New York Times, has been cited 374 times, and has stimulated a number of 

epidemiological and modeling-based studies aimed at understanding how humidity and temperature impact 

influenza at a population level. 

a. Lowen AC, Mubareka S, Steel J, and Palese P. 2007. Influenza virus transmission is dependent on 

relative humidity and temperature. PLOS Pathogens. 3(10):1470-1476. PMC2034399 

b. Lowen AC, Steel J, Mubareka S and Palese P. 2008. High temperature (30°C) blocks aerosol but not 

contact transmission of influenza virus. Journal of Virology. 82(11):5650-5652. PMC2395183 

c. Steel J, Palese P, Lowen AC. 2011. Transmission of a 2009 pandemic influenza virus shows a 

sensitivity to temperature and humidity similar to that of an H3N2 seasonal strain. Journal of Virology. 

85(3):1400-1402. PMC3020521 

d. Lowen AC and Steel J. 2014. Roles of humidity and temperature in shaping influenza seasonality. 

Journal of Virology. 88(14):7692-7695. PMC4097773 

4. Identification of determinants of influenza virus transmission. The efficiency with which influenza 

viruses transmit from one individual to the next is a key factor in determining the occurrence of influenza 

pandemics and the severity of influenza epidemics. In total, I have co-authored 19 publications focused on 

influenza virus transmission, a subject of clear significance to public health. This body of work has contributed 

significantly to the advancement of the field. While much remains to be learned, a picture of the viral, host and 

environmental factors required to support transmission among mammals is nowemerging. 

a. Steel J, Lowen AC, Mubareka S and Palese P. 2009. Transmission of influenza virus in a mammalian 

host is increased by PB2 amino acids 627K or 627E/701N. PLOS Pathogens. 3(10):1470-1476. 

PMC2603332 

b. Mubareka S, Lowen AC, Steel J, Coates AL, García-Sastre A and Palese P. 2009. Transmission of 

influenza virus via aerosols and fomites in the guinea pig model. Journal of Infectious Diseases. 

199(6):858-865. PMC4180291 

c. Lowen AC, Steel J, Mubareka S, Carnero E, García-Sastre A and Palese P. 2009. Blocking inter-host 

transmission of influenza virus by vaccination in the guinea pig model. Journal of Virology. 83(7):2803-

2818. PMC2655561 

d. Chutinimitkul S, Herfst S, Steel J, Lowen AC, Ye J, van Riel D, Schrauwen EJ, Bestebroer TM, Koel B, 

Burke DF, Sutherland-Cash KH, Whittleston CS, Russell CA, Wales DJ, Smith DJ, Jonges M, Meijer A, 

Koopmans M, Rimmelzwaan GF, Kuiken T, Osterhaus AD, García-Sastre A, Perez DR, Fouchier RA. 

2010. Virulence-associated substitution D222G in the hemagglutinin of 2009 pandemic influenza 

A(H1N1) virus affects receptor binding. Journal of Virology. 84(22):11802-13. PMC2977876 

5. A robust reverse genetics system for Bunyamwera virus. As a PhD student with Dr. Richard Elliott, I 

was fortunate to work with the only reverse genetics system available at that time for a virus of the 

Bunyaviridae. In addition to gaining novel insights into the bunyavirus life cycle, my work in the Elliott lab 

helped to vastly improve the efficiency of virus rescue and the simplicity of theprotocol. 

a. Lowen AC, Noonan C, McLees A, Elliott RM. Efficient bunyavirus rescue from cloned cDNA. 2004. 

Virology. 330(2):493-500. PMID: 15567443 

b. Kohl A, Lowen AC, Léonard VH, Elliott RM. 2006. Genetic elements regulating packaging of the 

Bunyamwera orthobunyavirus genome. Journal of General Virology. 87(1):177-87. PMID:16361430 

c. Lowen AC, Elliott RM. 2005. Mutational analyses of the nonconserved sequences in the Bunyamwera 

Orthobunyavirus S segment untranslated regions. Journal of Virology.79(20):12861-70.PMC1235861 

d. Lowen AC, Boyd A, Fazakerley JK, Elliott RM. 2005. Attenuation of bunyavirus replication by 

rearrangement of viral coding and noncoding sequences. Journal of virology. 79(11):6940-6. 

PMC1112153 

Complete List of Published Work in MyBibliography:

http://www.ncbi.nlm.nih.gov/sites/myncbi/anice.lowen.1/bibliography/40895322/public/?sort=date&direction=de 

scending 

Biosketches Page 28 
 

D. Research Support 

Ongoing Research Support 

Contact PD/PI: Schwartz, Samantha 

Title: Reassortment of influenza viruses in a co-infected host 

Number: R01 AI099000 

Principal investigator: Anice Lowen 

Funding Agency: National Institutes of Health 

Award period: 9/1/2012 – 8/31/2017 

The main goals of this project are to determine the baseline frequency of influenza virus reassortment under 

unbiased conditions, and test whether a number of factors, such as timing and dose of co-infection, increase or 

decrease that frequency. 

Title: Host adaptation, reassortment and transmission of influenza viruses at the animal-human interface 

Number: HHSN272201400004C 

Funding Agency: National Institutes of Health 

Principal investigator: Walt Orenstein 

Role: Co-project leader on Project 2 

Award period: 4/1/2014- 3/31/2021 

Project 2 within Emory/UGA Center of Excellence for Influenza Research and Surveillance NIH/NIAID contract. 

The main goals are to test the impact of host adaptation and host cell origin on reassortment outcomes, and to 

evaluate the potential for transmissible viruses to arise through reassortment. 

Title: Identification and Hit-To-Lead Development of Influenza A Virus Inhibitors 

Number: R21 AI119196 

Funding Agency: National Institutes of Health 

Principal investigator: Richard Plemper

Role: sub-contractor 

Award period: 7/1/2015 – 6/30/2017 

The main goal is to identify several novel small molecule inhibitors of influenza A viruses with potential for 

clinical development. 

Title: Dynamics and evolution of recall immune responses to influenza viruses 

Number: U19 AI117891 

Funding Agency: National Institutes of Health 

Principal investigator: Rustom Antia 

Role: Co-investigator 

Award period: 06/01/2015 – 05/31/2020 

The major aim is to develop a robust computational model, informed by experimental data, of humoral and cell 

mediated immune responses to influenza virus infection and vaccination. 

Title: Impact of selective genome packaging on influenza A virus reassortment 

Number: R01 AI125268 

Funding Agency: National Institutes of Health 

Principle investigator: Anice Lowen 

Award Period: 08/04/2016 – 07/31/2020 

The main aim of this project is to test the hypothesis that sequence divergence in RNA packaging signals limits 

reassortment between heterologous strains of influenza A virus. 

Title: Host dependence of influenza A virus reassortment 

Number: R01 AI127799 

Funding Agency: National Institutes of Health 

Principle investigator: Anice Lowen 

Award Period: 12/05/16-11/30/21 

Research funded through this grant will indicate the efficiency of influenza A virus reassortment in a broad set 

of natural hosts, reveal whether the prevalence of viral genetic exchange varies among host species, and give 

insight into the features of viral within-host dynamics that allow for co-infection (and therefore reassortment) to 

occur in vivo. 

Biosketches Page 29 
Completed Research Support 

Contact PD/PI: Schwartz, Samantha 

Title: Contribution of virion morphology to influenza viral fitness 

Number: HHSN266200700006C 

Principal investigator: Orenstein 

Funding Agency: National Institutes of Health 

Award period: 4/1/2011 – 3/31/2013

Role: Project lead of pilot project 

The main goal of this project is to define the relative fitness and transmissibility of matched spherical and 

filamentous influenza viruses. 

Biosketches Page 30 
Contact PD/PI: Schwartz, Samantha 

PHS Fellowship Supplemental Form OMB Number: 0925-0001 

Expiration Date: 10/31/2018 

Introduction 

1. Introduction 

(RESUBMISSION) 

Fellowship Applicant Section 

2. Applicant's Background and Goalsfor Fellowship Applicant_s_Background_and_Goals_for_Fellowship_Training_Schwartz103208959 

Training* 

Research Training Plan Section 

 

3. Specific Aims* Specific_Aims_Schwartz1032089674.pdf 

4. Research Strategy* Research_Strategy_Schwartz1032089676.pdf 

5. Respective Contributions* Respective_Contributions_Schwartz1032089594.pdf 

6. Selection of Sponsor and Institution* Selection_of_Sponsor_and_Institute_Schwartz1032089595.pdf 

7. Progress Report Publication List 

(RENEWAL) 

8. Training in the Responsible Conduct of Research* Responsible_Conduct_of_Research_Schwartz1032089596.pdf 

Sponsor(s), Collaborator(s) and Consultant(s) Section 

9. Sponsor and Co-Sponsor Statements Sponsor_Cosponsor_Training_Plan_Schwartz1032089592.pdf 

Letters of Support from Collaborators, Contributors 10. 

and Consultants 

LoS_Renhao_Li HDX_MS NIH_F31_Dec2016V21032089849.pdf 

Institutional Environment and Commitment to Training Section 

11. Description of Institutional Environment and 

Commitment to Training 

Institutional_Environment_and_Commitment_to_Training_Schwartz1032089602.pdf 

Other Research Training Plan Section 

Human Subjects 

Please note. The following item is taken from the Research & Related Other Project Information form. The response provided on that 

page, regarding the involvement of human subjects, is repeated here for your reference as you provide related responses for this 

Fellowship application. If you wish to change the answer to the item shown below, please do so on the Research & Related Other Project 

Information form; you will not be able to edit the response here. 

Are Human Subjects Involved? Yes ✔ No 

12. Human Subjects Involvement Indefinite? 

13. Clinical Trial? 

14. Agency-Defined Phase III Clinical Trial? 

15. Protection of Human Subjects 

16. Data Safety Monitoring Plan 

17. Inclusion of Women and Minorities 

18. Inclusion of Children 

Vertebrate Animals 

The following item is taken from the Research & Related Other Project Information form and repeated here for your reference. Any 

change to this item must be made on the Research & Related Other Project Information form. 

Are Vertebrate Animals Used? Yes ✔ No 

19. Vertebrate Animals Use Indefinite? 

3.pdf 

Page 31 

Tracking Number: GRANT12302947 Funding Opportunity Number: PA-16-309. Received Date: 

2016-12-08T16:40:52.000-05:00 
Contact PD/PI: Schwartz, Samantha 

PHS Fellowship Supplemental Form 

20. Are vertebrate animals euthanized? 

If "Yes" to euthanasia 

Is method consistent with American Veterinary 

Medical Association (AVMA) guidelines? 

If "No" to AVMA guidelines, describe method and 

provide scientific justification 

 

21. Vertebrate Animals 

Other Research Training Plan Information 

22. Select Agent Research 

23. Resource Sharing Plan Resource_Sharing_Plan_Schwartz1032089603.pdf 

24. Authentication of Key Biological and/or Chemical 

Resources 

Page 32 

Tracking Number: GRANT12302947 Funding Opportunity Number: PA-16-309. Received Date: 

2016-12-08T16:40:52.000-05:00 
Contact PD/PI: Schwartz, Samantha 

PHS Fellowship Supplemental Form 

Additional Information Section 

25. Human Embryonic Stem Cells

Does the proposed project involve human embryonic stemcells?* Yes ✔ No 

If the proposed project involves human embryonic stem cells, list below the registration number of the specific cell line(s), using the registr

information provided within the agency instructions. Or, if a specific stem cell line cannot be referenced at this time, please check the box 

indicating that one from the registry will be used: 

Specific stem cell line cannot be referenced at this time. One from the registry will be used. 

Cell Line(s): 

y

26. Alternate Phone Number:

27. Degree Sought During Proposed Award: 

 

Degree: 

PHD: Doctor of Philosophy 

If "other", please indicate degree type: Expected Completion Date (month/year): 

05/2021 

28. Field of Training for Current Proposal*: 100 Biochemistry 

29. Current Or Prior Kirschstein-NRSA Support?* ✔ Yes No 

If yes, please identify current and prior Kirschstein-NRSA support below: 

Level* 

Predoctoral 

Type* 

Institutional 

Start Date (if known) 

06/01/2016 

End Date (if known) 

05/31/2017 

Grant Number (if known) 

5T32GM008367-27 

30. Applications for Concurrent Support?* Yes ✔ No 

If yes, please describe in an attached file: 

31. Citizenship* 

U.S. Citizen U.S. Citizen or Non-Citizen National? ✔ Yes No 

Non-U.S. Citizen With a Permanent U.S. Resident Visa 

With a Temporary U.S. Visa 

If you are a non-U.S. citizen with a temporary visa who has applied for permanent resident status and expect to hold a permanent resident 

visa by the earliest possible start date of the award, please also checkhere. 

32. Change of Sponsoring Institution 

Page 33 

T Funding Opportunity Number: PA-16-309. Received Date: racking Number: GRANT12302947 

2016-12-08T16:40:52.000-05:00 

Name of Former Institution:*
 

Contact PD/PI: Schwartz, Samantha 

PHS Fellowship Supplemental Form 

Budget Section 

All Fellowship Applicants: 

1. Tuition and Fees*: 

None Requested ✔ Funds Requested 

Year 1 

Year 2 

Year 3 

Year 4 

Year 5 

Year 6 (when applicable) 

Total Funds Requested: 

Senior Fellowship Applicants Only: 

Amount Academic Period Number of Months 

2. Present Institutional Base Salary: 

3. Stipends/Salary During First Year of Proposed Fellowship: 

Amount Number of Months a. Federal Stipend Requested: 

Amount Number of Months 

b. Supplementation from other sources: 

Type (sabbatical leave, salary, etc.) 

Source 

Appendix 

Page 34 

T Funding Opportunity Number: PA-16-309. Received Date: racking Number: GRANT12302947 

2016-12-08T16:40:52.000-05:00 
 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Contact PD/PI: Schwartz, Samantha 

APPLICANT'S BACKGROUND AND GOALS FOR FELLOWSHIP TRAINING 

A. Doctoral Dissertation and Research Experience 

My previous research experiences have all revolved around microbiology, biochemistry, or a combination of 

the two. I had the opportunity to try two very different research experiences before entering graduate school at 

Emory University. I began my research career as an undergraduate at Armstrong State University and then 

worked for three years as a research technician at Emory University. Upon joining Emory University’s 

Biochemistry, Cell, and Developmental Biology (BCDB) Program, I completed three different laboratory 

rotations prior to joining the Conn lab in May 2016. 

As an undergraduate at Armstrong State University, I wholeheartedly applied myself to volunteering in Dr. 

Jennifer Brofft’s lab investigating microbes that penetrate sea turtle eggs and which are implicated with failed 

turtle embryo development. My research culminated in a poster presentation at two American Society for 

Microbiology meetings (Gainesville, Florida in 2011 and San Francisco, California in 2012), for which I was 

awarded travel funds via the National Science Foundation’s STEM program. I also gave a formal oral 

presentation at Armstrong State University's Student Scholars Symposium. Following this experience, I felt 

sure graduate school was in my future, but I wanted to explore additional areas of research before applying. 

While this research opportunity at my undergraduate institution was instrumental in my early development as a 

researcher, other options were limited in scope due to the small size of the institution. To broaden my horizons 

and develop an understanding of the rigors of a major research institution, I applied for a research specialist 

(technician) position at Emory University, an institute I had also identified as a potential top choice for graduate 

school. I took a leap and left for Atlanta for no other reason than to pursue academic research, despite my lack 

of exposure to graduate-level research and no family role model for highereducation. 

In Dr. Graeme Conn's lab at Emory University, I developed technical and organizational skills to efficiently 

carry out full-time research. My work ranged from laboratory prep work to troubleshooting complex assays and 

processing resultant data. My three years of lab experience as a research specialist provided an important 

initial exposure to aspects of being a researcher, such as reading of primary research articles, attending 

research seminars, giving presentations, and contributing to manuscript preparation. From these initial insights, 

I gained a clear concept of the critical skills I would develop for success in graduate school. My research in the 

Conn lab focused on elucidating the molecular details of protein kinase R (PKR) regulation by viral non-coding 

RNAs (VA RNAI and HIV-1 TAR) as part of the host innate immune response. I gained skills in RNA in vitro 

transcription and purification, and developed a new high-throughput version of the radiometric assay used by 

the lab to measure PKR activity. Developing this assay in particular permitted me to evolve from becoming 

frustrated by experimental road blocks to a scientist who is excited and driven by the often subtle complexities 

that define a highly reproducible, invaluable experimental tool. What initially began as a test of perseverance 

grew into a love of experimental science. It was in this transformation that I knew I was ready to take the next 

step: graduate school. Upon joining Emory University’s Biochemistry, Cell, and Developmental Biology (BCDB) 

Program, I completed three laboratory rotations prior to joining my thesis lab. 

My first rotation was in the research group of Dr. Christine Dunham. The Dunham lab uses X-ray 

crystallography to study ribosome structure and translational regulation. Here, my work focused on the toxin 

MazF-mt6 from Mycobacterium tuberculosis that inhibits protein synthesis during stress by cleaving 23S rRNA 

at Helix 70. The goal of my project was to determine MazF-mt6 residues important for cleavage of Helix 70 

RNA. Using X-ray crystal structures of MazF-mt6 and Bacillus subtilis MazF-mRNA complex as a guide, I 

substituted predicted catalytic residues with alanine and tested the variant MazF proteins for ribonuclease 

activity using an in vitro cleavage assay. Dr. Dunham also entrusted me with an X-ray crystallography side 

project where I attempted to co-crystallize a novel inhibitor compound with the ribosome. I gained experience 

setting trays, optimizing conditions, and testing crystals remotely at the SER-CAT synchrotron beamline at the 

Advanced Photon Source. 

My next rotation was with Dr. Daniel Reines’ research group. The Reines lab uses yeast as a model system to 

study RNA-binding proteins containing low complexity domains and their propensity to form amyloid filaments. 

Here, my work focused on the RNA-binding protein, Pcf11, a component of the cleavage and polyadenylation 

complex that is involved in orchestrating transcription termination in yeast. Computational analysis suggested 

that Pcf11 possesses a prion-like domain predicted to form amyloid filaments. The Reines lab has shown 

through biochemical data and electron microscopy imaging that the low complexity domain of Pcf11 alone was 

able to form amyloid filaments. The main focus of my project was to address whether or not the low complexity 

domain of Pcf11 could form filaments when linked to structure-containing domains, as it exists naturally in the 

full-length protein. During my rotation, I spent the majority of my time optimizing the expression and solubility of 

the full-length Pcf11 protein. I purified enough stable protein to perform a fluorescence assay with Thioflavin T 

as an indirect measurement of filament formation. My results were indicative of filament formation, but required 

confirmation by electron microscopy. A current graduate student is continuing my work on this project. 

Applicant's Background and Goals for Fellowship Training Page 35 
 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Contact PD/PI: Schwartz, Samantha 

My last rotation was with the Lowen lab. Dr. Anice Lowen’s group uses molecular and classical virology 

techniques to study influenza A virus reassortment, the process by which two viruses that co-infect the same 

cell exchange intact gene segments. Here, my work focused on developing a novel technique using droplet 

digital PCR (ddPCR) as a method for detecting influenza virus defective interfering (DI) particles within a virus 

preparation. Three A/Panama/2007/99 (H3N2) virus stocks were used in these experiments that were either 

enriched in DI particles, purified to remove possible DI’s, or unknown. My results revealed that ddPCR can 

successfully detect DI particles within these virus stocks and confirmed the approach to be more sensitive and 

precise when compared to traditional quantitative PCR methods. My ten-week rotation proved to be very 

successful: I collected publishable data, and wrote and published a methods paper. Perhaps most importantly, 

I forged an excellent mentor-mentee relationship with Dr. Lowen who is now the Co-sponsor on this fellowship 

application. During my rotation, she also encouraged me to attend the 14th Annual Southeastern Regional 

Virology Conference at Emory University and that we present my work at the 9th Annual NIAID Centers of 

Excellence for Influenza Research and Surveillance (CEIRS) Network Meeting at St. Jude Children’s Research 

Hospital. 

Narrative of Doctoral Dissertation. Since joining the Conn laboratory, I have focused my studies on the 

regulation of OAS1 by double-stranded RNA (dsRNA). Data from previous lab members showed that 

mutations to particular consensus sequence nucleotides cause stark differences in OAS1 activation. However, 

the molecular basis for these differences was not clear from available structural and functional data. The goal 

of my dissertation research is to understand how RNA features (sequences, structural motifs, etc.) contribute 

to OAS1 activation. Preliminary data suggests that the stark differences observed in OAS1 activity by these 

dsRNA are not due to differences in binding affinity. From these data, I hypothesize that the differences in 

OAS1 activity likely lie in differences in enzyme kinetics or structural rearrangements and will test these 

hypotheses as part of my current proposal. 

B. Training Goals and Objectives 

My first goal for the training period is to continue developing my skills in independent experimental design, 

execution, and interpretation of results obtained. To date, I have refined our expression and purification 

scheme for OAS1, resulting in a better yield of more active protein. As presented in the preliminary data in this 

proposal, I have also begun experiments using bio-layer interferometry (BLI) (using a new biotinylated OAS1 

construct I generated) and produced the samples for the hydrogen-deuterium exchange coupled to mass 

spectrometry (HDX-MS) peptide mapping study. 

The proposed research will aid my scientific career by first allowing me to acquire many new technical skills 

e.g. in performing and analyzing the results of BLI binding assays, HDX-MS analyses of protein dynamics, Xray crystallographic structure determination, OAS enzyme assays, cell culture, and viral infection assays. 

These new skills will complement those from my time as a research specialist (e.g. in RNA synthesis and 

purification, and protein kinase assays) as well deepen my knowledge of critical practical skills for any 

biochemist, such as protein expression and purification. I will be supported by my Sponsor and Co-sponsor in 

many of these approaches but will also be able to call on other researchers and experts to develop new 

protocols and troubleshoot difficult problems in approaches, including BLI and HDX-MS. I am excited to be 

contributing to bringing these new approaches into our lab’s repertoire. With the help of Drs. Conn and Lowen, 

I have developed an integrated plan to assess OAS1 regulation by specific RNA features using the above 

broad range of approaches. In Specific Aim 1, I will measure OAS1 enzyme kinetics and correlate the 

differences in vitro with their impact on the OAS1/RNase L pathway in human cells by measuring ribosomal 

RNA (rRNA) cleavage and transcript level changes of known RNase L targets, all of which is new to me. In 

Specific Aim 2, I will measure dsRNA binding kinetics (on/off rates) and OAS1 structural dynamics using BLI 

and HDX-MS, respectively, both entirely new techniques to me. These experiments will allow us to gain insight 

into exactly how the RNA can mechanistically alter OAS1 structure to achieve different levels of activation. By 

building upon my current foundation of knowledge, I am setting myself up for the best possible post-doctoral 

experiences available. 

I will also continue to develop my communication skills. Dr. Conn places a strong emphasis on perfecting 

presentation and writing skills, which is one of the main reasons I ultimately chose to join his lab for my thesis 

Applicant's Background and Goals for Fellowship Training Page 36 
Contact PD/PI: Schwartz, Samantha 

research. I practice my seminars in front of Dr. Conn and lab members to improve my style by becoming more 

clear and polished. The process of developing and writing this fellowship with Dr. Conn and others, and my 

manuscript with Dr. Lowen from my rotation in her lab, not only has been an amazing experience, but also it 

revealed I still have much to learn from them in this area. Developing both of these communication skills is an 

ongoing process as they are essential to my advancement in science. Throughout the training period, I will 

attend meetings to present my research and network with other scientists. These meetings will not only further 

my research through the critical feedback I will receive, but will also help me build connections in my chosen 

field. Additionally, I will take advantage of the many training opportunities provided by the BCDB graduate 

program (yearly student seminars, journal clubs, etc.) to refine and practice my communication skills. Finally, I 

will expand my writing skills to include the preparation and submission of my work for publication. My 

expectation is that, from the project I have developed, I will be able to publish at least two first-author peerreviewed papers in leading journals in my new field. 

My long-term career goal is to become an independent researcher using biochemical and virological 

approaches to study mechanisms underpinning cellular function and disease related to infection and immunity. 

Given my early stage in graduate school, I currently aim to keep an open mind about the ultimate setting in 

which I will build this career (e.g. academia, government lab, or industry). I plan to take advantage of 

opportunities to learn about all career options, including a career seminar series, “Pathways Beyond the 

Professoriate,” offered by the Laney Graduate School (LGS), and professionalization workshops offered by my 

program. One important strength of the BCDB Program is its requirement that students produce an individual 

development plan (IDP) in their first year and then update this plan on an annual basis, including short/ long 

term research goals and career plans. This process will help Dr. Conn and I ensure that my technical and other 

professional training continues to be well suited to my future career. Dr. Conn has been exceptionally 

supportive of my career goals to date, and I am optimistic that the training and mentorship I will receive from 

him and Dr. Lowen will allow me to reach my goal. My initial target following successful graduate work will be 

to secure a post-doctoral training position at a top research university in a lab working in the areas of innate 

immunity field but using approaches tangential from my current studies. Long term, I want to continue studying 

innate immunity with the goal that my research will lend insight into both basic cellular mechanisms and 

disease. 

C. Activities Planned Under this Award 

I am currently a second year in the BCDB graduate program at Emory University. As such, I have completed 

the majority of the required BCDB coursework, including the intensive, literature- and discussion-based course 

Foundations in BCDB I and II, Beginning Seminar, and research rotations in Year 1. I have also completed the 

Year 2 course “Hypothesis Design and Scientific Writing” in which I developed this proposal (see Respective 

Contributions for details). I also passed my written qualifying exam in April 2016. My remaining coursework and 

program-related activities include a Year 2 spring course on statistics for biology research and a semester-long 

teaching assistantship (as part of the formal LGS TATTO program). I am therefore currently focusing the 

majority of my time between research and coursework. I spent the summer prior to the fall semester of my 

second year writing up and publishing my methods paper with Dr. Lowen, and I have spent the fall semester 

obtaining preliminary data presented here and writing this proposal. I have also submitted an abstract for a 

poster presentation at the 14th Annual DSAC Student Research Symposium at Emory in January 2017. 

Importantly, both of my remaining Program obligations (biostatistics course and teaching assistantship) will be 

completed in the Spring 2017 semester before this NRSA F31 fellowship would be awarded. This will allow me 

to devote my time primarily to research and other related activities, including mentoring undergraduates or 

other junior lab members, preparing manuscripts, and attending local, national, or international conferences to 

present my work, as outlined in the Table below. 

Grad 

Year 

F31 

Year Research* Data collection/

analysis Mentoring Manuscript/thesis prep 

BCDB 

Program

Activities

Seminars, 

Conferences, 

& Symposia 

Applicant's Background and Goals for Fellowship Training Page 37 

3 1 90 75 5 10 3 7 

4 2 90 65 15 10 3 7 

5 3 90 55 5 30 3 7 

*Research time includes three specific activities: Data collection/ analysis, Mentoring, and Manuscript/ thesis prep. Therefore, 

the sum of these three categories equal the total percentage indicated for Research. 
Contact PD/PI: Schwartz, Samantha 

At Emory, I have the opportunity to attend and participate in many excellent seminars. I attend a weekly 

Advanced Seminar through the BCDB graduate program. Here, two students give half hour presentations on 

their research, and I am required to present once a year. I also participate in two monthly special interest 

seminars. The first is a Joint Structural Biology Groups meeting where one or more lab members from one of 

the Emory structural biology research groups gives a one-hour presentation on their project(s) and any 

problems or difficulties encountered using biophysical methods, including X-ray crystallography. This meeting 

involves four groups from the Department of Biochemistry (Drs. Conn, Dunham, Bo Liang, and Eric Ortlund) 

and others from across campus (e.g. Drs. Renhao Li and Elizabeth Wright from the Department of Pediatrics). 

The other special interest seminar series is the ‘Emory RNA club,’ which brings together labs with varied 

interests in RNA biology from both the School of Medicine (e.g. Drs. Conn, Dunham, and Daniel Reines from 

Biochemistry, and Gary Bassell from Cell Biology) and Emory College (e.g. Drs. Khalid Salaita and Anita 

Corbett from Chemistry and Biology, respectively). At these meetings, two students or postdocs each give a 30 

minute presentation on their research, with an emphasis on diverse methods used related to RNA biology (e.g. 

structural biology, cell biology, fluorescence microscopy, and RNA-seq/ bioinformatic methods). Here, I am 

exposed to the many techniques used to study RNA outside the mostly in vitro structure-function assays I 

perform. I will continue to participate in local scientific seminar series and plan to attend both national and 

international conferences. Future conferences I would like to attend include: RNA Society, American Society 

for Biochemistry and Molecular Biology, Cold Spring Harbor, Keystone, and a Gordon Conference. 

I also enjoy volunteering and contributing to the BCDB program and plan to maintain this level of involvement 

throughout my time at Emory. Currently, I am a “Student Director” for the first year Foundations course, an 

instructor for the Methods workshop, an editor for The Leading Edge BCDB Newsletter, and an organizer for 

the program’s Professionalization Workshops. I also helped to lead the organization of this year’s BCDB retreat 

(August 2016), and was asked to help organize recruitment for the 2017 admissions cycle. Being a part of 

these non-research activities will help me gain important transferable skills, like communication, organization, 

and collaboration that are essential for my professional development and are not achievable by exclusively 

working at the bench. It is important to me to give back to the program. I find these experiences incredibly 

valuable, and I want to contribute directly to future BCDB student’s personal and professional development. 

Applicant's Background and Goals for Fellowship Training Page 38 
SPECIFIC AIM 1: Define dsRNA features and their context that lead to potent activation of OAS1. 

Hypothesis: Extent of OAS1 activation is determined by the context of potentially overlapping RNA features 

with the ability to activate or inhibit OAS1. I will examine the role of specific RNA features in vitro by using an 

established assay to measure OAS1 enzyme kinetics in the presence of the wild-type and each variant dsRNA 

hairpin. I will correlate the differences in ability of each RNA to activate OAS1 in vitro with their impact on the 

OAS1/RNase L pathway by transfecting these dsRNAs into A549 cells and measuring cellular messenger RNA 

transcript level changes of known RNase L targets and cleavage of ribosomal RNA by RNase L. These 

experiments will provide important new insight into currently unknown features of dsRNA that result in potent 

OAS1 activation and the potential for competition between OAS1 bindingsites. 

SPECIFIC AIM 2: Determine the molecular mechanism(s) by which the “non-activating” and “hyperactivating” dsRNAs differ in their effects upon OAS1 activity. Hypothesis: “Non-activating” and “hyperactivating” RNAs exert their effects through different impacts on binding kinetics and/or OAS1 structural 

changes despite both having similar binding affinity. Biotinylated OAS1 will be immobilized on a streptavidin 

biosensor and dsRNA binding affinity and kinetics (on/off rates) measured using bio-layer interferometry. Next, 

I will use hydrogen-deuterium exchange coupled with mass spectrometry to determine the impact of each 

dsRNA hairpin on OAS1 conformational dynamics, including critical allosteric changes in the enzyme active 

site. Lastly, I will use x-ray crystallography to solve structures of dsRNA hairpins bound to OAS1. Collectively, 

these experiments will reveal the molecular mechanism(s) by which specific dsRNA signatures drive different 

levels of OAS1 activation. 

Contact PD/PI: Schwartz, Samantha 

SPECIFIC AIMS 

The innate immune system must accurately distinguish self from foreign molecules to provide a critical first line 

of defense against pathogens. Double-stranded RNAs (dsRNAs) are produced during the life cycles of many 

viruses and their detection by cellular sensors signals that infection has occurred and antiviral defenses should 

be activated. 2’-5’-oligoadenylate synthetase 1 (OAS1) is an important innate immune sensorof cytosolic 

dsRNA. OAS1 activates the latent ribonuclease (RNase L) via dsRNA-dependent productionof 2’-5’-

oligoadenylate second messengers. Activated RNase L then targets viral and cellular RNA for degradation and 

thereby halts viral replication. Attesting to the importance of the OAS1/RNase L pathway, viruses have evolved 

mechanisms to evade its effects by directly inhibiting OAS1, sequestering dsRNA produced as a result of viral 

infection, or producing 2’-5’-oligoadenylate analogs. Determining the molecular mechanism of dsRNAmediated regulation of OAS1 is vital for understanding how the OAS1/RNase L pathway controls viral infection. 

Previous structural studies revealed that dsRNA binding allosterically induces conformational changes 

in OAS1 to form its active site and thus drive polymerization of ATP into 2’-5’-oligoadenylates. These structures 

have given us some insight into how OAS1 is activated by dsRNA; however, we still understand very little 

about how specific features of the dsRNA contribute to the level of OAS1 activation. The dsRNA used in these 

structural studies contained two overlapping and antiparallel copies of a known OAS1 activation consensus 

sequence, one on each strand of the helix. Yet the dsRNA bound OAS1 in a single unique orientation. Our 

preliminary data indicate that this selectivity in binding orientation also exists in solution and plays a critical role 

in determining the potency of OAS1 activation. We designed three RNA hairpin constructs based on the model 

dsRNA used in the structural studies: the wild-type dsRNA hairpin with the two strands linked by a short stable 

loop, and two variants where a critical residue of one OAS1 consensus sequence was mutated. Remarkably, 

while mutation of one consensus sequence resulted in complete loss of OAS1 (“non-activating”), 

increased OAS1 (“hyper-activating”). Despite these differences in ability 

to activate OAS1, preliminary data from our lab suggested that both variants bind OAS1 with similar affinity. 

These findings suggest that the wild-type dsRNA hairpin contains competing OAS1 binding sites with 

remarkably different capacities to activate the protein. However, the molecular signatures defining these sites 

as activating and non-activating are unknown. The dsRNA hairpins we have generated are ideal tools for 

deciphering the structural requirements and molecular mechanisms of OAS1 activation. Thus, in the following 

two Specific Aims, I will use complementary assays of OAS1 activity in vitro and in human cells as well as 

biochemical, biophysical, and structural approaches to define the differences in protein-RNA interaction that 

lead to differential activation of OAS1 by these three dsRNA hairpin sequences. 

Summary: The goal of this project is to determine how specific features in dsRNA, as well as their context, 

control regulation of OAS1. Such studies are critical to gain a broader understanding of host-pathogen 

interactions and the fundamental mechanisms of cellular translational control. For example, this work will give 

insight into how viruses could mask otherwise activating motifs in order to evade detection by the innate 

immune system and may provide a foundation for the development of novel antiviral therapeutics. 

Specific Aims Page 39 
Research Strategy Page 40 

 

 

 

 

 

 

 

Contact PD/PI: Schwartz, Samantha 

RESEARCH STRATEGY 

A. SIGNIFICANCE 

2’-5’-oligoadenylate synthetase 1 (OAS1) is an important component of the innate immune system that 

provides a critical first line of defense against viral infection. OAS1 is a sensor of cytosolic double-stranded 

RNA (dsRNA) (1-3), a potent pathogen-associated molecular pattern (PAMP), present in some viral genomes 

or produced as a consequence of viral gene expression or replication (4). Viral dsRNA-promoted OAS1 

activation leads to subsequent activation of the latent endoribonuclease L (RNase L) via dsRNA-dependent 

production of 2’-5’-oligoadenylate secondary messengers. RNase L activation effectively halts viral replication 

through the degradation of target viral and cellular RNAs (Fig. 1A) (5-8). The goal of this project is to reveal 

novel insight into the importance of RNA sequence, structure, and context to dsRNA regulation of OAS1 

activity. These details will aid in our understanding of host-pathogen interactions and, for example, how viruses 

might circumvent the OAS1/RNase L pathway. 

Viruses have evolved ways of circumventing the innate immune system. As obligate parasites, viruses 

depend on the host cell to complete their life cycle. In particular, all viruses require the cellular translation 

machinery for expression of their proteins. Viruses must also avoid detection by innate antiviral factors that can 

potently restrict viral replication, often by interfering with cellular translation. Attesting to the specific importance 

of the OAS1/RNase L pathway in this process, many viruses have developed ways to evade detection by 

directly inhibiting OAS1, sequestering dsRNA produced as a result of viral infection, or producing 2’-5’-analogs 

(1,9-17). Therefore, determining the molecular mechanisms of dsRNA-mediated OAS1 regulation is a vital 

component of understanding how the OAS1/RNase L pathway contributes to the control of viral infection. 

OAS1 shuts down host translation through the OAS/RNase L pathway. OAS1 is an important innate 

immune sensor that detects cytosolic dsRNA produced as a consequence of viral replication (1-3). Previous 

structural studies revealed that dsRNA binding allosterically induces the conformational changes necessary in 

OAS1 to form its active site and thus drive polymerization of ATP into 2’-5’-linked oligoadenylates (18). These 

2’-5’-oligoadenylate secondary messengers promote the dimerization and 

subsequent activation of RNase L (Fig. 1A) (7,8). Activated RNase L degrades 

both viral and cellular RNA to halt viral replication and limit the spread of infection 

(19-22). RNase L targets specific messenger (m)RNA transcripts encoding 

proteins known to regulate cell adhesion and proliferation (23) as well as 

ribosomal (r)RNA to prevent translation and viral spread to neighboring cells (24). 

OAS1 is activated upon binding viral dsRNA. OAS1 lacks an RNA-binding 

motif and instead interacts with dsRNA through patches of positive residues on 

the protein’s surface (18). RNA binding to OAS1 requires double stranded regions 

with a minimum length of 18 base pairs (bp) (25). However, while OAS1 can be 

activated by dsRNA that meets this 18 bp requirement, activation is strongly 

potentiated by activating consensus sequences and the 3’-end single-stranded 

pyrimidine (3’-ssPy) motif that our lab recently identified (26-28). However, how 

these molecular signatures in dsRNA affect the level of OAS1 activity, and thus 

the potency of its antiviral effect, is not well understood. 

The dsRNA used in previous structural studies (18) contained two 

overlapping and antiparallel copies of a known OAS1 activation consensus 

sequence WWN9WG, where W is A or U, and N is any nucleotide (26). Although 

one consensus sequence was present on each strand of the helix, the dsRNA 

bound OAS1 in a single, unique orientation (18). Our preliminary data indicate 

that selectivity in binding orientation also exists in solution and plays a critical role 

in determining the potency of OAS1 activation. We designed a model dsRNA airpin construct based on the dsRNA used in these structural studies where the 

“wild-type” dsRNA strands are linked by a short stable loop (Fig. 1B). We chose 

 use short dsRNA hairpins for the studies proposed here to simplify preparation 

(by in vitro transcription), for ease of transfection, and because due to their small 

 size they should not activate other dsRNA sensors in cells. Two additional hairpin variants were also created where the G residue of one OAS1 consensus 

sequence was mutated. This G residue (in the top strand, green shaded 

onsensus; Fig 1B) was the only base-specific contact between OAS1 and the 

RNA in the crystal structure (18). Remarkably, our preliminary data showed that 

Fig. 1. OAS1/RNase L pathway and 

 n. 

s 

 te le 

 

 - h

). in 

(top)_with two overlapping and anti- to

parallel copies of a known OAS1 

activation consensus sequence 

(shaded blue and green). The tetra- loop added to connect the strands is 

 

 in 

c r-

 

dsRNA hairpin construct desig A, Upon binding dsRNA, OAS1 form

2’-5’-oligoadenylates which activa RNase L. The location of the stab

RNA tetraloop sequence added to 

my dsRNA constructs is shown by the dashed purple line on the OAS1

dsRNA crystal structure (PDB 4IG8

B, The wild-type dsRNA hairp

in purple. Single G to A mutations 

that result in dramatic differences 

OAS1 activation are indicated for the

“Non-activating” and “Hype

activating” dsRNA hairpin variants.
Contact PD/PI: Schwartz, Samantha 

while the mutation in the top strand consensus resulted in a complete loss of OAS1 activity (“Non-activating” 

variant), the equivalent change on the other stand increased OAS1 activity (“Hyper-activating” variant). Despite 

displaying stark differences in their ability to activate OAS1, both dsRNA hairpin variants retain the ability to 

bind OAS1 (see Approach section for details). 

Scientific Premise: Although crystal structures have been

solved of OAS1 in complex with dsRNA (18,29), we still do 

not fully understand the mechanisms OAS1 employs to

discriminate between viral and cellular RNAs. Some

previous work has been done to tease out the molecular

requirements for OAS1 activation (18,25-27), but our lab’s 

recent discovery of the novel motif suggests our

understanding of dsRNA-mediated OAS1 regulation is still

incomplete (28). Based on the preliminary findings

presented here, I hypothesize that the dsRNA hairpin

contains competing OAS1 binding sites with remarkably 

different capacities to activate the protein. However, the 

molecular signatures defining these sites as activating and

non-activating are not known. I will test my hypothesis 

through the following aims (summarized in Fig. 2). In Aim 1, I will use OAS1 kinetics assays and RNase L activation in

cells to define the features of dsRNA that lead to potent 

OAS1 activation using the model dsRNA hairpins. In Aim 2, 

I will determine the molecular mechanism(s) by which the 

“non-activating” and “hyper-activating” dsRNAs differ in their 

interaction with OAS1 and effects on OAS1 structural 

dynamics. Through these complementary specific aims, I will determine how specific features in dsRNA and 

their context contribute to regulation of OAS1. 

Fig. 2. Summary of Aims. In Aim 1, I will test my model for 

competition between OAS1 binding sites (top) using 

complementary assays of OAS1 activation in vitro and in A549 

cells using the “hyper-activating” (green arrow) or “non-activating” 

(red arrow) dsRNA variants. In Aim 2, I will examine RNA binding 

affinity and kinetics (top) and structural changes (bottom) to 

define the mechanistic basis to “hyper-activating” or “nonactivating” OAS1 binding sites in dsRNA. 

B. APPROACH 

SPECIFIC AIM 1: Define dsRNA features and their context that lead to potent activation of OAS 1. 

Rationale: dsRNA binding to OAS1 requires a minimum of 18 bp and activation is potentiated by the presence 

of recently identified molecular signatures, including 

However, how these molecular signatures act in concert or competition to affect the level of 

OAS1 activity and thus an innate antiviral response is unknown. Our preliminary data (Fig. 3) illustrate that 

in each of the two consensus sequences leads to opposing affects: one no longer activates 

OAS1 (“non-activating”) while the other dramatically increases OAS1 activation (“hyper-activating”). 

Determining which RNA features create a preferred OAS1 binding site activating or non-activating will give 

critical new insight into how viruses could mask otherwise activating motifs to evade detection by the innate 

immune system. Hypothesis: Extent of OAS1 activation is determined by the context of potentially overlapping 

RNA features with the ability to activate or inhibit OAS1. 

Overview of Experimental Design: I will examine how specific dsRNA features control the extent of OAS1 

activity in vitro by using our established chromogenic assay (28) to measure OAS1 enzyme kinetics for the 

wild-type and each variant dsRNA hairpin (see Fig. 1B). I will next compare the differences in the ability of 

each dsRNA to activate OAS1 in vitro with their impact on the OAS1/RNase L pathway in living cells. These 

experiments will provide important new insight into currently unknown features of dsRNA that result in potent 

OAS1 activation in vitro and in human cells. 

Aim 1.1: Define the features of dsRNA that lead to potent activation of OAS1 in vitro. 

Experimental Approach: I will in vitro transcribe the dsRNA hairpins from linearized plasmid DNA templates 

using T7 RNA polymerase and purify the RNAs by denaturing polyacrylamide gel electrophoresis using 

established protocols (30-33). Two “scrambled” versions of the dsRNA hairpin will also be transcribed as 

controls: Scramble 1 will maintain the wild-type activation consensus sequences, but will randomize all other 

nucleotides and in Scramble 2 all nucleotides will be randomized (while maintaining an 18 bp duplex in both 

RNAs). Human OAS1 will be expressed in E. coli BL21(DE3) and purified using sequential Ni2+-affinity, 

heparin-affinity, and gel filtration chromatography (28). I will use our lab’s established 96-well plate format in 

vitro chromogenic assay (28) to test the effects of mutations in defined RNA signatures in the dsRNA model 

Research Strategy Page 41 
Contact PD/PI: Schwartz, Samantha 

hairpin on OAS1 enzyme kinetics (Fig. 3A). This assay measures the amount of inorganic pyrophosphate (PPi)

produced as a consequence of 2’-5’-oligoadenylate synthesis as a readout of OAS1 activity. The PPi is 

detected by quantifying the change in color (Abs at 580 nm) upon adding an ammonium molybdate reagent, as 

shown for the initial enzyme progress curves at a single concentration of the wild-type (purple), “non-activating” 

(blue), and “hyper-activating” (green) dsRNA hairpins (Fig. 3B). In this subaim, I will perform assays at a range 

of RNA concentrations to determine enzyme kinetic parameters (Vmax and Kapp) (28) to fully define the capacity 

of each RNA to activate OAS1 in vitro. 

I will also perform competition assays

with a fixed amount of the “hyper-activating” 

dsRNA and titrating increasing amounts of the 

“non-activating” dsRNA. This experiment will 

directly test the consensus competition model

and show that the “non-activating” RNA interacts 

with OAS1 (as suggested by preliminary binding 

data, see Aim 2). The following controls will be 

used in all experiments in this subaim: ATP 

degradation (no OAS1), no RNA (negative), 

poly(rI:rC) dsRNA (positive), wild-type and both

scramble dsRNA hairpins. 

Fig. 3. In vitro OAS1 activation assay reveals stark differences between the 

two consensus sequence variants. A, OAS1 activity is measured via PP 

production during 2’-5’-oligoadenylate synthesis. A color product is produced 

upon the addition of ammonium molybdate and absorbance is measured at 580

nm using a BioTek Synergy 4 plate reader. B, OAS1 enzyme progress curves 

are shown for a single concentration of wild-type (purple), “hyper-activating” 

(green), and “non-activating” (blue) dsRNAs; a no RNA control (grey). Data Analysis/Rigor: To ensure rigorous and 

reproducible data are obtained, each experiment 

will be performed in three technical replicates and use at least two different preps of OAS1. Prep-to-prep 

variation in OAS activity will be assessed and controlled for by including poly(rI:rC) dsRNA and wild-type 

dsRNA samples on each plate. After background correction, absorbance measurements are converted to nmol 

PPi produced using a standard curve of known PPi concentrations. Data will be averaged and plotted using 

standard error of the mean on GraphPad Prism software and curves will be fit using non-linear regression to 

obtain Vmax and Kapp values using the Michaelis-Menten model equation, Y=(VmaxX)/(Kapp+X). 

Outcomes/Interpretations: This subaim will measure in vitro OAS1 enzyme activity to discern potential 

differences in OAS1 kinetic parameters (Vmax and Kapp) that lead to the dramatically different extents of OAS1 

activation by the dsRNA hairpins suggested by the preliminary studies using single RNA concentrations (Fig. 

3B). Our lab’s previous analysis of the (28) suggest that I may observe an increase in maximal 

enzyme rate (Vmax) for the “hyper-activating” and a decrease in this parameter for the “non-activating” dsRNA 

compared to “wild-type.” For each dsRNA, I may also observe a change in the apparent RNA affinity (Kapp). A 

decrease in apparent affinity from enzyme kinetic measurements for the “hyper-activating” dsRNA hairpin 

could, for example, reflect a mechanistic requirement for OAS1 to bind and release the dsRNA between 

rounds of catalysis. Competition experiments will explore a model that the “wild-type” dsRNA contains 

competing sites (productive vs non-productive); if the “non-activating” dsRNA can still bind OAS1 then it should 

be able to compete for binding (and thus regulation of OAS1) in trans. The mechanistic basis for the 

differences in OAS1 activation by different dsRNAs and the potential for competition between activating and 

inhibitory sequences with be fully explored in Aim 2. As these experiments progress, new dsRNA variants 

could be designed to answer additional questions such as whether consensus sequence position within the 

duplex influences activation by inserting/ deleting base pairs between the consensus G and the RNA terminus. 

Aim 1.2: Determine the ability of dsRNA hairpins to activate the OAS/RNase L pathway in living cells.

Experimental Approach: I will test the effects of the three dsRNA model hairpin variants (Fig. 1B) on OAS1 

activation by transfecting each dsRNA into human lung carcinoma (A549) cells and measuring OAS/RNase L 

activity. A549 cells are optimal for these experiments as they express OAS1 without interferon stimulation, thus 

reducing the complexity of experimental design. I will transfect cells with my three dsRNA hairpins using 

lipofectamine 2000 (ThermoFisher) accompanied by the following controls: mock (no RNA), poly(rI:rC) dsRNA 

(positive control), and the scramble dsRNA hairpins (see Aim 1.1). Mock transfections will allow me to confirm 

that the transfection process does not stimulate an innate immune response as well as assess RNA quality 

during extraction. I will isolate total RNA from A549 cells at specific established time points (e.g. 1 and 3 hours) 

post-transfection (23,34). RNase L activity will then be determined by: 1) reverse transcription droplet digital 

PCR (RT ddPCR) with primers for known specific RNase L targets (FAT4, FREM2, PCDHB5, and ZEB1) (23), 

and 2) assess ribosomal RNA (rRNA) cleavage via agarose gel (23,35-37). Partitioning of cDNAs intodroplets 

Research Strategy Page 42 
 

 

 

 

 

 

 

 

 

 

 

 

 

Contact PD/PI: Schwartz, Samantha 

prior to amplification makes ddPCR ideal for detecting small differences between samples or minor species in 

a population (36). ddPCR also allows for absolute quantification of cDNA copy number without the need for a 

standard curve. Pre-determining the number of cells in the starting material allows back calculation and precise 

quantification of the number of mRNA transcripts per cell. rRNA cleavage assays will be used to visualize 

cleavage patterns characteristic of RNase L activation and is well established in the field (19,20,34,35). These 

two methods will allow me to measure a gradation of OAS1 activation (e.g. ddPCR is sensitive tool that will 

allow weak activation to be detected, whereas robust activation can be monitored by rRNAcleavage). 

Data Analysis/Rigor: Each experiment will be performed in biological triplicates. Data will be plotted using 

GraphPad Prism software, replicates will be analyzed using standard deviation, and statistical significance 

determined using unpaired Student’s t-test (p<0.05). 

Outcomes/Interpretations: I anticipate that the cell data will recapitulate my in vitro results on OAS1 

activation, e.g. cellular mRNA and rRNA degradation following transfection with the “hyper-activating” and 

“non-activating” dsRNA hairpins will be significantly increased and decreased, respectively, compared to the 

“wild-type” RNA. These experiments will reveal the importance of the identified RNA signatures and their 

context on OAS1 activation in cells and will thus serve as an important validation of the in vitro enzymatic 

studies of this aim and the mechanistic studies in Aim 2. It is possible that differences in OAS1 (and thus 

RNase L) activation in cells might not be as dramatic as shown by the in vitro data. However, by testing RNAs 

with a range of potential capacities to activate OAS1, my experiments may reveal in more detail the nature of 

the cellular response to low extents of OAS1 activation. For example, does low level activation (which might 

reflect the early stages of infection) lead to only mRNA degradation, while extended time of high OAS1 

activation subsequently results in additional degradation of the cellular translational machinery? 

Potential Pitfalls/Alternative Approaches: The in vitro chromogenic assay outlined in Aim 1.1 is for OAS1 

enzyme kinetics assays established in our lab (28), and therefore I do not expect technical issues with these 

experiments. However, an alternative approach also used in our lab would be to analyze 2’-5’-oligoadenylate 

synthesis by [α32P]-ATP incorporation via denaturing sequencing gels (28). This method, unlike the 

chromogenic assay, is not high throughput but is useful to directly visualize 2’-5’-oligoadenylate products and 

measure very weak activation (18,25). In Aim 1.2, RT ddPCR is an established method that I have used in the 

Lowen lab previously (36) therefore I do not expect to run into technical issues adapting the method for the 

proposed analyses. However, qRT-PCR is an alternative method (23) that can be used if needed and is also 

well established in the Lowen lab. rRNA cleavage can also be determined using a Bioanalyzer (available in the 

Emory Integrated Genomics Core) if agarose gels prove to be inconclusive. Although my dsRNA constructs 

are designed to minimize activation of other innate immune sensor proteins in A549 cells such as dsRNAactivated protein kinase (PKR), if such issues are identified I would use knockout cell lines which have been 

constructed (38) or can be generated in the Lowen lab. 

SPECIFIC AIM 2: Determine the molecular mechanism(s) by which the “non-activating” and “hyperactivating” dsRNAs differ in their effects upon OAS1 activity. 

Rationale: Our preliminary data suggest that dsRNAs may contain potentially competing OAS1 binding sites 

with remarkably different capacities to activate the protein (see Aim 1 and Fig. 3). However, the molecular 

mechanisms defining these sites as activating and non-activating are unknown. Defining such differences will 

provide novel insight into the regulation of OAS1 and could reveal both potential new strategies to manipulate 

OAS1 for the design of effective treatments for viral infection and mechanisms by which viruses could 

potentially mask otherwise activating dsRNA motifs. Hypothesis: “Non-activating” and “hyper-activating” RNAs 

exert their effects through different impacts on binding kinetics and/or OAS1 structural changes despite having 

similar binding affinity. 

Overview of Experimental Design: I will elucidate the molecular mechanism(s) responsible for the dramatic 

differences in OAS1 activation by the dsRNA hairpins by measuring binding affinity and kinetics (on/off rates) 

using bio-layer interferometry (BLI), comparing dsRNA-induced changes in OAS1 structural dynamics using 

hydrogen-deuterium exchange coupled with mass spectrometry (HDX-MS), and determining x-ray crystal 

structures of the “non-activating” and “hyper-activating” dsRNAs bound to OAS1. These experiments will reveal 

important new insight into the molecular mechanisms that modulate OAS1 activation. 

Aim 2.1: Determine the impact of dsRNA binding affinity and/or kinetics on OAS1 activation. 

Experimental Approach: To immobilize OAS1 on a streptavidin biosensor for BLI OAS1-dsRNA interaction 

studies, I used inverse PCR to add an AviTag sequence to the C-terminus of OAS1 to create an OAS1-AviTag 

Research Strategy Page 43 
 

 

Contact PD/PI: Schwartz, Samantha 

construct (39,40). AviTag is a 15 amino acid tag (GSGLNDIFEAQKIEWHE) containing a specific recognition 

sequence for biotinylation by BirA biotin ligase (39). I purified biotinylated recombinant OAS1-AviTag from E. 

coli and showed, using the OAS1 activation assay (see Aim 1.1), that the C-terminal AviTag does not alter 

OAS1 activity (Fig. 4A,B). I have also shown that OAS1-AviTag can be successfully immobilized on 

streptavidin biosensors for RNA binding affinity (Kd) and kinetics (kon and koff) experiments on a state-of-art 

FortéBio OctetRED384 instrument (Fig. 4C) available to us through Emory’s Chemical Biology Discovery 

Center (see letter from Dr. Du). Preliminary BLI data shown here (Fig. 4C) not only demonstrates my ability to 

collect data using this method, but also the important finding that the “non-activating” dsRNA hairpin can still 

bind OAS1. Therefore, the observed non-activation by this hairpin in Aim 1.1 (see Fig. 3B) is not due to lack of 

OAS1 binding. Experiments will be performed at a fixed density of OAS1-AviTag (e.g. 180s loading, 20 μg/ml)

with increasing amounts of dsRNA (e.g. 0.1-100 μM). Each sensor will use a different RNA concentration and

on/off rates will be measured by dipping sensors into RNA (association) and then into buffer (dissociation). 

Controls will include: OAS1 in buffer only (background) and biocytin (a biotin analog) with and without RNA. 

Parameters that may require optimization include buffer conditions, OAS1 and dsRNA concentrations, 

molecule orientation, and reference sensors. I will test different assay buffers using the OAS1 activation assay 

(see Aim 1.1) buffer as a starting point. Loading density of biotinylated OAS1 and analyte concentration will be 

optimized to ensure the appropriate signal intensity is achieved. I will also verify that there is no preferred 

molecule orientation by performing experiments using immobilized biotinylated dsRNA. Although an important 

control, this set up is not ideal, as every dsRNA construct will need to be synthesized with a biotin modification. 

Fig. 4. OAS1-AviTag is active 

and can be biotinylated for 

BLI assays. A, Serially diluted 

wild-type OAS1 and OAS1-

AviTag were analyzed by SDSPAGE and visualized using 

silver stain (top) or blotted with 

streptavidin-horseradish 

peroxidase (bottom). B, OAS1 

activation by the “wild-type” 

RNA hairpin is shown for wild-type OAS1 (solid purple) and OAS1-AviTag (dashed purple). OAS1 activity was also measured using a no RNA control 

(grey). C, OAS1-AviTag was immobilized on a streptavidin biosensor and the “non-activating” RNA hairpin was added at 0.3 mM (blue) and 0.1 mM 

(red). Dotted lines show the curve fits for each concentration. These data show that OAS1-AviTag is specifically biotinylated, retains enzyme activity, 

and preliminary BLI data demonstrate our ability to measure protein-RNA binding affinity andkinetics. 

Data Analysis/Rigor: Data will be subtracted from reference streptavidin sensors coated with biocytin. After 

background correction, the interference shift (in nanometers) is plotted, fit, and analyzed using the Octet Data 

Analysis Software. To ensure rigorous and reproducible data, each experiment will be performed in three 

technical replicates using at least two different preps of OAS1 to address prep-to-prep variability. 

Outcomes/Interpretations: If the ability of a dsRNA to activate OAS1 is dependent on binding affinity or 

kinetics I expect to identify significant differences between “non-activating” and “hyper-activating” dsRNAs. For 

example, I may find that differences in binding affinity whereby higher affinity is correlated with either the more 

or less activating dsRNA. For the “hyper-activating” dsRNA, higher affinity could result in a great ability to drive 

OAS1 conformational changes (see Aim 2.2), while lower affinity with altered kinetics would be consistent with 

a mechanistic requirement to bind and release dsRNA between rounds of catalysis. It is thus also possible that 

the functionally critical difference could be based in alteration of a specific kinetic parameter (kon and/ or koff); a 

kinetic basis for regulation would be a novel finding. If both dsRNAs have the same (or similar) affinity and 

kinetics, this would suggest that binding differences are not the basis for their distinct capacities to activate 

OAS1. In this case, I will focus on the protein dynamics and structural approaches in Aims 2.2 and2.3. 

Aim 2.2: Define the role of dsRNA-driven structural changes in OAS1 enzyme activation. 

Experimental Approach: I performed an OAS1 peptide mapping experiment by in-line pepsin digest and MS 

on our HDX-MS system (see letter from Dr. Li) revealing my ability to achieve 100% OAS1 sequence coverage 

and high (33-fold) redundancy (Fig. 5A). An earlier comparative deuterium exchange experiment showed that 

OAS1 residues dsRNA-induced conformational changes (18), exhibited high deuterium 

uptake in apo OAS1, indicating the dynamic nature of these residues in the absence of RNA (Fig. 5B). These 

data show that HDX/MS will be an ideal tool to monitor differences in the capacity of my dsRNAs to functionally 

alter the OAS1 structure. I will therefore use HDX-MS to examine differences in OAS1 protein conformational 

dynamics in the absence or presence of the “wild-type,” “non-activating,” and “hyper-activating” dsRNA 

hairpins (see Fig. 1B). The automated system adds deuterium-containing solution to the sample (OAS1 alone 

Research Strategy Page 44 
 

 

 

 

 

 

 

 

 

 

Contact PD/PI: Schwartz, Samantha 

or OAS1-dsRNA complex), quenches the reaction at 4-5 individual time points (e.g. 0, 15, 60, 180, 600 

seconds), and injects the samples individually onto the in-line pepsin column prior to MS analysis. Differential 

deuterium uptake in each measured OAS1 peptide (apo vs each dsRNA, “hyper-activating” vs “non-activating”) 

will be calculated and mapped on to the OAS1 structure. 

Data Analysis/Rigor: Duplicate experiments will be conducted using protein from independent preps, with six 

separate injections of each sample into the MS to ensure high redundancy. I will analyze the data in the HDX 

core with Masslynx 4.1, PLGS 3.0, and Dynamix 3.2 software. 

Outcomes/Interpretations: If an ability to drive changes in 

OAS1 conformational dynamics contributes to differences 

observed in OAS1 activation, I expect that the “hyperactivating” dsRNA will causechanges in and 

potentially other activating changes elsewhere in OAS1. In 

contrast, the “non-activating” dsRNA may fail to induce the 

functionally critical changes in or may cause 

additional inhibitory changes that contribute to loss of OAS1 

activation. The role of newly identified regions in OAS1 that 

may be allosterically regulated by dsRNA could next be tested 

by mutagenesis and functional analyses like those of Aim1. 

Fig. 5. Preliminary HDX-MS data. A, OAS1 mappin

experiment demonstrating the potential for acquiring high

quality HDX-MS data (100% coverage, 33-fold redundancy). 

Each blue bar represents a unique peptide and the zoomed in

region shows the loop which undergoes 

formational change upon dsRNA binding. B, Deuterium

uptake from a pilot exchange experiment. These data show 

uptake only for demonstrating that RNAinduced changes can be monitored by this method. [Data in 

nel B collected by G. Conn]. 

Aim 2.3: Determine structures of ‘non-activating’ and 

‘hyper-activating’ dsRNA in complex with OAS1.

Experimental Approach: We have obtained initial crystals 

from 96-well screens for both the “non-activating” and “hyper- g 

activating” dsRNA complexes with OAS1 that diffract to 

medium resolution (~7 Å) (Fig. 6). I will next optimize these 

crystals using additional screens around the initial conditions, 

adjusting parameters such as the concentrations of OAS1- con

dsRNA complex, salt, or precipitant, pH, and temperature. If 

needed, I will also test detergents and other additives to 

improve crystal formation. Diffraction data sets will be collected pa

at the SER-CAT beamline at the APS. Once suitable quality data are obtained, I will determine the structure by 

molecular replacement using the structure of RNAbound OAS1 (PDB 4IG8) as a starting model. Our 

lab has all the software needed for structure 

determination, including HKL2000 for X-ray data 

processing (41); Phenix for molecular replacement, 

refinement, and validation (42); and Coot for manual 

model building (43). 

Fig. 6. Crystallization of OAS1:dsRNA complexes. A, OAS1 and dsRN

elute from a Superdex S200 gel filtration column. B, Demonstration that

crystals contain both RNA and protein. Crystals were (1) washed five times

with crystallization solution then (2) dissolved and analyzed by PAGE. C

Diffraction from a crystal taken from the drop shown in panel B extends to a

least 7Å (white arrows). These data demonstrate our ability to crystallize de OAS1 with a dsRNA hairpin from our library. [Data collected by B. Calderon 

and G. Conn]. 

A Data Analysis/Rigor: Structures will be validated coduring refinement with Phenix (42), and I will use the 

Protein Data Bank (PDB) server to ensure our data ,

t and final structures are of optimal quality prior to 

position (44). 

Outcomes/Interpretations: Structures of the OAS1-

dsRNA complexes will reveal the molecular details underpinning the differing ability of each dsRNA to activate 

OAS1. These structures will provide a detailed platform for interpretation of my findings in other subaims as 

well as allowing me to develop and test (by mutagenesis and functional assays) new hypotheses about critical 

OAS1-dsRNA interactions for potent activation or for dsRNA binding in the absence of OAS1activation. 

Potential Pitfalls/Alternative Approach: My preliminary data indicate BLI will be applicable to OAS-dsRNA 

binding affinity/ kinetics but, if needed other approaches are well established in our lab (45-47) and several 

options are available (e.g surface plasmon resonance or isothermal titration calorimetry in the Emory 

Comprehensive Glycomics core). I also do not anticipate technical issues with HDX-MS as our preliminary data 

(Fig. 5) clearly support the feasibility of this approach. Finally, X-ray crystallography is inherently full of 

potential pitfalls but progress in obtaining diffracting crystals of both complexes and our lab’s track record in 

structure determination (48-54) give strong cause for optimism that I will obtain high-resolution structures. 

Research Strategy Page 45 
 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Contact PD/PI: Schwartz, Samantha 

RESPECTIVE CONTRIBUTIONS 

The project described in this proposal is founded on an initial observation made by a previous Conn Lab 

graduate student, Dr. Virginia Vachon. Specifically, she found that single point mutations within each OAS1 

activation consensus sequence in the double-stranded RNA duplex used in previous structural studies had 

starkly different impacts on the ability of the RNA to activate OAS1. After I joined Dr. Conn’s lab for my thesis 

work, we discussed this observation and together outlined a set of experimental approaches that could tease 

out the molecular basis for how RNAs with similar affinity could have such different capacities to activate 

OAS1. 

Following these discussions in early summer 2016, I began developing a form of this proposal in the IBS 522r 

Hypothesis Design and Scientific Writing course taken as part of the Biochemistry, Cell, and Developmental 

Biology (BCDB) Program core curriculum. This course is co-directed by Drs. Conn, Anita Corbett, and Joanna 

Goldberg. The course includes all second year BCDB and Microbiology and Molecular Genetics (MMG) 

Program students, as well as other MD/PhD students enrolled in various graduate programs at Emory. This 

course taught us how to think critically and to communicate our science. As part of the course, I prepared an 

NRSA-format research proposal in a step-wise manner with weekly assignments to outline, write, and re-write 

each section of the proposal. As a result, I received feedback on my developing proposal from a large number 

of individuals. For each week’s assignment, Dr. Conn worked closely with me, typically through an initial 

discussion of ideas and then written comments on a draft version of the section to be submitted. During the 

entire process, Dr. Conn assisted by critically evaluating my writing and ideas and always followed up with 

helpful advice and suggestions. I worked very closely with my “class mentor,” Dr. Corbett, who would provide 

written comments on each week’s assignment to offer an additional perspective to help guide me as I 

developed, wrote, and re-wrote the various sections of my fellowship. In several of the classes, I also received 

feedback from classmates through a presentation of aims and a model figure and other in-class exercises. 

Once the complete proposal was compiled, I received additional comments from a senior BCDB student (Mr. 

Ed Quach) before finally “submitting” my proposal for review by two faculty members (all mentors of students in 

the class are required to review two “grants” of other students in the class). Comments from these anonymous 

reviews were also provided to me before I prepared the current proposal. Finally, I also received comments 

from Dr. Conn and my Co-sponsor, Dr. Lowen, on the version of my proposal that I ultimately submitted. 

The preliminary data presented in this proposal was collected and analyzed by me unless otherwise 

specifically noted in the corresponding figure legend. 

Moving forward, for the experiments described in this proposal, I will design, conduct, analyze, and interpret 

the results with assistance from Drs. Conn and Lowen. My sponsors will also assist me with correctly 

interpreting and presenting the results of my experiments, as well as advising me on experimental design for 

the next steps through both our regular scheduled meetings and informal discussions. Dr. Conn’s office is 

adjacent to the lab, and he is always available and eager to talk about experiments or data. Though I strive for 

independence in the execution of my experiments, his expertise and availability has been a tremendous asset 

to my training thus far. For preparation of manuscripts, I will construct a thorough outline prior to seeking 

assistance from Drs. Conn and Lowen so that we can further organize my thoughts and findings into a 

cohesive story. I will then write initial drafts with my sponsors’ guidance until I can piece together a well-written 

first draft independently. I will also seek feedback on my results and manuscripts from my thesis committee, 

other colleagues (e.g. Dr. Christine Dunham and her group, with whom we have joint lab meetings), and 

current Conn and Lowen lab members. 

Respective Contributions Page 46 
 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Contact PD/PI: Schwartz, Samantha 

SELECTION OF SPONSOR AND INSTITUTE 

After making my decision to pursue graduate school, I narrowed my difficult decision down to two excellent 

graduate programs: University of Texas Southwestern Medical Center’s Biological Sciences Umbrella Program 

and Emory University’s Biochemistry, Cell, and Developmental Biology (BCDB) Program. BCDB really stood 

apart from UTSW and the other programs I had considered because of the attractive training opportunities and 

the warm, close-knit feel the faculty and students share (and which I had had the opportunity to witness in 

detail through my role as a research specialist in a lab hosting BCDB students). These opportunities include a 

first year discussion-based course called “Foundations” that allows for extensive time one-on-one with the 

faculty and my peers, a first year seminar course that prepares students for public speaking and presentations, 

a second year scientific writing course where students write their own research proposals using an NRSA-style 

format, yearly student seminars, workshops to explore potential career opportunities, and a guaranteed stipend 

throughout training. BCDB also offers 1) a program retreat at the start of each academic year that is full of 

team-building activities, science, and the opportunity to catch up with BCDB alums to discuss their experiences 

and career paths, 2) a methods workshop (which I currently organize with two senior students in my program), 

and 3) a professionalization workshop (I currently organize this also!). As a result, BCDB students have many 

opportunities to hone their oral and written communication skills, as well as to access substantial education 

about career development. In addition, the pervasively collaborative and supportive environment of the BCDB 

program convinced me to attend. Professors and students routinely consult each other for advice or to develop 

new collaborations. In addition to my experience working at Emory, this strong graduate program environment 

was obvious to me at my interview because members of the program clearly knew each other and each other’s 

research, despite the breadth of research in the program. I see this type of environment being a particular 

asset to my career because I find it easy to approach a professor at an event or in their office to talk about an 

experimental method, my data, or my proposal. Although the BCDB program is relatively small (roughly 40 

students and 45 faculty), as one of nine programs in the Emory School of Medicine’s Graduate Division of 

Biological and Biomedical Sciences I am part of an exceptionally broad, dynamic, and exciting research and 

intellectual environment. As a result, on an institutional level, Emory’s graduate support structure and core 

facilities are outstanding (I am even implementing two of them in this proposal!). Collectively, these many 

strengths from the individual program level and across the whole of Emory assured me that I would have 

everything I need to perform cutting-edge research and all of the training opportunities to make me 

exceptionally competitive for my post-doctoral training and career in researchbeyond. 

As a first-generation college student, I was unsure about the next steps and not yet prepared to commit to 

graduate school following my graduation from Armstrong State University. At the time, I bounced back and 

forth between pursuing a Master’s or a Ph.D. but could not firmly commit to one field of study over another, 

having had limited research opportunities to that point. I knew, however, that Emory University was one of my 

top choices for graduate school, so I thought what better way to figure out my path than to work at a university I 

was interested in attending. This experience would allow me to work alongside the graduate students and 

principal investigators of programs I would potentially apply to. I worked for three years as a research 

technician in Dr. Conn’s lab. I had no prior experience working in a biochemistry lab, nor had I ever done 

bench science full-time, but Dr. Conn took a chance on me. I was able to witness first-hand how invested Dr. 

Conn was to training, mentoring, and challenging his students to improve. He carefully adapts his mentoring 

style to each of his students based on their individual needs. He will be hands-off when independence is 

needed or warranted, but always has an open door if you want to discuss a result or troubleshoot a problem. 

Dr. Conn is also always very involved in the graduate programs he is a member of, including BCDB of which 

he is currently the Director of Graduate Studies. He is one of the main instructors for the Hypothesis Design 

and Scientific Writing course and Foundations, and is a regular participant in student-lead seminars and 

workshops. Dr. Conn and I worked closely throughout my three years in his lab, from troubleshooting assays to 

writing a manuscript I coauthored with a postdoc in the lab, and this showed me the qualities I valued in a 

mentor and advisor. He was always very supportive of my decision to apply to graduate school, a career goal 

he knew of from the day I interviewed for the position. My experience as a technician was pivotal in my career, 

because without a “good” experience I am convinced I would have changed career paths. The time I spent in 

the Conn lab solidified for me that I was meant to pursue a career in research. Although I explored other 

options (at Dr. Conn’s insistence!) based on the qualities outlined above, I chose to stay at Emory to pursue 

my graduate school career. After three very different rotations (see Research Experience), I ultimately chose to 

return to Dr. Conn’s lab. Because of his unprecedented commitment to training and mentoring his students in 

all aspects of graduate student development, I was sold. 

Selection of Sponsor and Institution Page 47 
RESPONSIBLE CONDUCT OF RESEARCH 

All Emory University graduate students are required to take a six-hour ethics seminar course, called Jones 

Program in Ethics (JPE 600), at the start of their first year. The ethics course covers general topics applicable 

to all disciplines and is supported by the Laney Graduate School in collaboration with the Emory Center for 

Ethics. I am also required to attend at least four additional workshops sponsored by the Laney Graduate 

School or the Emory Center for Ethics. I attended my first workshop this semester, where I met the Editor-inChief of the European Journal of Neuroscience, Dr. Paul Bolam. We discussed the ethical conundrums that 

plague science publishing, such as the “crisis” in the peer review process, conflicts of interest, and plagiarism. 

He also gave us an inside look at the publishing timeline and the stages manuscripts must go through from 

submission to acceptance. 

As a graduate student in the Biochemistry, Cell, and Developmental Biology (BCDB) Program, I attend 

monthly, one-hour ethics workshops (eight per school year) sponsored by the program and currently directed 

by Drs. Guy Benian (Professor, Pathology) and William Dynan (Professor, Biochemistry). For my first two 

years in the program, I am required to attend all eight of the monthly ethics workshops. As a third year and 

beyond, I am required to attend at least one ethics workshop per semester. This requirement therefore meets 

the National Institutes of Health (NIH) requirement for retraining every four years. Students, typically a junior 

and senior student, are paired with a faculty advisor to put together each interactive, discussion-based 

workshop, supported by a Powerpoint presentation on one of the following topics outlined in the table below. 

Many of the faculty advisors attend multiple sessions, and other BCDB faculty, e.g. Drs. Richard Kahn 

(Biochemistry) and Michael Koval (Medicine), also attend to contribute to the discussions. 

Topic Year Faculty Advisor (Department) 

Conflict of Interest 2015-16* 

2016-17 

Paul Doetsch (Biochemistry) 

Kenneth Moberg (Cell Biology) 

Animal Experiments and IACUC 2015-16 

2016-17* 

David Pallas (Biochemistry) 

David Katz (Cell Biology) 

Human Subjects and Tissues 2015-16 

2016-17 Judy Fridovich-Keil (Human Genetics) 

Mentor-Mentee Responsibilities 

and Relationships 

2015-16 

2016-17 

G. Benian (Path.), W. Dynan (Biochem.) 

Keith Wilkinson (Biochemistry) 

Collaborative Research 2015-16 Eric Ortlund (Biochemistry) 

Peer Review 2015-16 

2016-17 

Graeme Conn (Biochemistry) 

Alexa Mattheyses (Cell Biology) 

Data Management and Sharing 2015-16 

2016-17 

Ichiro Matsumura (Biochemistry) 

Maureen Powers (Cell Biology) 

Research Misconduct and Data 

Manipulation 

2015-16 

2016-17 

Christine Dunham (Biochemistry) 

David Pallas (Biochemistry) 

Responsible Authorship and 

Publication 

2015-16 

2016-17 

Judy Fridovich-Keil (Human Genetics) 

William Kelly (Biology) 

Contact PD/PI: Schwartz, Samantha 

*Denotes the two ethics presentations I have given to date. 

Training in the Responsible Conduct of Research Page 48 
 

 

 

SPONSOR AND CO-SPONSOR STATEMENT 

A. RESEARCH SUPPORT AVAILABLE 

Contact PD/PI: Schwartz, Samantha 

Source Identifier Title PI Dates Direct $/ yr 

Current-Conn (Sponsor) 

NIH/ NIAID R01 

AI088025-07 

RNA modification and antibiotic 

resistance Conn 6/1/10-

5/30/20 $304,000 

Pending-Conn (Sponsor) 

Current-Lowen (Co-sponsor) 

NIH/ NIAID R01 AI099000 Reassortment of influenza viruses 

in a co-infected host Lowen 9/1/12-

8/31/17 $250,000 

NIH/ NIAID R01 AI125268 

Impact of selective genome 

packaging on influenza A virus 

reassortment 

Lowen 8/4/16-

7/31/20 $250,000 

NIH/ NIAID R01 AI127799 Host dependence of influenza A 

virus reassortment Lowen 12/5/16-

11/30/21 $493,000 

NIH HHSN2722014 

00004C 

Host adaptation, reassortment 

and transmission of influenza 

viruses at the animal-human 

interface 

Orenstein 

(Lowen, 

Project 2

Co-leader) 

4/1/14-

3/31/21 $259,462 

Pending-Lowen (Co-sponsor) 

 

 

B. SPONSOR’S/ CO-SPONSOR’S PREVIOUS FELLOWS/TRAINEES

Conn (Sponsor) 

 Eight (8) previous and three (3) current pre-doctoral trainees, including the applicant Ms.Schwartz. 

 Six (6) previous postdoctoral trainees. 

Five representative previous trainees:

Name Pre-/ Postdoctoral Current Position 

Miloje Savic Pre (Manchester)/ Post 

(Emory) 

Senior Advisor on Global Pharmaceutical Policy, 

Norwegian Institute of Public Health, Norway. 

Catherine Templeton Pre (Manchester, PhD) Senior Scientific Officer, Inst. for Cancer Research, UK 

Ahmed Wahid Pre (Manchester, PhD) Associate Prof., Biochemistry, Minia University, Egypt 

Emily Kuiper Pre (Emory BCDB program) Postdoctoral Fellow, Dana Farber Cancer Institute 

Pooja M. Desai Post (Emory) Research Scientist, Therapure Biopharma Inc., Canada 

Lowen (Co-sponsor) 

 Two (2) previous and two (2) current pre-doctoral trainees. 

 One (1) current postdoctoral trainee. 

Previous trainees: 

Name Pre-/ Postdoctoral Current Position 

Jillian Seladi-Schulman Pre (Emory MMG program) Associate Lab Project Set-up Manager, Quintiles, Atlanta 

Nicolle Marshall-Baird Pre (Emory MMG program) Postdoctoral Fellow, CDC Influenza Division 

Sponsor and Co-Sponsor Statements Page 49 

C. TRAINING PLAN, ENVIRONMENT AND RESEARCH FACILITIES 

C1. TRAINING PLAN. Samantha (Sam) Schwartz is a student in the Biochemistry, Cell & Developmental 

Biology (BCDB) Graduate Program at Emory University. Sam will be co-mentored by Dr. Graeme L. Conn 

(Associate Prof., Department of Biochemistry) and Dr. Anice Lowen (Assistant Prof., Department of 

Microbiology & Immunology). Dr. Conn has many years of mentoring experience and a research focus on 
 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Contact PD/PI: Schwartz, Samantha 

understanding the structures, interactions and biological functions of RNA molecules and their protein 

binding partners. Relevant to Sam’s proposal, Dr. Conn’s group has a well-established record in the area of 

viral non-coding RNAs and their interactions with innate immune proteins, PKR and OAS1. Dr. Lowen will 

additionally bring a distinct perspective to Sam’s mentoring and career guidance as well as outstanding 

expertise in molecular virology and the cell culture systems Sam will use in her proposal. 

Sponsor Background. I (Dr. Conn) place a great emphasis on student mentorship and development in my 

lab, and I have been actively engaged in graduate education since arriving at Emory in 2008 (please see 

my Biosketch Personal Statement for details). I am currently a member of two Emory Graduate programs, 

BCDB and Microbiology & Molecular Genetics (MMG), as well as the NIAID-funded T32 “Antimicrobial 

Resistance and Therapeutic Discovery Training Program (ART-DTP).” I currently serve on the Executive 

Committees of each of these programs, as the BCDB Program Director of Graduate Studies (DGS), and as 

one of four MMG Program student recruiters (along with Sam’s Co-sponsor Dr. Lowen). I am also actively 

involved in directing and teaching courses for each of these programs. In total, I have mentored 11 PhD 

students and served on the thesis committees of an additional 17 Emory graduate students. My lab 

currently consists of three graduate students (including Sam), and one senior (PhD level) Research 

Specialist Lead (technical staff). I am currently in the process of recruiting a postdoctoral fellow to my lab to 

work on our antibiotic-resistance rRNA methyltransferase project. In addition to the 8 PhD students who 

have graduated from my lab, I have mentored and trained 5 former postdoctoral researchers who have 

gone on to successful positions in academia and industry (e.g. see Table above). Through this experience I 

have developed, and try to continue to evolve, a broad perspective on training and mentorship. I recognize 

that each of my lab members may require a style of mentorship specifically tailored to them and I continually 

assess each individual’s strengths, weaknesses, expectations and ambitions. 

Co-Sponsor Background. Dr. Lowen is similarly engaged in graduate education having been an active 

member of the MMG and Immunology and Molecular Pathogenesis (IMP) programs since joining Emory in 

2011. Dr. Lowen teaches in “Principles of Basic Biomedical and Biological Sciences” and co-directs the 

“Virology” course required for students of both the MMG and IMP program, and which Sam will either audit 

or take as an elective to strengthen her fundamental virology knowledge. Dr. Lowen also serves on the 

MMG recruitment committee, regularly attends seminars hosted by both of her programs, and is currently a 

member of eight thesis committees. The Lowen lab currently comprises two PhD students, one post-doc, 

two senior technicians (Research Specialist Senior) and a more junior Research Specialist. The lab is 

expanding due to new funding and Dr. Lowen expects to take on an additional student and post-doc in the 

next year. Since starting her lab in 2011, Dr. Lowen has graduated two PhD students who are now 

employed in related fields (see Table above). She strives to provide constructive mentorship and scientific 

direction while leaving trainees enough independence to develop critical thinking and creativity. Dr. Lowen 

meets regularly with her trainees to discuss progress and plans, and is available for input asneeded. 

Overview of Training Objectives. My current trainees are engaged in projects investigating ribosomal 

RNA methyltransferase enzymes that confer bacterial resistance to antibiotics, or viral/ cellular non-coding 

RNA structure and activity against proteins of the human host cell antiviral response (PKR and OAS1). 

Sam’s project represents an important new direction in the latter area. My plans with Dr. Lowen to support 

Sam’s technical, professional and other training away from the bench are outlined in the following sections. 

Training in Diverse New Experimental Approaches. When Sam began her thesis work my lab last 

summer she chose to develop a new direction in our studies on OAS1 which had begun a couple of years 

earlier (see Vachon, V.K. et al. Nucleic Acids Res. 2015). Specifically, Sam decided to devise a project to 

investigate the molecular basis for an unexpected observation, made by former graduate student Dr. Ginny 

Vachon, that very small changes in a model dsRNA used for prior structural studies of the OAS1-dsRNA 

complex could either substantially increase OAS1 activation or completely eliminate it. Sam’s project will 

employ diverse approaches that will provide new training in biochemical (OAS1 enzyme kinetics), structural 

(x-ray crystallography) and other biophysical approaches (BLI and HDX-MS) to tease apart new details of 

OAS1 regulation by RNA. The use of cell culture approaches in Dr. Lowen’s lab will further broaden Sam’s 

technical training while also providing greater biological context to increase the impact of her findings. 

Plan for Mentorship, Professional Development, & Opportunities for Scientific Networking. Sam is 

part of a dynamic, interactive and collaborative group of researchers studying various aspects of RNA 

biology and translational control using many complementary biochemical, microbiological and biophysical 

techniques. Sam’s primary day-to-day interactions will be with me, Dr. Lowen, and the current members of 

our research groups. We also collaborate closely with Dr. Christine Dunham’s group in Biochemistry, with 

Sponsor and Co-Sponsor Statements Page 50 
 

 

Contact PD/PI: Schwartz, Samantha 

whom we have weekly joint lab meetings; Dr. Lowen’s group similarly works closely with that of Dr. John 

Steel in Microbiology & Immunology. In addition to the technical training and individual mentorship Sam will 

receive in my laboratory and that of her Co-sponsor Dr. Lowen, Sam’s project will bring a wealth of 

opportunities to interact with and learn from a diverse collection of scientists in the Emory University School 

of Medicine and more broadly across the Emory campus and its healthcare system. 

One-on-one meetings: My office is located adjacent to the lab and one door down from our shared 

student/ postdoc office; as far as possible, my door is “open” for informal discussions. Sam is very proactive 

in seeking my input (and that of Dr. Lowen) on her experimental plans, the subsequent interpretation of her 

results, and decisions on the next priorities. We typically meet briefly in my office or in the lab to discuss the 

latest developments at least 3-4 times a week. Should I feel such interactions are too infrequent, during 

periods of particular challenge, or when greater input might be needed (e.g. finalizing a manuscript), I 

typically schedule individual meetings (at least once a week) to give these one-on-one discussions 

additional structure. In Sam’s case, our meetings have largely been informal but through the Fall semester 

regular scheduled meetings helped us keep on track with my feedback on her weekly assignments for the 

intensive IBS522r Scientific Writing and Hypothesis Design course. Sam was also a willing volunteer to pilot 

the use of an electronic notebook in my lab, using “Findings” (http://findingsapp.com/), allowing us to share 

protocols and experimental results via Emory Box (an Emory-wide implementation of the Box.net file 

sharing and collaboration tool). This approach has allowed me to track progress with experiments, offer 

immediate input on record keeping, analysis, interpretation and, most importantly, prepare for our regular 

discussions with greater depth of insight. Dr. Lowen will also continue to be available to address Sam’s 

questions and discuss her project as needed, and will also begin meeting with Sam regularly once she 

reaches the stage of her project that relies on use of cell culture systems. Though I expect Sam to 

coordinate these interactions with Dr. Lowen, I plan to participate in any regular scheduledmeetings. 

Weekly laboratory meetings: My lab holds weekly joint meetings with Dr. Christine Dunham’s group 

who have related research interests in translation control, including bacterial toxin-antitoxin systems, 

ribosomal frameshifting, and ribosome quality control. At these meetings, one member of each lab will 

typically present either their latest results or a relevant paper from the recent literature. We also use these 

meetings as a forum for students and postdocs to practice formal presentations of a more complete “story”, 

e.g. prior to a conference talk or using the figures from anin prep manuscript to get group feedback. Dr. 

Lowen (and potentially members of her group) will attend the Conn/ Dunham lab meetings when Sam is 

presenting her work. Similarly, Dr. Lowen will include Sam on the regular presentation schedule for her 

group’s lab meetings which are held jointly with Dr. Steel’s group. Sam will be a regular participant in the 

Lowen/ Steel meetings and I will also attend when Sam is presenting. 

Presentations: I encourage my lab members to present their research early and often in order to hone 

their presentation skills. Sam has already benefited from the BCDB Program’s focus on improving 

presentation skills through the Year 1 Introductory Seminar class, and is scheduled to present her first 

BCDB “Advanced Seminar” on Feb. 15th 2017. Ahead of this presentation, I will work closely with Sam, as 

will all my students and postdocs, to ensure her presentation is clear, polished and successful in making its 

main points. As noted above, Sam will also be scheduled to present her talk at least a week before in our 

weekly lab meeting. I also expect that Sam will present her work extensively at local journal clubs, the 

monthly Joint Structural Biology Groups Meeting and Emory RNA Club, and the annual Emory Graduate 

Symposium organized by the Graduate Division Advisory Council (DSAC). Sam will present a poster at the 

next DSAC Symposium in January 2017 and my expectation is that Sam submit an abstract for this event 

each year and will request a podium presentation in the second and/ or third year of this fellowship. Dr. 

Lowen and I will also strongly encourage Sam to attend and present her work at local, e.g. the Southeastern 

Regional Virology Conference (SERVC), and national scientific meetings (see below). Sam attended 

SERVC held near Emory in April 2016 while rotating in the Lowen lab and this is an excellent forum for 

students to present their research in a workshopsetting. 

Scientific Conferences and Meetings: I will encourage Sam to attend at least one scientific meeting per 

year to present her results and to develop a network of interactions with senior colleagues and peers at 

other institutes. Specific conferences for Sam to target will be discussed ~6-9 months prior to planned 

attendance but over the course of her time in my lab will include both more focused meetings, like the GRC 

on Nucleic Acids or a Keystone meeting on Innate Immunity, and broader conferences such as the annual 

meetings of the RNA Society, American Society for Microbiology (ASM) or American Society for 

Biochemistry and Molecular Biology (Experimental Biology). A first priority for Sam will be attendance at a 

meeting of broader scope to immerse herself in her new field. As a goal of Sam’s technical training is to 

Sponsor and Co-Sponsor Statements Page 51 
C2. ENVIRONMENT 

 

 

 

 

Contact PD/PI: Schwartz, Samantha 

learn x-ray crystallography, I will also encourage Sam to attend an intensive training course in 

macromolecular crystallography and at least one conference related to this technique. Several courses on xray data collection and/or structure determination are held annually at US synchrotron sources and 

elsewhere, and I will encourage Sam to apply once she has fully embarked on that aspect of her project. 

Upon completing the second aim of her proposal I would encourage Sam to present her structures and 

complementary binding and protein dynamics (HDX-MS) data at the national meeting of the American 

Crystallographic Association. In addition to lab funds, the Laney Graduate School provides “Professional 

Development Support (PDS)” funds (up to per student, potentially more on a competitive basis) to 

support conference attendance for students to present their work (poster or talk is required). Dr. Lowen and 

I will also guide Sam in the preparation of applications for travel awards and other meeting fellowships to 

maximize the range of her conference attendance and experiences throughout her graduatecareer. 

Thesis Committee: Sam has assembled a thesis committee with diverse expertise to help guide her 

research and oversee her progress towards her career goals. In addition to Dr. Lowen and I, the committee 

comprises three Biochemistry Department faculty, Drs. Christine Dunham, Rick Kahn, and Daniel Reines. 

As noted above, Dr. Dunham brings relevant expertise in structural biology, protein synthesis and RNAprotein interactions. Dr. Reines was one of Sam’s BCDB rotation mentors and brings complementary 

expertise in RNA biology and protein structure related to transcriptional control. Dr. Kahn is a biochemist 

and cell biologist with expertise in cell signaling/ regulation by GTP-binding proteins, membrane traffic, cell 

division, and energy metabolism. Sam’s thesis committee will meet for 1-2 hours every six months as 

dictated by the BCDB program and she will meet individually with members of her committee as needed. 

Publications: All students in my laboratory are required to complete an independent project leading to 

first author publications. When Sam is nearing the point of preparing her first manuscript, I will assist her in 

developing a framework for the paper as she prepares draft figures (a process that may identify any “gaps” 

in the data). Next, Sam will write each section in turn to prepare a complete first draft: Methods, Results, 

Discussion, Introduction and finally the Abstract. In my lab we typically share manuscripts via OneDrive (for 

sharing and team editing), which allows me to track progress and offer quick comments as each section 

develops. Once Sam completes a first draft I will provide detailed feedback-usually I do this as handwritten 

comments on a printed copy. I will then sit down with her and discuss my comments and explain why I 

made specific suggestions. My experience is that students may go through several drafts before a final 

product is reached; this can be a time-consuming process (at least for the first manuscript), but one that I 

believe is critical arming my students with effective skills for scientific writing. 

Mentoring as a component of training: Later in her graduate career I plan to provide Sam with several 

opportunities to mentor undergraduates (we typically host one or two each summer), rotation or other junior 

graduate students, to gain skills as a mentor. My approach to this, as with previous trainees, will be to have 

an initial discussion with Sam and her mentee about the overall project goals and the timeframe, the 

general experimental plan, and the specific details of the first experiments. After this, I will allow Sam the 

freedom to train and mentor the student directly. I expect that Sam will be the first person her mentee will 

seek input from, e.g. on experimental details or later for reviews of abstracts, poster drafts, etc. However, I 

will schedule regular meetings with Sam and her mentee to ensure things are progressing well. At the end 

of the student’s time in the lab, I will discuss the outcomes with Sam and ask her to prepare a reference 

letter for the student on which I will provide feedback to help her develop this essentialskill. 

Biochemistry, Cell & Developmental Biology (BCDB) Program. Sam is a member of the BCDB program 

and will continue to follow the innovative BCDB curriculum (please see Institutional Environment and 

Commitment to Training). Sam has completed most requirements for Years 1-2 (a Spring semester in 

biostatistics and teaching assistantship remain). Beyond Year 2, coursework centers mostly on honing 

presentation and other professional skills, through courses such as BCDB Advanced Seminar and Ethics in 

Research. Sam will also attend a twice-monthly BCDB journal club, monthly Professionalization Workshops 

covering topics such as Individual Development Plans (IDP) and time management, and an annual scientific 

and team building retreat with other students and many of the Program faculty. 

Biochemistry Department. The Conn lab is part of the Biochemistry Department in the Emory University 

School of Medicine so Sam is also affiliated with the Department. Additional groups Sam will have 

opportunities to interact with (in addition to those already noted above) include those of Drs. Eric Ortlund 

(protein structure, protein-DNA/RNA interactions, X-ray crystallography), and Bo Liang (viral RNA 

polymerase structure, high-resolution cryo-EM). The Department hosts a weekly seminar series and 

students are invited to have lunch with the speakers. I encourage my students to participate in these 

Sponsor and Co-Sponsor Statements Page 52 
 

Contact PD/PI: Schwartz, Samantha 

meetings and I expect that Sam will have opportunities to meet with a seminar speaker 2-3 times/ semester. 

Microbiology & Immunology Department. The Lowen lab is part of the Microbiology & Immunology 

Department, located one floor below Biochemistry. Virology is a strength at Emory and Sam will have the 

opportunity to interact with trainees and PIs from the Steel, Speck, Mocarski, Ahmed, Suthar, Hunter and 

Grakoui laboratories, to name a few. Dr. Lowen is a member of the Emory-UGA Center of Excellence for 

Influenza Research and Surveillance (CEIRS), which offers a number of opportunities for trainees to 

present their work, meet virologists, and travel to other institutions to learn pertinenttechniques. 

Emory as an Outstanding Training Environment. Emory has an extremely collaborative research 

environment and many of our current studies rely on the expertise of colleagues. For our students, this 

collaborative environment creates a unique working environment where they can draw on the expertise of 

many individuals in the absence of formal training relationships. The interdisciplinary nature of the GDBBS 

graduate programs also enhances our research environment creating interactions and bonds between 

College departments (such as Biology and Chemistry) and those in the School of Medicine. Thus, students 

have the opportunity to broaden their training and learn new approaches from experienced experts. 

As noted above, the Graduate Division holds an annual student symposium providing opportunities for 

poster and oral research presentations. I require that my students submit an abstract each year and Sam 

will begin participating in January 2017. Various additional seminar series are available that will provide 

Sam with opportunities to become familiar with diverse techniques, biological systems and biomedical 

problems. These include: 1) Emory RNA Club, a bimonthly seminar series that brings together diverse 

research groups using biochemical, cellular, genetic, developmental, chemical biological and structural 

biological techniques that focus on understanding the emerging world of RNA biology. More than 10 

research groups at Emory are involved in this series that will provide an excellent forum for Sam to present 

her research and hone her presentation skills for a diverse audience. 2) Structural Biology Joint Group 

Meeting, a monthly meeting involving groups with expertise in x-ray crystallography (Drs. Conn, Dunham, 

and Ortlund), cryo-EM and tomography (Drs. Liang and Elizabeth Wright), and other biophysical 

approaches such as HDX-MS (Dr. Renhao Li). In both cases, students and postdocs give presentations on 

their work or recent literature in an informal setting where discussion is stronglyencouraged. 

Relationship of Training to Applicant’s Career Goals. Sam’s immediate goal after completing her PhD is 

to secure a postdoctoral position at a top research university to continue on the path to a career as an 

independent researcher. My goal in training Sam is to provide the laboratory setting, atmosphere and 

continuous mentorship and feedback that will allow her to develop the technical and professional skills 

necessary to accomplish this goal. Sam’s project will give her experience of experimental design and 

interpretation, and essential technical skills in protein expression/ purification of RNA, biochemical assays of 

enzyme activity, cell culture, and biophysical approaches to study protein structure, dynamics and 

interactions. I am also committed to ensuring Sam is trained as broadly as possible in all other essential 

professional skills, including scientific writing (e.g. manuscripts, grants), presentations (posters, talks) and in 

mentorship. Our efforts will be complemented by the comprehensive BCDB programmatic activities and the 

outstanding intellectual environment at Emory. Taken together, all the requisite resources are in place to 

promote Sam’s development as an independent research leader and an outstanding scientist. 

C3. RESEARCH FACILITIES 

The Conn and Lowen laboratories, Departments of Biochemistry and Microbiology and Immunology, and 

Emory core facilities will provide everything Sam needs to complete the experiments described in her 

proposal (please see Facilities and Resources and Equipment sections for more detail). Briefly, the Conn 

lab has dedicated spaces for bacterial culture (for protein expression, etc), radioisotope use, and 

macromolecular crystallography; a main lab space where each member has their own dedicated bench; 

and, is well equipped for protein and RNA preparation/purification and in vitro biochemical/ structural studies 

of OAS1 regulation by dsRNA. Of particular relevance for Sam’s cell culture experiments, the Lowen lab 

has three Class II biosafety cabinets, four CO2 incubators and a light microscope for cell culture work, and is 

also well equipped with quantitative PCR instrumentation. The Department of Biochemistry has modern xray crystallography suite with crystallization robotics and x-ray generator with sample mounting robot, and 

also provides regular scheduled time at the SER-CAT beamline at the Advanced Photon Source. These 

outstanding resources and regular availability of synchrotron beamtime at APS will expedite Sam’s research 

program and enhance her training in x-ray crystallography. Finally, Sam’s project will make use of 

equipment in two Emory core facilities (for HDX-MS and BLI analyses); it is important to note that both 

facilities require thorough user training from the core but will subsequently allow Sam to independently 

Sponsor and Co-Sponsor Statements Page 53 
E. APPLICANT’S QUALIFICATIONS AND POTENTIAL FOR A RESEARCHCAREER 

Contact PD/PI: Schwartz, Samantha 

design, run and analyze the results of her experiments under their expert guidance. 

D. NUMBER OF TRAINEES 

In addition to Sam, I currently advise two other pre-doctoral trainees and a PhD-level technician. I expect 

one student to graduate by summer 2017 and my lab is open to a new student for their thesis research. I 

am also actively recruiting a new postdoctoral fellow. Over my time at Emory, my group has typically had 5-

8 members (graduate students, postdocs and technicians) plus 1-2 undergrads or other visiting scientists. 

Dr. Lowen currently advises two pre-doctoral trainees and one postdoctoral fellow. Her lab has consistedof 

~4 members since its inception in 2011, but is currently transitioning to a larger group; Dr. Lowen plans to 

take one additional student and aims to recruit a postdoctoral fellow or staff scientist within the next year. 

Sponsor (Conn): Sam is smart, driven, and a careful and already highly competent experimentalist. These 

qualities, among many others, point to her outstanding potential as a future research leader. Not all these 

abilities are innate, some were built on hard work over 3 years as a research technician; some of them she 

now continues to develop in grad school. As Sam describes elsewhere, being a first generation college 

student and completing her undergrad degree at an institute with limited research opportunities, she took 

the (very mature) decision to gain further research experience before committing to grad school. As a result, 

I have in effect recruited Sam to my lab twice, each time with very different goals. When Sam applied for the 

open Research Specialist position in my lab in 2012, her CV made my short list but I had reservations both 

about her limited research experience and some “features” of her undergrad transcript. Needless to say, the 

interview convinced me she was the right choice for my lab. Two main factors contributed to this decision. 

The first was Sam’s clear objective to gain research experience with graduate school the future goal 

(something I felt my lab and I were well placed to help her achieve). Second, was how Sam dealt with my 

list of standard “lab tech” questions, gleaned from many co-interviews with experienced HR professionals, 

as mandated in Manchester for all tech hires. While I had unknowingly always found myself going too deep 

into specific research experiences or future career goals, these questions were simple, direct, and, to my 

initial surprise, highly discriminating. These included asking about task prioritization or how conflicts should 

be handled, to the seeming simple question, “If I asked you to make a 1M solution of NaCl, what would you 

need to know?” which completely throws >90% of my interviewees. How about one who got an F grade in 

Organic Chemistry? As with everything else I threw at her from my repertoire, Sam aced the answers (I 

suppose I should have known, since she retook the class and got an A!). I was completely convinced and 

Sam was a stellar technician. What about her potential for grad school and beyond? As Sam began to 

develop her innate scientific curiosity to complement her excellent experimental hands, I knew it was time 

she left. I encouraged Sam to explore broadly and she did (choosing an interview at UTSW over waiting on 

an invitation to the Emory BCDB event the same weekend). Having seen the BCDB Program up close 

already, she chose to stay at Emory (I didn’t blame her). Next, I insisted she explore other labs during her 

rotations. While she ultimately chose to return to a new project in my lab, she did so with a new perspective 

on her abilities, interests, and future goals and an outstanding co-mentor in Dr. Lowen! I cannot over state 

how different I view Sam’s future grad experience and training in my lab (and my role in that training) from 

what she has already experienced and accomplished. What I know is that I am fortunate to have an 

amazingly talented student in my lab who is destined for great things in her future career in research. 

Co-Sponsor (Lowen): During her rotation in my lab, Sam demonstrated excellent technical ability, maturity, 

organizational skills and an ideal balance of independence and willingness to ask for help. Sam’s 

impressive productivity during her 10-week rotation is evidenced by her publication on the use of ddPCR to 

detect and quantify defective viral genomes. Sam is the only author on this paper with me because she did 

all the experiments, analyzed the data and, with my guidance, interpreted the data and wrote the first draft 

of the paper. She accomplished all of this because she was thoughtful in her experimental design, ensuring 

that all necessary pilot experiments had been run and all reagents were in good condition before starting a 

larger series of experiments. Sam had very few, if any, failed experiments. Sam is also an excellent 

communicator: she reported her results regularly without me having to prompt her, she came to my door or 

set up meetings as needed to discuss future plans, and she worked very well with other group members. 

Although in my lab only briefly, Sam became our expert on ddPCR, which was new to us at the time of 

Sam’s rotation. I therefore asked her to write up a protocol and to train others to use the instrumentation 

and software; she took these tasks on willingly and did a great job. Sam was also a lot of fun to have in the 

lab because she is very enthusiastic about her research and science in general. She is ambitious, willing to 

work hard to achieve her goals, and has excellent potential for a successful career inresearch. 

Sponsor and Co-Sponsor Statements Page 54 
 

 

 

 

 

 

 

Contact PD/PI: Schwartz, Samantha 

INSTITUTIONAL ENVIRONMENT AND COMMITMENT TO TRAINING 

Samantha Schwartz is a 2nd-year student (rising 3rd year by time of potential award of this NRSA F31 

fellowship) in the interdepartmental Biochemistry, Cell, and Developmental Biology (BCDB) Graduate Program 

at Emory University. Sam has completed all required core Program coursework to date and passed her written 

qualifying exam in April 2016. Remaining Program commitments include a biostatistics course and a semesterlong teaching assistantship. Both of these obligations will be completed in the Spring 2017 semester prior to an 

award of this NRSA F31 fellowship. Sam has assembled her thesis committee, comprising Drs. Conn (Sam’s 

Sponsor on this application), Lowen (Co-sponsor), Christine Dunham, Rick Kahn, and Daniel Reines. 

Technical, Intellectual and Other Supporting Resources at Emory University. Sam’s research and 

professional training will benefit from outstanding technical, intellectual, and other resources available directly 

within the Conn and Lowen laboratories, as well as the Departments of Biochemistry (Conn) and Microbiology 

& Immunology (Lowen), the Emory School of Medicine and its Core facilities, the BCDB Graduate Program, 

and the Laney Graduate School (LGS) at Emory University. In terms of equipment and other facilities, both the 

Sponsor and Co-sponsor labs are well-equipped for the proposed studies. The Conn lab has the equipment 

and resources needed for modern biochemical and biophysical approaches to study the structures, 

interactions, and biological functions of biomedically important RNA and protein molecules. Additional shared 

facilities that Sam will use in her work include the Biochemistry structural biology facility, which contains 

robotics for automated crystallization screens and an X-ray generator for crystal screening. The Department 

also supports regular access to the SER-CAT beamlines at APS (see Equipment and Facilities sections for 

details). The Lowen lab is similarly well-equipped for cell culture and viral infection experiments. Sam will use 

several of Emory’s excellent core facilities, including the Emory Chemical Biology Discovery Core for their 

OctetRED384 and the HDX-MS Core. In both cases, Sam will work directly on protocol development, data 

collection, and analysis on these state-of-the-art instruments under the guidance of expert corestaff. 

Sam’s research is centered on understanding how a key component of the human innate immune system 

(OAS1) is regulated by specific features within double-stranded RNA (dsRNA) molecules. Among labs working 

today on the OAS1/ RNase L pathway, Sam’s project is unique with its specific focus on understanding the 

RNA features that potently activate OAS1 or that can lead to sequestration of its activity. Sam will extend the 

Conn lab’s strong record of using RNA biochemistry/structural biology approaches to investigate the regulation 

of dsRNA sensors of the innate immune system by viral and cellular non-coding RNAs. This project builds 

directly on that of a former graduate student (Dr. Virginia Vachon) and will complement that of a current BCDB 

graduate student (Ms. Brenda Calderon) whose project is centered on the cellular structured non-coding RNA 

nc886. The environments in which Sam will work are also enriched by other PhD and graduate student 

investigators working on RNA-protein interactions related to bacterial antibiotic resistance (Conn lab) and viral 

transmission, reassortment, and host immunity (Lowen lab). Outside of the Conn and Lowen labs, Sam will 

have the opportunity to interact with other faculty members and their teams in both informal and formal 

settings. For example, Sam’s thesis committee has three additional members in addition to Drs. Conn and 

Lowen who bring diverse expertise, including translational control and ribosome structural biology (Dunham), 

RNA biology and protein-RNA interactions related to eukaryotic transcription regulation (Reines), and cell and 

protein biology (Kahn). Other faculty members in Biochemistry with strong research programs in structural 

biology include Drs. Eric Ortlund (steroid hormone receptors, including protein-RNA interactions, using X-ray 

crystallography) and Bo Liang (viral RNA-dependent RNA polymerase structures by high-resolution cryo-EM). 

Sam will participate in the monthly Joint Structural Biology Groups (JSBG) meeting and the “Emory RNA Club,” 

which connects researchers with interests in RNA biology from Biochemistry, Biology, Cell Biology, and other 

departments across campus. More broadly, through her interactions with Dr. Lowen’s lab, Sam will benefit from 

exposure to the great strengths at Emory in virology and vaccine development. 

Sam will have many opportunities to present and receive feedback on her work. She will present research 

updates at least 3-4 times a year in bi-weekly joint Conn-Dunham and Lowen lab meetings. Sam will meet 

twice a year with her thesis committee and will present her latest research to faculty and students in the BCDB 

Advanced Seminar course once per year until graduation. Sam will present her work at the JSBG and RNA 

Club meetings, as well as at Emory symposia (including the Division Student Advisory Council (DSAC) Annual 

Research Symposium (sponsored by the LGS)) and other local meetings, such as the Southeastern Regional 

Virology Conference. The LGS also provides professional development support funds for students to present 

their work at national and international meetings. Finally, Sam will benefit from a number of innovative 

approaches the BCDB program has implemented to support student professional development, e.g. by 

requiring yearly updates to her individual development plan (IDP) and allocating time during thesis committee 

Description of Institutional Environment and Commitment to Training Page 58 
 

 

 

Contact PD/PI: Schwartz, Samantha 

meetings to discuss her career goals. Sam also has access to career seminars, such as “Pathways Beyond 

the Professoriate” and professionalization workshops offered by the BCDB program. 

ADDITIONAL EDUCATIONAL INFORMATION 

Program Structure. The BCDB Program is one of 9 graduate training programs in the Graduate Division of 

Biological and Biomedical Sciences (GDBBS), part of the LGS of Emory University. The BCDB Program is 

highly interdisciplinary with ~45 training faculty representing 13 basic science and clinical departments and 

offering an incredible breadth of potential training. Faculty research is grouped into four overarching themes: 

Biochemistry/ Structural Biology, Cancer Biology, Cell Biology, and Developmental Biology. The Program has 

a history of implementing innovative approaches to graduate education that emphasize oral and written 

communication skills, quantitative skills, career development, and professionalization, along with cutting edge 

technical research training. Our graduates are expected to have the technical, analytical, and communication 

skills necessary to pursue an independent career in academic, industrial, or government research or in careers 

where their training will facilitate the business, application, or public understanding of biomedicalresearch. 

Required Milestones & Timing. (a) Coursework. The BCDB curriculum is intended to provide students with 

the basic knowledge and skills to pursue doctoral dissertation research and a career in the disciplines 

represented by the Program. All required coursework is completed by the end of the Spring semester of Year 

2, and electives may be taken starting in Year 2 if desired. The following core courses are required for all 

BCDB students: Year 1, Foundations in BCDB I and II (BCDB 501/502), Beginning Seminar (BCDB 570r; 

including attendance at Advanced Seminar), and Jones Program in Ethics (JPE 600); Year 2, Statistical 

Design and Analysis of Experiments (IBS 538), Hypothesis Design and Scientific Writing (IBS 522r), and, 

Advanced Seminar (BCDB 790r). Additionally, three 10-week research rotations are completed in Year 1, and 

in most cases, students then select a thesis advisor (typically in May). (b) Teaching commitment. Formal 

instruction and experience in teaching is a requirement for all graduate students at Emory. The Teaching 

Assistant Training and Teaching Opportunity (TATTO) Program is administered by the LGS to provide teacher 

training, and BCDB Trainees fulfill this requirement in Year 2 by (i) participation in a 2-day teaching training 

workshop (TATT 600) covering methods and ethics of teaching, as well as content-specific practice sessions 

tailored to the discipline of the student, and (ii) serving as a Teaching Assistant (TA) for at least one semester, 

with the quality of the teaching experience being evaluated via reports from the course directors. Several 

options are available to BCDB students who wish to gain additional teaching experience and t o establish 

teaching credentials, subject to continued satisfactory progress in their dissertation research subject. (c) 

Qualifying exams (QE). The BCDB QE is completed in two parts. QE1 (May/June Year 1) is a written (essaytype question), closed-book examination administered over two days. QE1 is designed to test foundational 

knowledge and critical thinking/writing, and thus student preparedness to progress in the Program. QE2 (to be 

completed before June 1 of Year 2) is an oral examination designed to assess the student's ability to integrate 

different aspects of the first two years of graduate training including lab work, data interpretation, hypothesis 

development, research design, presentation of research, and all other course work. (d) Dissertation defense. 

The BCDB Program requires students to produce a rigorous body of novel research, including at least one firstauthor peer-reviewed research paper, published or accepted for publication, before the dissertation defense is 

scheduled. Before the PhD degree will be granted, the following tasks must then be completed in order: (i) 

submission of the written dissertation, (ii) a closed session oral examination (defense) by the student’s thesis 

committee, and (iii) an advertised public oral presentation of the thesis research. 

Monitoring and Evaluation of Student Progress. Student progress is monitored from initial entry into the 

Program via an established, formal process involving academic probation (based on coursework grades and 

average semester GPA) and the requirements for its resolution through improved performance. Failure to 

satisfy these criteria is grounds for termination from the BCDB Program. After completion of QE1 and no later 

than the Spring semester in Year 2, students must form a Dissertation Committee comprising the dissertation 

advisor and a minimum of four other faculty members, at least three of whom must be BCDB faculty members. 

The first committee meeting is held no later than six months after passing QE2, and thereafter meetings are 

required every six months (every four months after Year 5). Compliance is tracked by the BCDB Executive 

Committee. The Program requires the following slides in meeting presentations: (i) scientific update: 

techniques learned, papers, grants, presentations, awards, etc., (ii) short-term goals, and (iii) goals beyond 

graduate school. The average time to PhD degree for BCDB students over the last 10 years is 5.8 years. 

Sam is on track to graduate within this timeframe. 

Provided by Michael Koval, Ph.D. (BCDB Director) & Graeme L. Conn Ph.D. (BCDB Dir. Grad. Studies) 

Description of Institutional Environment and Commitment to Training Page 59 
Contact PD/PI: Schwartz, Samantha 

RESOURCE SHARING PLAN 

All reagents produced during the course of this research program will be shared in line with the policies of 

Emory University and the NIH (https://www.nlm.nih.gov/NIHbmic/nih_data_sharing_policies.html). Data will be 

shared freely between the PI, Sponsor, and Co-sponsor and members of their research teams, with colleagues 

at meetings and conferences, and through publications. Where appropriate, data will be deposited in a public 

repository, e.g. the RCSB Protein Data Bank for X-ray crystal structure coordinates and electron density maps. 

Resource Sharing Plan Page 60