Saeed A Khan, Ph.D.
Division of Microbiology
National Center for Toxicological Research
Jefferson, AR 72079

FDA Experience: 14 Yrs
 

Proposed Research Project for FDA Fellow: Gene expression profiling in pulmonary, gastrointestinal and cutaneous epithelial cell lines after infection with Bacillus anthracis Sterne.

Anthrax is a disease that manifests itself in three forms: cutaneous anthrax, gastrointestinal anthrax and pulmonary anthrax. The three forms of anthrax vary in the severity of disease and its outcome. The cutaneous anthrax is not fatal at all, gastrointestinal anthrax is somewhat fatal but the pulmonary anthrax is always fatal. The outcome of the disease is probably dependent upon the interaction of anthrax toxins with cellular targets at the site of infection. These can be better understood by studying the gene expression profiling after challenging different kinds of cell lines with Bacillus anthracis. The proposed study will look into the gene expression profile and signaling pathways that become active during cutaneous, pulmonary and gastrointestinal anthrax by infecting the epithelial cell lines derived from human skin, respiratory tract, or intestinal tract tissues with an avirulent strain of B. anthracis that has been rendered avirulent by loss of capsule production genes. The cellular RNA will be collected from the bacteria cultured alone or after contact with each type of epithelial cell and hybridized with B. anthracis genomic probes on microarray slides to detect differences in the expression of genes in the global genome. RNA samples from each epithelial cell line will be reverse-transcribed and the resultant cDNA mixtures will be used in quantitative real-time PCR reactions using primers and master mixes specifically designed for and limited to cellular response pathways (RT2 Profiler™ PCR Arrays, SuperArray Bioscience Corp., Fredrick, MD). The gene expression profiles will be compared to a pathway database to evaluate the cellular responses to B. anthracis. Differences between epithelial cell types will be evaluated in search of a molecular reason behind lethality differences between skin, lung, and intestinal anthrax.

Applicant Requirements: Ph.D. in related science; training in microbiology/molecular biology, cell culture and microarray techniques.
 

Selected Recent Publications:
1. Khan, S. A. and Nawaz, M. S. Direct in-gel Hybridization of DNA with digoxigenin-
labeled probes. Methods in Molecular Biology (book chapter). Elena Hilario and J. F.
Mackay (Eds). (2007) 353:93-103.
2. Nawaz, M., Khan, A. A., Khan, S. A., Sung, K. and Steele, R. Isolation and characterization of tetracycline-resistant Citrobacter spp. from catfish. Food Microbiol.
(2008) 25:85-91.
3. Khan, S. A., Sung, K., and Nawaz, M. Heteroresistance to vancomycin and novel point mutations in Tn1546 of Enterococcus faecium ATCC 51559. Int. J. Antimicrob. Agents. (2008) 31:27-36.
4. Sung, K., Khan, S. A., and Nawaz, M. Genetic diversity of Tn1546-like elements in clinical isolates of vancomycin-resistant enterococci. Int. J. Antimicrob. Agents (2008) 31: 549-54.
5. Khan, S. A., Sung, K., Nawaz, M., Cerniglia, C. E., Tamplin, M. L., Phillips, R. W., and L. C. Kelly. The survivability of Bacillus anthracis in processed liquid eggs. Food Microbiology (2009) 26:123-127.
 

Suzanne M. Morris, Ph.D.
Division of Genetic and Molecular Toxicology
National Center for Toxicological Research

Background:
BS, University of Florida
MS, Virginia Polytechnic Institute
PhD, Purdue University
Post-doctoral Fellow, Indiana University

FDA employment: 32 years
 

Research Interests:  Understanding the role of p53 in determining the response to DNA damaging agents; approaches include (1) determination of the type and frequency of mutations in transgenic cell lines which differ in p53 mutational status (2) utilization of gene expression profiling in transgenic cell lines to determine the effect of p53 status on the expression of the DNA damage response pathways; and (3) use of gene expression profiling and DNA adduct analyses in tumor-prone tissues of transgenic mice to determine the effect of p53 mutational status after the expression of the DNA damage response after exposure to a model carcinogen.

Proposed Research Project for FDA Fellow:  Participate in experiments designed to understand the role of p53 in determining the response to DNA damaging agents through the use of genetic and genomic methods for the analysis of gene expression. Both cell culture and animal models will be evaluated with the aid of targeted arrays, microRNA analysis, and deep RNA sequencing.

Applicant Requirements:

PhD with training in biochemistry, molecular biology, toxicology, genetics,

Selected Recent Publications:

1. Morris, S.M. (2002). A role for p53 in the frequency and spectrum of induced mutation. Mutation Research (Reviews in Mutation Research), 511:45-62.

2. Akerman, G.S., B.A. Rosenzweig, O.E. Domon, L.J. McGarrity, L.E. Blankenship, C.A. Tsai, S.J. Culp, J.T. MacGregor, F.D. Sistare, J.J. Chen and S.M. Morris. (2004) Gene expression profiles and genetic damage in BPDE-exposed TK6 cells. Mutation Research, 561, 43-64

3. Akerman, G.S., B.A. Rosenzweig, C.A. Tsai, O.E. Domon, M. E. Bishop, L.J. McGarrity, F.D. Sistare, J.T. MacGregor, J.J. Chen and S.M. Morris. (2005) Alterations in gene expression profiles and the DNA damage response in ionizing radiation-exposed TK6 cells. Environmental and Molecular Mutagenesis, 45:188-205.

4. S. M. Morris, G. S. Akerman, V. G. Desai, C.-a. Tsai, W. H. Tolleson, W. B. Melchior, Jr., C.-J. Lin, J. C. Fuscoe, D. A. Casciano, and J. J. Chen (2008) Effect of p53 genotype on gene expression profiles in murine liver. Mutation Research, 640: 54-73.

5. R. Kulkarni D. M. Petibone, C.-W. Chang, J. J. Chen, W. H.Tolleson, W. B. Melchior, Jr., M. I. Churchwell, F. A. Beland and S. M. Morris. (in press, 2009) Effect of p53 Genotype on Gene Expression and DNA Adducts in ENU-Exposed Mice. Handbook of Systems Toxicology (eds. Sahu and Casciano
 

Baitang Ning, Ph.D.
Genomics Laboratory
Division of Personalized Nutrition and Medicine
National Center for Toxicological Research
Jefferson, AR

Background:
B.S. Medicine
Ph.D. Biochemistry
Years of FDA employment: 10 years
 

Research Interests:

Pharmacogenomics and molecular basis of genetic/phonotypic variation in human populations, which include: genetic and biochemical characterization of human genetic polymorphisms that modulate drug metabolism; and metabolic genotyping/phenotyping of human populations and assessment of individual variability to nutrients and drugs.

Proposed Research Project for FDA Fellow:

Understanding genetic susceptibilities to drug responses (i.e., adverse reactions and efficacy) is critical to the implementation of personalized medicine. Next-generation sequencing is a powerful tool for decoding the genetic basis of human diseases and drug responses. Carbamazepine causes various types of skin hypersensitivity reaction, including Stevens-Johnson syndrome (SJS), toxic epidermal necrosis (TEN) and hypertensive syndrome (HSS). Genetic variants have been associated with adverse reactions to carbamazepine (HLA-B*1502 and HLA-A*3101), but these risk alleles predict only a portion of individuals who will develop SJS, TEN and HSS. This suggests that other rare or non-HLA related variants may also play an important role. Therefore, deep sequencing will provide single-base resolution of genetic information from patients with carbamazepine-induced skin injury and provide opportunities to identify causative genetic variants contributing to the disease leading to further predictive information for the safe use of carbamazepine.

This proposed study will perform whole-genome sequencing and genetic analysis to identify susceptibilities to carbamazepine-induced adverse drug reactions (ADRs) including SJS, TEN and HSS, providing essential single-base resolution information for prediction of such ADRs.

Applicant Requirements:

Ph.D. in genetics, molecular epidemiology, pharmacology, molecular biology, biochemistry or related scientific fields.

Selected Recent Publications:

Yang L, Price E, Chang C, Li Y, Huang Y, Guo L, Kaput J, Shi L and Ning B. Interindividual variability in the expression of drug metabolizing enzymes in human liver. In press.

Su Z., Ning B., Fang H., Hong H., Perkins R., Tong W. and Shi L. (2011) Next-generation sequencing and its applications in molecular diagnostics. Expert Review of Molecular Diagnostics. 11 (3) , 333-343

Guo L, Dial S, Shi L, Branham W, Liu J, Fang JL, Green B, Deng h, Kaput J, and Ning B. (2010) Similarities and differences in the expression of drug metabolizing enzymes between human hepatic cell lines and primary hepatocytes. Drug Metab Dispos. 2010 Dec. 13 [Epub ahead of print]

MAQC Consortium. (2010) The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-base predictive models. Nat Biotechnol. July 30 [Epub ahead of print]

Ning B., Dial S., Sun Y., Wang J., and Guo L. (2008) Systematic and simultaneous gene profiling of 84 drug-metabolizing genes in primary hepatocytes. J. Biomol. Screen. 13(3):194-201

Lin Z., Zhang Z., Tuo J., Guo Y., Green B., Chan C. C., Tan W., Huang Y., Ling W., Kadlubar F.F., Lin D., and Ning B. (2007). Variant of the Cockayne Syndrome B gene ERCC6 confers risk of lung cancer. Hum. Mut. Sep 13; [Epub ahead of print]

Tuo J., Ning B., Bojanowski C.M., Lin Z.N., Reed G., Shen D., Jiao X., Chew E., Kadlubar F.F., and Chan C.C. (2006). Synergetic Effect of Functional Variation in ERCC6 5’-Flanking Region and a CFH Variation Confers High Risk to Age-Related Macular Degeneration. Proceed. Nat. Acad. Sci. 103:9256-9261

 

Director of Electron Microscopy Group, NCTR/ORA Nanotechnology Core Facility, Office of Scientific Coordination, NCTR, FDA
3900 NCTR Road, Jefferson, Arkansas 72079

Background:
Ph.D., Microbiology, University of Texas, 1993
National Center for Molecular Imaging, Baylor College of Medicine, Houston, TX (1994-2004)
Assistant Professor and Director High Resolution Cryo-Electron Microscopy Facility, Department of Pathology & Laboratory Medicine, University of Texas Health Sciences Center, Houston, TX (2005-2011)
Director of Electron Microscopy Group, NCTR (2011-present) 

Research Interests:

Nanotechnology involves the study and manipulation of certain nano-scaled materials (~1-100 nm) for use in manufactured products. Some of these products include pharmaceuticals and medical devices, and from the FDA point of view, the potential adverse effect of these materials on human health is very important. For instance, many nanomaterials such as nano-silver, nano-gold, and nano-iron are being developed as drug delivery/organ targeting systems. My research goal is to use electron microscopy (EM) and computer aided 3D image reconstruction to investigate the structural basis of human cellular interaction with nanomaterials. As nanomaterials are introduced into a mammalian system, knowledge of the uptake, distribution, and disposition of the nanomaterial is critical for understanding potential benefit and risk. We will be using a state-of-the-art FEG Scanning Electron Microscope (SEM) with a novel new auto-ultramicrotome serial sectioning device (Gatan 3Veiw2) to look at the 3D structure of cells and organelles treated with nanomaterials. In particular, we are interested in the distribution of nanomaterial within the animal model and the effects these materials have at the cellular and organ level.

Proposed Research Project for FDA Fellow:

The Gatan 3View system is a new and extremely powerful technology that for the first time allows automated serial sectioning at the ultramicrotome level (10-50 nm sections) and visualization of tissues. The project for this Commissioners Fellow is to (1) use existing classical electron microscope (EM) technology to visualize nanomaterials and (2) compare the results with the new SEM serial sectioning methods. The methodology that will be employed is immuno-EM, where nanogold (5 nm) tagged antibodies are used to precisely map the location of epitopes (e.g. proteins, macromolecular structures, etc.) within the cellular structure using TEM and SEM. Because this technology is so new, techniques need to be developed to improve the power and range of the combination of SEM with serial sectioning with immuno-EM labeling. It is believed that merging immuno-EM with the resolution power of the serial sectioning system will create a new combinatorial technique for localizing the distribution of important epitopes within organisms. This technique could then be used to answer relevant questions about impact of nanomaterials (and other compounds) on cellular structure and function.

The National Center for Molecular Imaging at Baylor University and the High Resolution Cryo-Electron Microscopy Facility at University of Texas Health Sciences Center are state-of-the-art electron microscope facilities. During my tenure at Baylor, I trained over two-dozen graduate students and a dozen post-doctoral fellows and faculty on cryo-EM sample preparation and microscopy. While a graduate student at University of Texas, I taught graduate level courses on EM, where students (10-15/class) were given lecture and hands-on training in EM. At the University of Texas Health Sciences Center, I was the primary person responsible for the 300 kV Polara G2 very high resolution EM, and trained approximately one dozen post-doctoral fellows and faculty on the proper use of this expensive EM. At NCTR, I have already trained seven staff on the use of the 200 kV transmission electron microscope and seven staff on the variable-vacuum SEM, both of which are capable of cryo-EM. Currently a 120 kV transmission electron microscope is being installed, and the FEG SEM described above will provide sufficient EM platforms for training of the Commissioners Fellow on state-of-the-art EM.

Applicant Requirements:

The applicant should have a degree related to biological sciences with some experience in electron microscopy.

Selected Recent Publications:

1. Hernandez, R., Paredes, A.M., (2009) Sindbis virus as a model for studies of conformational changes in a metastable virus and the role of conformational changes in in vitro antibody neutralisation. Rev. Med. Virology. 19(5):257-72.
2. Kozar, R.A., Peng, Z., Holcomb, J.B., Pati, S., Park, P., Ko, T.C., Paredes, A., (2011) Plasma restoration of endothelial glycocalyx in a rodent model of hemorrhagic shock. Anesth. Analg., Vol. 112, No. 6, pp1289-95.
3. Fu, X., Walter, M.H., Paredes, A.M. , Morais, M.C., Lui, J., (2011) DNA Ejection by Cryo-Electron Tomography of spore-binding phage. Submitted.
4. Vancini, R., Paredes, A., Ribeiro, M., Ferreira, D., Hernandez, R., Brown, D., (2011) Espirito Santo Virus: A new Birnavirus that replicates in insect cells. Submitted.
 

BioImaging Lab / Division of Neurotoxicology NCTR
62/108, 3900 NCTR Rd, Jefferson AR 72079

Background/Experience:

MD/PhD in biochemistry/pharmacology (Russian State Medical University and National Center for Bioactive Compounds, Moscow, Russia)

7.5 years with Pfizer, Inc (Sr. Principal Scientist, Head of MRI)
2.5 years with FDA (Director of Bio-Imaging)

Mentorship Experience: 3 summer students, 1 graduate student, 3 postdoctoral fellows.
 

Research Interests:

- Utilization of Magnetic Resonance Imaging and Spectroscopy (MRI/MRS) in preclinical study design.
- Imaging biomarkers of neurotoxicity
- Translational biomarkers of addiction
- Novel MRI/MRS data acquisition and analysis

Proposed Research Project for FDA Fellow:

Development of MRI/MRS biomarkers of neurotoxicity in rats. Prototypic neurotoxic compounds will be used to induce brain lesions with the intent of identifying associated metabolic changes in affected tissue. Evaluation of quantitative imaging (MRI/MRS, positron emission tomography) for identifying new potentially translational biomarkers and predictors of efficacy and safety.

Applicant Requirements:

- basic knowledge of MRI physics
- animal handling experience
- MS or PhD in imaging science, biomedical engineering, medical physics, or related areas
- Experience in preclinical MRI is preferable

Selected Recent Publications:

1. Xie Z, Liachenko S, Chiao PC, Carvajal-Gonzalez S, Bove S, Bocan T. In vivo MRI assessment of knee cartilage in the medial meniscal tear model of osteoarthritis in rats. Med Image Comput Assist Interv. 2010; 13(Pt 3): 57-64.
2. Xu Y, Liachenko SM, Tang P, Chan PH. Faster recovery of cerebral perfusion in SOD1-overexpressed rats after cardiac arrest and resuscitation. Stroke. 2009; 40: 2512-8.
3. Major T, Dhamija S, Black N, Liachenko S, Morenko B, Sobocinski G, Okerberg C, Tinholt P, Madore S, Kowala M. The T- and L-Type Calcium Channel Blocker (CCB) Mibefradil Attenuates Leg Edema Induced by the L-Type CCB Nifedipine in the Spontaneously Hypertensive Rat. JPET J Pharmacol Exp Ther. 2008; 325: 723-31.
4. Liachenko S, Tang P, Xu Y. Deferoxamine improves early postresuscitation reperfusion after prolonged cardiac arrest in rats. J Cereb Blood Flow Metab. 2003; 23: 574-81.