Continuous secondary fermentation using immobilised yeast

An immobilised yeast, two-stage reactor system was applied to laboratory fermentations of wort. The first stage, the primary fermentation process was carried out in an up-flow gas-lift bioreactor, and in the second stage, fermentation was processed in column reactors consisting of eight packed-beds filled with both yeasts entrapped in three different polysaccharide hydrogels (calcium alginate, calcium pectate, sodium carrageenan) and with free yeast in parallel. The residence time for the two-stage immobilised system varied from 74 to 108 h. © Rapid Science Ltd. 1998     

A phylogenetically based secondary structure for the yeast telomerase RNA

BACKGROUND: Telomerase is a ribonucleoprotein complex whose RNA moiety dictates the addition of specific simple sequences onto chromosomes ends. While relevant for certain human genetic diseases, the contribution of the essential telomerase RNA to RNP assembly still remains unclear. Phylogenetic analyses of vertebrate and ciliate telomerase RNAs revealed conserved elements that potentially organize protein subunits for RNP function. In contrast, the yeast telomerase RNA could not be fitted to any known structural model, and the limited number of known sequences from Saccharomyces species did not permit the prediction of a yeast specific conserved structure. RESULTS: We cloned and analyzed the complete telomerase RNA loci (TLC1) from all known Saccharomyces species belonging to the "sensu stricto" group. Complementation analyses in S. cerevisiae and end mappings of mature RNAs ensured the relevance of the cloned sequences. By using phylogenetic comparative analysis coupled with in vitro enzymatic probing, we derived a secondary structure prediction of the Saccharomyces cerevisiae TLC1 RNA. This conserved secondary structure prediction includes a central domain that is likely to orchestrate DNA synthesis and at least two accessory domains important for RNA stability and telomerase recruitment. The structure also reveals a potential tertiary interaction between two loops in the central core. CONCLUSIONS: The predicted secondary structure of the TLC1 RNA of S. cerevisiae reveals a distinct folding pattern featuring well-separated but conserved functional elements. The predicted structure now allows for a detailed and rationally designed study to the structure-function relationships within the telomerase RNP-complex in a genetically tractable system.     

RNA isolation from yeast using silica matrices.

RNA isolation from yeast is complicated by the need to initially break the cell wall. While this can be accomplished by glass bead disruption or enzyme treatment, these approaches result in DNA contamination and/or the need for incubation periods. We have developed a protocol for the isolation of RNA samples from yeast that minimizes degradation by RNases and incorporates two purification steps: acid phenol extraction and binding to a silica matrix. The procedure requires no precipitation steps, facilitating automation, and can be completed in less than 90 min. The RNA quality is ideal for microarray analysis.     

Comparing multiple RNA secondary structures using tree comparisons

In a previous paper, an algorithm was presented for analyzingmultiple RNA secondary structures utilizing a multiple stringalignment algorithm. In this paper we present another approachto the problem of comparing many secondary structures by utilizinga very efficient tree-matching algorithm that will compare twotrees in O(|T₁|x|T₂|x L₁ x L₂) in the worst case and very closeto O(|T₁|x|T₂|) for average trees representing secondary structures.The result of the pairwise comparison algorithm is then usedwith acluster algorithm to produce a multiple structure clusteringwhich can be displayed in ataxonomy tree to show related structures. Received on September 15, 1989; accepted on June 12, 1990     

The genetic map of transfer RNA genes of yeast mitochondria: Correction and extension

Summary Ninety five rho^- mitochondrial DNA's of Saccharomyces cerevisiae were compared for their deletion structure by means of 15 genetic markers and 22 tRNA genes. The patterns of co-deletion and coretention of different tRNA genes allowed us to determine their positions with respect to each other. The deduced order of tRNA genes was consistent with the order of the genetic markers established by independent genetic approaches. Our previously proposed mitochondrial tRNA gene map has been revised and extended. Transfer RNA genes, corresponding to all 20 aminoacids, and two isoacceptor tRNA genes were localized. The possible position of each tRNA gene has been indicated on the physical map of mitochondrial DNA. Seventeen tRNA genes are carried by a narrow region representing less than 20% of the wild type genome.Abbreviations tRNA transfer RNA - mRNA messenger RNA - rRNA ribosomal RNA - mitDNA mitochondrial DNA - nucDNA nuclear DNA - EDTA ethylenediaminetetraacetate - C, E, O_I, O_II and P drug resistance genetic loci - Rib I, Rib III O_I, O_II and P_I respectively. The three letter symbols for amino acids (ala, cys, etc...) designate tRNA genes corresponding to each amino acid Formerly Fondation Curie, Institut du Radium     

Identification of consensus RNA secondary structures using suffix arrays

Background  

The identification of a consensus RNA motif often consists in finding a conserved secondary structure with minimum free energy in an ensemble of aligned sequences. However, an alignment is often difficult to obtain without prior structural information. Thus the need for tools to automate this process.     

Induction of immunologic deficiency by benzene and its correction by administration of anabol

Cellular immunity and activity of enzymes of xenobiotic metabolism have been investigated. It has been shown that administration of benzene induces a stable immune deficiency syndrome characterized by a decrease in the quantity if antibody-forming cells, T-killers and T-suppressors. The activity of enzymes (cytochrome P-450 and cytochrome C reductase) was also inhibited. It has been shown that anabol can stimulate the parameters of cellular immunity and enzyme activity. Benzene intoxication was demonstrated to be a model of immune deficiency syndrome similar to the clinical pattern. Anabol was shown to be an effective immunomodulator.     

Enantioselective hydrolysis of esters of secondary alcohols using lyophilized Bakers'' yeast

A number of acetoxycarboxylic acid esters were hydrolysed enantioselectively by Saccharomyces cerevisiae Hansen leading to chiral hydroxycarboxylic acid esters of high optical purity. The scope and limitations of this method with respect to the substitutional pattern of substrates were investigated. Subcellular localization of the hydrolytic activity on the plasma membrane led to the assumption that unspecific carboxyl esterases are responsible for hydrolysis of this type of substrate. Comparative experiments using viable cells and lyophilized cells as source of enzyme revealed the latter to be superior with respect to enantioselection and ease of handling.     

Recognition of RNA encapsidation signal by the yeast L-A double-stranded RNA virus

The encapsidation signal of the yeast L-A virus contains a 24-nucleotide stem-loop structure with a 5-nucleotide loop and an A bulged at the 5' side of the stem. The Pol part of the Gag-Pol fusion protein is responsible for encapsidation of viral RNA. Opened empty viral particles containing Gag-Pol specifically bind to this encapsidation signal in vitro. We found that binding to empty particles protected the bulged A and the flanking-two nucleotides from cleavage by Fe(II)-EDTA-generated hydroxyl radicals. The five nucleotides of the loop sequence ((4190)GAUCC(4194)) were not protected. However, T1 RNase protection and in vitro mutagenesis experiments indicated that G(4190) is essential for binding. Although the sequence of the other four nucleotides of the loop is not essential, data from RNase protection and chemical modification experiments suggested that C(4194) was also directly involved in binding to empty particles rather than indirectly through its potential base pairing with G(4190). These results suggest that the Pol domain of Gag-Pol contacts the encapsidation signal at two sites: one, the bulged A, and the other, G and C bases at the opening of the loop. These two sites are conserved in the encapsidation signal of M1, a satellite RNA of the L-A virus.