Nucleoside and Nucleotide Nomenclature

Current nomenclature in the area of nucleosides, nucleotides, and nucleic acids comprises a mixture of (1) common names that have gained official recognition, (2) guidelines that have been derived and officially recommended by the International Union of Pure and Applied Chemistry (IUPAC)/International Union of Biochemistry and Molecular Biology (IUBMB), and (3) evolving usage that is derived by individual scientists and laboratories and subjected to peer review through publication. A working group was commissioned in 1998 by IUBMB to review guidelines for nucleotide (including oligonucleotide) nomenclature. As those guidelines are developed and made available, they will be referenced in future updates of this appendix. The main purpose of this appendix is to provide pertinent references that will direct the reader to the relevant guidelines or evolving nomenclature as described in the literature. When additional suggestions or guidance are appropriate, those comments are included as well.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/143595/1/cpnca01d.pd

A ceramide analogue (PDMP) inhibits glycolipid synthesis in fish embryos

Glycolipids were depleted from medaka embryos using 1-phenyl-2-decanoylamino-3-morpholino-1-propanol (PDMP), an inhibitor of glucosylceramide synthetase. Embryos cultured in the presence of 20 [mu]M PDMP exhibited a dramatic decline in glycolipid synthesis and cell surface expression. Metabolic labeling of glucosylceramide declined by 87% on Days 3-6 of development and 72% on Days 7-10 (hatching occurred on Day 10). In parallel, PDMP-treated embryos exhibited a striking loss of several tissue-specific glycolipid antigens, including 9-O-acetyl GD3 from brain and retina, GT3/ GQ1C from brain, neural tube, and retina, and sulfated glycolipid from skin and gut. Despite these changes in glycolipid expression, PDMP-treated embryos were fully viable with no evidence of developmental abnormality. PDMP appears to provide a useful tool for identifying glycolipid antigens in embryos and investigating their role in development.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/30233/1/0000627.pd

The derivation of the formyl-group oxygen of chlorophyll b in higher plants from molecular oxygen.

The mechanism of formation of the formyl group of chlorophyll b has long been obscure but, in this paper, the origin of the 7-formyl-group oxygen of chlorophyll b in higher plants was determined by greening etiolated maize leaves, excised from dark-grown plants, by illumination under white light in the presence of either H218O or 18O2 and examining the newly synthesized chlorophylls by mass spectroscopy. To minimize the possible loss of 18O label from the 7-formyl substituent by reversible formation of chlorophyll b-71-gem-diol (hydrate) with unlabelled water in the cell, the formyl group was reduced to a hydroxymethyl group during extraction with methanol containing NaBH4: chlorophyll a remained unchanged during this rapid reductive extraction process. Mass spectra of chlorophyll a and [7-hydroxymethyl]-chlorophyll b extracted from leaves greened in the presence of either H218O or 18O2 revealed that 18O was incorporated only from molecular oxygen but into both chlorophylls: the mass spectra were consistent with molecular oxygen providing an oxygen atom not only for incorporation into the 7-formyl group of chlorophyll b but also for the well-documented incorporation into the 131-oxo group of both chlorophylls a and b [see Walker, C. J., Mansfield, K. E., Smith, K. M. & Castelfranco, P. A. (1989) Biochem. J. 257, 599–602]. The incorporation of isotope led to as much as 77% enrichment of the 131-oxo group of chlorophyll a: assuming identical incorporation into the 131 oxygen of chlorophyll b, then enrichment of the 7-formyl oxygen was as much as 93%. Isotope dilution by re-incorporation of photosynthetically produced oxygen from unlabelled water was negligible as shown by a greening experiment in the presence of 3-(3,4-dichlorophenyl)-1,1-dimethylurea. The high enrichment using 18O2, and the absence of labelling by H218O, unequivocally demonstrates that molecular oxygen is the sole precursor of the 7-formyl oxygen of chlorophyll b in higher plants and strongly suggests a single pathway for the formation of the chlorophyll b formyl group involving the participation of an oxygenase-type enzyme

Simple synthesis of 32P-labelled inositol hexakisphosphates for study of phosphate transformations

In many soils inositol hexakisphosphate in its various forms is as abundant as inorganic phosphate. The organismal and geochemical processes that exchange phosphate between inositol hexakisphosphate and other pools of soil phosphate are poorly defined, as are the organisms and enzymes involved. We rationalized that simple enzymic synthesis of inositol hexakisphosphate labeled with 32P would greatly enable study of transformation of soil inositol phosphates when combined with robust HPLC separations of different inositol phosphates

Bioactive characterization of Persea americana Mill. by-products: A rich source of inherent antioxidants

[EN] Avocado (Persea americana Mill.) is a worldwide consumed fruit, with great interest for cosmetic and pharmaceutical industries; however, 30% of avocado fruits are bio-wastes (peels and kernels), converting them into a potential source of bioactive compounds, such as phenolic compounds. Therefore, the hydroethanolic extracts of peels and kernels of Persea america Mill. var. Hass were analysed regarding their individual phenolic profile by HPLC-DAD/ESI-MS and correlated with their antioxidant, antimicrobial and cytotoxic activities. Avocado by-products presented a very distinct phenolic profile, presenting higher concentration in peels (227.9 mg/g of extract for total phenolic content), mainly in (epi)catechin derivatives (175 mg/g of extract), followed by chlorogenic derivatives (42.9 mg/g of extract). In this study hydrophilic and lipophilic antioxidant assays were performed together for the first time in P. americana by-products, and although kernels showed a great antioxidant potential (EC50 values ranging from 18.1 to 276 mu g/mL), peels presented the highest potential (EC50 ranging from 11.7 to 152 mu g/mL), mainly due to the presence of phenolic compounds, and an overall better performance in the antibacterial assays. Further studies needs to be conducted to better understand the correlation between the presence of phenolic compounds and bioactivities, however, the main objective is to implement these biocompounds in different products and industries, due to results obtained, P. americana peels could be a great alternative in the substitution of synthetic antioxidants.The authors are grateful to the Foundation for Science and Technology(FCT, Portugal) and FEDER under Program PT2020 for financial support to CIMO (UID/AGR/00690/2013) and L. Barros contract. The authors would like to thank the Interreg Espana-Portugal for financial support through the project 0377_Iberphenol_6_E. B. Melgar thanks CONACyT for his grant (No. 329930). The authors are also grateful to the Serbian Ministry of Education, Science and Technological Development, grant number 173032 for financial support.Melgar-Castañeda, B.; Dias, MI.; Ciric, A.; Sokovic, M.; Garcia-Castello, EM.; Rodríguez López, AD.; Barros, L.... (2018). Bioactive characterization of Persea americana Mill. by-products: A rich source of inherent antioxidants. Industrial Crops and Products. 111:212-218. https://doi.org/10.1016/j.indcrop.2017.10.024S21221811

Influence of naturally-occurring 5′-pyrophosphate-linked substituents on the binding of adenylic inhibitors to ribonuclease a: An X-ray crystallographic study

Ribonuclease A is the archetype of a functionally diverse superfamily of vertebrate-specific ribonucleases. Inhibitors of its action have potential use in the elucidation of the in vivo roles of these enzymes and in the treatment of pathologies associated therewith. Derivatives of adenosine 5′-pyrophosphate are the most potent nucleotide-based inhibitors known. Here, we use X-ray crystallography to visualize the binding of four naturally-occurring derivatives that contain 5′-pyrophosphate-linked extensions. 5′-ATP binds with the adenine occupying the B2 subsite in the manner of an RNA substrate but with the γ-phosphate at the P1 subsite. Diadenosine triphosphate (Ap3A) binds with the adenine in syn conformation, the β-phosphate as the principal P1 subsite ligand and without order beyond the γ-phosphate. NADPH and NADP+ bind with the adenine stacked against an alternative rotamer of His119, the 2′-phosphate at the P1 subsite, and without order beyond the 5′-α-phosphate. We also present the structure of the complex formed with pyrophosphate ion. The structural data enable existing kinetic data on the binding of these compounds to a variety of ribonucleases to be rationalized and suggest that as the complexity of the 5′-linked extension increases, the need to avoid unfavorable contacts places limitations on the number of possible binding modes. © 2009 Wiley Periodicals, Inc. Biopolymers 91: 995–1008, 2009

Structural analysis of the Ss sialoglycoprotein specific for Henshaw blood group from human erythrocyte membranes

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/66122/1/j.1432-1033.1984.tb08155.x.pd