Biomedical subjects

M L Shuler

Publications and source records attributed to M L Shuler.

At least 19 recordsLinked to original sources

PubMed2004

A modular minimal cell model: purine and pyrimidine transport and metabolism.

A more complete understanding of the relationship of cell physiology to genomic structure is desirable. Because of the intrinsic complexity of biological organisms, only the simplest cells will allow complete definition of all components and their interactions. The theoretical and experimental construction of a minimal cell has been suggested as a tool to develop such an understanding. Our ultimate goal is to convert a "coarse-grain" lumped parameter computer model of Escherichia coli into a genetically and chemically detailed model of a "minimal cell." The base E. coli model has been converted into a generalized model of a heterotrophic bacterium. This coarse-grain minimal cell model is functionally complete, with growth rate, composition, division, and changes in cell morphology as natural outputs from dynamic simulations where only the initial composition of the cell and of the medium are specified. A coarse-grain model uses pseudochemical species (or modules) that are aggregates of distinct chemical species that share similar chemistry and metabolic dynamics. This model provides a framework in which these modules can be "delumped" into chemical and genetic descriptions while maintaining connectivity to all other functional elements. Here we demonstrate that a detailed description of nucleotide precursors transport and metabolism is successfully integrated into the whole-cell model. This nucleotide submodel requires fewer (12) genes than other theoretical predictions in minimal cells. The demonstration of modularity suggests the possibility of developing modules in parallel and recombining them into a fully functional chemically and genetically detailed model of a prokaryote cell.

Adenylate Kinase↗

PubMed2003

A simple method for enhancing paclitaxel release from Taxus canadensis cell suspension cultures utilizing cell wall digesting enzymes.

Paclitaxel storage in Taxus suspension cell cultures was studied through the simple use of cell wall digesting enzymes. The application of cellulase (1%) and pectolyase (0.1%) to Taxus canadensis suspension cultures induced a significant increase in the paclitaxel present in the extracellular medium while maintaining membrane integrity, suggesting that paclitaxel is stored in the cell wall. The addition of cell wall digesting enzymes to a cell culture bioprocess may be an effective way of enhancing paclitaxel release to the extracellular medium and hence simplify product recovery.

Cell Wall↗

PubMed2001

The effects of pH and surface composition on Pb adsorption to natural freshwater biofilms.

Two dominant variables that control the adsorption of toxic trace metals to suspended particulate materials and aquatic surface coatings are surface composition and solution pH. A model for the pH-dependent adsorption of Pbto heterogeneous particulate surface mixtures was derived from experimental evaluation of Pb adsorption to laboratory-derived surrogates. The surrogate materials were selected to represent natural reactive surface components. Pb adsorption to both the laboratory surrogates and natural biofilms was determined in chemically defined solutions under controlled laboratory conditions. Pb adsorption was measured over a pH range of 5-8, with an initial Pb concentration in solution of 2.0 microM. The surface components considered include amorphous Fe oxide, biogenic Mn oxide produced by a Mn(II) oxidizing bacterium (Leptothrix discophora SS-1), Al oxide, the common green alga Chlorella vulgaris, and Leptothrix discophora SS-1 cells. A linearization of Pb adsorption data for each adsorbent was used to quantify the relationship between Pb adsorption and pH. The parameters for individual adsorbents were incorporated into an additive model to predict the total Pb adsorption in multiple-adsorbent natural surface coatings that were collected from Cayuga Lake, NY. Pb adsorption experiments on the natural surface coatings at variable pH were utilized to verify the additive model predictions based on the pH dependent behavior of the experimental laboratory surrogates. Observed Pb adsorption is consistent with the model predictions (within 1-24%) over the range of solution pH values considered. The experimental results indicate that the combination of Fe and biogenic Mn oxides can contribute as much as 90% of Pb adsorbed on Cayuga Lake biofilms, with the dominant adsorbent switching from Mn to Fe oxide with increasing pH.

Biofilms↗

PubMed2001

Towards the development of a minimal cell model by generalization of a model of Escherichia coli: use of dimensionless rate parameters.

A model of a minimal cell would be a valuable tool in identifying the organizing principles that relate the static sequence information of the genome to the dynamic functioning of the living cell. Our approach for developing a minimal cell model is to first generalize an existing model of Escherichia coli by expressing reaction rates as ratios to a set of reference parameters. This generalized model is a prototype minimal cell model that will be developed by adding detail to explicitly include each chemical species. We tested the concept of a generalized model by testing the effect of scaling all enzyme-catalyzed reactions in the E. coli model. The scaling has little effect on cellular function for a wide range of kinetic ratios, where the kinetic ratio is defined as the rate of all enzyme-catalyzed reactions in a given model relative to those in the E. coli model.

Computer Simulation↗

PubMed2001

Phenanthrene desorption from soil in the presence of bacterial extracellular polymer: observations and model predictions of dynamic behavior.

The extracellular polymer produced by a bacterium isolated from soil was employed in laboratory studies of desorption of a model polynuelear aromatic hydrocarbon (PAH), phenanthrene. The experimental results show that the selected extracellular polymer enhances the extent of release of soil-bound phenanthrene. A kinetic model was developed as an aid in interpreting the alterations in phenanthrene desorption resulting from polymer addition. The model employs a statistical gamma (gamma) distribution to describe spectrum of rate constants for transfer of phenanthrene from soil to water, and assumes instantaneous binding of phenanthrene to polymer and of polymer to the test soil. The relevant distribution coefficients and statistical parameters of the gamma distribution needed for the model were evaluated in independent experiments. Using these measured parameters, the model provides a satisfactory independent prediction of phenanthrene release from soil to aqueous phase at two test polymer concentrations, 50 mg TOC/L and 100 mg TOC/L. The success of the independent model predictions suggests a mechanism for the influence of extracellular polymer on phenanthrene desorption. The intrinsic, soil-specific, rate constants for solid to solution transfer of phenanthrene do not appear to be changed by bacterial polymer. Instead, polymer binding of phenanthrene in solution results in an increase in driving force for desorption by decreasing the solution concentration of the free, unbound, PAH molecule.

Bacteria↗

PubMed2000

Cell science and protein crystal growth research for the International Space Station.

The recent National Research Council report, Future Biotechnology Research on the International Space Station, evaluates NASA's plans for research in cell science and protein crystal growth to be conducted on the International Space Station. This report concludes that the NASA biotechnology programs have the potential to significantly impact relevant scientific fields and to increase understanding and insight into fundamental biological issues. In order to realize the potential impacts, NASA must focus its research programs by selecting specific questions related to gravitational forces' role in cell behavior and by using the microgravity environment as a tool to determine the structure of macromolecules with important biological implications. Given the time and volume constraints associated with space-based experiments, instrumentation to be used on the space station must be designed to maximize the productivity of researchers, and NASA's recruitment of investigators and support for space station experiments should aim to encourage and facilitate cutting-edge research.

Biotechnology↗

PubMed2000

Computer model for glucose-limited growth of a single cell of Escherichia coli B/r-A. Reprinted from Biotechnology and Bioengineering, Vol. 26, Issue 3, Pp 203-216 (1984).

A computer model is described which is capable of predicting changes in cell composition, cell size, cell shape, and the timing of chromosome synthesis in response to changes in external glucose limitation. The model is constructed primarily from information on unrestricted growth in glucose minimal medium. The ability of the model to make reasonable quantitative predictions under glucose-limitation is a test of the plausibility of the basic biochemical mechanisms included in the model. Such a model should be of use in differentiating among competing hypotheses for biological mechanisms and in suggesting as yet unobserved phenomena. The last two points are illustrated with the testing of a mechanism for the control of the initiation of DNA synthesis and predictions on cell-width variations during the division cycle.

Computer Simulation↗

PubMed2000

The effect of inoculum density and conditioned medium on the production of ajmalicine and catharanthine from immobilized Catharanthus roseus cells.

The effect of the cell-inoculum size and the addition of conditioned medium on ajmalicine and catharanthine production were studied using immobilized Catharanthus roseus cells. Higher specific-uptake rates of ammonium, nitrate, and sugars were observed in the low-inoculum-density cultures (50 g FW/L) compared to the high-inoculum-density cultures (100 g FW/L). Alkaloid production was not correlated with the exhaustion of a particular nutrient from the medium. The high-inoculum-density cultures produced higher ajmalicine concentrations throughout the experiment. Catharanthine production was similar between the two inoculum-density cultures. The addition of conditioned medium to MS-production medium dramatically improved the production of ajmalicine and catharanthine. The addition of conditioned medium enhanced ajmalicine production from immobilized Catharanthus roseus cultures on day 15 by at least two- to fourfold compared to media without the conditioning factors. Catharanthine production was increased by nearly fivefold in cultures with conditioned medium compared to those without conditioned medium. The enhancing effects of conditioned medium on alkaloid production were attributed to an unidentified factor produced and secreted by suspension cultures of C. roseus. The presence of conditioned medium also decreased the sucrose hydrolysis rate. The ajmalicine concentration in these immobilized cell cultures was found to be a function of the fresh-weight concentration, irrespective of the inoculum density or the culture medium. The medium choice and the inoculum density determined how rapidly fresh weight was accumulated and thus, how quickly ajmalicine was produced. Ajmalicine production correlated positively with fresh-weight concentration, but catharanthine production was not correlated with fresh-weight concentration.

Biotechnology↗

PubMed1999

Independent prediction of naphthalene transport and biodegradation in soil with a mathematical model.

Experiments were performed to test the ability of a mathematical model to predict naphthalene transport and biodegradation. Pseudomonas putida G7, a model bacterial strain capable of degrading naphthalene, was added to a column packed with the soil that had been pre-equilibrated with naphthalene. Model prediction for transport and degradation were based on predetermined parameters that described naphthalene desorption kinetics and the utilization of naphthalene by the test bacterium. However, initial prediction for naphthalene biodegradation was high, and the formation of cell aggregates is advanced as a plausible explanation. Access of substrate to cells in the interior of an aggregate would be restricted. When the numerical simulation was conducted with a factor to account for cell aggregation, it successfully described the experimental data. Thus, with a single adjustable parameter (an average effectiveness factor), the model predicted macroscopic responses of naphthalene in soil-columns where naphthalene was subject to transport and biodegradation.

Adsorption↗

PubMed1999

Single-cell models: promise and limitations.

This article describes the development of single-cell models, their uses and accomplishments, the barriers to the greater adoption, and a perspective on challenges to the biochemical engineering community where the single-cell model approach may be used advantageously. In particular, it may become an important tool in relating genomic information to cellular regulation and dynamics.

Animals↗

PubMed1999

Glycosylation of a recombinant protein in the Tn5B1-4 insect cell line: influence of ammonia, time of harvest, temperature, and dissolved oxygen.

Glycosylation is both cell line and protein dependent. Culture conditions can also influence the profile of glycoforms produced. To examine this possibility in the insect cell/baculovirus system, structures of N-linked oligosaccharides attached to SEAP (human secreted alkaline phosphatase), expressed under various culture conditions in BTI Tn5B1-4 cells, were characterized using FACE (fluorescence-assisted carbohydrate electrophoresis). Parameters varied were time of harvest, ammonia added during infection, dissolved oxygen, and temperature. It was found that glycosylation in the insect cell/baculovirus expression system is a robust, stable system that is less perturbed by variations in culture conditions than the level of protein expression. Addition of ammonia and low oxygen conditions affected SEAP expression, but not the oligosaccharide profile of SEAP. Time of SEAP harvest increased the amount of alpha-mannosidase resistant structures from 4.1% at 34 hours postinfection (h pi), to 5.0% at 100 h pi, and to 7.5% at 120 h pi. These structures were primarily sensitive to N-acetylhexosaminidase digest, although a small amount was insensitive to both mannosidase and N-acetyl-hexosaminidase digests. Lowering the temperature from 28 degrees C to 24 degrees C or even 20 degrees C, resulted in a twofold increase in oligosaccharides containing terminal alpha(1,3)-mannose residues. This condition did not affect the amount of mannosidase-resistant structures. However, this could result in more complete glycosylation of recombinant proteins in the BTI Tn5B1-4 cell line, because more structures with the potential for further processing would be produced.

Alkaline Phosphatase↗

PubMed1999

The kinetics of taxoid accumulation in cell suspension cultures of Taxus following elicitation with methyl jasmonate.

Cell suspension cultures of Taxus canadensis and Taxus cuspidata rapidly produced paclitaxel (Taxol) and other taxoids in response to elicitation with methyl jasmonate. By optimizing the concentration of the elicitor, and the timing of elicitation, we have achieved the most rapid accumulation of paclitaxel in a plant cell culture, yet reported. The greatest accumulation of paclitaxel occurred when methyl jasmonate was added to cultures at a final concentration of 200 microM on day 7 of the culture cycle. The concentration of paclitaxel increased in the extracellular (cell-free) medium to 117 mg/day within 5 days following elicitation, equivalent to a rate of 23.4 mg/L per day. Paclitaxel was only one of many taxoids whose concentrations increased significantly in response to elicitation. Despite the rapid accumulation and high concentration of paclitaxel, its concentration never exceeded 20% of the total taxoids produced in the elicited culture. Two other taxoids, 13-acetyl-9-dihydrobaccatin III and baccatin VI, accounted for 39% to 62% of the total taxoids in elicited cultures. The accumulation of baccatin III did not parallel the pattern of accumulation for paclitaxel. Baccatin III continued to accumulate until the end of the culture cycle, at which point most of the cells in the culture were dead, implying a possible role as a degradation product of taxoid biosynthesis, rather than as a precursor.

Acetates↗

PubMed1999

Isolation of labeled 9-dihydrobaccatin III and related taxoids from cell cultures of taxuscell cultures of taxus canadensis elicited with m.

Cell suspension cultures of Taxus canadensis rapidly produced paclitaxel (1) and other taxoids in response to elicitation with methyl jasmonate. Three of these taxoids, of potential value in the synthesis of taxoid analogues, have been isolated from cell cultures of Taxus canadensis and identified as 13-acetyl-9-dihydrobaccatin III (2), baccatin VI (3), and 9-dihydrobaccatin III (4). Of these metabolites, 9-dihydrobaccatin III (4) has not been isolated from any Taxus species, whereas 13-acetyl-9-dihydrobaccatin III (2) and baccatin VI (3) have been isolated from a number of natural sources. 2D NMR techniques, mass spectrometry, and partial synthesis were used to rigorously elucidate the structure and stereochemistry of these natural products.

Acetates↗

PubMed1998

Growth kinetics of Pseudomonas putida G7 on naphthalene and occurrence of naphthalene toxicity during nutrient deprivation.

The objectives of this work were (1) to demonstrate how the chemostat approach could be modified to allow determination of kinetic parameters for a sparingly soluble, volatile substrate such as naphthalene and (2) to examine the influence of the interactions of various nutrients on possible growth-inhibitory effects of naphthalene. Pseudomonas putida G7 was used as a model naphthalene-degrading microorganism. Naphthalene was found to be toxic to P. putida G7 in the absence of a nitrogen source or oxygen. The death rate of cells grown on minimal medium plus naphthalene and then exposed to naphthalene under anoxic conditions was higher than that observed under oxic conditions in the absence of a nitrogen source. The presence of necessary nutrients for the biodegradation of PAH compounds is indicated to be important for the survival of microorganisms that are capable of PAH degradation. The amounts of ammonia and oxygen necessary for naphthalene biodegradation and for suppression of naphthalene toxicity were calculated from growth yield coefficients. A chemostat culture of P. putida G7 using naphthalene as a carbon and energy source was accomplished by using a feed augmented with a methanol solution of naphthalene so as to provide sufficient growth to allow accurate evaluation of kinetic parameters. When naphthalene was the growth-limiting substrate, the degradation of naphthalene followed Monod kinetics. Maximum specific growth rate (micrometer) and Monod constant (Ks) were 0.627 +/- 0.007 h-1 and 0.234 +/- 0.0185 mg/L, respectively. The evaluation of biodegradation parameters will allow a mathematical model to be applied to predict the long-term behavior of PAH compounds in soil when combined with PAH transport parameters.

Ammonia↗

PubMed1998

N-glycosylation of a baculovirus-expressed recombinant glycoprotein in three insect cell lines.

The capacity of two Trichoplusia ni (TN-368 and BTI-Tn-5b 1-4) and a Spodoptera frugiperda (IPLB-SF-21A) cell lines to glycosylate recombinant, baculovirus-encoded, secreted, placental alkaline phosphatase was compared. The alkaline phosphatase from serum-containing, cell culture medium was purified by phosphate affinity column chromatography. The N-linked oligosaccharides were released from the purified protein with PNGase F and analyzed by fluorophore-assisted carbohydrate electrophoresis. The majority of oligosaccharide structures produced by the three cell lines contained two or three mannose residues, with and without core fucosylation, but there were structures containing up to seven mannose residues. The oligosaccharides that were qualitatively or quantitatively different between the cell lines were sequenced with glycosidase digestions. The S. frugiperda cells produced more fucosylated oligosaccharides than either of the T. ni cell lines. The smallest oligosaccharide produced by S. frugiperda cells was branched trimannose. In contrast, both T. ni cell lines produced predominantly dimannose and linear trimannose structures devoid of alpha 1-3-linked mannose.

Alkaline Phosphatase↗

PubMed1996

Kinetics of taxol production and nutrient use in suspension cultures of Taxus cuspidata in shake flasks and a Wilson-type bioreactor.

Suspension cultures of Taxus cuspidata were grown in shake flasks and Wilson-type reactors where bubbled air provided both agitation and mixing. Taxol titers of 22 mg l-1 were achieved for both configurations in 20 days for a volumetric productivity of 1.1 mg l-1 day-1. This productivity is many-fold higher than reported for other Taxus sp. suspension cultures. Taxol was released to the extracellular medium as it was produced with little intracellular retention (< or = 10%). Taxol production occurred during the last seven days of the cultivation period and was not growth-associated. Although the same taxol titers could be obtained in both reactor types, nutrient uptake rates were faster in the Wilson-type reactor than in shake flasks. Formation of a growth ring in the Wilson-type reactor reduced measured cell mass yields.

Antineoplastic Agents, Phytogenic↗

PubMed1995

Possible involvement of the Ah receptor in the induction of cytochrome P-450IA1 under conditions of hydrodynamic shear in microcarrier-attached hepatoma cell lines.

The exposure of two hepatoma cell lines, Hep G2 and Hepa-1, to moderate hydrodynamic shear, in microcarrier-attached suspension cultures, resulted in the transient induction of cytochrome P450IA1 (CYP1A1). Both cell lines have been characterized with respect to their Ah receptor (AhR) concentrations and induce CYP1A1 in response to exposure to xenobiotics such as 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). Using an AhR antagonist, alpha-naphthoflavone (alpha-NF) and a protein kinase C (PKC) inhibitor, staurosporine (ST), in the Hep G2 cell line, the induced CYP1A1 activity was modulated in the same manner as when the cells were coexposed to TCDD and either alpha-NF or ST. Exposure of the Hep G2 cell line to TCDD and shear resulted in both enhancement of the induced CYP1A1 activity in addition to a competitive response. Finally, using the wild type and AhR defective Hepa-1 cell lines, it was demonstrated that a functional AhR was required for shear-induced CYP1A1 expression. The data obtained in the three cell lines indicate a role for the AhR in the induction of CYP1A1 by shear in agitated microcarrier cultures.

Alkaloids↗

PubMed1995

Trace metal mobilization in soil by bacterial polymers.

Enhanced transport of trace metal in porous media can occur in the presence of a ligand or "carrier" that has a high affinity for binding the pollutant, is dispersed and mobile in the soil environment, is recalcitrant with respect to microbial degradation, and is acceptable to the public. These aspects of the facilitated transport to trace metals are discussed with respect to a naturally occurring carrier: extracellular polymers of bacterial origin. The literature is reviewed regarding the production and composition of bacterial extracellular polymers, the processes relevant to the facilitated transport of trace metals in soil by bacterial polymers, and potential for transformation of polymers in soils by microbial degradation. Model calculations of contaminant retardation are presented for the case of polymer-mediated transport of cadmium in a sandy aquifer material. The available information suggests that extracellular polymers can bind metal ions and are mobile in the soil environment. Extracellular polymers also appear to be relatively slowly degraded by soil microorganisms. These properties and the supporting model calculations indicate that extracellular polymers of bacterial origin merit consideration as agents that may be applied to contaminated soils to enhance trace metal mobility.

Bacteria↗