STUDENT ACCOMPLISHMENTS

2023-2024

Awards and Fellowships

2023 C. Werner and Kitty Hirs Travel Award- Emma Sheriff
2023 Colorado Immunology & Microbiology Conference Microbiology Program Poster Award – Cormac Lucas
2023 Ruth L. Kirschstein National Research Service Award (NRSA) Individual Predoctoral F31 Fellowship – Elizabeth Spear
2023 CCTSI Team Oriented Training across the Translational Sciences Spectrum T32 – Kaylee Mickens
2023 Molecular Pathogenesis of Infectious Disease (MIPD) Symposium 3rd Place Graduate Student Poster Prize Awardee - Elizabeth Nail
2023 American Society for Microbiology Future Leaders Mentoring Fellowship (FLMF) – Madeline Akbari
2024 Werner and Kitty Hirs Travel Award - Elizabeth Nail
2024 2nd Place Graduate Student Talk - Spring Rocky Mountain Branch – American Society for Microbiology – Madeline Akbari
2024 NIH NIAID F31 Fellowship – Madeline Akbari

2023-2024 Molecular Pathogenesis of Infectious Diseases Training Program Scholar Award
- Shirli Cohen
- Madeline Akbari
- Elizabeth Nail
Runner-up Best Graduate Poster Presentation; Rocky Mountain Branch – American Society for Microbiology – Shelby Andersen
First Place Graduate Entry; Love Data Week Visualization Contest - Shelby Andersen
Travel scholarship “President’s Diversity Fund for Development and Support” from CU Anschutz ($1000) – Grecia Rivera Palomino
Awarded 3rd Place Graduate Student Talk at the Rocky Mountain Branch Meeting of the American Society for Microbiology - Emma Sheriff
Honorable Mention, NSF Graduate Research Fellowship - Joanna Chau
American Association of Immunologists Young Investigator Award for poster presentation – Kaylee Mickens
Conference on retroviruses and opportunistic infections (CROI) New investigator scholarship – Kaylee Mickens

Thesis Defenses

Anna Burnet – Nagel and Rochford
Klara Keim - Horswill
Joshua Kirsch - Duerkop
Corman Lucas - Morrison
Laurie Lyon - Horswill
Emma Sheriff - Duerkop

Publications

Maier JL, Gin C, Callahan B, Sheriff EK, Duerkop BA, Kleiner M. Pseudo-pac site sequences used by phage P22 in generalized transduction of Salmonella PLoS Pathog. 2024;20(6):e1012301. doi: 10.1371/journal.ppat.1012301

Kirsch JM, Hryckowian AJ, Duerkop BA. A metagenomics pipeline reveals insertion sequence-driven evolution of the microbiota. Cell Host Microbe. 2024;32(5):739-754.e4. doi: 10.1016/j.chom.2024.03.005

Kirsch JM, Ely S, Stellfox ME, Hullahalli K, Luong P, Palmer KL, Van Tyne D, Duerkop BA. Targeted IS-element sequencing uncovers transposition dynamics during selective pressure in enterococci. PLoS Pathog. 2023;19(6):e1011424. doi: 10.1371/journal.ppat.1011424

Sheriff EK, Andersen SE, Chatterjee A, Duerkop BA. Complete genome sequence of enterococcal phage G01. Microbiol Resour Announc. 2024 Jan 31:e0121723. doi: 10.1128/mra.01217-23. Epub ahead of print. PMID: 38294211

Bullen NP*, Johnson CN*, Andersen SE, Arya G, Marotta SR, Whitney JC, Duerkop BA. 2024. An enterococcal phage protein broadly inhibits type IV restriction enzymes involved in antiphage defense. Nature Communications.

Sheriff E, Salvato F, Andersen SE, Chatterjee A, Kleiner M, Duerkop BA. Enterococcal quorum-controlled protease alters phage infection. 2024 April. FEMS Microbes.

Sharon BM, Arute AP, Nguyen A, Tiwari S, Bonthu SSR, Hulyalkar NV, Neugent ML, Araya DP, Dillon NA, Zimmern PE, Palmer KL, De Nisco NJ. Genetic and functional enrichments associated with Enterococcus faecalis isolated from the urinary tract. mBio. Published online November 14, 2023. doi:10.1128/mbio.02515-23

Cao AL, Mills KB, Nguyen A, Costa FG, Wall E, Horswill AR. Complete Genome Sequence of a Staphylococcus epidermidis Isolate from Healthy Skin with Upregulation of Protease EcpA. Microbiol Resour Announc. 2023;12(7):e0046323. doi:10.1128/mra.00463-23

McCaslin P*, Andersen SE*, Icardi C, Faris R, Weber MM. (2022). Identification and preliminary characterization of novel type III secreted proteins by Chlamydia trachomatis. IAI. 2023 June. https://doi.org/10.1128/iai.00491-22 *Co-first authors

Li FS, Carpentier KS, Hawman DW, Lucas CJ, Ander SE, Feldmann H, Morrison TE. Species-specific MARCO-alphavirus interactions dictate chikungunya virus viremia. Cell Rep. 2023 May 30;42(5):112418. doi: 10.1016/j.celrep.2023.112418. Epub 2023 Apr 21. PMID: 37083332; PMCID: PMC10290254.

Holmes AC, Lucas CJ, Brisse ME, Ware BC, Hickman HD, Morrison TE, Diamond MS. Ly6C+ monocytes in the skin promote systemic alphavirus dissemination. Cell Rep. 2024 Mar 26;43(3):113876. doi: 10.1016/j.celrep.2024.113876. Epub 2024 Mar 5. PMID: 38446669; PMCID: PMC11005330.

Ander SE, Parks MG, Davenport BJ, Li FS, Bosco-Lauth A, Carpentier KS, Sun C, Lucas CJ, Klimstra WB, Ebel GD, Morrison TE. Phagocyte-expressed glycosaminoglycans promote capture of alphaviruses from the blood circulation in a host species-specific manner. PNAS Nexus. 2024 Mar 20;3(4):pgae119. doi: 10.1093/pnasnexus/pgae119. PMID: 38560529; PMCID: PMC10978064.

Lucas CJ, Sheridan RM, Reynoso GV, Davenport BJ, McCarthy MK, Martin A, Hesselberth JR, Hickman HD, Tamburini BA, Morrison TE. Chikungunya virus infection disrupts lymph node lymphatic endothelial cell composition and function via MARCO. JCI Insight. 2024 Jan 9;9(4):e176537. doi: 10.1172/jci.insight.176537. PMID: 38194268; PMCID: PMC11143926

Sharon B, Ebraimzadeh T, Dahl H, Avadhanam N, Rajendran D, Abaragu A, Nguyen D, Phan L, Ramjee C, Thai M, Vragel G, Mehta I, Palmer K. 2024. Genome sequences of seven bacterial isolates collected from soil as part of a microbiology lab course. Microbiol Resour Announc 13:e00357-23. https://doi.org/10.1128/MRA.00357-23

Sheriff EK, Salvato F, Andersen SE, Chatterjee A, Kleiner M, Duerkop BA. Enterococcal quorum-controlled protease alters phage infection. bioRxiv [Preprint]. 2024 May 11:2024.05.10.593607. doi: 10.1101/2024.05.10.593607. PMID: 38766208; PMCID: PMC11100838.

Cohen S, Ost KS, Doran KS (2024) Impact of interkingdom microbial interactions in the vaginal tract. PLOS Pathogens 20(3): e1012018. https://doi.org/10.1371/journal.ppat.1012018

Neve RL, Giedraitis E, Akbari MS, Cohen S, Phelan VV (2024) Secondary metabolite profiling of Pseudomonas aeruginosa isolates reveals rare genomic traits. mSystems9: e00339-24. https://doi.org/10.1128/msystems.00339-24

Powers RA, June CM, Fernando MC, Fish ER, Maurer OL, Baumann RM, Beardsley TJ, Taracila MA, Rudin SD, Hujer KM, Hujer AM, Santi N, Villamil V, Introvigne ML, Prati F, Caselli E, Bonomo RA, Wallar BJ. Synthesis of a novel boronic acid transition state inhibitor (BATSI), MB076: a heterocyclic triazole effectively inhibits Acinetobacter-derived cephalosporinase (ADC) variants with an expanded-substrate spectrum. (2023) J. Med. Chem. doi:10.1021/acs.jmedchem.3c00144

Dopkins N, Fei T, Michael S, Liotta N, Guo K, Mickens KL, Barrett BS, Bendall ML, Dillon SM, Wilson CC, Santiago ML, Nixon DF. Endogenous retroelement expression in the gut microenvironment of people living with HIV-1. EBioMedicine. 2024 May;103:105133. doi: 10.1016/j.ebiom.2024.10513

Crosby HA, Keim K, Kwiecinski JM, Langouët-Astrié CJ, Oshima K, LaRivière WB, Schmidt EP, Horswill AR. Host-derived protease promotes aggregation of Staphylococcus aureus by cleaving the surface protein SasG. Cell Rep. 2024;43(4):114022. doi: 10.1016/j.celrep.2024.114022

Mills KB, Maciag JJ, Wang C, Crawford JA, Enroth TJ, Keim KC, Dufrêne YF, Robinson DA, Fey PD, Herr AB, Horswill AR. Staphylococcus aureus skin colonization is mediated by SasG lectin variation. Cell Rep. 2024;43(4):114022. doi: 10.1016/j.celrep.2024.114022

Spencer BL, Job AM, Robertson CM, Hameed ZA, Serchejian C, Wiafe-Kwakye CS, Mendonça JC, Apolonio MA, Nagao PE, Neely MN, Korotkova N, Korotkov KV, Patras KA, Doran KS. Heterogeneity of the group B streptococcal type VII secretion system and influence on colonization of the female genital tract. Mol Microbiol. 2023;120(2):258-275. doi: 10.1111/mmi.15115

Akbari MS, Keogh RA, Radin JN, Sanchez-Rosario Y, Johnson MDL, Horswill AR, Kehl-Fie TE, Burcham LR, Doran KS. The impact of nutritional immunity on Group B streptococcal pathogenesis during wound infection. mBio. 2023;14(4):e0030423. doi: 10.1128/mbio.00304-23

Manzer HS, Brunetti T, Doran KS. Identification of a DNA-cytosine methyltransferase that impacts global transcription to promote group B streptococcal vaginal colonization. mBio. 2023;14(6):e0230623. doi: 10.1128/mbio.02306-23

Manzer HS, Doran KS. Complete m6A and m4C methylomes for group B streptococcal clinical isolates CJB111, A909, COH1, and NEM316. Microbiol Resour Announc. 2024;13(1):e0073323. doi: 10.1128/mra.00733-23

Job AM, Doran KS, Spencer BL. A group B streptococcal type VII-secreted LXG toxin mediates interbacterial competition and colonization of the murine female genital tract. mBio. 2024:e0208824. doi: 10.1128/mbio.02088-24

Raab JE, Hamilton DJ, Harju TB, Huynh TN, Russo BC. Pushing boundaries: mechanisms enabling bacterial pathogens to spread between cells. Infect Immun. 2024;92(9):e0052423. doi: 10.1128/iai.00524-23

Presentations

Posters Presentations

2023 Viruses and Cells Gordon Research Conference Poster and Seminar Presentations – Cormac Lucas
March 2023 Conference on Retroviruses and Opportunistic Infections – Kaylee Mickens
June 2023 Andersen SE, Johnson CN, Kirsch JM, Bullen N, White LK, Arya G, Hesselberth JR, Whitney JC, Duerkop BA.
2023 June “Coevolution between phages and the microbiota reveals a novel method for discovering antiphage defense systems” Wind River Meeting on Prokaryotic Biology. Estes Park, CO. Poster.- Shelby Andersen
July 2023 Andersen SE, Johnson CN, Kirsch JM, Bullen N, White LK, Arya G, Hesselberth JR, Whitney JC, Duerkop BA.
2023 July “Coevolution between phages and the microbiota reveals a novel method for discovering antiphage defense systems” Lactic Acid Bacteria Biology, Symbioses and Applications Gordon Research Conference. Ventura, CA. Poster.- Shelby Andersen
July 2023 Nguyen A, Bunch ZL, Severn MM, Chekan JR, Cech NB, & Horswill AR. (July 2023) A novel Staphylococcus hominis bacteriocin shapes skin community structure. 22nd Annual Colorado Immunology and Microbiology Conference, Steamboat Springs, CO– Amber Nguyen
July 2023 Nguyen A, Bunch ZL, Severn MM, Chekan JR, Cech NB, & Horswill AR. (July 2023) A novel Staphylococcus hominis bacteriocin shapes skin community structure. Gordon Research Conference Microbial Adhesion and Signal Transduction, Newport, RI– Amber Nguyen
July 2023 Nguyen A, Bunch ZL, Severn MM, Chekan JR, Cech NB, & Horswill AR. (July 2023) A novel Staphylococcus hominis bacteriocin shapes skin community structure. Gordon Research Seminar Microbial Adhesion and Signal Transduction, Newport, RI– Amber Nguyen
July 2023 Poster at Gordon Research Conference on Lactic Acid Bacteria Biology, Symbioses, and Applications – Emma Sheriff
October 2023 Nguyen A, Bunch ZL, Severn MM, Chekan JR, Cech NB, & Horswill AR. (October 2023) A novel Staphylococcus hominis bacteriocin shapes skin community structure. Microbial Pathogenesis and Infectious Diseases Symposium, Aurora, CO – Amber Nguyen
April 2024 Andersen SE, Kirsch JM, Johnson CN, Bullen NP, Whitney JC, Duerkop BA. 2024 April “A conserved serine recombinase serves as bait for finding novel antiphage defense systems in diverse genomes” Symposium on the Immune Systems of Bacteria. Boston, MA. Poster. - Shelby Andersen
July 2024 Microbial Toxins and Pathogenicity Gordon Research Conference, July 12th- July 19th, 2024 – Elizabeth Nail

Oral Presentations

Rocky Mountain Branch Meeting of the American Society for Microbiology last weekend and was awarded 3rd place graduate student talk – Emma Sheriff
2023 3 Minute Thesis Competition - Gabrielle Vragel
2023 Presented a talk at the UK Hepacivirus and Flavivirus Conference – Elizabeth Spear
2023 3 Minute Thesis Competition - Kaylee Mickens
2023 Community Advisory Board of the Denver AIDS Clinical Trial Group - Kaylee Mickens
June 2023 Poster presentation at the Wind River Meeting on Prokaryotic Biology – Shelby Anderson
July 2023 “Serine Recombinase Linked to a Type IV Restriction Enzyme Identifies Diverse Antiphage Defense Systems in Lactic Acid Bacteria” Lactic Acid Bacteria Biology, Symbioses and Applications Gordon Research Conference, Ventura, CA - Shelby Andersen
July 2023 Invited talk at the Lactic Acid Bacteria Biology, Symbioses and Applications Gordon Research Conference – Shelby Anderson
2024 Invited Guest Speaker for the MSU Denver Chemistry and Biochemistry Seminar Series – Elizabeth Spear
2024 Wind River Conference on Prokaryotic Biology Presenters:
- Shirli Cohen
- Amber Nguyen
- Timothy Enroth
- Shelby Andersen
- John Thorstenson
2024 Cold Spring Harbor Retrovirology Meeting – Kaylee Mickens
June 2024 International Symposium on EBV & KSHV & Related Agents and Diseases - Gabrielle Vragel
June 2024 “A conserved serine recombinase serves as bait for finding novel antiphage defense systems in diverse genomes” Wind River Meeting on Prokaryotic Biology, Breckenridge, CO. - Shelby Andersen

Comprehensive Exams Completed

Jill Bilodeaux
Joanna Chau
Sarah Leach
Elizabeth Nail
Jack O’Connor
Grecia Rivera
Johnny Thorstenson
Erin Fish
Gabrielle Vragel

New Thesis Laboratories

Ari Crossen – Doran
Ana Fairbanks-Mahnke – Clark
Sydney Hall – Horswill
Anna-Sophia Leon – Horswill
Gabrielle Vragel – van Dyk
Charmie Vang – Ravi

2022-2023

Awards and Fellowships

2022 C. Werner and Kitty Hirs Merit Award- Joanna Chau
2022 Achievement Rewards for College Scientists (ARCS) Foundation Fellowship- Haider Manzer
2023, 2nd Place Graduate Student Poster Presentation – Spring RMB ASM- Haider Manzer
2022, Student Travel Award – International Conference on Gram Positive Pathogens- Haider Manzer
2023 National Science Foundation Graduate Research Fellowship Program (NSF-GRFP) Fellowship- Shelby Andersen
3rd place graduate student talk Rocky Mountain Branch - American Society for Microbiology meeting- Shelby Andersen
2022 T32 in Otolaryngology- Steven Shaw
Excellence in a graduate student poster presentation at the 2023 Front Range Microbiome Symposium- Shelby Andersen
2nd place Graduate Student Poster Presentation. Rocky Mountain Branch ASM Meeting- Amber Nguyen
Honorable Mention, NSF Graduate Research Fellowship- Amber Nguyen

Molecular Pathogenesis of Infectious Diseases T32

2022-2023

Cormac Lucas
Kaylee Mickens
Elizabeth Spear
Julie Raab

Thesis Defenses

Casey Martin- Lozupone
Brendan Monogue- Beckham
Joshua Frost- Tyler
Matthew Szucs- Kieft
Monica Graham- Beckham
Haider Manzer- Doran

Publications

Zhaohui Wang, Matteo Boretto, Rosemary Millen, Naveen Natesh, Elena S. Reckzeh, Carolyn Hsu, Haipei Yao, William Quayle, Brook E. Heaton, Alfred T. Harding, Shree Bose, Else Driehuis, Joep Beumer, Grecia O. Rivera et al. (2022). “Rapid tissue prototyping with micro-organospheres.” Stem Cell Reports 17(9): 1959-1975. DOI: https://doi.org/10.1016/j.stemcr.2022.07.016

Voorhies M* and Cohen S*, Shea TP, Petrus S, Muñoz JF, Poplawski S, Goldman WE, Michael TP, Cuomo CA, Sil A, Beyhan S. (2022). Chromosome-level genome assembly of a human fungal pathogen reveals synteny among geographically distinct species. mBio. *Co-first author. doi:10.1128/mbio.02574-21

Nicholas S. Giroux, Shengli Ding, Micah T. McClain, Thomas W. Burke, Elizabeth Petzold, Hong A. Chung, Grecia O. Rivera, Ergang Wang et al. (2023). Author Correction: “Differential chromatin accessibility in peripheral blood mononuclear cells underlies COVID-19 disease severity prior to seroconversion.” Scientific Reports 13, 6462. DOI: https://doi.org/10.1038/s41598-023-33323-8

Rana M, Yilmaz T, Cohen S, Beyhan S, Argun AA. (2023). A novel biosensor for ultrasensitive detection of fungal genes. Biosensors and Bioelectronics. doi:10.1016/j.bios.2022.114986

Iwamoto C, Lesteberg KE, Lamb MM, Calvimontes DM, Guo K, Barrett BS, Mickens KL, Duca LM, Monzon J, Chard AN, Guzman G, Barrios E, Rojop N, Arias K, Gomez M, Paiz C, Bolanos GA, Edwards KM, Zielinski Gutierrez E, Azziz-Baumgartner E, Asturias EJ, Santiago ML, Beckham JD, Olson D. High SARS-CoV-2 Seroprevalence and Rapid Neutralizing Antibody Decline among Agricultural Workers in Rural Guatemala, June 2020–March 2021. Vaccines. 2022; 10(7):1160.

Guo K, Barrett BS, Morrison JH, Mickens KL, VladarEK, Hasenkrug KJ, Poeschla EM, Santiago ML. Interferon resistance of emerging SARS-CoV-2 variants. Proc Natl Acad Sci USA. 2022;119(32):e2203760119. doi:10.1073/pnas.2203760119

Manzer H.S., Nguyen D.T., Park J.Y., Park N., Seo K.S., Thornton J.A., Nobbs A.H., and Doran K.S. (2022). The Group B Streptococcal Adhesin BspC Interacts with Host Cytokeratin 19 to Promote Colonization of the Female Reproductive Tract. mBio, doi: 10.1128/mbio.01781-22

Shipman BM, Nguyen A, Sharon BM, Zimmern PE, De Nisco NJ. (2022) Complete Genome Sequences of Three Lactobacillus gasseri Urine Isolates Obtained from Postmenopausal Women. Microbiology resource announcement. 2022;11(9):e0048122.

Neugent ML, Kumar A, Hulyalkar NV, Lutz KC, Nguyen VH, Fuentes JL, Zhang C, Nguyen A, Sharon BM, Kuprasertkul A, Arute AP, Li Q, Xing C, Shulaev V, Zimmern PE, Palmer KL, & De Nisco NJ. (2022) Recurrent urinary tract infection and estrogen shape the taxonomic ecology and function of the postmenopausal urogenital microbiome. Cell Reports Medicine. 2022;1000753.

Presentations

Posters Presentations

August 2022: Poster at Gordon Research Seminar for Streptococcal Biology- Emma Sheriff
August 2022: Poster at Gordon Research Conference for Streptococcal Biology- Emma Sheriff
August 2022: Molecular Biology of Infectious Disease Symposium- Emma Sheriff
November 2022: American Society for Microbiology Rocky Mountain Fall Branch Meeting- Emma Sheriff
April 2023: American Society for Microbiology Rocky Mountain Spring Branch Meeting- Emma Sheriff
April 2023: Front Range Microbiome Symposium- Emma Sheriff
32nd International Workshop on Retroviral Pathogenesis, Vail, CO- Kaylee Mickens
2023 STEM Poster Day at the Capitol- Kaylee Mickens
2023, ARCS Foundation Gala- Haider Manzer
2023, Spring Rocky Mountain Branch ASM Meeting- Haider Manzer
2022, GRS and GRC on Streptococcal and Enterococcal Biology-- Haider Manzer
2022, Colorado immunology Conference- Haider Manzer
2023 Front Range Microbiome Symposium- Shelby Andersen
2022 Rocky Mountain Branch - American Society for Microbiology meeting- Shelby Andersen
2022- 8th International Conference on Gram Positive Pathogens- Amber Nguyen
2023- Gordon Research Conference Microbial Adhesion and Signal Transduction- Amber Nguyen

Oral Presentations

3rd Place Graduate Poster at American Society for Microbiology Rocky Mountain Branch Meeting- Emma Sheriff
2022, Molecular Pathogenesis of Infectious Disease Symposium- Haider Manzer
2023 Rocky Mountain Branch - American Society for Microbiology meeting- Shelby Andersen
2023 Aurora Science and Technology Middle School Seminar Series- Shelby Andersen

Comprehensive Exams Completed

Shelby Andersen
Shirli Cohen
Tim Encroth
Alyx Job
Amber Nguyen
Steven Shaw
Elena Wall

New Thesis Laboratories

Jill Bilodeaux - Hesselberth
Joanna Chau- Duerkop
Elizabeth Nail- Keestra-Gounder
Sarah Leach- Guthmiller
Grecia Rivera – Theiss

2021-2022

Awards and Fellowships

2022 Ruth L. Kirschstein NRSA Individual Predoctoral Fellowship (F31) - Joshua Kirsch
2021 C. Werner and Kitty Hirs Merit Award - Amber Nguyen
2nd place Graduate Student Oral Presentation, Rocky Mountain Branch ASM Meeting Fall 2021 - Laurie Lyon
Wind River Conference on Prokaryotic Biology 2022 Travel Award - Laurie Lyon
Instructor SEA-PHAGES course on campus in partnership with Aurora Community College - Emma Sheriff
Runner Up Best Graduate Student Poster at the Rocky Mountain Branch - American Society for Microbiology - Shelby Andersen
AGI SMRT Sequencing Grant - Haider Manzer
3rd place graduate student talk, 21st Annual Rocky Mountain Virology Association meeting - Monica Graham
N.E.B. Gisela Monsig award for excellence in bacteriophage research - Cydney Johnson

Molecular Pathogenesis of Infectious Diseases T32

2021-2022

Joshua Kirsch
Laurie Lyon
Anna Burnet
Klara Keim

Thesis Defenses

Sarah Stonedahl- Tyler
Ashley Knox- Van Dyk
Morgan Severn- Horswill
Cydney Johnson- Duerkop
Rachel Neve- Phelan
Hadrian Sparks- Beckham

Publications

Neugent ML, Kumar A, Hulyalkar NV, Lutz KC, Nguyen VH, Fuentes JL, Zhang C, Nguyen A, Sharon BM, Kuprasertkul A, Arute AP, Li Q, Xing C, Shulaev V, Zimmern PE, Palmer KL, & De Nisco NJ. (2021). Recurrent urinary tract infection and estrogen shape the taxonomic ecology and functional potential of the postmenopausal urobiome. bioRxiv 2021.11.06.467345

Kleinschmidt, R.A., Lyon, L.M., Smith, S.L., Rittenberry, J., Lawless, K.M., Acosta, A.A., Donze, D. (2021). Genetic screen for suppressors of increased silencing in rpd3 mutants in Saccharomyces cerevisiae identifies a potential role for H3K4 methylation. G3 Genes|Genomes|Genetics,11(11). PMCID: PMC8527511

Severn, M.M., Williams, M.R., Shahabandi, A., Bunch, Z.L., Lyon, L.M., Nguyen, A., Zaramela, L.S., Todd, D.A., Zengler, K., Cech, N.B., Gallo, R.L., Horswill, A.R. (2022). The Ubiquitous Human Skin Commensal Staphylococcus hominis Protects against Opportunistic Pathogens. mBio, 13(3). PMCID: PMC9239047.

Burcham, L.R., Bath, J.R., Werlang, C.A., Lyon, L.M., Liu, N., Evans, C., Ribbeck, K., Doran, K.S. (2022). Role of MUC5B during Group B Streptococcal Vaginal Colonization. mBio, 13(2). PMCID: PMC9040740.

Lyon, L.M. and Doran, K.S. (2022) Human Milk Oligosaccharides vs. Streptococcus: How a Human-Made Natural Product Protects Us from Pathogens. mSphere, 7(1). PMCID: PMC8849339

Barrett BS, Nguyen DH, Xu J, Guo K, Shetty S, Jones ST, Mickens KL, Shepard C, Roers A, Behrendt R, Wu L, Kim B, Santiago ML. SAMHD1 Promotes the Antiretroviral Adaptive Immune Response in Mice Exposed to Lipopolysaccharide. J Immunology. 2022. 208 (2) 444-453.

Dillon SM, Mickens KL, Thompson TA, Cooper EH, Nesladek S, Christians AJ, Castleman M, Guo K, Wood C, Frank DN, Kechris K, Santiago ML & Wilson CC. Granzyme B+ CD4 T cells accumulate in the colon during chronic HIV-1 infection. Gut Microbes. 2022. 14:1.

Burcham LR, Akbari MS, Alhajjar N, Keogh RA, Radin JN, Kehl-Fie TE, Belew AT, El-Sayed NM, McIver KS, Doran KS. Genomic Analyses Identify Manganese Homeostasis as a Driver of Group B Streptococcal Vaginal Colonization. mBio. 2022 Jun 28;13(3):e0098522. doi: 10.1128/mbio.00985-22. Epub 2022 Jun 6. PMID: 35658538; PMCID: PMC9239048.

Akbari MS, Doran KS, Burcham LR. Metal homeostasis in pathogenic Streptococci. Microorganisms. 2022; 10(8):1501. doi: 10.3390/microorganisms10081501

Burcham LR, Burcham ZM, Akbari MS, Metcalf J, and Doran KS. Interrelated effects of zinc deficiency and the microbiome on Group B Streptococcal vaginal colonization. mSphere. 2022. Accepted.

Severn M.M., Cho Y.S., Manzer H.S., Bunch Z.L., Shahbandi A., Todd D.A., Cech N.B., Horswill A.R. (2022). The commensal Staphylococcus warneri makes peptide inhibitors of MRSA quorum sensing that protect skin from atopic or necrotic damage. J. Invest. Dermatol, doi: 10.1016/j.jid.2022.05.1092.

Manzer H.S., Villarreal R., & Doran K.S. (2022). Targeting the BspC-vimentin interaction to develop anti-virulence therapies during Group B streptococcal meningitis. PLoS Path, doi: 10.1371/journal.ppat.1010397.

Joyce L.R., Manzer H.S., Mendonca J.C., Villarreal R., Doran K.S., Palmer K.L., Guan Z. (2022). Identification of a novel cationic glycolipid in Streptococcus agalactiae that contributes to brain entry and meningitis. PLoS Biol., doi: 10.1371/journal.pbio.3001555.

Villarreal R., Manzer H.S., Keestra-Gounder A.M., Doran K.S. (2021). Vimentin Regulates Chemokine Expression and NOD2 Activation in Brain Endothelium During Group B Streptococcal Infection. Infect. Immun., doi: 10.1128/IAI.00340-21.

Lucas CJ, Davenport BJ, Carpentier KS, Tinega AN, Morrison TE. Two Conserved Phenylalanine Residues in the E1 Fusion Loop of Alphaviruses Are Essential for Viral Infectivity. J Virol. 2022 May 11;96(9):e0006422. doi: 10.1128/jvi.00064-22.

Lucas, CJ, Morrison, TE. (2022) Animal Models of Alphavirus Infection and Human Disease. Advances in Virus Research (in press).

Hamilton MK, Wall ES, Robinson CD, Guillemin K, Eisen JS (2022) Enteric nervous system modulation of luminal pH modifies the microbial environment to promote intestinal health. PLoS Pathog 18(2): e1009989.

Johnson CN* and Palacios Araya D*, Schink V, Islam M, Mangalea MR, DeCurtis EK, Ngo TC, Palmer KL, Duerkop BA. “Genetically distant bacteriophages select for unique genomic changes in Enterococcus faecalis”. MicrobiologyOpen. 2022. *Co-first author DOI: 10.1002/mbo3.1273

Presentations

Posters Presentations

RNA Society Meeting- Elizabeth Spear
2022 Streptococcal Biology Gordon Research Conference Symposium- Madeline Akbari
2022 Streptococcal Biology Gordon Research Seminar Symposium- Madeline Akbari
2021 Molecular Pathogenesis of Infectious Disease Symposium- Madeline Akbari
2022- Positive Strand RNA Viruses Keystone Symposia, Keystone, CO- Cormac Lucas
American Society for Virology 41st Annual meeting- Monica Graham
2022 Keystone Symposia Positive-Strand RNA Viruses- Monica Graham
2022 A mobile plasmid of Enterococcus faecalis encodes an anti-phage system, American Society of Microbiology Microbe, Washington, DC- Cydney Johnson

Oral Presentations

2022 Wind River Conference on Prokaryotic Biology- Laurie Lyon
2022 Wind River Conference on Prokaryotic Biology- Haider Manzer
2021 Mountain Virology Conference, Pingree Park, CO- Cormac Lucas
21st Annual Rocky Mountain Virology Association meeting- Monica Graham
Rocky Mountain ASM Branch Meeting, Online- Cydney Johnson
American Society of Microbiology Microbe, Washington, DC- Cydney Johnson

Comprehensive Exams Completed

Madeline Akbari
Kaylee Mickens
Julie Raab
Elizabeth Spear

New Thesis Laboratories

Shelby Andersen - Duerkop
Shirli Cohen- Doran
Timothy Enroth- Horswill
Reed Haney- Kvaratskhelia
Alyx Job- Doran
Amber Nguyen- Horswill
Elena Wall- Lozupone

2020-2021

Awards and Fellowships

Ruth L. Kirschstein NRSA Individual Predoctoral Fellowship (F31) - Cydney Johnson
Ruth L. Kirschstein NRSA Individual Predoctoral Fellowship (F31) - Morgan Brown
Ruth L. Kirschstein NRSA Individual Predoctoral Fellowship (F31) - Haider Manzer
Ruth L. Kirschstein NRSA Individual Predoctoral Fellowship (F31) - Matthew Szucs
Ruth L. Kirschstein NRSA Individual Predoctoral Fellowship for Students at Institutions with Dual-Degree Training Programs (F30) - Frances Li
2nd place for STEM Oral Presentation at the Research and Creative Activities Symposium (CU) - Haider Manzer
1st place for Graduate Student Oral Presentation at the Rocky Mountain Branch ASM meeting - Haider Manzer
Gisela Mosig Award for Outstanding Bacteriophage Resaerch, ASM World Microbe - Joshua Kirsch
2020 RNA Bioscience Initiative RNA Scholar Award- Matthew Szucs
ASM World Microbe Forum Student Travel Award - Haider Manzer
ASM Rocky Mountain Branch “National Presence” Travel Award - Haider Manzer
2021 RNA Bioscience Initiative RNA Scholar Award - Cormac Lucas

Molecular Pathogenesis of Infectious Diseases T32

2020

Morgan Brown
Haider Manzer
Brendan Monogue

2021

Joshua Kirsch
Laurie Lyon
Anna Burnet
Klara Keim

Thesis Defenses

Norhan Alhajjar - Doran
Ricardo Villarreal - Doran
Frank Santoriello - Pukatzki
Sarah Born - Voskuil
Zoe O'Donoghue - Kieft
Gabriela Samayoa-Reyes - Rochford
Christopher Covey - Voskuil
Ari Simenauer - Cota-Gomez

Publications

Carpentier KS, Sheridan RM, Lucas CJ, Davenport BJ, Li FS, Lucas ED, McCarthy MK, Reynoso GV, May NA, Tamburini BAJ, Hesselberth JR, et al. MARCO+ lymphatic endothelial cells sequester arthritogenic alphaviruses to limit viremia and viral dissemination. EMBO J. 2021. e108966
Akiyama BM, Graham ME, O′Donoghue Z, Beckham JD, Kieft JS. Three-dimensional structure of a flavivirus dumbbell RNA reveals molecular details of an RNA regulator of replication. Nucleic Acids Res. 2021. 49 (12): 7122–7138
Stonedahl S, Clarke P, Tyler KL. The Role of Microglia during West Nile Virus Infection of the Central Nervous System. Vaccines (Basel). 2020. 8(3):485
Johnson CN, Sheriff EK, Duerkop BA, Chatterjee A. Let me upgrade you: Impact of mobile genetic elements on enterococcal adaption and evolution. J Bacteriol. 2021. In Press.
Szucs MJ, Nichols PJ, Jones RA, Vicens Q, Kieft JS. A new subclass of exoribonuclease-resistant RNA found in multiple genera of Flaviviridae. mBio. 2020. 11:e02352-20
Kirsch JM, Brzozowski RS, Faith D, Round JL, Secor PR, Duerkop BA. Bacteriophage-bacteria interactions in the gut - from invertebrates to mammals. Annu Rev Virol. 2021. 8:17.1–17.19
Canfield GS, Chatterjee A, Espinosa J, Mangalea MR, Sheriff EK, Keidan M, McBride SW, McCollister BD, Hang HC, Duerkop BA. Lytic bacteriophages facilitate antibiotic sensitization of Enterococcus faecium. Antimicrob Agents Chemother. 2021. 65:e00143-21.
Keeley R, Rodriguez-Gonzalez L, USF Genomics Class, Briggs G, Frazier V, Mancera P, Manzer HS, Ergas SJ, Scott K. Degenerate PCR Primers for Assays to Track Steps of Nitrogen Metabolism by Taxonomically Diverse Microorganisms in a Variety of Environments. J Microbiol Methods. 2020. 175:105990.
Manzer HS, Nobbs AH, Doran KS. The Multifaceted Nature of Streptococcal Antigen I/II Proteins in Colonization and Disease Pathogenesis. Front Microbiol. 2020. 11:602305
SalamAM, Porras G, Cho YSC, Brown MM, Lyles JT, Bacsa J, Horswill AR, Quave CL. Castaneroxy A from the leaves of Castanea sativa inhibits virulence in Staphylococcus aureus. Front Pharmacol. 2021. In Press.
Brown MM, Horswill AR. Staphylococcus epidermidis – skin friend or foe? PLoS Pathog. 2021. 16(11):e1009026
Brown MM, Kwiecinski J, Cruz L, Shahbandi A, Todd D, Cech N, Horswill AR. Novel peptide from commensal Staphylococcus simulans blocks MRSA quorum sensing and protects host skin from damage. Antimicrob Agents Chemother. 2020. 64:e00172-20.
Tang H, Porras G, Brown MM, Lyles J, Bacsa J, Horswill AR, Quave CL. Triterpenoids isolated from Schinus terebinthifolia fruits reduces S. aureus capacity for virulence and pathogenesis. Sci Rep. 2020. 10:8046.
Hasenkrug KJ, Feldmann F, Myers L, Santiago ML, Guo K, Barrett BS, Mickens KL, Carmody A, Okumura A, Rao D, Collins MM, et al. Recovery from acute SARS-CoV-2 infection and development of anamnestic immune responses in T cell-depleted rhesus macaques. mBio. 2021. e0150321.
Santoriello FJ, Michel L, Unterweger D, Pukatzki S. Pandemic Vibrio cholerae shuts down site-specific recombination to retain an interbacterial defence mechanism. Nat Commum. 2020. 11(1):6246.
Walter ND, Born SEM, Robertson GT, Reichlen M, Dide-Agossou C, Ektnitphong VA, Rossmassler K, Ramey ME, Bauman AA, Ozols V, et al. Mycobacterium tuberculosis precursor rRNA as a measure of treatment-shortening activity of drugs and regimens. Nat Commun. 2021. 12(1):2899.
Alhajjar N, Chatterjee A, Spencer BL, Burcham LR, Willett JLE, Dunny GM, Duerkop BA, Doran KS. Genome-wide mutagenesis identifies factors involved in Enterococcus faecalis vaginal adherence and persistence. Infect Immun. 2020. 88(10):e00270-20.
Knox AN, Mueller A, Medina EV, Clambey ET, van Dyk LF. Lytic infection with murine gammaherpesvirus 68 activates host and viral RNA polymerase III promoters and enhances noncoding RNA expression. J Virol. 2021. 95(14):e0007921.
Sparks H, Monogue B, Akiyama B, Kieft J, Beckham JD. Disruption of Zika virus xrRNA1-dependent sfRNA1 production results in tissue-specific attenuated viral replication. Viruses. 2020. 12(10):1177.
Wiles TJ, Schlomann BH, Wall ES, Betancourt R, Parthasarathy R, Guillemin K. Swimming motility of a gut bacterial symbiont promotes resistance to intestinal expulsion and enhances inflammation. PLoS Biol. 2020. 18(3): e3000661.

Presentations

Posters Presentations

2020 Molecular Pathogenesis of Infectious Diseases Symposium - Monica Graham
35th Annual University of Colorado School of Medicine Student Research Forum - Cydney Johnson
ASM World Microbe Forum -Cydney Johnson
ASM World Microbe Forum - Joshua Kirsch
ASM World Microbe Forum - Haider Manzer
FASEB Microbial Pathogenesis Conference: Mechanisms of Infectious Disease - Cydney Johnson
6th Annual St. Jude Children's Research Hospital Future Fellows Research Conference - Cydney Johnson
2021 Wind River Conference on Prokaryotic Biology - Haider Manzer

Oral Presentations

20th Annual Rocky Mountain Virology Association Meeting - Monica Graham
20th Annual Rocky Mountain Virology Association Meeting - Sarah Stonedahl
39th Annual American Society for Virology Meeting - Sarah Stonedahl
40th Annual American Society for Virology Meeting - Sarah Stonedahl
40th Annual American Society for Virology Meeting - Monica Graham
ASM World Microbe Forum, Division M Meeting - Joshua Kirsch
World Enterococcus Day - Emma Sheriff
2020 Molecular Pathogenesis of Infectious Diseases Symposium - Emma Sheriff
2020 Molecular Pathogenesis of Infectious Diseases Symposium - Haider Manzer
2021 CU Research and Creative Activities Symposium - Haider Manzer
2021 Rocky Mountain Branch American Society for Microbiology Meeting - Haider Manzer

Comprehensive Exams Completed

Joshua Kirsch
Emma Sheriff
Cormac Lucas
Francis Li
Krista Mills
Klara Keim
Anna Burnet
Laurie Lyon

New Thesis Laboratories

Kaylee Mickens - Santiago/Wilson
Julie Raab - Russo
Elizabeth Spear - Kieft
Madeline Akbari - Doran

2018-2019

Awards and Fellowships

Program Award for Research Excellence in Microbiology: Abigail Armstrong
2018 Skaggs School of Pharmacy and Pharmaceutical Sciences Annual Retreat, Best Student Poster: Rachel Neve
2018 Metabolism and Infectious Diseases Symposium, Student Travel Award: Rachel Neve
2018 RMB-ASM, Student Travel Scholarship: Frank Santoriello
2018 RMB-ASM (Fall), 1st Place PhD Best Poster: Norhan Alhajjar
2018 RMB-ASM (Fall), 1st Place PhD Best Oral Presentation: Frank Santoriello
2019 RMB-ASM (Spring), 1st Place PhD Best Oral Presentation: Frank Santoriello
2019 RMB-ASM (Spring), Award winner PhD Oral Presentation: Abigail Armstrong
2019 ASM Microbe, Student Travel Award: Rachel Neve

Thesis Defenses

Scott Seitz, Postdoctoral Fellow at Boston University, laboratory of John H. Connor, Ph.D.

Publications

Pharmacologic Depletion of Microglia Increases Viral Load in the Brain and Enhances Mortality in Murine Models of Flavivirus-Induced Encephalitis. Seitz S, Clarke P, Tyler KL. J Virol. 2018 Jul 31;92(16). pii: e00525-18.
Antibiotic Lethality and Membrane Bioenergetics. Voskuil MI, Covey CR, Walter ND. Adv Microb Physiol. 2018;73:77-122.
Gut microbiota from high-risk men who have sex with men drive immune activation in gnotobiotic mice and in vitro HIV infection. Li SX, Sen S, Schneider JM, Xiong KN, Nusbacher NM, Moreno-Huizar N, Shaffer M, Armstrong AJS, Severs E, Kuhn K, Neff CP, McCarter M, Campbell T, Lozupone CA, Palmer BE. PLoS Pathog. 2019 Apr 4;15(4):e1007611.
An exploration of Prevotella-rich microbiomes in HIV and men who have sex with men. Armstrong AJS, Shaffer M, Nusbacher NM, Griesmer C, Fiorillo S, Schneider JM, Preston Neff C, Li SX, Fontenot AP, Campbell T, Palmer BE, Lozupone CA. Microbiome. 2018 Nov 5;6(1):198.
Repression of Nrf2/ARE regulated antioxidant genes and dysregulation of the cellular redox environment by the HIV Transactivator of Transcription. Simenauer A, Assefa B, Rios-Ochoa J, Geraci K, Hybertson B, Gao B, McCord J, Elajaili H, Nozik-Grayck E, Cota-Gomez A. Free Radic Biol Med. 2019 Jun 22;141:244-252.
SODB1 is essential for Leishmania major infection of macrophages and pathogenesis in mice. Davenport BJ, Martin CG, Beverley SM, Orlicky DJ, Vazquez-Torres A, Morrison TE. PLoS Negl Trop Dis. 2018 Oct 29;12(10):e0006921.
Low diversity gut microbiota dysbiosis: drivers, functional implications and recovery. Kriss M, Hazleton KZ, Nusbacher NM, Martin CG, Lozupone CA. Curr Opin Microbiol. 2018 Aug;44:34-40.
Multidimensional analysis of Gammaherpesvirus RNA expression reveals unexpected heterogeneity of gene expression. Oko LM, Kimball AK, Kaspar RE, Knox AN, Coleman CB, Rochford R, Chang T, Alderete B, van Dyk LF, Clambey ET. PLoS Pathog. 2019 Jun 5;15(6):e1007849.
Commensal Staphylococci Influence Staphylococcus aureus Skin Colonization and Disease. Parlet CP, Brown MM, Horswill AR. Trends Microbiol. 2019 Jun;27(6):497-507.
Bacteriophage Resistance Alters Antibiotic-Mediated Intestinal Expansion of Enterococci. Chatterjee A, Johnson CN, Luong P, Hullahalli K, McBride SW, Schubert AM, Palmer KL, Carlson PE Jr, Duerkop BA. Infect Immun. 2019 May 21;87(6).
Activation of the endoplasmic reticulum stress response impacts the NOD1 signaling pathway. Mendez JM, Kolora LD, Lemon JS, Dupree SL, Keestra-Gounder AM. Infect Immun. 2019 May 20

Presentations

Posters Presentations

1st Annual Front Range Microbiome Symposium: Abigail Armstrong
2018 Rocky Mountain Branch-ASM: Norhan Alhajjar
2018 Rocky Mountain Branch-ASM: Rachel Neve
2018 Skaggs School of Pharmacy and Pharmaceutical Sciences Annual Retreat: Rachel Neve
Society for Investigative Dermatology 77th Annual Meeting: Morgan Brown
International Conference on Gram-Positive Pathogens: Morgan Brown
The 18th Rocky Mountain Virology Association Meeting: Sarah Stonedahl
2019 Rocky Mountain Branch-ASM: Haider Manzer
2019 Keystone Symposia-Host and Environment in IBD: Jonathan Mendez
2019 Gordon Research Conference-Salmonella Biology and Pathogenesis: Jonathan Mendez
2019 Keystone Symposia-Positive-Strand RNA Viruses (E2): Zoe O’Donoghue
2019 Colorado Biological Mass Spectrometry Society Meeting: Rachel Neve
2019 ASM Microbe: Frank Santoriello
2019 ASM Microbe: Rachel Neve

Oral Presentations

The 18th Rocky Mountain Virology Association Meeting: Jennifer Berger
The 18th Rocky Mountain Virology Association Meeting: Sarah Stonedahl
Simons Foundation – 3rd Workshop on Statistical and Algorithmic Challenges in Microbiome Data Analysis: Abigail Armstrong
2018 Rocky Mountain Branch-ASM: Haider Manzer
2018 Rocky Mountain Branch-ASM: Frank Santoriello
2018 Annual Colorado Immunology Conference: Sarah Born
2018 MPID Symposium: Sarah Born
2018 Metabolism and Infectious Diseases Symposium: Rachel Neve
2019 Rocky Mountain Branch-ASM: Frank Santoriello
2019 Rocky Mountain Branch ASM: Abigail Armstrong
2019 Rocky Mountain Branch ASM: Katie Arnolds
2019 Rocky Mountain Branch ASM: Rachel Neve
2019 ASM Microbe Rapid Fire Talk: Rachel Neve
Calvin College Biology Seminar: Abigail Armstrong
UC School of Medicine Research Symposium: Hadrian Sparks
Wind River Conference on Prokaryotic Biology: Cydney Johnson

Comprehensive Exams Completed

Cydney Johnson
Norhan Alhajjar
Jonathan Mendez
Morgan Brown
Josh Frost
Brendan Monogue
Matthew Szucs
Monica Graham

New Thesis Laboratories

Haider Manzer – Kelly Doran
Hailey Kinsland – Vanessa Phelan

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