Arthrobacter enclensis sp. nov., isolated from sediment sample

A novel bacterial strain designated as NIO-1008^T was isolated from marine sediments sample in Chorao Island India. Cells of the strains were gram positive and non-motile, displayed a rod–coccus life cycle and formed cream to light grey colonies on nutrient agar. Strain NIO-1008^T had the chemotaxonomic markers that were consistent for classification in the genus Arthrobacter, i.e. MK-9(H₂) (50.3 %), as the major menaquinone, and the minor amount of MK-7 (H₂-27.5 %), MK-8 (H₄-11.6 %) and MK-8 (H₂-10.4 %). anteiso-C_15:0, iso-C_15:0, iso-C_16:0 and C_15:0 were the predominant fatty acids. Galactose, glucose and rhamnose are the cell-wall sugars, and DNA G+C content was 61.3 mol%. Phylogenetic analysis, based on 16S rRNA gene sequencing, showed that the strains were most similar to Arthrobacter equi IMMIB L-1606^T, Arthrobacter chlorophenolicus DSM 12829^T, Arthrobacter defluvii KCTC 19209^T and Arthrobacter niigatensis CCTCC AB 206012^T with 98.5, 98.4, 98.0 and 97.8 %, respectively, and formed a separate lineage. Combined phenotypic data and DNA–DNA hybridization data supported the conclusion that strains NIO-1008^T represent a novel species within the genus Arthrobacter, for which the name Arthrobacter enclensis sp. nov., is proposed. The type strain is NIO-1008^T = (NCIM 5488^T = DSM 25279^T).     

Purification and characterization of 2S albumin from Nelumbo nucifera

The 2S albumins are a group of seed storage proteins that have recently attracted considerable attention in the field of allergen science due to their allergenic potential. A new 2S albumin from seeds of Nelumbo nucifera (Nn-2S alb) was purified to electrophoretic homogeneity by the combination of ammonium sulfate fractionation, gel filtration, and ion exchange chromatography. The protein has a molecular mass of about 12 kDa estimated by SDS–PAGE, in good agreement with 12.5 ± 0.01 kDa determined by ESI–MS. Circular dichroism data showed that protein contained about 66% α-helices as estimated by K2D3, indicating that the protein was predominantly helical. The sedimentation coefficient (s°_20,w) of the predicted model was 1.72 ± 0.21 S. The predicted 3-dimensional structure of the Nn-2S alb revealed that the protein has a region of 12 amino acids which largely corresponds to the conserved immuno-dominant epitope of 2S allergens.     

Novelty of Axin 2 and lack of Axin 1 gene mutation in colorectal cancer: a study in Kashmiri population

Colorectal cancer is (CRC) one of the leading causes of mortality and morbidity. Various genetic factors have been reported to be involved in the development of colorectal cancers including Axin gene. Axin, a major scaffold protein, plays an important role in various bio signaling pathways. We aim to study mutational pattern of Axin gene in colorectal cancer patients of Kashmiri population. The paired tumor and adjacent normal tissue specimens of 50 consecutive patients with CRC were used in our study. The DNA preparations were evaluated for the occurrence of Axin 1 and Axin 2 gene mutations by direct DNA sequencing. We analyzed exon 1a, 1b, 1c, 2, 4, 6, and 10 of Axin 1 and exon 7 of Axin 2. In this study, we found a novel mutation of G>T (GCT>TCT) transversion in exon 7 of Axin 2 gene at codon G695T (p.alanine >?serine) at a frequency of 6% (3/50). In the same exon of Axin 2 gene a single nucleotide polymorphism (SNP) was detected in codon L688L (CCT>CTT) at a frequency of 36% (18/50). In exon 1c of Axin 1 a SNP was detected at codon D726D (GAT>GAC) at a frequency of 62.5% (31/50). Both the SNPs were synonymous hence do not lead to change of amino acid. Although Axin 1 and Axin 2 gene mutations have been found to be involved in the development of colorectal cancers, it seems to be a relatively rare event in Kashmiri population. However, an interesting finding of this study is the novelty of Axin 2 gene mutations which may be a predisposing factor in ethnic Kashmiri population to CRC.     

Design,synthesis, and biological evaluation of selective and potent Carbazole-based butyrylcholinesterase inhibitors

Alzheimer’s disease (AD) is the most common form of dementia. Inhibition of BChE might be a useful therapeutic target for AD. A new series of Carbazole-Benzyl Pyridine derivatives were designed synthesized and evaluated as butyrylcholinesterase (BChE) inhibitors. In vitro assay revealed that all of the derivatives had selective and potent anti- BChE activities. 3-((9H-Carbazol-9-yl)methyl)-1-(4-chlorobenzyl)pyridin-1-ium chloride (compound 8f) had the most potent anti-BChE activity (IC₅₀ value?=?0.073?μM), the highest BChE selectivity and mixed-type inhibition. Docking study revealed that 8f interacted with the peripheral site, the choline binding site, catalytic site and the acyl pocket of BChE. Physicochemical properties were accurate to Lipinski's rule. In addition, compound 8f demonstrated neuroprotective activity at 10?µM. This compound could also inhibit AChE-induced and self-induced Aβ peptide aggregation at concentration of 100?µM and 10?µM respectively. The in-vivo study showed that compound 8f in 10?mg/kg increased the time spent in target quadrant in the probe day and decreased mean training period scape latency in rats. All results suggest that new sets of potent selective inhibitors of BChE have a therapeutic potential for the treatment of AD.     

Recent Advances in the Regulation of Citric Acid Metabolism in Citrus Fruit

The regulation of citric acid metabolism during fruit ripening has a major impact on the production of high-quality fruit. The impact of citric acid on organoleptic fruit quality attributes, fruit storage performance and the synthesis of several secondary metabolites has led to an exponential increase in research efforts during the last two decades. Recent research has focused on the relationship among citric acid biosynthesis, transportation, storage, and utilization. Among citrate metabolic processes, activities of a proton pump, especially the plasma membrane H⁺-ATPase on tonoplast and citrate catabolism in cytosol play important roles in the regulation of citrate accumulation in cell vacuoles. Moreover, we highlight recent advances and provide an overview of citrate metabolism, postharvest physiology of citrate metabolism, and the influence of agro-climatic factors on citrus fruits. It is the first review that provides a comprehensive model for citrate metabolism in citrus fruit juice sacs. We anticipate that this model for the regulation of citrate metabolism will facilitate the study of fruit acidity in citrus and other nonclimacteric fruits.     

A comparative study of cell classifiers for image-based high-throughput screening

Background

Millions of cells are present in thousands of images created in high-throughput screening (HTS). Biologists could classify each of these cells into a phenotype by visual inspection. But in the presence of millions of cells this visual classification task becomes infeasible. Biologists train classification models on a few thousand visually classified example cells and iteratively improve the training data by visual inspection of the important misclassified phenotypes. Classification methods differ in performance and performance evaluation time. We present a comparative study of computational performance of gentle boosting, joint boosting CellProfiler Analyst (CPA), support vector machines (linear and radial basis function) and linear discriminant analysis (LDA) on two data sets of HT29 and HeLa cancer cells.

Results

For the HT29 data set we find that gentle boosting, SVM (linear) and SVM (RBF) are close in performance but SVM (linear) is faster than gentle boosting and SVM (RBF). For the HT29 data set the average performance difference between SVM (RBF) and SVM (linear) is 0.42 %. For the HeLa data set we find that SVM (RBF) outperforms other classification methods and is on average 1.41 % better in performance than SVM (linear).

Conclusions

Our study proposes SVM (linear) for iterative improvement of the training data and SVM (RBF) for the final classifier to classify all unlabeled cells in the whole data set.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2105-15-342) contains supplementary material, which is available to authorized users.     

Structural studies of water-soluble polysaccharides of an edible mushroom, Termitomyces eurhizus. A reinvestigation

The structure of two polysaccharides isolated from the hot aqueous extract of fruiting bodies of the mushroom, Termitomyces eurhizus, have been reinvestigated. These consist of two homogeneous fractions PS-I and PS-II. PS-I contains only D-glucose as the monosaccharide constituent. From methylation analysis and periodate oxidation studies, followed by GLC-MS analysis the linkages, the sugar units in PS-I were identified as (1-->3)-D-Glcp and (1-->6)-D-Glcp. PS-II contains D-glucose, and the mode of linkage of d-glucose was identified as (1-->6)-D-Glcp. Finally, the following possible structures of the polysaccharides were assigned using 1H, 2D-COSY, TOCSY, NOESY and 13C NMR spectral analysis: [carbohydrate structure: see text].