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Pascal J Lopez

Publications and source records attributed to Pascal J Lopez.

7 recordsLinked to original sources
PubMed2006

Biomimetic growth of silica tubes in confined media.

Polymer membranes were used as biomimetic environments to study the effect of confinement on silica formation. Within membrane pores, silica tubes were formed, consisting of a dense silica shell incorporating nanoparticle aggregates. The shell structure does not depend on the membrane pore size, suggesting that its formation proceeds via interfacial interactions with the pore surface. In contrast, the size of primary nanoparticles within core aggregates is influenced by pore dimensions, indicating an effect of confinement on the diffusion-limited growth of silica. A parallel can be drawn with reported roles of confinement in biomineralization processes, providing a basis for future developments in biosilicification mimetic approaches and biofunctional nanomaterials design.

Biomimetics↗
PubMed2005

A mutation in T7 RNA polymerase that facilitates promoter clearance.

Like multisubunit RNA polymerases (RNAPs), T7 RNAP frequently releases its transcript over the initial 8-12 transcribed nucleotides, when it still contacts the promoter. This abortive cycling, which is most prominent with initial sequences that deviate from those of T7 late genes, eventually compromises productive transcription. Starting from an in vivo situation where transcription of a target gene by T7 RNAP is virtually abolished because of extensive abortive cycling, we have selected a mutation in RNAP that restores target gene expression. In vitro, this mutation (P266L) weakens promoter binding but markedly reduces abortive cycling over a variety of initial sequences by stabilizing the transcription complex at nucleotides 5-8. Other substitutions of P266 have similar effects. X-ray data show that during the transition from initial to elongation complex, the N-terminal region undergoes a major structural switch of which P266 constitutes one of the hinges. How the mutation might facilitate this switch is tentatively discussed. On the practical side, the mutation can significantly improve in vitro transcription, particularly from templates carrying unfavorable initial sequences.

Amino Acid Substitution↗
PubMed2005

Unravelling the mechanism of RNA-polymerase forward motion by using mechanical force.

Polymerases form a class of enzymes that act as molecular motors as they move along their nucleic acid substrate during catalysis, incorporating nucleotide triphosphates at the end of the growing chain and consuming chemical energy. A debated issue is how the enzyme converts chemical energy into motion [J. Gelles and R. Landick, Cell 93, 13 (1998)]. In a single molecule assay, we studied how an opposing mechanical force affects the translocation rate of T7 RNA polymerase. Our measurements show that force acts as a competitive inhibitor of nucleotide binding. This result is interpreted in the context of possible models, and with respect to published crystal structures of T7 RNA polymerase. The transcribing complex appears to utilize only a small fraction of the energy of hydrolysis to perform mechanical work, with the remainder being converted to heat.

Adenosine Triphosphate↗
PubMed2005

Prospects in diatom research.

Diatoms are unicellular photosynthetic eukaryotes that play a major role in the global cycling of carbon and silicon. They are believed to have arisen from a secondary endosymbiotic event between two eukaryotes, a red alga and a flagellated heterotroph. Recent analysis of a diatom genome indeed reveals a 'mosaic' nature, with genes derived from plant, animal and bacterial lineages. Advances in molecular genomics are facilitating the use of diatom-specific genes or pathways for biotechnology. Another interest is in understanding the artistry of the amorphous silica shell and the underlying biomineralization process. Materials scientists and chemists are now exploiting diatoms to develop new biomimetic approaches and to create silicon-based microdevices with specific features.

Biotechnology↗
PubMed2005

Diatomics: toward diatom functional genomics.

For diatom biologists one of the most interesting research areas over the next years will be in linking mathematical models for pattern formation with information derived from molecular genetic, biochemical, and physiological studies. A major goal of this research is to exploit diatom proficiency in biogenic silica formation to develop strategies for bio-inspired nanofabrication of silicon based materials. Development of high-throughput methods for the functional analysis of diatom genes is a key step toward this goal. In this article we review the different techniques available to investigate gene and protein function in diatoms. Furthermore, to make diatom research as effective as possible the research community must address the question of which diatom species should be developed as a model. Choice of a diatom model organism should be made on the basis of several criteria, such as the ease of genetic manipulation, ecological relevance, or biomineralization capability. Phaeodactylum tricornutum is one of the principal three species that are candidates for such a model. For this species we have accomplished the first large-scale analysis of 12000 expressed sequence tags (ESTs) and have organized it in a queryable database, Phaeodactylum tricornutum database (PtDB). A summary of the functional analysis of this EST collection is presented, and genes of particular interest are highlighted.

Chromosome Mapping↗