I am interested in the interaction of intracellular pathogens with host cells. I am particularly interested in the organisms known as "amoeba-resistant bacteria." Many of these bacteria are unculturable on laboratory media and thus often go undetected. However, many infect not only amoeba but human cells as well and may be responsible for pneumonia and other infectious diseases. These bacteria exist in both environmental and anthropogenic water sources, although many have not yet been described. The goal of the laboratory is to isolate and identify novel bacteria from amoeba and to characterize their interaction with both amoeba and human host cells utilizing techniques such as DNA sequencing, real-time quantitative PCR, and cellular staining and microscopy, including brightfield, fluorescent, confocal, and transmission electron microscopy techniques.

Other interests are the role of protozoa in sequesting bacteria responsible for foodborne disease as well as the development of novel therapeutics for microbes, including bacteria, fungi, and viruses.

I have been involved in collaborative projects with faculty members in other departments. My interest in bacteria responsible for infectious disease has led to collaboration with members of the Anthropology and Agriscience departments during which we studies the aerobic decomposition of animals and my roles involve the prevention of environmental contamination with disease-causing microorganism as well as biodegradation of euthanizing chemicals. I have also collaborated with members of Chemistry and Mathematics departments to study the importance of various amino acids in enzyme activity. My role in this project was the mutagenesis of the DNA for bases encoding specific amino acids.

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• Alqahtani FM, Handy ST, Sutton CL, Farone MB.  Combining genome-wide gene expression analysis (RNA-seq) and a gene editing platform (CRISPR-Cas9) to uncover the selectively pro-oxidant activity of aurone compounds against Candida albicans.  
• Alqahtani FM, Arivett BA, Taylor ZE, Handy ST, Farone AL, Farone MB. Chemogenomic profiling to understand the antifungal action of a bioactive aurone compound. PLoS One. 2019; 14(12):e0226068. doi: 10.1371/journal.pone.0226068. eCollection 2019.
• Chamberlain NB, Mehari YT, Hayes BJ, Roden CM, Kidane DT, Swehla AJ, Lorenzana-DeWitt MA, Farone AL, Gunderson JH, Berk SG, Farone MB. Infection and nuclear interaction in mammalian cells by 'Candidatus Berkiella cookevillensis', a novel bacterium isolated from amoebae. BMC Microbiol. 2019 May 9;19(1):91. doi: 10.1186/s12866-019-1457-z. 
• Tran T, Chiem K, Jani S, Arivett BA, Lin DL, Lad R, Jimenez V, Farone MB, Debevec G, Santos R, Giulianotti M, Pinilla C, Tolmasky ME. Identification of a small molecule inhibitor of the aminoglycoside 6'-N-acetyltransferase type Ib [AAC(6')-Ib] using mixture-based combinatorial libraries. Int J Antimicrob Agents. 2018 May;51(5):752-761. doi: 10.1016/j.ijantimicag.2018.01.019. 
• Bagsby C, Saha A, Goodin G, Siddiqi S, Farone M, Farone A, Kline PC. Stability of pentobarbital in soil. J Environ Sci Health B. 2018 Mar 4;53(3):207-213. doi: 10.1080/03601234.2017.1406714. Epub 2017 Dec 29. PubMed PMID: 29286885.
• Kidane DT, Arivett BA, Crigler J, Vick EJ, Farone AL, Farone MB. Draft genome sequence of Gardnerella vaginalis strain ATCC 49145 associated with bacterial vaginosis. Genome Announc. 2017 May 4;5(18). doi: 10.1128/genomeA.00286-17.
• Sutton CL, Taylor ZE, Farone MB, Handy ST. Antifungal activity of substituted aurones. Bioorg Med Chem Lett. 2017 Feb 15;27(4):901-903. doi: 10.1016/j.bmcl.2017.01.012. Epub 2017 Jan 6. PubMed PMID: 28094180.
• Park HS, Nelson DE, Taylor ZE, Hayes JB, Cunningham KD, Arivett BA, Ghosh R, Wolf LC, Taylor KM, Farone MB, Handy ST, Farone AL. Suppression of LPS-induced NF-κB activity in macrophages by the synthetic aurone, (Z)-2-((5-(hydroxymethyl) furan-2-yl) methylene) benzofuran-3(2H)-one. Int Immunopharmacol. 2017 Feb;43:116-128. doi: 10.1016/j.intimp.2016.12.004. Epub 2016 Dec 16. 
• Park HS, Vick EJ, Gao Y, He C, Almosnid NM, Farone M, Farone AL. Cis- and Trans-gnetin H from Paeonia suffruticosa suppress inhibitor kappa B kinase phosphorylation in LPS-stimulated human THP-1 cells. J Ethnopharmacol. 2016 Aug 2;189:202-9. doi: 10.1016/j.jep.2016.05.042. Epub 2016 May 16. 
• Mehari YT, Arivett BA, Farone AL, Gunderson JH, Farone MB. Draft genome sequences of two novel amoeba-resistant intranuclear bacteria, "Candidatus Berkiella cookevillensis" and "Candidatus Berkiella aquae". Genome Announc. 2016 Feb 18;4(1). doi: 10.1128/genomeA.01732-15. 
• Mehari YT, Hayes JB, Redding KS, Mariappan PVG, Gunderson JH, Farone AL, Farone MB. Description of 'Candidatus Berkiella aquae' and 'Candidatus Berkiella cookevillensis', two intranuclear bacteria of freshwater amoebae. Int J Syst Evol Microbiol. 2016 Feb;66:536-541. doi: 10.1099/ijsem.0.000750. Epub 2015 Nov 9.
• Vick EJ, Park HS, Huff KA, Brooks KM, Farone AL, Farone MB. Gardnerella vaginalis triggers NLRP3 inflammasome recruitment in THP-1 monocytes. J Reprod Immunol. 2014 Dec;106:67-75. doi: 10.1016/j.jri.2014.08.005. Epub 2014 Sep 16.
• Arivett B, Farone M, Masiragani R, Burden A, Judge S, Osinloye A, Minici C, Degano M, Robinson M, Kline P. Characterization of inosine-uridine nucleoside hydrolase (RihC) from Escherichia coli. Biochim Biophys Acta. 2014 Mar;1844(3):656-62. doi: 10.1016/j.bbapap.2014.01.010. Epub 2014 Jan 25. PubMed PMID: 24473221.
• Pellizzaro, A., Farone, A. Farone, M., Mushi, R. Aguinaga, M., and D. Erenso.2012. Direct laser trapping for measuring the behavior of transfused erythrocytes in a sickle cell anemia patient. Biomed Optics Express. 3:2190-2199.
• Jackson JC, Farone AL, Farone MB. 2011. Bacterial enteropathogens associated with diarrhea in a rural population of Haiti. Res Rep Trop Med. 2:129-133.
• Trim R, Skinner MA, Farone MB, Newsome AL. 2011. Use of PCR to detect Entamoeba gingivalis in diseased gingival pockets and demonstrate its absence in healthy gingival sites.  Parasitol Res.109:857-864.
• Farone, A., Farone, M., Kline, P., and Z. Sinkala. 2010. A practical approach for computing the active site of the ribonucleoside hydrolase of E.coli encoded by rihC. Adv Exp Med Biol. 680:437-443.
• Farone, A., Farone, M., Khaliq, A., Kline, P., Quinn, T., and Z. Sinkala, 2009. Identifying the active site of ribonucleoside hydrolase of E. coli encoded by RihC. Proceedings of the 2009 International Conference on Bioinformatics & Computational Biology: BIOCOMP2009 Vol. I, Editors: H.R. Arabnia and M. Q. Yang, CSREA Press, USA, pp 216-218.
• Sharp R, Farone M.  2007.  Smooth and rough colony variants of Shigella sonnei on Congo Red Agar.  ©Sharpe R and M Farone, authors.  Microbe Library. Licensed for use, ASM MicrobeLibrary 9/28/2007 (linked to http://www.microbelibrary.org).
• Ward, R.L., McNeal, M.M., Farone, M.B., and A.L. Farone. 2007. "The Reoviridae" In: The Mouse in Biomedical Research. (A.Smith, ed.) 2nd Edition. Elsevier Scientific Publishing, Inc., New York. pp. 235-268.
• Berk, S.G., Gunderson, J.H., Newsome A.L., Farone, A.L., Skolasinski, W.S., Hayes, B.J., Redding, K.S., Uddin, N., William, E.L., Reid, A., Ventrice, J.A., Skimmyhorn, J. and Farone, M. B. 2006. Occurrence of infected amoebae in cooling towers environments compared with natural aquatic environments: implications for emerging diseases. Environ. Sci. Technology 40:7440-7444.
• Farone, A. L., O'Donnell, S.M., Brooks, C. S., Young, K. M., Pierce, J., Wetzel, D., Dermody, T. S. and Farone, M. B. 2006. Reovirus serotype-dependent inflammatory cytokine repsonses and replication patterns in a human monocyte cell line. Viral Immunol. 19:546-557
• Farone, A. L., Farone, M. B., McNeal, M., Ward, R. Reoviridae and Epizootic Diarrhea of Infant Mice. 2006. In: The Mouse in Biomedical Research, 2nd Edition, J.G. Fox, C. Newcomer, A. Smith, S. Barthold, F. Quimby, M. Davisson, Eds. Academic Press, NY.
• Farone, M., and Farone, A. 2005. Detecting mold spores in school buildings: An exercise in biodiversity. Am. Biol. Teach. 67: 401-410.
• Newsome AL, Farone MB, Berk SG, Gunderson JH. 2001. Free living amoebae as opportunistic hosts for intracellular bacterial parasites. J Euk Microbiol. Suppl:13-14.
• Desai R, Welsh C, Summy M, Farone M, Newsome AL. 1999.  The potential of in situ hybridization and an immunogold assay to identify Legionella associations with other microorganisms. J Microbiol Meth. 37:155-164.
• Farone A., Frevert CW, Farone MB, Morin MJ, Fields BN, Paulauskis J, Kobzik L. 1996. Serotype-dependent induction of pulmonary neutrophilia and inflammatory cytokine gene expression by reovirus. J Virol. 70:7079-7084.

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