Primers‐4‐Yeast: a comprehensive web tool for planning primers for Saccharomyces cerevisiae

The budding yeast Saccharomyces cerevisiae is a key model organism of functional genomics, due to its ease and speed of genetic manipulations. In fact, in this yeast, the requirement for homologous sequences for recombination purposes is so small that 40 base pairs (bp) are sufficient. Hence, an enormous variety of genetic manipulations can be performed by simply planning primers with the correct homology, using a defined set of transformation plasmids. Although designing primers for yeast transformations and for the verification of their correct insertion is a common task in all yeast laboratories, primer planning is usually done manually and a tool that would enable easy, automated primer planning for the yeast research community is still lacking. Here we introduce Primers‐4‐Yeast, a web tool that allows primers to be designed in batches for S. cerevisiae gene‐targeting transformations, and for the validation of correct insertions. This novel tool enables fast, automated, accurate primer planning for large sets of genes, introduces consistency in primer planning and is therefore suggested to serve as a standard in yeast research. Primers‐4‐Yeast is available at: http://www.weizmann.ac.il/Primers‐4‐Yeast Copyright © 2013 John Wiley & Sons, Ltd.     

Next‐generation biofuels: a new challenge for yeast

Economic growth depends strongly on the availability and price of fuels. There are various reasons in different parts of the world for efforts to decrease the consumption of fossil fuels, but biofuels are one of the main solutions considered towards achieving this aim globally. As the major bioethanol producer, the yeast Saccharomyces cerevisiae has a central position among biofuel‐producing organisms. However, unprecedented challenges for yeast biotechnology lie ahead, as future biofuels will have to be produced on a large scale from sustainable feedstocks that do not interfere with food production, and which are generally not the traditional carbon source for S. cerevisiae. Additionally, the current trend in the development of biofuels is to synthesize molecules that can be used as drop‐in fuels for existing engines. Their properties should therefore be more similar to those of oil‐derived fuels than those of ethanol. Recent developments and challenges lying ahead for cost‐effective production of such designed biofuels, using S. cerevisiae‐based cell factories, are presented in this review. Copyright © 2015 John Wiley & Sons, Ltd.     

Application of a picrate semi‐quantitative screening assay for the cyanogenic potential of cassava roots at a remote field site

The purpose of this research was to test the accuracy of the picrate screening assay (PSA) in the evaluation of the cyanogenic potential of cassava roots at a remote field site under conditions of unusual difficulty. To do this, a PSA was conducted in the field and compared to data collected previously on five of the same cassava varieties using the Cooke colorimetric enzymic assay. PSA data were collected for 10 different cassava varieties in the Tukanoan Indian village of Yapú in the Colombian Amazon region. The PSA results agree with Tukanoan classifications of cassava; that is, those classified as ‘sweet’ by the Tukanoans generally had low‐to‐moderate parenchymal cyanogenic potential (0–50 mg kg⁻¹ fwb of HCN), while those that they classify as ‘bitter’ had high parenchymal cyanogenic potential (≥100 mg kg⁻¹ fwb of HCN). The PSA results also agree with the data collected using the Cooke colorimetric enzymic assay. The data suggest that the PSA is an appropriate test of the cyanogenic potential of cassava roots in remote field sites. © 2000 Society of Chemical Industry     

Near‐infrared transmittance spectroscopy: a potential tool for non‐destructive determination of oil content in groundnuts

The oil content of 64 samples of groundnut kernels, representing 47 genotypes, was determined by the conventional Soxhlet extraction procedure (Oil^SOX). The values of Oil^SOX ranged from 403 to 536 g kg⁻¹. The optical densities (ODs) of these samples were determined at 12 wavelengths (918, 928, 940, 950, 968, 975, 985, 998, 1010, 1023, 1037 and 1045 nm) in the near‐infrared (NIR) region using a food composition analyser (essentially a filter‐based NIR spectrophotometer). The instrument also recorded the temperatures of the sample (Temp^S) and the air (Temp^A) surrounding it. A sample holder (75 mm × 150 mm; optical path length 25 mm) was used for optical density measurement. The data obtained were subjected to multiple linear regression analysis using the ODs at 12 wavelengths, Temp^S and Temp^A as the independent (predictor) variables, and Oil^SOX as the dependent variable. The multiple linear regression equation comprising 14 predictors showed a significant relationship between predicted values of oil content (Oil^NIR) and Oil^SOX. The standard error of calibration and the coefficient of determination for calibration (R) were 3.54 and 0.821 respectively, while the standard error of prediction and the coefficient of determination for prediction were 5.82 and 0.865 respectively. The ratio of standard error of calibration and standard error of prediction was 0.608. The differences between Oil^SOX and Oil^NIR were less than ± 20 g kg⁻¹ for samples having oil contents in the range from 480 to 510 g kg⁻¹. However, for samples having Oil^SOX lower than 480 g kg⁻¹ or higher than 510 g kg⁻¹, differences greater than ± 20 g kg⁻¹ were observed. There exists scope for further refining the regression equation by using a larger number of samples for generating optical data. The results demonstrated the potential of NIR transmittance spectroscopy for determining the oil content of groundnuts in a non‐destructive manner. © 2000 Society of Chemical Industry     

Application of matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry as a monitoring tool for in‐house brewer's yeast contamination: a proof of concept

Contamination of brewer's pitching yeast cultures with wild‐type yeasts or bacteria is unwanted as it can corrupt the fermentation outcome and causes huge economic losses for the brewing industry. The applicability of matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry (MALDI‐TOF MS) as a fast tool to monitor the purity of brewer's yeast cultures was investigated. This proof of concept was examined for a brewer's yeast strain contaminated with wild‐type yeast and for bottled beer produced by fermentation with that particular contaminated brewer's yeast strain. The data demonstrated that MALDI‐TOF MS is very suitable to discriminate between brewing and non‐brewing yeast strains. Copyright © 2014 The Institute of Brewing & Distilling     

In‐house validation of a high‐performance liquid chromatography analytical method for quantification of ochratoxin A in unfermented grape juice

A validated high‐performance liquid chromatography (HPLC) method with fluorescence detection for the quantitative analysis of ochratoxin A (OTA) in unfermented grape juice is described. Five millilitres of unfermented grape juice was mixed with 45 mL of PBS, and the pH was adjusted to 7.2. Then the mixture was filtered under vacuum through a glass microfibre filter and cleaned up with immunoaffinity columns prior to analysis by HPLC. Validation of the analytical method was based on the following criteria: selectivity, linearity, limit of detection and quantification, precision (within‐day and between‐day variability) and recovery and uncertainty estimation. Detection and quantification limits obtained were 0.02 µg L^?1 and 0.05 µg L^?1 respectively. The percentage recovery was 91.5% (RSD = 3.9). This method was applied to the measurement of 30 veraison stage unfermented grape juice samples. Copyright © 2007 Society of Chemical Industry