Mapping of a Gene for Long QT Syndrome to Chromosome 4q25-27

Long QT syndrome (LQTS) is a heterogeneous inherited disorder causing syncope and sudden death from ventricular arrhythmias. A first locus for this disorder was mapped to chromosome 11p15.5. However, locus heterogeneity has been demonstrated in several families, and two other loci have recently been located on chromosomes 7q35-36 and 3p21-24. We used linkage analysis to map the locus in a 65-member family in which LQTS was associated with more marked sinus bradycardia than usual, leading to sinus node dysfunction. Linkage to chromosome 11p15.5, 7q35-36, or 3p21-24 was excluded. Positive linkage was obtained for markers located on chromosome 4q25-27. A maximal LOD score of 7.05 was found for marker D4S402. The identification of a fourth locus for LQTS confirms its genetic heterogeneity. Locus 4q25-27 is associated with a peculiar phenotype within the LQTS entity.     

The respective roles of polar/nonpolar binary patterns and amino acid composition in protein regular secondary structures explored exhaustively using hydrophobic cluster analysis

Several studies have highlighted the leading role of the sequence periodicity of polar and nonpolar amino acids (binary patterns) in the formation of regular secondary structures (RSS). However, these were based on the analysis of only a few simple cases, with no direct mean to correlate binary patterns with the limits of RSS. Here, HCA‐derived hydrophobic clusters (HC) which are conditioned binary patterns whose positions fit well those of RSS, were considered. All the HC types, defined by unique binary patterns, which were commonly observed in three‐dimensional (3D) structures of globular domains, were analyzed. The 180 HC types with preferences for either α‐helices or β‐strands distinctly contain basic binary units typical of these RSS. Therefore a general trend supporting the “binary pattern preference” assumption was observed. HC for which observed RSS are in disagreement with their expected behavior (discordant HC) were also examined. They were separated in HC types with moderate preferences for RSS, having “weak” binary patterns and versatile RSS and HC types with high preferences for RSS, having “strong” binary patterns and then displaying nonpolar amino acids at the protein surface. It was shown that in both cases, discordant HC could be distinguished from concordant ones by well‐differentiated amino acid compositions. The obtained results could, thus, help to complement the currently available methods for the accurate prediction of secondary structures in proteins from the only information of a single amino acid sequence. This can be especially useful for characterizing orphan sequences and for assisting protein engineering and design. Proteins 2016; 84:624–638. © 2016 Wiley Periodicals, Inc.     

Biochemical and Immunocytological Characterizations of Arabidopsis Pollen Tube Cell Wall

During plant sexual reproduction, pollen germination and tube growth require development under tight spatial and temporal control for the proper delivery of the sperm cells to the ovules. Pollen tubes are fast growing tip-polarized cells able to perceive multiple guiding signals emitted by the female organ. Adhesion of pollen tubes via cell wall molecules may be part of the battery of signals. In order to study these processes, we investigated the cell wall characteristics of in vitro-grown Arabidopsis (Arabidopsis thaliana) pollen tubes using a combination of immunocytochemical and biochemical techniques. Results showed a well-defined localization of cell wall epitopes. Low esterified homogalacturonan epitopes were found mostly in the pollen tube wall back from the tip. Xyloglucan and arabinan from rhamnogalacturonan I epitopes were detected along the entire tube within the two wall layers and the outer wall layer, respectively. In contrast, highly esterified homogalacturonan and arabinogalactan protein epitopes were found associated predominantly with the tip region. Chemical analysis of the pollen tube cell wall revealed an important content of arabinosyl residues (43%) originating mostly from (1→5)-α-l-arabinan, the side chains of rhamnogalacturonan I. Finally, matrix-assisted laser desorption ionization time-of-flight mass spectrometry analysis of endo-glucanase-sensitive xyloglucan showed mass spectra with two dominant oligosaccharides (XLXG/XXLG and XXFG), both being mono O-acetylated, and accounting for over 68% of the total ion signals. These findings demonstrate that the Arabidopsis pollen tube wall has its own characteristics compared with other cell types in the Arabidopsis sporophyte. These structural features are discussed in terms of pollen tube cell wall biosynthesis and growth dynamics.Fertilization of flowering plants requires the delivery of the two sperm cells, carried by a fast growing tip-polarized pollen tube, to the egg cell. In plants with dry stigma and solid style such as Arabidopsis (Arabidopsis thaliana), this process begins with the deposition and specific adhesion of the pollen grains on the stigmatic tissue, subsequent hydration of the pollen grains, and germination of pollen tubes (Palanivelu and Preuss, 2000). Pollen tubes invade the papillae cell wall of the stigma, enter the short style, and grow through the apoplast of the specialized transmitting tract (TT) that is filled with a nutrient-rich extracellular matrix (Kandasamy et al., 1994; Lennon et al., 1998). During this invasive growth, pollen tubes are guided to the ovules via signals that need to pass through the cell wall to reach their membrane-associated or intracellular targets (Lord and Russell, 2002; Kim et al., 2003; Boavida et al., 2005; McCormick and Yang, 2005; Johnson and Lord, 2006). In plant species with wet stigma and hollow style such as lily (Lilium longiflorum), adhesion between the pollen tube wall and the TT epidermis extracellular matrix is important for the growth of the pollen tubes toward the ovules (Mollet et al., 2000, 2007; Park et al., 2000; Chae et al., 2007). In addition to being the interface between the tube cells and the surroundings (female sporophyte or culture medium), the pollen tube wall also controls the cell shape, protects the generative cells, and allows resistance against turgor pressure (Geitmann and Steer, 2006; Geitmann, 2010).Most of our knowledge on cell wall polymers of higher plants comes from investigations on vegetative organs in which cells have diffuse growth. The cell wall is mainly composed of polysaccharides (cellulose, hemicellulose, pectin, and occasionally callose, depending on the tissue) and proteoglycans (e.g. extensin and arabinogalactan proteins [AGPs]) forming a complex network with processing enzymes.Pectins are complex wall macromolecules with uncertain supramolecular organization (Vincken et al., 2003) consisting of homogalacturonan (HG) that can be methylesterified and acetylesterified, rhamnogalacturonan I (RG-I), rhamnogalacturonan II (RG-II), and xylogalacturonan (Carpita and McCann, 2000). HG is a polymer of repeated units of (1→4)-α-d-GalUA that can be cross-linked with calcium upon block-wise action of pectin methylesterases (PMEs) on methylesterified HG (Micheli, 2001). RG-II has the same homopolymer backbone as HG but is substituted with four different oligosaccharides composed of unusual sugars, such as apiose, aceric acid, and 3-deoxy-d-manno-2-octulosonic acid, of unknown function (for review, see Caffall and Mohnen, 2009). RG-I consists of the repeating disaccharide (1→4)-α-d-GalUA-(1→2)-α-l-Rha, with a wide variety of side chains attached to the rhamnosyl residues, ranging from monomers to large oligosaccharides such as (1→4)-β-d-galactan, (1→5)-α-l-arabinan, and/or type I arabinogalactan (Caffall and Mohnen, 2009).Xyloglucan (XyG) is the major hemicellulosic polysaccharide of the primary wall of flowering plants. Classic XyG consists of a (1→4)-β-d-glucan backbone substituted with Xyl, Gal-Xyl, or Fuc-Gal-Xyl motifs, which correspond, according to the one-letter code proposed by Fry et al. (1993), to X, L, and F, respectively, G being the unsubstituted glucosyl residue of the glucan backbone. The main XyG fragments released after endo-glucanase treatment of the cell wall from wild-type Arabidopsis vegetative organs are generally XXXG, XXLG/XLXG, XXFG, and XLFG (Zablackis et al., 1995; Lerouxel et al., 2002; Nguema-Ona et al., 2006; Obel et al., 2009). In addition, O-acetylation of XyG can occur, most generally on the galactosyl residues, but its biological function is unknown (Cavalier et al., 2008). In the primary wall, XyG interacts with cellulose microfibrils via hydrogen bonds and participates in the control of cell expansion (Cosgrove, 1999).AGPs and extensin belong to the Hyp-rich glycoproteins superfamily with very high levels of type II arabinogalactan glycosylation (Nothnagel, 1997; Showalter, 2001). These proteoglycans have been implicated in many aspects of plant development, including cell expansion, cell signaling and communication, embryogenesis, wound response, and pollen tube guidance (Wu et al., 1995; Nothnagel, 1997; Seifert and Roberts, 2007; Driouich and Baskin, 2008).Despite the importance of pollen tubes for the delivery of the sperm cells to the egg, little is known about the underlying molecular mechanisms that regulate the mechanical interaction of pollen tubes with female floral tissues. There are very scarce data concerning the different components of the pollen tube cell wall. Past approaches to characterize the pollen tube cell wall are limited to a few plant genera, including Camellia (Nakamura and Suzuki, 1981), Lilium (Jauh and Lord, 1996; Mollet et al., 2002), Nicotiana (Rae et al.,1985; Li et al., 1995; Ferguson et al., 1998; Qin et al., 2007), Pinus (Derksen et al., 1999), and Zea (Rubinstein et al., 1995), and are mostly based on immunocytochemistry. These studies revealed that, depending on the species, the pollen tube cell wall contains epitopes that are found in the polymers described above, including HGs with varying levels of methylesterification, AGPs, extensin-like proteins, and low amounts of cellulose. Unlike most other plant cells, callose, a (1→3)-β-glucan, is predominant and is deposited in the wall back from the tip. Moreover, it is deposited at regular intervals to form callose plugs that maintain the tube cell in the apical expanding region of the tube and separate the viable from the degenerating region of the tube (for review, see Geitmann and Steer, 2006). Only a few reports have investigated the pollen tube of the model plant Arabidopsis. They have focused either on in vivo-grown or on in vitro-grown pollen tubes using monoclonal antibodies (MAbs) directed against a subset of cell wall epitopes present in HG, XyG, and AGPs (Lennon and Lord, 2000; Freshour et al., 2003; Pereira et al., 2006), but quantitative chemical analyses are lacking. This lack of information is most likely due to the fact that substantial amounts of pollen tube material are needed for chemical analysis, and a reproducible and efficient method for liquid culture of Arabidopsis pollen tubes had not been established until recently (Boavida and McCormick, 2007; Bou Daher et al., 2009).Here, we report the composition and localization of different cell wall polymers of in vitro-grown wild-type Arabidopsis pollen tubes based on biochemical analyses coupled to immunocytochemical investigations both at light and transmission electron microscopy (TEM) levels using recently developed MAbs. Our results show distinct patterns of labeling (tip, whole tube, and shank of the tube) depending on the recognized epitope. The most striking observations are (1) the abundance of (1→5)-α-l-arabinan in the tube wall (greater than 40 mol % of Ara), mostly localized, with LM6 and LM13, in the outer wall layer of the tube and (2) an atypical XyG matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) profile with over 68% of the oligosaccharide fragments being O-acetylated.     

Ligand scaffold hopping combining 3D maximal substructure search and molecular similarity

Background  

Virtual screening methods are now well established as effective to identify hit and lead candidates and are fully integrated in most drug discovery programs. Ligand-based approaches make use of physico-chemical, structural and energetics properties of known active compounds to search large chemical libraries for related and novel chemotypes. While 2D-similarity search tools are known to be fast and efficient, the use of 3D-similarity search methods can be very valuable to many research projects as integration of "3D knowledge" can facilitate the identification of not only related molecules but also of chemicals possessing distant scaffolds as compared to the query and therefore be more inclined to scaffolds hopping. To date, very few methods performing this task are easily available to the scientific community.     

Centromere binding specificity in assembly of the F plasmid partition complex

The segregation of plasmid F of Escherichia coli is highly reliable. The Sop partition locus, responsible for this stable maintenance, is composed of two genes, sopA and sopB and a centromere, sopC, consisting of 12 direct repeats of 43 bp. Each repeat carries a 16-bp inverted repeat motif to which SopB binds to form a nucleoprotein assembly called the partition complex. A database search for sequences closely related to sopC revealed unexpected features that appeared highly conserved. We have investigated the requirements for specific SopB–sopC interactions using a surface plasmon resonance imaging technique. We show that (i) only 10 repeats interact specifically with SopB, (ii) no base outside the 16-bp sopC sites is involved in binding specificity, whereas five bases present in each arm are required for interactions, and (iii) the A-C central bases contribute to binding efficiency by conforming to a need for a purine–pyrimidine dinucleotide. We have refined the SopB–sopC binding pattern by electro-mobility shift assay and found that all 16 bp are necessary for optimal SopB binding. These data and the model we propose, define the basis of the high binding specificity of F partition complex assembly, without which, dispersal of SopB over DNA would result in defective segregation.     

Pollen tube cell walls of wild and domesticated tomatoes contain arabinosylated and fucosylated xyloglucan

Background and Aims In flowering plants, fertilization relies on the delivery of the sperm cells carried by the pollen tube to the ovule. During the tip growth of the pollen tube, proper assembly of the cell wall polymers is required to maintain the mechanical properties of the cell wall. Xyloglucan (XyG) is a cell wall polymer known for maintaining the wall integrity and thus allowing cell expansion. In most angiosperms, the XyG of somatic cells is fucosylated, except in the Asterid clade (including the Solanaceae), where the fucosyl residues are replaced by arabinose, presumably due to an adaptive and/or selective diversification. However, it has been shown recently that XyG of Nicotiana alata pollen tubes is mostly fucosylated. The objective of the present work was to determine whether such structural differences between somatic and gametophytic cells are a common feature of Nicotiana and Solanum (more precisely tomato) genera.Methods XyGs of pollen tubes of domesticated (Solanum lycopersicum var. cerasiforme and var. Saint-Pierre) and wild (S. pimpinellifolium and S. peruvianum) tomatoes and tobacco (Nicotiana tabacum) were analysed by immunolabelling, oligosaccharide mass profiling and GC-MS analyses.Key Results Pollen tubes from all the species were labelled with the mAb CCRC-M1, a monoclonal antibody that recognizes epitopes associated with fucosylated XyG motifs. Analyses of the cell wall did not highlight major structural differences between previously studied N. alata and N. tabacum XyG. In contrast, XyG of tomato pollen tubes contained fucosylated and arabinosylated motifs. The highest levels of fucosylated XyG were found in pollen tubes from the wild species.Conclusions The results clearly indicate that the male gametophyte (pollen tube) and the sporophyte have structurally different XyG. This suggests that fucosylated XyG may have an important role in the tip growth of pollen tubes, and that they must have a specific set of functional XyG fucosyltransferases, which are yet to be characterized.     

Emotional Meaning in Context in Relation to Hypomanic Personality Traits: An ERP Study

The ability to integrate contextual information is important for the comprehension of emotional and social situations. While some studies have shown that emotional processes and social cognition are impaired in people with hypomanic personality trait, no results have been reported concerning the neurophysiological processes mediating the processing of emotional information during the integration of contextual social information in this population. We therefore chose to conduct an ERP study dealing with the integration of emotional information in a population with hypomanic personality trait. Healthy participants were evaluated using the Hypomanic Personality Scale (HPS), and ERPs were recorded during a linguistic task in which participants silently read sentence pairs describing short social situations. The first sentence implicitly conveyed the positive or negative emotional state of a character. The second sentence was emotionally congruent or incongruent with the first sentence. We analyzed the difference in the modulation of two components (N400 and LPC) in response to the emotional word present at the end of the “target” sentences as a function of the HPS score and the emotional valence of the context. Our results showed a possible modulation of the N400 component in response to both positive and negative context among the participants who scored high on the Mood Volatility subscale of the Hypomanic Personality Scale. These results seem to indicate that the participants with hypomanic personality traits exhibited specificities in the integration of emotions at the level of the early-mobilized neurocognitive processes (N400). Participants with hypomanic personality traits found it difficult to integrate negative emotional contexts, while simultaneously exhibiting an enhanced integration of positive emotional contexts.     

Importance of traditional protected areas for the collection of medicinal plants,Kongo‐Central (DRC)

The Mbanza‐Ngungu region (Kongo‐Central province, DRC) currently faces continued forest deterioration. Many of these forests were traditionally protected areas of which to date, only traces are left. The aim of this study was to evaluate and compare the importance of forest remnants and other components of the landscape for the collection of medicinal plants in the Mbanza‐Ngungu Region, DRC. Between February 2009 and May 2012, semi‐structured interviews and participatory observations were conducted in this region with 51 traditional healers selected by means of the ‘snowball method’. Local importance of medicinal plants was determined by the medicinal Use Value parameter. Statistical analyses were carried out with SPSS 20.0 and based on chi‐square test, analysis of variance and post hoc comparison of means. Our results show that the forest remnants remain the main medicinal species provider: 68 species against 62 for agro‐ecosystems. However, the total number of citations for medicinal species uses is higher for agro‐ecosystems (293) than for forest remnants (233), and this difference is significant (P < 0·05). This could be explained, among others, by the fact that some forest remnants are respected or protected by the villagers for religious and ritual purposes (Sangi). This also points to the importance of agro‐ecosystems and secondary vegetation as provider of medicinal plants around rural villages, as seen elsewhere in the tropics.     

Global Conservation of Protein Status between Cell Lines and Xenografts

Common preclinical models for testing anticancer treatment include cultured human tumor cell lines in monolayer, and xenografts derived from these cell lines in immunodeficient mice. Our goal was to determine how similar the xenografts are compared with their original cell line and to determine whether it is possible to predict the stability of a xenograft model beforehand. We studied a selection of 89 protein markers of interest in 14 human cell cultures and respective subcutaneous xenografts using the reverse-phase protein array technology. We specifically focused on proteins and posttranslational modifications involved in DNA repair, PI3K pathway, apoptosis, tyrosine kinase signaling, stress, cell cycle, MAPK/ERK signaling, SAPK/JNK signaling, NFκB signaling, and adhesion/cytoskeleton. Using hierarchical clustering, most cell culture-xenograft pairs cluster together, suggesting a global conservation of protein signature. Particularly, Akt, NFkB, EGFR, and Vimentin showed very stable protein expression and phosphorylation levels highlighting that 4 of 10 pathways were highly correlated whatever the model. Other proteins were heterogeneously conserved depending on the cell line. Finally, cell line models with low Akt pathway activation and low levels of Vimentin gave rise to more reliable xenograft models. These results may be useful for the extrapolation of cell culture experiments to in vivo models in novel targeted drug discovery.