N-arylsulfonyl-2-vinyltryptamines as new 5-HT6 serotonin receptor ligands

Several new 2-vinyl-Nb,Nb-dimethyltryptamines were prepared using Fischer indole synthesis followed by simple functional group transformations and evaluated on 5-HT4, 5-HT5, 5-HT6 and 5-HT7 serotonin receptors. It was found that 2-vinyl substitution conferred a potent and selective 5-HT6 binding activity to these molecules which could be enhanced by Na-arylsulfonyl substituents.     

Vipp1: a very important protein in plastids?!

As a key feature in oxygenic photosynthesis, thylakoid membranes play an essential role in the physiology of plants, algae, and cyanobacteria. Despite their importance in the process of oxygenic photosynthesis, their biogenesis has remained a mystery to the present day. A decade ago, vesicle-inducing protein in plastids 1 (Vipp1) was described to be involved in thylakoid membrane formation in chloroplasts and cyanobacteria. Most follow-up studies clearly linked Vipp1 to membranes and Vipp1 interactions as well as the defects observed after Vipp1 depletion in chloroplasts and cyanobacteria indicate that Vipp1 directly binds to membranes, locally stabilizes bilayer structures, and thereby retains membrane integrity. Here current knowledge about the structure and function of Vipp1 is summarized with a special focus on its relationship to the bacterial phage shock protein A (PspA), as both proteins share a common origin and appear to have retained many similarities in structure and function.     

Learned Vocal Variation Is Associated with Abrupt Cryptic Genetic Change in a Parrot Species Complex

Contact zones between subspecies or closely related species offer valuable insights into speciation processes. A typical feature of such zones is the presence of clinal variation in multiple traits. The nature of these traits and the concordance among clines are expected to influence whether and how quickly speciation will proceed. Learned signals, such as vocalizations in species having vocal learning (e.g. humans, many birds, bats and cetaceans), can exhibit rapid change and may accelerate reproductive isolation between populations. Therefore, particularly strong concordance among clines in learned signals and population genetic structure may be expected, even among continuous populations in the early stages of speciation. However, empirical evidence for this pattern is often limited because differences in vocalisations between populations are driven by habitat differences or have evolved in allopatry. We tested for this pattern in a unique system where we may be able to separate effects of habitat and evolutionary history. We studied geographic variation in the vocalizations of the crimson rosella (Platycercus elegans) parrot species complex. Parrots are well known for their life-long vocal learning and cognitive abilities. We analysed contact calls across a ca 1300 km transect encompassing populations that differed in neutral genetic markers and plumage colour. We found steep clinal changes in two acoustic variables (fundamental frequency and peak frequency position). The positions of the two clines in vocal traits were concordant with a steep cline in microsatellite-based genetic variation, but were discordant with the steep clines in mtDNA, plumage and habitat. Our study provides new evidence that vocal variation, in a species with vocal learning, can coincide with areas of restricted gene flow across geographically continuous populations. Our results suggest that traits that evolve culturally can be strongly associated with reduced gene flow between populations, and therefore may promote speciation, even in the absence of other barriers.     

Barriers to HIV testing in Côte d'Ivoire: the role of individual characteristics and testing modalities

Background

Expanding HIV testing requires a better understanding of barriers to its uptake. We investigated barriers to HIV testing in Côte d''Ivoire, taking into account test circumstances (client vs. provider-initiated).

Methods

We used data from the 2005 nationally representative Demographic and Health Survey conducted in Côte d''Ivoire. Socio-demographic characteristics, sexual behaviour and knowledge and attitudes toward HIV/AIDS associated with recent (<2 years) HIV testing were identified using gender-specific univariate and multivariate logistic regressions. Among women, differential effects of barriers to testing according to test circumstance (whether they have been offered for a prenatal test or not) were assessed through interaction tests.

Results

Recent HIV testing was reported by 6.1% of men and 9.5% of women (including 4.6% as part of antenatal care). Among men, having a low socioeconomic status, having a low HIV-related knowledge level and being employed [compared to those inactive: adjusted Odds Ratio (aOR) 0.46; 95% confidence interval (CI) 0.25–0.87] were associated with lower proportions of recent HIV testing. Among women without a prenatal HIV testing offer, living outside the capital (aOR 0.38; CI 0.19–0.77) and reporting a unique lifetime sexual partner constituted additional barriers to HIV testing. By contrast, among women recently offered to be tested in prenatal care, none of these variables was found to be associated with recent HIV testing.

Conclusions

Various dimensions of individuals'' characteristics constituted significant barriers to HIV testing in Côte d''Ivoire in 2005, with gender specificities. Such barriers are substantially reduced when testing was proposed in the framework of antenatal care. This suggests that provider-initiated testing strategies may help overcome individual barriers to HIV testing.     

Does Facial Resemblance Enhance Cooperation?

Facial self-resemblance has been proposed to serve as a kinship cue that facilitates cooperation between kin. In the present study, facial resemblance was manipulated by morphing stimulus faces with the participants'' own faces or control faces (resulting in self-resemblant or other-resemblant composite faces). A norming study showed that the perceived degree of kinship was higher for the participants and the self-resemblant composite faces than for actual first-degree relatives. Effects of facial self-resemblance on trust and cooperation were tested in a paradigm that has proven to be sensitive to facial trustworthiness, facial likability, and facial expression. First, participants played a cooperation game in which the composite faces were shown. Then, likability ratings were assessed. In a source memory test, participants were required to identify old and new faces, and were asked to remember whether the faces belonged to cooperators or cheaters in the cooperation game. Old-new recognition was enhanced for self-resemblant faces in comparison to other-resemblant faces. However, facial self-resemblance had no effects on the degree of cooperation in the cooperation game, on the emotional evaluation of the faces as reflected in the likability judgments, and on the expectation that a face belonged to a cooperator rather than to a cheater. Therefore, the present results are clearly inconsistent with the assumption of an evolved kin recognition module built into the human face recognition system.     

Spectral trees as a robust annotation tool in LC–MS based metabolomics

The identification of large series of metabolites detectable by mass spectrometry (MS) in crude extracts is a challenging task. In order to test and apply the so-called multistage mass spectrometry (MS ⁿ ) spectral tree approach as tool in metabolite identification in complex sample extracts, we firstly performed liquid chromatography (LC) with online electrospray ionization (ESI)?CMS ⁿ , using crude extracts from both tomato fruit and Arabidopsis leaf. Secondly, the extracts were automatically fractionated by a NanoMate LC-fraction collector/injection robot (Advion) and selected LC-fractions were subsequently analyzed using nanospray-direct infusion to generate offline in-depth MS ⁿ spectral trees at high mass resolution. Characterization and subsequent annotation of metabolites was achieved by detailed analysis of the MS ⁿ spectral trees, thereby focusing on two major plant secondary metabolite classes: phenolics and glucosinolates. Following this approach, we were able to discriminate all selected flavonoid glycosides, based on their unique MS ⁿ fragmentation patterns in either negative or positive ionization mode. As a proof of principle, we report here 127 annotated metabolites in the tomato and Arabidopsis extracts, including 21 novel metabolites. Our results indicate that online LC?CMS ⁿ fragmentation in combination with databases of in-depth spectral trees generated offline can provide a fast and reliable characterization and annotation of metabolites present in complex crude extracts such as those from plants.     

Bio-samtools: Ruby bindings for SAMtools, a library for accessing BAM files containing high-throughput sequence alignments

ABSTRACT: BACKGROUND: The SAMtools utilities comprise a very useful and widely used suite of software for manipulating files and alignments in the SAM and BAM format, used in a wide range of genetic analyses. The SAMtools utilities are implemented in C and provide an API for programmatic access, to help make this functionality available to programmers wishing to develop in the high level Ruby language we have developed bio-samtools, a Ruby binding to the SAMtools library. RESULTS: The utility of SAMtools is encapsulated in 3 main classes, Bio::DB::Sam, representing the alignment files and providing access to the data in them, Bio::DB::Alignment, representing the individual read alignments inside the files and Bio::DB::Pileup, representing the summarised nucleotides of reads over a single point in the nucleotide sequence to which the reads are aligned. CONCLUSIONS: bio-samtools is a flexible and easy to use interface that programmers of many levels of experience can use to access the information in the popular and common SAM/BAM format.     

Dimers of light-harvesting complex 2 from Rhodobacter sphaeroides characterized in reconstituted 2D crystals with atomic force microscopy

Microscopic and light spectroscopic investigations on the supramolecular architecture of bacterial photosynthetic membranes have revealed the photosynthetic protein complexes to be arranged in a densely packed energy-transducing network. Protein packing may play a determining role in the formation of functional photosynthetic domains and membrane curvature. To further investigate in detail the packing effects of like-protein photosynthetic complexes, we report an atomic force microscopy investigation on artificially created 2D crystals of the peripheral photosynthetic light-harvesting complexes 2 (LH2's) from the bacterium Rhodobacter sphaeroides. Instead of the usually observed one or two different crystallization lattices for one specific preparation protocol, we find seven different packing lattices. The most abundant crystal types all show a tilting of LH2. Most surprisingly, although LH2 is a monomeric protein complex in vivo, we find an LH2 dimer packing motif. We further characterize two different dimer configurations: in type 1, the LH2's are tilted inwards, and in type 2, they are tilted outwards. Closer inspection of the lattices surrounding the LH2 dimers indicates their close resemblance to those LH2's that constitute a lattice of zig-zagging LH2's. In addition, analyses of the tilt of the LH2's within the zig-zag lattice and that observed within the dimers corroborate their similar packing motifs. The type 2 dimer configuration exhibits a tilt that, in the absence of up-down packing, could bend the lipid bilayer, leading to the strong curvature of the LH2 domains as observed in Rhodobacter sphaeroides photosynthetic membranes in vivo.     

Landscape composition and spatial prediction of alveolar echinococcosis in southern Ningxia, China

Background

Alveolar echinococcosis (AE) presents a serious public health challenge within China. Mass screening ultrasound surveys can detect pre-symptomatic AE, but targeting areas identified from hospital records is inefficient regarding AE. Prediction of undetected or emerging hotspots would increase detection rates. Voles and lemmings of the subfamily Arvicolinae are important intermediate hosts in sylvatic transmission systems. Their populations reach high densities in productive grasslands where food and cover are abundant. Habitat availability is thought to affect arvicoline population dynamic patterns and definitive host–intermediate host interactions. Arvicoline habitat correlates with AE prevalence in Western Europe and southern Gansu Province, China.

Methods and Findings

Xiji County, Ningxia Hui Autonomous Region, borders southern Gansu. The aims of this study were to map AE prevalence across Xiji and test arvicoline habitat as a predictor. Land cover was mapped using remotely sensed (Landsat) imagery. Infection status of 3,205 individuals screened in 2002–2003 was related, using generalised additive mixed models, to covariates: gender; farming; ethnicity; dog ownership; water source; and areal cover of mountain pasture and lowland pasture. A Markov random field modelled additional spatial variation and uncertainty. Mountain pasture and lowland pasture were associated with below and above average AE prevalence, respectively.

Conclusions

Low values of the normalised difference vegetation index indicated sub-optimality of lowland pasture for grassland arvicolines. Unlike other known endemic areas, grassland arvicolines probably did not provide the principal reservoir for Echinococcus multilocularis in Xiji. This result is consistent with recent small mammal surveys reporting low arvicoline densities and high densities of hamsters, pikas and jerboas, all suitable intermediate hosts for E. multilocularis, in reforested lowland pasture. The risk of re-emergence is discussed. We recommend extending monitoring to: southern Haiyuan County, where predicted prevalence was high; southern Xiji County, where prediction uncertainty was high; and monitoring small mammal community dynamics and the infection status of dogs.     

Peters Plus syndrome is a new congenital disorder of glycosylation and involves defective Omicron-glycosylation of thrombospondin type 1 repeats

Peters Plus syndrome is an autosomal recessive disorder characterized by anterior eye chamber defects, disproportionate short stature, developmental delay, and cleft lip and/or palate. It is caused by splice site mutations in what was thought to be a beta1,3-galactosyltransferase-like gene (B3GALTL). Recently, we and others found this gene to encode a beta1,3-glucosyltransferase involved in the synthesis of the disaccharide Glc-beta1,3-Fuc-Omicron-that occurs on thrombospondin type 1 repeats of many biologically important proteins. No functional tests have been performed to date on the presumed glycosylation defect in Peters Plus syndrome. We have established a sensitive immunopurification-mass spectrometry method, using multiple reaction monitoring, to analyze Omicron-fucosyl glycans. It was used to compare the reporter protein properdin from Peters Plus patients with that from control heterozygous relatives. In properdin from patients, we could not detect the Glc-beta1,3-Fuc-Omicron-disaccharide, and we only found Fuc-Omicron-at all four Omicron-fucosylation sites. In contrast, properdin from heterozygous relatives and a healthy volunteer carried the Glc-beta1,3-Fuc-Omicron-disaccharide. These data firmly establish Peters Plus syndrome as a new congenital disorder of glycosylation.