Biomedical subjects

Mohammad M Ataai

Publications and source records attributed to Mohammad M Ataai.

6 recordsLinked to original sources

PubMed2006

A three-level problem-centric strategy for selecting NMR precursor labeling and analytes.

We have developed a sequential set of computational screens that may prove useful for evaluating analyte sets for their ability to accurately report on metabolic fluxes. The methodology is problem-centric in that the screens are used in the context of a particular metabolic engineering problem. That is, flux bounds and alternative flux routings are first identified for a particular problem, and then the information is used to inform the design of nuclear magnetic resonance (NMR) experiments. After obtaining the flux bounds via MILP, analytes are first screened for whether the predicted NMR spectra associated with various analytes can differentiate between different extreme point (or linear combinations of extreme point) flux solutions. The second screen entails determining whether the analytes provide unique flux values or multiple flux solutions. Finally, the economics associated with using different analytes is considered in order to further refine the analyte selection process in terms of an overall utility index, where the index summarizes the cost-benefit attributes by quantifying benefit (contrast power) per cost (e.g., NMR instrument time required). We also demonstrate the use of an alternative strategy, the Analytical Hierarchy Process, for ranking analytes based on the individual experimentalist's-generated weights assigned for the relative value of flux scenario contrast, unique inversion of NMR data to fluxes, etc.

Algorithms↗

PubMed2004

Immobilized cobalt affinity chromatography provides a novel, efficient method for herpes simplex virus type 1 gene vector purification.

Herpes simplex virus type 1 (HSV-1) is a promising vector for gene therapy applications, particularly at peripheral nerves, the natural site of virus latency. Many gene vectors require large particle numbers for even early-phase clinical trials, emphasizing the need for high-yield, scalable manufacturing processes that result in virus preparations that are nearly free of cellular DNA and protein contaminants. HSV-1 is an enveloped virus that requires the development of gentle purification methods. Ideally, such methods should avoid centrifugation and may employ selective purification processes that rely on the recognition of a unique envelope surface chemistry. Here we describe a novel method that fulfills these criteria. An immobilized metal affinity chromatography (IMAC) method was developed for the selective purification of vectors engineered to display a high-affinity binding peptide. Feasibility studies involving various transition metal ions (Cu2+, Zn2+, Ni2+, and Co2+) showed that cobalt had the most desirable features, which include a low level of interaction with either the normal virus envelope or contaminating DNA and proteins. The introduction of a cobalt-specific recognition element into the virus envelope may provide a suitable target for cobalt-dependent purification. To test this possibility, we engineered a peptide with affinity for immobilized cobalt in frame in the heparan sulfate binding domain of HSV-1 glycoprotein B, which is known to be exposed on the surface of the virion particle and recombined into the viral genome. By optimizing the IMAC loading conditions and reducing cobalt ion leakage, we recovered 78% of the tagged HSV-1 recombinant virus, with a >96% reduction in contaminating proteins and DNA.

Adsorption↗

PubMed2004

Tagging retrovirus vectors with a metal binding peptide and one-step purification by immobilized metal affinity chromatography.

Retroviral vectors produced from packaging cells are invariably contaminated by protein, nucleic acid, and other substances introduced in the manufacturing process. Elimination of these contaminants from retroviral vector preparations is helpful to reduce unwanted side effects, and purified vector preparations are desirable to improve reproducibility of therapeutic effect. Here we report a novel approach to engineer a metal binding peptide (MBP)-tagged murine leukemia virus (MuLV), allowing for one-step purification of retroviral vectors by immobilized metal affinity chromatography (IMAC). We inserted a His6 peptide into an ecotropic envelope protein (Env) by replacing part of its hypervariable region sequence with a sequence encoding the His6 peptide. Display of the His6 tag on the surface of Env endowed the vectors with a high affinity for immobilized metal ions, such as nickel. We demonstrated that the His6-tagged MuLV could be produced to high titers and could be highly purified by one-step IMAC. The protein and DNA contaminants in the purified vector supernatants were below 7 microg/ml and 25 pg/ml, respectively, indicating a 1,229-fold reduction in protein contaminant level and a 6,800-fold reduction in DNA contaminant level. About 56% of the viral vectors were recovered in the IMAC purification. The purified vectors retained their functionality and infectivity. These results establish that an MBP can be functionally displayed on the surface of ecotropic retroviruses without interfering with their integrity, and MBP-tagged retroviral vectors can be highly purified by one-step IMAC.

Amino Acid Sequence↗

PubMed2002

Effect of genetic background and culture conditions on the production of herpesvirus-based gene therapy vectors.

Herpes simplex virus type-1 (HSV-1) represents a unique vehicle for the introduction of foreign DNA to cells of a variety of tissues. The nature of the vector, the cell line used for propagation of the vector, and the culture conditions will significantly impact vector yield. An ideal vector should be deficient in genes essential for replication as well as those that contribute to its cytotoxicity. Advances in the engineering of replication-defective HSV-1 vectors to reduce vector-associated cytotoxicity and attain sustained expression of target genes make HSV-1 an attractive gene-delivery vehicle. However, the yield of the less-cytotoxic vectors produced in standard tissue-culture systems is at least three order of magnitudes lower than that achieved with wild-type virus. The low overall yield and the complexity involved in the preparation of HSV vectors at high concentrations represent major obstacles in use of replication-defective HSV-derived vectors in gene therapy applications. In this work, the dependence of the vector yield on the genetic background of the virus is examined. In addition, we investigated the production of the least toxic, lowest-yield vector in a CellCube bioreactor system. After initial optimization of the operational parameters of the cellcube system, we were able to attain virus yields similar to or better than those values attained using the tissue culture flask system for vector production with significant savings with respect to time, labor, and cost.

Bioreactors↗

PubMedDate not supplied

Evaluation of infection parameters in the production of replication-defective HSV-1 viral vectors.

Herpes simplex virus type-1 (HSV-1) is a neurotrophic human pathogen that establishes life-long latency in the nervous system. Our laboratory has extensively engineered this virus to retain the ability to persist in neurons without expression of lytic genes or disease phenotype. Highly defective, replication-incompetent HSV mutants are thus potentially ideal for transfer of therapeutic transgenes to human nerves where long-term therapy of nervous system disease may be provided. A prerequisite for using recombinant HSV vectors for therapeutic gene delivery to humans is the development of methods for large-scale manufacture of HSV vectors. Here we report studies to identify infection parameters that result in high-yield production of immediate early gene deletion mutant HSV vectors in complementing cells that supply the deleted essential viral functions in trans. Virus yield was correlated with various culture media conditions that included pH, glucose metabolism, and serum levels. The results demonstrated that systematic media exchange to remove lactate derived from high-level glucose consumption, maintenance of tissue culture pH at 6.8, and the use of 5% fetal bovine serum gave the highest yield of infectious virus. The data indicate that these are important parameters to consider for high-yield, large-scale virus production.

Animals↗

PubMedDate not supplied

Regulating expression of pyruvate kinase in Bacillus subtilis for control of growth rate and formation of acidic byproducts.

Our prior work has shown that a pyk mutant of Bacillus subtilis exhibited diminished acidic byproduct accumulation, dramatically elevated phosphoenolpyruvate (PEP) pool, and reduced growth rate. To determine if a low acetate-producing but fast-growing strain of B. subtilis could be developed, we placed the expression of the pyk gene under the control of an inducible promoter. Enzyme measurements proved that PYK activity of the inducible PYK mutant (iPYK) increases with the isopropyl-beta-d-thiogalactopyranoside concentration. Batch growth experiments showed that growth rate and acid formation are closely related to the induction level of pyk. Measurements of cell growth rate and acetate formation of the iPYK mutant at different induction levels revealed that a PYK activity of about 12% of wild-type allows for good growth rate (0.4 h(-)(1) versus 0.63 h(-)(1) of wild-type) and low acetate production (0.26 g/L versus 1.05 g/L of wild-type). This is the first report to our knowledge of a metabolically engineered B. subtilis strain that allows good growth rate and low acid production in batch cultures. Finally, it was found that, by varying the pyk induction level, intracellular PEP concentration can be controlled over a wide range. The intracellular PEP concentration is intimately connected to the regulation of the transport of phosphotransferase system (PTS) sugars in the presence of glucose. Because there is no other method for modulating intracellular PEP levels, this finding represents a major advance in one's ability to dissect the function of the PTS and sugar metabolism in bacteria.

Bacillus subtilis↗