MUCKE aims to mine a large volume of images, to structure them conceptually and to use this conceptual structuring in order to improve large-scale image retrieval. The last decade witnessed important progress concerning low-level image representations. However, there are a number problems which need to be solved in order to unleash the full potential of image mining in applications. The central problem with low-level representations is the mismatch between them and the human interpretation of image content. This problem can be instantiated, for instance, by the incapability of existing descriptors to capture spatial relationships between the concepts represented or by their incapability to convey an explanation of why two images are similar in a content-based image retrieval framework. We start by assessing existing local descriptors for image classification and by proposing to use co-occurrence matrices to better capture spatial relationships in images. The main focus in MUCKE is on cleaning large scale Web image corpora and on proposing image representations which are closer to the human interpretation of images. Consequently, we introduce methods which tackle these two problems and compare results to state of the art methods. Note: some aspects of this deliverable are withheld at this time as they are pending review. Please contact the authors for a preview.

http://ieeexplore.ieee.org/iel2/4524/12820/00592460.pdf

Image Processing

Data-independent acquisition (DIA) in liquid chromatography (LC) coupled to tandem mass spectrometry (MS/MS) provides comprehensive untargeted acquisition of molecular data. We provide an open-source software pipeline, which we call MS-DIAL, for DIA-based identification and quantification of small molecules by mass spectral deconvolution. For a reversed-phase LC-MS/MS analysis of nine algal strains, MS-DIAL using an enriched LipidBlast library identified 1,023 lipid compounds, highlighting the chemotaxonomic relationships between the algal strains.

/pdf/ms-dial-data-independent-ms-ms-deconvolution-for-3nkasaw72n.pdf

MS-DIAL: data-independent MS/MS deconvolution for comprehensive metabolome analysis.

Historically, natural products have been used since ancient times and in folklore for the treatment of many diseases and illnesses. Classical natural product chemistry methodologies enabled a vast array of bioactive secondary metabolites from terrestrial and marine sources to be discovered. Many of these natural products have gone on to become current drug candidates. This brief review aims to highlight historically significant bioactive marine and terrestrial natural products, their use in folklore and dereplication techniques to rapidly facilitate their discovery. Furthermore a discussion of how natural product chemistry has resulted in the identification of many drug candidates; the application of advanced hyphenated spectroscopic techniques to aid in their discovery, the future of natural product chemistry and finally adopting metabolomic profiling and dereplication approaches for the comprehensive study of natural product extracts will be discussed.

https://minerva-access.unimelb.edu.au/bitstream/handle/11343/265172/PMC3901206.pdf

A historical overview of natural products in drug discovery.

Starch is the most widespread and abundant storage carbohydrate in plants. We depend upon starch for our nutrition, exploit its unique properties in industry, and use it as a feedstock for bioethanol production. Here, we review recent advances in research in three key areas. First, we assess progress in identifying the enzymatic machinery required for the synthesis of amylopectin, the glucose polymer responsible for the insoluble nature of starch. Second, we discuss the pathways of starch degradation, focusing on the emerging role of transient glucan phosphorylation in plastids as a mechanism for solubilizing the surface of the starch granule. We contrast this pathway in leaves with the degradation of starch in the endosperm of germinated cereal seeds. Third, we consider the evolution of starch biosynthesis in plants from the ancestral ability to make glycogen. Finally, we discuss how this basic knowledge has been utilized to improve and diversify starch crops.

/pdf/starch-its-metabolism-evolution-and-biotechnological-33cbtthksl.pdf

Starch: its metabolism, evolution, and biotechnological modification in plants.

Wheat is the most important staple crop in temperate zones and is in increasing demand in countries undergoing urbanization and industrialization. In addition to being a major source of starch and energy, wheat also provides substantial amounts of a number of components which are essential or beneficial for health, notably protein, vitamins (notably B vitamins), dietary fiber, and phytochemicals. Of these, wheat is a particularly important source of dietary fiber, with bread alone providing 20% of the daily intake in the UK, and well-established relationships between the consumption of cereal dietary fiber and reduced risk of cardio-vascular disease, type 2 diabetes, and forms of cancer (notably colo-rectal cancer). Wheat shows high variability in the contents and compositions of beneficial components, with some (including dietary fiber) showing high heritability. Hence, plant breeders should be able to select for enhanced health benefits in addition to increased crop yield.

https://onlinelibrary.wiley.com/doi/pdf/10.1002/fes3.64

The contribution of wheat to human diet and health

Factors affecting the postharvest soluble solids and sugar content of tomato (Solanum lycopersicum L.) fruit

Effects of environmental factors on cereal starch biosynthesis and composition

The occurrence of an extra-plastidial isoform of ADP-glucose (Glc) pyrophosphorylase (AGPase) among starch-storing organs was investigated in two ways. First, the possibility that an extra-plastidial isoform arose during the domestication of cereals was studied by comparing the intracellular distribution of enzyme activity and protein in developing endosperm of noncultivated Hordeum species with that previously reported for cultivated barley (Hordeum vulgare). As in cultivated barley, the AGPase of H. vulgare subsp. spontaneum and Hordeum murinum endosperm is accounted for by a major extra-plastidial and a minor plastidial isoform. Second, the ratio of ADP-Glc to UDP-Glc was used as an indication of the intracellular location of the AGPase activity in a wide range of starch-synthesizing organs. The ratio is expected to be high in organs in which UDP-Glc and ADP-Glc are synthesized primarily in the cytosol, because the reactions catalyzed by AGPase and UDP-Glc pyrophosphorylase will be coupled and close to equilibrium. This study revealed that ADP-Glc contents and the ratio of ADP-Glc to UDP-Glc were higher in developing graminaceous endosperms than in any other starch-storing organs. Taken as a whole the results indicate that an extra-plastidial AGPase is important in ADP-Glc synthesis in graminaceous endosperms, but not in other starch-storing organs.

/pdf/a-cytosolic-adp-glucose-pyrophosphorylase-is-a-feature-of-4wjbetk29x.pdf

A cytosolic ADP-glucose pyrophosphorylase is a feature of graminaceous endosperms, but not of other starch-storing organs.

Dynamic changes in the starch-sugar interconversion within plant source and sink tissues promote a better abiotic stress response.

Stressful environments can alter starch biosynthesis in cereal endosperm. The aim of this review is to carefully examine how starch functional properties are altered when plants encounter environmental parameters outside of the normal range. This is important because while growers and processors require grain yield stability and product uniformity this will be challenging in an era of variable weather patterns. Being able to predict the general physico-chemical nature of the starch as a result of growth status is a step towards the precise agriculture required for the 21st century. Variations in soil moisture and nutrient availability, ambient temperature, and atmospheric composition were all shown to affect starch functionality. Elevated temperature led to the most significant changes in both tropical and temperate cereals and amylose content was the most sensitive parameter under various environmental conditions. Genotypic variation appears to be a primary contributor for the response of cereal starches to environmental stress. Nonetheless, while a large amount of data from single controlled environmental stress experiment is currently available, comparably little is known about whether similar results would be achieved in multifactorial and large-scale settings. The challenges in terms of the need for more detailed experimental descriptions to lessen the study-to-study discrepancies of data and to enhance their interpretability were also discussed. © 2013 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim.

/pdf/how-environmental-stress-affects-starch-composition-and-31n2ptg9z7.pdf

Diane M. Beckles

Papers

Factors affecting the postharvest soluble solids and sugar content of tomato (Solanum lycopersicum L.) fruit

Effects of environmental factors on cereal starch biosynthesis and composition

A cytosolic ADP-glucose pyrophosphorylase is a feature of graminaceous endosperms, but not of other starch-storing organs.

Dynamic changes in the starch-sugar interconversion within plant source and sink tissues promote a better abiotic stress response.

How environmental stress affects starch composition and functionality in cereal endosperm