Prediction of rice texture from starch profiles measured using high-performance liquid chromatography

Starch determines a large proportion of the textural properties of cooked rice. The amylose: amylopectin ratio plays a significant role in the functionality of native starch. In this study a medium-grain rice cultivar, ‘Bengal’, was used for starch structure characterization using high performance size-exclusion chromatography (HPSEC). This cultivar is characterized by having lower amylose content (15% to 20%) than long grain cultivars and being sticky when cooked, similar to short-grain cultivars. Rice samples were harvested in 1999 from five locations around Arkansas at state verification trials where cultural practices are closely monitored. Samples of this cultivar stored at a specified moisture level for a pre-determined period of time were also subjected to texture analysis by means of a Texture Analyzer. The data measured with the HPSEC was related to instrumental texture attributes. Chemical characterization data (carbohydrate profiles) of rice samples were used to predict texture attributes of cooked rice such as hardness and stickiness. Instrumental texture attributes of hardness and stickiness were successfully predicted for Bengal rice from starch-profile data obtained though HPSEC analyses. Both attributes proved to be well predicted, based on their high coefficients of determination of 0.97 and 0.85, respectively. The statistical analysis indicates that starch structure characterization using HPSEC may be related to instrumental measurements of texture attributes

Design of nucleotide-mimetic and non-nucleotide inhibitors of the translation initiation factor eIF4E: Synthesis, structural and functional characterisation.

Eukaryotic translation initiation factor 4E (eIF4E) is considered as the corner stone in the cap-dependent translation initiation machinery. Its role is to recruit mRNA to the ribosome through recognition of the 5'-terminal mRNA cap structure (m7GpppN, where G is guanosine, N is any nucleotide). eIF4E is implicated in cell transformation, tumourigenesis, and angiogenesis by facilitating translation of oncogenic mRNAs; it is thus regarded as an attractive anticancer drug target. We have used two approaches to design cap-binding inhibitors of eIF4E by modifying the N7-substituent of m7GMP and replacing the phosphate group with isosteres such as squaramides, sulfonamides, and tetrazoles, as well as by structure-based virtual screening aimed at identifying non-nucleotide cap-binding antagonists. Phosphomimetic nucleotide derivatives and highly ranking virtual hits were evaluated in a series of in vitro and cell-based assays to identify the first non-nucleotide eIF4E cap-binding inhibitor with activities in cell-based assays, N-[(5,6-dihydro-6-oxo-1,3-dioxolo[4,5-g]quinolin-7-yl)methyl]-N'-(2-methyl-propyl)-N-(phenyl-methyl)thiourea (14), including down-regulation of oncogenic proteins and suppression of RNA incorporation into polysomes. Although we did not observe cellular activity with any of our modified m7GMP phosphate isostere compounds, we obtained X-ray crystallography structures of three such compounds in complex with eIF4E, 5'-deoxy-5'-(1,2-dioxo-3-hydroxycyclobut-3-en-4-yl)amino-N7-methyl-guanosine (4a), N7-3-chlorobenzyl-5'-deoxy-5'-(1,2-dioxo-3-hydroxy-cyclobut-3-en-4-yl)amino-guanosine (4f), and N7-benzyl-5'-deoxy-5'-(trifluoromethyl-sulfamoyl)guanosine (7a). Collectively, the data we present on structure-based design of eIF4E cap-binding inhibitors should facilitate the optimisation of such compounds as potential anticancer agents

Design of nucleotide-mimetic and non-nucleotide inhibitors of the translation initiation factor eIF4E: Synthesis, structural and functional characterisation.

Eukaryotic translation initiation factor 4E (eIF4E) is considered as the corner stone in the cap-dependent translation initiation machinery. Its role is to recruit mRNA to the ribosome through recognition of the 5'-terminal mRNA cap structure (m7GpppN, where G is guanosine, N is any nucleotide). eIF4E is implicated in cell transformation, tumourigenesis, and angiogenesis by facilitating translation of oncogenic mRNAs; it is thus regarded as an attractive anticancer drug target. We have used two approaches to design cap-binding inhibitors of eIF4E by modifying the N7-substituent of m7GMP and replacing the phosphate group with isosteres such as squaramides, sulfonamides, and tetrazoles, as well as by structure-based virtual screening aimed at identifying non-nucleotide cap-binding antagonists. Phosphomimetic nucleotide derivatives and highly ranking virtual hits were evaluated in a series of in vitro and cell-based assays to identify the first non-nucleotide eIF4E cap-binding inhibitor with activities in cell-based assays, N-[(5,6-dihydro-6-oxo-1,3-dioxolo[4,5-g]quinolin-7-yl)methyl]-N'-(2-methyl-propyl)-N-(phenyl-methyl)thiourea (14), including down-regulation of oncogenic proteins and suppression of RNA incorporation into polysomes. Although we did not observe cellular activity with any of our modified m7GMP phosphate isostere compounds, we obtained X-ray crystallography structures of three such compounds in complex with eIF4E, 5'-deoxy-5'-(1,2-dioxo-3-hydroxycyclobut-3-en-4-yl)amino-N7-methyl-guanosine (4a), N7-3-chlorobenzyl-5'-deoxy-5'-(1,2-dioxo-3-hydroxy-cyclobut-3-en-4-yl)amino-guanosine (4f), and N7-benzyl-5'-deoxy-5'-(trifluoromethyl-sulfamoyl)guanosine (7a). Collectively, the data we present on structure-based design of eIF4E cap-binding inhibitors should facilitate the optimisation of such compounds as potential anticancer agents

A method for increasing expressivity of Gene Ontology annotations using a compositional approach.

BACKGROUND: The Gene Ontology project integrates data about the function of gene products across a diverse range of organisms, allowing the transfer of knowledge from model organisms to humans, and enabling computational analyses for interpretation of high-throughput experimental and clinical data. The core data structure is the annotation, an association between a gene product and a term from one of the three ontologies comprising the GO. Historically, it has not been possible to provide additional information about the context of a GO term, such as the target gene or the location of a molecular function. This has limited the specificity of knowledge that can be expressed by GO annotations. RESULTS: The GO Consortium has introduced annotation extensions that enable manually curated GO annotations to capture additional contextual details. Extensions represent effector-target relationships such as localization dependencies, substrates of protein modifiers and regulation targets of signaling pathways and transcription factors as well as spatial and temporal aspects of processes such as cell or tissue type or developmental stage. We describe the content and structure of annotation extensions, provide examples, and summarize the current usage of annotation extensions. CONCLUSIONS: The additional contextual information captured by annotation extensions improves the utility of functional annotation by representing dependencies between annotations to terms in the different ontologies of GO, external ontologies, or an organism's gene products. These enhanced annotations can also support sophisticated queries and reasoning, and will provide curated, directional links between many gene products to support pathway and network reconstruction

Advantages of sous-vide cooked red cabbage: structural, nutritional and sensory aspects

The comparison between equivalent cooking treatments should be applied in a systematic way. This study proposes a methodical way to provide cooked samples with similar firmness using two cooking treatments. In addition, the structural, nutritional and sensory properties of red cabbage cooked with sous-vide treatment in comparison with traditional cooking (boiling water) was evaluated. Changes in texture, color and anthocyanin content were measured in samples cooked with traditional cooking (for different times) and sous-vide (modifying time and temperature according to a Response Surface Methodology). Consumers described sensory properties and preferences between samples. Cryoscanning electron microscopy was used to study the samples microstructure. The firmness of samples, traditionally cooked for 11 min and preferred by consumers, was achieved in samples cooked with sous-vide treatment by optimizing of the cooking conditions (87 C/50 min or 91 C/30 min). Sous-vide treatment was preferred to traditional cooking by consumers. Sous-vide samples were more purple, more aromatic and tastier than traditionally cooked ones. The loss of anthocyanins in traditional cooking was twice that in sous-vide samples. Micrographs from different treatments showed different degrees of cell wall damage. Sous-vide treatment could be recommended as a treatment for the catering industry providing better quality products.Author Iborra-Bernad was supported by the Generalitat Valenciana under FPI (Researcher Formation Program) grant. Author Tarrega was financially supported by the Juan de la Cierva programme.Iborra Bernad, MDC.; Tárrega, A.; García Segovia, P.; Martínez Monzó, J. (2014). Advantages of sous-vide cooked red cabbage: structural, nutritional and sensory aspects. Food Science and Technology. 56(2):451-460. doi:10.1016/j.lwt.2013.12.027S45146056