New PCR-based methods for yeast identification

AIMS: To characterize reference yeast strains and identify indigenous strains isolated from wine fermentations by PCR methods. METHODS AND RESULTS: We compared several PCR techniques for yeast identification. We used oligonucleotide primers that are complementary to (i) intron splice sites, (ii) REP and (iii) ERIC elements to produce PCR fingerprints that display specific patterns between the different yeast species. These three techniques were used to characterize 41 reference yeast strains belonging to 15 different species and to identify 40 indigenous strains isolated from grape must and wine fermentations. Species-specific banding patterns were obtained with the three PCR-techniques with different degrees of intraspecific differentiation depending on the method. By comparing the PCR fingerprints of unknown isolates with those produced by reference strains, we identified yeast strains isolated from an industrial wine fermentation. CONCLUSIONS: All three PCR techniques are rapid, reliable and simple methods of yeast identification. As far as we know, this is the first time that the primers designed for amplifying repetitive elements in bacteria have been successfully used in yeast. SIGNIFICANCE AND IMPACT OF THE STUDY: Industry needs rapid, reliable and simple methods of yeast identification. The proposed PCR techniques will allow to achieve this objective.     

Computational methods for yeast prion curing curves

If the chemical guanidine hydrochloride is added to a dividing culture of yeast cells in which some of the protein Sup35p is in its prion form, the proportion of cells that carry replicating units of the prion, termed propagons, decreases gradually over time. Stochastic models to describe this process of ‘curing’ have been developed in earlier work. The present paper investigates the use of numerical methods of Laplace transform inversion to calculate curing curves and contrasts this with an alternative, more direct, approach that involves numerical integration. Transform inversion is found to provide a much more efficient computational approach that allows different models to be investigated with minimal programming effort. The method is used to investigate the robustness of the curing curve to changes in the assumed distribution of cell generation times. Matlab code is available for carrying out the calculations.     

Genetic methods for characterizing the cis-acting components of yeast DNA replication origins.

Small circular plasmids containing replication origins and, in some cases, centromeres, can replicate autonomously in the nuclei of all tested yeast species. Because this autonomous replication is dependent on the replication origin within the plasmid, measurements of the efficiency of autonomous replication (by the methods summarized here) permit evaluation of the effects of mutations on origin function. Although alternative methods are available for genetic characterization of replication origins in other organisms, the simplicity of the autonomous replication assay in yeasts has permitted development of the deepest understanding to date of eukaryotic replication origin structure. This information has come primarily from studies with Saccharomyces cerevisiae. However, there are many other yeast species, each with its own variety of replication origins. Use of the methods summarized here to characterize origins in other yeast species is likely to provide additional insights into eukaryotic replication origin structure.     

A comparison of methods for assessing yeast viability

Summary Eight different methods were used to assess the cell viability of four strains of Saccharomyces. Staining with Mg-ANS, primuline yellow, FITC and methylene blue gave a good index of yeast cell viability. The standard plate count technique and microcolony formation also gave a good measure of cell viability. Fluorescent staining with acridine orange was the least useful of the methods tested. INT dye reduction gave a good index of respiring cells depending upon the yeast strain tested.     

Effects of yeast, fermentation time, and preservation methods on tarhana

The physicochemical properties of tarhana soup produced with different dough treatments, fermentation times, and preservation methods were examined. Tarhana doughs were prepared with yogurt (control) or baker's yeast (Saccharomyces cerevisiae) and fermented for 3 days. Samples were taken at 24, 48, and 72 hr. Samples were then preserved via one of four methods: sun dried, dried in the shade, vacumn dried, and frozen. Frozen samples produced lower organic acid levels after 72 hr of fermentation in both control (0.68 g/100 g) and yeast (0.61 g/100 g) applications than samples that were dried (0.94 g/100 g control samples; 0.81 g/100 g samples with yeast). Increasing fermentation time resulted in a significant effect on the formation of organic acid in the tarhana (p < .01). At 72 hr of fermentation, total acidity increased 11%, 17%, and 23% for tarhana samples vacumn-dried, sun-dried, and dried in the shade, respectively. Preservation methods also affected the moisture, ash, crude protein, total acidity, pH, salt, fat, reducing sugar levels, and the sensory assestment of tarhana soup (p < .01). Sensory characteristics were not significantly affected by baker's yeast in any of the preservation methods used (p > .01). However, sensory scores for tarhana prepared from the samples dried in a sheltered area showed a reduction in color desireablilty as the fermentation time increased. The soup prepared from frozen tarhana (72 hr fermentation, with yeast) had the highest scores with respect to color, mouth feel, flavor, and overall acceptability. Vacuum-dried samples' scores in these areas were also high in comparison to the two other drying methods.     

Recent writings on yeast recombination.

The analysis of recombination mechanisms in Saccharomyces cerevisiae produces a lively literature spanning classical genetics, enzymology and the physical analysis of intermediates. Recent papers include excellent examples from each of these areas.     

Evaluation of methods for total selenium determination in yeast

The selenium determination in biological materials by the classical fluorometric method (FM) is time-consuming and also hazardous, as it requires the destruction of the organic matrix samples with hot HNO₃/HClO₄ mixtures prior to analysis. Accordingly, commercial analytical laboratories are increasingly using faster instrumental methods; for sample digestion, avoid using HClO₄. Because of these procedural changes, the results obtained by commercial laboratories may be unreliable, especially for samples containing Se in organic forms. One such “difficult” substrate is Se yeast, which contains most of its Se as selenomethionine. To establish which methods for Se analysis and sample digestion are applicable, samples of Se yeast and of selenomethionine standards were sent to laboratories employing either flame atomic absorption spectrometry (FAAS), inductively coupled plasma-mass spectrometry (ICP-MS), or hydride generation atomic absorption spectrometry (HGAAS). The result were compared with those obtained by FM and non-destructive instrumental neutron activation analysis (INAA). ICP-MS, after microwave digestion of sample with HNO₃/H₂O₂, produced results within 5% of the expected values, as did those obtained by FM and INAA. With FAAS, acceptable results were obtained after digestion with HNO₃/HCl. With HGAAS, sample digestion with HNO₃/H₂O₂ produced values that were systematically elevated by about 10% and exhibited standard deviations of ≥10%. Thus, current methods of sample digestion are applicable for Se yeast analysis by ICP-MS and FAAS, but not by HGAAS.     

酵母及与藻类搭配对萼花臂尾轮虫饵料效果的研究

研究了２种酵母单独投喂萼花臂尾轮虫的最适密度、饵料效果及与藻类搭配的投喂效果．结果表明,在５种密度下,面包酵母和啤酒酵母的最适密度分别为１０和５×１０６个·ｍｌ－１．用面包酵母和啤酒酵母培养轮虫所得到的种群密度和瞬时增长率分别是用蛋白核小球藻培养的４０．２％、２６．０％和８５．５％、７６．６％．用面包酵母和蛋白核小球藻适当比例搭配投喂轮虫,其效果接近或超过单一用小球藻在最适密度下的培养效果．     

酵母双杂交相关方法的改良及应用

对酵母双杂交实验过程中较为耗时的阳性克隆鉴定过程进行改进,以期建立一种快速有效的鉴定方法。分别采用液氮冻融法、超声破碎法、渗透压破壁法以及煮沸裂解法裂解酵母细胞,获得质粒作为PCR模板,直接测序鉴定筛选到的相互作用蛋白。以液氮冻融法和超声破碎法裂解细胞获得的质粒为模板进行PCR,得到特异的产物,测序鉴定结果明确,与经典的鉴定方法相比效果相当,但更加经济快捷;而渗透压破壁法和煮沸裂解法则效果不好。说明前两种方法可代替常规方法用于阳性克隆的鉴定,从而加快酵母双杂交实验中大量阳性克隆的筛查工作。