Optimization and modeling of phenanthrene degradation by <Emphasis Type="Italic">Mycobacterium</Emphasis> sp. 6PY1 in a biphasic medium using response-surface methodology

In the present paper, the degradation of phenanthrene, a model polycyclic aromatic hydrocarbon compound, by the Mycobacterium strain 6PY1 was optimized in a biphasic culture medium. The optimization and modeling were performed using the design of experiments methodology. The temperature, the silicone oil/mineral salts medium volume ratio, and the initial cell concentration, were used as the central composite design parameters. In all experiments, the phenanthrene was degraded to undetectable levels. Response surface methodology was successfully employed to derive an empirical model describing the rate and time of degradation and to deduce the optimal degradation conditions. As a result of the optimization processes, the optimal responses for the degradation rate, the volumetric degradation rate, and the 90% degradation time were estimated to be 0.172 mg h⁻¹, 22 mg l⁻¹ h⁻¹, and 18 h, respectively.     

Combining Position Weight Matrices and Document-Term Matrix for Efficient Extraction of Associations of Methylated Genes and Diseases from Free Text

Background

In a number of diseases, certain genes are reported to be strongly methylated and thus can serve as diagnostic markers in many cases. Scientific literature in digital form is an important source of information about methylated genes implicated in particular diseases. The large volume of the electronic text makes it difficult and impractical to search for this information manually.

Methodology

We developed a novel text mining methodology based on a new concept of position weight matrices (PWMs) for text representation and feature generation. We applied PWMs in conjunction with the document-term matrix to extract with high accuracy associations between methylated genes and diseases from free text. The performance results are based on large manually-classified data. Additionally, we developed a web-tool, DEMGD, which automates extraction of these associations from free text. DEMGD presents the extracted associations in summary tables and full reports in addition to evidence tagging of text with respect to genes, diseases and methylation words. The methodology we developed in this study can be applied to similar association extraction problems from free text.

Conclusion

The new methodology developed in this study allows for efficient identification of associations between concepts. Our method applied to methylated genes in different diseases is implemented as a Web-tool, DEMGD, which is freely available at http://www.cbrc.kaust.edu.sa/demgd/. The data is available for online browsing and download.     

Ecrg4 Attenuates the Inflammatory Proliferative Response of Mucosal Epithelial Cells to Infection

We report an inverse relationship between expression of the orphan candidate tumor suppressor gene esophageal cancer related gene 4 (Ecrg4), and the mucosal epithelial cell response to infection in the middle ear (ME). First, we found constitutive Ecrg4 mRNA expression in normal, quiescent ME mucosa that was confirmed by immunostainning of mucosal epithelial cells and immunoblotting of tissue lysates for the 14 kDa Ecrg4 protein. Upon experimental ME infection, Ecrg4 gene expression rapidly decreased by over 80%, between 3 to 48 hrs, post infection. When explants of this infected mucosa were placed in culture and transduced with an adenovirus (AD) encoding Ecrg4 gene (ADEcrg4), the proliferative and migratory responses of mucosal cells were significantly inhibited. ADEcrg4 transduction of control explants from uninfected MEs had no effect on basal growth and migration. Over-expression of Ecrg4 in vivo, by pre-injecting MEs with ADEcrg4 48 hrs prior to infection, prevented the natural down-regulation of Ecrg4, reduced mucosal proliferation and prevented inflammatory cell infiltration normally observed after infection. Taken together, these data support a hypothesis that Ecrg4 plays a role in coordinating the inflammatory and proliferative response to infection of mucosal epithelium suggesting a possible mechanism for its putative anti-tumor activity.     

PHYTODESALINATION OF A MODERATELY-SALT-AFFECTED SOIL BY SULLA CARNOSA

The aim of this investigation was to evaluate the ability of the indifferent halophyte Sulla carnosa Desf. to desalinize a moderately-salt-affected soil. Seeds were sown on a fertile soil added or not with 1.5 g NaCl. kg^?1. Analogous treatments without plantation (control and salinized) were also used. Plant culture was performed under greenhouse conditions in non-perforated pots containing 10 kg soil each and irrigated with non-saline tap water. After 80 days of treatment, shoots were harvested. Soil samples were also collected after division of soil column in each pot into two horizons. Our results showed that salt addition increased electrical conductivity of saturation paste extract (ECe) from 3.3 to 8.4 dS. m^?1 and soluble sodium concentration from 0.32 to 1.15 g. kg^?1 soil in the upper horizon. In the lower horizon however, Na⁺ concentration was quasi-constant and then ECe was less increased. Plant culture inversed this pattern of sodium accumulation and salinity. Its productivity and phytodesalination capacity in 80 days were 5.0 t DW. ha^?1 and 0.3 t Na⁺. ha^?1 (24% of the added quantity), respectively. Interestingly, sodium dilution within biomass (41.5–45.6 mg. g^?1 DW) and the non-altered nutrition make this plant suitable for forage as second use after phytodesalination.     

Utilization of cellulose and ulvan from the green seaweed Ulva lactuca in the development of composite edible films with natural antioxidant properties

Journal of Applied Phycology - Cellulose and ulvan were extracted sequentially from the green seaweed Ulva lactuca and were used for the development of edible films with natural antioxidant...