Association of candidate genes with flowering time and water-soluble carbohydrate content in Lolium perenne (L.)

Sk?t, L., Humphreys, J., Humphreys, M. O., Thorogood, D., Gallagher, J. A., Sanderson, R., Armstead, I. P., Thomas, I. D. (2007). Association of candidate genes with flowering time and water-soluble carbohydrate content in Lolium perenne (L.). Genetics, 177 (1), 535-547. Sponsorship: BBSRC RAE2008

Anopheles gambiae and climate in Brazil

Christopher J Thomas (2003). Anopheles gambiae and climate in Brazil. The Lancet, Infectious Diseases, 3 (6), 326-326. RAE2008

Safe Compositional Specification of Networking Systems

The Science of Network Service Composition has clearly emerged as one of the grand themes driving many of our research questions in the networking field today [NeXtworking 2003]. This driving force stems from the rise of sophisticated applications and new networking paradigms. By "service composition" we mean that the performance and correctness properties local to the various constituent components of a service can be readily composed into global (end-to-end) properties without re-analyzing any of the constituent components in isolation, or as part of the whole composite service. The set of laws that would govern such composition is what will constitute that new science of composition. The combined heterogeneity and dynamic open nature of network systems makes composition quite challenging, and thus programming network services has been largely inaccessible to the average user. We identify (and outline) a research agenda in which we aim to develop a specification language that is expressive enough to describe different components of a network service, and that will include type hierarchies inspired by type systems in general programming languages that enable the safe composition of software components. We envision this new science of composition to be built upon several theories (e.g., control theory, game theory, network calculus, percolation theory, economics, queuing theory). In essence, different theories may provide different languages by which certain properties of system components can be expressed and composed into larger systems. We then seek to lift these lower-level specifications to a higher level by abstracting away details that are irrelevant for safe composition at the higher level, thus making theories scalable and useful to the average user. In this paper we focus on services built upon an overlay management architecture, and we use control theory and QoS theory as example theories from which we lift up compositional specifications.

ImageRover: A Content-Based Image Browser for the World Wide Web

ImageRover is a search by image content navigation tool for the world wide web. To gather images expediently, the image collection subsystem utilizes a distributed fleet of WWW robots running on different computers. The image robots gather information about the images they find, computing the appropriate image decompositions and indices, and store this extracted information in vector form for searches based on image content. At search time, users can iteratively guide the search through the selection of relevant examples. Search performance is made efficient through the use of an approximate, optimized k-d tree algorithm. The system employs a novel relevance feedback algorithm that selects the distance metrics appropriate for a particular query.

Characterisation of the microbiota of traditional fermented beverages and screening these and other populations for novel antimicrobial producers and gene clusters

To screen for novel ribosomally synthesised antimicrobials, in-silico genome mining was performed on all publically available fully sequenced bacterial genomes. 49 novel type 1 lantibiotic clusters were identified from a number of species, genera and phyla not usually associated with lantibiotic production, and indicates high prevalence. A crucial step towards the commercialisation of fermented beverages is the characterisation of the microbial content. To achieve this goal, we applied next-generation sequencing techniques to analyse the bacterial and yeast populations of the organic, symbiotically-fermented beverages kefir, water kefir and kombucha. A number of minor components were revealed, many of which had not previously been associated with these beverages. The dominant microorganism in each of the water kefir grains and fermentates was Zymomonas, an ethanol-producing bacterium that had not previously been detected on such a scale. These studies represent the most accurate description of these populations to date, and should aid in future starter design and in determining which species are responsible for specific attributes of the beverages. Finally, high-throughput robotics was applied to screen for the presence of antimicrobial producers associated with these beverages. This revealed a low frequency of bacteriocin production amongst the bacterial isolates, with only lactococcins A, B and LcnN of lactococcin M being identified. However, a proteinaceous antimicrobial produced by the yeast Dekkera bruxellensis, isolated from kombucha, was found to be active against Lactobacillus bulgaricus. This peptide was patially purified.

Mitochondrial DNA polymorphism A4917G is independently associated with age-related macular degeneration.

The objective of this study was to determine if MTND2*LHON4917G (4917G), a specific non-synonymous polymorphism in the mitochondrial genome previously associated with neurodegenerative phenotypes, is associated with increased risk for age-related macular degeneration (AMD). A preliminary study of 393 individuals (293 cases and 100 controls) ascertained at Vanderbilt revealed an increased occurrence of 4917G in cases compared to controls (15.4% vs.9.0%, p = 0.11). Since there was a significant age difference between cases and controls in this initial analysis, we extended the study by selecting Caucasian pairs matched at the exact age at examination. From the 1547 individuals in the Vanderbilt/Duke AMD population association study (including 157 in the preliminary study), we were able to match 560 (280 cases and 280 unaffected) on exact age at examination. This study population was genotyped for 4917G plus specific AMD-associated nuclear genome polymorphisms in CFH, LOC387715 and ApoE. Following adjustment for the listed nuclear genome polymorphisms, 4917G independently predicts the presence of AMD (OR = 2.16, 95%CI 1.20-3.91, p = 0.01). In conclusion, a specific mitochondrial polymorphism previously implicated in other neurodegenerative phenotypes (4917G) appears to convey risk for AMD independent of recently discovered nuclear DNA polymorphisms.

beta-Arrestin 1 and 2 differentially regulate heptahelical receptor signaling and trafficking.

The two widely coexpressed isoforms of beta-arrestin (termed beta arrestin 1 and 2) are highly similar in amino acid sequence. The beta-arrestins bind phosphorylated heptahelical receptors to desensitize and target them to clathrin-coated pits for endocytosis. To better define differences in the roles of beta-arrestin 1 and 2, we prepared mouse embryonic fibroblasts from knockout mice that lack one of the beta-arrestins (beta arr1-KO and beta arr2-KO) or both (beta arr1/2-KO), as well as their wild-type (WT) littermate controls. These cells were analyzed for their ability to support desensitization and sequestration of the beta(2)-adrenergic receptor (beta(2)-AR) and the angiotensin II type 1A receptor (AT(1A)-R). Both beta arr1-KO and beta arr2-KO cells showed similar impairment in agonist-stimulated beta(2)-AR and AT(1A)-R desensitization, when compared with their WT control cells, and the beta arr1/2-KO cells were even further impaired. Sequestration of the beta(2)-AR in the beta arr2-KO cells was compromised significantly (87% reduction), whereas in the beta arr1-KO cells it was not. Agonist-stimulated internalization of the AT(1A)-R was only slightly reduced in the beta arr1-KO but was unaffected in the beta arr2-KO cells. In the beta arr1/2-KO cells, the sequestration of both receptors was dramatically reduced. Comparison of the ability of the two beta-arrestins to sequester the beta(2)-AR revealed beta-arrestin 2 to be 100-fold more potent than beta-arrestin 1. Down-regulation of the beta(2)-AR was also prevented in the beta arr1/2-KO cells, whereas no change was observed in the single knockout cells. These findings suggest that sequestration of various heptahelical receptors is regulated differently by the two beta-arrestins, whereas both isoforms are capable of supporting receptor desensitization and down-regulation.

Molecular characterization of chordoma xenografts generated from a novel primary chordoma cell source and two chordoma cell lines.

OBJECT: Chordoma cells can generate solid-like tumors in xenograft models that express some molecular characteristics of the parent tumor, including positivity for brachyury and cytokeratins. However, there is a dearth of molecular markers that relate to chordoma tumor growth, as well as the cell lines needed to advance treatment. The objective in this study was to isolate a novel primary chordoma cell source and analyze the characteristics of tumor growth in a mouse xenograft model for comparison with the established U-CH1 and U-CH2b cell lines. METHODS: Primary cells from a sacral chordoma, called "DVC-4," were cultured alongside U-CH1 and U-CH2b cells for more than 20 passages and characterized for expression of CD24 and brachyury. While brachyury is believed essential for driving tumor formation, CD24 is associated with healthy nucleus pulposus cells. Each cell type was subcutaneously implanted in NOD/SCID/IL2Rγ(null) mice. The percentage of solid tumors formed, time to maximum tumor size, and immunostaining scores for CD24 and brachyury (intensity scores of 0-3, heterogeneity scores of 0-1) were reported and evaluated to test differences across groups. RESULTS: The DVC-4 cells retained chordoma-like morphology in culture and exhibited CD24 and brachyury expression profiles in vitro that were similar to those for U-CH1 and U-CH2b. Both U-CH1 and DVC-4 cells grew tumors at rates that were faster than those for U-CH2b cells. Gross tumor developed at nearly every site (95%) injected with U-CH1 and at most sites (75%) injected with DVC-4. In contrast, U-CH2b cells produced grossly visible tumors in less than 50% of injected sites. Brachyury staining was similar among tumors derived from all 3 cell types and was intensely positive (scores of 2-3) in a majority of tissue sections. In contrast, differences in the pattern and intensity of staining for CD24 were noted among the 3 types of cell-derived tumors (p < 0.05, chi-square test), with evidence of intense and uniform staining in a majority of U-CH1 tumor sections (score of 3) and more than half of the DVC-4 tumor sections (scores of 2-3). In contrast, a majority of sections from U-CH2b cells stained modestly for CD24 (scores of 1-2) with a predominantly heterogeneous staining pattern. CONCLUSIONS: This is the first report on xenografts generated from U-CH2b cells in which a low tumorigenicity was discovered despite evidence of chordoma-like characteristics in vitro. For tumors derived from a primary chordoma cell and U-CH1 cell line, similarly intense staining for CD24 was observed, which may correspond to their similar potential to grow tumors. In contrast, U-CH2b tumors stained less intensely for CD24. These results emphasize that many markers, including CD24, may be useful in distinguishing among chordoma cell types and their tumorigenicity in vivo.

Ins-4 and daf-28 function redundantly to regulate C. elegans L1 arrest

© 2014 The Authors.Caenorhabditis elegans larvae reversibly arrest development in the first larval stage in response to starvation (L1 arrest or L1 diapause). Insulin-like signaling is a critical regulator of L1 arrest. However, the C. elegans genome encodes 40 insulin-like peptides, and it is unknown which peptides participate in nutritional control of L1 development. Work in other contexts has revealed that insulin-like genes can promote development ("agonists") or developmental arrest ("antagonists"), suggesting that such agonists promote L1 development in response to feeding. We measured mRNA expression dynamics with high temporal resolution for all 40 insulin-like genes during entry into and recovery from L1 arrest. Nutrient availability influences expression of the majority of insulin-like genes, with variable dynamics suggesting complex regulation. We identified thirteen candidate agonists and eight candidate antagonists based on expression in response to nutrient availability. We selected ten candidate agonists (. daf-28, ins-3, ins-4, ins-5, ins-6, ins-7, ins-9, ins-26, ins-33 and ins-35) for further characterization in L1 stage larvae. We used destabilized reporter genes to determine spatial expression patterns. Expression of candidate agonists is largely overlapping in L1 stage larvae, suggesting a role of the intestine, chemosensory neurons ASI and ASJ, and the interneuron PVT in control of L1 development. Transcriptional regulation of candidate agonists is most significant in the intestine, as if internal nutrient status is a more important influence on transcription than sensory perception. Phenotypic analysis of single and compound deletion mutants did not reveal effects on L1 developmental dynamics, though simultaneous disruption of ins-4 and daf-28 increases survival of L1 arrest. Furthermore, overexpression of ins-4, ins-6 or daf-28 alone decreases survival and promotes cell division during starvation. These results suggest extensive functional overlap among insulin-like genes in nutritional control of L1 development while highlighting the role of ins-4, daf-28 and to a lesser extent ins-6.

Computational fluid dynamics: advancements in technology for modeling iron and steelmaking processes

Computational fluid dynamics (CFD) software technology has formed the basis of many investigations into the behavior and optimization of primary iron and steelmaking processes for the last 25+ years. The objective of this contribution is to review the progress in CFD technologies over the last decade or so and how this can be brought to bear in advancing the process analysis capability of primary ferrous operations. In particular, progress on key challenges such as compute performance, fluid-structure transformation and interaction, and increasingly complex geometries are highlighted.

Investigation of wall-slip behaviour in lead-free solder pastes and isotropic conductive adhesives

Slippage due to wall depletion effect is well-known in rheological investigation. The aim of this study was to investigate the influence of the paste microstructure on slip formation for the paste materials (lead-free solder paste and isotropic conductive adhesives). The effect of different flowgeometries, gap heights and surface roughness on the paste viscosity was investigated. The utilisation of different measuring geometries has not clearly showed the presence of wall-slip in the paste samples. The existence of wall-slip was found to be pronounced when gap heights were varied using the parallel plate geometry. It was also found that altering the surface roughness of the parallel plate measuring geometry did not significantly eliminate wall-slip as expected. But results indicate that the use of a relatively rough surface helps to increase paste adhesion to the plates and to a certain extent inducing structural breakdown in the paste. Most importantly, the study also demonstrated on how the wall-slip formation in the paste material could be utilised for understanding of the paste microstructure and its flow behaviour.

Venetian time and the meander

Argues that the past is necessary to architectural modernity for its self-definition. Goes on to look at Le Corbusier and the past in relation to his revolutionary architectural manifesto, 'Vers une architecture' (1923), and his and Tafuri's views on Venice. Also considers Le Corbusier's 'law of meander' as a strategy for urbanism and his Venice Hospital project