Glutamate Dehydrogenase in Cerebellar Mutant Mice: Gene Localization and Enzyme Activity in Different Tissues

Many similarities of both the inheritance pattern and the neuropathology can be observed between olivopontocerebellar atrophies, or so-called multiple system atrophies (MSAs), and murine cerebellar mutations like Purkinje cell degeneration, nervous, staggerer, weaver, and reeler. Our study aimed to test whether the glutamate dehydrogenase (GDH) deficiency observed in some MSA patients could be found also in any of the murine mutants. GDH activity was assayed in several organs of these mutants, and no general deficiency was detected. By contrast, the level was found to be elevated in the cerebellum. The GDH gene was localized on mouse chromosome 14 and does not map close to any known neurological mutation in the mouse. We conclude, for the moment, that none of these cerebellar mutant mice can be considered as an animal model for GDH-deficient MSA.     

Effects of material methadone administration on ornithine decarboxylase in brain and heart of the offspring: Relationships of enzyme activity to dose and to growth impairment in the rat

Administration of 5 mg/kg of methadone daily to pregnant and nursing rats produced substantial retardation of body, brain and heart growth in the offspring; alterations in biochemical development also were present in the methadone-exposed pups, as evidenced by delays in the maturational declines of brain and heart ornithine decarboxylase (ODC) activity. Lowering the dose of methadone to levels which did not affect growth or brain ODC, still resulted in pro-found abnormalities in the developmental pattern of heart ODC. These studies indicate that downward adjustment of maternal methadone dosage to a point where birthweights and body and organ growth rates are normal, does not eliminate all of the biochemical alterations associated with the perinatal opiate syndrome.     

Methanogenic activity tests by Infrared Tunable Diode Laser Absorption Spectroscopy

Methanogenic activity (MA) tests are commonly carried out to estimate the capability of anaerobic biomass to treat effluents, to evaluate anaerobic activity in bioreactors or natural ecosystems, or to quantify inhibitory effects on methanogenic activity. These activity tests are usually based on the measurement of the volume of biogas produced by volumetric, pressure increase or gas chromatography (GC) methods. In this study, we present an alternative method for non-invasive measurement of methane produced during activity tests in closed vials, based on Infrared Tunable Diode Laser Absorption Spectroscopy (MA-TDLAS). This new method was tested during model acetoclastic and hydrogenotrophic methanogenic activity tests and was compared to a more traditional method based on gas chromatography. From the results obtained, the CH(4) detection limit of the method was estimated to 60ppm and the minimum measurable methane production rate was estimated to 1.09(.)10(-3)mgl(-1)h(-1), which is below CH(4) production rate usually reported in both anaerobic reactors and natural ecosystems. Additionally to sensitivity, the method has several potential interests compared to more traditional methods among which short measurements time allowing the measurement of a large number of MA test vials, non-invasive measurements avoiding leakage or external interferences and similar cost to GC based methods. It is concluded that MA-TDLAS is a promising method that could be of interest not only in the field of anaerobic digestion but also, in the field of environmental ecology where CH(4) production rates are usually very low.     

Iron Oxidation and Deposition in the Biofilm Covering Montacuta ferruginosa (Mollusca,Bivalvia)

The shell of the bivalve Montacuta ferruginosa is covered with a rust-colored biofilm. This biofilm includes filamentous bacteria and protozoa encrusted with a mineral, rich in ferric ion and phosphate. The aim of this research was to study two possible microbial iron precipitation pathways in the biofilm, namely, microbial iron oxidation and microbial degradation of organic Fe(III) complexes. The iron-oxidizing activity was assayed spectrophotometrically by monitoring the formation of the dye Wurster blue in biofilm extracts. Iron-oxidizing activity was effectively detected in extracts obtained by oxalic acid treatment of biofilm fragments. Extracts obtained without oxalic acid treatment, heated extracts, or extracts supplemented with HgCl 2 did not show any activity. This suggests that an iron-oxidizing factor (IOF), possibly an enzyme, coprecipitated with the mineral. Additional information gathered by using sodium dodecyl sulfate-polyacrylamide gel electrophoresis, gel-filtration chromatography, and UV spectrophotometry indicate that the IOF would be a small peptide or glycopeptide (1,350 Da). Microbial degradation of organic Fe(III) complexes was assayed with biofilm fragments incubated in a medium containing ferric citrate. Analysis of the supernatants after various intervals revealed that the complex was degraded by living microorganisms much faster than in the heat-killed negative controls. We conclude that ferric iron precipitation in the biofilm may proceed by way of microbial Fe(II) oxidation as well as microbial degradation of organic Fe(III) complexes.     

Aquacultured Rainbow Trout (Oncorhynchus mykiss) Possess a Large Core Intestinal Microbiota That Is Resistant to Variation in Diet and Rearing Density

As global aquaculture fish production continues to expand, an improved understanding of how environmental factors interact in fish health and production is needed. Significant advances have been made toward economical alternatives to costly fishmeal-based diets, such as grain-based formulations, and toward defining the effect of rearing density on fish health and production. Little research, however, has examined the effects of fishmeal- and grain-based diets in combination with alterations in rearing density. Moreover, it is unknown whether interactions between rearing density and diet impact the composition of the fish intestinal microbiota, which might in turn impact fish health and production. We fed aquacultured adult rainbow trout (Oncorhynchus mykiss) fishmeal- or grain-based diets, reared them under high- or low-density conditions for 10 months in a single aquaculture facility, and evaluated individual fish growth, production, fin indices, and intestinal microbiota composition using 16S rRNA gene sequencing. We found that the intestinal microbiotas were dominated by a shared core microbiota consisting of 52 bacterial lineages observed across all individuals, diets, and rearing densities. Variations in diet and rearing density resulted in only minor changes in intestinal microbiota composition despite significant effects of these variables on fish growth, performance, fillet quality, and welfare. Significant interactions between diet and rearing density were observed only in evaluations of fin indices and the relative abundance of the bacterial genus Staphylococcus. These results demonstrate that aquacultured rainbow trout can achieve remarkable consistency in intestinal microbiota composition and suggest the possibility of developing novel aquaculture strategies without overtly altering intestinal microbiota composition.     

Bioinformatics Analysis Identify Novel OB Fold Protein Coding Genes in C. elegans

Background

The C. elegans genome has been extensively annotated by the WormBase consortium that uses state of the art bioinformatics pipelines, functional genomics and manual curation approaches. As a result, the identification of novel genes in silico in this model organism is becoming more challenging requiring new approaches. The Oligonucleotide-oligosaccharide binding (OB) fold is a highly divergent protein family, in which protein sequences, in spite of having the same fold, share very little sequence identity (5–25%). Therefore, evidence from sequence-based annotation may not be sufficient to identify all the members of this family. In C. elegans, the number of OB-fold proteins reported is remarkably low (n = 46) compared to other evolutionary-related eukaryotes, such as yeast S. cerevisiae (n = 344) or fruit fly D. melanogaster (n = 84). Gene loss during evolution or differences in the level of annotation for this protein family, may explain these discrepancies.

Methodology/Principal Findings

This study examines the possibility that novel OB-fold coding genes exist in the worm. We developed a bioinformatics approach that uses the most sensitive sequence-sequence, sequence-profile and profile-profile similarity search methods followed by 3D-structure prediction as a filtering step to eliminate false positive candidate sequences. We have predicted 18 coding genes containing the OB-fold that have remarkably partially been characterized in C. elegans.

Conclusions/Significance

This study raises the possibility that the annotation of highly divergent protein fold families can be improved in C. elegans. Similar strategies could be implemented for large scale analysis by the WormBase consortium when novel versions of the genome sequence of C. elegans, or other evolutionary related species are being released. This approach is of general interest to the scientific community since it can be used to annotate any genome.