Identification of the GPR55 agonist binding site using a novel set of high-potency GPR55 selective ligands

Marijuana is the most widely abused illegal drug, and its spectrum of effects suggests that several receptors are responsible for the activity. Two cannabinoid receptor subtypes, CB1 and CB2, have been identified, but the complex pharmacological properties of exogenous cannabinoids and endocannabinoids are not fully explained by their signaling. The orphan receptor GPR55 binds a subset of CB1 and CB2 ligands and has been proposed as a cannabinoid receptor. This designation, however, is controversial as a result of recent studies in which lysophosphatidylinositol (LPI) was identified as a GPR55 agonist. Defining a biological role for GPR55 requires GPR55 selective ligands that have been unavailable. From a β-arrestin, high-throughput, high-content screen of 300000 compounds run in collaboration with the Molecular Libraries Probe Production Centers Network initiative (PubChem AID1965), we identified potent GPR55 selective agonists. By modeling of the GPR55 activated state, we compared the GPR55 binding conformations of three of the novel agonists obtained from the screen, CID1792197, CID1172084, and CID2440433 (PubChem Compound IDs), with that of LPI. Our modeling indicates the molecular shapes and electrostatic potential distributions of these agonists mimic those of LPI; the GPR55 binding site accommodates ligands that have inverted-L or T shapes with long, thin profiles that can fit vertically deep in the receptor binding pocket while their broad head regions occupy a horizontal binding pocket near the GPR55 extracellular loops. Our results will allow the optimization and design of second-generation GPR55 ligands and provide a means for distinguishing GPR55 selective ligands from those interacting with cannabinoid receptors.     

Increased level of cytokines and matrix metalloproteinases in osteoarthritic subchondral bone

OBJECTIVE: The aim of this study was to investigate the expression of several cytokines, matrix metalloproteinases (MMPs), and tissue inhibitor of matrix metalloproteinases (TIMP)-1 in osteoarthritis (OA) and control sera and different joint tissues. METHODS: Serum, synovial fluid, cartilage, synovial and subchondral bone tissues were examined in OA and control subjects. The protein level of tumor necrosis factor (TNF)-alpha, interleukin (IL)-1alpha, IL-8, IL-10 and MMP-2, MMP-3, MMP-9, and TIMP-1 were measured by immunoanalysis. RESULTS: Serum levels of TNF-alpha, MMP-3 and -9 were significantly higher in OA patients than in controls. Conversely, serum IL-10 was decreased in OA patients. CRP was elevated when compared to healthy controls and decreased significantly 6 months after the surgery. In contrast to control samples, OA cartilage and synovium revealed significantly higher MMP-2, -3, -9 and IL-10. IL-1alpha was significantly higher in OA cartilage and IL-8 in OA synovium. Interestingly, MMP-3, -9, TIMP-1 and all tested cytokines were up-regulated in OA subchondral bone. DISCUSSION: This study demonstrates pro-inflammatory condition of OA pathology and supports the idea that vascularized subchondral region may increase the synthesis of cytokines and MMPs leading to degradation of adjacent cartilage.     

The peptide nucleic acids (PNAs): "high-tech" probes for genetic and molecular cytogenetic investigations

The peptide nucleic acids (PNAs) constitute a remarkable new class of synthetic nucleic acids analogs, in which the sugar phosphate backbone is replaced by repeating N-(2-aminoethyl) glycine units linked by amine bonds and to which the nucleobases are fixed. This structure gives to PNAs the capacity to hybridize with high affinity and specificity to complementary RNA and DNA sequences, and a great resistance to nucleases and proteinases. Originally conceived as ligands for the study of double stranded DNA, the unique physico-chemical properties of PNAs have led to the development of a large variety of research and diagnostic assays, including antigene and antisense therapy and genome mapping. Several sensitive and robust PNA-dependent methods have been designed for modulating polymerase chain reactions, detecting genomic polymorphisms and mutations or capturing nucleic acids. Over the last few years, the use of PNAs has proven its powerful usefulness in cytogenetics for the rapid in situ identification of human chromosomes and the detection of aneuploidies. Recent studies have reported the successful use of chromosome-specific PNA probes on human lymphocytes, amniocytes, spermatozoa as well as on isolated oocytes and blastomeres. Muticolor PNA protocols have been described for the identification of several human chromosomes, indicating that PNAs could become a powerful tool for in situ chromosomal investigation.     

Towards resolving the Knautia arvensis agg. (Dipsacaceae) puzzle: primary and secondary contact zones and ploidy segregation at landscape and microgeographic scales

Background and Aims

Detailed knowledge of variations in ploidy levels and their geographic distributions is one of the key tasks faced in polyploid research in natural systems. Flow cytometry has greatly facilitated the field of cytogeography by allowing characterization of ploidy levels at both the regional and population scale, and at multiple stages of the life cycle. In the present study, flow cytometry was employed to investigate the patterns and dynamics of ploidy variation in the taxonomically challenging complex Knautia arvensis (Dipsacaceae) and some of its allies (K. dipsacifolia, K. slovaca) in Central Europe.

Methods

DNA ploidy levels were estimated by DAPI flow cytometry in 5205 adult plants, 228 seedlings and 400 seeds collected from 292 Knautia populations in seven European countries. The flow cytometric data were supplemented with conventional chromosome counts. A subset of 79 accessions was subjected to estimation of the absolute genome size using propidium iodide flow cytometry.

Key Results and Conclusions

Five different ploidy levels (from 2x to 6x) were found, with triploids of K. arvensis being recorded for the first time. The species also exhibited variation in the monoploid genome size, corresponding to the types of habitats occupied (grassland diploid populations had larger genome sizes than relict and subalpine diploid populations). Disregarding relict populations, the distribution of 2x and 4x cytotypes was largely parapatric, with a diffuse secondary contact zone running along the north-west margin of the Pannonian basin. Spatial segregation of the cytotypes was also observed on regional and microgeographic scales. The newly detected sympatric growth of diploids and tetraploids in isolated relict habitats most likely represents the primary zone of cytotype contact. Ploidy level was found to be a major determinant of the strength of inter-cytotype reproductive barriers. While mixed 2x + 4x populations virtually lacked the intermediate ploidy level at any ontogenetic stage, pentaploid hybrids were common in 4x +6x populations, despite the cytotypes representing different taxonomic entities.Key words: Contact zone, cytogeography, flow cytometry, genome size, hybridization, Knautia arvensis, ploidy mixture, polyploidy, relict, reproductive isolation, serpentine     

Micro-habitat use within a guild of newt larvae (Trituridae) in an Alpine lake

Population and ecological parameters such as numbers of larvae, microhabitat use, niche breadth and niche overlap of three species of syntopic larval newts (Alpine newt Triturus alpestris, Italian crested newt T. carnifex, and common newt T. vulgaris) were studied for two years in a small pond at 1160 m a.s.l. in NE Slovenia. Differences in microhabitat partitioning among larval newts were small. The largest niche breadth was estimated for larval T. alpestris, and the narrowest estimate was for larval T. carnifex in both years. Ecological differences seem to be very small and quite variable among sites and years. It appears that the developmental stage and size of newt larvae are more important in explaining resource partitioning than the characteristics of each species. Because of the absence of potential invertebrate predators and adult newts in the second half of the breeding season, the injuries could only be caused by intra-and interspecific predation attempts.     

Exploring Nitrilase Sequence Space for Enantioselective Catalysis

Nitrilases are important in the biosphere as participants in synthesis and degradation pathways for naturally occurring, as well as xenobiotically derived, nitriles. Because of their inherent enantioselectivity, nitrilases are also attractive as mild, selective catalysts for setting chiral centers in fine chemical synthesis. Unfortunately, <20 nitrilases have been reported in the scientific and patent literature, and because of stability or specificity shortcomings, their utility has been largely unrealized. In this study, 137 unique nitrilases, discovered from screening of >600 biotope-specific environmental DNA (eDNA) libraries, were characterized. Using culture-independent means, phylogenetically diverse genomes were captured from entire biotopes, and their genes were expressed heterologously in a common cloning host. Nitrilase genes were targeted in a selection-based expression assay of clonal populations numbering 10⁶ to 10¹⁰ members per eDNA library. A phylogenetic analysis of the novel sequences discovered revealed the presence of at least five major sequence clades within the nitrilase subfamily. Using three nitrile substrates targeted for their potential in chiral pharmaceutical synthesis, the enzymes were characterized for substrate specificity and stereospecificity. A number of important correlations were found between sequence clades and the selective properties of these nitrilases. These enzymes, discovered using a high-throughput, culture-independent method, provide a catalytic toolbox for enantiospecific synthesis of a variety of carboxylic acid derivatives, as well as an intriguing library for evolutionary and structural analyses.     

One-electron oxidation of beta-amyloid peptide: sequence modulation of reactivity

Amyloid beta peptide (Abeta) is a 39 to 43 amino-acid-long peptide implicated in Alzheimer's disease. One of its mechanisms of toxicity is related to its redox properties. Therefore we studied its one electron oxidation using azide free radicals produced in gamma and pulse radiolysis, and compared the results with those obtained with the reverse sequence Abeta(40-1). HPLC analysis combined with absorption, fluorescence, Raman spectroscopy, and MALDI-TOF MS were used for product identification. Met35 was shown to be the target in Abeta(1-40); oxidation leads to a major compound that is Abeta with methionine sulfoxide. Similarly, oxidation of fragment Abeta(29-40) also leads to methionine sulfoxide. For Abeta(40-1), Met35 is not reactive and Tyr10 is the target of azide radicals. The major products are peptide dimer linked by dityrosine and trimer. The lowering of the one-electron reduction potential of the MetS+/Met couple, which was proposed, is in agreement with our findings. To our knowledge, this is the first time that such a drastic effect of the primary sequence is observed in a small peptide. In addition, it is also the first experimental demonstration of the sensitivity of the one-electron reduction potential of methionine on neighboring groups.     

Determination of PRKAG1 coding sequence and mapping of PRKAG1 and PRKAG2 relatively to porcine back fat thickness QTL

PRKAG1, PRKAG2 and PRKAG3 encode three isoforms of AMP-activated protein kinase gamma chain. A major effect on meat quality and a medium effect on back fat thickness of the RN- mutation in the PRKAG3 gene has previously been reported. We have now mapped PRKAG1 and PRKAG2 at expected locations on SSC5 and SSC18 by analysis of radiation hybrids (IMpRH panel). PRKAG2 has been mapped in a region where no quantitative trait loci (QTL) has been reported. PRKAG1 has been mapped close to (but probably outside) a region containing a QTL influencing fatness traits. We have determined the full coding sequence of PRKAG1. No missense mutation was identified when comparing the coding sequence of one Meishan and one Large White boars. Further work is, however, required to determine if a polymorphism in PRKAG1 could be responsible for a part of the variability observed on fatness traits.     

Structural diversity of Papaver somniferum L. cell surfaces in vitro depending on particular steps of plant regeneration and morphogenetic program

Culture of Papaver somniferum in vitro was used for a characterisation of cell surface structures and mode of cell adhesion and cell separation during cell differentiation and plant regeneration in somatic embryogenesis and shoot organogenesis. In early stages of somatic embryogenesis, cell type-specific and developmentally regulated change of cell morphogenesis was demonstrated. Cell wall of separated embryonic cells were self-covered with external tubular network, whereas morphogenetic co-ordination of adhered cells of somatic proembryos was supported by fine and fibrillar external cell wall continuum of peripheral cells, interconnecting also local sites of cell separation. Such type of cell contacts disappeared during histogenesis, when the protodermis formation took place. Tight cell adhesion of activated cells with polar cell wall thickening, and production of extent mucilage on the periphery were the crucial aspects of meristemoids. Fine amorphous layer covered developing shoot primordia, but we have not observed such comparable external fibrillar network. On the contrary intercellular separation of differentiated cells in regenerated organs, and accepting distinct developmental system of somatic embryogenesis and shoot organogenesis, cell adhesion in early stages and ultrastructural changes associated with tissue disorganisation, and the subsequent reorganisation into either embryos or shoots appear to be regulatory morphogenetical events of plant regeneration in vitro.