A. M. Findley

Genetic coding: approaches to theory construction☆

Abstract A new approach to genetic coding theory, the generalized genetic code (GGC), is presented. It is shown how the GGC reunifies ambiguous codon assignments within the standard genetic code, thereby redefining genetic code universality in a modified form. An extensive survey of ambiguous codings (> 100 assignments) is presented as a critical test of the GGC and all assignments are successfully analyzed within the GGC Finally, the operative nature of biological contexts is investigated and discussed.

Status report on the camd project

Abstract The LSU Center for Advanced Microstructures and Devices (CAMD) is a DOE-funded materials science and engineering laboratory which will include a normal-conducting compact electron storage ring optimized for the production of soft X-rays. The focus of CAMD is the fundamental study of processing and analysis technologies — including X-ray lithography — important to microstructure fabrication and electronic device development. Design details of the storage ring, which is being acquired commercially, are presented in this paper. In addition, the overall research mission of CAMD is described.

Peroxisomal Catalase in Extrusion Apparatus Posterior Vacuole of Microsporidian Spores

A remarkable survival adaptation of microsporidians is the spore extrusion apparatus (EXA), which is equipped to explosively discharge a tube through which the infective sporoplasm is sent into a host cell. The EXA consists of a membrane-associated aperture, polaroplast, polar filament protein, and a posterior vacuole. When the spore activates, the EXA discharges a long, fine tube by an apparent eversion process. When the tube is fully formed, the sporoplasm moves down the tube and ends up in an enveloped compartment thought to be derived from the everted extrusion apparatus membrane. The energy source for spore discharge is believed to reside in the EXA posterior vacuole. In activated spores, the posterior vacuole swells before and during spore extrusion. We report here the presence of catalase in the posterior vacuole of the spores of a microsporidian, Spraguea lophii. This was first made evident when significant levels of molecular oxygen were detected in a medium containing the discharging spores. Clarkstyle oxygen microelectrodes (Model 7376C, Diamond General, Ann Arbor, Michigan) were used to measure dissolved oxygen in the medium. The oxygen appeared only when low levels of hydrogen peroxide were added to the medium, either before or during spore discharge. In the absence of hydrogen peroxide, no oxygen formed in the medium containing the firing spores. The medium was recovered from the fired spores and was analyzed for catalase enzyme using western blot analysis and using the protocol described earlier (1). The results indicate that catalase was present in the medium, and that the molecular weight corresponded to control catalase (Fig. 1A). This finding supports the old hypothesis that the EXA contents may be released directly into the surrounding medium during tube eversion. Catalase crystals were successfully isolated using the protocol described by Reinlein (2). The catalase-rich medium was placed in 10% NaCl, containing 2 mM KH2PO4 at pH 5.5, and after 1 h, this was dialyzed against 1 mM ammonium chloride (pH 5.5). To recrystalize the catalase, there were two cycles of 10-h dialysis. For clean crystals, the entire sample was recycled through the procedure a second time. The crystals tested positive for catalase on the basis of western blots with rabbit anti-bovine catalase (Rockland Immunochemicals, Gilbertsville, Pennsylvania). To identify the specific location of the catalase, spores of S. lophii were subjected to the alkaline-diaminobenzidine (DAB) procedure as reported by Novikoff and Goldfischer (3). The DAB reaction localized to the posterior vacuole before and during spore activation (Fig. 1B). After spore discharge, no detectable DAB activity was found in either the spore ghosts or the extruded sporoplasms. Although the mechanism by which catalase works in the posterior vacuole is unclear, it may be associated with the oxidation of long chain fatty acids. Docosahexaenoic acid, commonly associated with peroxisomes, is significantly represented in S. lophii spores (4). A function of peroxisomes is to manage the betaoxidation of long chain fatty acids. Acyl-coA oxidase, an essential enzyme in this process, produces hydrogen peroxide. The catalase in the area can convert the hydrogen peroxide to water and oxygen. The rapid oxidation of the long chain fatty acids may effect the swelling of the posterior vacuole and induce spore discharge.

LSU Center for Advanced Microstructures and Devices

The LSU Center for Advanced Microstructures and Devices (CAMD) is a DOE‐funded materials science and engineering laboratory which will include a normal‐conducting compact electron storage ring optimized for the production of soft x rays. The focus of CAMD is the fundamental study of processing and analysis technologies—including x‐ray lithography—important to microstructure fabrication and electronic device development. Design details of the storage ring, which is being acquired commercially, are presented in this article.

Systematics in the ionization energies of rare gas clusters

Abstract A linear correlation plot is presented for the first ionization energy of the rare-gas n-mers, which extrapolates to a similar correlation for the photoemission threshold of the solid rare gases. Also a simple correlation is described for the heteronuclear rare-gas dimers, the correlation parameter being defined as an appropriate average ionization energy of the two rare-gas atoms in the dimer.

Applications of differential geometry to molecular genetics

A mathematical formalism is presented in which changes in information content of an evolving DNA (deoxyribonucleic acid) molecule may be described. The basic construct is a 65-dimensional differentiable manifold (the informational space-time manifold) in a coordinate structure such that the manifold points represent (i) the number of each codon type in a DNA molecule, and (ii) the evolutionary time of that DNA. It is shown that this manifold cannot be Euclidean but must be taken, at least conditionally, to be Riemannian. Evolutionary motions in the informational space-time manifold are initially postulated to be geodesics, and evolutionary equations-of-motion are elaborated. These equations are governed by an evolutionary field which is produced by the intrinsic structure of the manifold. The concept of genetic cosmology is introduced, and a manifold in which the evolutionary field is weak and depends only upon the evolutionary time is investigated. The nature of empirical input into genetic cosmology is discussed.

A web-based restriction endonuclease tool for mycobacteriophage cluster prediction

A recent explosion in the amount of genomic data has revealed a large genetic diversity in the bacteriophages that infect Mycobacterium smegmatis. In an effort to assess the novelty of newly described mycobacteriophage isolates and provide a preliminary determination of their probable cluster assignment prior to full genome sequencing, we have developed a systematic approach that relies on restriction endonuclease analysis. We demonstrate that a web‐based tool, the Phage Enzyme Tool (or PET), is capable of rapidly facilitating this analysis and exhibits reliability in the putative placement of mycobacteriophages into specific clusters of previously sequenced phages. We propose that this tool represents a useful analytical step in the initial study of phage genomes and that this tool will increase the efficiency of phage genome characterization and enhance the educational activities involving mycobacteriophage discovery.

Photoionization Spectroscopy of Highly Polar Aromatics. Halobenzonitriles

We report the first adiabatic ionization energy (I1) of benzene, and the ortho, meta and para isomers of fluoro-, chloro- and bromobenzonitrile, extracted from gas-phase photoionization spectra measured up to the LiF cut-off. In every case, I1 for the disubstituted benzene species is blue-shifted from I1 in benzene. Moreover, I1 decreases along the series F, Cl, Br. We explain these trends qualitatively by invoking destabilization/stabilization of the topmost filled π MO of benzene by donor/acceptor substituents.