Mining the 3′UTR of Autism-implicated Genes for SNPs Perturbing MicroRNA Regulation

Autism spectrum disorder(ASD) refers to a group of childhood neurodevelopmental disorders with polygenic etiology. The expression of many genes implicated in ASD is tightly regulated by various factors including microRNAs(miRNAs), a class of noncoding RNAs 22 nucleotides in length that function to suppress translation by pairing with ‘miRNA recognition elements'(MREs) present in the 30untranslated region(30UTR) of target mRNAs. This emphasizes the role played by miRNAs in regulating neurogenesis, brain development and differentiation and hence any perturbations in this regulatory mechanism might affect these processes as well. Recently, single nucleotide polymorphisms(SNPs) present within 30UTRs of mRNAs have been shown to modulate existing MREs or even create new MREs. Therefore, we hypothesized that SNPs perturbing miRNA-mediated gene regulation might lead to aberrant expression of autism-implicated genes, thus resulting in disease predisposition or pathogenesis in at least a subpopulation of ASD individuals. We developed a systematic computational pipeline that integrates data from well-established databases. By following a stringent selection criterion, we identified 9 MRE-modulating SNPs and another 12 MRE-creating SNPs in the 30UTR of autism-implicated genes. These high-confidence candidate SNPs may play roles in ASD and hence would be valuable for further functional validation.     

Effect of Shadowing on Survival of Bacteria under Conditions Simulating the Martian Atmosphere and UV Radiation

Spacecraft-associated spores and four non-spore-forming bacterial isolates were prepared in Atacama Desert soil suspensions and tested both in solution and in a desiccated state to elucidate the shadowing effect of soil particulates on bacterial survival under simulated Martian atmospheric and UV irradiation conditions. All non-spore-forming cells that were prepared in nutrient-depleted, 0.2-μm-filtered desert soil (DSE) microcosms and desiccated for 75 days on aluminum died, whereas cells prepared similarly in 60-μm-filtered desert soil (DS) microcosms survived such conditions. Among the bacterial cells tested, Microbacterium schleiferi and Arthrobacter sp. exhibited elevated resistance to 254-nm UV irradiation (low-pressure Hg lamp), and their survival indices were comparable to those of DS- and DSE-associated Bacillus pumilus spores. Desiccated DSE-associated spores survived exposure to full Martian UV irradiation (200 to 400 nm) for 5 min and were only slightly affected by Martian atmospheric conditions in the absence of UV irradiation. Although prolonged UV irradiation (5 min to 12 h) killed substantial portions of the spores in DSE microcosms (~5- to 6-log reduction with Martian UV irradiation), dramatic survival of spores was apparent in DS-spore microcosms. The survival of soil-associated wild-type spores under Martian conditions could have repercussions for forward contamination of extraterrestrial environments, especially Mars.     

Isolation and characterization of a methanol-utilizing strain ofCandida boidinii from cow dung which is able to grow on paraffin

A methanol-utilizing yeast,Candida boidinii, was isolated from cow dung. It could grow on a medium containing methanol or liquid paraffin as the only carbon source. Its cell yield after 7 days of growth on methanol was 0.34 g g^–1 and on paraffin 0.30 g g^–1. The organism was able to tolerate up to 4% (v/v) methanol.

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Résumé On a isolé une souche deCandida boidinii, levure utilisant le méthanol, à partir de bouse de vache. La souche était capable de croître sur un milieu contenant le méthanol ou la paraffine liquide, comme seule souche de carbone. Le rendement cellulaire après 7 jours de croissance était de 0.34 g par g de méthanol et 0.30 g par g de paraffine. L'organisme était capable de tolérer jusqu'à 4% (v/v) de méthanol.

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This work was carried out while K. Kannan was at the Tamil Nadu Agricultural University.     

Biogenesis of peptide antibiotics

A simple synthetic medium with glycine,l-tryptophan anddl-alanine was developed for study of antimycin A biogenesis. The strain produced 550 mg of mycelium dry weight and 200 μg of antimycin A per 100 ml of this medium. Intense biosynthesis of antibiotic was initiated in early fermentation and optimum yields were achieved after an additional 96 h incubation. No absolute relationship between growth rate and antimycin A production intensity was found. Biogenesis of antimycin A via tryptophan and formylkynurenine is suggested and similarity in early biogenesis of both antimycin A and actinomycin is considered.     

Activation of the mitochondrial apoptotic pathway contributes to methotrexate‐induced small intestinal injury in rats

The efficacy of methotrexate (MTX), a commonly used chemotherapeutic drug, is limited by intestinal injury. As the mechanism of MTX‐induced small intestinal injury is not clear, there is no definitive treatment for MTX‐induced gastrointestinal injury. The present study investigates the role of mitochondrial apoptotic pathway in MTX‐induced small intestinal injury and examines whether aminoguanidine is effective in preventing the damage. Eight Wistar rats were administered 3 consecutive i.p. injections of 7 mg/kg body wt. MTX. Some rats were pretreated with 30 mg or 50 mg/kg body wt. of aminoguanidine (n = 6 in each group). Protein expressions of cytochrome c, caspases 3 and 9, and PARP‐1 were determined in the small intestines by immunohistochemistry and western blot. Mitochondrial pathway of apoptosis was activated in the small intestines of MTX‐treated rats as evidenced by intense immunostaining for cyt c, caspases 9 and 3, and PARP‐1 and mitochondrial release of cyt c, activation of caspases, and PARP‐1 cleavage by Western blot. Immunofluorescence revealed increased nuclear localization of PARP‐1. Aminoguanidine pretreatment ameliorated MTX‐induced small intestinal injury in dose‐dependent manner and inactivated the mitochondrial apoptotic pathway. Aminoguanidine may possess beneficial intestinal protective effects as an adjuvant co‐drug against MTX intestinal toxicity during cancer chemotherapy. As the mechanism of MTX‐induced small intestinal injury is not clear, there is no definitive treatment for MTX‐induced gastrointestinal injury. The results of the present study show that the mitochondrial pathway of apoptosis plays a role in MTX‐induced small intestinal injury as evidenced by cytochrome c release, activation of caspases 9 and 3, PARP‐1 cleavage, and DNA fragmentation. Aminoguanidine (AG) pretreatment attenuates the severity of small‐intestinal injury induced in rats by MTX treatment. The mechanisms of action of AG involve inhibition of iNOS, and mitochondrial pathway of apoptosis. It is suggested that aminoguanidine may possess beneficial intestinal protective effects as an adjuvant co‐drug against MTX intestinal toxicity during cancer chemotherapy.     

Extended fuzzy c-means: an analyzing data clustering problems

In recent years the use of fuzzy clustering techniques in medical diagnosis is increasing steadily, because of the effectiveness of fuzzy clustering techniques in recognizing the systems in the medical database to help medical experts in diagnosing diseases. This study focuses on clustering lung cancer dataset into three types of cancers which are leading cause of cancer death in the world. This paper invents effective fuzzy clustering techniques by incorporating hyper tangent kernel function, and entropy methods for analyzing the Lung Cancer database to assist physician in diagnosing lung cancer. Further this paper proposes an algorithm to initialize the cluster centers to speed up the process of the algorithms. The effectiveness of the proposed methods has been proved through the experimental works on synthetic dataset, Wine dataset and IRIS dataset in terms of running time, number of iterations, visual segmentation effects and clustering accuracy. And then this paper proposes the proposed method on Lung cancer database to divide it into three types of lung cancers. In addition this paper proves the superiority of the proposed methods by comparing the obtained classes with reference classes through Error Matrix.     

Developmental Changes in the in Vitro Activated Regenerative Activity of Primitive Mammary Epithelial Cells

Many normal adult tissues contain rare stem cells with extensive self-maintaining regenerative potential. During development, the stem cells of the hematopoietic and neural systems undergo intrinsically specified changes in their self-renewal potential. In the mouse, mammary stem cells with transplantable regenerative activity are first detectable a few days before birth. They share some phenotypic properties with their adult counterparts but are enriched in a subpopulation that displays a distinct gene expression profile. Here we show that fetal mammary epithelial cells have a greater direct and inducible growth potential than their adult counterparts. The latter feature is revealed in a novel culture system that enables large numbers of in vitro clonogenic progenitors as well as mammary stem cells with serially transplantable activity to be produced within 7 days from single fetal or adult input cells. We further show that these responses are highly dependent on novel factors produced by fibroblasts. These findings provide new avenues for elucidating mechanisms that regulate normal mammary epithelial stem cell properties at the single-cell level, how these change during development, and how their perturbation may contribute to transformation.