Current range characteristics of Swiss stone pine (Pinus cembra L.) along the Carpathians revealed by chloroplast SSR markers.

We investigated the diversity pattern of nine Swiss stone pine (Pinus cembra L.) populations along the Carpathian range including the High Tatras, by using six chloroplast DNA microsatellites (cpSSR). Our aim was to detect genetically distinct regions by clustering of populations, and to tackle possible historical colonization routes. Our analysis referred to an investigated geographical range with the two most distant populations situated at about 500 air km. We found that the most diverse populations are situated at the two edges of the investigated part, in the Retezat Mts. (South Carpathians) and the High Tatras, and diversity decreases towards the populations of the Eastern Carpathians. Hierarchical clustering and NMDS revealed that the populations of the South Carpathians with the Tatras form a distinct cluster, significantly separated from those of the Eastern Carpathians. Moreover, based on the most variable chloroplast microsatellites, the four populations of the two range edges are not significantly different. Our results, supported also by palynological and late glacial macrofossil evidences, indicate refugial territories within the Retezat Mts. that conserved rich haplotype composition. From this refugial territory Pinus cembra might have colonized the Eastern Carpathians, and this was accompanied by a gradual decrease in population diversity. Populations of the High Tatras might have had the same role in the colonizing events of the Carpathians, as positive correlation was detected among populations lying from each other at a distance of 280 km, the maximum distance between neighbouring populations

Conservation value of the native Hungarian wild grape (Vitis sylvestris Gmel.) evaluated by microsatellite markers

Wild grape (Vitis sylvestris GMEL.) has became a highly threatened species in Europe because of habitat loss, competition with alien grape species and intensive forest exploitation. Twenty-three Vitis spp. samples were analysed at 8 microsatellite loci to estimate the genetic diversity of the natural Vitis sylvestris specimens. In order to analyse the morphological traits and to perform molecular analysis, 11 native individuals were sampled from 6 remnant Hungarian habitats of the wild grape. To compare the genetic relationships among the wild specimens, samples from Turkish habitats, as well as cultivars of Vitis vinifera, Vitis labrusca and Vitis riparia were also included. Genetic diversity was higher within the Hungarian wild grape locations, with a mean of He = 0.74, which was higher that of samples originating from a larger area of Turkey, He = 0.69. Most of the Hungarian samples formed a well-defined, separate branch on the NJ tree. Based on the morphological traits and molecular analysis on the territory of Szentendre Island, formerly considered to be one of the largest native locations of wild grape, interspecific hybrids of Vitis sylvestris and Vitis riparia were identified. It can be concluded from the results that most of the Hungarian habitats studied could be valuable for the conservation. This paper reports on Hungarian Vitis sylvestris habitats, providing the first genetic study on diversity and on the relationship of Vitis sylvestris to other Vitis specimens, wild or cultivated, in the central part of the Carpathian Basin

Transcriptome pathways unique to dehydration tolerant relatives of modern wheat

Among abiotic stressors, drought is a major factor responsible for dramatic yield loss in agriculture. In order to reveal differences in global expression profiles of drought tolerant and sensitive wild emmer wheat genotypes, a previously deployed shock-like dehydration process was utilized to compare transcriptomes at two time points in root and leaf tissues using the Affymetrix GeneChip(R) Wheat Genome Array hybridization. The comparison of transcriptomes reveal several unique genes or expression patterns such as differential usage of IP(3)-dependent signal transduction pathways, ethylene- and abscisic acid (ABA)-dependent signaling, and preferential or faster induction of ABA-dependent transcription factors by the tolerant genotype that distinguish contrasting genotypes indicative of distinctive stress response pathways. The data also show that wild emmer wheat is capable of engaging known drought stress responsive mechanisms. The global comparison of transcriptomes in the absence of and after dehydration underlined the gene networks especially in root tissues that may have been lost in the selection processes generating modern bread wheats

Cranial and ventricular size following shunting or endoscopic third ventriculostomy (ETV) in infants with aqueductal stenosis: further insights from the International Infant Hydrocephalus Study (IIHS)

Purpose: The craniometrics of head circumference (HC) and ventricular size are part of the clinical assessment of infants with hydrocephalus and are often utilized in conjunction with other clinical and radiological parameters to determine the success of treatment. We aimed to assess the effect of endoscopic third ventriculostomy (ETV) and shunting on craniometric measurements during the follow-up of a cohort of infants with symptomatic triventricular hydrocephalus secondary to aqueductal stenosis. Methods: We performed a post hoc analysis of data from the International Infant Hydrocephalus Study (IIHS)—a prospective, multicenter study of infants (\u3c 24 months old) with hydrocephalus from aqueductal stenosis who were treated with either an ETV or shunt. During various stages of a 5-year follow-up period, the following craniometrics were measured: HC, HC centile, HC z-score, and frontal-occipital horn ratio (FOR). Data were compared in an analysis of covariance, adjusting for baseline variables including age at surgery and sex. Results: Of 158 enrolled patients, 115 underwent an ETV, while 43 received a shunt. Both procedures led to improvements in the mean HC centile position and z-score, a trend which continued until the 5-year assessment point. A similar trend was noted for FOR which was measured at 12 months and 3 years following initial treatment. Although the values were consistently higher for ETV compared with shunt, the differences in HC value, centile, and z-score were not significant. ETV was associated with a significantly higher FOR compared with shunting at 12 months (0.52 vs 0.44; p = 0.002) and 3 years (0.46 vs 0.38; p = 0.03) of follow-up. Conclusion: ETV and shunting led to improvements in HC centile, z-score, and FOR measurements during long-term follow-up of infants with hydrocephalus secondary to aqueductal stenosis. Head size did not significantly differ between the treatment groups during follow-up, however ventricle size was greater in those undergoing ETV when measured at 1 and 3 years following treatment

Network of Epistatic Interactions Within a Yeast snoRNA

Epistatic interactions play a fundamental role in molecular evolution, but little is known about the spatial distribution of these interactions within genes. To systematically survey a model landscape of intragenic epistasis, we quantified the fitness of similar to 60,000 Saccharomyces cerevisiae strains expressing randomly mutated variants of the 333-nucleotide-long U3 small nucleolar RNA (snoRNA). The fitness effects of individual mutations were correlated with evolutionary conservation and structural stability. Many mutations had small individual effects but had large effects in the context of additional mutations, which indicated negative epistasis. Clusters of negative interactions were explained by local thermodynamic threshold effects, whereas positive interactions were enriched among large-effect sites and between base-paired nucleotides. We conclude that high-throughput mapping of intragenic epistasis can identify key structural and functional features of macromolecules

Two terpene synthases are responsible for the major sesquiterpenes emitted from the flowers of kiwifruit (Actinidia deliciosa)

Kiwifruit vines rely on bees for pollen transfer between spatially separated male and female individuals and require synchronized flowering to ensure pollination. Volatile terpene compounds, which are important cues for insect pollinator attraction, were studied by dynamic headspace sampling in the major green-fleshed kiwifruit (Actinidia deliciosa) cultivar ‘Hayward’ and its male pollinator ‘Chieftain’. Terpene volatile levels showed a profile dominated by the sesquiterpenes α-farnesene and germacrene D. These two compounds were emitted by all floral tissues and could be observed throughout the day, with lower levels at night. The monoterpene (E)-β-ocimene was also detected in flowers but was emitted predominantly during the day and only from petal tissue. Using a functional genomics approach, two terpene synthase (TPS) genes were isolated from a ‘Hayward’ petal EST library. Bacterial expression and transient in planta data combined with analysis by enantioselective gas chromatography revealed that one TPS produced primarily (E,E)-α-farnesene and small amounts of (E)-β-ocimene, whereas the second TPS produced primarily (+)-germacrene D. Subcellular localization using GFP fusions showed that both enzymes were localized in the cytoplasm, the site for sesquiterpene production. Real-time PCR analysis revealed that both TPS genes were expressed in the same tissues and at the same times as the corresponding floral volatiles. The results indicate that two genes can account for the major floral sesquiterpene volatiles observed in both male and female A. deliciosa flowers

Helicobacter pylori Type IV Secretion Apparatus Exploits β1 Integrin in a Novel RGD-Independent Manner

Translocation of the Helicobacter pylori (Hp) cytotoxin-associated gene A (CagA) effector protein via the cag-Type IV Secretion System (T4SS) into host cells is a major risk factor for severe gastric diseases, including gastric cancer. However, the mechanism of translocation and the requirements from the host cell for that event are not well understood. The T4SS consists of inner- and outer membrane-spanning Cag protein complexes and a surface-located pilus. Previously an arginine-glycine-aspartate (RGD)-dependent typical integrin/ligand type interaction of CagL with α5β1 integrin was reported to be essential for CagA translocation. Here we report a specific binding of the T4SS-pilus-associated components CagY and the effector protein CagA to the host cell β1 Integrin receptor. Surface plasmon resonance measurements revealed that CagA binding to α5β1 integrin is rather strong (dissociation constant, KD of 0.15 nM), in comparison to the reported RGD-dependent integrin/fibronectin interaction (KD of 15 nM). For CagA translocation the extracellular part of the β1 integrin subunit is necessary, but not its cytoplasmic domain, nor downstream signalling via integrin-linked kinase. A set of β1 integrin-specific monoclonal antibodies directed against various defined β1 integrin epitopes, such as the PSI, the I-like, the EGF or the β-tail domain, were unable to interfere with CagA translocation. However, a specific antibody (9EG7), which stabilises the open active conformation of β1 integrin heterodimers, efficiently blocked CagA translocation. Our data support a novel model in which the cag-T4SS exploits the β1 integrin receptor by an RGD-independent interaction that involves a conformational switch from the open (extended) to the closed (bent) conformation, to initiate effector protein translocation

Bayesian computing with INLA: New features

The INLA approach for approximate Bayesian inference for latent Gaussian models has been shown to give fast and accurate estimates of posterior marginals and also to be a valuable tool in practice via the R-package R-INLA. In this paper we formalize new developments in the R-INLA package and show how these features greatly extend the scope of models that can be analyzed by this interface. We also discuss the current default method in R-INLA to approximate posterior marginals of the hyperparameters using only a modest number of evaluations of the joint posterior distribution of the hyperparameters, without any need for numerical integration

Conserved and variable correlated mutations in the plant MADS protein network

<p>Abstract</p> <p>Background</p> <p>Plant MADS domain proteins are involved in a variety of developmental processes for which their ability to form various interactions is a key requisite. However, not much is known about the structure of these proteins or their complexes, whereas such knowledge would be valuable for a better understanding of their function. Here, we analyze those proteins and the complexes they form using a correlated mutation approach in combination with available structural, bioinformatics and experimental data.</p> <p>Results</p> <p>Correlated mutations are affected by several types of noise, which is difficult to disentangle from the real signal. In our analysis of the MADS domain proteins, we apply for the first time a correlated mutation analysis to a family of interacting proteins. This provides a unique way to investigate the amount of signal that is present in correlated mutations because it allows direct comparison of mutations in various family members and assessing their conservation. We show that correlated mutations in general are conserved within the various family members, and if not, the variability at the respective positions is less in the proteins in which the correlated mutation does not occur. Also, intermolecular correlated mutation signals for interacting pairs of proteins display clear overlap with other bioinformatics data, which is not the case for non-interacting protein pairs, an observation which validates the intermolecular correlated mutations. Having validated the correlated mutation results, we apply them to infer the structural organization of the MADS domain proteins.</p> <p>Conclusion</p> <p>Our analysis enables understanding of the structural organization of the MADS domain proteins, including support for predicted helices based on correlated mutation patterns, and evidence for a specific interaction site in those proteins.</p