Sheema Mir, PhD

BS (Honors) 1999 Biochemistry - Aligarh Muslim University, Aligarh, India

MS 2001 Biochemistry - Aligarh Muslim University, Aligarh, India

PhD 2007 Biochemistry - Aligarh Muslim University, Aligarh, India

2007-2009.Post Doctorate Fellow (University of New Mexico, Albuquerque, NM, USA)

2009-2012.Post Doctorate Fellow (University of Florida, Gainesville, USA)

2012-2016. Research Scientist (Viracor Eurofins labs, Lee Summit, MO, USA)

2016-2020. Senior Research Scientist (Applied BioCode, Santa Fe springs, CA, USA)

First / Second Year Problem Based Learning

Virology, Infectious Diseases and Diagnostics (BSL/MCB)

Food and Feed (Molecular Diagnostics) Third Year

1. Infectious Disease Diagnostics: The early detection of infectious pathogens determines the outcome of an infectious disease. The overall goal of my research program is to develop highly sensitive and cost effective diagnostic tools for the rapid detection of diagnostic markers during the early stages of infectious disease. My research team at Applied BioCode Inc. focused on developing nucleic acid based multiplex diagnostic technology that can simultaneously detect numerous pathogens from a single patient sample. I supervised the overall research program from initial concept, feasibility, verification, validation studies, clinical trials to the final delivery of the 510k IVD product. I developed diagnostic assays that are used in diagnostic facilities nationwide with FDA approval. A brief overview of the infectious disease diagnostic tools developed under my supervision is below.

(i).Multiplex diagnostics of Respiratory Infectious Pathogens:A diagnostic test for the following respiratory infectiouspathogens, which includes seventeen viruses and three bacterial targets. Viruses (•Adenovirus •Coronavirus 229E •Coronavirus HKU1 •Coronavirus NL63 •Coronavirus OC43 •Influenza A - H1, seasonal - H1N1 2009 pdm, H3 subtype •Influenza B •Metapneumovirus (HMPV) •Parainfluenza virus type 1 •Parainfluenza virus type 2 •Parainfluenza virus type 3 •Parainfluenza virus type 4 •Respiratory Syncytial Virus (RSV) •Rhinovirus/ Enterovirus. Bacteria (• Bordetella pertusssis • Chlamydophila pneumonia • Mycoplasma pneumoniae)

FDA Approval:Device 510(k)# k192485

(ii).Multiplex diagnostics of Gastrointestinal Infectious Pathogens: A diagnostic test for the below Gastrointestinal Infectious PathogensBacteria (• Campylobacter •Clostridium difficiletoxins A and B •E. coliO157 • EnterotoxigenicE. coliLT/ST (ETEC) • Salmonella • Shiga-like toxin producingE. colistx1/stx2 (STEC) • Shigella/ EnteroinvasiveE. coli(EIEC) • Vibro/Vibro parahemolyticus•Yersinia enterocolitica. Viruses (• Adenovirus 40/41 • Norovirus GI/GII • Rotavirus A). Parasites (•Cryptosporidium•Entamoeba histolytica•Giardia lamblia).

FDA Approval: Device 510(k)# K181548

(iii).Diagnostics of Upper Respiratory Tract Infectious Pathogens: A multiplex qPCR diagnostic assay for upper respiratory pathogens including both viral and bacterial pathogens at Viracor Eurofins labs, Lee Summit, MO, USA.

(iv).Diagnostics of Zika virus infection: ZIKA virus qPCR and ZIKA virus IgM, IgG serology (ELISA) assays.

2. Replication of negative strand RNA viruses: The nucleocapsid protein of negative strand RNA viruses encapsidates the viral genome and generates the ribonucleocapsids that are used as templates by the RdRp during transcription and replication of the viral genome. I demonstrated for the first time that Crimean Congo Hemorrhagic fever virus (CCHFV) nucleocapsid protein has two RNA binding sites in the stalk and head domains. I showed that double strand panhandle structure formed by the vRNA termini, and single strand RNA, bind to the RNA binding sites in the stalk and head domains, respectively. I demonstrated that panhandle binding site located in the stalk domain plays a key role in the replication of viral RNA genome in conjunction with RdRp. I also showed that nucleocapsid protein of hantavirus, another negative strand RNA virus, has distinct 5’ cap and RNA binding sites that play key roles in the hantavirus replication. I showed for the first time that hantavirus RdRp requires a host cell factor for cap snatching. The host cell factor is required for specific cleavage of the long capped RNA fragments at a “G” residue located 10-14 nucleotides downstream of the 5’ cap. The long capped RNA fragments are rescued from degradation by the nucleocapsid protein. After specific cleavage, the short RNA molecules are used as primers by the RdRp to initiate transcription/replication of the viral genome.

1. Wang Z, Ren S, Li Q, Royster AD, Lin L, Liu S, Ganaie SS, Qiu J, Mir Sheema*, Mir MA.2021. Hantaviruses use the endogenous host factor P58IPK to combat the PKR antiviral response. PLoS Pathog 17:e1010007.

2. Royster, A, Mir Sheema* and Mir MA: A novel approach for the purification of aggregation prone proteins. PLOS One. 2021 Nov 22;16(11): e0260143.doi: 10.1371/journal.pone.0260143.eCollection 2021.eeva S, Mir S, Velasquez A, Ragan J, Leka A, Wu S, Sevarany AT, Royster AD, Almeida NA, Chan F, O'Brien L, Mir MA. Crimean-Congo hemorrhagic fever virus nucleocapsid protein harbors distinct RNA binding sites in the stalk and head domains. J Biol Chem. 2019 Mar 29;294(13):5023-5037. doi: 10.1074/jbc.RA118.004976. Epub 2019 Feb 5.

3. Jeeva S, Mir S, Velasquez A, Weathers BA, Leka A, Wu S, Sevarany AT, Mir M. Hantavirus RdRp requires a host cell factor for cap snatching. J Virol.2019 Feb 19;93(5). pii: e02088-18. doi: 10.1128/JVI.02088-18. Print 2019 Mar 1.

4. Cheng E, Haque A, Rimmer MA, Hussein IT, Sheema S, Little A and Mir MA. Characterization of the Interaction between Hantavirus nucleocapsid protein (N) and ribosomal protein S19 (RPS19). J Biol Chem. 2011 Apr 1; 286(13).

3. DNA repair by nonhomologous endjoining:

Given its significant role in the maintenance of genomic stability, histone methylation has been postulated to regulate DNA repair. Histone methylation mediates localization of 53BP1 to a DNA double-strand break (DSB) during homologous recombination repair, but a role in DSB repair by nonhomologous end-joining (NHEJ) has not been defined. By screening for histone methylation after DSB induction by ionizing radiation I demonstrated for the first time that generation of dimethyl histone H3 lysine 36 (H3K36me2) was the major event. Using a novel human cell system that rapidly generates a single defined DSB in the vast majority of cells, I showed that the DNA repair protein Metnase (also SETMAR), which has a SET histone methylase domain, localized to an induced DSB and directly mediated the formation of H3K36me2 near the induced DSB. This dimethylation of H3K36 improved the association of early DNA repair components, including NBS1 and Ku70, with the induced DSB, and enhanced DSB repair. In addition, expression of JHDM1a (an H3K36me2 demethylase) or histone H3 in which K36 was mutated to A36 or R36 to prevent H3K36me2 formation decreased the association of early NHEJ repair components with an induced DSB and decreased DSB repair. Thus, these experiments define a histone methylation event that enhances DNA DSB repair by NHEJ.

1. Sheema Fnu, Williamson EA, Deharo LP, Brenneman M, Wray J, Shaheen M, Radhakrishnan K, Lee SH, Nickoloff JA, and Hromas R. Methylation of Histone H3 lysine 36 enhances DNA repair by nonhomologous end joining. Proc. Natl, Acad, Sci, USA. 2011 Jan 11; 108(2)

2. Hromas R, Williamson EA, Sheema Fnu, Lee YJ, Nickoloff JA and Lee SH. Chk1 phosphorylation of metnase enhances DNA repair but inhibits replication fork resart.Oncogene.2012 Jan 9

3. Wray J, Willaimson EA, Sheema S, Lee SH, Willman CL, Nickoloff JA, and Hromas R. Metnase mediates chromosome decatenation in acute leukemia cells. Blood. 2009 Aug 27; 114(9).

American Society for Microbiology

American Society of Virology

One Health

I have 12 years of research experience in working with diverse areas of biology with more technical focus on virology and diagnostics. My basic research studies have contributed in understand the mechanism of RNA virus replication, and the role of DNA repair protein Metnase, in nonhomologousendjoining. My translational research program is focused on revolutionary rapid identification of emerging pathogens to accelerate development of improved infectious disease diagnostics and to see these new methods better integrated into clinical care. A critical objective of my research is to foster frequent, impactful collaboration among applied researchers and clinicians across diverse research environments from academia to industry. My past experience in the area molecular diagnostics will be of paramount importance in future development of multiplex diagnostic approaches for other emerging respiratory pathogens. Besides research, I enjoy interaction with students that are highly interested in research. My teaching covers Molecular Diagnostics in Animal Food and Feed besides Basic Virology and Molecular Cell Biology courses.