Doctoral Dissertation And Other Research Experience Sample

Table of Contents

SF 424 R&R Face Page

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PICalix, Juan
TitleThe role of wcjE disruption in pneumococcal serotype 11A humoral escape
Application ID1 F31 AI093103-01
OrganizationUniversity of Alabama at Birmingham
Clinical TrialNo
Current HS Code10
New InvestigatorNo
Early Stage InvestigatorNo

Performance Sites

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Research & Related Other Project Information

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Are Human Subjects Involved?No
If YES to Human Subjects
Is the Project Exempt from Federal regulations?NA
If yes, check appropriate exemption number.NA
If no, is the IRB review Pending?NA
IRB Approval Date:NA
Human Subject Assurance Number:NA
Are Vertebrate Animals Used?Yes
If YES to Vertebrate Animals
Is the IACUC review Pending?Yes
IACUC Approval Date:NA
Animal Welfare Assurance NumberA3244-01

Project Summary

The success of Streptococcus pneumoniae (pneumococcus) as a human pathogen is largely due to its capability to employ a polysaccharide (PS) capsule to avoid host immunity. Recent discovery and characterization of the pneumococcal serotype 11E strongly suggested that inactivation of the capsule synthesis gene wcjE¸ which encodes a putative O-acetyltransferase, plays an important role in escaping a host humoral immune response to the closely related serotype 11A. Since many epidemiologically prevalent serotypes also contain the gene, discerning the effects of WcjE-mediated variable O-acetylation on the serological properties of serotypes 11A and 11E will aid in understanding pneumococcal pathology, in determining trends of emerging pneumococcal serotypes and in designing effective PS-based vaccines.

Previously serotyped as 11A, the true epidemiological nature of 11E is unclear. Clinical isolates originally serotyped as 11A will be readdressed for the expression of 11E capsule using serospecific monoclonal antibodies. To understand the serological flexibility of these serotypes, the genetic properties that lead to seroswitching between 11A and 11E will be further studied.

Additionally, the role wcjE inactivation plays in avoiding a human humoral response will be evaluated using an in vitro opsonophagocytosis killing assay (OPKA) with sera from humans vaccinated with the 23- valent polysaccharide vaccine, which includes 11A PS. Independent and competitive OPKA survival of strains expressing 11A and 11E capsule will be compared, and the capacity of purified 11A and 11E PS to inhibit functional antibodies will be determined. 

Finally, the capacity of serotype 11A to escape an 11A-specific humoral response through wcjEinactivation in vivo and the effects on pathology will be verified in a murine infection model. The survival of 11A and 11E strains will be compared under naïve conditions, with passive 11A-specific immunization, and with preimmunization against 11A and 11E PS. These assays will also provide preliminary information on the use of 11E as a potential vaccine against both serotypes. 

Public Health Relevance Statement (Project Narrative)

Understanding how Streptococcus pneumoniae serotypes escape an immune response is important for the design of interventional and preventative strategies against this significant human pathogen. This proposed research will study the effects of O-acetylation modification of S. pneumoniae capsule on antibody-dependent clearance of the bacteria, in relation to the prevalent serotype 11A and the closely related serotype 11E. 

Bibliography and References Cited

  1. Kadioglu A, Weiser JN, Paton JC, Andrew PW. The role of Streptococcus pneumoniae virulence factors in host respiratory colonization and disease. Nat Rev Microbiol. 2008;6(4):288-301.
  2. Park IH, Pritchard DG, Cartee R, Brandao A, Brandileone MC, Nahm MH. Discovery of a new capsular serotype (6C) within serogroup 6 of Streptococcus pneumoniae. J Clin Microbiol. 2007;45(4):1225-33.
  3. Henrichsen J. Six newly recognized types of Streptococcus pneumoniae. J Clin Microbiol. 1995;33(10):2759-62.
  4. Bratcher PE, Kim KH, Kang JH, Hong JY, Nahm MH. Identification of natural pneumococcal isolates expressing serotype 6D by genetic, biochemical, and serological characterization. Microbiology. 2009
  5. Calix JJ, Nahm MH. A new pneumococcal serotype, 11E, has variably inactivated wcjE gene. J Infect Dis. 2010;In Print.
  6. Bentley SD, Aanensen DM, Mavroidi A, Saunders D, Rabbinowitsch E, Collins M, Donohoe K, Harris D, Murphy L, Quail MA, Samuel G, Skovsted IC, Kaltoft MS, Barrell B, Reeves PR, Parkhill J, Spratt BG. Genetic analysis of the capsular biosynthetic locus from all 90 pneumococcal serotypes. Pub Lib of Sci Genet. 2006;2(3):e31.
  7. Sjostrom K, Spindler C, Ortqvist A, Kalin M, Sandgren A, Kuhlmann-Berenzon S, Henriques-Normark B. Clonal and capsular types decide whether pneumococci will act as a primary or opportunistic pathogen. Clin Infect Dis. 2006;42(4):451-9.
  8. Yu J, Carvalho Mda G, Beall B, Nahm MH. A rapid pneumococcal serotyping system based on monoclonal antibodies and PCR. J Med Microbiol. 2008;57(Pt 2):171-8.
  9. Lin J, Kaltoft MS, Brandao AP, Echaniz-Aviles G, Brandileone MC, Hollingshead SK, Benjamin WH, Nahm MH. Validation of a multiplex pneumococcal serotyping assay with clinical samples. J Clin Microbiol. 2006;44(2):383-8.
  10. Zartler ER, Porambo RJ, Anderson CL, Chen LH, Yu J, Nahm MH. The structure of the capsular polysaccharide of pneumococcal serotype 11A reveals a novel acetyl-glycerol that is the structural basis for 11A subtypes. J Biol Chem. 2009;284(11):7318-29.
  11. Shelly MA, Jacoby H, Riley GJ, Graves BT, Pichichero M, Treanor JJ. Comparison of pneumococcal polysaccharide and CRM197-conjugated pneumococcal oligosaccharide vaccines in young and elderly adults. Infect Immun. 1997;65(1):242-7.
  12. Whitney CG, Farley MM, Hadler J, Harrison LH, Bennett NM, Lynfield R, Reingold A, Cieslak PR, Pilishvili T, Jackson D, Facklam RR, Jorgensen JH, Schuchat A. Decline in invasive pneumococcal disease after the introduction of protein-polysaccharide conjugate vaccine. N Engl J Med. 2003;348(18):1737-46.
  13. Poehling KA, Talbot TR, Griffin MR, Craig AS, Whitney CG, Zell E, Lexau CA, Thomas AR, Harrison LH, Reingold AL, Hadler JL, Farley MM, Anderson BJ, Schaffner W. Invasive pneumococcal disease among infants before and after introduction of pneumococcal conjugate vaccine. Jama. 2006;295(14):1668-74.
  14. Richter SS, Heilmann KP, Dohrn CL, Riahi F, Beekmann SE, Doern GV. Changing epidemiology of antimicrobial-resistant Streptococcus pneumoniae in the United States, 2004-2005. Clin Infect Dis. 2009;48(3):e23-33.
  15. Huang SS, Hinrichsen VL, Stevenson AE, Rifas-Shiman SL, Kleinman K, Pelton SI, Lipsitch M, Hanage WP, Lee GM, Finkelstein JA. Continued impact of pneumococcal conjugate vaccine on carriage in young children. Pediatrics. 2009;124(1):e1-11.
  16. Kellner JD, Scheifele D, Vanderkooi OG, Macdonald J, Church DL, Tyrrell GJ. Effects of routine infant vaccination with the 7-valent pneumococcal conjugate vaccine on nasopharyngeal colonization with streptococcus pneumoniae in children in Calgary, Canada. Pediatr Infect Dis J. 2008;27(6):526-32.
  17. Park SY, Moore MR, Bruden DL, Hyde TB, Reasonover AL, Harker-Jones M, Rudolph KM, Hurlburt DA, Parks DJ, Parkinson AJ, Schuchat A, Hennessy TW. Impact of conjugate vaccine on transmission of antimicrobial-resistant Streptococcus pneumoniae among Alaskan children. Pediatr Infect Dis J. 2008;27(4):335-40.
  18. Harboe ZB, Thomsen RW, Riis A, Valentiner-Branth P, Christensen JJ, Lambertsen L, Krogfelt KA, Konradsen HB, Benfield TL. Pneumococcal serotypes and mortality following invasive pneumococcal disease: a population-based cohort study. PLoS Med. 2009;6(5):e1000081.
  19. Rajam G, Carlone GM, Romero-Steiner S. Functional antibodies to the O-acetylated pneumococcal serotype 15B capsular polysaccharide have low cross-reactivities with serotype 15C. Clin Vaccine Immunol. 2007;14(9):1223-7.
  20. McNeely TB, Staub JM, Rusk CM, Blum MJ, Donnelly JJ. Antibody responses to capsular polysaccharide backbone and O-acetate side groups of Streptococcus pneumoniae type 9V in humans and rhesus macaques. Infect Immun. 1998;66(8):3705-10.
  21. Aanensen DM, Mavroidi A, Bentley SD, Reeves PR, Spratt BG. Predicted functions and linkage specificities of the products of the Streptococcus pneumoniae capsular biosynthetic loci. J Bacteriol. 2007;189(21):7856-76.
  22. Fusco PC, Farley EK, Huang CH, Moore S, Michon F. Protective meningococcal capsular polysaccharide epitopes and the role of O acetylation. Clin Vaccine Immunol. 2007;14(5):577-84. PMCID: 1865638.
  23. Bender MH, Cartee RT, Yother J. Positive correlation between tyrosine phosphorylation of CpsD and capsular polysaccharide production in Streptococcus pneumoniae. J Bacteriol. 2003;185(20):6057-66.
  24. Trzcinski K, Thompson CM, Lipsitch M. Construction of otherwise isogenic serotype 6B, 7F, 14, and 19F capsular variants of Streptococcus pneumoniae strain TIGR4. Appl Environ Microbiol. 2003;69(12):7364-70.
  25. Wernette CM, Frasch CE, Madore D, Carlone G, Goldblatt D, Plikaytis B, Benjamin W, Quataert SA, Hildreth S, Sikkema DJ, Kayhty H, Jonsdottir I, Nahm MH. Enzyme-linked immunosorbent assay for quantitation of human antibodies to pneumococcal polysaccharides. Clin Diagn Lab Immunol. 2003;10(4):514-9.
  26. Romero-Steiner S, Libutti D, Pais LB, Dykes J, Anderson P, Whitin JC, Keyserling HL, Carlone GM. Standardization of an opsonophagocytic assay for the measurement of functional antibody activity against Streptococcus pneumoniae using differentiated HL-60 cells. Clin Diagn Lab Immunol. 1997;4:41522.
  27. Burton RL, Nahm MH. Development and validation of a fourfold multiplexed opsonization assay (MOPA4) for pneumococcal antibodies. Clin Vaccine Immunol. 2006;13(9):1004-9.
  28. Wu HY, Nahm MH, Guo Y, Russell MW, Briles DE. Intranasal immunization of mice with PspA(pneumococcal surface protein A) can prevent intranasal carriage, pulmonary infection, and sepsis with Streptococcus pneumoniae. J Infect Dis. 1997;175(4):839-46.
  29. Glover DT, Hollingshead SK, Briles DE. Streptococcus pneumoniae surface protein PcpA elicits protection against lung infection and fatal sepsis. Infect Immun. 2008;76(6):2767-76.
  30. Balachandran P, Brooks-Walter A, Virolainen-Julkunen A, Hollingshead SK, Briles DE. Role of pneumococcal surface protein C in nasopharyngeal carriage and pneumonia and its ability to elicit protection against carriage of Streptococcus pneumoniae. Infect Immun. 2002;70(5):2526-34.
  31. Briles DE, Forman C, Crain M. Mouse antibody to phosphocholine can protect mice from infection with mouse-virulent human isolates of Streptococcus pneumoniae. Infect Immun. 1992;60:1957-62.
  32. Yu J, Lin J, Benjamin WH, Jr., Waites KB, Lee CH, Nahm MH. Rapid multiplex assay for serotyping pneumococci with monoclonal and polyclonal antibodies. J Clin Microbiol. 2005;43(1):156-62.
  33. Jakobsen H, Sigurdsson VD, Sigurdardottir S, Schulz D, Jonsdottir I. Pneumococcal serotype 19F conjugate vaccine induces cross-protective immunity to serotype 19A in a murine pneumococcal pneumonia model. Infect Immun. 2003;71(5):2956-9

Facilities and Other Resources

University: UAB has many investigators studying various aspects of pneumococcal pathogenesis and immunology. These include: Susan Hollingshead and Janet Yother for pneumococcal pathogenesis; David Briles for pneumococcal infection mouse models; Suzanne Michalek and Robin Lorenz for mucosal immunology; Kevin Dyvbig for bacterial genetics; David Pritchard for biochemistry of pneumococcal polysaccharide. The Medical Scientist Training Program provide exceptional support for the training of its students, and putting them in contact with potential mentors and collaborators on-site.

Laboratory: Dr. Nahm's laboratory occupies about 2500 square feet in the Bevill Biomedical Research Building (BBRB 614) on the UAB Campus. This building houses laboratories of many microbiologists in the UAB. Drs. Hollingshead, Briles, and Yother, who study pneumococci, have laboratories in the same floor as the PI and supervisor. Dr. Hollingshead specializes in the genetic evolution of pneumococcus; Dr. Yother specializes in bacterial genetics and physiology; and Dr. Briles is an expert in the application of animal models in the research of bacterial pathogen. Having this many specialized investigators makes for a specially suitable environment in which to execute this research and training plan. All these investigators will be regularly consulted for guidance in executing this proposal.

Information technology: There are various personal computers in Dr. Nahm's laboratory and in his office. Dr. Nahm's laboratory has a flow cytometry data analysis computer station. These computers are connected to internet and files can be shared electronically with co-investigators via internet and departmental servers. 

Animal facility: An animal facility is located in the basement of Bevill Biomedical Research Building and has a specially designed room for housing mice that are used for pneumococcal infections. The facility also has a staff that provides adequate veterinary care and living conditions to all experimental animals.

Clinical: UAB medical school is a part of a medical center that includes a university hospital, a veteran's hospital, a children's hospital, and a clinic. The hospital has more than 900 beds and has all the major clinical departments. The clinic has more than 800 physicians and handles 400,000 clinic visits per year. All the hospitals are involved in the clinical training of medical and MD/PhD students. The university also contains a Center for Clincial and Translational Research which sponsors and supports the training of physician scientists. 


Dr. Nahm's laboratory is equipped for various microbiological, serological, and immunological work. His laboratory has various centrifuges, water bath, spectrophotometer, pH meter, analytical balances, isoelectric focusing get station, tissue culture hoods, CO2 incubators, ELISA plate readers, ELISA plate washer, SDSPAGE apparatus, power supplies, various glassware adequate for polysaccharide purification, fraction collectors, lyophilizer, various microscopes (including a fluorescence microscope), PCR machine, bacteria colony counter for opsonization assays, liquid nitrogen freezers, and various freezers (-20oC, -70 oC). His laboratory has a FACSarray analyzer which permits us semi-automate pneumococcal serotyping (multibead serotyping assays).

One FACScalibur machine is available one floor above our laboratory for general flow cytometry and FACSbased serotyping assays. If any polysaccharide biochemical work becomes necessary, a GLC/MS (Varian 4000) system used for polysaccharide analysis is available on the same floor. In addition, UAB has several core laboratories including the fermentation facility, NMR center, and mass-spectrometry laboratory. 

List of Referees

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Sponsor and Co-Sponsor Information

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Research & Related Senior/Key Person Profile

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NAMEJuan Jose Calix 
POSITION TITLEGraduate Student Trainee
 Loyola University New Orleans (LOYNO) B.S. (MCL) 05/2005 Biological Sciences
 University of Alabama in Birmingham (UABSOM) MD/Ph.D. 05/2014 Microbiology

A. Personal Statement

I am currently seeking a MD/PhD degree with an emphasis on microbiology and am pursuing a career as an academic physician in pediatric infectious disease. My past academic training has prepared me to make significant contributions in the fields of infectious disease and vaccine development. For my undergraduate research I had the opportunity to work in two labs. I did a summer undergraduate research fellowship at Albert Einstein College of Medicine, where I worked in the lab of Dr. Jurgen Brojatsch studying the kinetics of anthrax-toxin mediated killing of macrophages. Later, I then spent a year in the lab of Dr. Patricia Dorn at Loyola University New Orleans, where I studied the genetic flow of the Central American vector for American trypanosomiasis, Triatoma dimidiata. These experiences provided a strong foundation in basic laboratory techniques and exposed me to the lifestyles of an academic scientist. They also provided opportunities to present research at the local, regional and national levels. I am currently pursuing my doctoral thesis in the laboratory of Dr. Moon Nahm, whose research focuses on the immunological and pathological implications of Streptococcus pneumoniae capsule biology. Dr. Nahm has served on various advisory WHO boards and his lab is currently the NIH Bacterial Respiratory Pathogen Reference Laboratory. His mentorship and the lab environment provide an advantage for someone seeking to work and make a contribution in my preferred field. My proposed project focuses on S. pneumoniae, a significant pediatric pathogen, and how its antigenic polysaccharide capsule can be modified to escape the host humoral response. The long term goal of this project is to gain a better understanding of the mechanisms that contribute to capsule diversity and aid in the design of future vaccines against the bacterium. This project is multidisciplinary and offers the chance to interact and collaborate with scientists at different institutions. I have also had the chance to mentor younger graduate students who have contributed to this project. The experience and expertise I obtain from this work will contribute to both the overall knowledge of the field of S. pneumoniae disease prevention and to my personal goals of being a physician scientist on the translational front of infectious disease intervention. 

B. Positions and Honors

Projects Coordinator10/0512/05Non-profit administrationCatholic Charities New OrleansDr. Elmore Rigamer, Medical Director
Small Projects Coordinator12/0507/06Non-profit administrationCatholic Community Services Baton RougeDeborah Roe, CEO

C. Publications

Research Publications

  • Calix JJ and Nahm MH. A new pneumococcal serotype, 11E, has variably inactivated wcjE gene. J Infect Dis. 2010. In Press.
  • Franco CM, Andrade AL, Andrade JG, Almeida e Silva S, Oliveira CR, Pimenta FC, Lamaro-Cardoso J, Brandão AP, Almeida SC, Calix JJ, Nahm MH, de Cunto Brandileone MC. Survey of nonsusceptible nasopharyngeal Streptococcus pneumoniae isolates in children attending day-care centers in Brazil. Pediatr Infect Dis J. 2010 Jan;29(1):77-9

Published Abstracts

  • Calix JJ and Nahm MH. 2009. “Genetic Basis for a New Pneumococcal Serotype, 11E.” Abstract for Poster Presentation. American Society for Microbiology 109th General Meeting. Philadelphia, PA.
  • Calix JJ and Dorn P. 2006. “Gene flow among Triatoma Dimidiata populations across Central America and Mexico” Abstract for poster and oral presentation. 54th Annual American Society of Tropical Medicine and Hygiene Conference. Washington DC.

D. Scholastic Performance

[Redacted from this sample.]

Biographical Sketch

NAMEMoon Hea Nahm
POSITION TITLEProfessor of Pathology
Washington University, St. Louis, MOA.B. (SCL)1970Physics
Washington University, St. Louis, MOM.D.1974Medicine
Washington University, St. Louis, MOPost-doctoral1977-1980Microbiology/Immunology

A. Personal Statement

My laboratory has been studying diversity of pneumococcal capsule and pneumococcal antibodies. We investigated diversity of polyclonal and monoclonal antibodies to polysaccharide (PS) capsules of Streptococcus pneumoniae using their isoelectric points, peptide sequences, DNA sequences, binding affinity (avidity), cross-reactions, and peptide mimotopes. Using monoclonal antibodies specific to pneumococcal capsules, we have begun to investigate diversity of pneumococcal capsule. We recently discovered many new pneumococcal serotypes including serotypes 6C, 6D, and 11E. We have now studied the genetic and biochemical basis of these new serotypes using DNA sequencing, 2D-NMR and mass spectrometry techniques. Discovery of serotype 6C was important since the 7-valent pneumococcal conjugate vaccine did not provide cross-protection against 6C and its prevalence significantly increased in the past several years and future vaccines should provide protection against 6C. Our studies led us to develop ways to accurately measure vaccine-induced antibodies to pneumococcal capsule and also developed a multiplexed opsonophagocytosis assay. My laboratory currently serves as the reference laboratory for NIH and WHO. 

B. Positions and Honors

1974-76 Internship and Residency, Department of Medicine, Jewish Hospital, Washington University Medical School, St. Louis, Missouri
1976-80 Resident, Laboratory Medicine Division, Barnes Hospital, Washington University Medical School, St. Louis, Missouri
1980-89 Assistant Professor, Division of Laboratory Medicine, Departments of Medicine and Pathology, Washington University School of Medicine, St. Louis, Missouri
1989-96 Associate Professor, Division of Laboratory Medicine, Departments of Medicine and Pathology, Washington University School of Medicine, St. Louis, Missouri
1996-01 Professor, Departments of Pediatrics, Pathology, and Medicine, University of Rochester School of Medicine and Dentistry, Rochester, New York
1996-01 Director of NIH Pneumococcal and H. influenzae Reference Laboratory University of Rochester Medical Center, Rochester, NY
2001- Director of NIH Bacterial Respiratory Pathogens Reference Laboratory University of Alabama at Birmingham, Birmingham, AL
2001- Professor, Departments of Pathology and Microbiology & Director of the Clinical Immunology Laboratory, University of Alabama at Birmingham, Birmingham, Alabama

C. Selected peer-reviewed publications (Selected from more than 160 publications)

Most relevant to the current application

  1. Zartler ER, Porambo RJ, Anderson CL, Chen LH, Yu J, Nahm MH. Structure of the capsular polysaccharide of pneumococcal serotype 11A reveals a novel acetylglycerol that is the structural basis for 11A subtypes. J Biol Chem. 2009 Mar 13;284(11):7318-29. Epub 2008 Dec 29. [PMCID: PMC2652282]
  2. Wernette CM, Frasch CE, Madore D, Carlone G, Goldblatt D, Plikaytis B, Benjamin W, Quataert SA, Hildreth S, Sikkema DJ, Käyhty H, Jonsdottir I, and Nahm MH: Enzyme-linked Immunosorbent assay for quantitation of human antibodies to pneumococcal polysaccharides. Clin Diagn Lab Immuno 2003;10:514-519 (Describes specific pneumococcal antibody ELISA)
  3. Bratcher PE, Kim KH, Kang JH, Hong JY, Nahm MH. Identification of natural pneumococcal isolates expressing serotype 6D by genetic, biochemical and serological characterization. Microbiology. 2010 Feb;156(Pt 2):555-60. Epub 2009 Nov 26. PubMed PMID: 19942663.
  4. Park IH, Pritchard DG, Cartee R, Brandao A, Brandileone MCC, Nahm MH: Discovery of a new capsular serotype (6C) within serogroup of Streptococcus pneumoniae. J Clin Microbiol. 2007;45:1225-1233.
  5. [Redacted publication in press]

Additional recent publications of importance to the field

  1. Shin JS, Yu J, Lin J, Zhong L, Bren KL, Nahm MH: Peptide mimotopes of pneumococcal capsular PS of 6B serotype. A peptide mimotope can bind to two unrelated antibodies. J Immunol 2002;168:6273-6278
  2. Burton R and Nahm MH: A four-fold multiplexed OPA for pneumococcal antibodies, Clin Vaccine Immunol 2006 Sep;13(9):1004-1009.
  3. Jackson LA, Neuzil, KM, Nahm MH, Whitney CG, Yu O, Nelson JC, Starkovich PT, Dunstan M, Carste B, Shay DK, Baggs J, Carlone GM: Immunogenicity of varying dosages of 7-valent pneumococcal polysaccharide-protein conjugate vaccine in seniors previously vaccinated with 23-valent pneumococcal polysaccharide vaccine. Vaccine 2007;25:4029-4037.
  4. Park IH, Park S, Hollingshead SK, Nahm MH: Genetic basis for the new pneumococcal serotype 6C. Infect Immun 2007;75:4482-4489.
  5. Seo HS, Michalek SM, Nahm MH: Lipoteichoic acid is important in innate immune responses to grampositive bacteria. Infect Immun. 2008;76(1):206-13. [PMCID: PMC2223632] (The article was spotlighted by the journal. Infect Immun. 2008;76(1):21).
  6. Seo HS, Cartee RT, Pritchard DG, Nahm MH: A new model of pneumococcal lipoteichoic acid structure resolves biochemical, biosynthetic, and serologic inconsistencies of the current model. J. Bacteriol. 2008; 190:2379-2387. [PMCID: PMC2293179]
  7. Schenkein JG, Park S, Nahm MH: Pneumococcal vaccination in older adults induces antibodies with low opsonic capacity and reduced antibody potency. Vaccine 2008;26:5521-5526. PMID: 18706464 (PMCID: PMC2574975).
  8. Park IH, Moore MR, Treanor JJ, Pelton SI, Pilishvili T, Beall B, Shelly MA, Mahon BE, Nahm MH, the Active Bacterial Core Surveillance Team: Differential effects of pneumococcal vaccines against serotypes 6A and 6C. J Infect Dis. 2008 Dec 15; 198(12):1818-22. [PMID: 18983249]
  9. Nahm MH, Lin J, Finkelstein JA, Pelton SI. Increase in the prevalence of the newly discovered pneumococcal serotype 6C in the nasopharynx after introduction of pneumococcal conjugate vaccine. J Infect Dis. 2009;199(3):320-325. PMID: 19099489 (PMCID: PMC2743180)
  10. Park S, Parameswar AR, Demchenko AV, Nahm MH. Identification of a simple chemical structure associated with protective human antibodies against multiple pneumococcal serogroups. Infect Immun. 2009 Aug;77(8):3374-9. Epub 2009 May 18. PubMed PMID: 19451241; PubMed Central PMCID: PMC2715663.

D. Research Support

Ongoing Research Support

Nahm, Moon H. (PI) 
02/01/07 – 01/31/12
Title: Impact of a new group 6 serotype on pneumococcal vaccines
The purpose of the grant is to study biochemical, genetic and serological basis of the newly identified pneumococcal serotypes 6C and 6D.
Role: PI

Nahm, Moon H. (PI) 
06/30/03 - 6/29/10 (extended to 9/30/11)
Title: Bacterial Respiratory Pathogens Reference Laboratory
The major goal of this contract is to support the effort of NIH in studying the infections by respiratory pathogens by providing new analytical solutions and/or standardizing the assays. Pneumococci are used as the model pathogen. Our laboratory has developed the 3rd generation pneumococcal antibody ELISA and a multiplexed opsonization assay for pneumococcal antibodies. We are now spearheading the international effort to standardize pneumococcal antibody opsonization assays. These pneumococcal antibody assays will be important in performing the studies described in the current proposal.
Role: PI

Nahm, Moon H. (PI) 
04/01/06 – 03/31/10
Title: Pneumococcal conjugate vaccines and old adults
The goal of this grant is to study pneumococcal antibodies induced in old adults. We will compare the
opsonizing capacity and antibody avidities of pneumococcal antibodies to serotypes 14 and 23F induced with a
polysaccharide and a conjugate vaccine. The current proposal is a continuation of this study.
Role: PI

Completed Research Support

[Outside research support redacted from sample.]

PHS Fellowship Supplemental Form, Research Plan

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Specific Aims

The role of wcjE disruption in pneumococcal serotype 11A humoral escape 

Rationale: Serotype 11E is a novel pneumococcal serotype, previously unidentified due to its serological similarity to the epidemiologically prevalent 11A, a significant serotype in both asymptomatic carriage and disease-causing strains. Genetic findings indicate that each 11E strain emerged independently in separate hosts. 11E differs from 11A due to a disruption of the wcjE capsule synthesis gene, which encodes an Oacetyltranferase that targets 1-phosphoglycerol in capsule polysaccharide. We hypothesize that disruption of the gene allows a strain initially expressing 11A capsule to avoid a host humoral response by changing its capsule structure, resulting in an 11E infection. Given that no previous studies have recognized 11E as a separate serotype, we aim to determine the extent of the role 11E plays following initial 11A infection, setting the stage for future studies addressing the prevention and control of disease caused by serotype 11A. 

Aim 1. Examine nasopharyngeal (NP) isolates for the presence of 11E strains
(1A) Develop a FACS-based assay for efficient detection and distinction of 11A and 11E strains.
(1B) Identify additional 11E clinical strains, focusing on NP isolates originally typed as serotype 11A.
(1C) Examine newly identified 11E isolates for heterogeneity of wcjE disruption.

Aim 2. Determine whether a human humoral immune response can be selective for 11A and not 11E in vitro
(2A) Generate isogenic 11A and 11E strains for comparative studies.
(2B) Determine antibody specificity for 11A or 11E PS in sera from individuals vaccinated with the pneumococcal vaccine PPV-23 (PPV-23 sera) by using ELISA.
(2C) Detect functional anti-11A and anti-11E antibodies in PPV-23 sera by using Single Opsonophagocytic Killing Assay (SOPKA) of 11A and 11E.
(2D) Determine competitive advantage of 11E by immunological escape in PPV-23 sera by using Multiplex Opsonophagocytic Killing Assay (MOPKA).
(2E) Verify the role of anti-capsular PS antibodies in 11A and 11E opsonization.

Aim 3. Determine that 11E has a selective advantage in an immune response against 11A in vivo and whether 11E infection emerges from initial infection with 11A
(3A) Develop an 11A and 11E mouse infection model.
(3B) Detect total and functional anti-11A and anti-11E antibodies in murine sera following 11A and 11E infection.
(3C) Determine in vivo survival of 11A and 11E in mice actively immunized against 11A and 11E PS.
(3D) Assess in vivo survival of 11A and 11E in mice passively immunized with 11A-specific monoclonal antibodies.

A. Significance

Streptococcus pneumoniae, also known as the pneumococcus, is a commensal gram-positive diplococcus that ubiquitously colonizes the human nasopharyngeal (NP) tract. However, pneumococcus can spread to normally sterile sites and cause diseases such as pneumonia, meningitis and otitis media. Especially susceptible populations include infant, elderly and immunocompromised individuals. Despite the development of effective vaccines and antimicrobial therapies, the adaptable pneumococcus continues to have a widespread impact as a pathogen. 

The bacterium’s most significant virulence factor and a prerequisite for almost all pneumococcal disease is its polysaccharide (PS) capsule. The capsule is composed of chains of PS repeat units that surround and protect the bacterium against the host immune system, e.g. antibody-independent opsonophagocytosis (1). Host exposure to the capsule antigen following either natural infection or vaccination can elicit a capsule-specific antibody response. This selective pressure has contributed to the diversification of capsular structures into the 93 currently recognized pneumococcal serotypes (2-5). This diversity is directly reflected in comparison of the genetic contents in the capsule PS synthesis (cps) loci of different serotypes, which contain the genes necessary for the synthesis of each serotype’s particular PS subunits (6). Despite the large diversity of capsule structure, only a few prevalent serotypes are responsible for most of pneumococcal disease (7).

Classically, serotypes were designated according to the Quellung reaction, in which a strain is tested for reactivity with polyclonal antisera. However, serological assays that make use of more antigenically specific monoclonal antibodies (mAb) have been developed and have led to the identification of new serotypes (2, 4, 8). Using a mAb assay, we identified two subtypes within strains typed as 11A according to classical Quellung methods (8, 9). Subsequent studies determined that the subtypes were serologically, structurally and genetically distinct serotypes, 11A and a novel serotype 11E (5, 10). An NMR spectroscopy study of the closely related serotypes identified the presence of an O-acetylated 1-phosphoglycerol (1-P-Gro) on 50% of the capsular PS repeat units on 11A, whereas all 11E 1-P-Gro are not acetylated (10). Serological and structural changes are attributed to disruption of the capsule synthesis gene wcjE in all 11E strains, indicating that the gene encodes an O-acetyltransferase (OAcT) (5). In each 11E strain examined the mutation in wcjE was different.

Serotypes that are prevalent in the population are the targets for the current polysaccharide-based vaccines. A 23-valent pneumococcal polysaccharide vaccine (PPV-23), which includes 11A PS, is administered to at-risk adult populations, but is ineffective in pediatric populations. A 7-valent conjugate vaccine (PCV-7), which is effective for children under the age of two and does not include 11A PS, has been in use since 2000 (11). The latter vaccine has been effective in lowering the incidence of invasive pneumococcal disease (12, 13). However, pediatric carriage rates have not declined, and there is growing concern that non- PCV-7 serotypes are filling the void left by widespread vaccination (14-16). Development and implementation of new, more inclusive vaccines (e.g. PCV-10 and PCV-13) is underway to address the concern over emerging serotypes. Recent epidemiological studies place serotype 11A among the top five occurring serotypes isolated from disease and colonized individuals (14-16). The 11A serotype appears to be filling the void left by widespread use of the pediatric vaccine in North America (15-17) and has been associated with greater rates of 30-day mortality relative to other serotypes (18). These findings make a strong case for the consideration of 11A in future vaccine design. However, all these studies were done before the discovery of 11E, and preliminary results suggest that 10-25% of invasive disease isolates serotyped as 11A may actually be 11E (8). Furthermore, we have not identified any 11E isolates associated with NP carriage.

The unrelated disruptive mutations observed in all 11E isolates indicate that each strain emerged independently. It also suggests a barrier to host-to-host spread of these strains. Because these strains were capable of independently emerging and surviving in hosts, we speculate that serotype 11E emerges from an initial 11A infection, competitively survives in a state of co-infection, and goes on to cause disease. We hypothesize that in certain individuals that mount an 11A-specific humoral response, selective pressure to escape host’s immunity favors loss of wcjE in 11A; this leads to disease caused by 11E. 

B. Innovation

Vertebrate Animals

Previous studies have shown that antibodies to one serotype can be non-reactive to another serotype with identical capsule structures except for the lack of O-acetylation (19, 20). However, these studies did not address competitive survival between counterpart serotypes and may have understated the effects of loss of O-acetylation. Furthermore, no study has shown in vivo seroswitching in response to an O-acetylationdependent immune response. Comparative studies of these closely related serotypes may reveal what roles capsular O-acetylation plays in pneumococcal pathology. Indeed, sequencing of the wcjE pseudogenes in multiple strains of serotype 9A and the vaccine serotype 33F (the wcjE-inactivated counterparts of serotypes 9V and 33A, respectively) shows the existence of heterogeneous disruption of the wcjE gene (data not shown), suggesting that loss of O-acetylation may be playing a similar role in serotypes beyond serogroup 11. Half of the known serotypes, including 8 current vaccine targets, contain a putative OAcT in their respective cps locus (21). Identifying the conditions that contribute to the adaptation or loss of capsular O-acetylation is important for anticipating serotype emergence and can be translated into future vaccine design. This study also begins to validate the use of de-O-acetylated PS in pneumococcal vaccines for disease prevention, a similar strategy to what is being developed against other bacterial pathogens (22).

C. Approach

Aim 1. Examine nasopharyngeal (NP) isolates for the presence of 11E strains. To confirm whether previous results apply to the entire population of clinical isolates previously serotyped as 11A, we must readdress further clinical isolates from NP carriage states. Furthermore, we will define the genetic characteristics of wcjE inactivation in additional strains. These results will indicate whether inter-host transmission of 11E occurs, and whether 11E emerges in the NP tract. 

a. Develop FACS-based serotyping method for efficient detection and distinction of 11A and 11E. To facilitate the study of serotypes that readily seroswitch, we must develop methods that can detect and distinguish clones expressing closely related serotypes within a culture. We have previously shown the validity of using monoclonal antibodies (mAb) to serotype clinical isolates (8). However, these assays are based on the capacity for soluble capsular PS to inhibit binding of mAbs to PS-coated beads or plates, thus, indirectly detecting the presence of a serotype. This method does not readily detect subpopulations within a culture. We have developed FACS-based methods to distinguish between the clinically significant 9V and the closely related serotype 9A, which genetically differ only by wcjE disruption in 9A. The assay takes advantage of the fact that most mAb made against 9V bind exclusively to 9V capsule, but one mAb (Hyp9VM5) is cross-reactive to both 9A and 9V (Fig 1). Given that preliminary ELISA results show that some mAb display crossreactivity to both 11A and 11E serotypes and some are selective for 11A (data not shown), we will develop a method similar to the 9A/9V protocol, for detection of 11A and 11E individual clones in culture. To validate the specificity of the method, mAb reactivity to the closely re serotypes 11F, 11B, 11C, and 11D will be evaluated. A successful method to distinguish the two serotypes will aid in studies outlined below. 

b. Identify additional 11E clinical strains, focusing on NP isolates originally typed as serotype 11A. Serotype 11A has recently been among the top five serotypes isolated from NP colonization strains (15, 17), however, no epidemiological study has distinguished 11E from 11A isolates. From previous studies we can extrapolate that 11E may represent a significant portion of isolates typed as 11A by Quellung (5). Furthermore, to date all 11E strains have been isolated from blood and cerebral spinal fluid, i.e. have been invasive disease strains. If 11E is capable o emerging and being selected for in the NP, we expect to identify 11E strains in carriage isolates previously typed as 11A. Through collaboration with groups studying NP isolates, we will screen using methods established in our lab (8, 9). We are currently collaborating with Dr. Stephen Pelton in the Department of Pediatrics at Boston University School of Medicine to identify NP isolates from pediatric patients and originally serotyped as 11A (15). If no 11E isolates are detected, we can interpret that 11E is either a rare serotype or it only emerges following infection of sterile sites (i.e. lung, blood or cerebral spinal fluid).

c. Examine newly identified 11E isolates for genetic heterogeneity. We showed that all 11E isolate identified to date contain disruptive mutations unrelated to each other (5). This result strongly suggests that a) the 11E serotype is capable of emerging independently in different hosts and b) there is a barrier to the epidemiological spread of an 11E strain. However, only a few invasive disease isolates have been examined. To support or dismiss initial conclusions that 11E is not transmissible, 11E carriage isolates must be analyzed genetically in search for evidence of clonal expansion between hosts, i.e. two separate isolates with identical disruptive mutations. Using PCR and sequencing methods as previously published (5), we will genetically characterize isolates identified in Aim 1B. If the degree of previously observed genetic heterogeneity applies to further isolates, then the hypothesis of 11E emergence in separate individuals is supported. 

Aim 2. Determine whether a human humoral immune response can be selective for 11A and not 11E in vitro. Our hypothesis presumes that a humoral response made against serotype 11A is more effective at opsonizing an 11A strain than an 11E strain. Indeed, evidence shows that individuals may be capable of mounting an immune response that is not cross-reactive to serotypes where the only difference is Oacetylation, i.e. 15B and 15C, and 9A and 9V (19, 20). Our study is designed to confirm whether 11E strains have a competitive advantage over 11A strains against opsonization by sera of humans vaccinated against 11A, and whether this response is PS specific.

a. Generate isogenic 11A and 11E strains for comparative studies. To closely study the effects of 11A and 11E PS expression, we will create two isogenic strains that can be readily selected for by means other than serological differences. We will transform the rpsL gene from the streptomycin-resistant strain TIGR4 into a clinical isolate of 11A (i.e. MNZ270); rpsL from TIGR4 has been shown to confer resistance to streptomycin. Alternatively, MNZ270 will be passaged in sequentially higher concentrations of streptomycin to isolate a streptomycin-resistant 11A strain by artificial selection. However, this method may introduce additional non-related mutations that may affect further studies. 

Next, we will transform the streptomycin resistant strain with a Janus cassette containing a kanamycin resistance gene and a streptomycin susceptibility gene, to disrupt wcjE, as previously described (5). This method will result in a streptomycin resistant 11A and a kanamycin resistant 11E strain, respectively referred to as 11Astr and 11Ekan for the remainder of this proposal. Both strains will be validated for correct serology using ELISA. Studies in this lab have verified that in vitro disruption of wcjE results in loss of O-acetylated 1- P-Gro according to NMR analysis (data not shown).

To control for any other confounding factors that may influence results in the following assays, independent and competitive in vitro growth, average bacterial chain length and average capsule production will be examined in these strains. Growth will be monitored using OD600 measurements and serial dilutions on antibiotic selective plates. Average bacterial chain length will be determined by microscopy. Average capsule production will be determined by measuring capsule thickness according to electron microscopy and by comparing purified PS capsule chain length on SDS gel as previously determined (23). Preliminary studies of 11A and 11E clinical co-isolates of identical multilocus sequence types suggest that independent or competitive growth are not affected by serotype expression (Fig 2). If differences are detected in capsule production, we will design additional experiments to examine protective features, such as complement deposition, etc. However, small capsule expression differences will have minimal effect on antibodymediated opsonophagocytosis. 

In addition to 11Astr and 11Ekan, we will transform TIGR-JS (a TIGR-4 background with its cps locus deleted through recombination with a Janus cassette (24)) with 11A cps to create the streptomycin resistant TIGR11A. Following the same procedures for the creation of 11Ekan, we will create the kanamycin resistant TIGR11E. These two strains will be used interchangeably in the assays mentioned in this proposal to verify that capsule alone can confer any of the observed results, independent of a strain’s genetic background. 

b. Determine antibody specificity for 11A or 11E in sera from individuals vaccinated with pneumococcal vaccine PPV-23 by using ELISA. Total antibody concentrations will be determined according to a previously established ELISA protocol (25). Briefly, sera will be absorbed with cell wall polysaccharide and serotype 23F PS. Resulting sera will then be incubated in ELISA plates coated with equal concentrations of purified 11A or 11E PS and detected with anti-human IgG, IgM and IgA alkaline phosphatase conjugated secondary antibodies. PS will be purified from 11Astr and 11Ekan using ethanol precipitation. A standard assay has been developed to detect absolute concentrations of 11A-specific antibody (25). Since no corresponding assay exists for 11E specific antibodies, anti-11E concentrations will be determined as binding signal relative to11A. 

Polyclonal sera may display similar reactivity to both PS. To analyze the crossreactivity of this sera to 11A and 11E PS, sera will be inhibited by soluble PS of either serotype previous to being analyzed by ELISA. This will determine the amount of 11A- or 11E- specific antibody in the samples. By using different concentrations of inhibitory PS, we can also determine total affinity of sera to 11A or 11E PS. Though PS may be altered, i.e. de-O-acetylated or misfolding of epitopes, by the purification process or adhesion to ELISA plates, these assays will identify any major specificity differences of vaccinated sera to these serotypes.

c. Detect functional anti-11A and anti-11E antibodies in PPV-23 human sera using Single Opsonophagocytic Killing Assay (SOPKA) of 11A and 11E. We hypothesize that individuals may mount a functional immune response specifically to serotype 11A, but in which strains with 11E capsule have a competitive advantage over 11A. To test this hypothesis, we will examine the capacity of sera from PPV-23 vaccinated patients to induce opsonophagocytosis of 11A and 11E in the well established SOPKA (26). In this assay, bacteria, rabbit complement, serial dilutions of an individual’s serum and activated HL60 granulocytic cells are incubated to induce bacterial killing. Following incubation, tissues cells are lysed and the bacteria are plated to determine amount of viable colony forming units (CFU). If the serum contains functional antibodies against the bacteria, killing of bacteria is increased. Bacterial killing is measured as a function of titers, here defined as the inverse of the concentration of sera needed to obtain 50% maximum killing in vitro. Since these sera are obtained from patients vaccinated with a polysaccharide vaccine, titers are dependent on the capsule structure the bacteria. If our hypothesis is correct, some individuals will display higher titers against 11A than against 11E. Various sera may need to be tested, since previous studies have shown that not all patients mount O-acetylation-dependent responses (20). Additionally, surviving 11A CFU will be routinely screened serologically and genetically to verify that escape from OPK was not due to in vitro seroswitching. 

d. Determine competitive advantage of 11E by immunological escape in PPV-23 human sera by using Multiplex Opsonophagocytic Killing Assay (MOPKA). A limitation of SOPKA is that we will use sera from patients immunized with vaccines containing purified 11A PS. O-acetyl groups are susceptible to mild hydrolysis and other factors, such as storage time, so the degree of O-acetylation of 11A may have decreased during preparation, storage and administration of the vaccine. Thus, these sera may not be representative of an individual whose first exposure to an 11A antigen was natural, potentially resulting in difference between 11A and 11E OPKA that are too small to detect when tested in separate systems. Furthermore, to support our hypothesis, we need to detect 11E competitively surviving against 11A in the same OPKA system.

To better visualize the effects of seroswitching in a system more closely resembling 11A and 11E competition within a host, we will adopt the MOPKA that has been established in our lab (27). The procedures will resemble those in aim 2c, except that 11Astr and 11Ekan will be co-incubated in the OPKA systems with increasing dilutions of human sera. After incubation, surviving bacteria will be spotted on plates containing antibiotic selective media, so that surviving 11Astr CFU will be enumerated on streptomycin plates, and 11Ekan CFU on kanamycin plates (Fig 3). Opsonization with 11A specific monoclonal antibodies will serve as a positive control. This multiplexing will allow us to detect the effect of the two serotypes within a single host, and if our hypothesis is correct, we expect 11E survival to be significantly greater than 11A. Conversely, 11E titers will be lower than 11A titers. To our knowledge, the competitive survival of closely related serotypes has never been examined in the same system. 

e. Verify the role of anti-capsular PS antibodies in 11A and 11E opsonization. We hypothesize that seroconversion of 11A to 11E is advantageous because de-Oacetylated PS has lower affinity to functional antibodies against 11A. To confirm this, we will attempt to inhibit OPKA with absorption of sera with whole 11A and 11E bacteria and with soluble 11A and 11E PS (see aim 2b). Human sera at optimal dilutions (according to Aim 2c) will be absorbed with increasing concentrations of purified PS, and we will detect for decreases in killing. Inhibition curves by 11A and 11E PS, and concentrations of PS that inhibit 50% killing will be compared. If an individual produces a predominantly 11A-specific humoral response (Aim 2b and 2c), we expect that 11A PS inhibit killing of both 11Astr and will 11Ekan at lower concentrations than 11E PS. 

Aim 3. Determine that 11E has a selective advantage in an immune response against 11A in vivo and whether 11E infection emerges from initial infection with 11A. To verify our hypothesis, it must be shown that an initial 11A infection can result in an 11E disease isolate in vivo under the selective pressure of an 11Aspecific response. To recreate this scenario, we will develop and employ a murine model of 11A infection. All protocols specified below will conform to local and national guideline and will be reviewed by the UAB internal review board for the correct usage of animal subjects. This aim will be performed in close collaboration with Dr. David Briles who specializes in the development and use of murine models of pneumococcal disease. 

a. Create and 11A and 11E mouse infection model. Murine models of pneumococcal infection have been well established (28, 29). However, currently there is no in vivo model for infection with serotype 11A. Given the rise in prevalence of the 11A serotype, a murine model is pertinent for future studies. Preliminary infection of C57BL/6 mice will include nasopharangeal (NP) and intravenous (IV) inoculations according to previous studies (30, 31). The 11A clinical isolate MNZ270 and its 11E coisolate MNZ269 will be used separately to assess the capability of the serotype to colonize and/or persist in the NP and blood. NP colonization and pneumonia can be achieved by NP inoculation with different CFU amounts (30). Successful infections will be assessed by sacrificing mice 5 days post-infection with variable concentrations of bacteria, and determining CFU counts from blood, long, nasal wash and nasal tissue. Successful infections will then be followed over 14-21 days to detect time from infection until mice exhibit moribund behavior. Following optimization of an infection protocol, we will assess infection with 11Astr and 11Ekan. This latter method will allow us to the monitor the competitive survival of each serotype using selective antibiotic plates. 

Since there is no evidence of 11E host-to-host dissemination, it is uncertain whether an 11E strain can successfully colonize a host following NP infection, or whether 11E can survive in the blood without emerging from an 11A predecessor. In order to achieve infection, 11E may be infected intraperitonealy (31). 

b. Detect total and functional anti-11A and anti-11E antibodies in murine sera following 11A and 11E infection. Sera from mice infected NP and IV with 11A and 11E will be assessed for reactivity to capsular PS. Total antibody concentrations will be determined akin to aim 2b, and functional antibody levels will be determined akin to aims 2c and 2d. Since any influence of capsule differences may be masked by a humoral response to non-capsule antigens, sera will be absorbed with a nonencapsulated strain (e.g. TIGR-JS). If 11A infection is capable of producing an O-acetylation specific response, we expect sera from 11A infected mice to preferably bind and opsonize 11A PS and bacteria. Since 11E epitopes are present on both 11E and 11A bacteria, we expect difference between the binding and opsonization of both serotypes by sera from11E infected mice to be minimal. Humoral responses will be assessed from every mice used in this study to determine correlations between titers and bacterial growth in hosts. 

c. Determine in vivo survival of 11A and 11E in mice actively immunized against 11A and 11E PS. If the above studies reveal that mice can develop a humoral response that selectively targets the 11A serotype over 11E, we will assess the survival of the bacteria in vivo following immunization. Purified 11A PS will be conjugated to ovalbumin through cyanylation with CNBr, and the resulting compound will be injected subcutaneously into mice three times at two week intervals. This process was capable to induce antibodies that are specific for 11A PS and not 11E PS (32), so we assume that O-acetylation is at least partially conserved in the immunization product. Successful immunization will be verified by collecting sera from vaccinated mice and testing for 11A specific antibodies by ELISA and OPKA. If functional antibody levels are not detected, different protocols for vaccine synthesis or IP administration will be used. 

A week after final immunization, mice will be co-infected NP or IV with both 11Astr and 11Ekan according to optimal protocols determined in aim 3a. At 2 and 5 days after infection, CFU counts from lung, NP tissue, nasal wash and blood will be determined by growth on selective plates to determine 11Astr and 11Ekan levels. Alternatively, we will employ FACS based methods developed above, since antibiotic resistance may be lost during in vivo growth and 11E clones may emerge de novo from 11Astr. If our hyptothesis is correct, we expect levels of 11E to be significantly higher than levels of 11A upon collection of isolates. 

In a similar manner, 11E conjugated vaccine will be created and administered to mice prior to coinfection. Since 11E PS may contain epitopes found on both 11A and 11E strains, we hypothesize that in vivo growth will be affected in both serotypes. This preliminary data begins to validate the use of 11E as a vaccine target.

d. Assess in vivo survival of 11A and 11E in mice passively immunized with 11A specific monoclonal antibodies.Since aim 3c will be using conjugated vaccine, it is likely that subject mice will not develop an exclusively anti-11A response. To test the growth of 11A and 11E in an exclusively anti-11A environment in vivo, we will employ passive immunization with murine mAb prior to co-infection with 11Astr and 11Ekan. Antibodies will be assessed for exclusive or near exclusive opsonization of 11A in vitro using OPKA described above. Antibodies will be administered prior and during infection and CFU numbers will be determined in all the tissues mentioned above. 

We will compare bacteria isolated from two groups of mice infected only with 11Astr, a control group and a passively immunized group. Special interest will be paid to streptomycin resistant strains with 11E serology according to FACS analysis, as this population would constitute strains that seroswitched from 11A to 11E during infection. We would expect a higher population of de novo 11E to emerge in the passively immunized mice compared to the control group. If so, this would confirm our hypothesis that 11E emerges in following initial 11A infection in response to an anti-11A immune response. 


1a) Carriage Model Description. 

We will determine whether 11A and 11E strains are capable of establishing nasopharyngeal carriage in mice. It has been established that nasal colonization of mice with pneumococcus is a reasonable model of colonization in man. Most of these mice will exhibit no life-threatening infections. They will be euthanized after about 7 days and the numbers of CFU in their nasal tissue and nasal wash will be determined by growth on plates. Although most remain healthy until the end of the experiment, a small number (about 5%) will become ill. Once they become moribund (as defined below) they will be euthanized and recorded as having reached the moribund state. Various doses of pneumococcus will be used to find the dose of the new serotypes resulting in carriage in 50% of cases.

1b) Infection Model Description. 

We will also study the ability of the new pneumococcal types to cause bacteremia and sepsis. This is an important endpoint, because virtually all of the human deaths due to pneumococcal pneumonia are associated with sepsis. In this study some mice will be bled retrorbitally up to four times over 2 day period by removal of 35 ul blood at each bleeding. Various doses of pneumococci will be used to find LD50 CFU of the new serotypes. In some cases, protective antibody will be given passively. We will do quantitative determination of CFU in these samples by plating the pneumococci. In all studies following i.v. infection mice will be monitored until they become unresponsive to touch and scored as being moribund (as described below). The time at which they become moribund will be recorded. 

1c) Immunization Description.

After establishing colonization and bacteremia models of infection, we will validate whether preimmunization with conjugated polysaccharide incurs a protective humoral response against infection. We will immunize mice three times with conjugated polysachharides and peripheral blood samples will be obtained before each immunization or two weeks after the final immunization. The candidate PS will be mixed with an adjuvant (quilA or alum). Serum from blood samples will be analyzed for pneumococcal antibody levels (determined by ELISA) and capacity to opsonize pneumococci (determined by opsonophagocytic killing assay). Preimmunized mice will also be analyzed for protection from infection using the protocols mentioned above.

Mice will be considered moribund when they reach the following clinical presentation: mice that hardly move, fail to right themselves, or fail to respond to touch will be examined to determine their surface temperature. The surface temperature of a normal mouse is 30º C. When the surface temperature falls below ≤25º C the mice will be considered "moribund" and will be euthanized. The surface temperature will be monitored by using an infrared thermometer (Model: 15-077-966 from Control Company [Friendswood, TX]). Temperature will always be recorded by scanning the back of the mouse in question.

The reason that some of the mice will be studied until they become moribund is that this is the most sensitive measure of protection against sepsis. Even amounts of antibody that give unconvincing changes in blood clearance of bacteria can be protective. A study (33) reported that passively given antibody did not affect the degree of bacteremia at 12 hours post infection, but it resulted in a median time to become moribund of 8 days whereas mice without antibody became moribund in one day. By 24 hours mice in the unprotected group were dying, thus greatly complicating comparisons of CFU between the groups since there were no longer enough control mice still alive for statistical analysis.

Mice are infected with pathogenic bacteria (Streptococcus pneumoniae), which probably causes discomfort, but no real pain as such. No pain relieving agents can be used to eliminate this discomfort without interfering with the validity of the study. Pain relieving agents such as aspirin or ibuprofen reduce inflammation and thus decrease resistance to infection. For this reason, they cannot be used in these studies. Their use would compromise our ability to identify relevant mechanisms of disease and resistance to infections. 

2) Justification.

There are no ways to determine in vivo survival of these strains or to describe the humoral response to live infection or vaccination without using actual animal models. We propose to use mice for this study because mice have been widely used for this purpose and therefore are well established. We will make every effort to use the fewest animals compatible with obtaining reliable data. 

3) Veterinary care.

The animals will be housed in our school facilities, which are supervised by professional veterinarians.

4) Limiting discomfort.

Immunization and phlebotomy without anesthesia are not thought to be painful procedures. Nevertheless, we will have trained and experienced persons to perform the procedure. If any animal show any sign of discomfort (e.g., due to infections), we will euthanize them. 

5) Euthanasia. 

The mice will be euthanized with carbon dioxide as recommended by the UAB Comparative Medicine Department. 


This training plan was initially conceived by the Principal Investigator (PI, Calix) and Supervisor (Nahm) according to work done in the lab by the PI. Writing of the proposal was performed by the PI. After completion of the initial draft, the proposal was submitted to the PI’s steering committee for comments. Minor editings were made by the PI and Supervisor according to suggestions by the committee. 


Sponsor: Dr. Nahm is currently the director of the UAB Clinical Immunology Laboratory, of the WHO (World Health Organization) Pneumococcal Serology Reference Laboratory, and of the NIH Respiratory Bacterial Pathogens Reference Laboratory. He has served on multiple international advisory boards in matters of vaccine implementation, and his lab currently focuses on developing and monitoring the efficacy of vaccines. I selected Dr. Nahm as my research mentor because his expertise on both the medical and basic science components of research makes him an ideal mentor for students pursuing careers as medical scientist. Given that Dr. Nahm specializes in the immunological response to respiratory pathogens, his mentorship offers crucial support to the aims of this proposal. Furthermore, his laboratory, employed scientists and the facilities available to the Nahm lab offer a helpful environment for experimental work. 

Institution: I decided to attend the University of Alabama Birmingham (UAB) because it is among the largest biomedical centers in the United States of America and is among the top ranked hospital systems in the country. As such, the UAB school of medicine offers advantageous opportunities for students seeking a career in academic science. Accordingly, the Medical Scientist Training Program (MSTP) is nationally recognized and was recently recommended for expansion according to a national MSTP review committee. The program and university has offered me many opportunities for both academic and personal growth. 

Furthermore, UAB has a valued tradition of infectious disease research. Currently four laboratories (Dr. Moon Nahm, Dr. Janet Yother, Dr. David Briles and Dr. Susan Hollingshead) collaborate on research in the field of S. pneumoniae pathogenesis and hold inter-laboratory meetings every month. The sharing of resources and ideas among these labs promotes interdisciplinary approaches to questions including pneumococcal genetics, vaccinology, in vivo pathology, etc. This is a special instance that an unusually large group of investigators focus on a same pathogen, and this makes for an ideal environment for me to address the hypothesis of this proposal. 


The University of Alabama at Birmingham (UAB) has a strong and ongoing commitment to the responsible conduct of research. The UAB campus offers many opportunities for such training including formal courses through graduate school programs and additional educational opportunities as detailed below. 

MSTP trainees specifically take two courses:

(1) Medical Ethics

NIH F-series Grant Tips and Example

I successfully applied to the NIH F31 grant in 2015. I recently terminated it to accept a new NIH F99/K00 grant. Here are some of the things I’ve learned and some advice for writing an outstanding NIH grant as a PhD Student. I’ve included my NIH F31 grant and full summary statements as an example. Enjoy and good luck!


The NIH F-series of grants is appropriate for trainees, primarily at the graduate level. Much much much more information can be found on the NIH website.

Applying for an NIH F-series grant is very different from helping your PI with a grant because the F-series grants are awarded to the trainee, who serve as the principal investigator (you are your own PI!)

This blog post will mostly focus on the F31 (The Ruth L. Kirschstein Predoctoral Individual National Research Service Award - to provide predoctoral individuals with supervised research training in specified health and health-related areas leading toward the research doctoral degree).

Who should apply to the NIH F31

  • Current PhD students in their 2nd or 3rd year of graduate studies. Those in their 4th year are still eligible but should consider applying to the F99/K00 if possible.
  • Must be a U.S. citizen or permanent resident, enrolled in a research doctoral degree program.
  • Must be pursuing health-related research. Can be basic or clinical.

But my PI is well funded. Why should I write a grant?

“Because getting this grant will help you get the next one” is what Dr. Paul Avillach often reminds me. Indeed, my NSF grant introduced me to this whole grant writing system, which made putting together my F31 that much more feasible, which then made putting together my F99/K00 substantially easier.

Also, having your own grant means you have your own money, which, in theory, should mean you will have more leverage. Negotiating for a better computer? Want to go to more conferences? Some schools/programs will even provide additional travel and educational allowances for those who bring in their own grants.

In my opinion, if you think you may want a career in academia, a surprising portion of your life will be spent writing grants. So better to get some practice to at least see if you like it!

My grant as an example

There are A LOT of documents to put together. I personally find it really overwhelming to read the NIH website and prefer to just look at actual examples. Big thanks to my mentor Dr. Peter Kharchenko for sharing his successful R01, to Dr. Nils Gehlenborg for sharing his successful K99, and to Yu-Han Hsu sharing her successful F31! So now I’m passing on their generosity by sharing my successful F31 grant as well.

All the documents you need (as of 2015) are as follows:

All about your research (what you should spend the most time on)

All about you (don’t be modest)

All about your training environment (would not recommend spending too much time on these documents)

The good news is that a lot of these documents are pretty boiler plate. Ask your PI or others at your institution for her/his grants. The Cover letter, Selection of Institution, Facilities and Resources, Equipment, Resource Sharing Plan, and many other text will be nearly the same.

General Tips and Advice

Beyond having a great research topic and strong preliminary data, here are a few tips to improve your grant based on my experience and the criticism I received for my F31.

Tip 1: Start early, especially if you are dealing with human data of any kind

If you are dealing at all with human data, get your IRB straightened out NOW! Even though I only deal with non-identifiable sequencing data from patients and do not directly interface with patients or even collect data myself, I still needed an IRB according to this document from the NIH. The NIH only requests for the appropriate IRBs AFTER your grant is awarded; so it would be such a shame if your grant was awarded but you can’t accept it because you don’t have your IRB!

I was my advisor’s first PhD student. As such, he had no track record of mentoring PhD students. I was advised to choose a co-sponsor with a good track record of mentoring PhD students to counter-balance my advisor’s deficits. My advisor’s advisor from his PhD training was George Church, who was and is now even moreso a super big shot, for lack of a better word. Hundreds of PhD students have gone through his lab so his track record for mentorship on paper is superb. However, my choice of Dr. Church as a co-sponsor was the primary criticism from almost every reviewer. And in hindsight, they were absolutely right. One reviewer worded things particularly well: “Co-sponsor’s letter and offered level of input came across as weak and distant; seemed to be there to prevent criticism of a young sponsor. This is a proposal that could benefit from a co-sponsor bringing some other expertise and with a way to push this young woman’s training.” The purpose of a co-sponsor is to have someone to mentor you in areas where your primary advisor can not or does not have a track record of doing well. Dr. Church’s purpose in my training was to mentor me on how to mentor. Yet, during the duration of my F31, I did not interact at all with Dr. Church. Indeed, he served more for ‘inspiration’ than actual mentorship. Reviewers knew this would happen. They were right to criticize.

Tip 3: Choose an appropriate agency

Doing research on blood cancers? Should you submit to the National Cancer Institute (NCI) or National Heart, Lung, and Blood Institution (NHBLI)? Ideally, the choice of agency shouldn’t matter but if you send your grant to a completely irrelevant agency, that will of course hurt you. But when there are multiple appropriate agencies, a more calculated choice may be warranted. On one hand, NCI generally has more funding and will be able to fund more grants. But NHBLI may be ‘less competition’ and can fund grants with lower scores even if fewer grants are funded by them in general. It’s worth looking into historical data of funding paylines, funding availability, and other statistics. Ask for advisor for recommendations as well especially if they have a track record of funding from a particular agency.

Tip 4: Ask for recommendation letters from old mentors

Did you do research in undergrad? Ask that mentor for a recommendation letter. Don’t be shy! Establish a record for research and contribution to science.

Tip 5: Take your training plan seriously

Sure, there is nothing to substitute a solid research plan, but an F31 is a training grant. You should have a clear plan as to how you will develop the necessary skills towards independence. Are you going to mentor students? How are you going to acquire these students and assess your effectiveness as a mentor? Are you going to attend conferences? Which ones are you planning to go to? As with the rest of your grant, the more specific your plan the better.

Final tip: Understand that a majority of accepted applications are resubmissions

So if you don’t get the grant the first time, try again! Maybe the funding payline was really harsh this year, maybe you were just unlucky. There are 3 opportunities per year to submit an F31. So plenty of chances to try again!

Best of luck with your grant!

What to expect after you submit

After you submit your grant, it will be assigned to a study section comprised of senior scientists in your agency’s field. Your study section will physically meet together many many months later and judge your grant on its Overall Impact using five criteria: Applicant, Sponsor(s), Research Training Plan, Training Potential, and Institutional Environment & Commitment. Three reviewers will score each aspect on a scale of 1 to 9, where 1 is the best score. The 3 sets of scores are averaged and multiplied by 10 to arrive at a final score that will range from 10 to 90, with 10 being the best score. These scores and comments will be sent to you as your Summary Statements.

Here are my Summary Statements for your reference

Many many months after your Summary Statements are available, each agency will issue its payline. If you grant falls within the payline ie. lower/better score than the payline, then congrats (but don’t celebrate too soon)! If not, depending on how far from the payline your score is, it will be worth discussing with your Program Director as to the best course of action. Maybe transfer to another agency, maybe apply again.

If you are within the payline, your Program Director will be in touch with you to get the necessary IRBs, certificates on ethics and human subject research training, and other paperwork. Many many months after this, you will receive a ‘Just In Time’ (JIT) that you will need to complete with the help of your sponsoring official. Then many many months after this, you will receive a ‘Notice of Award’ (NOA) and finally, after this, your grant manager will receive the award money in your accounts. The grant can theoretically be lost at any of these steps (such as failure to provide IRBs, etc).

Getting grants is a very anticlimactic experience!


Jumping a little ahead, but eventually the NIH will start sending you emails asking for your Tuition and confirmations for other numbers. NEVER RESPOND BY YOURSELF (I made this mistake). Even though NIH will address the email to you, they will add at the way bottom of every email, “All correspondence must be submitted through your sponsoring official” which means you should forward the emails to your sponsoring official and let them deal with it.

Caveat to the last tip: DO TALK TO YOUR PROGRAM DIRECTOR

She is often very helpful! As soon as you get your Summary Statements, it may be worth shooting your Program Director a short email to get a sense for if your score is within the funding payline. She won’t be able to tell you for sure, but she’ll give you a good guess.

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