Biotext: Exploiting Biological-like format for text mining

The large amount of existing textual data justifies the development of new text mining tools. Bioinformatics tools can be brought to Text Mining, increasing the arsenal of resources. Here, we present Biotext, a package of strategies for converting natural language text into biological-like information data, providing a general protocol with standardized functions, allowing to share, encode and decode textual data for amino acid data. The package was used to encode the arbitrary information present in the headings of the biological sequences found in a BLAST survey. The protocol implemented in this study consists of 12 steps, which can be easily executed and/ or changed by the user, depending on the study area. Biotext empowers user to perform text mining using bioinformatics tools. Biotext is Freely available at https://pypi.org/project/biotext/ (Python package) and https://sourceforge.net/projects/biotext-tools/files/AMINOcode_GUI/ (Standalone tool).

First sequencing of ancient coral skeletal proteins

Here we report the first recovery, sequencing, and identification of fossil biomineral proteins from a Pleistocene fossil invertebrate, the stony coral Orbicella annularis. This fossil retains total hydrolysable amino acids of a roughly similar composition to extracts from modern O. annularis skeletons, with the amino acid data rich in Asx (Asp + Asn) and Glx (Glu + Gln) typical of invertebrate skeletal proteins. It also retains several proteins, including a highly acidic protein, also known from modern coral skeletal proteomes that we sequenced by LC–MS/MS over multiple trials in the best-preserved fossil coral specimen. A combination of degradation or amino acid racemization inhibition of trypsin digestion appears to limit greater recovery. Nevertheless, our workflow determines optimal samples for effective sequencing of fossil coral proteins, allowing comparison of modern and fossil invertebrate protein sequences, and will likely lead to further improvements of the methods. Sequencing of endogenous organic molecules in fossil invertebrate biominerals provides an ancient record of composition, potentially clarifying evolutionary changes and biotic responses to paleoenvironments.

Determination of Whey Protein Content in Bovine Milk-Based Infant Formula Finished Products Using Amino Acids Calculation Method: AOAC First Action 2012.08

A method for the calculation of the whey protein fraction was developed for milk-based infant formula products based upon amino acid ratio calculated from asparagine/aspartic acid, alanine, proline, and phenylalanine amino acid data. Historical and literature amino acid data were combined to establish the reference amino acid values used in the validation study. This method has been evaluated for accuracy versus label claim for 12 products, with results from 90 to 107.5% of label claim and an overall average of 98.7%. Repeatability and intermediate precision were determined over 4 different days. Repeatability results were 4.75, 2.06, 4.18, and 2.44% RSD, respectively, with an overall intermediate precision of 3.68% RSD. Since the amino acid profile of infant formula finished products depends on the amino acid profile of ingredients used, the applicability of the method needs to be confirmed for specific types of infant formula, for which data will be gathered. Additional reference material data are being gathered for better estimation of milk and whey reference values, which are based on being normalized to total amino acid content, during the two year AOAC INTERNATIONAL Official Methods of Analysis method approval process.

The complete mitochondrial genome sequence of Euphausia pacifica (Malacostraca: Euphausiacea) reveals a novel gene order and unusual tandem repeats

Euphausiid krill are dominant organisms in the zooplankton population and play a central role in marine ecosystems. Euphausia pacifica (Malacostraca: Euphausiacea) is one of the most important and dominant crustaceans in the North Pacific Ocean. In this paper, we described the gene content, organization, and codon usage of the E. pacifica mitochondrial genome. The mitochondrial genome of E. pacifica is 16 898 bp in length and contains a standard set of 13 protein-coding genes, 2 ribosomal RNA genes, and 22 transfer RNA genes. Translocation of three transfer RNAs (trnL1, trnL2, and trnW) was found in the E. pacifica mitochondrial genome when comparing with the pancrustacean ground pattern. The rate of Ka/Ks in 13 protein-coding genes among three krill is much less than 1, which indicates a strong purifying selection within this group. The largest noncoding region in the E. pacifica mitochondrial genome contains one section with tandem repeats (4.7 × 154 bp), which are the largest tandem repeats found in malacostracan mitochondrial genomes so far. All analyses based on nucleotide and amino acid data strongly support the monophyly of Stomatopoda, Penaeidae, Caridea, Brachyura, and Euphausiacea. The Bayesian analysis of nucleotide and amino acid datasets strongly supports the close relationship between Euphausiacea and Decapoda, which confirms traditional findings. The maximum likelihood analysis based on amino acid data strongly supports the close relationship between Euphausiacea and Penaeidae, which destroys the monophyly of Decapoda.

Biological identifications through DNA barcodes: the case of the Crustacea

The ability of a 650 base pair section of the mitochondrial cytochrome c oxidase I (COI) gene to provide species-level identifications has been demonstrated for large taxonomic assemblages of animals such as insects, birds, and fishes, but not for the subphylum Crustacea, one of the most diverse groups of arthropods. In this study, we test the ability of COI to provide identifications in this group, examining two disparate levels in the taxonomic hierarchy — orders and species. The first phase of our study involved the development of a sequence profile for 23 dominant crustacean orders, based upon the analysis of 150 species, each belonging to a different family. The COI amino acid data placed these taxa into cohesive assemblages whose membership coincided with currently accepted boundaries at the order, superorder, and subclass levels. Species-level resolution was subsequently examined in an assemblage of Decapoda and in representatives of the genera Daphnia (Cladocera) and Gammarus (Amphipoda). These studies revealed that levels of nucleotide sequence divergence were from 19 to 48 times greater between congeneric species than between individuals of a species. We conclude that sequence variation in the COI barcode region will be very effective for discriminating species of Crustacea.

Postprandial body protein synthesis and amino acid catabolism measured with leucine and phenylalanine-tyrosine tracers

Whether phenylalanine-tyrosine (Phe-Tyr) tracers yield estimates of postprandial protein synthesis comparable to those of the widely used leucine (Leu) tracer is unclear. We measured Leu oxidation (Ox), Phe hydroxylation (Hy), and their disposal into whole body protein synthesis before and after the administration of a mixed meal (62 kJ/kg body wt, 22% of energy as protein), over 4 h in healthy subjects. Both plasma and intracellular precursor pools were used. The amino acid data were extrapolated to body protein by assuming a fixed ratio of Leu to Phe in the proteins. In the postabsorptive state, whole body protein synthesis (expressed as mg · kg−1 · min−1) was similar between Leu and Phe-Tyr tracers irrespective of the precursor pool used. After the meal, Leu Ox, Phe Hy, and body protein synthesis increased ( P ≤ 0.01 vs. basal). With the use of intracellular precursor pools, the increase of protein synthesis with Phe-Tyr (+0.51 ±0.21 mg · kg−1 · min−1) and Leu tracers (+0.57 ± 0.14) were similar ( P = not significant). In contrast, with plasma pools the increase of protein synthesis was more than twofold greater with Phe-Tyr (+1.17 ± 0.19 mg · kg−1 · min−1) than that with Leu (0.50 ± 0.13 mg · kg−1 · min−1, P < 0.01). Direct correlations were found between Leu and Ox [using both plasma and intracellular pools ( r ≤ 0.65, P ≤ 0.01)] but not between Phe and either plasma or intracellular Hy. In conclusion, 1) Phe-Tyr and Leu tracers yield comparable estimates of body protein synthesis postprandially, provided that intracellular precursor pools are used; 2) both Leu Ox and Phe Hy are stimulated by a mixed meal; 3) Phe does not correlate with Hy, which might be better related to the (unknown) portal Phe.