Evaluation of the role of heterogeneous nuclear ribonucleoprotein A1 as a host factor in murine coronavirus discontinuous transcription and genome replication

Viruses with RNA genomes often capture and redirect host cell components to assist in mechanisms particular to RNA-dependent RNA synthesis. The nidoviruses are an order of positive-stranded RNA viruses, comprising coronaviruses and arteriviruses, that employ a unique strategy of discontinuous transcription, producing a series of subgenomic mRNAs linking a 5′ leader to distal portions of the genome. For the prototype coronavirus mouse hepatitis virus (MHV), heterogeneous nuclear ribonucleoprotein (hnRNP) A1 has been shown to be able to bind in vitro to the negative strand of the intergenic sequence, a cis-acting element found in the leader RNA and preceding each downstream ORF in the genome. hnRNP A1 thus has been proposed as a host factor in MHV transcription. To test this hypothesis genetically, we initially constructed MHV mutants with a very high-affinity hnRNP A1 binding site inserted in place of, or adjacent to, an intergenic sequence in the MHV genome. This inserted hnRNP A1 binding site was not able to functionally replace, or enhance transcription from, the intergenic sequence. This finding led us to test more directly the role of hnRNP A1 by analysis of MHV replication and RNA synthesis in a murine cell line that does not express this protein. The cellular absence of hnRNP A1 had no detectable effect on the production of infectious virus, the synthesis of genomic RNA, or the quantity or quality of subgenomic mRNAs. These results strongly suggest that hnRNP A1 is not a required host factor for MHV discontinuous transcription or genome replication.

Heterogeneous transcription of an indoleacetic acid biosynthetic gene in Erwinia herbicola on plant surfaces

We investigated the spatial pattern of expression of ipdC, a plant inducible gene involved in indoleacetic acid biosynthesis in Erwinia herbicola, among individual cells on plants to gain a better understanding of the role of this phenotype in the epiphytic ecology of bacteria and the factors involved in the regulation of ipdC. Nonpathogenic E. herbicola strain 299R harboring a transcriptional fusion of ipdC to gfp was inoculated onto bean plants, recovered from individual leaves 48 h after inoculation, and subjected to fluorescence in situ hybridization using a 16S rRNA oligonucleotide probe specific to strain 299R. Epifluorescence images captured through a rhodamine filter were used to distinguish the 5carboxytetramethylrhodamine-labeled cells of strain 299R from other leaf microflora. Quantification of the green fluorescence intensity of individual cells by analysis of digital images revealed that about 65% of the 299R cells recovered from bean leaves had higher ipdC expression than in culture. Additionally, 10% of the cells exhibited much higher levels of green fluorescence than the median fluorescence intensity, indicating that they are more heterogeneous with respect to ipdC expression on plants than in culture. Examination of 299R cells in situ on leaf surfaces by confocal laser scanning microscopy after fluorescence in situ hybridization of cells on leaf samples showed that even cells that were in close proximity exhibited dramatically different green fluorescence intensities, and thus, were in a physical or chemical microenvironment that induced differential expression of ipdC.

Nonuniformity of the constitutive law parameters for shear rupture and quasistatic nucleation to dynamic rupture: a physical model of earthquake generation processes.

Based on the recent high-resolution laboratory experiments on propagating shear rupture, the constitutive law that governs shear rupture processes is discussed in view of the physical principles and constraints, and a specific constitutive law is proposed for shear rupture. It is demonstrated that nonuniform distributions of the constitutive law parameters on the fault are necessary for creating the nucleation process, which consists of two phases: (i) a stable, quasistatic phase, and (ii) the subsequent accelerating phase. Physical models of the breakdown zone and the nucleation zone are presented for shear rupture in the brittle regime. The constitutive law for shear rupture explicitly includes a scaling parameter Dc that enables one to give a common interpretation to both small scale rupture in the laboratory and large scale rupture as earthquake source in the Earth. Both the breakdown zone size Xc and the nucleation zone size L are prescribed and scaled by Dc, which in turn is prescribed by a characteristic length lambda c representing geometrical irregularities of the fault. The models presented here make it possible to understand the earthquake generation process from nucleation to unstable, dynamic rupture propagation in terms of physics. Since the nucleation process itself is an immediate earthquake precursor, deep understanding of the nucleation process in terms of physics is crucial for the short-term (or immediate) earthquake prediction.

Slip complexity in earthquake fault models.

We summarize studies of earthquake fault models that give rise to slip complexities like those in natural earthquakes. For models of smooth faults between elastically deformable continua, it is critical that the friction laws involve a characteristic distance for slip weakening or evolution of surface state. That results in a finite nucleation size, or coherent slip patch size, h*. Models of smooth faults, using numerical cell size properly small compared to h*, show periodic response or complex and apparently chaotic histories of large events but have not been found to show small event complexity like the self-similar (power law) Gutenberg-Richter frequency-size statistics. This conclusion is supported in the present paper by fully inertial elastodynamic modeling of earthquake sequences. In contrast, some models of locally heterogeneous faults with quasi-independent fault segments, represented approximately by simulations with cell size larger than h* so that the model becomes "inherently discrete," do show small event complexity of the Gutenberg-Richter type. Models based on classical friction laws without a weakening length scale or for which the numerical procedure imposes an abrupt strength drop at the onset of slip have h* = 0 and hence always fall into the inherently discrete class. We suggest that the small-event complexity that some such models show will not survive regularization of the constitutive description, by inclusion of an appropriate length scale leading to a finite h*, and a corresponding reduction of numerical grid size.

The nucleation of receptor-mediated endocytosis.

A theory of the mechanical origins of receptor-mediated endocytosis shows that a spontaneous membrane complex formation can provide the stimulus for a local membrane motion toward the cytosol. This motion is identified with a nucleation stage of receptor-mediated endocytosis. When membrane complexes cluster, membrane deformation is predicted to be most rapid. The rate of growth of membrane depressions depends upon the relative rates of approach of aqueous cytosolic and extracellular fluids toward the cell membrane. With cytosolic and extracellular media characterized by apparent viscosities, the rate of growth of membrane depressions is predicted to increase as the extracellular viscosity nears the apparent viscosity of the cytosol and then to decrease when the extracellular viscosity exceeds that of the cytosol. To determine whether these trends would be apparent in the overall endocytosis rate constant, an experimental study of transferrin-mediated endocytosis in two different cell lines was conducted. The experimental results reveal the same dependence of internalization rate on extracellular viscosity as predicted by the theory. These and other comparisons with experimental data suggest that the nucleation stage of receptor-mediated endocytosis is important in the overall endocytosis process.

Optimization of rates of protein folding: the nucleation-condensation mechanism and its implications.

Small, single-module proteins that fold in a single cooperative step may be paradigms for understanding early events in protein-folding pathways generally. Recent experimental studies of the 64-residue chymotrypsin inhibitor 2 (CI2) support a nucleation mechanism for folding, as do some computer stimulations. CI2 has a nucleation site that develops only in the transition state for folding. The nucleus is composed of a set of adjacent residues (an alpha-helix), stabilized by long-range interactions that are formed as the rest of the protein collapses around it. A simple analysis of the optimization of the rate of protein folding predicts that rates are highest when the denatured state has little residual structure under physiological conditions and no intermediates accumulate. This implies that any potential nucleation site that is composed mainly of adjacent residues should be just weakly populated in the denatured state and become structured only in a high-energy intermediate or transition state when it is stabilized by interactions elsewhere in the protein. Hierarchical mechanisms of folding in which stable elements of structure accrete are unfavorable. The nucleation-condensation mechanism of CI2 fulfills the criteria for fast folding. On the other hand, stable intermediates do form in the folding of more complex proteins, and this may be an unavoidable consequence of increasing size and nucleation at more than one site.

Genetic dissection of Alzheimer disease, a heterogeneous disorder.

The genetics of Alzheimer disease (AD) are complex and not completely understood. Mutations in the amyloid precursor protein gene (APP) can cause early-onset autosomal dominant AD. In vitro studies indicate that cells expressing mutant APPs overproduce pathogenic forms of the A beta peptide, the major component of AD amyloid. However, mutations in the APP gene are responsible for 5% or less of all early-onset familial AD. A locus on chromosome 14 is responsible for AD in other early-onset AD families and represents the most severe form of the disease in terms of age of onset and rate of decline. Attempts to identify the AD3 gene by positional cloning methods are underway. At least one additional early-onset AD locus remains to be located. In late-onset AD, the apolipoprotein E gene allele epsilon 4 is a risk factor for AD. This allele appears to act as a dose-dependent age-of-onset modifier. The epsilon 2 allele of this gene may be protective. Other late-onset susceptibility factors remain to be identified.

Heterogeneous catalysts for environmentally sustainable reactions

This PhD work deals with problems of synthetic organic chemistry with particular attention to the development of environmentally friendly processes. In particular, new synthetic strategies have been studied based on the use of low cost heterogeneous catalysts, non-toxic reagents and mild operating conditions that do not involve, when possible, the use of solvents. The catalysts examined are both basic and acids, commercial or prepared by hetereogenization of homogeneous catalysts synthesized by tethering or impregnation. In particular it will be discussed the catalytic activity of oxides (Al2O3 and TiO2), supported sulphonic acids and hydrotalcites for the reactions of selective monoesterificazion of dicarboxylic acids, dehydrogenation of butane in gas phase, esterification of levulinic acid, Friedel-Craft acylations, C-C and C-P coupling. The use of these materials has allowed the development of simple processes with low environmental impact. The operating conditions are in fact mild and reaction times short. The selectivity for the desired products is in all reported cases very high and the catalysts can be recycled maintaining their optimum performances.

Image Noise Removal on Heterogeneous CPU-GPU Configurations

A parallel algorithm to remove impulsive noise in digital images using heterogeneous CPU/GPU computing is proposed. The parallel denoising algorithm is based on the peer group concept and uses an Euclidean metric. In order to identify the amount of pixels to be allocated in multi-core and GPUs, a performance analysis using large images is presented. A comparison of the parallel implementation in multi-core, GPUs and a combination of both is performed. Performance has been evaluated in terms of execution time and Megapixels/second. We present several optimization strategies especially effective for the multi-core environment, and demonstrate significant performance improvements. The main advantage of the proposed noise removal methodology is its computational speed, which enables efficient filtering of color images in real-time applications.

Copper-Impregnated Magnetite as a Heterogeneous Catalyst for the Homocoupling of Terminal Alkynes

Copper-impregnated magnetite is a versatile heterogeneous catalytic system for the synthesis of 1,3-diynes by the homocoupling of terminal alkynes. This catalyst does not require the use of pressurized oxygen as the oxidant and it does not need a solvent or harsh conditions to give the expected products. Moreover, the catalyst can be removed from the reaction medium simply by using a magnet. The reaction occurs at the lowest copper loading reported for any heterogeneous catalyst.

Cobalt-Impregnated Magnetite as General Heterogeneous Catalyst for the Hydroacylation Reaction of Azodicarboxylates

Catalysts consisting of cobalt and nickel impregnated on magnetite have been prepared, characterized and used for the hydroacylation reaction of different azodicarboxylate compounds with aldehydes, using nearly stoichiometric amounts of both reagents in only 3 h. Furthermore, this reaction has been conducted with the smallest amount of catalyst. The cobalt catalyst is stable enough to be removed by magnetic decantation and recycled ten-fold without any detrimental effect on the results.

Osmium impregnated on magnetite as a heterogeneous catalyst for the syn-dihydroxylation of alkenes

A new catalyst derived from osmium has been prepared, fully characterized and tested in the dihydroxylation of alkenes. The catalyst was prepared by wet impregnation methodology of OsCl3·3H2O on a commercial micro-magnetite surface. The catalyst allowed the reaction with one of the lowest osmium loadings for a heterogeneous catalyst and was selective for the monodihydroxylation of 1,5-dienes. Moreover, the catalyst was easily removed from the reaction medium by the simple use of a magnet. The selectivity of catalyst is very high with conversions up to 99%. Preliminary kinetics studies showed a first-order reaction rate with respect to the catalyst.

Gold Nanoparticles Supported on Polyacrylamide Containing a Phosphorus Ligand as an Efficient Heterogeneous Catalyst for Three-Component Synthesis of Propargylamines in Water

Gold nanoparticles supported on a polyacrylamide containing a phosphinite ligand have been synthesized and characterized using different techniques such as TEM, SEM, EDX, XPS, and solid UV analyses. The new material was successfully applied as a heterogeneous catalyst for the three-component A3 coupling of amines, aldehydes, and alkynes to give propargylamines. Reactions are performed in neat water at 80 °C with only 0.05 mol% catalyst loading. The heterogeneous catalyst is recyclable during seven consecutive runs with small decrease in activity.