New antitumor leads from a peptidomimetic library

A parallel combinatorial library of over 1600 compounds has been designed and synthesized for the development of new potential peptidomimetic protein tyrosine kinase (PTK) inhibitor leads. These peptidomimetic molecules are aimed at intervening with the substrate binding site of the pp60^c-src enzyme. The new structures were based on known PTK inhibitors with at least two variously substituted aromatic moieties attached by spacer groups of different length and flexibility. Eleven bis-aryl-type inhibitory compounds were found in the range of 18–100 μM IC₅₀ concentrations from combinations of 12 different substituents. Molecular modeling of the active compounds showed a characteristic distance of 12–14 Å between the farthest sp² carbon atoms of the two aromatic rings. Conformational analysis of several peptide substrates recently found for pp60^c-src PTK showed that the energy-minimized conformers had the same distance between the two aromatic moieties. Several compounds in the library not only showed remarkable PTK inhibitory activity but also a significant apoptosis-inducing effect on HT-29 human colon tumor cells.     

Patch Size and Tree Species Influence the Number and Duration of Bird Visits in Forest Restoration Plots in Southern Costa Rica

Efforts to restore tropical forest in abandoned pasture are likely to be more successful when bird visitation is promoted because birds disperse seeds and eat herbivorous arthropods that damage leaves. Thus, it is critical to understand bird behavior in relation to different restoration strategies. We measured the likelihood of visitation, number of visits, and duration of visits for all birds and for Cherrie's Tanager ( Ramphocelus costaricensis ), a common seed disperser, in five sizes of forest restoration patches planted with four tree species in southern Costa Rica. We predicted that the largest patches, and the tree species with the greatest canopy cover, would be visited most frequently and have the longest visits because we assumed that these patch types had the greatest food resources and the lowest predation risk. We found that birds were more likely to visit large patches and the tree species with the highest canopy cover ( Inga edulis ). Birds visited Inga trees more often and stayed in Inga and Erythrina poeppigiana trees for longer periods of time than in other tree species. We found similar results for Cherrie's Tanagers. Thus, we identified two factors, tree species and patch size, which may be manipulated in restoration projects to increase bird visitation.     

Population trends of European common birds are predicted by characteristics of their climatic niche

Temperate species are projected to experience the greatest temperature increases across a range of modelled climate change scenarios, and climate warming has been linked to geographical range and population changes of individual species at such latitudes. However, beyond the multiple modelling approaches, we lack empirical evidence of contemporary climate change impacts on populations in broad taxonomic groups and at continental scales. Identifying reliable predictors of species resilience or susceptibility to climate warming is of critical importance in assessing potential risks to species, ecosystems and ecosystem services. Here we analysed long‐term trends of 110 common breeding birds across Europe (20 countries), to identify climate niche characteristics, adjusted to other environmental and life history traits, that predict large‐scale population changes accounting for phylogenetic relatedness among species. Beyond the now well‐documented decline of farmland specialists, we found that species with the lowest thermal maxima (as the mean spring and summer temperature of the hottest part of the breeding distribution in Europe) showed the sharpest declines between 1980 and 2005. Thermal maximum predicted the recent trends independently of other potential predictors. This study emphasizes the need to account for both land‐use and climate changes to assess the fate of species. Moreover, we highlight that thermal maximum appears as a reliable and simple predictor of the long‐term trends of such endothermic species facing climate change.     

Role of syndecan-1 proteoglycan in the invasiveness of HT-1080 fibrosarcoma

Syndecan-1 is a transmembrane heparan sulfate proteoglycan which plays pivotal role in cell-cell and cell-extracellular matrix interactions. However, its implication in the establishment of malignant phenotype is still controversial. Its expression indicates differentiated phenotype in certain tumors, while it confers invasive nature for others. For the better understanding of the role of syndecan-1 in cancer we transfected HT-1080 fibrosarcoma cell line with the full and a truncated construct of syndecan-1 and established stable cell lines with them. We studied the in vitro and in vivo growth capacity and metastatic potential of the transfectants in comparison with the cell line bearing only the EGFP expression vector. Our results showed that the growth rate of syndecan transfectants increased and they developed more lung metastases than the control cells. As local growth of the full transfectant was faster than that of the 78sig we presume that the full protein and maybe the shedding is needed for the local development of the tumor, but the intracellular and transmembrane domain is sufficient to promote metastasis formation.     

Deficiency of the Metalloproteinase-Disintegrin ADAM8 Is Associated with Thymic Hyper-Cellularity

Background

Thymopoiesis requires thymocyte-stroma interactions and proteases that promote cell migration by degrading extracellular matrix and releasing essential cytokines and chemokines. A role for several members of the A Disintegrin and Metalloprotease (ADAM) family in T cell development has been reported in the past.

Methodology/Principal Findings

Here, we present data indicating that the family member ADAM8 plays a role in thymic T cell development. We used qrtPCR on FACS sorted thymic subsets together with immunofluorescene to analyze thymic ADAM8 expression. We found that ADAM8 was expressed in murine thymic stromal cells and at lower levels in thymocytes where its expression increased as cell matured, suggesting involvement of ADAM8 in thymopoiesis. Further flow cytometry analysis revealed that ADAM8 deficient mice showed normal development and expansion of immature thymocyte subsets. There was however an intrathymic accumulation of single positive CD4 and CD8 T cells which was most noticeable in the late mature T cell subsets. Accumulation of single positive T cells coincided with changes in the thymic architecture manifest in a decreased cortex/medulla ratio and an increase in medullary epithelial cells as determined by histology and flow cytometry. The increase in single positive T cells was thymus-intrinsic, independent of progenitor homing to the thymus or thymic exit rate of mature T cells. Chemotaxis assays revealed that ADAM8 deficiency was associated with reduced migration of single positive thymocytes towards CCL21.

Conclusions/Significance

Our results show that ADAM8 is involved in T cell maturation in the medulla and suggest a role for this protease in fine-tuning maturation of thymocytes in the medulla. In contrast to ADAM10 and ADAM17 lack of ADAM8 appears to have a relatively minor impact on T cell development, which was unexpected given that maturation of thymocytes is dependent on proper localization and timing of migration.     

Molecular studies resolve Nyholmiella (Orthotrichaceae) as separated genus

Two Orthotrichum species of the subgenus Orthophyllum were compared with other representatives of this genus using the internally transcribed spacer regions 1 and 2, the chloroplast trnH-psbA region and ISSR and ISJ DNA markers. The applied DNA markers revealed many bands and mutations specific only to O. gymnostomum and O. obtusifolium. A phylogenetic analysis clearly supported the previous concepts postulating that species of the subgenus Orthophyllum should be recognized as separate genus Nyholmiella.     

Free energy simulation to investigate the effect of amino acid sequence environment on the severity of osteogenesis imperfecta by glycine mutations in collagen

Molecular dynamics simulations were carried out to calculate the free energy change difference of two collagen-like peptide models for Gly --> Ser mutations causing two different osteogenesis imperfecta phenotypes. These simulations were performed to investigate the impact of local amino acid sequence environment adjacent to a mutation site on the stability of the collagen. The average free energy differences for a Gly --> Ser mutant relative to a wild type are 3.4 kcal/mol and 8.2 kcal/mol for a nonlethal site and a lethal site, respectively. The free energy change differences of mutant containing two Ser residues relative to the wild type at the nonlethal and lethal mutation sites are 4.6 and 9.8 kcal/mol, respectively. Although electrostatic interactions stabilize mutants containing one or two Ser residues at both mutation sites, van der Waals interactions are of sufficient magnitude to cause a net destabilization. The presence of Gln and Arg near the mutation site, which contain large and polar side chains, provide more destabilization than amino acids containing small and nonpolar side chains.     

Plexin-D1 is a novel regulator of germinal centers and humoral immune responses

Long-lived humoral immune responses depend upon the generation of memory B cells and long-lived plasma cells during the germinal center (GC) reaction. These memory compartments, characterized by class-switched IgG and high-affinity Abs, are the basis for successful vaccination. We report that a new member of the plexin family of molecules, plexin-D1, controls the GC reaction and is required for secondary humoral immune responses. Plexin-D1 was not required for B cell maturation, marginal zone precursor development, dark and light zone formation, Igλ(+) and Igκ(+) B cell skewing, B1/B2 development, and the initial extrafollicular response. Plexin-D1 expression was increased following B cell activation, and PlxnD1(-/-) mice exhibited defective GC reactions during T-dependent immune activation. PlxnD1(-/-) B cells showed a defect in migration toward the GC chemokines, CXCL12, CXCL13, and CCL19. Accordingly, PlxnD1(-/-) mice exhibited defective production of IgG1 and IgG2b, but not IgG3 serum Ab, accompanied by reductions in long-lived bone marrow plasmacytes and recall humoral memory responses. These data show a new role for immune plexins in the GC reaction and generation of immunologic memory.     

Tissue MicroRNAs as Predictors of Outcome in Patients with Metastatic Colorectal Cancer Treated with First Line Capecitabine and Oxaliplatin with or without Bevacizumab

Purpose

We tested the hypothesis that expression of microRNAs (miRNAs) in cancer tissue can predict effectiveness of bevacizumab added to capecitabine and oxaliplatin (CAPEOX) in patients with metastatic colorectal cancer (mCRC).

Experimental Design

Patients with mCRC treated with first line CAPEOX and bevacizumab (CAPEOXBEV): screening (n = 212) and validation (n = 121) cohorts, or CAPEOX alone: control cohort (n = 127), were identified retrospectively and archival primary tumor samples were collected. Expression of 754 miRNAs was analyzed in the screening cohort using polymerase chain reaction (PCR) arrays and expression levels were related to time to disease progression (TTP) and overall survival (OS). Significant miRNAs from the screening study were analyzed in all three cohorts using custom PCR arrays. In situ hybridization (ISH) was done for selected miRNAs.

Results

In the screening study, 26 miRNAs were significantly correlated with outcome in multivariate analyses. Twenty-two miRNAs were selected for further study. Higher miR-664-3p expression and lower miR-455-5p expression were predictive of improved outcome in the CAPEOXBEV cohorts and showed a significant interaction with bevacizumab effectiveness. The effects were strongest for OS. Both miRNAs showed high expression in stromal cells. Higher expression of miR-196b-5p and miR-592 predicted improved outcome regardless of bevacizumab treatment, with similar effect estimates in all three cohorts.

Conclusions

We have identified potentially predictive miRNAs for bevacizumab effectiveness and additional miRNAs that could be related to chemotherapy effectiveness or prognosis in patients with mCRC. Our findings need further validation in large cohorts, preferably from completed randomized trials.