Bindley Bioscience Center

COVID-19 Research Preparedness

Use the help of Bindley experts in your COVID-19 research

The Bindley Bioscience Center (BBC) is a multidisciplinary life-sciences research facility providing access to the unique expertise of the resident scientists, as well as numerous biochemistry, biophysics, bioengineering, and bioinformatics tools. BBC serves the broad community of Purdue scientists, offering not only unique instruments and infrastructure but also skills and competence of the resident faculty, facility directors, and technicians with multiple years of experience in biomolecular imaging, cytometry, various spectroscopies, and biological data analysis technologies. BBC is distinctively positioned to aid and support the Purdue researchers in their COVID-19-related studies.

Our research resources, techniques, and methods relevant to COVID-19 include  

Proteomics Facility 

  • Plasma, tissue cell lysates or body fluids proteome analysis performed in the context of diagnostic biomarkers, evaluation of disease progression, and drug development for SARS-CoV-1, SARS-CoV-2, and MERS coronaviruses [1,2]
  • Identification and analysis of peptides composing the viral proteins
  • Identification and quantitation of antibodies in plasma.
  • Analysis and identification of nucleocapsid proteins [3]

Metabolite Profiling Facility 

  • Identification of various viruses using MALDI-TOF techniques [4]
  • Identification of in vitro metabolites of various anti-viral drugs relevant for COVID-19 treatment
  • High throughput small molecule (lipids and metabolites) biomarker discovery [5–7]
  • Metabolomic profiling, comparative analysis, and pathway analysis of t issue cell lysates or body fluids [8,9]
  • Evaluation and quantification of lipid metabolism in cells/tissues of patients exposed/recovered from SARS-CoV or other respiratory infections [10,11]
  • Mass spectrometry imaging of metabolites, lipids, peptides, and proteins in tissues exposed to viruses [12,13]

Imaging Facility 

Note: all the specimens must be fixed and labeled before they are brought to the facility

  • Spatial localization, and three-dimensional visualization of proteins involved in SARS-CoV-1, SARS-CoV-2 and MERS replication studies (ACE2, CD26, TMPRSS2) [14]
  • Identification of SARS-CoV-2 in Vero E6 cells [15].
  • SARS-CoV infection studies using a multi-color TIRF system evaluating cellular attachment, internalization, replication, and release stages [16].
  • Localization and colocalization of expression sites of the viral proteins [17]

Flow Cytometry and Cell Separation Facility 

  • Quantification of expression of proteins involved in SARS-CoV-1, SARS-CoV-2 and MERS cell entry (ACE2, CD26, TMPRSS2) [18–20]
  • Cytometry cytokine bead assays for studying “cytokine storm” and immune responses in COVID-19 [21]
  • Analysis of immunophenotypic changes due to COVID-19 infection and detection of cells responsible for “cytokine storm” [22,23]


Genomics Facility (contact Phillip San Miguel at pmiguel@purdue.edu)

  • RNA and protein quantification/electrophoretic sizing using Agilent Bioanalyzer and ThermoFisher Qubit instruments
  • Illumina library quantitation and pooling to facilitate high throughput sequencing
  • 10X Genomics single-cell transcriptome library construction for the analysis of the immune and inflammatory pathways activated during the COVID-19 infection [24].


Computational biology, bioinformatics and machine learning (contact Bartek Rajwa at brajwa@purdue.edu)

  • Help with statistical analysis of research and clinical data.
  • Power analysis and experimental design for research and clinical studies. Statistical assistance with IRB completion related to COVID-19 studies.
  • Implementation and use of algorithms allowing search for unique biomarkers of COVID-19 using mass spec data
  • Data reduction, unsupervised learning, and data visualization of research and clinical data. Classification and feature selection


Gene Editing and Transgenic Mouse Facilities (contact Wen-hung Wang at wwang@purdue.edu and Wen-hung Wang at halletje@purdue.edu )

  • Help and assistance with acquiring and maintaining animals used as models for SARS and MERS research, such as K18-hACE2 transgenic mice expressing human ACE2 receptor [25], hDPP4-transgenic mice expressing human CD26 [26], and engineered DPP4-mouse [27]
  • Development of primary cell models suitable for SARS-CoV-1, SARS-CoV-2 and MERS studies.

References

[1] Chen J-H, Chang Y-W, Yao C-W, Chiueh T-S, Huang S-C, Chien K-Y, et al. Plasma proteome of severe acute respiratory syndrome analyzed by two-dimensional gel electrophoresis and mass spectrometry. PNAS 2004;101:17039–44. https://doi.org/10.1073/pnas.0407992101.

[2] Kang X, Xu Y, Wu X, Liang Y, Wang C, Guo J, et al. Proteomic fingerprints for potential application to early diagnosis of severe acute respiratory syndrome. Clin Chem 2005;51:56–64. https://doi.org/10.1373/clinchem.2004.032458.

[3] Mark J, Li X, Cyr T, Fournier S, Jaentschke B, Hefford MA. SARS coronavirus: Unusual lability of the nucleocapsid protein. Biochem Biophys Res Commun 2008;377:429–33. https://doi.org/10.1016/j.bbrc.2008.09.153.

[4] Xiu L, Zhang C, Wu Z, Peng J. Establishment and Application of a Universal Coronavirus Screening Method Using MALDI-TOF Mass Spectrometry. Front Microbiol 2017;8. https://doi.org/10.3389/fmicb.2017.01510.

[5] Franco J, Ferreira C, Sobreira TJP, Sundberg JP, HogenEsch H. Profiling of epidermal lipids in a mouse model of dermatitis: Identification of potential biomarkers. PLOS ONE 2018;13:e0196595. https://doi.org/10.1371/journal.pone.0196595.

[6] Xie Z, Gonzalez LE, Ferreira CR, Vorsilak A, Frabutt D, Sobreira TJP, et al. Multiple reaction monitoring profiling (MRM-profiling) of lipids to distinguish strain-level differences in microbial resistance in Escherichia coli. Anal Chem 2019;91:11349–54. https://doi.org/10.1021/acs.analchem.9b02465.

[7] Yannell KE, Ferreira CR, Tichy SE, Cooks RG. Multiple reaction monitoring (MRM)-profiling with biomarker identification by LC-QTOF to characterize coronary artery disease. Analyst 2018;143:5014–22. https://doi.org/10.1039/C8AN01017J.

[8] Ferreira CR, Yannell KE, Mollenhauer B, Espy RD, Cordeiro FB, Ouyang Z, et al. Chemical profiling of cerebrospinal fluid by multiple reaction monitoring mass spectrometry. Analyst 2016;141:5252–5. https://doi.org/10.1039/C6AN01618A.

[9] Adamson SX-F, Wang R, Wu W, Cooper B, Shannahan J. Metabolomic insights of macrophage responses to graphene nanoplatelets: Role of scavenger receptor CD36. PLOS ONE 2018;13:e0207042. https://doi.org/10.1371/journal.pone.0207042.

[10] Woods PS, Doolittle LM, Rosas LE, Joseph LM, Calomeni EP, Davis IC. Lethal H1N1 influenza A virus infection alters the murine alveolar type II cell surfactant lipidome. American Journal of Physiology-Lung Cellular and Molecular Physiology 2016;311:L1160–9. https://doi.org/10.1152/ajplung.00339.2016.

[11] Zheng Y-Y, Ma Y-T, Zhang J-Y, Xie X. COVID-19 and the cardiovascular system. Nat Rev Cardiol 2020;17:259–60. https://doi.org/10.1038/s41569-020-0360-5.

[12] Cazares LH, Van Tongeren SA, Costantino J, Kenny T, Garza NL, Donnelly G, et al. Heat fixation inactivates viral and bacterial pathogens and is compatible with downstream MALDI mass spectrometry tissue imaging. BMC Microbiology 2015;15:101. https://doi.org/10.1186/s12866-015-0431-7.

[13] Schleyer G, Shahaf N, Ziv C, Dong Y, Meoded RA, Helfrich EJN, et al. In plaque-mass spectrometry imaging of a bloom-forming alga during viral infection reveals a metabolic shift towards odd-chain fatty acid lipids. Nat Microbiol 2019;4:527–38. https://doi.org/10.1038/s41564-018-0336-y.

[14] Zhou P, Yang X-L, Wang X-G, Hu B, Zhang L, Zhang W, et al. A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature 2020;579:270–3. https://doi.org/10.1038/s41586-020-2012-7.

[15] Ogando NS, Dalebout TJ, Zevenhoven-Dobbe JC, Limpens RW, Meer Y van der, Caly L, et al. SARS-coronavirus-2 replication in Vero E6 cells: replication kinetics, rapid adaptation and cytopathology. BioRxiv 2020:2020.04.20.049924. https://doi.org/10.1101/2020.04.20.049924.

[16] Millet JK, Kien F, Cheung C-Y, Siu Y-L, Chan W-L, Li H, et al. Ezrin Interacts with the SARS Coronavirus Spike Protein and Restrains Infection at the Entry Stage. PLOS ONE 2012;7:e49566. https://doi.org/10.1371/journal.pone.0049566.

[17] Geng H, Liu Y-M, Chan W-S, Lo AW-I, Au DM-Y, Waye MM-Y, et al. The putative protein 6 of the severe acute respiratory syndrome-associated coronavirus: Expression and functional characterization. FEBS Letters 2005;579:6763–8. https://doi.org/10.1016/j.febslet.2005.11.007.

[18] Matsuyama S, Nao N, Shirato K, Kawase M, Saito S, Takayama I, et al. Enhanced isolation of SARS-CoV-2 by TMPRSS2-expressing cells. PNAS 2020;117:7001–3. https://doi.org/10.1073/pnas.2002589117.

[19] Qing E, Hantak MP, Galpalli GG, Gallagher T. Evaluating MERS-CoV entry pathways. MERS Coronavirus 2020:9–20. https://doi.org/10.1007/978-1-0716-0211-9_2.

[20] Yan R, Zhang Y, Li Y, Xia L, Guo Y, Zhou Q. Structural basis for the recognition of SARS-CoV-2 by full-length human ACE2. Science 2020;367:1444–8. https://doi.org/10.1126/science.abb2762.

[21] Moore BJB, June CH. Cytokine release syndrome in severe COVID-19. Science 2020. https://doi.org/10.1126/science.abb8925.

[22] Cossarizza A, Biasi SD, Guaraldi G, Girardis M, Mussini C. SARS-CoV-2, the virus that causes COVID-19: cytometry and the new challenge for global health. Cytometry Part A 2020;in press. https://doi.org/10.1002/cyto.a.24002.

[23] Wang X, Xu W, Hu G, Xia S, Sun Z, Liu Z, et al. SARS-CoV-2 infects T lymphocytes through its spike protein-mediated membrane fusion. Cell Mol Immunol 2020:1–3. https://doi.org/10.1038/s41423-020-0424-9.

[24] Liao M, Liu Y, Yuan J, Wen Y, Xu G, Zhao J, et al. The landscape of lung bronchoalveolar immune cells in COVID-19 revealed by single-cell RNA sequencing. MedRxiv 2020:2020.02.23.20026690. https://doi.org/10.1101/2020.02.23.20026690.

[25] McCray PB, Pewe L, Wohlford-Lenane C, Hickey M, Manzel L, Shi L, et al. Lethal infection of K18-hACE2 mice infected with severe acute respiratory syndrome coronavirus. Journal of Virology 2007;81:813–21. https://doi.org/10.1128/JVI.02012-06.

[26] Kim J, Yang YL, Jeong Y, Jang Y-S. Middle east respiratory syndrome-coronavirus infection into established hDPP4-transgenic mice accelerates lung damage via activation of the pro-inflammatory response and pulmonary fibrosis. Journal of Microbiology and Biotechnology 2020;30:427–38. https://doi.org/10.4014/jmb.1910.10055.

[27] Leist SR, Cockrell AS. Genetically engineering a susceptible mouse model for MERS-CoV-induced acute respiratory distress syndrome. MERS Coronavirus 2020:137–59. https://doi.org/10.1007/978-1-0716-0211-9_12.