Improved ontology for eukaryotic single-exon coding sequences in biological databases

Indexación: Scopus.Efficient extraction of knowledge from biological data requires the development of structured vocabularies to unambiguously define biological terms. This paper proposes descriptions and definitions to disambiguate the term 'single-exon gene'. Eukaryotic Single-Exon Genes (SEGs) have been defined as genes that do not have introns in their protein coding sequences. They have been studied not only to determine their origin and evolution but also because their expression has been linked to several types of human cancer and neurological/developmental disorders and many exhibit tissue-specific transcription. Unfortunately, the term 'SEGs' is rife with ambiguity, leading to biological misinterpretations. In the classic definition, no distinction is made between SEGs that harbor introns in their untranslated regions (UTRs) versus those without. This distinction is important to make because the presence of introns in UTRs affects transcriptional regulation and post-transcriptional processing of the mRNA. In addition, recent whole-transcriptome shotgun sequencing has led to the discovery of many examples of single-exon mRNAs that arise from alternative splicing of multi-exon genes, these single-exon isoforms are being confused with SEGs despite their clearly different origin. The increasing expansion of RNA-seq datasets makes it imperative to distinguish the different SEG types before annotation errors become indelibly propagated in biological databases. This paper develops a structured vocabulary for their disambiguation, allowing a major reassessment of their evolutionary trajectories, regulation, RNA processing and transport, and provides the opportunity to improve the detection of gene associations with disorders including cancers, neurological and developmental diseases. © The Author(s) 2018. Published by Oxford University Press.https://academic.oup.com/database/article/doi/10.1093/database/bay089/509943

Extraction of silymarin compounds from milk thistle (Silybum marianum) seed using hot, liquid water as the solvent

High-value specialty chemicals are usually obtained from natural products by extracting with generally regarded as safe (GRAS) solvents. Because organic solvents are quite often used, high operating and disposal costs occur. When compared to traditional solvents, water is an interesting alternative because of its low operating and disposal costs. Milk thistle contains compounds (taxifolin, silychristin, silydianin, silybinin A, and silybinin B) that display hepatoxic protection properties. This paper examines the batch extraction of silymarin compounds from milk thistle seed meal in 50°C, 70°C, 85°C and 100°C water as a function of time. For taxifolin, silychristin, silybinin A, and silybinin B, extraction with 100°C water resulted in the highest yields. After 210 min of extraction at 100°C, the yield of taxifolin was 1.2 mg/g of seed while the yields of silychristin, silybinin A, and silybinin B were 5.0, 1.8 and 3.3 mg/g of seed, respectively. The ratios of the extracted compounds, and particularly the ratios at long extraction times, showed that the more polar compounds (taxifolin and silychristin) were preferentially extracted at 85°C, while the less polar silybinin was preferentially extracted at 100°C

Dietitians Plan for Future

Miss Nell C. Clausen, Dietitian, Milwaukee Children\u27s Hospital, and President of the American Dietetic Association, expresses her vision of the future of dietetics in these excerpts of her report to the dietitians\u27 meeting at the Tri-State Hospital Assembly meeting in Chicago

The Privilege of Speech in a Pleasantly Authoritarian Country

Giving credence to Alexis de Tocqueville\u27s argument that in democratic societies the love of equality is greater than the love of freedom is a recently emerging trend among Western nations to legally proscribe speech critical of homosexuality. Such laws, in various forms, now exist in a large and growing minority of countries in Europe and North America. The goal of these laws is much grander than preventing discrimination against homosexuals; rather, the objective is seemingly to promote the social acceptance of gay and lesbian lifestyles. These laws provide for civil remedies and in some instances even criminal sanctions for speech considered offensive or degrading to homosexuals, and constitutional-rights objections to them--on the basis of speech and religious liberty guarantees--have been largely unavailing. Thus, achieving the social equality of homosexuals--conceived in sweeping terms--has, in many Western countries, outstripped legal protections for speech and religious freedoms. In this Note, the Author examines Canada\u27s extensive legal regime proscribing speech critical of homosexuality. The Author illustrates how the Canadian judiciary\u27s zeal for promoting the social acceptance of homosexuality has greatly diminished fundamental legal protections for open discourse and religious liberty

Quantum state conversion by cross-Kerr interaction

A generalized Mach-Zehnder-type interferometer equipped with cross-Kerr elements is proposed to convert N-photon truncated single-mode quantum states into (N+1)-mode single-photon states, which are suitable for further state manipulation by means of beam splitter arrays and ON/OFF-detections, and vice versa. Applications to the realization of unitary and non-unitary transformations, quantum state reconstruction, and quantum telemanipulation are studied.Comment: 22 pages, 4 figures, using a4.st

The bend stiffness of S-DNA

We formulate and solve a two-state model for the elasticity of nicked, double-stranded DNA that borrows features from both the Worm Like Chain and the Bragg--Zimm model. Our model is computationally simple, and gives an excellent fit to recent experimental data through the entire overstretching transition. The fit gives the first value for the bending stiffness of the overstretched state as about 10 nm*kbt, a value quite different from either B-form or single-stranded DNA.Comment: 7 pages, 1 figur

Two-color nonlinear localized photonic modes

We analyze second-harmonic generation (SHG) at a thin effectively quadratic nonlinear interface between two linear optical media. We predict multistability of SHG for both plane and localized waves, and also describe two-color localized photonic modes composed of a fundamental wave and its second harmonic coupled together by parametric interaction at the interface.Comment: 4 pages, 5 figures (updated references