A dynamically growing self-organizing tree (DGSOT) for hierarchical clustering gene expression profiles

MOTIVATION: The increasing use of microarray technologies is generating large amounts of data that must be processed in order to extract useful and rational fundamental patterns of gene expression. Hierarchical clustering technology is one method used to analyze gene expression data, but traditional hierarchical clustering algorithms suffer from several drawbacks (e.g. fixed topology structure; mis-clustered data which cannot be reevaluated). In this paper, we introduce a new hierarchical clustering algorithm that overcomes some of these drawbacks. RESULT: We propose a new tree-structure self-organizing neural network, called dynamically growing self-organizing tree (DGSOT) algorithm for hierarchical clustering. The DGSOT constructs a hierarchy from top to bottom by division. At each hierarchical level, the DGSOT optimizes the number of clusters, from which the proper hierarchical structure of the underlying dataset can be found. In addition, we propose a new cluster validation criterion based on the geometric property of the Voronoi partition of the dataset in order to find the proper number of clusters at each hierarchical level. This criterion uses the Minimum Spanning Tree (MST) concept of graph theory and is computationally inexpensive for large datasets. A K-level up distribution (KLD) mechanism, which increases the scope of data distribution in the hierarchy construction, was used to improve the clustering accuracy. The KLD mechanism allows the data misclustered in the early stages to be reevaluated at a later stage and increases the accuracy of the final clustering result. The clustering result of the DGSOT is easily displayed as a dendrogram for visualization. Based on a yeast cell cycle microarray expression dataset, we found that our algorithm extracts gene expression patterns at different levels. Furthermore, the biological functionality enrichment in the clusters is considerably high and the hierarchical structure of the clusters is more reasonable. AVAILABILITY: DGSOT is available upon request from the authors.     

Improvement of the antibody-dependent respiratory burst assay for assessing protective immune responses to malaria

The antibody-dependent respiratory burst (ADRB) assay is a sensitive isoluminol-based chemiluminescence (CL) functional assay designed to assess the capacity of opsonizing antibodies against merozoites to induce neutrophil respiratory burst. ADRB was shown to measure protective immunity against malaria in endemic areas, but the assay needed further improvement to ensure better sensitivity and reproducibility. Here, we adjusted parameters such as the freezing–thawing procedure of merozoites, merozoites''s concentration and the buffer solution''s pH, and we used the improved assay to measure ADRB activity of 207 sera from 97 and 110 individuals living, respectively, in Dielmo and Ndiop villages with differing malaria endemicity. The improvement led to increased CL intensity and assay sensitivity, and a higher reproducibility. In both areas, ADRB activity correlated with malaria endemicity and individual''s age discriminated groups with and without clinical malaria episodes, and significantly correlated with in vivo clinical protection from Plasmodium falciparum malaria. Our results demonstrate that the improved ADRB assay can be valuably used to assess acquired immunity during monitoring by control programmes and/or clinical trials.     

Smc5-Smc6 mediate DNA double-strand-break repair by promoting sister-chromatid recombination

DNA double-strand breaks (DSB) can arise during DNA replication, or after exposure to DNA-damaging agents, and their correct repair is fundamental for cell survival and genomic stability. Here, we show that the Smc5-Smc6 complex is recruited to DSBs de novo to support their repair by homologous recombination between sister chromatids. In addition, we demonstrate that Smc5-Smc6 is necessary to suppress gross chromosomal rearrangements. Our findings show that the Smc5-Smc6 complex is essential for genome stability as it promotes repair of DSBs by error-free sister-chromatid recombination (SCR), thereby suppressing inappropriate non-sister recombination events.     

Heterochromatin is refractory to gamma-H2AX modification in yeast and mammals

Double-strand break (DSB) damage in yeast and mammalian cells induces the rapid ATM (ataxia telangiectasia mutated)/ATR (ataxia telangiectasia and Rad3 related)-dependent phosphorylation of histone H2AX (gamma-H2AX). In budding yeast, a single endonuclease-induced DSB triggers gamma-H2AX modification of 50 kb on either side of the DSB. The extent of gamma-H2AX spreading does not depend on the chromosomal sequences. DNA resection after DSB formation causes the slow, progressive loss of gamma-H2AX from single-stranded DNA and, after several hours, the Mec1 (ATR)-dependent spreading of gamma-H2AX to more distant regions. Heterochromatic sequences are only weakly modified upon insertion of a 3-kb silent HMR locus into a gamma-H2AX-covered region. The presence of heterochromatin does not stop the phosphorylation of chromatin more distant from the DSB. In mouse embryo fibroblasts, gamma-H2AX distribution shows that gamma-H2AX foci increase in size as chromatin becomes more accessible. In yeast, we see a high level of constitutive gamma-H2AX in telomere regions in the absence of any exogenous DNA damage, suggesting that yeast chromosome ends are transiently detected as DSBs.     

Biofilm formation by Acinetobacter baumannii strains isolated from urinary tract infection and urinary catheters

Systemic infections in avian species caused by avian pathogenic Escherichia coli (APEC) are economically devastating to poultry industries worldwide. To unravel factors possibly involved in APEC pathogenicity, suppression subtractive hybridization was applied, leading to the identification of a putative APEC autotransporter adhesin gene aatA in our previous study. In this study, pathogenic mechanism of AatA was further determined. A deletion mutant of aatA was constructed in the APEC DE205B, which results in the reduced capacity to adhere to DF-1 cells, defective virulence in vivo, and decreased colonization capacity in lung during the systemic infection compared with the wild-type strain. Furthermore, these capacities were restored in the complementation strains. These results indicated that AatA makes a significant contribution to APEC virulence through bacterial adherence to host tissues in vivo and in vitro. In addition, aggregation assays for strain AAEC189 expressing aatA indicated that AatA mediates cell aggregation and settling of cells. However, this cell aggregation is blocked by Type I fimbriae. This study illustrates the first examination of the role of AatA in aggregation and systemic infection.     

Biotreatment of Total Petroleum Hydrocarbons from an oily Sludge Using Co-Composting Approach

Discharging of non-treated oily sludge from oil refineries has undesirable impacts on the environment. In this research, the biotreatment of total petroleum hydrocarbons (TPHs) from Abadan Petroleum Refinery, Iran was done using co-composting method. A 5 kg mixture of oily sludge and compost (oily sludge: compost ratios 1:0, 1:0.1, 1:0.3, 1:0.5, and 1:0.7 w/w) and a bulking agent of wheat straw were used as treatments. All treatments were placed in a wooden box inside a laboratory and aerated every 2–3 days by mixing during two months of the experiments. The variation of TPHs concentration, bacterial density, C/N ratio, pH, and temperature were assessed during the 63 days- experiments. Results showed that the majority of TPHs of samples was removed at first 30 days. The maximum TPHs removal (65%) was obtained in the sludge: compost = 1:0.5 at the operation time of 63 day. The significant different between removal efficiency of oily sludge: compost ratios and the control sample (p value < 0.05) indicated the appropriate density of TPHs degrader-bacteria in treated samples. The highest variation in C/N ratio was observed 15± 0.58 in the oily sludge: compost = 1:0.1. At the beginning of experiments, the pH values of all treatments was alkaline, but became neutral at the end of the reaction time. The TPHs degradation kinetic for all oily sludge: compost ratios followed pseudo second-order model. In general, co-composting has high efficiency in oily sludge remediation and can be potentially applied as a simple and cost-effective approach for remediation of oily sludge.     

Characterization of plant-growth-promoting traits of Acinetobacter species isolated from rhizosphere of Pennisetum glaucum

A total of 31 Acinetobacter isolates were obtained from the rhizosphere of Pennisetum glaucum and evaluated for their plant-growth-promoting traits. Two isolates, namely Acinetobacter sp. PUCM1007 and A. baumannii PUCM1029, produced indole acetic acid (10-13 microgram/ml). A total of 26 and 27 isolates solubilized phosphates and zinc oxide, respectively. Among the mineral-solubilizing strains, A. calcoaceticus PUCM1006 solubilized phosphate most efficiently (84 mg/ml), whereas zinc oxide was solubilized by A. calcoaceticus PUCM1025 at the highest solubilization efficiency of 918%. All the Acinetobacter isolates, except PUCM1010, produced siderophores. The highest siderophore production (85.0 siderophore units) was exhibited by A. calcoaceticus PUCM1016. Strains PUCM1001 and PUCM1019 (both A. calcoaceticus) and PUCM1022 (Acinetobacter sp.) produced both hydroxamate- and catechol-type siderophores, whereas all the other strains only produced catechol-type siderophores. In vitro inhibition of Fusarium oxysporum under iron-limited conditions was demonstrated by the siderophore-producing Acinetobacter strains, where PUCM1018 was the most potent inhibitor of the fungal phytopathogen. Acinetobacter sp. PUCM1022 significantly enhanced the shoot height, root length, and root dry weights of pearl millet seedlings in pot experiments when compared with controls, underscoring the plant-growth-promoting potential of these isolates.