Effect of galactomannan hydrocolloids on gelatinization and retrogradation of tapioca and corn starch

The aim of the present study was to investigate the effect of galactomannan hydrocolloids (guar gum and locust bean gum) on gelatinization and retrogradation of tapioca and corn starch. Differential scanning calorimetry (DSC) was used to characterize the behaviour of tapioca and corn starch with and without additives. Results showed that guar gum and locust bean gum retarded the retrogradation of tapioca and corn starch at both investigated temperatures (4 and 25 °C). Guar gum retarded retrogradation of tapioca starch more than locust bean gum, on the other hand, locust bean gum had a greater effect on reduction of the recrystallization of corn starch. Temperatures of gelatinization did not vary significantly in starch-hydrocolloid systems. Additions of galactomannan hydrocolloids caused a decrease in gelatinization enthalpy of both starches

Speeding up all-against-all protein comparisons while maintaining sensitivity by considering subsequence-level homology.

Orthology inference and other sequence analyses across multiple genomes typically start by performing exhaustive pairwise sequence comparisons, a process referred to as "all-against-all". As this process scales quadratically in terms of the number of sequences analysed, this step can become a bottleneck, thus limiting the number of genomes that can be simultaneously analysed. Here, we explored ways of speeding-up the all-against-all step while maintaining its sensitivity. By exploiting the transitivity of homology and, crucially, ensuring that homology is defined in terms of consistent protein subsequences, our proof-of-concept resulted in a 4× speedup while recovering >99.6% of all homologs identified by the full all-against-all procedure on empirical sequences sets. In comparison, state-of-the-art k-mer approaches are orders of magnitude faster but only recover 3-14% of all homologous pairs. We also outline ideas to further improve the speed and recall of the new approach. An open source implementation is provided as part of the OMA standalone software at http://omabrowser.org/standalone

Phylogenetic approaches to identifying fragments of the same gene, with application to the wheat genome.

As the time and cost of sequencing decrease, the number of available genomes and transcriptomes rapidly increases. Yet the quality of the assemblies and the gene annotations varies considerably and often remains poor, affecting downstream analyses. This is particularly true when fragments of the same gene are annotated as distinct genes, which may cause them to be mistaken as paralogs. In this study, we introduce two novel phylogenetic tests to infer non-overlapping or partially overlapping genes that are in fact parts of the same gene. One approach collapses branches with low bootstrap support and the other computes a likelihood ratio test. We extensively validated these methods by (i) introducing and recovering fragmentation on the bread wheat, Triticum aestivum cv. Chinese Spring, chromosome 3B; (ii) by applying the methods to the low-quality 3B assembly and validating predictions against the high-quality 3B assembly; and (iii) by comparing the performance of the proposed methods to the performance of existing methods, namely Ensembl Compara and ESPRIT. Application of this combination to a draft shotgun assembly of the entire bread wheat genome revealed 1221 pairs of genes that are highly likely to be fragments of the same gene. Our approach demonstrates the power of fine-grained evolutionary inferences across multiple species to improving genome assemblies and annotations. An open source software tool is available at https://github.com/DessimozLab/esprit2. Supplementary data are available at Bioinformatics online

Effect of galactomannan hydrocolloids on gelatinization and retrogradation of tapioca and corn starch

original scientific paper Summary The aim of the present study was to investigate the effect of galactomannan hydrocolloids (guar gum and locust bean gum) on gelatinization and retrogradation of tapioca and corn starch. Differential scanning calorimetry (DSC) was used to characterize the behaviour of tapioca and corn starch with and without additives. Results showed that guar gum and locust bean gum retarded the retrogradation of tapioca and corn starch at both investigated temperatures (4 and 25 °C). Guar gum retarded retrogradation of tapioca starch more than locust bean gum, on the other hand, locust bean gum had a greater effect on reduction of the recrystallization of corn starch. Temperatures of gelatinization did not vary significantly in starch-hydrocolloid systems. Additions of galactomannan hydrocolloids caused a decrease in gelatinization enthalpy of both starches

Anthocyanins, phenols, and antioxidant activity in blackberry juice with plant extracts addition during heating

In this work the influence of addition of different plant extracts (olive leaf, green tea, pine bark PE 95%, pine bark PE 5:1, red wine PE 30%, red wine PE 4:1, and bioflavonoids) to blackberry juice during heating (at 30, 50, 70 and 90 °C) on the anthocyanin and phenol contents, polymeric colour, and antioxidant activity was investigated. Also, reaction rate constant, half-lives of degradation, and activation energy were calculated. Control sample was juice without addition of extracts. The highest anthocyanin content at 30 °C was in samples with the addition of olive leaf and green tea. At 90 °C the highest anthocyanin content was measured in samples with the addition of extract of red wine and bioflavonoides. Samples supplemented with the extracts had much higher antioxidant activity in comparison to the control sample. Results showed that at 90 °C the sample with green tea supplementation had the lowest reaction rate constant and the highest half-life. Activation energy ranged from 29 to 44 kJ mol−1

The OMA orthology database in 2015: function predictions, better plant support, synteny view and other improvements

International audienceThe Orthologous Matrix (OMA) project is a method and associated database inferring evolutionary relationships amongst currently 1706 complete proteomes (i.e. the protein sequence associated for every protein-coding gene in all genomes). In this update article, we present six major new developments in OMA: (i) a new web interface; (ii) Gene Ontology function predictions as part of the OMA pipeline; (iii) better support for plant genomes and in particular homeologs in the wheat genome; (iv) a new synteny viewer providing the genomic context of orthologs; (v) statically computed hierarchical orthologous groups subsets downloadable in OrthoXML format; and (vi) possibility to export parts of the all-against-all computations and to combine them with custom data for 'client-side' orthology prediction. OMA can be accessed through the OMA Browser and various programmatic interfaces at http://omabrowser.org