PUBLICATIONS
A complete listing of publications can be found here: https://www.ncbi.nlm.nih.gov/myncbi/scott.lindner.2/bibliography/public/
As an Associate Professor at Penn State, 2020-Present (17)
Biorxiv Preprints Currently Undergoing Peer Review:
Caloba, C., Sturtz, A., Ramachandran, A. John, L., Malkina, K., Minns, A.M., Lindner, S.E., & Vijay, R.
“Exogenous 4-1BB co-stimulation enhances memory B cell response during malaria.”
Biorxiv Preprint: https://www.biorxiv.org/content/10.1101/2023.09.12.557411v1?ct=
Publications:
54. Patel, D.R., Minns, A.M., Sim, D.G., Field, C.F., Kerr, A.E., Heinly, T., Luley, E.H., Rossi, R.M., Bator, C., Mostafa, I.M., Hafenstein, S.L., Lindner, S.E. # & Sutton, T.C.# "Intranasal virus-particle mimicking vaccine enhances SARS-CoV-2 clearance in the Syrian hamster model." (# co-corresponding authors)
Biorxiv Preprint: https://www.biorxiv.org/content/10.1101/2022.10.27.514054v2
Microbiology Spectrum. Accepted January 17, 2024.
53. Sassmannshausen, J., Bennink, S., Distler, U., Kuchenhoff, J., Minns, A.M., Lindner, S.E., Burda, P-C., Tenzer, S., Gilberger, T.W., & Pradel, G. “Comparative proteomics of vesicles essential for the egress of Plasmodium falciparum gametocytes from red blood cells.” Molecular Microbiology. 2023 Jul 26. Doi: 10.1111/mmi.15125.
52. Godin, M.J.*, Sebastian, A.*, Albert, I#, & Lindner, S.E.# “Long-Read Genome Assembly and Gene Model Annotations for the Rodent Malaria Parasite Plasmodium yoelii 17XNL” (* equal contribution, # co-corresponding authors)
Journal of Biological Chemistry. 2023 May 27: 104871. doi: 10.1016/j.jbc.2023.104871.
51. McGee, J.M., Armache, J.P., & Lindner, S.E. "Specialized Ribosomes of Plasmodium Parasites"
PLoS Pathogens. 2023 Apr 13;19(4):e1011267. doi: 10.1371/journal.ppat.1011267. Invited Review.
50. Zhang, K., Wang, Z., Liu, H., Perea-Lopez, N., Ranasinghe, J., Bepete, G., Minns, A.M., Rossi, R.M., Lindner, S.E., Huang, X., Terrones, M., & Huang, S. “Understanding the excitation wavelength dependence and thermal stability of SARS-CoV-2 receptor-binding domain using surface-enhanced Raman scattering and machine learning.”
ACS Photonics. 2022 Aug 25; 9,9,2963-2972. doi.org/10.1021/acsphotonics.2c00456
49. Lamb, I., Rios, K.T., Shukla, A., Ahiya, A.I., Morrisey, J.M., Lindner, S.E., Mather, M.W., & Vaidya, A. “Mitochondrially targeted proximity biotinylation and proteomic analysis in Plasmodium falciparum.”
PLoS One. 2022 Aug 19;17(8):e0273357. doi.org/10.1371/journal.pone.0273357.
48. Clements, R.L., Morano, A.A., Narvarro, F.M., McGee, J.P., Du, E.W., Streva, V.A., Lindner, S.E., & Dvorin, J.D.
“A novel basal complex protein is essential for the maturation of transmission-stage malaria parasites.”
PNAS. 2022 Aug 23; 119*34):e2204167119. doi.org/10.1073/pnas.2204167119
47. Marques-da-Silva, C., Peissig, K., Walker, M.P., Shiau, J. Kyle, D.E., Vijay, R., Lindner, S.E. & Kurup, S.P.
“Direct Type I Interferon Signaling in Hepatocytes Controls Malaria.”
Cell Reports. 2022, July 19. Vol 40, Issue 3, 111098. https://doi.org/10.1016/j.celrep.2022.111098
46. Gontu, A., Marlin, E.A., Ramasamy, S., Neerukonda, S., Anil, G., Morgan, J., Quraishi, M., Chen, C., Boorla, V.S., Nissly, R.H., Jakka, P., Chothe, S.K., Ravichandran, A., Kodali, N., Amirthalingam, S., LaBella, L., Kelly, K., Natesan, P., Minns, A.M., Rossi, R.M., Werner, J.R., Hovingh, E., Lindner, S.E., Tewari, D., Kapur, V., Vandegrift, K.J., Maranas, C.D., Nair, M. & Kuchipudi, S.V. “Development and validation of indirect enzyme-linked immunosorbent assays for detecting antibodies to SARS-CoV-2 in cattle, swine, and chicken.”
Viruses. 2022 14(7), 1358; doi.org/10.3390/v14071358
45. Rios, K.T., Dickson, T., & Lindner, S.E. “Sulfadiazine enrichment of gametocytes causes unexpected effects on Plasmodium transmission.”
mSphere. 2022 May 19; e0010622. doi: 10.1128/msphere.00106-22.
44. Hart, K.J., Power, B.J.*, Rios, K.T.*, Sebastian, A., & Lindner, S.E. “The Plasmodium NOT1-G Paralogue Acts Is an Essential Regulator of Sexual Stage Maturation and Parasite Transmission.”
PLOS Biology. 2021 Oct 21; 19(10): e3001434. (* equal contribution) doi: 10.1371/journal.pbio.3001434
43. Kumar, R., Christensen, N.D., Kaddis Maldonado, R.J., Bewley, M.C., Ostman, A., Sudol, M., Chen, E.C., Buchkovich, N.W., Gontu, A., Surendran Nair, M., Nissly, R.H., Minns, A.M., Kapur, V., Rossi, R., Kuchipudi, S.V., Lindner, S.E., Parent, L.J., Flanagan, J.M., & Buchkovich, N.J. "Monoclonal Antibodies to S and N SARS-CoV-2 Proteins as Probe to Assess Structural and Antigenic Properties of Coronaviruses."
Viruses. 2021 Sep 22; 13(10):1899. doi: 10.3390/v13101899
42. Holyk, A.*, Lindner A.H.*, Lindner S.E., & Shippert, B.W. “Compatibility during simulated Y-site administration of Normosol-R with selected ICU infusions used in Coronavirus Disease 2019 (COVID-19 patients.”
American Journal of Health-System Pharmacy. 2021 Aug 14;zxab329. (* equal contribution) doi: 10.1093/ajhp/zxab329
41. Godin, M.J. & Lindner, S.E. “NEB Monarch HMW DNA Extraction Kit improves sample preparation for Oxford Nanopore Technologies sequencing of malaria parasites.” (Note: Non-Peer Reviewed Publication)
New England Biolabs Application Note. July 15, 2021. https://tinyurl.com/NEB-HMW-Nanopore
40. Gontu, A.*, Srinivasan, S.*, Salazar, E.*, Nair, M.S., Nissly, R.H., Greenawalt, D., Bird, I.M., Herzog, C., Ferrari, M.J., Poojary, I., Katani, R., Lindner, S.E., Minns, A.M., Rossi, R., Christensen, P.A., Castillo, B., Chen, J., Eagar, T.N., Yi, X., Zhao, P., Leveque, C., Olsen, R.J., Bernard, D.W., Gollihar, J., Kuchipudi, S.V.#, Musser, J.M. #, & Kapur, V. # “Limited window for donation of convalescent plasma with high live-virus neutralizing antibodies for COVID-19 immunotherapy.”
Communications Biology. 2021 Feb; 4:267 doi: 10.1038/s42003-021-01813-y. (* equal contribution, # co-corresponding authors)
39. Bowman, L.M.*, Finger, L.E.*, Hart, K.J., & Lindner, S.E. “Definition of Constitutive and Stage-Enriched Promoters in the Rodent Malaria Parasite, Plasmodium yoelii.”
Malaria Journal. 2020 Nov 23; 19(1):424. Doi: 10.1186/s12936-020-03498-2. (* equal contribution)
38. Gray, S.L., Tiedge, T.M., Butkus, J.M., Earp, T.J., Lindner, S.E., & Roy, R. “Determination of Human Identity from Anopheles stephensi Mosquito Blood Meals Using Direct Amplification and Massively Parallel Sequencing.”
Forensic Science International: Genetics. 2020 Sep; 48:102347. Doi: 10.1016/j.fsigen.2020.102347.
As an Assistant Professor at Penn State, 2013-2020 (20)
37. Rios, K.T. & Lindner S.E.
“Protein-RNA Interactions Important for Plasmodium Transmission.”
PLoS Pathogens. 2019 Dec 26; 15(12):e1008095. doi: 10.1371/journal/ppat.1008095. Invited Review.
36. Lindner, S.E.*, #, Swearingen, K.E.*, Shears, M., Walker, M.P., Vrana, E.N., Hart, K.J., Minns, A.M., Sinnis, P., Moritz, R.L., & Kappe, S.H.I. #
“Transcriptomics and proteomics reveal two waves of translational repression during the maturation of malaria parasite sporozoites.”
Nature Communications. 2019 Oct 31; 10(1):4964. doi: 10.1038/s42467-019-12936-6.
(* equal contribution, # joint supervision/co-corresponding authors)
Addendum: 2022 Jan 6. https://www.nature.com/articles/s41467-021-27767-7
35. Lee, M., Lindner, S.E., Marco-Rubio, J.J., & Llinás, M.
“Cutting back malaria: CRISPR/Cas9 genome editing of Plasmodium.”
Briefings in Functional Genomics. 2019 Jul 29. pii:elz012. 1-9. doi: 10.1093/bfgp/elz012. Invited Review.
34. Vivax Sporozoite Consortium (Alphabetical): Ansell, B., Charnaud, S., Duffy, M., Emery-Corbin, S.J., Flannery, E., Jex, A., Kappe, S.H., Koepfli, C., Mikolajczak, S., Muller, I., Lerch, A., Lindner, S.E., Merrienne, N., Patrapuvich, R., Petter, M., Sattabongkot, J., Smith, J., and Swearingen, K.E..
“Transcriptome and histone epigenome of Plasmodium vivax salivary-gland sporozoites point to tight regulatory control and mechanisms for liver-stage differentiation in relapsing malaria.”
International Journal for Parasitology. 2019 Jun; 49(8):501-513 doi: 10.1016/j.ijpara.2019.02.007.
33. Walker M.P., & Lindner, S.E.
“Ribozyme-Mediated, Multiplex CRISPR Gene Editing and CRISPR interference (CRISPRi) in rodent-infectious Plasmodium yoelii.”
Journal of Biological Chemistry. 2019 Jun 14; 294(24):9555-9566. doi: 10.1074/jbc.RA118.007121
**Featured as one of the Top 50 most viewed JBC papers in May and June 2019.
32. Hart, K.J., Oberstaller, J., Walker, M.P., Minns, A.M., Kennedy, M.F., Padykula, I., Adams, J.H., & Lindner, S.E.
“Plasmodium male gametocyte development and transmission are critically regulated by the two putative deadenylases of the CAF1/CCR4/NOT Complex.”
PLoS Pathogens. 2019 Jan 31; 15(1):e1007164. 1-28.
**Selected as the week’s Featured Research Article.
31. Swearingen, K.E. & Lindner S.E.
“Plasmodium Parasites Viewed Through Proteomics”
Trends in Parasitology. 2018 Nov; 37(11): 945-960. doi: 10.1016/j.pt.2018.08.003. Invited Review.
**Featured as the Cover Image/Publication for November 2018.
30. Bennink, S., von Bohl, A., Ngwa, C., Henschel, L., Kuehn, A., Pilch, N., Weibbach, T., Rosinksi, A.N., Scheuermayer, M., Repnik, U., Przyborski, J.M., Minns, A.M., Orchard, L.M., Lindner, S.E., Griffiths, G., Llinás , M., & Pradel, G.
“A seven-helix protein constitutes stress granules crucial for regulating translation during human-to-mosquito transmission of Plasmodium falciparum.”
PLoS Pathogens. 2018 Aug 22; 14(8):e1007249. 1-36.
29. Liang, X., Hart, K.J., Gang, D., Siddiqui, F.A., Sebastian, A., Li, X., Albert, I., Miao, J., Lindner, S.E., & Cui, L.
“Puf3 participates in ribosomal biogenesis in malaria parasites.”
Journal of Cell Science. 2018 Mar 26; 131(6). doi: 1.1242/jcs.212597.
28. Hahn, W.O., Butler, N.S., Lindner, S.E., Akilesh, H.M., Sather, D.N., Kappe, S.H.I., Hamerman, J.A., Gale Jr., M., Liles, W. C., & Pepper, M.
“cGAS-mediated control of blood-stage malaria promotes Plasmodium-specific germinal center responses.”
JCI Insight. 2018 Jan 25;3(2). 1-19. doi: 10.1172/jci.inisight.94132
27. Minns, A.M., Hart, K.J., Subramanian, S., Hafenstein, S., & Lindner S.E.
“Nuclear, Cytosolic, and Surface Localized Poly(A)-Binding Proteins of Plasmodium yoelii.”
mSphere. 2018 Jan 10; 3(1). 1-13. pii:e00435-17. doi: 10.1128/mSphere.00435-17.
26. Zander, R.A., Vijay, R., Pack, A.D., Guthmiller, J.J., Graham, A.C., Lindner, S.E., Vaughan, A.M., Kappe, S.H., & Butler N.S.
“Th1-like Plasmodium-specific memory CD4+ T cells support humoral immunity.”
Cell Reports. 2017 Nov 14; 21(7): 1839-1852. doi: 10.1016/j.celrep.2017.10.077
25. Munoz, E. E., Hart, K. J., Walker, M. P., Kennedy, M. F., Shipley, M. M., & Lindner, S.E.
“ALBA4 modulates its stage-specific interactions and specific mRNA fates during Plasmodium yoelii growth and transmission.”
Molecular Microbiology. 2017 Oct; 106(2):266-284. doi: 10.1111/mmi.13762
24. Swearingen, K. E., Lindner, S.E., Flannery, E., Vaughan A.M., Patrapuvich, R., Kopfli, C., Muller, I., Jex, A., Moritz, R.L., Kappe, S.H.I., Sattabongkot, J. & Mikolajczak, S.
“Proteogenomic analysis of the total and surface-exposed proteomes of Plasmodium vivax salivary gland sporozoites.”
PLoS Neglected Tropical Diseases. 2017 Jul 31; 11(7):e0005791. 1-36. doi: 10.1371/journal/pntd.005791.
23. El-Manzalawy, Y., Munoz, E.M., Lindner, S.E.*, & Honavar, V.*
“PlasmoSEP: Predicting Surface Exposed Proteins on the Malaria Parasite Using Semi-supervised, Self-training, and Expert-annotated Data.”
Proteomics. 2016 Dec; 16(23):2967-2976.
(* joint supervision/co-corresponding authors)
22. Huang, W., Hulverson, M.A., Zhang, Z., Choi, R., Hart, K.J., Kennedy, M., Subba Rao Vidadala, R., Maly, D.J., Van Voorhis, W.C., Lindner, S.E., Fan, E., & Ojo, K.K.
“5-Aminopyrazole-4-carboxamide analogues are selective inhibitors of Plasmodium falciparum microgametocyte exflagellation and potential malaria transmission blocking agents.”
Bioorganic & Medicinal Chemistry Letters. 2016 Nov 15; 26 (22):5487-5491. doi: 10.1016/j.bmcl.2016.10.014
21. Swearingen, K.E.*, Lindner, S.E.*, Shi, L., Shears, M.J., Harupa, A., Hopp, C.S., Vaughan, A.M., Springer, T.A., Moritz, R.L., Kappe, S.H., & Sinnis, P.
“Interrogating the Plasmodium Sporozoite Surface: Identification of Surface-Exposed Proteins and Demonstration of Glycosylation on CSP and TRAP by Mass Spectrometry-Based Proteomics.”
PLoS Pathogens. 2016 Apr 29; 12(4):e1005606. 1-32. doi: 10.1371/journal.ppat.1005606.
(* equal contribution)
**Recognized as one of the “Top 50 Most Downloaded” articles of the year for PLoS Pathogens.
20. Reddy, B.P.N., Shrestha, S., Hart, K.J., Liang, X., Kemirembe, K., Cui, L., & Lindner, S.E.
“A bioinformatic survey of RNA-binding proteins in Plasmodium.”
BMC Genomics. 2015 Nov 2; 16:890. 1-26. doi: 10.1186/s12864-015-2092-1
19. Mikolajczak, S.A.*, Vaughan, A.V.*, Kangwanrangsan, N., Yimamnuaychok, N., Rezakhani, N., Fishbauger, M., Lakshmanan, V., Singh, N., Kaushansky, A., Baldwin, M., Lindner, S.E., Adams, J.H., Prachumsri, J., & Kappe, S.H.
“Plasmodium vivax liver stage development and hypnozoite persistence in human liver-chimeric mice.”
Cell Host & Microbe. 2015 Apr 8; 17(4): 526-35. doi: 10.1016/j.chom.2015.02.011. (* equal contribution)
18. Cui, L., Lindner, S., & Miao, J.
“Translational regulation during stage transitions in malaria parasites.”
The Annals of the New York Academy of Sciences. 2015 Apr; 1342:1-9 doi: 10.1111/nyas.12573. Invited Review.
As a Post-Doc/Staff Scientist at Seattle Biomedical Research Institute, 2009-2013 (11)
17. Harupa, A., Sack, B., Lakshmanan, V., Arang, N., Douglass, A., Oliver, B., Stuart, A., Sather, D.N., Lindner, S.E., Hybiske, K., Torii, M., & Kappe, S.H.I.
“SSP3 is a novel Plasmodium yoelii sporozoite surface protein with a role in gliding motility.”
Infection and Immunity. 2014 Nov; 82(11): 4643-4653. doi: 10.1128/IAI.01800-14.
16. Lindner, S.E., Sartain, M.J., Hayes, K., Harupa, A., Moritz, R.L., Kappe, S.H.I. & Vaughan, A.M.
“Enzymes involved in plastid-targeted phosphatidic acid synthesis are essential for Plasmodium yoelii liver-stage development.”
Molecular Microbiology. 2014 Feb; 91(4): 679-693. doi: 10.1111/mmi.12485
**Featured as the Cover Image/Publication
15. Mailu, B.M., Ramasamay, G., Mudeppa, D.G., Li, L., Lindner, S.E., Peterson, M.J., DeRocher, A.E., Kappe, S.H.I., Rathod, P.K., & Gardner, M.J.
"A nondiscriminating glutamyl-tRNA synthetase in the Plasmodium apicoplast: the first enzyme in an indirect aminoacylation pathway.”
Journal of Biological Chemistry. 2013 Nov 8; 288(45):32539-52. doi: 10.1074/jbc.M113.507467
14. Pei, Y. *, Miller, J.L. *, Lindner, S.E., Vaughan, A.M., Torii, M., & Kappe, S.H.I.
“Plasmodium yoelii inhibitor of cysteine proteases is exported to exomembrane structures and interacts with yoelipain-2 during asexual blood-stage development.”
Cellular Microbiology. 2013 Sep; 15(9):1508-1526. doi: 10.1111/cmi.12124.
(* equal contribution)
13. Lindner, S.E., Mikolajczak, S.A., Vaughan, A.M., Moon, W., Joyce, B.R., Sullivan, W.J., & Kappe, S.H.I.
“Perturbations of Plasmodium Puf2 expression and RNA-seq of Puf2-deficient sporozoites reveal a critical role in maintaining RNA homeostasis and parasite transmissibility.”
Cellular Microbiology. 2013 Jul; 15(7):1266-1283. doi: 10.1111/cmi.12116.
12. Lindner, S.E.*, Swearingen, K.E.*, Harupa, A., Vaughan, A.M., Sinnis, P., Moritz, R.L., & Kappe, S.H.I.
“Total and putative surface proteomics of malaria parasite salivary gland sporozoites.”
Molecular and Cellular Proteomics. 2013 May; 12(5): 1127-1143. doi:10.1074/mcp.M112.024505
(* equal contribution)
11. Kennedy, M., Fishbaugher, M.E., Vaughan, A.M., Patrapuvich, R., Boonhok, R., Yimamnuaychok, N., Rezakhani, N., Metzger, P., Ponpuak, M., Sattabongkot, J., Kappe, S.H., Hume, J.C.C., & Lindner, S.E.
“A rapid and scalable density gradient purification method for Plasmodium sporozoites.”
Malaria Journal. 2012 Dec 17; 11:421. 1-10. doi: 10.1186/1475-2875-11-421.
10. Vaughan, A.M., Mikolajczak, S. A., Camargo, N., Lakshmanan, V., Kennedy, M., Lindner, S.E., Miller, J.L., & Kappe, S.H.
“A transgenic Plasmodium falciparum NF54 strain that expresses GFP-luciferase throughout the parasite life cycle.”
Molecular and Biochemical Parasitology. 2012 Dec;186(2): 143-147. doi: 10.1016/j.molbiopara.2012.10.004.
9. Lindner, S.E.*, Miller, J.L.*, & Kappe, S.H.
“Malaria parasite pre-erythrocytic infection: preparation meets opportunity.”
Cellular Microbiology. 2012 Mar; 14(3): 316-324. doi: 10.1111/j.1462-5822.2011.01734.x.
(* equal contribution) Invited Review.
8. Lindner, S.E., Llinás, M., Keck, J.L., & Kappe, S.H.
“The primase domain of PfPrex is a proteolytically matured, essential enzyme of the apicoplast.”
Molecular and Biochemical Parasitology. 2011 Dec; 180(2): 69-75. doi: 10.1016/j.molbiopara.2011.08.002.
7. Aly, A.S.I, Lindner, S.E., MacKellar, D.C., Peng, X., & Kappe, S.H.
“SAP1 is a critical post-transcriptional regulator of infectivity in malaria parasite sporozoite stages.”
Molecular Microbiology. 2011 Feb; 79(4): 929-939. doi: 10.1111/j.1365-2958.2010.07497.x.
As a Post-Doc at the University of Wisconsin, 2007-2009 (3)
6. Kolonko, E.M, Albaugh, B.N., Lindner, S.E., Chen, Y, Satyshur, K.A., Keck, J.L., Kaufman, P.D., & Denu, J.M.
“Catalytic activation of histone acetyltransferase Rtt109 by a histone chaperone.”
Proceedings of the National Academy of Sciences USA. 2010 Nov 23; 107(47): 20275-20280. doi: 10.1073/pnas.1009860107.
5. Lindner, S.E., De Silva, E., Keck, J.L. & Llinás, M.
“Structural determinants of DNA binding by a P. falciparum ApiAP2 transcriptional regulator.”
Journal of Molecular Biology. 2010 Jan 22; 395(3): 558-567. doi: 10.1016/j.jmb.2009.11.004.
4. Berndsen, C.E., Tsubota, T., Lindner, S.E., Lee, S., Holton, J.M., Kaufman, P.D., Keck, J.L., & Denu, J.M.
“Molecular functions of the histone acetyltransferase chaperone complex Rtt109-Vps75.”
Nature Structural and Molecular Biology. 2008 Sep; 15(9): 948-956.
As a Ph.D. Student at the University of Wisconsin, 2001-2006 (3)
3. Lindner, S.E., Zeller, K., Schepers, A., & Sugden, B.
“The affinity of EBNA1 for its origin of DNA synthesis is a determinant of the origin’s replicative efficiency.”
Journal of Virology. 2008 Jun; 82(12): 5693-5702. doi: 10.1128/JVI.00332-08.
2. Lindner, S.E. & Sugden, B.
“The plasmid replicon of Epstein-Bar Virus: mechanistic insights into efficient, licensed, extrachromosomal replication in human cells.”
Plasmid. 2007 Jul; 58(1): 1-12. Invited Review.
1. Wang, J.*, Lindner, S.E.*, Leight, E.R., & Sugden, B. “Essential elements of a licensed, mammalian plasmid origin of DNA synthesis.”
Molecular and Cellular Biology. 2006 Feb; 26(3): 1124-1134.
(* equal contribution)