Indiana University Bloomington
Flow Cytometry Core Facility

Publications by FCCF Users

Please acknowledge the IUB FCCF in any publications that utilized facility instrumentation.

SH800 instrument: "This equipment was supported in part, with support from the Indiana Clinical and Translational Sciences Institute, funded in part by Grant Number UL1 TR002529 from the National Institutes of Health, National Center for Advancing Translational Sciences, Clinical and Translational Sciences Award."


Rajalekshmy Shyam, Diego G. Ogando, Moonjung Choi, Paloma B. Liton, and Joseph A. Bonanno. Mitochondrial ROS Induced Lysosomal Dysfunction and Autophagy Impairment in an Animal Model of Congenital Hereditary Endothelial Dystrophy. Invest. Ophthalmol. Vis. Sci. 2021 Sep 2;62(12):15. PMID 34533563.

Targeting Ovarian Cancer Stem Cells by Dual Inhibition of HOTAIR and DNA Methylation. Wang W, Fang F, Ozes A, Nephew KP. Mol Cancer Ther. 2021 Jun;20(6):1092-1101. doi: 10.1158/1535-7163.MCT-20-0826. Epub 2021 Mar 30. PMID: 33785648

Generation of Drosophila attP containing cell lines using CRISPR-Cas9. Mariyappa D, Luhur A, Overton D, Zelhof AC. G3 (Bethesda). 2021 May 8;11(8):jkab161. doi: 10.1093/g3journal/jkab161. Online ahead of print. PMID: 33963853 Free PMC article.

Million, KM, A Bhattacharya, ZM Dinges, S Montgomery, E Smith, and CM Lively. 2021. DNA content variation and SNP diversity within a single population of asexual snails. Journal of Heredity, 112(1):58-66. 

Rajendren S, Dhakal A, Vadlamani P, Townsend J, Deffit SN, Hundley HA. Profiling neural editomes reveals a molecular mechanism to regulate RNA editing during development. Genome Res. 2021 Jan;31(1):27-39. doi: 10.1101/gr.267575.120. PMID: 33355311; PMCID: PMC7849389.


Adapting Drosophila melanogaster Cell Lines to Serum-Free Culture Conditions. Luhur A, Mariyappa D, Klueg KM, Buddika K, Tennessen JM, Zelhof AC. G3 (Bethesda). 2020 Dec 3;10(12):4541-4551. doi: 10.1534/g3.120.401769. PMID: 33028628

EZH2-Mediated Downregulation of the Tumor Suppressor DAB2IP Maintains Ovarian Cancer Stem Cells. Zong X, Wang W, Ozes A, Fang F, Sandusky GE, Nephew KP. Cancer Res. 2020 Oct 15;80(20):4371-4385. doi: 10.1158/0008-5472.CAN-20-0458. Epub 2020 Aug 19. PMID: 32816909

Ashok N, Bauer CE. Evidence of defined temporal expression patterns that lead a gram-negative cell out of dormancy. PLoS Genet. 2020;16(3):e1008660. Published 2020 Mar 23. doi:10.1371/journal.pgen.1008660

Harrington HR, Zimmer MH, Chamness LM, et al. Cotranslational folding stimulates programmed ribosomal frameshifting in the alphavirus structural polyprotein. J Biol Chem. 2020;295(20):6798-6808. doi:10.1074/jbc.RA120.012706

Penn WD, McKee AG, Kuntz CP, et al. Probing biophysical sequence constraints within the transmembrane domains of rhodopsin by deep mutational scanning. Sci Adv. 2020;6(10):eaay7505. Published 2020 Mar 4. doi:10.1126/sciadv.aay7505

Leung JM, Nagayasu E, Hwang YC, et al. A doublecortin-domain protein of Toxoplasma and its orthologues bind to and modify the structure and organization of tubulin polymers. BMC Mol Cell Biol. 2020;21(1):8. Published 2020 Feb 28. doi:10.1186/s12860-020-0249-5


Li W, Yan J, Yu Y. Geometrical reorganization of Dectin-1 and TLR2 on single phagosomes alters their synergistic immune signaling. Proc Natl Acad Sci U S A. 2019;116(50):25106-25114. doi:10.1073/pnas.1909870116 

Diego G. Ogando, Moonjung Choi, Rajalekshmy Shyam, Shimin Li, Joseph A. Bonanno, Ammonia sensitive SLC4A11 mitochondrial uncoupling reduces glutamine induced oxidative stress, Redox Biology, Volume 26, 2019, 101260, ISSN 2213-2317,

Rotelli, M.D., Policastro, R., Bolling, A.M., Killion, A.W., Weinberg, A.J., Dixon, M.J., Zentner, G., Lilly, M., Walczak, C., and Calvi, B.R. (2019) A Cyclin A - Myb-MuvB - Aurora B network regulates the choice between mitotic cycles and polyploid endoreplication cycles. PLoS Genet 15: e1008253. PMC6645565

Takemata, N., Samson, R.Y., Bell, S.D. (2019) Physical and functional compartmentalization of archaeal chromosomes. Cell. 179 (1): 165-179. doi: 10.1016/j.cell.2019.08.036. PMID: 31539494


IL-6 mediates platinum-induced enrichment of ovarian cancer stem cells. Wang Y, Zong X, Mitra S, Mitra AK, Matei D, Nephew KP. JCI Insight. 2018 Dec 6;3(23). pii: 122360. doi: 10.1172/jci.insight.122360. PMID: 30518684

Hustmyer CM, Simpson CA, Olney SG, Rusch DB, Bochman ML, van Kessel JC. Promoter Boundaries for the luxCDABE and betIBA-proXWV Operons in Vibrio harveyi Defined by the Method Rapid Arbitrary PCR Insertion Libraries (RAIL). J Bacteriol. 2018 May 9;200(11). pii: e00724-17. doi: 10.1128/JB.00724-17.

Pu M, Rowe-Magnus DA. A Tad pilus promotes the establishment and resistance of Vibrio vulnificus biofilms to mechanical clearance. NPJ Biofilms Microbiomes. 2018 Apr 23;4:10. doi: 10.1038/s41522-018-0052-7. PMID: 29707230; PMCID: PMC5913241.


Shoemaker WR, Lennon JT (2017) Evolution with a seed bank: the population genetic consequences of microbial dormancy. Evolutionary Applications

Deffit SN, Yee BA, Manning AC, Rajendren S, Vadlamani P, Wheeler EC, Domissy A, Washburn MC, Yeo GW, Hundley HA. The C. elegans neural editome reveals an ADAR target mRNA required for proper chemotaxis. Elife. 2017 Sep 19;6. pii: e28625. doi: 10.7554/eLife.28625. PMID: 28925356

Porter MR, Lindahl SE, Lietzke A, Metzger EM, Wang Q, Henck E, Chen CH, Niu H, Zaleski JM. Metal-mediated diradical tuning for DNA replication arrest via template strand scission. Proc Natl Acad Sci U S A. 2017 Sep 5;114(36):E7405-E7414. doi: 10.1073/pnas.1621349114. Epub 2017 Jul 31. PMID: 28760964

Gibson AK, Delph LF, Lively CM. The two-fold cost of sex: experimental evidence from a natural system. Evol Lett. 2017 May;1(1):6-15. doi: 10.1002/evl3.1. Epub 2017 May 3. PMID: 30233811; PMCID: PMC6089407.

Özes, A.R., Wang, Y., Zong, X. et al. Therapeutic targeting using tumor specific peptides inhibits long non-coding RNA HOTAIR activity in ovarian and breast cancer. Sci Rep 7, 894 (2017) doi:10.1038/s41598-017-00966-3

Wu H-J, On JW, Spandau DF, Tholpady S, Diaz J, Schroeder LJ Offutt CD, Glick A., Plikus M Koyama S. Foley J. Estrogen modulates mesenchymal-epidermal interactions in the adult nipple. Development. 2017 Apr 15;144(8):1498-1509. doi: 10.1242/dev.141630.


Zheng Y, Phillips LJ, Hartman R, An J, Dann CT. Ectopic POU5F1 in the male germ lineage disrupts differentiation and spermatogenesis in mice. Reproduction. 2016 Oct;152(4):363-77. doi: 10.1530/REP-16-0140.

Thete D, Snyder AJ, Mainou B, Danthi P. Reovirus μ1 Protein Affects Infection by Altering Virus-Receptor Interactions.  J Virol. 2016 Sep 28. pii: JVI.01843-16. [Epub ahead of print]

Gibson AK, Xu JY, Lively CM. Within-population covariation between sexual reproduction and susceptibility to local parasites. Evolution. 2016 Sep;70(9):2049-60. doi: 10.1111/evo.13001.

Shidal C, Al-Rayyan N, Yaddanapudi K, Davis KR. Lunasin is a novel therapeutic agent for targeting melanoma cancer stem cells. Oncotarget. 2016 Aug 23. doi: 10.18632/oncotarget.11554. [Epub ahead of print]

Chen S, Stout JR, Dharmaiah S, Yde S, Calvi BR, Walczak CE. Transient Endoreplication Down-Regulates the Kinesin-14 HSET and Contributes to Genomic Instability. Mol Biol Cell. 2016 Aug 3. pii: mbc.E16-03-0159. [Epub ahead of print]

Haley J, Tomar S, Pulliam N, et al. Functional characterization of a panel of high-grade serous ovarian cancer cell lines as representative experimental models of the disease. Oncotarget. 2016; May 31. 7(22):32810-32820. doi:10.18632/oncotarget.9053.

Qi, S., and Calvi, B.R. (2016) Different cell cycle modifications repress apoptosis at different steps independent of developmental signaling in Drosophila. Mol. Biol. Cell, 10.1091/mbc.E16-03-0139

Liu J, He Y, Benmerzouga I, Sullivan WJ Jr, Morrissette NS, Murray JM, Hu K. An ensemble of specifically targeted proteins stabilizes cortical microtubules in the human parasite Toxoplasma gondii. Mol Biol Cell. 2016 Feb 1;27(3):549-71. doi: 10.1091/mbc.E15-11-0754. [link]

Samson RY, Abeyrathne PD, Bell SD. Mechanism of Archaeal MCM Helicase Recruitment to DNA Replication Origins. Mol Cell. 2016 Jan 21;61(2):287-96. doi: 10.1016/j.molcel.2015.12.005. Epub 2015 Dec 24.


Cherbas, L., Hackney, J., Gong, L., Salzer, C., Mauser, E., Zhang, D., & Cherbas, P. (2015). Tools for Targeted Genome Engineering of Established Drosophila Cell Lines. Genetics, 201(4), 1307–1318. [link]

Bradley E. Hiller, Angela K. Berger, Pranav Danthi. Viral gene expression potentiates reovirus-induced necrosis. Virology, Volume 484, October 2015, Pages 386-394, ISSN 0042-6822, [link]

Kah Tan Allen, Helen Chin-Sinex, Thomas DeLuca, Joseph R. Pomerening, Jeremy Sherer, John B. Watkins III, John Foley, Jerry M. Jesseph, Marc S. Mendonca. Dichloroacetate alters Warburg metabolism, inhibits cell growth, and increases the X-ray sensitivity of human A549 and H1299 NSC lung cancer cells. Free Radical Biology and Medicine, Volume 89, December 2015, Pages 263-273, ISSN 0891-5849,

Deepti Thete, Pranav Danthi. Conformational changes required for reovirus cell entry are sensitive to pH. Virology, Volume 483, September 2015, Pages 291-301, ISSN 0042-6822, [link]

Xu S, Ackerman MS, Long H, Bright L, Spitze K, Ramsdell JS, Thomas WK, Lynch M. A Male-Specific Genetic Map of the Microcrustacean Daphnia pulex Based on Single-Sperm Whole-Genome Sequencing. Genetics. 2015 Sep;201(1):31-8. doi: 10.1534/genetics.115.179028. Epub 2015 Jun 26. [link]

Hsin-Jung Wu, Teresa Easwaran, Carlos D. Offutt, Richard Levi Elgar, Dan F. Spandau, Sachiko Koyama, John Foley. Expansion of specialized epidermis induced by hormonal state and mechanical strain. Mechanisms of Development. Volume 136, May 2015, Pages 73-86, ISSN 0925-4773, [link]

Wheeler EC, Washburn MC, Major F, Rusch DB, Hundley HA. Noncoding regions of C. elegans mRNA undergo selective adenosine to inosine deamination and contain a small number of editing sites per transcript. RNA Biol. 2015;12(2):162-74. doi: 10.1080/15476286.2015.1017220. PMID: 25826568; PMCID: PMC4615841.


Merritt, P. M., Nero, T., Bohman, L., Felek, S., Krukonis, E. S. and Marketon, M. M. (Nov. 2014) Yersinia pestis targets neutrophils via complement receptor 3. Cellular Microbiology. doi: 10.1111/cmi.12391 [link]

Gao X, Dong X, Subramanian S, et al. Engineering of Bacillus subtilis Strains To Allow Rapid Characterization of Heterologous Diguanylate Cyclases and Phosphodiesterases. Liu S-J, ed. Applied and Environmental Microbiology. 2014;80(19):6167-6174. doi:10.1128/AEM.01638-14. [link]

Y. Zheng, A. Thomas, C.M. Schmidt, and C.T. Dann. Quantitative detection of human spermatogonia for optimization of spermatogonial stem cell culture. Hum. Reprod. (2014) 29 (11): 2497-2511 first published online September 29, 2014 doi:10.1093/humrep/deu232 [link]

Daniela Vergara, Jukka Jokela, and Curtis M. Lively. (August 2014) Infection Dynamics in Coexisting Sexual and Asexual Host Populations: Support for the Red Queen Hypothesis. The American Naturalist, Vol. 184, No. S1, Disease Ecology and Evolution A Symposium, pp. S22-S30 [link]

Fanslow DA, Wirt SE, Barker JC, Connelly JP, Porteus MH, et al. (2014) Genome Editing in Mouse Spermatogonial Stem/Progenitor Cells Using Engineered Nucleases. PLoS ONE 9(11): e112652. doi:10.1371/journal.pone.0112652 [link]

Yinu Wang, Horacio Cardenas, et al. Epigenetic Targeting of Ovarian Cancer Stem Cells. Cancer Res. 2014 Jul 17 [link]

Washburn MC, Kakaradov B, Sundararaman B, Wheeler E, Hoon S, Yeo GW, and Hundley HA. The dsRBP and inactive editor, ADR-1, utilizes dsRNA binding to regulate A-to-I RNA editing across the C. elegans transcriptome. Cell Reports, Volume 6, Issue 4, 599-607, 06 February 2014. [link]


He K, Marden JN, Quardokus EM, Bauer CE (2013) Phosphate Flow between Hybrid Histidine Kinases CheA3 and CheS3 Controls Rhodospirillum centenum Cyst Formation. PLoS Genet 9(12): e1004002. [link]

Christiane Hassel, Bingqing Zhang, Michael Dixon and Brian R. Calvi. Induction of endocycles represses apoptosis independently of differentiation and predisposes cells to genome instability. Development (2014) 141, 1-12. Epub 2013 Nov 27. [link]

Liu J, Wetzel L, Zhang Y, Nagayasu E, Ems-McClung S, Florens L, Hu K. Novel thioredoxin-like proteins are components of a protein complex coating the cortical microtubules of Toxoplasma gondii.  Eukaryot Cell. 2013 Dec;12(12):1588-99. Epub 2013 Jul 19. [link]

Frederic Pontvianne, Todd Blevins, Chinmayi Chandrasekhara, Iva Mozgová, Christiane Hassel, Olga M F Pontes, Sarah Tucker, Petr Mokros, Veronika Muchová, Jirí Fajkus, Craig S Pikaard. Subnuclear partitioning of rRNA genes between the nucleolus and nucleoplasm reflects alternative epiallelic states. Genes & Development. 07/2013; 27(14):1545-50. [link]


Soper DM, Delph LF, Lively CM. Multiple paternity in the freshwater snail, Potamopyrgus antipodarum. Ecology and Evolution. 2012;2(12):3179-3185. doi:10.1002/ece3.408. [link]

Madren SM, Hoffman MD, Brown PJ, Kysela DT, Brun YV, Jacobson SC. Microfluidic device for automated synchronization of bacterial cells. Anal Chem. 2012 Oct 16;84(20):8571-8. doi: 10.1021/ac301565g. Epub 2012 Oct 3. [link]

Fontaine SN, Bauer SP, Lin X, Poorfarahani S, Ybe JA. Replacement of charged and polar residues in the coiled-coiled interface of huntingtin-interacting protein 1 (HIP1) causes aggregation and cell death. FEBS Letters Volume 586, Issue 19, 21 September 2012, Pages 3030–3036. PMID: 22835334 [link]

Frédéric Pontvianne, Todd Blevins, Chinmayi Chandrasekhara, Wei Feng, Hume Stroud, Steven E. Jacobsen, Scott D. Michaels, and Craig S. Pikaard. Histone methyltransferases regulating rRNA gene dose and dosage control in Arabidopsis. Genes Dev. May 1, 2012 26: 945-957 [link]


Mazumdar M, Sung MH, Misteli T. Chromatin maintenance by a molecular motor protein. Nucleus. 2011 Nov-Dec;2(6):591-600. Epub 2011 Nov 1. [link]

Williams AB, Hetrick KM, Foster PL. 2011. Double-Strand Break Repair and Holliday Junction Processing Are Required for Chromosome Processing in Stationary-Phase Escherichia coli Cells. g3 1:417-426; doi:10.1534/g3.111.001057 [link]

Dewoody R, Merritt PM, Houppert AS, Marketon MM. 2011. YopK regulates the Yersinia pestis type III secretion system from within host cells. Mol Microbiol. Mar;79(6):1445-61. doi: 10.1111/j.1365-2958.2011.07534.x. [link]


Yannick Jacob, Hume Stroud, Chantal LeBlanc, Suhua Feng, Luting Zhou, Elena Caro, Christiane Hassel, Crisanto Gutierrez, Scott D. Michaels and Steven E. Jacobsen. 2010. Two histone H3 lysine 27 methyltransferases, ATXR5 and ATXR6, regulate heterochromatic DNA replication. Nature, doi:10.1038/nature09290. [link]

Williams AB, Hetrick KM, Foster PL. 2010. Interplay of DNA repair, homologous recombination, and DNA polymerases in resistance to the DNA damaging agent 4-nitroquinoline-1-oxide in Escherichia coli. DNA Repair (Amst). October 5; 9(10): 1090–1097. [link]


Dongmei Xing, Joseph A. Bonanno. Hypoxia reduces TGFβ1-induced corneal keratocyte myofibroblast transformation. Mol Vis. 2009; 15: 1827–1834. [link]

Xing D, Bonanno JA. 2009. Effect of cAMP on TGFbeta1-induced corneal keratocyte-myofibroblast transformation. Invest Ophthalmol Vis Sci. 50(2): 626-633.
Epub 2008 Oct 20. PMID: 18936144 [PubMed - indexed for MEDLINE] [link]


journal cover artShu Zhang, Curt Balch, Michael W. Chan, Hung-Cheng Lai, Daniela Matei, Jeanne M. Schilder, Pearlly S. Yan, Tim H-M. Huang and Kenneth P. Nephew. 2008. Identification and Characterization of Ovarian Cancer-Initiating Cell from Primary Human Tumors. Cancer Research 68: 4311-4320. [cover article link]

Hedrick DG, Stout JR, Walczak CE. 2008. Effects of anti-microtubule agents on microtubule organization in cells lacking the kinesin-13 MCAK. Cell Cycle 7(14):2146-56. Epub 2008 May 7. PMID: 18635958 [PubMed - indexed for MEDLINE] [link]

Xing D, Bonanno JA. Effect of cAMP on TGFbeta1-induced corneal keratocyte-myofibroblast transformation. Invest Ophthalmol Vis Sci. 2009 Feb;50(2):626-33. doi: 10.1167/iovs.08-2444. Epub 2008 Oct 20. PMID: 18936144; PMCID: PMC2810623.


Qiang Cheng, Tracy Nguyen, Hongxin Song and Joseph Bonanno (2007) Hypoxia Protects Human Corneal Endothelium from Tertiary Butyl Hydroperoxide and Paraquat-Induced Cell Death In Vitro. Experimental Biology and Medicine 232:445-453. [link]

E. E. OSNAS, C. M. LIVELY. 2006. Host ploidy, parasitism and immune defence in a coevolutionary snail-trematode system. Journal of Evolutionary Biology 19 (1), 42–48. [link]
Eric J. Baack, Kenneth D. Whitney, Loren H. Rieseberg. 2005. Hybridization and genome size evolution: timing and magnitude of nuclear DNA content increases in Helianthus homoploid hybrid species. New Phytologist 167 (2), 623–630. [link]