Effect of aluminum and iron on lipid metabolism in aquatic invertebrates

Methods of thin-layer, gas-liquid, and liquid chromatography were applied to the study of the effect of various concentrations of aluminum and iron salts on the contents of phospholipids, cholesterol, and fatty acids in the aquatic invertebrate Hydropsyche contubernalis L. (Trichoptera). It was found that the effect of the metals under study on lipid contents in living organisms depended on the composition of the aqueous medium and concentrations of the metals. Aluminum and iron altered the value of the cholesterol-to-phospholipid molar ratio. In the absence of lethal effects, this was indicative of attempts to switch adaptational biochemical mechanisms to stabilize cellular structures.Translated from Prikladnaya Biokhimiya i Mikrobiologiya, Vol. 41, No. 2, 2005, pp. 220–227.Original Russian Text Copyright © 2005 by Regerand, Nefedova, Nemova, Ruokolainen, Toivonen, Dubrovina, Vuori, Markova.     

Biomine: predicting links between biological entities using network models of heterogeneous databases

ABSTRACT: BACKGROUND: Biological databases contain large amounts of data concerning the functions and associationsof genes and proteins. Integration of data from several such databases into a single repositorycan aid the discovery of previously unknown connections spanning multiple types ofrelationships and databases. RESULTS: Biomine is a system that integrates cross-references from several biological databases into agraph model with multiple types of edges, such as protein interactions, gene-diseaseassociations and gene ontology annotations. Edges are weighted based on their type,reliability, and informativeness. We present Biomine and evaluate its performance in linkprediction, where the goal is to predict pairs of nodes that will be connected in the future,based on current data. In particular, we formulate protein interaction prediction and diseasegene prioritization tasks as instances of link prediction. The predictions are based on aproximity measure computed on the integrated graph. We consider and experiment withseveral such measures, and perform a parameter optimization procedure where different edgetypes are weighted to optimize link prediction accuracy. We also propose a novel method fordisease-gene prioritization, defined as finding a subset of candidate genes that cluster togetherin the graph. We experimentally evaluate Biomine by predicting future annotations in thesource databases and prioritizing lists of putative disease genes. CONCLUSIONS: The experimental results show that Biomine has strong potential for predicting links when aset of selected candidate links is available. The predictions obtained using the entire Biominedataset are shown to clearly outperform ones obtained using any single source of data alone,when different types of links are suitably weighted. In the gene prioritization task, anestablished reference set of disease-associated genes is useful, but the results show that underfavorable conditions, Biomine can also perform well when no such information is available.The Biomine system is a proof of concept. Its current version contains 1.1 million entities and8.1 million relations between them, with focus on human genetics. Some of its functionalitiesare available in a public query interface at http://biomine.cs.helsinki.fi, allowing searching forand visualizing connections between given biological entities.     

Optimization of the dilute maleic acid pretreatment of wheat straw

Background  

In this study, the dilute maleic acid pretreatment of wheat straw is optimized, using pretreatment time, temperature and maleic acid concentration as design variables. A central composite design was applied to the experimental set up. The response factors used in this study are: (1) glucose benefits from improved enzymatic digestibility of wheat straw solids; (2) xylose benefits from the solubilization of xylan to the liquid phase during the pretreatment; (3) maleic acid replenishment costs; (4) neutralization costs of pretreated material; (5) costs due to furfural production; and (6) heating costs of the input materials. For each response factor, experimental data were fitted mathematically. After data translation to €/Mg dry straw, determining the relative contribution of each response factor, an economic optimization was calculated within the limits of the design variables.     

What Data to Use for Forest Conservation Planning? A Comparison of Coarse Open and Detailed Proprietary Forest Inventory Data in Finland

The boreal region is facing intensifying resource extraction pressure, but the lack of comprehensive biodiversity data makes operative forest conservation planning difficult. Many countries have implemented forest inventory schemes and are making extensive and up-to-date forest databases increasingly available. Some of the more detailed inventory databases, however, remain proprietary and unavailable for conservation planning. Here, we investigate how well different open and proprietary forest inventory data sets suit the purpose of conservation prioritization in Finland. We also explore how much priorities are affected by using the less accurate but open data. First, we construct a set of indices for forest conservation value based on quantitative information commonly found in forest inventories. These include the maturity of the trees, tree species composition, and site fertility. Secondly, using these data and accounting for connectivity between forest types, we investigate the patterns in conservation priority. For prioritization, we use Zonation, a method and software for spatial conservation prioritization. We then validate the prioritizations by comparing them to known areas of high conservation value. We show that the overall priority patterns are relatively consistent across different data sources and analysis options. However, the coarse data cannot be used to accurately identify the high-priority areas as it misses much of the fine-scale variation in forest structures. We conclude that, while inventory data collected for forestry purposes may be useful for forest conservation purposes, it needs to be detailed enough to be able to account for more fine-scaled features of high conservation value. These results underline the importance of making detailed inventory data publicly available. Finally, we discuss how the prioritization methodology we used could be integrated into operative forest management, especially in countries in the boreal zone.     

Gene dosage and selective expression modify phenotype in a Drosophila model of human mitochondrial disease

Human mitochondrial disease manifests with a wide range of clinical phenotypes of varying severity. To create a model for these disorders, we have manipulated the Drosophila gene technical knockout, encoding mitoribosomal protein S12. Various permutations of endogenous and transgenic alleles create a range of phenotypes, varying from larval developmental arrest through to mild neurological defects in the adult, and also mimic threshold effects associated with human mtDNA disease. Nuclear genetic background influences mutant phenotype by a compensatory mechanism affecting mitochondrial RNA levels. Selective expression of the wild-type allele indicates critical times and cell-types in development, in which mitochondrial protein synthesis deficiency leads to specific phenotypic outcomes.     

Large-volume cytocentrifuge for processing alcohol-fixed cytologic specimens. Application in urinary cytology

The use of a large-volume cytocentrifuge for the routine processing of urine specimens was investigated. Most specimens arrived in the laboratory mixed with 50% ethanol. Polyethylene glycol was added to the fixative supplied to the clinicians or to the cell suspension received in the laboratory. The slides used in the cytocentrifuge were coated with gelatin or poly-L-lysine to minimize cell loss. The resulting monolayers of cells, with occasional true tissue fragments, were stained by the Papanicolaou method. When indicated, immunocytochemical and histochemical stains were used. The technique gave good morphologic details, good cell yield and consistent staining quality. This method has also been applied to other cytologic specimens, such as serous fluids and fine needle aspirates, with good results. The method saves the time of cytotechnologists, and slides prepared by this technique are suitable for automatic staining.