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Ilia V. Baskakov, PhD

Academic Title:


Primary Appointment:


Secondary Appointment(s):

BioChemistry&Molecular Biology


GRB, 111 S. Penn St., 307C

Phone (Primary):

(410) 706-4562


(410) 706-8184

Education and Training

I graduated from Moscow University with a M.S. degree in bioorganic chemistry and obtained a Ph.D. degree in biophysics from the Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow. I received postdoctoral training in biophysics and protein folding with Wayne Bolen at University of Texas Medical Branch and on prions with Nobel laureate Stanley Prusiner at UCSF. In UTMB, I established a pioneering approach for folding natively unfolded proteins. With Dr. Bolen, we described a new thermodynamic force that contributes to protein folding and stability more than 40 years after Kauzmann introduced four basic thermodynamic forces responsible for protein folding. As a postdoctoral fellow with Stanley Prusiner, I laid the ground work on synthetic prions and showed for the very first time that the transmissible prion disease can be induced in animals using amyloid fibrils prepared in vitro.


1996-1998       Postdoctoral Fellow, University of Texas Medical Branch, Galveston, TX, Supervisor Dr. D.W. Bolen

1999-2001       Postdoctoral Fellow, University of California, San Francisco, CA, Supervisor Dr. S.B. Prusiner

2001-2006       Assistant Professor, Medical Biotechnology Center, University of Maryland Biotechnology Institute, Baltimore, MD, USA

2006-2009       Associate Professor, Medical Biotechnology Center, University of Maryland Biotechnology Institute, Baltimore, MD, USA.

2010-2013       Associate Professor, Center for Biomedical Engineering and Technology and Department of Anatomy and Neurobiology, University of Maryland School of Medicine, Baltimore, MD, USA

2013 – present Professor, Center for Biomedical Engineering and Technology and Department of Anatomy and Neurobiology, University of Maryland School of Medicine, Baltimore, MD, USA

Research/Clinical Keywords

neurodegenerative diseases, prion diseases, neuroinflammation, reactive astrocytes, reactive microglia, Alzheimer's disease

Highlighted Publications

Bocharova, O., Fisher, A., Pandit, N.P, Molesworth, K., Mychko, O., Scott, A.J., Makarava, N., Ritzel, R., Baskakov, I.V. 2022 Ab plaques do not protect against HSV-1 infection in a mouse model of familial Alzheimer’s disease, and HSV-1 does not induce Ab pathology in a model of late onset Alzheimer’s disease. Brain Pathology, e13116.

Kushwaha, R., Sinha, A., Makarava, N., Molesworth, K., Baskakov, I.V. 2021 Non-cell autonomous astrocyte-mediated neuronal toxicity in prion diseases. Acta Neuropathol Commun. 9(1): e22. PMCID: PMC7866439.

Makarava, N., Mychko, O., Chang, J.C.Y., Molesworth, K., Baskakov, I.V. 2021 The degree of astrocyte activation is predictive of the incubation time to prion diseases. Acta Neuropathol Commun. 9(1): e87. PMCID: PMC8114720.

Makarava, N., Chang, J.C., Molesworth, K., Baskakov, I.V. 2020 Posttranslational modifications define course of prion strain adaptation and disease phenotype. J Clin Invest.  V130(8) p.4382-4395, PMID: 32484800

Makarava, N., Chang, J.C., Molesworth, K., Baskakov, I.V. 2020 Region-specific glial homeostatic signature in prion diseases is replaced by a uniform neuroinflammation signature, common for brain regions and prion strains with different cell tropism. Neurobiol Disease 137:104783 PMID: 32001329

Makarava, N., Savtchenko, R., Lasch, P., Beekes, M. Baskakov, I.V. 2018 Preserving prion strain identity upon replication of prions in vitro using recombinant prion protein. Acta Neuropathol Commun. 6(1): e92. PMCID: PMC6134792

Srivastava, S., Katorcha, E., Makarava, N., Barrett, J.P., Loane, D.J., Baskakov, I.V. 2018 Inflammation response of microglia is controlled by sialylation of PrPSc. Sci Rep., v.8, e11326. 

Katorcha, E., Gonzalez-Montalban, N., Makarava, N.., Kovacs, G.G., Baskakov, I.V. 2018 Prion replication environment defines the fate of prion strain adaptation. PLoS Pathogen, v.13(8), e1006563. PMCID: PMC6013019

Katorcha, E., Makarava, N., Lee, Y.J., Lindberg, I., Monteiro, M.J., Kovacs, G.G., Baskakov, I.V. 2017 Cross-seeding of prions by aggregated a-synuclein leads to transmissible spongiform encephalopathy, PLoS Pathog., v.13(8), e1006563. PMCID: PMC5567908

Srivastava, S., Katorcha, E., Daus, M.L., Lasch, P., Beekes, M., Baskakov, I.V. 2017 Sialylation controls prion fate in vivo. J.Biol.Chem. v. 292, p.2359-2368. PMID: 27998976 PMCID: PMC5313106

Katorcha, E., Daus, M.L., Gonzalez-Montalban, N., Makarava, N., Lasch, P., Beekes, M., Baskakov, I.V. 2016 Reversible off and on switching of prion infectivity via removing and reinstalling prion sialylation. Sci Rep., v.6, e33119.

Makarava, N., Savtchenko, R., Alexeeva , I., Rohwer , R.G., Baskakov, I.V. 2016 New molecular insight into mechanism of evolution of mammalian synthetic prions. American Journal of Pathology, v. 186(4), p. 1006-1014. PMCID: in process

Srivastava, S., Makarava, N., Katorcha, E., Savtchenko, R., Brossmer, R., Baskakov, I.V. 2015 Post-conversion sialylation of prions in lymphoid tissues. Proc. Natl. Acad. Sci. USA PLUS, p.E6654-6662

Katorcha, E., Makarava, N., Savtchenko, R., D’Arzo, A., Baskakov, I.V. 2014 Sialylation of prion protein controls the rate of prion amplification, the cross-species barrier, the ratio of PrPSc glycoform and prion infectivity. PLoS Pathog.,  v.10, e1004366

Makarava, N., Kovacs, G.G., Savtchenko, R., Alexeeva, I., Ostapchenko, V., Budka, H., Rohwer, R.G., Baskakov, I.V. 2012,  A New Mechanism for Transmissible Prion Diseases. J. Neurosci, v..32, p. 7345-7355. 

Makarava, N., Savtchenko, R., Alexeeva, I., Rohwer, R.G., Baskakov, I.V. 2012, Fast and ultrasensitive method for quantitating prion infectivity titre. Nature Commun., v. 3, p.741.

Makarava, N., Kovacs, G.G., Bocharova, O., Savtchenko, R., Alexeeva , I., Budka, H., Rohwer , R.G., Baskakov, I.V. 2010  Recombinant prion protein induces a new transmissible prion disease in wild type animals, Acta Neuropathol. 119, p177-178; PMID: 20052481.




Additional Publication Citations

Research Interests

Our laboratory use animal pathology, transcriptome analysis, neuroimmunology and cell biology along with structural, biochemical and imaging approaches to gain new knowledge on prion-induced neurodegeneration.  Prion diseases, or transmissible spongiform encephalopathies, are fatal neurodegenerative disorders that can arise spontaneously, be inherited or acquired through transmission. The transmissible agent of prion diseases devoid of nucleic acids, but instead consists of a prion protein in its abnormal, β-sheet rich state (PrPSc), which is capable of replicating itself according to the template-assisted mechanism.

Evolution of prion strains and deformed templating. In a series of studies conducted over 15 years, we introduced a new concept that transmissible prion diseases can be induced in wild type animals by PrP structures with a folding pattern fundamentally different from that of authentic prions or PrPSc. These studies provided compelling evidence that noninfectious amyloids with a structure different from that of PrPSc could lead to transmissible prion disease via a mechanism referred to as deformed templating. Moreover, using new imaging approach developed by my laboratory that combines atomic force and fluorescence microscopy, we showed for the first time that, indeed, a folding pattern can switch from one cross-b pattern to an alternative cross-b pattern within individual amyloid fibrils. This work provided important insights into the genesis of the transmissible protein states and has numerous implications for understanding the etiology of neurodegenerative diseases in general.

Establishing a causative relationship between prion strain-specific structure and disease phenotype. While existence of multiple prion strains have been well established, the question how individual strains elicit multiple disease phenotypes is one of the most puzzling in prion and other neurodegenerative diseases. Prion protein is posttranslationally modified with two sialylated N-linked glycans. We showed that among hundreds of PrPC sialoglycoforms expressed by a cell, individual prion strains selectively recruit those PrPC sialoglycoforms that can be accommodated within a strain-specific structure. We illustrated that strain-specific patterns of carbohydrate groups are formed on a surface of PrPSc particles that dictate a strength of proinflammatory response of microglia. Since posttranslational modifications are common among proteins implicated in neurodegenerative diseases (tau, a-synuclein), the novel mechanism on strain-specific selective recruitment described in our work has broad implication beyond the prion diseases.

Role of prion protein sialylation determining prion fate in an organism. Through appreciation of the roles sialylation plays in biology, our recent studies put forward key evidence illustrating that sialylation of N-glycans of prion protein is essential for understanding prion biology. We demonstrated that sialylation of PrPSc N-linked glycans controls prion fate in organisms, dictates neuroinflammation status and the outcomes of prion infection. In particular, we showed that challenge of a host with PrPSc with reduced sialylation levels does not cause prion infection or prion disease. Moreover, prion infectivity could be switched off and on reversibly via removing and reinstalling PrPSc sialylation. Removing PrPSc sialylation was found to abolish prion lymphotropism, i.e. selective trafficking of prions to secondary lymphoid organs that are known to be the first sites of prion replication upon peripheral challenge.

Role of microglia in pathogenesis of prion diseases. Discovering the relationship between PrPSc sialylation status and neuroinflammation led to the next quest as to whether neuroinflammation drives disease progression. Toward this question, transcriptome analysis of 17 animal groups revealed very strong inverse correlation between the degree of neuroinflammation and the incubation time to diseases suggesting that phenotypic changes in glia contribute to faster progression of diseases and, perhaps, even drive the disease pathogenesis Transcriptome analysis revealed that with the disease progression, the region-specific microglial homeostatic signatures were replaced by the region-independent neuroinflammation signature characterized by significant upregulation in microglial phagocytic pathways. Consistent with gene expression analysis, reactive microglia isolated from prion-infected mice showed dramatic increase in phagocytic uptake of both disease-associated and normal synaptosomes. The current projects in the lab examine the role of microglia-driven phagocytosis in prion disease pathogenesis.  In particular, we are interested whether phagocytic activity should be targeted as a potential therapeutic strategy for treating prion diseases.

Defining the role of reactive astrocytes in pathogenesis of prion diseases. Our recent studies found that astrocytes responded to prion infection earlier than microglia. Region-specific transcriptome analysis revealed a global dysregulation across multiple homeostatic functions including loss in neuronal support in reactive astrocyte. Moreover, we observed very strong inverse correlation between the degree of astrocyte reactivity and the incubation time to diseases suggesting that phenotypic changes in astrocytes contribute to faster progression of diseases and, perhaps, even drive the disease pathogenesis. In support of this hypothesis, reactive astrocytes isolated from prion-infected mice had deleterious effects on primary neurons. The current projects in the lab seek to establish the role of reactive astrocyte in prion diseaseas and test whether transformation of astrocytes into reactive states drives pathogenesis of the disease.


Lab Techniques and Equipment

Our laboratory use animal pathology, transcriptome analysis, neuroimmunology and cell biology along with structural, biochemical and imaging approaches to gain new knowledge on prion-induced neurodegeneration.  Our laboratory is equipped with Atomic Force Microscope PicoLE combined with the inverted fluorescence microscop, CD spectrophotometer J- 810 (Jacso); FTIR spectrometer Tensor 27 equipped (Bruker); fluorimeter FlouroMax-3 (Jobin Yvon); dynamic light scattering DynaPro-MS/X (Protein Solutions); HPLC system with fluorescence and photodiode detectors (Shimadzu); FPLC system Akta prime (Amersham); fluorescence inverted microscope TE-2000 (Nikon); automated sonicators Misonix S-4000.

Lab Members

Natallia Makarava, B.S., Research Associate
Rajesh Kushwaha, Ph.D., Postdoctoral Fellow
Olga Bocharova, Ph.D., Postdoctoral Fellow
Kara Molesworth, B.S., Animal Specialist
Olga Mychko, B.S., Laboratory Technician
Narayan Pandit, M.S., Laboratory Technician