A novel multivariate approach to phenotyping and association mapping of multi-locus gametophytic self-incompatibility reveals S, Z and other loci in a perennial ryegrass (Poaceae) population

Self-incompatibility (SI) is a mechanism that many flowering plants employ to preventfertilisation by self- and self-like pollen ensuring heterozygosity and hybrid vigour.Although a number of single locus mechanisms have been characterised in detail, nomulti-locus systems have been fully elucidated. Historically, examples of the geneticanalysis of multi-locus SI, to make analysis tractable, are either made on the progenyof bi-parental crosses, where the number of alleles at each locus is restricted, or oncrosses prepared in such a way that only one of the SI loci segregates. Perennial ryegrass(Lolium perenne L.) possesses a well-documented two locus (S and Z) gametophyticincompatibility system. A more universal, realistic proof of principle study was conductedin a perennial ryegrass population in which allelic and non-allelic diversity was notartificially restricted. A complex pattern of pollinations from a diallel cross was revealedwhich could not possibly be interpreted easily per se, even with an already establishedgenetic model. Instead, pollination scores were distilled into principal component scoresdescribed as Compatibility Components (CC1-CC3). These were then subjected toa conventional genome-wide association analysis. CC1 associated with markers onlinkage groups (LGs) 1, 2, 3, and 6, CC2 exclusively with markers in a genomic regionon LG 2, and CC3 with markers on LG 1. BLAST alignment with the Brachypodiumphysical map revealed highly significantly associated markers with peak associationswith genes adjacent and four genes away from the chromosomal locations of candidateSI genes, S- and Z-DUF247, respectively. Further significant associations were found in aBrachypodium distachyon chromosome 3 region, having shared synteny with Lolium LG1, suggesting further SI loci linked to S or extensive micro-re-arrangement of the genomebetween B. distachyon and L. perenne. Significant associations with gene sequencesaligning with marker sequences on Lolium LGs 3 and 6 were also identified. We thereforedemonstrate the power of a novel association genetics approach to identify the genescontrolling multi-locus gametophytic SI systems and to identify novel loci potentiallyinvolved in already established SI systems.publishersversionPeer reviewe

Wnt activity guides facial branchiomotor neuron migration, and involves the PCP pathway and JNK and ROCK kinases

<p>Abstract</p> <p>Background</p> <p>Wnt proteins play roles in many biological processes, including axon guidance and cell migration. In the mammalian hindbrain, facial branchiomotor (FBM) neurons undergo a striking rostral to caudal migration, yet little is known of the underlying molecular mechanisms. In this study, we investigated a possible role of Wnts and the planar cell polarity (PCP) pathway in this process.</p> <p>Results</p> <p>Here we demonstrate a novel role for Wnt proteins in guiding FBM neurons during their rostral to caudal migration in the hindbrain. We found that <it>Wnt5a </it>is expressed in a caudal^highto rostral^lowgradient in the hindbrain. Wnt-coated beads chemoattracted FBM neurons to ectopic positions in an explant migration assay. The rostrocaudal FBM migration was moderately perturbed in <it>Wnt5a </it>mutant embryos and severely disrupted in <it>Frizzled3 </it>mutant mouse embryos, and was aberrant following inhibition of Wnt function by secreted Frizzled-related proteins. We also show the involvement of the Wnt/PCP pathway in mammalian FBM neuron migration. Thus, mutations in two PCP genes, <it>Vangl2 </it>and <it>Scribble</it>, caused severe defects in FBM migration. Inhibition of JNK and ROCK kinases strongly and specifically reduced the FBM migration, as well as blocked the chemoattractant effects of ectopic Wnt proteins.</p> <p>Conclusion</p> <p>These results provide <it>in vivo </it>evidence that Wnts chemoattract mammalian FBM neurons and that Wnt5a is a candidate to mediate this process. Molecules of the PCP pathway and the JNK and ROCK kinases also play a role in the FBM migration and are likely mediators of Wnt signalling.</p

A heterogeneous microbial consortium producing short-chain fatty acids from lignocellulose.

Microbial consortia are a promising alternative to monocultures of genetically modified microorganisms for complex biotransformations. We developed a versatile consortium-based strategy for the direct conversion of lignocellulose to short-chain fatty acids, which included the funneling of the lignocellulosic carbohydrates to lactate as a central intermediate in engineered food chains. A spatial niche enabled in situ cellulolytic enzyme production by an aerobic fungus next to facultative anaerobic lactic acid bacteria and the product-forming anaerobes. Clostridium tyrobutyricum, Veillonella criceti, or Megasphaera elsdenii were integrated into the lactate platform to produce 196 kilograms of butyric acid per metric ton of beechwood. The lactate platform demonstrates the benefits of mixed cultures, such as their modularity and their ability to convert complex substrates into valuable biochemicals

Past, present and future of information and knowledge sharing in the construction industry: Towards semantic service-based e-construction

The paper reviews product data technology initiatives in the construction sector and provides a synthesis of related ICT industry needs. A comparison between (a) the data centric characteristics of Product Data Technology (PDT) and (b) ontology with a focus on semantics, is given, highlighting the pros and cons of each approach. The paper advocates the migration from data-centric application integration to ontology-based business process support, and proposes inter-enterprise collaboration architectures and frameworks based on semantic services, underpinned by ontology-based knowledge structures. The paper discusses the main reasons behind the low industry take up of product data technology, and proposes a preliminary roadmap for the wide industry diffusion of the proposed approach. In this respect, the paper stresses the value of adopting alliance-based modes of operation

Complex patterns of local adaptation in teosinte

Populations of widely distributed species often encounter and adapt to specific environmental conditions. However, comprehensive characterization of the genetic basis of adaptation is demanding, requiring genome-wide genotype data, multiple sampled populations, and a good understanding of population structure. We have used environmental and high-density genotype data to describe the genetic basis of local adaptation in 21 populations of teosinte, the wild ancestor of maize. We found that altitude, dispersal events and admixture among subspecies formed a complex hierarchical genetic structure within teosinte. Patterns of linkage disequilibrium revealed four mega-base scale inversions that segregated among populations and had altitudinal clines. Based on patterns of differentiation and correlation with environmental variation, inversions and nongenic regions play an important role in local adaptation of teosinte. Further, we note that strongly differentiated individual populations can bias the identification of adaptive loci. The role of inversions in local adaptation has been predicted by theory and requires attention as genome-wide data become available for additional plant species. These results also suggest a potentially important role for noncoding variation, especially in large plant genomes in which the gene space represents a fraction of the entire genome

Testing the Ortholog Conjecture with Comparative Functional Genomic Data from Mammals

A common assumption in comparative genomics is that orthologous genes share greater functional similarity than do paralogous genes (the “ortholog conjecture”). Many methods used to computationally predict protein function are based on this assumption, even though it is largely untested. Here we present the first large-scale test of the ortholog conjecture using comparative functional genomic data from human and mouse. We use the experimentally derived functions of more than 8,900 genes, as well as an independent microarray dataset, to directly assess our ability to predict function using both orthologs and paralogs. Both datasets show that paralogs are often a much better predictor of function than are orthologs, even at lower sequence identities. Among paralogs, those found within the same species are consistently more functionally similar than those found in a different species. We also find that paralogous pairs residing on the same chromosome are more functionally similar than those on different chromosomes, perhaps due to higher levels of interlocus gene conversion between these pairs. In addition to offering implications for the computational prediction of protein function, our results shed light on the relationship between sequence divergence and functional divergence. We conclude that the most important factor in the evolution of function is not amino acid sequence, but rather the cellular context in which proteins act

Writing in Britain and Ireland, c. 400 to c. 800

No abstract available

A review of nitrogen isotopic alteration in marine sediments

Key Points: Use of sedimentary nitrogen isotopes is examined; On average, sediment 15N/14N increases approx. 2 per mil during early burial; Isotopic alteration scales with water depth Abstract: Nitrogen isotopes are an important tool for evaluating past biogeochemical cycling from the paleoceanographic record. However, bulk sedimentary nitrogen isotope ratios, which can be determined routinely and at minimal cost, may be altered during burial and early sedimentary diagenesis, particularly outside of continental margin settings. The causes and detailed mechanisms of isotopic alteration are still under investigation. Case studies of the Mediterranean and South China Seas underscore the complexities of investigating isotopic alteration. In an effort to evaluate the evidence for alteration of the sedimentary N isotopic signal and try to quantify the net effect, we have compiled and compared data demonstrating alteration from the published literature. A >100 point comparison of sediment trap and surface sedimentary nitrogen isotope values demonstrates that, at sites located off of the continental margins, an increase in sediment 15N/14N occurs during early burial, likely at the seafloor. The extent of isotopic alteration appears to be a function of water depth. Depth-related differences in oxygen exposure time at the seafloor are likely the dominant control on the extent of N isotopic alteration. Moreover, the compiled data suggest that the degree of alteration is likely to be uniform through time at most sites so that bulk sedimentary isotope records likely provide a good means for evaluating relative changes in the global N cycle