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

LMSD: LIPID MAPS structure database

The LIPID MAPS Structure Database (LMSD) is a relational database encompassing structures and annotations of biologically relevant lipids. Structures of lipids in the database come from four sources: (i) LIPID MAPS Consortium's core laboratories and partners; (ii) lipids identified by LIPID MAPS experiments; (iii) computationally generated structures for appropriate lipid classes; (iv) biologically relevant lipids manually curated from LIPID BANK, LIPIDAT and other public sources. All the lipid structures in LMSD are drawn in a consistent fashion. In addition to a classification-based retrieval of lipids, users can search LMSD using either text-based or structure-based search options. The text-based search implementation supports data retrieval by any combination of these data fields: LIPID MAPS ID, systematic or common name, mass, formula, category, main class, and subclass data fields. The structure-based search, in conjunction with optional data fields, provides the capability to perform a substructure search or exact match for the structure drawn by the user. Search results, in addition to structure and annotations, also include relevant links to external databases. The LMSD is publicly available a

How finicky is mitochondrial protein import?

Recently it was reported that artificial targeting signals or signals specific for organelles other than mitochondria could direct proteins into mitochondria. Here we discuss findings which suggest that specific steps of mitochondrial protein import can be bypassed. Non-specific targeting signals appear to use this bypass pathway. Such import occurs at very low rates under physiological conditions and therefore does not affect the uniqueness of mitochondrial protein composition

FastaValidator: an open-source Java library to parse and validate FASTA formatted sequences

Background: Advances in sequencing technologies challenge the efficient importing and validation of FASTA formatted sequence data which is still a prerequisite for most bioinformatic tools and pipelines. Comparative analysis of commonly used Bio*-frameworks (BioPerl, BioJava and Biopython) shows that their scalability and accuracy is hampered. Findings: FastaValidator represents a platform-independent, standardized, light-weight software library written in the Java programming language. It targets computer scientists and bioinformaticians writing software which needs to parse quickly and accurately large amounts of sequence data. For end-users FastaValidator includes an interactive out-of-the-box validation of FASTA formatted files, as well as a non-interactive mode designed for high-throughput validation in software pipelines. Conclusions: The accuracy and performance of the FastaValidator library qualifies it for large data sets such as those commonly produced by massive parallel (NGS) technologies. It offers scientists a fast, accurate and standardized method for parsing and validating FASTA formatted sequence data

Nucleotides: Structure and Properties

Nucleotides consist of a nitrogen-containing base, a five-carbon sugar, and one or more phosphate groups. Cells contain many types of nucleotides, which play a central role in a wide variety of cellular processes, including metabolic regulation and the storage and utilization of genetic information

α-L-Aspartylglycine Monohydrate

C6H10N2O5, H2O, orthorhombic, P212121, a = 4·844 (5), b = 9·916 (3), c = 18·070(4) Å, V = 868·05 Å3, Z = 4, Dc = 1·59, Dm (flotation in chloroform/iodoform) = l·60 (1) Mg m-3; R1 = 0·040, R2 = 0·033 for 1088 observations. The dipeptide crystallizes as a zwitterion with the main-chain carboxyl ionized and the side-chain amino group protonated. The overall dipeptide conformation is highly extended and the molecule is extensively hydrogen bonded

α-L-Glutamylglycine

C7H12N 2O5, orthorhombic, P212121, a = 5·525(5), b = 12·565(4), c = 13·211(6) Å, Z = 4, Dc = l·48, Dm (flotation in chloroform/ methylene chloride) = 1·48(1) Mg m-3, R1 = 0·039, R2 = 0·040 for 1172 observations. The dipeptide crystallizes as a zwitterion with the main-chain carboxyl ionized and the amino terminus protonated. The conformation of the peptide group is trans; the glutamyl side chain is extended, but the carboxy terminus is held by hydrogen bonding in a non-extended conformation with a torsional angle ΦGly = -74.1°

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

l-Alanylglycylhistamine dihydro­chloride

In the title compound {systematic name: 4-[2-({N-[(2S)-2-ammonio­propano­yl]glyc­yl}amino)­eth­yl]-1H-imidazol-3-ium dichloride}, C10H19N5O2 2+·2Cl−, the pseudo-tripeptide l-alanyl­glycyl­histamine is protonated at both the terminal amino group and the histidine N2 atom. The resulting positive charges are neutralized by two chloride anions. In the crystal, the organic cation adopts a twisted conformation about the CH2—CH2 bond of histamine and about the C—N bond in the main chain, stabilized by a short intra­molecular C—H⋯O contact. In the crystal, N+—H⋯O and N+—H⋯Cl− hydrogen bonds link the mol­ecules into infinite sheets parallel to the (100) plane. The stacking of these sheets along the a axis is supported by Namide—H⋯Cl− hydrogen bonds