A computer filtering method to drive out tiny genes from the yeast genome

The authors of the first yeast chromosome sequence defined a minimum threshold requirement of 100 codons, above which an open reading frame (ORF) is retained as a putative coding sequence. However, at least 58 yeast genes shorter than 100 codons have an assigned protein function. Therefore, the yeast genome may contain other tiny but functionally important genes that are discarded from analyses by this simple filtering rule. We have established discriminant functions from the in-phase hexamer frequencies of functional genes and of simulated ORFs derived from a stationary Markov chain model. Fifty-two out of the 58 genes were recognized as coding ORFs by our discriminating method. The test was also applied to all the small ORFs (36 to 100 codons) found in the intergenic regions of published chromosomes. It retained 140 new potential tiny coding sequences, among which we identified seven new genes by similarity searches. Our method, used conjointly with similarity searches, can also highlight sequencing errors resulting from the disruption of the coding frame of longer ORFs. This method, by its ability to detect potential coding ORFs, can be a very useful tool for functional analysis.     

Effect of Diffusion Length in Modeling of Equiaxed Dendritic Solidification under Buoyancy Flow in a Configuration of Hebditch–Hunt Experiment

Metallurgical and Materials Transactions B - Modeling of equiaxed solidification is vital for understanding the solidification process of metallic alloys. In this work, an extended literature...     

Adventitial Tertiary Lymphoid Organs as Potential Source of MicroRNA Biomarkers for Abdominal Aortic Aneurysm

Abdominal aortic aneurysm (AAA) is an inflammatory disease associated with marked changes in the cellular composition of the aortic wall. This study aims to identify microRNA (miRNA) expression in aneurysmal inflammatory cells isolated by laser microdissection from human tissue samples. The distribution of inflammatory cells (neutrophils, B and T lymphocytes, mast cells) was evaluated in human AAA biopsies. We observed in half of the samples that adventitial tertiary lymphoid organs (ATLOs) with a thickness from 0.5 to 2 mm were located exclusively in the adventitia. Out of the 850 miRNA that were screened by microarray in isolated ATLOs (n = 2), 164 miRNAs were detected in ATLOs. The three miRNAs (miR-15a-3p, miR-30a-5p and miR-489-3p) with the highest expression levels were chosen and their expression quantified by RT-PCR in isolated ATLOs (n = 4), M1 (n = 2) and M2 macrophages (n = 2) and entire aneurysmal biopsies (n = 3). Except for the miR-30a-5p, a similar modulation was found in ATLOs and the two subtypes of macrophages. The modulated miRNAs were then evaluated in the plasma of AAA patients for their potential as AAA biomarkers. Our data emphasize the potential of miR-15a-3p and miR-30a-5p as biomarkers of AAA but also as triggers of ATLO evolution. Further investigations will be required to evaluate their targets in order to better understand AAA pathophysiology.     

The methionine precursor dl-2-hydroxy-(4-methylthio)butanoic acid protects intestinal epithelial barrier function

dl-2-hydroxy-(4-methylthio)butanoic acid (HMTBA) is a source of dietary methionine (Met) that is widely used in poultry nutrition. We have previously shown that HMTBA is preferentially diverted to the transsulfuration pathway, which gives antioxidant metabolites such as taurine and glutathione. Therefore, here we hypothesize that this Met source can protect epithelial barrier function in an in vitro model of intestinal inflammation of Caco-2 cells. The results show that HMTBA prevents the increase in paracellular permeability induced by H₂O₂ or tumour necrosis factor-α. This effect can be attributed to the increased production of taurine and reduced glutathione. Similar results were obtained for dl-Met, although the protective role of the amino acid was less pronounced than that of the hydroxy analogue. In conclusion, the diversion to the transsulfuration pathway means that this Met precursor is of greater value than previously thought, due to its capacity to improve intestinal homeostasis and the quality of poultry products destined for human consumption.     

Evolution of the localisation and composition of phenolics in grape skin between veraison and maturity in relation to water availability and some climatic conditions

BACKGROUND: Several studies have investigated the composition of phenolics in grape skin during grape maturation under various conditions of light exposure, water stress, nitrogen supply and mineral nutrition, but their localisation during berry development is not well known. In this study the composition and localisation of proanthocyanidins were monitored for three years on four plots known to induce a distinctive behaviour of the vine (Cabernet Franc). The composition of phenolics was determined by spectrophotometry; also, in one year, proanthocyanidins were determined by high‐performance liquid chromatography. Further information was obtained histochemically by means of toluidine blue O staining and image analysis. RESULTS: The results indicated that clear differences in phenolic quantification existed between the biochemical and histochemical approaches; the proportion of cells without phenolics was not linked with the quantity determined by the analytical methods used. The histochemical method showed the evolution of the localisation and typology of cells with and without phenolics during ripening. The number of cells without any phenolic compounds appeared to be very dependent on the mesoclimatic conditions and only slightly dependent on the site water status. CONCLUSION: Clear differences in phenolic quantification existed between the biochemical and histochemical approaches; the proportion of cells with phenolics was not linked with the quantity determined by biochemistry. The histochemical method showed an evolution of the localisation and typology of cells with and without phenolics in which mesoclimatic conditions were the most influential factor. Finally, the study showed some advantages of the histochemical approach: it gives information about the anatomy of the tissue as well as the nature and distribution of some of the large macromolecules and allows reconstruction of the three‐dimensional plant structure. Copyright © 2011 Society of Chemical Industry     

Characterization of activated sludge flocs by confocal laser scanning microscopy and image analysis

In this study we present a new approach to determine volumes, heterogeneity factors, and compositions of the bacterial population of activated sludge flocs by 3D confocal imaging. After staining the fresh flocs with fluorescein-isothiocyanate, 75 stacks of images (containing approx. 3000 flocs) were acquired with a confocal laser scanning microscope. The self-developed macro 3D volume and surface determination for the KS 400 software package combined the images of one stack to a 3D image and calculated the real floc volume and surface. We determined heterogeneity factors like the ratio of real floc surface to the surface of a sphere with the respective volume and the fractal dimension (D(f)). According to their significant influence on floc integrity and quality, we also investigated the chemical composition of flocs and quantified their bacterial population structure by using group-specific rRNA-targeted probes for fluorescence in situ hybridization. By a settling experiment we enriched flocs with poor settling properties and determined the above-mentioned parameters. This approach revealed shifts in floc volume, heterogeneity, and bacterial and chemical composition according to the settling quality of the flocs.     

Interlinking Music-Related Data on the Web

This article describes how Semantic Web technologies can be used to interlink musical data sources that have traditionally been isolated and difficult to integrate.     

Lipid oxidation products of heated soybeans as a possible cause of protection from ruminal biohydrogenation

Heating oilseeds has been shown to improve the milk fatty acid profile when given to dairy cows, compared to raw oilseeds. However, results from published studies are conflicting. The conditions of heating and storage of the oilseeds could be responsible for these differences, probably partly through their effects on lipid oxidation, the products of which could act on ruminal biohydrogenation (BH). Thus, 15 different treatments were applied to ground soybeans: three levels of heating (no heating, 30 min at 110 or 150°C) × 5 ambient storage durations (0, 1, 2, 4, or 6 months). Soybeans were incubated in vitro with ruminal fluid for 6 h. Triacylglycerol (TAG) polymers, hydroperoxides and hydroxyacids (HOA), aldehydes, and fatty acids were assayed in soybeans and ruminal culture. No TAG polymer was detected in any treatment. Soybeans stored for a long time had a high content of HOA, whereas those heated at 150°C, whatever the storage duration, had high aldehyde contents. The percentage disappearance of cis‐9,cis‐12 18:2 and cis‐9,cis‐12,cis‐15 18:3 in incubates decreased significantly in cultures with heated soybeans, especially at 150°C, suggesting that this partial protection of polyunsaturated fatty acids (PUFA) from BH was at least in part linked to the aldehyde content of the heated soybeans. Practical applications: Oilseeds given to ruminants are often heated, and heat treatment is known to generate oxidation products. Knowing what oxidation products influence ruminal biohydrogenation of unsaturated fatty acids could result in technological processes allowing a better transfer of unsaturated fatty acids from oilseeds to ruminant products.