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

Whole grain cereals are a good source of nutrients. Several cutting-edge metabolomic platforms have been deployed to identify various phenolic compounds and enhance cereal bioactive bioavailability. A diet rich in cereal phenolics may modify the microbial composition, support gut homeostasis, and increase gut health, thereby lowering the risk of non-communicable illness.In this work, we reviewed current metabolomic breakthroughs in cereal phenolic profiling and their effects on human health via gut microbiota modulation. We argue that the information presented in this paper will assist in the development of nutritionally superior cereal breeds and functional foods.Most cereal grains contain ferulic acid derivatives, caffeoyl glycerides, and feruloyl and coumaroyl esters. While there has been significant progress in discovering novel phenolic compounds in cereals, quantifying these molecules, and translating their therapeutic effects from animal model systems to humans remains a challenge. To this end, metabolomics, and other high-throughput-omics-based platforms must be integrated to further examine the structure and functionality of phenolic metabolites to breed nutritionally rich cereals as well as map their influence on human health benefits. Rare alleles must be introduced to improve bioactive content in cereal grains while maintaining yield. Following that, these exceptional varieties must be effectively processed to maximize phenolic bioavailability. 

Metabolomics based inferences to unravel phenolic compound diversity in cereals and its implications for human gut health

Rice (Oryza sativa L.) is the staple food of the majority of the population, particularly in Asia and Africa. Enriching rice with nutritional and therapeutic contents can improve its benefits for patients with lifestyle disorders. This study aimed to profile the phytochemical contents of the therapeutically known traditional rice Mappillai Samba against white rice CBMAS 14065 using non-targeted gas chromatography–mass spectrometry (GC-MS/MS). An analysis of the data using a mass spectrometry–data independent analysis (MS-DIAL) and MetaboAnalyst identified 113 metabolites belonging to 21 different classes of metabolites. A partial least square-discriminant analysis (PLS-DA) revealed 43 variable importance in projection (VIP) metabolites. This study identified therapeutically important metabolites, including phenylpropanoids, phytosterols, flavonoids, and polyamines, in the grains of Mappillai Samba. Three significant metabolic pathways, viz., phenylpropanoid biosynthesis, ubiquinone and other terpenoid-quinone biosynthesis, and steroid biosynthesis, were responsible for the grain metabolome variation between CBMAS 14065 and Mappillai Samba. Overall, the results of this study unravelled the biochemical complexity of Mappillai Samba, paving the way for the genetic mapping of the therapeutic compound accumulation in rice and the development of similar therapeutic rice varieties through molecular breeding.

/pdf/a-comparative-metabolomic-analysis-reveals-the-nutritional-1gzssmk3.pdf

A Comparative Metabolomic Analysis Reveals the Nutritional and Therapeutic Potential of Grains of the Traditional Rice Variety Mappillai Samba

Introduction Buckwheat (Fagopyrum tataricum), an important food crop, also has medicinal uses. It is widely planted in Southwest China, overlapping with planting areas remarkably polluted by cadmium (Cd). Therefore, it is of great significance to study the response mechanism of buckwheat under Cd stress and further develop varieties with excellent Cd tolerance. Methods In this study, two critical periods of Cd stress treatment (days 7 and 14 after Cd treatment) of cultivated buckwheat (Pinku-1, named K33) and perennial species (F. tatari-cymosum Q.F. Chen) (duoku, named DK19) were analyzed using transcriptome and metabolomics. Results The results showed that Cd stress led to changes in reactive oxygen species (ROS) and the chlorophyll system. Moreover, Cd-response genes related to stress response, amino acid metabolism, and ROS scavenging were enriched or activated in DK19. Transcriptome and metabolomic analyses highlighted the important role of galactose, lipid (glycerophosphatide metabolism and glycerophosphatide metabolism), and glutathione metabolism in response to Cd stress in buckwheat, which are significantly enriched at the gene and metabolic levels in DK19. Discussion The results of the present study provide valuable information for a better understanding of the molecular mechanisms underlying Cd tolerance in buckwheat and useful clues for the genetic improvement of drought tolerance in buckwheat.

/pdf/integrated-transcriptome-and-metabonomic-analysis-of-key-1gan1k37.pdf

Integrated transcriptome and metabonomic analysis of key metabolic pathways in response to cadmium stress in novel buckwheat and cultivated species

Advanced glycation end products (AGEs), the products of non-enzymatic browning reactions between the active carbonyl groups of reducing sugars and the free amines of amino acids, are largely considered oxidative derivatives resulting from diabetic hyperglycemia, which are further recognized as a potential risk for insulin resistance (IR) and type 2 diabetes (T2D). The accumulation of AGEs can trigger numerous negative effects such as oxidative stress, carbonyl stress, inflammation, autophagy dysfunction and imbalance of gut microbiota. Recently, studies have shown that cereal polyphenols have the ability to inhibit the formation of AGEs, thereby preventing and alleviating T2D. In the meanwhile, phenolics compounds could produce different biological effects due to the quantitative structure activity-relationship. This review highlights the effects of cereal polyphenols as a nonpharmacologic intervention in anti-AGEs and alleviating T2D based on the effects of oxidative stress, carbonyl stress, inflammation, autophagy, and gut microbiota, which also provides a new perspective on the etiology and treatment of diabetes.

Cereal polyphenols inhibition mechanisms on advanced glycation end products and regulation on type 2 diabetes.

Sorghum is one of the most important food and feed cereal crops and has been gaining industrial importance in recent years for its biofuel, nutraceutical and antioxidant values. A genetic profile variation study was undertaken for the accumulation of phytochemicals in 61 diverse sorghum accessions differing in their growth habitat and grain color through non-targeted Gas Chromatography-Mass Spectrometry (GC-MS/MS) analysis. Mass Spectrometry-Data Independent AnaLysis (MS-DIAL) and MetaboAnalyst identified 221 metabolites belonging to 27 different phytochemicals. Tropical and temperate sorghums were distinct in their metabolic profiles with minimum overlaps, and 51 different metabolites were crucial in differentiating the two groups. Temperate sorghums had the ability to accumulate more of phenolic acids, phytosterols, flavonoids, carotenoids, and tropical sorghums for stress-related amino acids, sugars and fatty acids. Grain-color-based Partial Least Square-Discriminant Analysis (PLS-DA) analysis identified 94 Variable Importance in Projections (VIP) metabolites containing majority of flavonoids, phenylpropanoids and phytosterols. This study identified two sorghum lines (IS 7748 and IS 14861) with rich amounts of antioxidants (catechins and epicatechins) belonging to the group of condensed tannins that otherwise do not accumulate commonly in sorghum. Out of 13 metabolic pathways identified, flavonoid biosynthesis showed the highest expression. This study provided new opportunities for developing biofortified sorghum with enhanced nutraceutical and therapeutics through molecular breeding and metabolic engineering.

Large-Scale Non-Targeted Metabolomics Reveals Antioxidant, Nutraceutical and Therapeutic Potentials of Sorghum.

Drought is the most devastating stress which causes a severe decline in crop yield than any other environmental stress. The ability of plants to access water from deep soil solely depends on the root system development. In water-limited conditions, the capacity of the root system plays a critical role to adapt the situation. Maize and sorghum are the best examples that can switch to the water stress condition.

In vitro Root Architectural Screening for Early Drought Adaptive Traits in Sorghum (Sorghum bicolor L.)

Stomata regulates conductance, transpiration and photosynthetic traits in plants. Increased stomatal density may contribute to enhanced water loss and thereby help improve the transpirational cooling process and mitigate the high temperature-induced yield losses. However, genetic manipulation of stomatal traits through conventional breeding still remains a challenge due to problems involved in phenotyping and the lack of suitable genetic materials. Recent advances in functional genomics in rice identified major effect genes determining stomatal traits, including its number and size. Widespread applications of CRISPR/Cas9 in creating targeted mutations paved the way for fine tuning the stomatal traits for enhancing climate resilience in crops. In the current study, attempts were made to create novel alleles of OsEPF1 (Epidermal Patterning Factor), a negative regulator of stomatal frequency/density in a popular rice variety, ASD 16, using the CRISPR/Cas9 approach. Evaluation of 17 T0 progenies identified varying mutations (seven multiallelic, seven biallelic and three monoallelic mutations). T0 mutant lines showed a 3.7–44.3% increase in the stomatal density, and all the mutations were successfully inherited into the T1 generation. Evaluation of T1 progenies through sequencing identified three homozygous mutants for one bp insertion. Overall, T1 plants showed 54–95% increased stomatal density. The homozygous T1 lines (# E1-1-4, # E1-1-9 and # E1-1-11) showed significant increase in the stomatal conductance (60–65%), photosynthetic rate (14–31%) and the transpiration rate (58–62%) compared to the nontransgenic ASD 16. Results demonstrated that the genetic alterations in OsEPF1 altered the stomatal density, stomatal conductance and photosynthetic efficiency in rice. Further experiments are needed to associate this technology with canopy cooling and high temperature tolerance.

/pdf/altering-stomatal-density-for-manipulating-transpiration-and-1od9d2uw.pdf

Williams Mohanavel

Papers

Large-Scale Non-Targeted Metabolomics Reveals Antioxidant, Nutraceutical and Therapeutic Potentials of Sorghum.

In vitro Root Architectural Screening for Early Drought Adaptive Traits in Sorghum (Sorghum bicolor L.)

Altering Stomatal Density for Manipulating Transpiration and Photosynthetic Traits in Rice through CRISPR/Cas9 Mutagenesis