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Biomedical subjects

V Nagarajan

Publications and source records attributed to V Nagarajan.

At least 19 recordsLinked to original sources
PubMed2005

Spectroscopic imaging of protein crystals in crystallization drops.

Automatic imaging and scoring of crystallization drops is an essential step in high-throughput crystallography. Presently, white-light images of crystallization drops are acquired robotically and the images are analyzed and scored using pattern recognition algorithms. However, the scoring part remains unreliable as crystals and microcrystals are not always recognized by existing feature-extraction and recognition algorithms. We propose a fundamental shift in crystal monitoring through spectroscopic imaging of crystallization drops. This method converts the problem of automatic crystal detection from one of pattern recognition into one of intensity (concentration) analysis. The latter can be more robust and reliable.

Crystallization↗
PubMed2003

Effects of ionizable residues on the absorption spectrum and initial electron-transfer kinetics in the photosynthetic reaction center of Rhodobacter sphaeroides.

Effects of ionizable amino acids on spectroscopic properties and electron-transfer kinetics in the photosynthetic reaction center (RC) of Rhodobacter sphaeroides are investigated by site-directed mutations designed to alter the electrostatic environment of the bacteriochlorophyll dimer that serves as the photochemical electron donor (P). Arginine residues at homologous positions in the L and M subunits (L135 and M164) are changed independently: Arg L135 is replaced by Lys, Leu, Glu, and Gln and Arg M164 by Leu and Glu. Asp L155 also is mutated to Asn, Tyr L164 to Phe, and Cys L247 to Lys and Asp. The mutations at L155, L164, and M164 have little effect on the absorption spectrum, whereas those at L135 and L247 shift the long-wavelength absorption band of P to higher energies. Fits to the ground-state absorption and hole-burned spectra indicate that the blue shift and increased width of the absorption band in the L135 mutants are due partly to changes in the distribution of energies for the zero-phonon absorption line and partly to stronger electron-phonon coupling. The initial electron-transfer kinetics are not changed significantly in most of the mutants, but the time constant increases from 3.0 +/- 0.2 in wild-type RCs to 4.7 +/- 0.2 in C(L247)D and 7.0 +/- 0.3 ps in C(L247)K. The effects of the mutations on the solvation free energies of the product of the initial electron-transfer reaction (P(+)) and the charge-transfer states that contribute to the absorption spectrum ( and ) were calculated by using a distance-dependent electrostatic screening factor. The results are qualitatively in accord with the view that electrostatic interactions of the bacteriochlorophylls with ionized residues of the protein are strongly screened and make only minor contributions to the energetics and dynamics of charge separation. However, the slowing of electron transfer in the Cys L247 mutants and the blue shift of the spectrum in some of the Arg L135 and Cys L247 mutants cannot be explained consistently by electrostatic interactions of the mutated residues with P and B(L); we ascribe these effects tentatively to structural changes caused by the mutations.

Amino Acid Substitution↗
PubMed2003

Bacterial diversity in an industrial wastewater bioreactor.

Industrial wastewater bioreactors are potentially important sources of novel biocatalysts. However, the microbial populations in these bioreactors are not well characterized. The microbial community in an industrial wastewater bioreactor was surveyed by extracting DNA from a sample of activated sludge, followed by PCR amplification and sequencing of cloned 16S rRNA genes. A total of 407 cloned 16S rRNA gene sequences were compared with 88 bacterial isolates cultured from the same sample of sludge using a variety of standard media. Most of the bacteria detected by the PCR-based approach were beta-subdivision Proteobacteria, whereas most of the cultured bacteria were gamma-subdivision Proteobacteria. Only a few types of bacteria were detected by both approaches. These observations indicate that multiple techniques are necessary to characterize the microbial diversity in any complex ecosystem.

Bacteria↗
PubMed2003

Epitaxial BiFeO3 multiferroic thin film heterostructures.

Enhancement of polarization and related properties in heteroepitaxially constrained thin films of the ferroelectromagnet, BiFeO3, is reported. Structure analysis indicates that the crystal structure of film is monoclinic in contrast to bulk, which is rhombohedral. The films display a room-temperature spontaneous polarization (50 to 60 microcoulombs per square centimeter) almost an order of magnitude higher than that of the bulk (6.1 microcoulombs per square centimeter). The observed enhancement is corroborated by first-principles calculations and found to originate from a high sensitivity of the polarization to small changes in lattice parameters. The films also exhibit enhanced thickness-dependent magnetism compared with the bulk. These enhanced and combined functional responses in thin film form present an opportunity to create and implement thin film devices that actively couple the magnetic and ferroelectric order parameters.

Journal Article↗
PubMed2003

A small cryptic plasmid from Rhodococcus erythropolis: characterization and utility for gene expression.

Exploration of metabolically diverse rhodococci is generally hampered by the lack of genetic tools. A small cryptic plasmid (pAN12) isolated from Rhodococcus erythropolis strain AN12 was sequenced. Plasmid pAN12 encodes proteins that share homology to replication proteins and putative cell division proteins. Based on in vitro transposon mutagenesis, we determined that the Rep protein of pAN12 is essential for plasmid replication in Rhodococcus spp., and the putative cell division protein Div is important for plasmid stability. The pAN12 replicon is able to replicate in R. erythropolis strains AN12 and CW23 (ATCC 47072) and is compatible with the nocardiophage Q4 replicon present on a Rhodococcus shuttle plasmid pDA71. pAN12 appears to belong to the pIJ101/pJV1 family of rolling circle replication plasmids. Expression of an isoprenoid pathway gene ( dxs) on the pAN12-derived multicopy shuttle vector increased production of carotenoid pigments in R. erythropolis ATCC 47072.

Adenosine Triphosphatases↗
PubMed2003

Dynamics of ferroelastic domains in ferroelectric thin films.

Dynamics of domain interfaces in a broad range of functional thin-film materials is an area of great current interest. In ferroelectric thin films, a significantly enhanced piezoelectric response should be observed if non-180 degrees domain walls were to switch under electric field excitation. However, in continuous thin films they are clamped by the substrate, and therefore their contribution to the piezoelectric response is limited. In this paper we show that when the ferroelectric layer is patterned into discrete islands using a focused ion beam, the clamping effect is significantly reduced, thereby facilitating the movement of ferroelastic walls. Piezo-response scanning force microscopy images of such islands in PbZr0.2Ti0.8O3 thin films clearly point out that the 90 degrees domain walls can move. Capacitors 1 microm2 show a doubling of the remanent polarization at voltages higher than approximately 15 V, associated with 90 degrees domain switching, coupled with a d33 piezoelectric coefficient of approximately 250 pm V-1 at remanence, which is approximately three times the predicted value of 87 pm V-1 for a single domain single crystal.

Biomedical Engineering↗
PubMed2002

Biotransformation of p-xylene and 2,6-dimethylnaphthalene by xylene monooxygenase cloned from a Sphingomonas isolate.

Sphingomonas strain ASU1 was isolated from an industrial wastewater bioreactor and grew on 2,6-dimethylnaphthalene (2,6-DMN) as the sole carbon/energy source. The genes for a xylene monooxygenase were cloned from strain ASU1. Expression of the ASU1 xylene monooxygenase was compared to expression of the pWWO xylene monooxygenase in Escherichia coli. Both monooxygenases transformed p-xylene and 2,6-DMN by initially hydroxylating one methyl group. In addition, the ASU1 monooxygenase also hydroxylated the second methyl group on p-xylene and 2,6-DMN whereas the pWWO monooxygenase hydroxylated the second methyl group only on p-xylene. Endogenous E. coli enzymes contributed to further oxidation of the resulting aromatic alcohols to form aromatic carboxylates.

Chromosome Mapping↗
PubMed2002

Pure bacterial isolates that convert p-xylene to terephthalic acid.

Bacteria that grow on p-xylene, p-toluic acid, and terephthalic acid (TPA) were isolated from a wastewater bioreactor that is used to treat a waste stream that contains all three of these compounds. Although previously described aerobic bacteria degrade p-xylene by initially oxidizing a single methyl group to form p-toluic acid and then cleaving the aromatic ring, some of the bacteria isolated during this study transformed p-xylene by oxidizing both methyl groups to produce TPA.

Bioreactors↗
PubMed2002

Nanoscale phenomena in synthetic functional oxide heterostructures.

This paper reviews nanoscale phenomena such as polarization relaxation dynamics and piezoelectric characterization in model ferroelectric thin films and nanostructures using voltage-modulated scanning force microscopy. Using this technique we show the three-dimensional reconstruction of the polarization vector in lead zirconate titanate (PZT) thin films. Second, the time-dependent relaxation of remanent polarization in epitaxial PZT ferroelectric thin films, containing a uniform two-dimensional grid of 90 degrees domains (c-axis in the plane of the film), has been investigated extensively. The 90 degrees domain walls preferentially nucleate the 180 degrees reverse domains during relaxation. Relaxation occurs through the nucleation and growth of reverse 180 degrees domains, which subsequently coalesce and consume the entire region as a function of relaxation time. In addition we also present results on investigation of the relaxation phenomenon on a very local scale, where pinning and bowing of domain walls has been observed. We also show how this technique is used for obtaining quantitative information on piezoelectric constants and by engineering special structures, and how we realize ultrahigh values of piezoconstants. Last, we also show direct hysteresis measurements on nanoscale capacitors, where there is no observable loss of polarization in capacitors as small as 0.16 microm2 in area.

Crystallization↗
PubMed2001

Crystal structures of substrate free and complex forms of reactivated BphC, an extradiol type ring-cleavage dioxygenase.

BphC derived from Pseudomonas sp. strain KKS102, an extradiol type catecholic dioxygenase, is a non-heam iron-containing enzyme, playing an important role in the degradation of biphenyl/PCB (Poly Chlorinated Biphenyls) in the microbe. Although we had earlier solved the crystal structure of KKS102 BphC, it was the inactive form with Fe(III) in the active site. In order to determine the active form structure, BphC was re-activated by anaerobic incubation with Fe(II) and ascorbate, and crystallized anaerobically. The crystal structures of activated BphC and its substrate complex (E x S complex) were determined at 2.0 A resolution under cryogenic condition. In addition, crystal structures of unactivated BphC in substrate free and complex forms were also re-determined. Comparison of activated and unactivated E x S complexes reveals that the orientation of the bound substrate in the active site is significantly different between the two. The structural comparison of the substrate free and complex forms of activated BphC show certain small conformational shifts around the active site upon substrate binding. As a result of the conformational shifts, His194, which has been suggested as the catalytic base, takes part in a weak hydrogen bond with hydroxyl group of the substrate.

Anaerobiosis↗
PubMed2001

Near-field second harmonic imaging of the c/a/c/a polydomain structure of epitaxial PbZrxTi(1-x)O3 thin films.

Near-field optical second harmonic microscopy has been applied to imaging of the c/a/c/a polydomain structure of epitaxial PbZrxTi1-xO3 thin films in the 0 < x < 0.4 range. Comparison of the near-field optical images and the results of atomic force microscopy and X-ray diffraction studies show that an optical resolution of the order of 100 nm is achieved. Symmetry properties of the near-field second harmonic signal allow us to obtain good optical contrast between the local second harmonic generation in c- and a-domains. Experimentally measured near-field second harmonic images have been compared with the results of theoretical calculations. Good agreement between theory and experiment is demonstrated.

Journal Article↗
PubMed2001

Cloning and characterization of a gene cluster for cyclododecanone oxidation in Rhodococcus ruber SC1.

Biological oxidation of cyclic ketones normally results in formation of the corresponding dicarboxylic acids, which are further metabolized in the cell. Rhodococcus ruber strain SC1 was isolated from an industrial wastewater bioreactor that was able to utilize cyclododecanone as the sole carbon source. A reverse genetic approach was used to isolate a 10-kb gene cluster containing all genes required for oxidative conversion of cyclododecanone to 1,12-dodecanedioic acid (DDDA). The genes required for cyclododecanone oxidation were only marginally similar to the analogous genes for cyclohexanone oxidation. The biochemical function of the enzymes encoded on the 10-kb gene cluster, the flavin monooxygenase, the lactone hydrolase, the alcohol dehydrogenase, and the aldehyde dehydrogenase, was determined in Escherichia coli based on the ability to convert cyclododecanone. Recombinant E. coli strains grown in the presence of cyclododecanone accumulated lauryl lactone, 12-hydroxylauric acid, and/or DDDA depending on the genes cloned. The cyclododecanone monooxygenase is a type 1 Baeyer-Villiger flavin monooxygenase (FAD as cofactor) and exhibited substrate specificity towards long-chain cyclic ketones (C11 to C15), which is different from the specificity of cyclohexanone monooxygenase favoring short-chain cyclic compounds (C5 to C7).

Amino Acid Sequence↗
PubMed2000

Measurement of internal stresses via the polarization in epitaxial ferroelectric films

The relations between electrical and mechanical properties of constrained ferroelectric films are analyzed. It is shown that the internal stresses and the elastic constants can be determined through the measurement of the electrical response. The change in the polarization is proportional to internal stresses due to film-substrate misfit, whereas the linear electrical and electromechanical responses to external field do not depend on the misfit and are determined by the film constraint. The theoretical results are successfully applied to PbZr 0.2Ti 0.8O (3) films on (001) LaAlO (3) substrate which exhibit a considerable increase in the saturation polarization due to epitaxial stresses. Significant recovery in the piezoelectric constant and susceptibility is theoretically predicted and experimentally verified for specific film configurations which reduce the degree of constraint. The concept presented in this Letter can be expanded to constrained ferromagnetic and superconductor films.

Journal Article↗
PubMed2000

The impact of biotechnology on the chemical industry in the 21st century.

Although the overall size of the industrial chemicals business is US$1.4 trillion worldwide, growth has slowed in some market segments. In order to reestablish and sustain growth, materials with higher information content and improved economics based on renewable resources will be required. These challenges have motivated the pursuit of biotechnology by several traditional chemical companies, such as DuPont, Dow, BASF and Monsanto. Even though each company might differ in their strategic approach, their common goal is the same: to create high-value materials using biotechnology.

Biotechnology↗
PubMed2000

Industrial wastewater bioreactors: sources of novel microorganisms for biotechnology.

Microorganisms exist in nature as members of complex, mixed communities. The microbial communities in industrial wastewater bioreactors can be used as model systems to study the evolution of new metabolic pathways in natural ecosystems. The evolution of microbial metabolic capability in these bioreactors is presumably analogous to phenomena that occur in natural ecosystems. The microorganisms in these bioreactors compete for different carbon sources and constantly have to evolve new metabolic capabilities for survival. Thus, industrial bioreactors should be a rich source of novel biocatalysts.

Bacteria↗
PubMed2000

Genetic analysis of a gene cluster for cyclohexanol oxidation in Acinetobacter sp. Strain SE19 by in vitro transposition.

Biological oxidation of cyclic alcohols normally results in formation of the corresponding dicarboxylic acids, which are further metabolized and enter the central carbon metabolism in the cell. We isolated an Acinetobacter sp. from an industrial wastewater bioreactor that utilized cyclohexanol as a sole carbon source. A cosmid library was constructed from Acinetobacter sp. strain SE19, and oxidation of cyclohexanol to adipic acid was demonstrated in recombinant Escherichia coli carrying a SE19 DNA segment. A region that was essential for cyclohexanol oxidation was localized to a 14-kb fragment on the cosmid DNA. Several putative open reading frames (ORFs) that were expected to encode enzymes catalyzing the conversion of cyclohexanol to adipic acid were identified. Whereas one ORF showed high homology to cyclohexanone monooxygenase from Acinetobacter sp. strain NCIB 9871, most of the ORFs showed only moderate homology to proteins in GenBank. In order to assign functions of the various ORFs, in vitro transposon mutagenesis was performed using the cosmid DNA as a target. A set of transposon mutants with a single insertion in each of the ORFs was screened for cyclohexanol oxidation in E. coli. Several of the transposon mutants accumulated a variety of cyclohexanol oxidation intermediates. The in vitro transposon mutagenesis technique was shown to be a powerful tool for rapidly assigning gene functions to all ORFs in the pathway.

Acinetobacter↗
PubMed1999

Structure analysis of a collagen-model peptide with a (Pro-Hyp-Gly) sequence repeat.

The crystal structure of a triple helical peptide (Pro-Hyp-Gly)10 has been determined at 1.9 A resolution. Single crystals grown by the hanging drop method, diffracted to a resolution of 1.8 A. The polymer-like structure of the triple helical repeat Pro-Hyp-Gly was in accordance with the 7/2 model proposed for collagen and very similar to the previously determined structure with a Pro-Pro-Gly sequence repeat. The solvent structure was also very similar to that previously observed, showing similar hydration patterns, but different crystal packing. The presence of hydroxyproline did not have any effect on the molecular structure or the hydration structure. This is in accordance with the recent finding that the inductive effect of the hydroxyl group attached to the Cgamma atom of hydroxyproline enhances collagen stability rather than the extensive water network.

Collagen↗