Calibration, validation and the NERC Airborne Remote Sensing Facility

The application of airborne and satellite remote sensing to terrestrial applications has been dominated by empirically-based, semi-quantitative approaches, in contrast to those developed in the marine and atmospheric sciences which have often developed from rigorous physically-based models. Furthermore, the traceability of EO data and the methodological basis of many applications has often been taken for granted, with the result that the repeatability of analyses and the reliability of many terrestrial EO products can be questioned. ‘NCAVEO’ is a recently established network of Earth Observation experts and data users committed to exchanging knowledge and understanding in the area of remote sensing data calibration and validation. It aims to provide a UK-based forum to collate available knowledge and expertise associated with the calibration and validation of EO-based products from both UK and overseas providers, in different discipline areas including land, ocean and atmosphere. This paper will introduce NCAVEO and highlight some of the contributions it hopes to make to airborne remote sensing in the UK

Development of airborne hemispheric spectrometer

A new concept of hyperspectral instrument is presented. Novel design of hyperspectral skydome allows retrieval of atmospheric constituents and properties from a snapshot of spectral solar radiation over entire sky, regardless of platform motion either on ground or aircraft. Design and description of subsystems of the instrument are given followed by preliminary tolerance analysis, whose results are to be added in the retrieval algorithm along with hardware specifications. Extended application of the hyperspectral skydome is being carried out filling in the gap in the imaging spectrometry

Pd catalysed C-C & C-O bond formation using bis-(dialkyl/diarylphosphino)ferrocene ligands

A brief introduction explaining phosphine ligand properties, Pd catalysed cross-coupling reactions; the importance of the steps involved in the catalytic cycle (oxidative addition, transmetalation & reductive elimination), mechanistic studies and a comparison of various reactions will give an overview of important cross-coupling reactions and their limitations.The development of a “super-concentrated” (5M) Pd catalysed Kumada type coupling reaction has been developed for coupling a range of aryl bromide and chloride substrates with the Grignard reagents ((p-CF₃-C₆H₄)MgBr)) and PhMgBr in methyl-tetrahydrofuran (Me-THF). Using a range of bidentate ligands such as bis-phosphinoferrocenyl ligands, good conversions were achieved using small amounts of solvent; up to 10 times less than typical procedures in THF. The unsymmetrical Pt complexes of the form [Pt(P-P)Br₂], [Pt(P-P)(Ph)Br] and [Pt(P-P)Ph₂] have been synthesised and characterised. The variations of substituents on the ligand system and the steric bulk have been shown to have a dramatic effect on the rate of transmetalation. The results provide one explanation why 1,1’-bis(di tert-butylphosphino)ferrocene (dtbpf), an excellent ligand for certain Suzuki reactions, is quite poor in reactions where transmetalation is more difficult. Palladium dichloride complexes of the ferrocenylphosphine based ligands 1,1’-bis- (diphenylphosphino)ferrocene (dppf), 1,1’-bis-(diisopropylphosphino)ferrocene (dippf) and 1,1’-bis-(di-tert-butylphosphino)ferrocene (dtbpf) have been shown to be active in the Hiyama cross-coupling of p-bromoacetophenone and vinyltrimethoxysilane (CHCH₂Si(OMe₃)) in the presence of TBAF under thermal heating and microwave conditions. Ligands with the optimum balance for promoting the transmetalation, oxidative addition and reductive elimination steps along the reaction pathway have been identified. Competition experiments are consistent with slow transmetalation being an issue with the Hiyama reaction relative to the Suzuki coupling.A novel protocol has been developed for the synthesis of aryl-alkyl ethers via C-O bond activation under Pd catalysed conditions. Utilising the unsymmetrical 1-bis-(ditertbutyl-1’- bis-diphenylphosphino)ferrocene (dtbdppf) under optimised conditions with silicon based nucleophiles and NaOH or TBAF as an activator, the formation of methyl, ethyl, n-propyl and n-butyl ethers with a range of aryl halides was achieved in good yield

\u3cem\u3eDENND5B\u3c/em\u3e Regulates Intestinal Triglyceride Absorption and Body Mass

Regulation of lipid absorption by enterocytes can influence metabolic status in humans and contribute to obesity and related complications. The intracellular steps of chylomicron biogenesis and transport from the Endoplasmic Reticulum (ER) to the Golgi complex have been described, but the mechanisms for post-Golgi transport and secretion of chylomicrons have not been identified. Using a newly generated Dennd5b−/− mouse, we demonstrate an essential role for this gene in Golgi to plasma membrane transport of chylomicron secretory vesicles. In mice, loss of Dennd5b results in resistance to western diet induced obesity, changes in plasma lipids, and reduced aortic atherosclerosis. In humans, two independent exome sequencing studies reveal that a common DENND5B variant, p.(R52K), is correlated with body mass index. These studies establish an important role for DENND5B in post-Golgi chylomicron secretion and a subsequent influence on body composition and peripheral lipoprotein metabolism

Pervasive effects of a dominant foliar endophytic fungus on host genetic and phenotypic expression in a tropical tree

It is increasingly recognized that macro-organisms (corals, insects, plants, vertebrates) consist of both host tissues and multiple microbial symbionts that play essential roles in their host’s ecological and evolutionary success. Consequently, identifying benefits and costs of symbioses, as well as mechanisms underlying them are research priorities. All plants surveyed under natural conditions harbor foliar endophytic fungi (FEF) in their leaf tissues, often at high densities. Despite producing no visible effects on their hosts, experiments have nonetheless shown that FEF reduce pathogen and herbivore damage. Here, combining results from three genomic, and two physiological experiments, we demonstrate pervasive genetic and phenotypic effects of the apparently asymptomatic endophytes on their hosts. Specifically, inoculation of endophyte-free (E−) Theobroma cacao leaves with Colletotrichum tropicale (E+), the dominant FEF species in healthy T. cacao, induces consistent changes in the expression of hundreds of host genes, including many with known defensive functions. Further, E+ plants exhibited increased lignin and cellulose content, reduced maximum rates of photosynthesis (Amax), and enrichment of nitrogen-15 and carbon-13 isotopes. These phenotypic changes observed in E+ plants correspond to changes in expression of specific functional genes in related pathways. Moreover, a cacao gene (Tc00g04254) highly up-regulated by C. tropicale also confers resistance to pathogen damage in the absence of endophytes or their products in host tissues. Thus, the benefits of increased pathogen resistance in E+ plants are derived in part from up-regulation of intrinsic host defense responses, and appear to be offset by potential costs including reduced photosynthesis, altered host nitrogen metabolism, and endophyte heterotrophy of host tissues. Similar effects are likely in most plant-endophyte interactions, and should be recognized in the design and interpretation of genetic and phenotypic studies of plantsIt is increasingly recognized that macro-organisms (corals, insects, plants, vertebrates) consist of both host tissues and multiple microbial symbionts that play essential roles in their host’s ecological and evolutionary success. Consequently, identifying benefits and costs of symbioses, as well as mechanisms underlying them are research priorities. All plants surveyed under natural conditions harbor foliar endophytic fungi (FEF) in their leaf tissues, often at high densities. Despite producing no visible effects on their hosts, experiments have nonetheless shown that FEF reduce pathogen and herbivore damage. Here, combining results from three genomic, and two physiological experiments, we demonstrate pervasive genetic and phenotypic effects of the apparently asymptomatic endophytes on their hosts. Specifically, inoculation of endophyte-free (E−) Theobroma cacao leaves with Colletotrichum tropicale (E+), the dominant FEF species in healthy T. cacao, induces consistent changes in the expression of hundreds of host genes, including many with known defensive functions. Further, E+ plants exhibited increased lignin and cellulose content, reduced maximum rates of photosynthesis (Amax), and enrichment of nitrogen-15 and carbon-13 isotopes. These phenotypic changes observed in E+ plants correspond to changes in expression of specific functional genes in related pathways. Moreover, a cacao gene (Tc00g04254) highly up-regulated by C. tropicale also confers resistance to pathogen damage in the absence of endophytes or their products in host tissues. Thus, the benefits of increased pathogen resistance in E+ plants are derived in part from up-regulation of intrinsic host defense responses, and appear to be offset by potential costs including reduced photosynthesis, altered host nitrogen metabolism, and endophyte heterotrophy of host tissues. Similar effects are likely in most plant-endophyte interactions, and should be recognized in the design and interpretation of genetic and phenotypic studies of plant

Alternative processing of human HTT mRNA with implications for Huntington's disease therapeutics

Huntington disease is caused by a CAG repeat expansion in exon 1 of the huntingtin gene (HTT) that is translated into a polyglutamine stretch in the huntingtin protein (HTT). We previously showed that HTT mRNA carrying an expanded CAG repeat was incompletely spliced to generate HTT1a, an exon 1 only transcript, which was translated to produce the highly aggregation-prone and pathogenic exon 1 HTT protein. This occurred in all knock-in mouse models of Huntington's disease and could be detected in patient cell lines and post-mortem brains. To extend these findings to a model system expressing human HTT, we took advantage of YAC128 mice that are transgenic for a yeast artificial chromosome carrying human HTT with an expanded CAG repeat. We discovered that the HTT1a transcript could be detected throughout the brains of YAC128 mice. We implemented RNAscope to visualise HTT transcripts at the single molecule level and found that full-length HTT and HTT1a were retained together in large nuclear RNA clusters, as well as being present as single transcripts in the cytoplasm. Homogeneous time-resolved fluorescence analysis demonstrated that the HTT1a transcript had been translated to produce the exon 1 HTT protein. The levels of exon 1 HTT in YAC128 mice, correlated with HTT aggregation, supportive of the hypothesis that exon 1 HTT initiates the aggregation process. Huntingtin-lowering strategies are a major focus of therapeutic development for Huntington's disease. These approaches often target full-length HTT alone and would not be expected to reduce pathogenic exon 1 HTT levels. We have established YAC128 mouse embryonic fibroblast lines and shown that, together with our QuantiGene multiplex assay, these provide an effective screening tool for agents that target HTT transcripts. The effects of current targeting strategies on nuclear RNA clusters are unknown, structures that may have a pathogenic role, or alternatively could be protective by retaining HTT1a in the nucleus and preventing it from being translated. In light of recently halted antisense oligonucleotide trials, it is vital that agents targeting HTT1a are developed, and that the effects of HTT-lowering strategies on the subcellular levels of all HTT transcripts and their various HTT protein isoforms are understood

LC-HRMS-Database Screening Metrics for Rapid Prioritization of Samples to Accelerate the Discovery of Structurally New Natural Products

In order to accelerate the isolation and characterization of structurally new or novel secondary metabolites, it is crucial to develop efficient strategies that prioritize samples with greatest promise early in the workflow so that resources can be utilized in a more efficient and cost-effective manner. We have developed a metrics-based prioritization approach using exact LC-HRMS, which uses data for 24 618 marine natural products held in the PharmaSea database. Each sample was evaluated and allocated a metric score by a software algorithm based on the ratio of new masses over the total (sample novelty), ratio of known masses over the total (chemical novelty), number of peaks above a defined peak area threshold (sample complexity), and peak area (sample diversity). Samples were then ranked and prioritized based on these metric scores. To validate the approach, eight marine sponges and six tunicate samples collected from the Fiji Islands were analyzed, metric scores calculated, and samples targeted for isolation and characterization of new compounds. Structures of new compounds were elucidated by spectroscopic techniques, including 1D and 2D NMR, MS, and MS/MS. Structures were confirmed by computer-assisted structure elucidation methods (CASE) using the ACD/Structure Elucidator Suite