An enhanced RNA alignment benchmark for sequence alignment programs

Background  

The performance of alignment programs is traditionally tested on sets of protein sequences, of which a reference alignment is known. Conclusions drawn from such protein benchmarks do not necessarily hold for the RNA alignment problem, as was demonstrated in the first RNA alignment benchmark published so far. For example, the twilight zone – the similarity range where alignment quality drops drastically – starts at 60 % for RNAs in comparison to 20 % for proteins. In this study we enhance the previous benchmark.     

Melting curves on less than 1 μg of nucleic acid

Two types of microcuvettes were developed for the registration of melting curves in normal uv-spectrophotometers. Nucleic acid (0.5–1 μg) is required to determine changes in absorption with an accuracy of 0.1 mA. The quartz cuvette allows the registration of equilibrium melting curves up to 100°C. The other type of cuvette made from gilded brass allows to measure slow temperature jumps up to 80°C and equilibrium melting curves up to 70°C. The time range of ～3 s to several hours is accessible complementing the Eigen/De Mayer temperature-jump technique (1963, in Techniques of Organic Chemistry, Vol. VIII/2, pp. 895–1054, Wiley, New York). Temperature jumps of high amplitude as well as jumps to lower temperatures are possible. Examples of measurements on viroids and double-stranded viral RNA are presented.     

The occurrence of malolactic fermentation in brandy base wine and its influence on brandy quality

AIMS: In this study we determined the extent to which lactic acid bacteria (LAB) occurred in brandy base wines, their ability to catalyse the malolactic fermentation (MLF) and the effect of MLF on the quality of the base wine and the brandy distillate. METHODS AND RESULTS: Lactic acid bacteria were isolated and enumerated from grape juice, experimental and commercially produced brandy base wines. Spontaneous MLF occurred in approximately 50% of the commercial base wines. The occurrence of MLF had an influence on the quality of the base wines and the resulting distillates. In samples where MLF occurred there was a loss of fruitiness and in the intensity of aroma. Volatile compounds like iso-amyl acetate, ethyl acetate, ethyl caproate, 2-phenethyl acetate and hexyl acetate decreased in samples having undergone MLF, while ethyl lactate, acetic acid and diethyl succinate increased in the same samples. CONCLUSIONS: Spontaneous malolactic fermentation does occur in commercial brandy base wines and it has an influence on base wine and brandy quality. SIGNIFICANCE AND IMPACT OF THE STUDY: This study showed that MLF influences the quality of the base wine and the resulting distillate and with this in mind commercial base wine producers should be able to produce brandy of higher quality.     

The selection of yeast strains for the production of premium quality South African brandy base products

One hundred seven yeast strains were screened for their ability to produce a brandy base wine of exceptional sensory quality. Volatile acids, esters and higher alcohols were quantified and the results were interpreted using a multivariate analysis of variance (MANOVA) and an average linkage cluster analysis. Significant differences between yeast strains for higher alcohol, fatty acid ester and acetate concentrations were observed. On the basis of their chemical profiles, 16 strains were selected and re-evaluated in larger-scale fermentations and subsequent double distillations. Results show that the yeast lees can have an important effect on the final concentration of higher alcohols and esters in the distillate. Highly elevated levels of ethyl acetate and iso-amyl acetate were found to be undesirable. Elevated levels of all the esters present contributed positively to the overall potential quality of the brandy base product. Too low higher alcohol concentrations were also not desirable. Sensory evaluations showed that, since the panel was composed of representatives of the three largest brandy-producing companies, each company preferred a different yeast strain most suitable for their style of brandy. For these reasons, three strains, B7, LL2 and 20-2, warranted further evaluation on a semi-commercial scale for each of the respective companies. Journal of Industrial Microbiology & Biotechnology (2000) 24, 431–440. Received 17 November 1999/ Accepted in revised form 07 March 2000     

Deficiency of immunoreactive somatostatin in the median eminence of Snell dwarf mice

Snell dwarf mice (dw/dw) are characterized by a genetically determined, congenital lack of pituitary GH, TSH and prolactin. Given that hypothalamic somatostatin is involved in the regulation of pituitary GH and TSH release, it was decided to investigate the content of immunoreactive somatostatin (IRS) in the median eminence of dw/dw and phenotypically normal mice of the same strain. The content of IRS in the pyloric antrum and pineal gland of these animals was also examined. The effects of ovariectomy and of hyperprolactinemia (induced by a pituitary graft under the kidney capsule) on the median eminence content of IRS were also studied in both normal and dwarf mice. Median eminence IRS content was significantly lower in the dw/dw (23.6 +/- 1.8 ng) than in normal mice (57.4 +/- 7.1 ng); no difference was found in the pyloric IRS content of dw/dw (16.9 +/- 1.6 ng/mg of protein) and normal animals (13.8 +/- 1.9 ng/mg of protein), nor in the pineal content of IRS (639.4 +/- 64.4 pg/gland in the dw/dw; 732 +/- 265 pg/gland in normals). Neither ovariectomy nor hyperprolactinemia were found to affect the IRS content in the tissues studied in normal or dwarf mice. Treatment of an additional group of 9 dwarf mice with L-thyroxine (L-T4 2 micrograms/48 h. s.c. for 2 weeks) significantly increased the animals weight (10.2 +/- 0.4 g versus 7.4 +/- 0.3 g) and produced maturation of facial features; however, it did not change the IRS content in any of the tissues studied. It is concluded that the content of IRS in the median eminence of mice with a congenital lack of GH, TSH and prolactin is significantly reduced and that this is unlikely to be related to the deficiency of thyroid hormones in these animals.     

Two novel proteins activate superoxide generation by the NADPH oxidase NOX1

NOX1, an NADPH oxidase expressed predominantly in colon epithelium, shows a high degree of similarity to the phagocyte NADPH oxidase. However, superoxide generation by NOX1 has been difficult to demonstrate. Here we show that NOX1 generates superoxide when co-expressed with the p47(phox) and p67(phox) subunits of the phagocyte NADPH oxidase but not when expressed by itself. Since p47(phox) and p67(phox) are restricted mainly to myeloid cells, we searched for their homologues and identified two novel cDNAs. The mRNAs of both homologues were found predominantly in colon epithelium. Differences between the homologues and the phagocyte NADPH oxidase subunits included the lack of the autoinhibitory domain and the protein kinase C phosphorylation sites in the p47(phox) homologue as well as the absence of the first Src homology 3 domain and the presence of a hydrophobic stretch in the p67(phox) homologue. Co-expression of NOX1 with the two novel proteins led to stimulus-independent high level superoxide generation. Stimulus dependence of NOX1 was restored when p47(phox) was used to replace its homologue. In conclusion, NOX1 is a superoxide-generating enzyme that is activated by two novel proteins, which we propose to name NOXO1 (NOX organizer 1) and NOXA1 (NOX activator 1).