A consensus classification and nomenclature are defined for RNA backbone structure using all of the backbone torsion angles. By a consensus of several independent analysis methods, 46 discrete conformers are identified as suitably clustered in a qualityfiltered, multidimensional dihedral angle distribution. Most of these conformers represent identifiable features or roles within RNA structures. The conformers are given two-character names that reflect the seven-angle dezabgd combinations empirically found favorable for the sugar-to-sugar ''suite'' unit within which the angle correlations are strongest (e.g., 1a for A-form, 5z for the start of S-motifs). Since the half-nucleotides are specified by a number for dez and a lowercase letter for abgd, this modular system can also be parsed to describe traditional nucleotide units (e.g., a1) or the dinucleotides (e.g., a1a1) that are especially useful at the level of crystallographic map fitting. This nomenclature can also be written as a string with two-character suite names between the uppercase letters of the base sequence (N1aG1gN1aR1aA1cN1a for a GNRA tetraloop), facilitating bioinformatic comparisons. Cluster means, standard deviations, coordinates, and examples are made available, as well as the Suitename software that assigns suite conformer names and conformer match quality (suiteness) from atomic coordinates. The RNA Ontology Consortium will combine this new backbone system with others that define base pairs, base-stacking, and hydrogen-bond relationships to provide a full description of RNA structural motifs.

1997;45:354-360 Reactive AA amyloidosis can be induced in mice in a model of sustained inflammation following daily casein subcutaneous injections. However, the development of AA amyloidosis is known to vary in different strains of mice. The C57BL/6 strain is susceptible to the development of amyloidosis while the A/J strain is resistant. The degradation of purified serum amyloid A (SAA) protein by human monocytes as well as by mouse macrophages has been shown. The resistance/susceptibility of different mouse strains to the development of systemic amyloidosis may therefore be related to a difference in the ability of macrophages to degrade SAA. The authors have used bone marrow-derived macrophage cell lines obtained from susceptible C57BL/6 (ANA-1) and resistant A/J (A/J 10) mouse strains to compare their ability to degrade HDL-SAA in vitro. Cells were incubated with HDL-SAA for up to 72 h and the culture medium was analysed by SDS-PAGE to determine the rate of SAA degradation by the macrophages. The A/J 10 cells (resistant) were found to initiate a constant HDL-SAA degradation promptly whereas ANA-1 cells (susceptible) showed an intermittent block in the degradation of the precursor. Activation of macrophages by lipopolysaccharide (LPS) or interferon-g (IFN-g) hampered the precursor degradation suggesting that the activation process may favour extracellular accumulation of the precursor leading to a partial degradation and fibril formation.

Probiotics are a nutritional tool for disease prevention. It has been proposed that stimulation of immune response could affect the growth-promoting properties of antimicrobial growth promoters as well as the control of foodborne pathogens. The current study compares immune response in the blood of 280 non-infected and Salmonella-infected chickens fed either with the growth promoter avilamycin or with one of five probiotic strains of Lactobacillus and Bifidobacterium, which also showed growth-promoting properties. All of the probiotic strains stimulated superoxide anion production and the proliferation of leukocytes, while raising lysozyme and γ-globulin levels (by up to 65%, p < 0.01), which are important factors in native and cell-mediated immune defense against pathogens. In contrast, among the two strains examined, specific Salmonella antibodies were induced only by L. salivarius, and not by B. animalis, as assessed by the ELISA method and confirmed by an agglutination reaction (p < 0.05). In the avilamycin-fed group, both non-infected and infected chickens showed decreased levels of these immune markers (by 30%) and increased levels of ceruloplasmin by up to 35%. In contrast, the probiotics suppressed acute-phase response assessed by ceruloplasmin by up to 32%. This correlation implies that various antimicrobial feed additives have a distinct effect on immunomodulation, which may affect different mechanisms in the nutrition-related metabolism associated with the rate of weight gain in chickens. The data could contribute to the design of innovative antimicrobial feed additives in the food industry and consequently to well-being of humans.

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