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.     

Kaposi's sarcoma-associated herpesvirus forms a multimolecular complex of integrins (alphaVbeta5, alphaVbeta3, and alpha3beta1) and CD98-xCT during infection of human dermal microvascular endothelial cells, and CD98-xCT is essential for the postentry stage of infection

Kaposi's sarcoma-associated herpesvirus (KSHV) interacts with cell surface heparan sulfate (HS) and α3β1 integrin during the early stages of infection of human dermal microvascular endothelial cells (HMVEC-d) and human foreskin fibroblasts (HFF), and these interactions are followed by virus entry overlapping with the induction of preexisting host cell signal pathways. KSHV also utilizes the amino acid transporter protein xCT for infection of adherent cells, and the xCT molecule is part of the cell surface heterodimeric membrane glycoprotein CD98 (4F2 antigen) complex known to interact with α3β1 and αVβ3 integrins. KSHV gB mediates adhesion of HMVEC-d, CV-1, and HT-1080 cells and HFF via its RGD sequence. Anti-αV and -β1 integrin antibodies inhibited the cell adhesion mediated by KSHV-gB. Variable levels of neutralization of HMVEC-d and HFF infection were observed with antibodies against αVβ3 and αVβ5 integrins. Similarly, variable levels of inhibition of virus entry into adherent HMVEC-d, 293 and Vero cells, and HFF was observed by preincubating virus with soluble α3β1, αVβ3, and αVβ5 integrins, and cumulative inhibition was observed with a combination of integrins. We were unable to infect HT1080 cells. Virus binding and DNA internalization studies suggest that αVβ3 and αVβ5 integrins also play roles in KSHV entry. We observed time-dependent temporal KSHV interactions with HMVEC-d integrins and CD98/xCT with three different patterns of association and dissociation. Integrin αVβ5 interaction with CD98/xCT predominantly occurred by 1 min postinfection (p.i.) and dissociated at 10 min p.i., whereas α3β1-CD98/xCT interaction was maximal at 10 min p.i. and dissociated at 30 min p.i., and αVβ3-CD98/xCT interaction was maximal at 10 min p.i. and remained at the observed 30 min p.i. Fluorescence microscopy also showed a similar time-dependent interaction of αVβ5-CD98. Confocal-microscopy studies confirmed the association of CD98/xCT with α3β1 and KSHV. Preincubation of KSHV with soluble heparin and α3β1 significantly inhibited this association, suggesting that the first contact with HS and integrin is an essential element in subsequent CD98-xCT interactions. Anti-CD98 and xCT antibodies did not block virus binding and entry and nuclear delivery of viral DNA; however, viral-gene expression was significantly inhibited, suggesting that CD98-xCT play roles in the post-entry stage of infection, possibly in mediating signal cascades essential for viral-gene expression. Together, these studies suggest that KSHV interacts with functionally related integrins (αVβ3, α3β1, and αVβ5) and CD98/xCT molecules in a temporal fashion to form a multimolecular complex during the early stages of endothelial cell infection, probably mediating multiple roles in entry, signal transduction, and viral-gene expression.     

Membrane degradation, accumulation of Phosphatidic acid, stimulation of catalase activity and nuclear DNA fragmentation during 2,4-d-induced leaf senescence in mustard

We investigated 2,4-D-induced leaf senescence in young mustard seedlings. A set of morphometric, biochemical and molecular parameters were analyzed to characterize senescence markers. In accordance with earlier reports, chloroplast-membrane degradation marked the early phase of leaf senescence based on the analysis of the galactolipid fraction. Degradation of grana occurred earlier to that of the envelope, as revealed by the relative level of their specific galactolipids, namely, monogalactosyl diglyceride and digalactosyl diglyceride. Phospholipids showed extensive degradation resulting in the accumulation of lyso-derivatives of major phospholipids and phosphatidic acid (PA) in senescing leaves. Catalase activity was stimulated by 2,4-D and reflected scavenging of reactive oxygen species. Nuclear DNA degradation, a previously known death signal that represented a point of no return from progression of senescence, occurred late on the 4th day subsequent to 2,4-D supplementation. AgNO₃, an inhibitor of ethylene biosynthesis, inhibited leaf senescence by ca. 54% based on PA content Involvement of 2,4-D, ethylene and abscisic acid in leaf senescence is discussed in relation to hormonal interplay.     

From Life Cycle Assessment to Life Cycle Management

Life cycle assessment (LCA) is a widely accepted methodology to support decision‐making processes in which one compares alternatives, and that helps prevent shifting of environmental burdens along the value chain or among impact categories. According to regulation in the European Union (EU), the movement of waste needs to be reduced and, if unavoidable, the environmental gain from a specific waste treatment option requiring transport must be larger than the losses arising from transport. The EU explicitly recommends the use of LCA or life cycle thinking for the formulation of new waste management plans. In the last two revisions of the Industrial Waste Management Programme of Catalonia (PROGRIC), the use of a life cycle thinking approach to waste policy was mandated. In this article we explain the process developed to arrive at practical life cycle management (LCM) from what started as an LCA project. LCM principles we have labeled the “3/3” principle or the “good enough is best” principle were found to be essential to obtain simplified models that are easy to understand for legislators and industries, useful in waste management regulation, and, ultimately, feasible. In this article, we present the four models of options for the management of waste solvent to be addressed under Catalan industrial waste management regulation. All involved actors concluded that the models are sufficiently robust, are easy to apply, and accomplish the aim of limiting the transport of waste outside Catalonia, according to the principles of proximity and sufficiency.     

7-Azaindole-3-acetic acid derivatives: Potent and selective CRTh2 receptor antagonists

High throughput screening identified a 7-azaindole-3-acetic acid scaffold as a novel CRTh2 receptor antagonist chemotype, which could be optimised to furnish a highly selective compound with good functional potency for inhibition of human eosinophil shape change in whole blood and oral bioavailability in the rat.     

Characterization of the human placental receptor for basic somatomedin

We have determined optimal conditions for the solubilization of the basic somatomedin (SM) receptor from human placental membranes and for the measurement of the binding of basic SM to the solubilized receptor. Further, we have developed conditions under which the basic SM receptor, in the presence of equivalent amounts of insulin receptor, can be selectively and specifically affinity-labeled with 125I-labeled basic SM, using the cross-linking reagent disuccinimidyl suberate (DSS). Our results with these developed methods indicate that the properties of the soluble basic SM receptor (pH optimum for ligand binding, pH 7 to 9; adsorption to lectin-agarose derivatives; sedimentation coefficient in detergent-sucrose solutions, 11S) closely parallel data previously reported for the insulin receptor. Based on the sedimentation coefficient and the previously estimated Stokes radius of the soluble receptor (7.2 nm), a molecular weight of 402 000 can be calculated for the detergent-receptor complex. Electrophoretic analysis of the basic SM receptor, selectively cross-linked to 125I-labeled basic SM with DSS in the presence of excess unlabeled insulin revealed, under reducing conditions, a major labeled constituent of 140 kdaltons, substantiating our previous work employing a photoaffinity labeling reagent. DSS cross-linking also demonstrated the presence of less intensely labeled components with apparent molecular weights of 54 000, 43 000 and 35 000 but failed to reveal a distinct 90- to 100-kdalton species visualized in parallel experiments with insulin. The 53-kdalton species was not detected in similar experiments with insulin. A specifically labeled basic SM receptor component of 300 kdaltons was also observed under reducing conditions; in the absence of beta-mercaptoethanol, all labeled components migrated in the 300-kdalton range. In comparison, selective DSS labeling of the insulin receptor in the presence of excess basic SM revealed components which, upon electrophoresis under reducing conditions, exhibited apparent molecular weights of 300 000, 140 000, 90 000--100 000, 43 000 and 35 000. The major insulin-labeled component (140 000) comigrated with the major constituent (140 000) selectively labeled with basic SM. Chymotryptic digestion of the receptors selectively DSS labeled with either 125I-labeled insulin or 125I-labeled basic SM yielded quite similar, but distinctive, gel electrophoretic maps. We conclude that the receptors for basic SM and insulin are highly homologous structures, particularly with respect to their glycoprotein nature, their hydrodynamic properties, their disulphide cross-linked composition, and with respect to the size of the major constituent detected by selective affinity labeling. Nonetheless, the detection of electrophoretically distinct labeled receptor substituents upon analysis of specifically labeled material, both before and after chymotryptic cleavage, points to subtle differences between the polypeptide compositions of the two receptors.     

Inhibition of thymidine kinase activity by hydroxyurea during highly and less proliferative regions of rat brain

Hydroxyurea, when injected intraperitoneally, exerted marked inhibition on the activity of thymidine kinase in 5 day old postnatal cerebellum and 15 day old embryonic cerebrum. However, it failed to show any sustained inhibition on thymidine kinase activity in 5 day old postnatal cerebrum. In this case, the marginal decrease of thymidine kinase activity noticed during early intervals reversed back to more than normal value at a later time interval. These results along with our earlier findings are taken to indicate the differential action of this drug on thymidine kinase activity in rapidly and slowly proliferating regions of rat brain