Automatic segmentation and supervised learning-based selection of nuclei in cancer tissue images

Analysis of preferential localization of certain genes within the cell nuclei is emerging as a new technique for the diagnosis of breast cancer. Quantitation requires accurate segmentation of 100-200 cell nuclei in each tissue section to draw a statistically significant result. Thus, for large-scale analysis, manual processing is too time consuming and subjective. Fortuitously, acquired images generally contain many more nuclei than are needed for analysis. Therefore, we developed an integrated workflow that selects, following automatic segmentation, a subpopulation of accurately delineated nuclei for positioning of fluorescence in situ hybridization-labeled genes of interest. Segmentation was performed by a multistage watershed-based algorithm and screening by an artificial neural network-based pattern recognition engine. The performance of the workflow was quantified in terms of the fraction of automatically selected nuclei that were visually confirmed as well segmented and by the boundary accuracy of the well-segmented nuclei relative to a 2D dynamic programming-based reference segmentation method. Application of the method was demonstrated for discriminating normal and cancerous breast tissue sections based on the differential positioning of the HES5 gene. Automatic results agreed with manual analysis in 11 out of 14 cancers, all four normal cases, and all five noncancerous breast disease cases, thus showing the accuracy and robustness of the proposed approach. ? Published 2012 Wiley Periodicals, Inc.     

A new monorchiid trematode, <Emphasis Type="Italic">Paramonorcheides selaris</Emphasis> n. sp., from the carangid fish <Emphasis Type="Italic">Selar crumenophthalmus</Emphasis> in the Bay of Bengal off the Visakhapatnam coast of India

Paramonorcheides selaris n. sp. is described from the intestine of the carangid fish Selar crumenophthalmus (Bloch) off the Visakhapatnam coast, Bay of Bengal. It is closest to the Australian species P. pseudocaranxi Dove & Cribb, 1998, but differs in its shorter cirrus-sac extending only to the level of the ovary rather than to the level of the testes, in lacking eye-spot pigment and in details of the armature of the terminal genitalia. P. pseudocaranxi of Machida (2005) is regarded as identical to the new species. The validity of Allobacciger Hafeezullah & Siddiqi, 1970, as distinct from Monorcheides Odhner, 1905, is discussed. A key to the six species of Paramonorcheides Yamaguti, 1938 is presented.     

Disease-specific gene repositioning in breast cancer

Genomes are nonrandomly organized within the three-dimensional space of the cell nucleus. Here, we have identified several genes whose nuclear positions are altered in human invasive breast cancer compared with normal breast tissue. The changes in positioning are gene specific and are not a reflection of genomic instability within the cancer tissue. Repositioning events are specific to cancer and do not generally occur in noncancerous breast disease. Moreover, we show that the spatial positions of genes are highly consistent between individuals. Our data indicate that cancer cells have disease-specific gene distributions. These interphase gene positioning patterns may be used to identify cancer tissues.     

Evaluating the biochemical traits of novel Trichoderma-based biofilms for use as plant growth-promoting inoculants

Bacteria-mediated plant growth promotion is a well-established and complex phenomenon that is often achieved by the activities of more than one plant growth-promoting (PGP) trait, which may not always be present in a single organism. Biofilms developed using a combination of two organisms with useful plant growth-promoting rhizobacteria (PGPR) traits may provide a definite advantage. In this context, in vitro studies were conducted evaluating the PGP traits of novel biofilms developed using Trichoderma as matrix and agriculturally important bacteria (Azotobacter chroococcum, Pseudomonas fluorescens and Bacillus subtilis) as partners. Such biofilms exhibited higher values for various biochemical attributes as compared to the individual organisms and dual cultures. Trichoderma–Bacillus and Trichoderma–Pseudomonas biofilms exhibited enhanced antifungal activity, ammonia, indole acetic acid (IAA) and siderophore production, as compared to the other treatments. Trichoderma–Azotobacter biofilm recorded the highest nitrogenase activity and 1-aminocyclopropane-1-carboxylic (ACC) deaminase activity. The synergism in terms of the PGP traits in the biofilms revealed their promise as superior PGP inoculants.     

Synthesis and structure-activity relationship of novel conformationally restricted analogues of serotonin as 5-HT6 receptor ligands

5-Hydroxytryptamine 6 receptors (5-HT(6)R) are being perceived as the possible target for treatment of cognitive disorders as well as obesity. The present article deals with the design, synthesis, in vitro binding and structure-activity relationship of a novel series of tetracyclic tryptamines with the rigidized N-arylsulphonyl, N-arylcarbonyl and N-benzyl substituents as 5-HT(6) receptor ligands. The chiral sulphonyl derivatives 15a and 17a showed high affinity at 5-HT(6)R with the K(i) of 23.4 and 20.5?nM, respectively. The lead compound from the series 15a has acceptable ADME properties, adequate brain penetration and is active in animal models of cognition like Novel Object Recognition Task (NORT) and water maze.     

Attenuation of hydrogen peroxide-mediated oxidative stress by Brassica juncea annexin-3 counteracts thiol-specific antioxidant (TSA1) deficiency in Saccharomyces cerevisiae

Brassica juncea annexin-3 (BjAnn3) was functionally characterized for its ability to modulate H₂O₂-mediated oxidative stress in Saccharomyces cerevisiae. BjAnn3 showed a significant protective role in cellular-defense against oxidative stress and partially alleviated inhibition of mitochondrial respiration in presence of exogenously applied H₂O₂. Heterologous expression of BjAnn3 protected membranes from oxidative stress-mediated damage and positively regulated antioxidant gene expression for ROS detoxification. We conclude that, BjAnn3 partially counteracts the effects of thioredoxin peroxidase 1 (TSA1) deficiency and aids in cellular-protection across kingdoms. Despite partial compensation of TSA1 by BjAnn3 in cell-viability tests, the over-complementation in ROS-related features suggests the existence of both redundant (e.g. ROS detoxification) and distinct features (e.g. membrane protection versus proximity-based redox regulator) of both proteins.     

Optimization of conditions for in vitro development of <Emphasis Type="Italic">Trichoderma viride</Emphasis>-based biofilms as potential inoculants

Biofilms represent mixed communities present in a diverse range of environments; however, their utility as inoculants is less investigated. Our investigation was aimed towards in vitro development of biofilms using fungal mycelia (Trichoderma viride) as matrices and nitrogen-fixing and P-solubilizing bacteria as partners, as a prelude to their use as biofertilizers (biofilmed biofertilizers, BBs) and biocontrol agents for different crops. The most suitable media in terms of population counts, fresh mass and dry biomass for Trichoderma and Bacillus subtilis/Pseudomonas fluorescens was found to be Pikovskaya broth ± 1 % CaCO_3, while for Trichoderma and Azotobacter chroococcum, Jensen’s medium was most optimal. The respective media were then used for optimization of the inoculation rate of the partners in terms of sequence of addition of partners, fresh/dry mass of biofilms and population counts of partners for efficient film formation. Microscopic observations revealed significant differences in the progress of growth of biofilms and dual cultures. In the biofilms, the bacteria were observed growing intermingled within the fungal mycelia mat. Further, biofilm formation was compared under static and shaking conditions and the fresh mass of biofilms was higher in the former. Such biofilms are being further characterized under in vitro conditions, before using them as inoculants with crops.     

Design, synthesis and pharmacological evaluation of conformationally restricted N-arylsulfonyl-3-aminoalkoxy indoles as a potential 5-HT6 receptor ligands

A series of novel conformationally restricted N(1)-arylsulfonyl-3-aminoalkoxy indoles were designed and synthesized as 5-HT(6) receptor (5-HT(6)R) ligands. Many of the synthesized compounds have moderate in vitro-binding affinities at 5-HT(6)R. The lead compound 8b (% inhibition?=?97.2 at 1 μM) from this series has good pharmacokinetic profile in male Wister rats and is active in animal model of cognition like Morris water maze. The details of chemistry, SAR, pharmacokinetics and pharmacological data constitute the subject matter of this report.     

The effect of level of forage and oil supplement on biohydrogenation intermediates and bacteria in continuous cultures

The objective of this study was to investigate how level of forage and oils in ruminant animals’ diet affect selected strains of ruminal bacteria believed to be involved in biohydrogenation (BH). Four continuous culture fermenters were used in 4 × 4 Latin square design with a 2 × 2 factorial arrangement over four consecutive periods of 10 days each. The experimental diets used in this study were: high forage diet (700:300 g/kg (DM basis) forage to concentrate; HFC), high forage with oil supplement (HFO), high forage diet (300:700 g/kg (DM basis) forage to concentrate; LFC), and high forage with oil supplement (HFO). The oil supplement was a blend of fish oil (FO) and soybean oil (SBO) added at 10 and 20 g/kg DM, respectively. Acetate concentration was greater (P<0.01) with the high forage diets whereas propionate concentration was greater (P<0.02) with the low forage diets and both decreased (P<0.05) with oil supplementation. The concentrations of t11 C18:1 (vaccenic acid, VA) and c9t11 conjugated linoleic acid (CLA) were greater (P<0.01) with the high than the low forage diets and concentrations increased (P<0.01) with oil supplementation particularly when added with the high forage diet. The concentrations of t10 C18:1 and t10c12 CLA were greater (P<0.01) with the low than the high forage diets and concentrations increased (P<0.01) with oil supplementation particularly when added with the low forage diet. The DNA abundance of Butyrivibrio fibrisolvens, Ruminococcus albus, Ruminococcus flavefaciens, Anaerovibrio lipolytica and Butyrivibrio proteoclasticum were greater (P<0.03) with the high than the low forage diets. Oil supplementation reduced (P<0.05) the DNA abundance only for R. flavefaciens, B. fibrisolvens and R. albus especially when added with the high forage diet. Results from this study suggest that the greater trans fatty acids (FA) production seen with the high forage diets may be related to greater activity of B. fibrisolvens, R. flavefaciens and R. albus, and B. proteoclasticum appears to play a minor role in the production of C18:0 from trans C18:1.     

Identification of dual kinase inhibitors of CK2 and GSK3β: combined qualitative and quantitative pharmacophore modeling approach

PTEN, a tumor suppressor protein, gets deactivated by casein kinase 2 (CK2) and glycogen synthase kinase 3β (GSK3β), which are the major causes of PI3K/AKT-driven tumors. To surmount this problem, the multi-target inhibitor strategy may be of great significance. The goal of this study was to design dual-target inhibitors of CK2 and GSK3β using a combination of pharmacophore modeling and molecular docking studies. The common feature-based (qualitative) and 3DQSAR-based (quantitative) pharmacophore models were generated and validated. The best pharmacophore models (Pharm18 and Hypo1) comprised two hydrogen-bond acceptors, one hydrophobic, and one ring aromatic features. The models were used to screen various chemical database and top mapped compounds from each database were selected. They were processed for Lipinski filter, Absorption, Distribution, Metabolism, Excretion, and Toxicity (ADMET) analysis, and docking studies. We have obtained six hits with comparable dock score to the reported inhibitors. We have concluded Hit15 as a competent candidate based on its docking and Density Functional Theory (DFT) calculations. It showed 140.73 and 130.79 dock score in CK2 and GSK3β, respectively. The electronic property of Hit 15 showed the lowest energy gap (0.021) compared to other hits and active ligands which suggest its higher reactivity. In conclusion, this study may assist in the development of new potent dual kinase inhibitors of CK2 and GSK3β. Also, the overture effort of combined qualitative and quantitative modeling for the development of multi-target inhibitors may support the future endeavors.