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P Dhurjati

Publications and source records attributed to P Dhurjati.

15 recordsLinked to original sources
PubMed2006

Modeling and observer design for recombinant Escherichia coli strain.

A mathematical model for recombinant bacteria which includes foreign protein production is developed. The experimental system consists of an Escherichia Coli strain and plasmid pIT34 containing genes for bioluminescence and production of a protein, beta-galactosidase. This recombinant strain is constructed to facilitate on-line estimation and control in a complex bioprocess. Several batch experiments are designed and performed to validate the developed model. The design of a model structure, the identification of the model parameters and the estimation problem are three parts of a joint design problem. A nonlinear observer is designed and an experimental evaluation is performed on a batch fermentation process to estimate the substrate consumption.

Bioreactors↗
PubMed2000

Quaternary ammonium functionalized poly(propylene imine) dendrimers as effective antimicrobials: structure-activity studies.

Quaternary ammonium functionalized poly(propyleneimine) dendrimers were synthesized and their antibacterial properties were evaluated using a bioluminescence method. These quaternary ammonium dendrimers are very potent biocides. The antibacterial properties depend on the size of the dendrimer, the length of hydrophobic chains in the quaternary ammonium groups, and the counteranion. Since these dendrimers are well characterized and monodisperse, they also serve as an effective system to study the structure-activity relationship. The antimicrobial properties of these dendrimer biocides have a parabolic dependence on molecular weight, which is different from the bell-shaped molecular weight dependence of conventional polymer biocides. The dependence on the hydrophobic chain of the quaternary ammonium structure is similar to conventional polymer biocides, and shows a parabolic relationship with dendrimer biocides carrying C10 hydrophobes the most potent. The antimicrobial properties of these novel biocides with bromide anions are more potent than those with chloride anions. Biocides derived from hyperbranched polymers were also synthesized and found to possess somewhat lower effectiveness.

Anti-Bacterial Agents↗
PubMed1995

Synthesis of non-translating or translating specialized ribosomes causes feedback regulation of ribosomal RNA synthesis in Escherichia coli.

Specialized ribosomes carry a mutant anti-Shine-Dalgarno region that disrupts the complementary base pairing that stabilizes the translation initiation complex with E. coli mRNAs. It has been reported that production of specialized ribosomes does not cause the inhibition of chromosomal rRNA synthesis that follows production of wild-type ribosomes. We proposed that enabling translation on specialized ribosomes by providing mRNA with a complementary mutation in the Shine-Dalgarno region would restore feedback regulation and inhibit chromosomal rRNA synthesis. With both our system and the system studied previously, we saw feedback regulation regardless of whether the specialized ribosomes were translating. As reported previously, transcription from plasmid-borne promoters decreased as chromosomal rRNA synthesis was repressed, suggesting that the lambda PL and tac promoters may be sensitive to the effector(s) of feedback regulation.

Base Sequence↗
PubMed1995

Protein aggregation kinetics in an Escherichia coli strain overexpressing a Salmonella typhimurium CheY mutant gene.

The tendency of recombinant protein in bacteria to partition into soluble and insoluble forms is attributed, in general, to a kinetic competition between protein folding and aggregation. However, little experimental work has actually been performed in vivo on the kinetics and mechanisms of protein folding and aggregation. Results are presented here from radiolabeling experiments which monitored the kinetics of recombinant protein aggregation in actively growing cultures. The strain used was an Escherichia coli strain overexpressing a Salmonella typhimurium CheY mutant gene. The rate of CheY aggregation was found to be time dependent in that the tendency of CheY to aggregate was greater for newly translated molecules, i.e., those translated within the previous several minutes, than for molecules translated less recently. CheY protein molecules that were translated less recently continued to aggregate for several hours but at a lower rate. The movement of soluble CheY to the insoluble form was enhanced at elevated growth temperatures and inhibited by the presence of chloramphenicol. The latter observation suggests that ongoing translation facilitates the movement of soluble CheY to the insoluble form. The implications of these results for the mechanism of protein aggregation in vivo, i.e., inclusion body formation, are discussed.

Bacterial Proteins↗
PubMed1994

Mathematical model of temperature-sensitive plasmid replication.

The copy number of a series of plasmids constructed at Odense University is regulated by the lambda PR/PRM promoters and the temperature-sensitive cI857 repressor. At low temperatures, these plasmids exhibit the low copy number of the parent plasmid R1 (5-6 per cell). At high temperatures, the plasmids exhibit runaway replication, reaching copy numbers of greater than 1,000 per cell. A detailed mathematical model of the temperature-sensitive replication of these plasmids has been developed incorporating three features: replication of the parent plasmid, regulation of the lambda PR/PRM promoters by the cI repressor, and thermal denaturation of the cI857 repressor. Models of the first two of these features have been described by others. We revised and extended those models, described the thermal denaturation of the cI857 repressor, and integrated these features to give a comprehensive model of temperature-sensitive plasmid replication. Model predictions were compared to experimental measurements of both steady-state copy numbers as a function of temperature and the change in copy number following temperature shifts up and down. The model accurately describes the qualitative behavior of the system and gives reasonable quantitative results. This is particularly significant since all the parameter values used in this model were determined independently: that is, there was no adjustment of parameter values to match our experimental data. The regulatory system that gives rise to the temperature-sensitive replication of these plasmids is widely used in biotechnology applications, so the elements of the model related to this regulation should be applicable to a wide variety of systems.

Bacterial Outer Membrane Proteins↗
PubMed1993

Properties conferred on Clostridium thermocellum endoglucanase CelC by grafting the duplicated segment of endoglucanase CelD.

The DNA sequence encoding the duplicated 22 amino acid segment of Clostridium thermocellum endoglucanase CelD was fused to the 3'-terminus of the celC gene encoding C.thermocellum endoglucanase CelC. The presence of the duplicated segment endowed CelC with the capacity to form cytoplasmic inclusion bodies containing active enzyme when the hybrid gene was expressed in Escherichia coli. Inclusion body formation prevented proteolytic cleavage of the duplicated segment. The intact hybrid protein CelC-Cel'D was purified from inclusion bodies and characterized. In contrast to CelC, CelC-Cel'D was able to bind to CipA, a protein acting as a scaffolding component of the C.thermocellum cellulase complex (cellulosome). However, the catalytic properties of CelC-Cel'D were similar to those of CelC. These results suggest that foreign proteins tagged with the duplicated segment could be incorporated into the cellulosome in order to modify the enzymatic properties of the complex. The formation of inclusion bodies by proteins carrying the duplicated segment may also prove a convenient means of purifying cloned gene products that are sensitive to proteolytic degradation.

Amino Acid Sequence↗
PubMed1991

Interaction of the duplicated segment carried by Clostridium thermocellum cellulases with cellulosome components.

The function of the non-catalytic, duplicated segment found in C. thermocellum cellulases was investigated. Rabbit antibodies reacting with the duplicated segment of endoglucanase CelD cross-reacted with a variety of cellulosome components ranging between 50 and 100 kDa. 125I-labeled forms of CelD and of xylanase XynZ carrying the duplicated segment bound to a set of cellulosome proteins ranging between 66 and 250 kDa, particularly to the 250 kDa SL (or S1) subunit. 125I-labeled forms of CelD and XynZ devoid of the duplicated segment failed to bind to any cellulosome protein. The duplicated segment appears thus to serve to anchor the various cellulosome subunits to the complex by binding to SL, which may be a scaffolding element of the cellulosome.

Animals↗
PubMed1991

High activity of inclusion bodies formed in Escherichia coli overproducing Clostridium thermocellum endoglucanase D.

The formation of cytoplasmic inclusion bodies by Escherichia coli overproducing Clostridium thermocellum endoglucanase D (EGD) was investigated. EGD was found in inclusion bodies as a 68 kDa form, whereas the size of the cytoplasmic form was 65 kDa. Upon solubilization with urea followed by dialysis, the 68 kDa form was converted to the 65 kDa species. Proteolysis occurred within the COOH-terminal, reiterated region of the 68 kDa form, which is conserved among most C. thermocellum endoglucanases, but is not required for catalytic activity. The specific activity of the enzyme embedded in inclusion bodies was close to that of the purified protein. Thus, inclusion body formation does not involve denaturation of the catalytic domain of EGD, but, more likely, the participation of the reiterated, conserved region in intermolecular interactions.

Blotting, Western↗
PubMed1987

Isolation of high-molecular-weight nucleic acids for copy number analysis using high-performance liquid chromatography.

The Nucleogen DEAE 4000-10 high-performance liquid chromatography (HPLC) column was shown to isolate tRNA, rRNA, and DNA from crude cell lysates in the presence of a denaturant. Chromosomal DNA and plasmid DNA coeluted and retention was independent of size. An HPLC technique for plasmid copy number determination was then developed, verified, and optimized. The assay was successfully applied to a recombinant yeast system. Similar results were obtained earlier for recombinant Escherichia coli. The copy number can be calculated from the ratio of plasmid DNA to rRNA, then calculated to a per-cell basis using literature and measured constants. Chromosomal DNA coeluted with plasmid DNA and so was removed prior to analysis. For recombinant systems were the rRNA content is not constant, the plasmid area along with cell concentration can be used to calculate plasmid copy number. Nucleic acids' responses were linear, and plasmid copy number results using peak ratios had a low percent standard deviation. Errors increased when the absolute plasmid area was used to calculate plasmid copy number.

Chromatography, DEAE-Cellulose↗
PubMedDate not supplied

Fractional factorial study of hybridoma behavior. 1. Kinetics of growth and antibody production.

A comprehensive approach was taken toward the quantitative study of hybridoma growth and antibody production. A fractional factorial experimental method was used to identify important variables and variable interactions affecting hybridoma behavior. The variables studied include temperature, pH, dissolved oxygen, glucose, glutamine, base medium, serum, lactate, and ammonium. The growth rate was strongly affected by the levels of dissolved oxygen, pH, temperature, and base medium. Interactions between temperature, pH, and dissolved oxygen were important. The optimal pH for growth depends upon the temperature and dissolved oxygen concentration. In general, growth was fastest at low dissolved oxygen levels. The growth rate was very sensitive to low concentrations of base medium, but was relatively insensitive to the serum concentration at levels above 2.5%. Antibody production was stimulated by high concentrations of base medium and serum and inhibited by ammonium and lactate. Antibody production increased linearly with serum concentration. In general, conditions that favored a high growth rate also favored a high specific rate of antibody production. The functional dependencies of antibody production on base medium and ammonium were similar to those for cell growth; however, antibody production and cell growth exhibited different dependencies on serum. Mathematical descriptions of cell growth and antibody production were developed. These experimental results have significant implications for the optimization of hybridoma growth in bioreactors.

Antibodies, Monoclonal↗
PubMedDate not supplied

Fractional factorial study of hybridoma behavior. 2. Kinetics of nutrient uptake and waste production.

A fractional factorial experimental method was used to identify important variables and variable interactions which affect nutrient uptake and waste production. The variables studied include glucose, glutamine, base medium, lactate, and ammonium. Cellular glucose uptake was stimulated by glucose and glutamine and inhibited by lactate. Glucose, base medium, and glutamine all had large stimulative effects on lactate production. Glucose uptake and lactate production both exhibited Monod-type dependencies on the glucose concentration. Ammonium production was sensitive to the glucose and lactate concentrations at levels below about 8 and 20 mM, respectively. Mathematical descriptions of glucose uptake and of lactate and ammonium production were developed. These experimental results have significant implications for the optimization of hybridoma growth in bioreactors.

Cell Division↗
PubMedDate not supplied

Construction and characterization of a specialized ribosome system for the overproduction of proteins in Escherichia coli.

A recombinant Escherichia coli system was constructed to overexpress proteins using the specialized ribosomes developed by Herman de Boer and co-workers at Genentech. Specialized ribosomes carry a mutation in the anti-Shine-Dalgarno region of 16 S ribosomal RNA, which is the site of messenger RNA binding. A complementary mutation in the ribosome binding site (the Shine-Dalgarno region) of a particular mRNA results in specific and efficient translation of this mRNA on the specialized ribosomes. Production of beta-galactosidase with this system was characterized with respect to transcription, translation, plasmid replication, and cell growth rate. Translation of specialized mRNA on specialized ribosomes gave 5 times more enzyme activity than did translation of wild-type mRNA on wild-type ribosomes under similar conditions. The system described here offers a number of advantages when compared to a similar system described recently: (1) two separate specialized systems were constructed; (ii) the genes for specialized mRNA and specialized rRNA are on separate plasmids, allowing for different combinations of mRNA and rRNA; and (iii) appropriate controls were constructed for each plasmid.

Base Sequence↗
PubMedDate not supplied

Specialized ribosomes in Escherichia coli.

Specialized ribosomes, developed by de Boer and co-workers at Genentech, carry a mutation in the anti-Shine-Dalgarno region of 16 S ribosomal RNA, the site of messenger RNA binding. A complementary mutation in the ribosome binding site (the Shine-Dalgarno region) of a particular messenger RNA results in specific and efficient translation of that messenger RNA on the specialized ribosomes. With this system, a fraction of the cell's ribosomes can be dedicated to the translation of a single messenger RNA; the remaining wild-type ribosomes carry out the normal cellular translation processes. Specialized ribosomes have been used for the overproduction of proteins, analysis of the feedback regulation of ribosomal RNA synthesis, and mutational analysis of 16 S ribosomal RNA. Experimental results related to each of these topics are summarized and discussed, and other potential applications are described. In particular, we propose a novel technique for mutational analysis of 23 S ribosomal RNA, the primary RNA constituent of the large ribosomal subunit, using the specialized ribosome approach.

Base Sequence↗
PubMedDate not supplied

Monitoring of recombinant protein production using bioluminescence in a semiautomated fermentation process.

On-line optimization of fermentation processes can be greatly aided by the availability of information on the physiological state of the cell. The goal of our "BioLux" research project was to design a recombinant cell capable of intracellular monitoring of product synthesis and to use it as part of an automated fermentation system. A recombinant plasmid was constructed containing an inducible promoter that controls the gene coding for a model protein and the genes necessary for bioluminescence. The cells were cultured in microfermenters equipped with an on-line turbidity sensor and a specially designed on-line light sensor capable of continuous measurement of bioluminescence. Initial studies were done under simple culture conditions, and a linear correlation between luminescence and protein production was obtained. Such specially designed recombinant bioluminescent cells can potentially be applied for model-based inference of intracellular product formation, as well as for optimization and control of recombinant fermentation processes.

Bioreactors↗