A proposed nomenclature for bile acids.

A proposal is made for a system of nomenclature of the more common unconjugated and conjugated bile acids. Acceptable trivial names for bile acids are tabulated, and guidelines are proposed for using these existing trivial names as roots to create acceptable semi-systematic names for other bile acids, as well as for new natural bile acids that will be discovered in the future. The term alpha-hyocholic is recommended to replace hyocholic, and beta-hyocholic to replace omega-muricholic. The term murideoxycholic acid is recommended for 3 alpha,6 beta-dihydroxy-5 beta-cholan-24-oic acid. Proposals are also made for bile acids with epimeric hydroxy groups, for unsaturated bile acids, and for bile acids with oxo- and/or hydroxy-oxo- substituents on the nucleus and/or on the side chain. For conjugated bile acids, the term "aminoacyl amidates" is recommended to replace "amidates" for bile acids conjugated in N-acyl linkage with amino acids. Nomenclature for other types of conjugates (sulfates, glucuronides, glucosides) is included as well as abbreviations. It is recommended that the historic tradition of naming a newly discovered bile acid after the species from which it was isolated be abandoned, and that in the future such a bile acid should be named using the principles contained in this paper.     

Chloroplast and mitochondrial proteases in Arabidopsis. A proposed nomenclature

The identity and scope of chloroplast and mitochondrial proteases in higher plants has only started to become apparent in recent years. Biochemical and molecular studies suggested the existence of Clp, FtsH, and DegP proteases in chloroplasts, and a Lon protease in mitochondria, although currently the full extent of their role in organellar biogenesis and function remains poorly understood. Rapidly accumulating DNA sequence data, especially from Arabidopsis, has revealed that these proteolytic enzymes are found in plant cells in multiple isomeric forms. As a consequence, a systematic approach was taken to catalog all these isomers, to predict their intracellular location and putative processing sites, and to propose a standard nomenclature to avoid confusion and facilitate scientific communication. For the Clp protease most of the ClpP isomers are found in chloroplasts, whereas one is mitochondrial. Of the ATPase subunits, the one ClpD and two ClpC isomers are located in chloroplasts, whereas both ClpX isomers are present in mitochondria. Isomers of the Lon protease are predicted in both compartments, as are the different forms of FtsH protease. DegP, the least characterized protease in plant cells, has the most number of isomers and they are predicted to localize in several cell compartments. These predictions, along with the proposed nomenclature, will serve as a framework for future studies of all four families of proteases and their individual isomers.     

Conserved main-chain peptide distortions: a proposed role for Ile203 in catalysis by dihydrodipicolinate synthase

In recent years, dihydrodipicolinate synthase (DHDPS, E.C. 4.2.1.52) has received considerable attention from a mechanistic and structural viewpoint. DHDPS catalyzes the reaction of (S)-aspartate-beta-semialdehyde with pyruvate, which is bound via a Schiff base to a conserved active-site lysine (Lys161 in the enzyme from Escherichia coli). To probe the mechanism of DHDPS, we have studied the inhibition of E. coli DHDPS by the substrate analog, beta-hydroxypyruvate. The K (i) was determined to be 0.21 (+/-0.02) mM, similar to that of the allosteric inhibitor, (S)-lysine, and beta-hydroxypyruvate was observed to cause time-dependent inhibition. The inhibitory reaction with beta-hydroxypyruvate could be qualitatively followed by mass spectrometry, which showed initial noncovalent adduct formation, followed by the slow formation of the covalent adduct. It is unclear whether beta-hydroxypyruvate plays a role in regulating the biosynthesis of meso-diaminopimelate and (S)-lysine in E. coli, although we note that it is present in vivo. The crystal structure of DHDPS complexed with beta-hydroxypyruvate was solved. The active site clearly showed the presence of the inhibitor covalently bound to the Lys161. Interestingly, the hydroxyl group of beta-hydroxypyruvate was hydrogen-bonded to the main-chain carbonyl of Ile203. This provides insight into the possible catalytic role played by this peptide unit, which has a highly strained torsion angle (omega approximately 201 degrees ). A survey of the known DHDPS structures from other organisms shows this distortion to be a highly conserved feature of the DHDPS active site, and we propose that this peptide unit plays a critical role in catalysis.     

Mitogen-activated protein kinase cascades in plants: a new nomenclature

Mitogen-activated protein kinase (MAPK) cascades are universal signal transduction modules in eukaryotes, including yeasts, animals and plants. These protein phosphorylation cascades link extracellular stimuli to a wide range of cellular responses. In plants, MAPK cascades are involved in responses to various biotic and abiotic stresses, hormones, cell division and developmental processes. Completion of the Arabidopsis genome-sequencing project has revealed the existence of 20 MAPKs, 10 MAPK kinases and 60 MAPK kinase kinases. Here, we propose a simplified nomenclature for Arabidopsis MAPKs and MAPK kinases that might also serve as a basis for standard annotation of these gene families in all plants.     

Beta-turns in serine-containing linear and cyclic models

Tetrapeptides, Cbz-Gly-X-Y-Gly-OSt ( 1 – 4 )—as well as cyclic systems, cyclo[NH-(CH₂)_n-CO-Gly-Ser(OX)-Ser(OX)-Gly] ( 5 and 6 ; n = 4 and 2, X = Bu^t or H), have been synthesized in order to compare the CD spectrum of linear and cyclic β-turn models containing either a protected or a free hydroxyl of the serine residue. In extremely dilute cyclohexane solution the linear models Cbz-Gly-Ser-Y-Gly-OSt ( 1 – 3a ) show class B spectra with very strong positive bands, contrary to other members of the series. Based on 200-MHz ¹H nuclear overhauser enhancement and Fourier transform ir studies, Cbz-Gly-Ser-Ser(OBu^t)-Gly-OSt ( 3a ) in dilute chloroform solution assumes a distorted type II β-turn conformation fixed by an extended system of intramolecular H bonds. As evidenced by ¹H-nmr and FT-IR experiments, the cyclic model cyclo[NH-(CH₂)₄-CO-Gly-Ser(OBu^t)- Ser(OBu^t)-Gly] ( 5a ) in a 1 : 1 mixture of (CD₃)₂SO-CDCl₃ is also characterized by a type II β-turn encompassing the Ser³(OBu^t)-Gly⁴ sequence. In water, a class B pattern was measured for this model, in good agreement with theoretical and experimental studies that show that type II β-turns are generally characterized by class B spectra. In the protected and free OH cyclic models, cyclo[NH-(CH₂)₂-CO-Gly-Ser(OX)-Ser(OX)-Gly] ( 5b and 6b , X = Bu^t or H) distortions of the peptide backbone due to the loss of two CH₂ groups result in the appearance of CD spectra characterized by a strong negative band near 200 nm, interpreted as a sign of the lack of β-turn structures in these models. This observation, together with other CD data discussed in this paper, clearly show that the CD of serine-containing β-turn sequences strongly depends on long-range backbone and local side-chain interactions.     

Towards standardization of canine STRs: a proposed nomenclature for six markers from the ISAG comparison-test panel

Eight short tandem repeat markers included in the International Society for Animal Genetics panel of 24 loci investigated in canine comparison tests were analysed in a sample of pure-breed dogs, with the purpose of defining an allele nomenclature based on the number of repeats. A regression analysis of the raw data produced by the sequencer, coupled with the direct sequencing of selected alleles, allowed us to propose a system of nomenclature for six of the eight loci (four di-nucleotidic: AHT121, AHTh137, REN169018 and REN64E19, and two tetra-nucleotidic: FH2001 and FH2328). The remaining two loci (INU055 and FH2848) showed a pattern of fragments that did not resolve in a simple allele series. This work may be useful to establish a basis for comparing data across different laboratories for a set of validated canine markers, which can be used in population genetics, forensics and other analyses.     

Immunological templates: a new model and proposed mechanism of immunogenicity

Immunogenicity of an antigen is dependent both on possession of antigenic determinants, including the haptenic portion(s) of the antigen, and binding groups. The binding groups are necessary for processing of the antigen to occur whereas the antigenic determinants specify the antibody structure. Some arrangements of these antigenic determinants in relation to the binding groups are proposed, as well as the relationships of these ligands during processing on a cellular processing template to form an antibody RNA. The antibody RNA is manufactured by a unique mode of inverse translation.     

Pharmacogenetically hazardous drugs: a proposed new scoring method.

Similar doses of a drug given to different individuals can result in widely disparate plasma concentrations and hence effects. Beside intraindividual differences also inter-ethnic differences of drug response must be taken into consideration. Both inter-individual and inter-ethnic variations of drug response are mostly related to genetic factors (polymorphism) involved in drug metabolism and kinetics. The farmacogenetic disorders involved clinically result in pharmacogenetic side effects. In order to avoid pharmacogenetic side effects, beside phenotyping of the patients, selection of drugs subjected to different pharmacogenetic disorders may be of great clinical importance. Therefore, a scoring method was carried out for the selection of pharmacogenetically hazardous drugs. With regard to both genetic and environmental factors influencing the drug response, 140 suspicious drugs were studied and classified with the method. Eighteen was the maximum point value for genetic and 12 for contributing factors involved, so 30 was the maximum point number in each drug studied. Out of 140 substances 50 drugs (qualified with 20 points or more) proved to be hazardous in different pharmacogenetic disorders, among them several widely used agents, e.g. Diazepam, Isoniazid, Phenytoin, Warfarin, Quinidine, Tolbutamide, etc. The article sums up the findings in a Table and comments them. This scoring method may be useful in drug safety and preventive medicine.     

Osmium tetroxide: a new probe for site-specific distortions in supercoiled DNAs.

Supercoiled plasmids Col E1 and cDm 506 (a Col E1 derivative carrying the D. melanogaster histone gene repeat) were treated with OsO4 in presence of pyridine and the reaction products were analyzed using different approaches. Gel electrophoresis showed that OsO4 binding to supercoiled DNA induced its relaxation without nicking. The amount of osmium bound to DNA (as determined electrochemically) increased with the extent of DNA relaxation. As a result of osmium modification of supercoiled cDm 506, a single denaturation "bubble" was observed in the electron microscope. Mapping of the osmium binding site by S1 nuclease cleavage followed by restriction enzyme digestion has revealed one major site in the intergenic spacer between the H1 and H3 histone genes of D. melanogaster. This site differs from the site cleaved by S1 nuclease in supercoiled DNA in the absence of osmium.     

A proposed nomenclature for antimicrobial peptides from frogs of the genus Leptodactylus

It is proposed that the current nomenclature by which individual antimicrobial peptides from the skins of frogs belonging to the genus Leptodactylus are named from the species of frog from which they were isolated should be replaced by one that emphasizes the fact that these peptides are evolutionarily related. As the ocellatins from Leptodactylus ocellatus were the first such peptides to be characterized, it is suggested that all orthologous peptides should be described as "ocellatins". Consistent with accepted terminology for other families of antimicrobial peptides, the upper case initial letter of the species is used to indicate their origin and isoforms are designated by numbers. When two species begin with the same initial letter, a second distinguishing letter shall be employed. Thus, the terms ocellatin-1, -2, -3, and -4 are retained for the parent peptides. Fallaxin is replaced by ocellatin-F1, pentadactylin by ocellatin-P1, laticeptin by ocellatin-L1, syphaxin by ocellatin-S1, and the paralogs from L. validus are termed ocellatin-V1, -V2, and -V3.     

Towards a new classification of Leguminosae: Naming clades using non-Linnaean phylogenetic nomenclature

The past three decades of research have greatly advanced our understanding of phylogenetic relationships in the family Leguminosae. It has become clear in recent years that our classification system is in need of significant updating if it is to reflect our current understanding of the phylogeny of the family and facilitate effective communication of that knowledge. The goal of this paper is to suggest a set of guidelines for formally defining and naming clades, which draws on many of the recommendations embodied in the draft International Code of Phylogenetic Nomenclature or “PhyloCode”. I provide specific examples of phylogenetic nomenclature applied to several well recognized and well-supported, informally named papilionoid clades to serve as a model for standardizing legume clade names by the legume community in the future. For the most part the clades named here are below subfamily and above tribal ranks in the Linnaean system. It is my contention that a new Linnaean classification, designed to reflect phylogeny, and a clade-based system of phylogenetic nomenclature are mutually complementary approaches to achieving a new classification of the legume family.     

Introduction of a nomenclature: Leukotrienes

The structure of a slow reacting substance (SRS) from mouse mastocytoma cells was recently reported (Murphy, R.C., Hammarström, S. and Samuelsson, B. (1979) Proc. Natl. Acad. Sci. USA, in press). We proposed that SRS is formed from a previously described unstable epoxide intermediate in the formation of dihydroxylated arachidonic acid metabolites in leukocytes. The term is introduced for compounds which like SRS are non-cyclized C₂₀ carboxylic acids with one or two oxygen substituents and three conjugated double bonds.     

A note: ortho-phthalaldehyde: proposed mechanism of action of a new antimicrobial agent

Ortho-phthalaldehyde (OPA) is a new aromatic dialdehyde antimicrobial agent, the mechanism of action of which has been little studied. The aims of this paper are to examine what is currently known about its mechanism of action, to compare the action with that of a widely investigated aliphatic dialdehyde, glutaraldehyde (GTA), and to put forward a hypothesis that would, in the light of current knowledge, explain how OPA inactivates micro-organisms, including GTA-resistant Mycobacterium chelonae.