Soundarapandian (Vijay) Vijayakumar

vijay
Title:
Assistant Professor
E-mail: vijayas@cobleskill.edu
Office Location: WH 200
Office Phone: 518-255-5462

Additional Title: Adjunct Associate Research Scientist, Columbia University

 

Areas of Expertise: Cell Biology, Biochemistry, Bioinformatics, Physiology

Courses Taught: Biology 1 (BIOL 111), Biology 2 (BIOL 112), Microbiology )BIOL 219), Anatomy & Physiology (BIOL 258X)

About Vijay:

Before coming to Cobleskill, I served as the Assistant Professor of Pediatrics as well as of Pharmacology & Physiology at the University of Rochester. During my tenure at the University of Rochester, I developed an independent research project investigating the role of extracellular matrix in Polycystic Kidney Disease, and mentored undergraduate and high school research students. I have held research positions at the Columbia University in the City of New York as well as the University of Texas Southwestern Medical Center, Dallas, TX. As a young scientist, I have spent time at the University of Ulm, Germany and International Center for Theoretical Physics, Italy. I have published in several leading peer-reviewed journals such as the Journal of Cell Biology and Journal of Clinical Investigation, primarily on the role of hensin in acid-base physiology. My research interests include structure of membrane proteins (CFTR, P450scc), Origin and evolution of life (primitive tRNA), Bioinformatics & genomics (P450scc, Polycystic Kidney Disease) as well as Developmental biology of the Kidney.

I have extraordinary interest in STEM education and interdisciplinary thought. I have served as adjunct faculty at the Bryant & Stratton College, Henrietta and at the College of Mount Saint Vincent at Bronx, NY. I routinely participate in the First Lego League events primarily in the Judging area as well as in the NYC Science & Engineering Fair. I am devoted to making concepts easily understandable to students, active learning strategies and mentoring.

 

Curriculum Vitae:

EDUCATION:

Rensselaer Polytechnic Institute, Troy, NY
• Ph.D. in Biology, 1993
• Thesis: Structural Investigations on Cytochrome P450scc

Rensselaer Polytechnic Institute, Troy, NY
• M.S. in Biology, 1992

RKM Vivekananda College, University of Madras, India
• M.Sc. in Physics, 1985
• Thesis: Lattice Dynamics of Strontium Oxide: Three Body Force Shell Model

RKM Vivekananda College, University of Madras, India
• B.Sc. in Physics, 1983

 

TEACHING EXPERIENCE:

Assistant Professor, Department of Natural Sciences & Mathematics, SUNY Cobleskill, Cobleskill, NY; Aug 2013 to present

• Prepare and present BIOL 111, BIOL 112 lectures to a large class-size audience (60 students)
• Interact with students in regularly scheduled office-hours as well as on ad-hoc basis
• Develop course syllabus, calendar, exams etc., and conducted two BIOL 258X Anatomy & Physiology labs
• Instructor for BIOL 111X lab section
• Participate in department and campus-wide meetings

Assistant Professor, Departments of Pharmacology & Physiology and Pediatrics, University of Rochester, Rochester, NY. Dec 2010 to present

• Undergraduate teaching: independent study (PHP 395- Spring 2012 & Spring 2013).
• Led Problem Based Learning (PBL) sessions entitled Just Say Yes! A patient odyssey through a cornucopia of pharmacopeia to medical students (one course/year)
• Mentored undergraduate students Alisa Johnson, Aditi Mulgund, Nicole Hook, Thomas Dieringer, Michael Hsu, Avni Patel and Suparna Dang in cell & developmental biology/protein biochemistry research on kidney diseases.
• Interviewed graduate students to the Pharmacology & Physiology graduate program
• Actively participated in faculty development workshops arranged by the Dean’s office

Adjunct Professor, Department of Natural Sciences, College of Mount Saint Vincent, Bronx, NY Sep 2012 to June 2013

• As the instructor for Anatomy & Physiology I Lab, worked with other adjuncts and professors to finalize the syllabus and calendar
• Prepared power-point presentations from various sources to thoroughly illustrate various anatomical structures to undergraduate students
• Conducted practical labs such as dissecting the pig-brain and dialysis experiment
• Led classes using an active learning strategy that included assigning group work, pop-quizzes and improptu student participation
• Planned the practical exams, administered and graded them
• Earned the respect and appreciation of students that led to many of them waking up before 5AM to sign up for my next semester Anatomy & Physiology II class

Adjunct Professor, Allied Health Program, Bryant & Stratton College, Rochester, NY
April 2010 to June 2013 (every semester)

• Taught Anatomy & Physiology II and Pharmacology courses to students from diverse backgrounds by incorporating kinetic, visual and auditory learning tools
• Worked efficiently with the program director to develop the syllabus, tracking calendar, reflective essay and research project topics
• Incorporated puzzles and games to encourage reciprocity and cooperation among students
• Actively sought student suggestions to improve their learning outcomes and incorporated their suggestions such as providing hand-outs of the presentation and introducing “make your own word bank” assignment
• Significantly improved sustained student engagement in a three-hour long class by giving in-class assignments in their work-book, text book and models
• Clearly explained the learning outcomes and work place relation of the topics at the beginning of the class and communicated high expectation
• Guided students in their writing projects such as the disease project by giving prompt and constructive feedbacks on their first and second draft
• Incorporated multiple choice questions and by reviewing a list of study material before their tests to enhance student success in CMA testing
• Actively participated in faculty development process by responding to Class Room Observation critiques

Teaching Assistant, Department of Biology, Rensselaer Polytechnic Institute, Troy, NY
Sep 1990 to Aug 1993

• Led undergraduate students in Advanced Biophysics laboratory course for three semesters and trained them in molecular modeling, bioinformatics and spectroscopic techniques (Instructor: Prof. John Salerno)
• Introduced bioinformatics and molecular modeling component to the course by designing the syllabus, lab exercises and tests
• Led undergraduate students in Advanced Biochemistry laboratory course for two semesters and trained students in the purification of cytochrome c from bovine heart and ferredoxin from spinach and in UV-Vis based protein assays and SDS-PAGE (Instructor: Prof. John Salerno)
• As a teaching assistant for Biochemistry course (lecture), acted as the preceptor for a small group of about 20 students by helping them with questions and concerns and grading their tests and quizzes (Instructors: Drs. Jane Koretz and Joyce Diwan)
• Led undergraduate students in Embryology lab course for three summer semesters
• As a teaching assistant for the Introduction to cell and molecular biology lab trained students in DNA extraction, cloning and agarose gel electrophoresis

RESEARCH EXPERIENCE:

University of Rochester, Rochester, NY, Departments of Pediatrics and Pharmacology & Physiology: Assistant Professor, Dec 2010 to present; Research Asst Professor Dec 2007 to Dec 2010)

Established a novel research program in Polycystic Kidney Disease (PKD) that included CTSI grant funded basic research and an industry sponsored clinical research project; successfully identified a novel biologic (laminin-332) for the treatment of PKD.

• Applying technical expertise in Cell Biology and Protein Biochemistry identified novel targets (galecti-3, laminin-332) PKD and renal fibrosis, hensin and integrin v1 in metabolic acidosis and DMBT1 in Prostate Cancer. Identified a lead biologic (laminin-332 antibody) for PKD.
• Planned the research project and as the Principal Investigator, developed the budget, drafted grant proposals, obtained funding, procured equipments, identified external and internal collaborators, obtained rat and mice model systems, designed animal care protocols and established new research program.
• Recruited Otsuka sponsored PKD clinical study to the University of Rochester and, as a sub-investigator, coordinated the study including obtaining IRB and ORPA approval, patient recruitment and enrollment.
• Edited a book on kidney diseases, published in peer-reviewed journals and presented lectures at the Brookhaven National Lab, American Society of Nephrology and at the Mayo Clinic.

Columbia University, New York, NY, Departments of Medicine: Associate Research Scientist, Jul 1996 to Dec 2007; Postdoctoral Research Fellow, Nov 1995 to Jun 1996

Discovered the function of a novel ECM protein, hensin, in terminal differentiation of kidney, prostate and intestinal epithelia. Discovered novel targets (hensin/DMBT1, integrin v1 and galectin-3) in kidney disease and prostate cancer using cell biological and proteomics tools.

• Identified integrin v1’s role in the matrix assembly of hensin (an alternatively spliced form of putative tumor suppressor protein DMBT1; published with cover picture in the Journal of American Society of Nephrology).
• Established the role of hensin in the differentiation of kidney, prostate and intestinal epithelial cells (published in the Journal of Cell Biology).
• Collaborated with other researchers in elucidating the role of hensin in prostate-cancer, alachlor-induced oncogenesis in rat olfactory mucosa and in metabolic acidosis of the kidney.
• Collaborated in identifying a novel protein, kanadaptin, and elucidated the influence of apical and basolateral lipids on chloride-bicarbonate exchanger protein

University of Texas Southwestern Medical Center, Dallas, TX, Department of Physiology: Postdoctoral Research Scientist, Sep 1993 to Nov 1995

Developed and executed a research project to determine the structure-function relationship of the membrane domain of Cystic Fibrosis Transmembrane Receptor (CFTR).

• Purified CFTR transmembrane peptides using HPLC, CE-MEKC and ESI-MS methods.
• Using biophysical techniques including circular dichroism (CD), discovered the conformational flexibility of a transmembrane peptide in the cystic fibrosis transmembrane regulator (CFTR) (published in Biochemistry)
• Developed novel techniques to express and purify full-length recombinant Cystic Fibrosis protein (CFTR) in Sf9-baculovirus expression system

Rensselaer Polytechnic Institute, Troy, NY, Department of Biology: Graduate student, Sep 1990 to Aug 1993

Successfully modeled the structure of Cytochrome P450scc, a protein that regulates steroid biogenesis and identified the active site and membrane binding domains.

• Using bioinformatics, computer modeling and EPR spectroscopy modeled the 3D structure of P450scc, a membrane protein involved in the biosynthesis of steroid hormones (P450scc) and predicted the active site, heme and membrane binding regions of this protein.
• Deposited the structure data in the Protein Data Bank (pdb:1scc) and published the findings in the Biochimica et Biophysica Acta
• Invited to present at the ASBMB and Biophysical Society Joint meeting, Houston, TX and participated in Second Albany Conference on Computational Biology, Albany, NY.
• Participated in the Frontiers of Life Conference, Blois, France and was visiting student at the International Center for Theoretical Physics, Trieste, Italy
COMMUNITY SERVICE:

• Volunteer Judge/Referee, First Lego League, New York since 2005
• New York City Science & Engineering Fair Judge since 2013
Research Mentoring Experience:
- T. Wiederholt, Graduate student from Germany (2000)
- Tanya Johnson,Graduate student from Nephro-Urology unit, University College London, London, UK (2002)
- Michael Hsu, Northwestern University, Illinois (Summer 2008)
- Avni Patel, University of Rochester, Rochester, NY (Summer 2009)
- Thomas Dieringer, University of Rochester, Rochester, NY (Summer 2010)
- Nicole Hook, Rochester Institute of Technology, Rochester, NY (Summer 2010)
- Aditi Mulgund, University of Akron, Ohio (Summer 2010)
- Alisa Johnson, University of Rochester, (Summer 2011 & Independent Research Course, Spring 2012)
- Suparna Dang, University of Rochester Undergraduate (Summer 2012)
- Several High School students through Friends of Strong, University of Rochester, Rochester, NY (2008-2012)
HONORS:

1. The role of Microfibril-associated protein 4 in vascular morphogenesis and in the development of vascular diseases. Lundbeck Foundation Dec 2007-2009; 1,000,000 kroners (declined)
2. Travel Grants from International Society for the study of Origins of Life, NASA and International Center for Theoretical Physics (1987-95).
3. Junior Research Fellowships from the Department of Science and Technology, India & University Grants Commission India (1986-89).
4. Best student of the College, RKM Vivekananda College, Chennai, India (1983).
MEMBERSHIP IN PROFESSIONAL SOCIETIES:

2008 – Present: Recessive PKD Core Center, Univ. of Alabama, Birmingham, AL 35294
2003-Current: American Society for Cell Biology, Bethesda, MD, USA
2003- Current: American Society of Nephrology, Washington DC, USA
1995-1997: Cystic Fibrosis Foundation. Bethesda, MD, USA
1988-1990: Society for Biomolecular Recognition
1991-1995: Biophysical Society
1987-2000: International Society for the Study of Origins of Life (ISSOL)

Selected Presentations and Participations in Conferences and Workshops:
- Investigation of the role of aberrant laminin assembly in PKD cystogenesis, Mayo Translational PKD Center Retreat, Mayo Clinic, Rochester, MN (May 11, 2012)

- Jim Hensin, A New Puppeteer In Epithelial Morphogenesis, Invited Speaker, Dept of Biology, Brookhaven National Laboratory, Brookhaven, NY (Feb 19, 2010)

- GSK-3/mTOR signaling regulates extracellular matrix deposition of hensin, a key regulator of kidney adaptation to metabolic acidosis by blocking galectin-3 secretion. American Society of Nephrology Renal Week, San Diego, CA (Oct 1, 2009)

- Molecular mechanisms of epithelial differentiation regulated by hensin, the rabbit homologue of innate immunity defense protein gp340/DMBT1. Invited speaker, University of Southern Denmark, Odense, Denmark (Jun 14, 2007)

- Cyclosporin Causes Distal Renal Tubular Acidosis by Preventing Hensin Polymerization, American Society of Nephrology Renal Week, San Diego, CA (Sep 30, 2003)

- Structural Investigations on P450scc and Cystic Fibrosis Transmembrane Receptor, National Cancer Institute, Frederick, MD (1995)

- Predicted three-dimensional structure of P450scc. American Society for Biochemistry & Molecular Biology and Biophysical Society Joint Annual meeting, Houston, Texas (Feb 1992)

- A primitive tRNA model for the genetic decoding machinery, Invited Speaker and Visiting Scholar, International Center for Theoretical Physics, Trieste, Italy (1992)

- A primitive tRNA model for the genetic decoding machinery, Sektion Polymere, Univ. of. Ulm, Germany (1987)
Research Grants:

1. Title: SUNY Cobleskill’s multi-pronged, targeted initiative to enhance STEM retention
Principal Investigator: Dr. S. Vijayakumar, Ph.D
Agency: National Science Foundation
Project Period: 06/01/2014 – 05/30/2017 Budget: $269,000 [PENDING]

2. Title: A Multi-Center, Longitudinal, Observational Study of Patients with Autosomal Dominant Polycystic Kidney Disease (ADPKD) to Establish the Rate, Characteristics, and Determinants of Disease Progression
Principal Investigator: Dr. Jeremy Taylor, M.D;
Role of Dr. S. Vijayakumar, Ph.D: Sub-Investigator
Agency: Otsuka Pharmacutical
Study Period: Nov 2011- Oct 2014; Budget: approximately $58,000
(Dr. S. Vijayakumar initiated the efforts for bringing this study to the University of Rochester)

3. Title: Bicarbonate Transport by the Maturing Renal Tubule
NIH RO1 2 R01 DK050603-31A1 Agency: NIDDK (NIH)
Principal Investigator: Dr. George Schwartz, M.D.
Role of Dr. S. Vijayakumar: Co-investigator; Percent effort 20%
Period: July 01, 2011- June 30 2015; Budget: approximately $430,000 per year

Completed:
1. Title: Role of Galectin-3 Mediated Extracellular Matrix Assembly in ARPKD Cystogenesis
Principal Investigator: S. Vijayakumar
Agency: NIH/NCRR (The University of Rochester’s Clinical and Translational Science Institute)
Funding Period: 07/01/2010 – 06/30/2011; Budget: $20,000

2. Title: Role of galectin-3 in Autosomal Recessive Polycystic Kidney Disease
Principal Investigator: S. Vijayakumar, Ph.D
Agency: Strong Childrens Research Center Small grants Program, University of Rochester
Funding Period: July 2008 – June 2010; Budget: $10,000
Peer-reviewed Publications:

1. Vijayakumar S, Dang S, Marinkovich MP, Lazarova Z, Yoder B, Torres V and Wallace D. (2013) Aberrant Expression of Laminin-332 in ARPKD Contributes to Cystogenesis by Altering Principal Cell Proliferation. American Journal of Physiology(ePublished ahead of Print Dec 26, 2013)

2. Vijayakumar S, Peng H and Schwartz GJ. (2013) Galectin-3 Mediates Oligomerization of Secreted Hensin Using its Carbohydrate Recognition Domain. Am. J. Physiol. 305:F90-99

3. Peng H, Vijayakumar S, Schiene-Fischer C, Li H, Purkerson JM, Malesevic M, Liebscher J, Al-Awqati Q Schwartz GJ.(2009). Secreted Cyclophilin A, A peptidyl prolyl cis/trans isomerase mediates matrix assembly of hensin, a protein implicated in epithelial differentiation. J Biol Chem. 10: 6465-6475. (* Equal first author)

4. S. Vijayakumar, H.Erdjument-Bromage, P.Tempst and Q. Al-Awqati. (2008) Role of Integrins in Hensin Assembly and Function in Cultured Intercalated Cells. J. Am. Soc. Neph. 19: 1079–1091

5. S. Vijayakumar, J. Takito, X. Gao, GJ. Schwartz and Q. Al-Awqati. (2006) Differentiation of columnar epithelia: the hensin pathway. J Cell Sci. 119:4797-801.

6. A.L. Schwaderer, S. Vijayakumar, Q. Al-Awqati, G. J. Schwartz (2006) Galectin-3 Expression is Induced in Renal -Intercalated Cells during Metabolic Acidosis. Am J Physiol Renal Physiol. 290:F148-58

7. S. Watanabe, S. Tsuroka, S. Vijayakumar and G. J. Schwartz. (2005) Cyclosporin produces Distal Renal Tubular Acidosis by blocking hensin polymerization. Am. J Physiol. 288(1): F40-47

8. Q. Al-Awqati, S. Vijayakumar, J. Takito. (2003). Terminal differentiation of epithelia. Biol Chem, 384:1255-1258.

9. Q. Al-Awqati, S. Vijayakumar, and J. Takito. (2003) Terminal differentiation of epithelia from trophectoderm to the intercalated cell: the role of hensin. J Am Soc Nephrol. 14 Suppl 1:S16-21.

10. M. B. Genter, DM. Burman, S. Vijayakumar, CL. Ebert and B. J. Aronow. (2002) Genomic analysis of alachlor-induced oncogenesis in rat olfactory mucosa. Physiol Genomics 12: 35-45.

11. G. J. Schwartz, S. Tsuroko, S. Vijayakumar, S. Petrovic, A. Milan and Q. Al-Awqati. (2002) Acid incubation reverses the polarity of intercalated cell transporters: An effect mediated by hensin. J. Clin. Inves. 102, 89-99.

12. J. F. Ma, J. Takito, S. Vijayakumar, D. M. Peehl, C. A. Olsson and Q. Al-Awqati. (2001) Prostatic expression of hensin, a protein implicated in epithelial terminal differentiation. The Prostate. 49(1): 9-18.

13. G. J. Schwartz, A.M. Kittelberger, D. A. Barnhart and S. Vijayakumar. (2000) Carbonic anhydrase IV is expressed in H+-secreting cells of rabbit kidney. Am. J Physiol. 278, F894-F904.

14. Q. Al-Awqati, S. Vijayakumar, J. Takito,C. Hikita, L. Yan & Wiederholt (2000) Phenotypic plasticity and terminal differentiation of the intercalated cell: the hensin pathway. Exp Nephrol. 8,66-71.

15. C. Hikita, S. Vijayakumar, J.Takito, H.Erdjument-Bromage, P.Tempst and Q.Al-Awqati. (2000) Induction of terminal differentiation in epithelial cells requires polymerization of hensin by galectin-3. J Cell Biol. 151, 1235-1246.

16. S. Vijayakumar, J. Takito, C. Hikita and Q. Al-Awqati. (1999) Hensin remodels the apical cytoskeleton and induces columnarization of intercalated epithelial cells: processes that resemble terminal differentiation. J. Cell. Biol. 144, 1057-1067.

17. C. Hikita, J. Takito, S. Vijayakumar and Q. Al-Awqati. (1999) Only multimeric hensin located in the ECM induces apical endocytosis and reversal of polarity in intercalated cells. J. Biol. Chem. 274, 17671-17676.

18. J. Takito, L.Yan, J. Ma, C. Hikita, S. Vijayakumar, D. Warburton and Q. Al-Awqati. (1999) Hensin, the polarity reversal protein, is encoded by DMBT1, a gene frequently deleted in malignant gliomas. Am. J. Physiol. 277, F277-F289.

19. Q. Al-Awqati, S. Vijayakumar, J. Takito, C. Hikita, L. Yan and T. Wiederholt. (1999) Terminal differentiation in epithelia: the Hensin pathway in intercalated cells. Semin Nephrol. 19, 415-

20. W. C. Wigley, S. Vijayakumar, J.D. Jones, C. Slaughter and P. J. Thomas. (1998) Transmembrane domain of Cystic fibrosis transmembrane conductance regulator: Design, characterization and secondary structure of synthetic peptides m1-m6. Biochemistry. 37, 844-853.

21. Q. Al-Awqati, S. Vijayakumar, C. Hikita, J. Chen and J. Takito. (1998) Phenotypic plasticity in the intercalated cell: the hensin pathway. Am. J. Physiol. 275: F183-F190.

22. J. Chen, S. Vijayakumar, X. Li and Q. Al-Awqati. (1998) Kanadaptin is a protein that interacts with the kidney but not the erythroid form of Band 3. J. Biol. Chem. 273, 1038-1043.

23. W. Van’t hof, A. Malik, S. Vijayakumar, J. Qiao, J. van Adelsberg and Q. Al-Awqati. (1997) The effect of apical and basolateral lipids on the function of the Band 3 anion exchange protein. J. Cell. Biol. 139, 941-949.

24. S. Vijayakumar and J. C. Salerno. (1992) Molecular modeling of the 3-D structure of cytochrome P-450scc. Biochim. Biophys. Acta. 1160, 281-286.

25. S. Vijayakumar and R. Balasubramanian, R. (1989) Origin of the discriminatory mechanism of proteinous
aminoacids from the non-proteinous aminoacids by the protein synthesizing machinery. Origins of Life and Evolution of the Biosphere. 19: 370-372.

Book Chapter:
Extracellular Matrix Abnormalities in Polycystic Kidney Disease,
In: Novel Insights on Chronic Kidney Disease, Acute Kidney Injury and Polycystic Kidney Disease, (Editor: S. Vijayakumar) Intech Publishing, Croatia ISBN 978-953-51-0234-2

http://www.intechopen.com/books/novel-insights-on-chronic-kidney-disease-acute-kidney-injury-and-polycystic-kidney-disease

Manuscripts under preparation:
3) PI3 kinase regulates galectin-3 synthesis in a kidney intercalated cell line (Journal of Biological Chemistry/ American Journal of Physiology)


In the News: 
http://www.intechopen.com/books/novel-insights-on-chronic-kidney-disease-acute-kidney-injury-and-polycystic-kidney-disease