Erdogan Gulari

Accurate multiplex gene synthesis from programmable DNA microchips.

Testing the many hypotheses from genomics and systems biology experiments demands accurate and cost-effective gene and genome synthesis. Here we describe a microchip-based technology for multiplex gene synthesis. Pools of thousands of ‘construction’ oligonucleotides and tagged complementary ‘selection’ oligonucleotides are synthesized on photo-programmable microfluidic chips, released, amplified and selected by hybridization to reduce synthesis errors ninefold. A one-step polymerase assembly multiplexing reaction assembles these into multiple genes. This technology enabled us to synthesize all 21 genes that encode the proteins of the Escherichia coli 30S ribosomal subunit, and to optimize their translation efficiency in vitro through alteration of codon bias. This is a significant step towards the synthesis of ribosomes in vitro and should have utility for synthetic biology in general.

Selective CO oxidation over Pt/alumina catalysts for fuel cell applications

It has been demonstrated that even traces of CO present in the hydrogen rich feed gas to proton exchange membrane (PEM) fuel cells can poison the platinum anode electrode and dramatically reduce the power output. The tolerable level of CO is around 10 ppm. In this paper, we present the results of selective CO oxidation in simulated reformate gas over single-step sol–gel prepared Pt/alumina catalysts. The effect of water vapor, carbon dioxide, CO and oxygen concentrations, temperature, and Pt loading on the activity and selectivity are presented. Our results show that a 2% Pt/alumina sol–gel catalyst can selectively oxidize CO down to a few ppm with constant selectivity and high space velocity. Water vapor in the feed increases the activity of the catalysts dramatically and in the absence of water vapor, CO 2 in the feed stream decreases the activity of the catalysts significantly.

Optical properties of silicon nitride films deposited by hot filament chemical vapor deposition

Silicon nitride films were deposited at low temperatures (245–370 °C) and high deposition rates (500–1700 A/min) by hot filament assisted chemical vapor deposition (HFCVD). Optical properties of these amorphous silicon nitride thin films have been extensively characterized by absorption, photoluminescence (PL), photoluminescence excitation, and electroluminescence measurements. The optical band gap of the films was varied between 2.43 and 4.74 eV by adjusting the flow rate of the disilane source gas. Three broad peaks at 1.8, 2.4, and 3.0 eV were observed in the PL spectra from these films. A simple qualitative model based on nitrogen and silicon dangling bonds adequately explains the observed PL features. The photoluminescence intensity observed in these films was 8–10 times stronger than films deposited by plasma enhanced chemical vapor deposition, under similar conditions. The high deposition rates obtained by HFCVD is believed to introduce a large number of these optically active defects.

Dynamics of growth of silica particles from ammonia-catalyzed hydrolysis of tetra-ethyl-orthosilicate

The NH3-catalyzed formation of colloidal silica particles from tetra-ethyl-orthosilicate (TEOS) in methanol and ethanol is studied by means of light scattering and Raman spectroscopy. We find that the growth is characterized by an incubation period after which no significant nucleation takes place. The particles have uniform, non-fractal structure and show low polydispersity. In the presence of excess water, the rate-limiting step is the hydrolysis, which is a first-order process in the orthosilicate concentration.

Comparative studies of low-temperature water-gas shift reaction over Pt/CeO2, Au/CeO2, and Au/Fe2O3 catalysts

We studied catalytic low-temperature water–gas shift (WGS) reaction over the Pt=CeO2 ,A u=CeO2 and Au=Fe2O3 catalysts. The activity of these catalysts was tested in the composition of 4% CO, 2.6–20% H2O and helium in the range of 120–360 C. It was found that CO and H2O concentrations have significant effects on the catalytic activity. The 1% Pt=CeO2 was substantially more active than other catalysts in the presence of 20% H2O. The catalytic activity of these catalysts was compared in the presence of H2 and deactivation test was also performed. BET, XRD, SEM and TEM analyses give additional information on the morphological structure of investigated samples. 2003 Elsevier Science B.V. All rights reserved.

Individually addressable parallel peptide synthesis on microchips

Miniaturized, spatially addressable microchips of peptides and peptidomimetics are powerful tools for high-throughput biomedical and pharmaceutical research and the advancement of proteomics. Here we report an efficient and flexible method for the parallel synthesis of peptides on individually addressable microchips, using digital photolithography and photogenerated acid in the deprotection step. We demonstrate that we are able to synthesize thousands of peptides in a 1 cm2 area on a microchip using 20 natural amino acids as well as synthetic amino acid analogs, with high stepwise yields and short reaction-cycle times. Epitope screening experiments using a p53 antibody (PAb240) produced clearly defined binding patterns. The peptidomimetic sequences on the microchip show specific antibody binding and provide insights into the molecular details responsible for specificity of epitope binding. Our approach requires just a conventional synthesizer and a computer-controllable optical module, thereby allowing potential development of peptide microchips for various pharmaceutical and proteomic applications in routine research laboratories.

Molybdena on titania. I: Preparation and characterization by Raman and Fourier transform infrared spectroscopy

Titania-supported molybdenum and cobalt-molybdenum catalysts were prepared by the dry impregnation and equilibrium adsorption techniques. Raman and Fourier Transform Infrared spectroscopy were used to follow the changes the catalysts underwent during the drying and calcination stages. The results indicate that the nature of the surface species depends on the loading, pH of the starting solution and the method of catalyst loading. It was found, for coverages calculated to be less than a monolayer, that the main surface species are tetrahedral molybdates. As the loading increases, octahedrally coordinated polymeric surface species form. Above the monolayer coverage, MoO3 is also formed. After calcination the spectra of catalysts prepared by the equilibrium adsorption technique change much less than those for catalysts prepared by the dry impregnation technique. Addition of cobalt to titania-supported molybdenum catalysts suppresses the formation of bulk MoO3 and leads to the formation of a cobalt molybdate phase. The results show that surface molybdates interact strongly with the support, TiO2.

Monomer-addition growth with a slow initiation step: A growth model for silica particles from alkoxides

A simplified monomer-addition model with a first-order activation step is developed to describe the dynamics of growth of silica particles from alkoxides. In the fimit of slow hydrolysis, we obtain expressions for the evolution of the particle mass and particle polydispersity, as well as an expression for the particle size as a function of the hydrolysis rate constant, the polymerization rate constant, and the initial concentration of the orthosilicate. We find that the formation of the particles is adequately modeled by a reaction limited growth.

Evolution combined with genomic study elucidates genetic bases of isobutanol tolerance in Escherichia coli

BackgroundIsobutanol is a promising next-generation biofuel with demonstrated high yield microbial production, but the toxicity of this molecule reduces fermentation volumetric productivity and final titer. Organic solvent tolerance is a complex, multigenic phenotype that has been recalcitrant to rational engineering approaches. We apply experimental evolution followed by genome resequencing and a gene expression study to elucidate genetic bases of adaptation to exogenous isobutanol stress.ResultsThe adaptations acquired in our evolved lineages exhibit antagonistic pleiotropy between minimal and rich medium, and appear to be specific to the effects of longer chain alcohols. By examining genotypic adaptation in multiple independent lineages, we find evidence of parallel evolution in marC, hfq, mdh, acrAB, gatYZABCD, and rph genes. Many isobutanol tolerant lineages show reduced RpoS activity, perhaps related to mutations in hfq or acrAB. Consistent with the complex, multigenic nature of solvent tolerance, we observe adaptations in a diversity of cellular processes. Many adaptations appear to involve epistasis between different mutations, implying a rugged fitness landscape for isobutanol tolerance. We observe a trend of evolution targeting post-transcriptional regulation and high centrality nodes of biochemical networks. Collectively, the genotypic adaptations we observe suggest mechanisms of adaptation to isobutanol stress based on remodeling the cell envelope and surprisingly, stress response attenuation.ConclusionsWe have discovered a set of genotypic adaptations that confer increased tolerance to exogenous isobutanol stress. Our results are immediately useful to further efforts to engineer more isobutanol tolerant host strains of E. coli for isobutanol production. We suggest that rpoS and post-transcriptional regulators, such as hfq, RNA helicases, and sRNAs may be interesting mutagenesis targets for future global phenotype engineering.

Gene-Z: a device for point of care genetic testing using a smartphone

By 2012, point of care (POC) testing will constitute roughly one third of the