A new electron microscopic method of determining acidification in phagocyte subcellular structures

A new method is elaborated for detecting acidification in phagocytes on the ultrastructural level. The method is based on the reaction between Cu2+ and [Fe(CN)6]4- which form a pellet of cupric ferrocyanide in the neutral medium. It is possible to induce pellet formation under definitely determined pH values on adding different amounts of chelating agent (citrate) to the reaction mixture. The fine-grained electron dense pellet of cupric ferrocyanide persists throughout the whole subsequent procedure of fixation, dehydration and embedding of the biological material for electron microscopy. Data are presented on the degree of acidification and its localization in subcellular structures of the phagocyte during phagocytosis.     

A fluorescent-cytochemical method for selective detection of yeast mitochondrial DNA

Yeast mitochondrial DNA (mDNA) can selectively be detected using a specific dye (DAPI). Nuclear DNA (nDNA) was stained along with mDNA only in three out of the fifteen studied yeast strains. Visualisation with a luminescent microscope showed that mDNA content varied among different yeast species as well as the size and shape of fluorescent mitochondrial nuclei. Intensive nDNA fluorescence was detected when a fixed specimen was treated with DAPI. Under these conditions, mDNA was revealed only in yeast cells with its high content. The process of fixation was shown to interfere with the integrity of mitochondria. It is also possible that the structure of DNA was modified to affect its interaction with the dye and thus the level of fluorescence. The developed technique of selective mDNA staining and the experimental results make it possible to gain a more accurate quantitative information about DNA content at the cellular level using cyto- and spectrofluorimetric techniques. This study involves important aspects pertinent to the dye interaction with yeast nuclear and mitochondrial DNA, both native and subjected to different fixation procedures.     

Factors affecting the outcome of the acidification power test of yeast quality: Critical reappraisal

Brewery bottom yeast strain 95 from the Pilsner Urquell propagation unit was used to reappraise the efficiency of the acidification power (AP) test consisting in determining the spontaneous (oxygen-induced) and glucose-induced medium acidification caused by yeast and lactic acid bacteria under standard conditions, and used widely for assessing and predicting the vitality of industrial strains. AP was evaluated in yeast stored for different periods of time (0-28 d) at 4 degrees C, at different temperatures before and during the test (0-55 degrees C), and at different concentrations of cells and glucose and different cells-to-glucose ratios. All these factors had a strong effect on acidification kinetics and the AP value. By contrast, the duration of the lag period between yeast collection and the test (0-6 h) had no perceptible effect on the AP value. The best results were achieved at saturation concentrations of cells (> 10 g pressed yeast or approximately 14 g yeast slurry per 100 mL) and glucose (approximately 3 %) and at 25 degrees C. Since an exact evaluation of acidification characteristics depends strongly on the kinetics of the process, the AP test should include monitoring the time course of the acidification.     

A new method of isolation and a new form of transketolase from baker's yeast]

A new procedure for the isolation of homogeneous transketolase from baker's yeast based on the use of enzyme-specific antibodies immobilized on a insoluble matrix has been developed. The enzyme yield is 90% of its total content in the original yeast extract. The eluate from the immunocolumn was found to contain a previously unknown form of transketolase which represents an enzyme-RNA complex.     

A method for the detection of Issatchenkia orientalis in a baker's yeast factory

Summary A method for the detection of Issatchenkia orientalis (Candida krusei), a contaminant of bakers' yeast, is described. Nine different liquid medium types were compared and maximum specific growth rates for the yeast contaminant were determined in each medium. Issatchenkia orientalis grew fastest in malt extract broth (0,37 h^-1) and potato dextrose broth (0,36 h^-1). Five antibiotics were tested for selective inhibition of seven different bakers' yeast strains in malt extract broth. Nystatin was the only antibiotic tested that inhibited the growth of all the bakers' yeast strains used, but did not affect the growth of I. orientalis.     

A new method for isolation of S-adenosylmethionine (SAM)-accumulating yeast

S-Adenosylmethionine (SAM) is an important metabolite that participates in many reactions as a methyl group donor in all organisms, and has attracted much interest in clinical research because of its potential to improve many diseases, such as depression, liver disease, and osteoarthritis. Because of these potential applications, a more efficient means is needed to produce SAM. Accordingly, we developed a positive selection method to isolate SAM-accumulating yeast in this study. In Saccharomyces cerevisiae, one of the main reactions consuming SAM is thought to be the methylation reaction in the biosynthesis of ergosterol that is catalyzed by Erg6p. Mutants with deficiencies in ergosterol biosynthesis may accumulate SAM as a result of the reduction of SAM consumption in ergosterol biosynthesis. We have applied this method to isolate SAM-accumulating yeasts with nystatin, which has been used to select mutants with deficiencies in ergosterol biosynthesis. SAM-accumulating mutants from S. cerevisiae K-9 and X2180-1A were efficiently isolated through this method. These mutants accumulated 1.7–5.5 times more SAM than their parental strains. NMR and GC-MS analyses suggested that two mutants from K-9 have a mutation in the erg4 gene, and erg4 disruptants from laboratory strains also accumulated more SAM than their parental strains. These results indicate that mutants having mutations in the genes for enzymes that act downstream of Erg6p in ergosterol biosynthesis are effective in accumulating SAM.     

A new repeat-masking method enables specific detection of homologous sequences

Biological sequences are often analyzed by detecting homologous regions between them. Homology search is confounded by simple repeats, which give rise to strong similarities that are not homologies. Standard repeat-masking methods fail to eliminate this problem, and they are especially ill-suited to AT-rich DNA such as malaria and slime-mould genomes. We present a new repeat-masking method, tantan, which is motivated by the mechanisms that create simple repeats. This method thoroughly eliminates spurious homology predictions for DNA–DNA, protein–protein and DNA–protein comparisons. Moreover, it enables accurate homology search for non-coding DNA with extreme A + T composition.     

A new electrophoretic-autoradiographic method for the visual detection of phosphotransferases

In this paper we present the details of a slab acrylamide, lanthanum precipitation, autoradiographic technique and show it to be useful for the visualization of at least four different enzymes. We believe that with appropriate separation conditions and reaction mixtures this technique could be extended to a larger number of enzymes, theoretically all those whose isotopically labeled product could be specifically precipitated within the matrix of a polyacrylamide gel. It will be interesting to use this technique with other gel buffer systems, particularly those with a lower pH that have recently been reported (21). In addition, it might be useful to combine it with isoelectric focusing in slab gels (10). The technique would appear to be particularly useful for phosphotransferases and, to date, it has been applied to thymidine kinase and adenosine kinase with encouraging results. Work with other enzymes, and adapting the technique to starch gels, is also in progress.     

Genomic detection of new yeast pre-mRNA 3'-end-processing signals.

To investigate Saccharomyces cerevisiae 3'-end-processing signals, a set of 1352 unique pre-mRNA 3'-end-processing sites, corresponding to 861 different genes, was identified by alignment of expressed sequence tag sequences with the complete yeast genome. Nucleotide word frequencies in the vicinity of the cleavage sites were analyzed to reveal the signal element features. In addition to previously recognized processing signals, two previously uncharacterized components of the 3'-end-processing signal sequence were discovered, specifically a predominance of U-rich sequences located on either side of the cleavage site. One of these, the downstream U-rich signal, provides a further link between the 3'-end-processing mechanisms of yeast and higher eukaryotes. Analysis of the complete set of 3'-end-processing sites by means of a discrimination function supports a 'contextual' model in which the sum total effectiveness of the signals in all four elements determines whether or not processing occurs.     

A new method for the determination of optical purity of synthetic peptides

A novel and very accurate method was established for the determination of the optical purity of a peptide by use of the following procedure: (1) hydrolysis of the peptide in deuterium chloride, (2) gas chromatographic separation of each amino acid enantiomer on a chiral phase, and (3) determination of the D /L ratio by mass fragmentography. In this manner, one can estimate the true chiral purity of each amino acid residue with an accuracy of ～0.2%. The recemization effected during hydrolysis could be eliminated in principle, since the artificially formed DL -amino acids are necessarily labeled at the α-position with deuterium and can thus be distinguished mass spectrometrically from the D - and L -isomer originally present in the peptide. The versatility of the method was proven by analysis of model peptides, as well as by a racemization test in fragment condensation.     

A new method for the detection of carotenoids in chlorophyll samples

Summary A new method is developed for the detection of carotenoids in chlorophyll samples.The typical colour curve of chlorophyll in 80 % methyl alcohol exhibits marked absorption in 690 to 610 and less absorption in 500 to 430. The colour curve of chlorophyll contaminated with carotenoids exhibits higher values in the region 530 to 430. If carotin is present, the band maximum in the region 530 to 430 is located at 500, and if xanthophyll is the impurity the band maximum is shifted to 430. On a comparison of the colour curve of the sample to be tested with that of the typical colour curve of chlorophyll the presence of carotenoids at once becomes evident, and carotin and xanthophyll are identified separately by the positions of the band maxima in the region 500 to 430.Carotenoids in as low a concentration as 0.05 % are detected by the new method described.     

基于连接酶—ELISA反应的单核苷酸多态性分型新方法

随着大量与人类疾病和药物治疗相关的单核苷酸多态性（Single-nucleotide polymorphism,SNP）的发现,出现了多种SNP分型检测的方法和技术。然而,大多数方法由于受限于检测灵敏度低或对检测设备和实验条件要求较高,不适宜于在一般实验条件下进行常规临床检测。通过建立一种基于连接酶-ELISA的SNP快速分型新方法,以非小细胞肺癌个体化治疗中,酪氨酸激酶抑制剂药物的生物标记基因—表皮生长因子受体基因（EGFR）为检测对象,对EGFR,c.2573T〉G（L858R）,EGFR,c.2582T〉A（L861Q）和EGFR,c.2155 G〉T（G719C）3个SNP位点进行了突变检测。经过18~28个循环的PCR扩增,能够通过琼脂糖凝胶电泳和ELISA反应,根据电泳条带的有无和ELISA显色值清晰判断检测位点的基因型,并且能够从混合等位基因样本中检测出5%的突变型等位基因。结果表明,方法具有较高的特异性和灵敏度,适合于在常规实验条件下从不均一的样本中进行突变等位基因的检测。     

Alternative mechanisms of vacuolar acidification in H(+)-ATPase-deficient yeast

Acidification of the endosomal/lysosomal pathway by the vacuolar-type proton translocating ATPase (V-ATPase) is necessary for a variety of essential eukaryotic cellular functions. Nevertheless, yeasts lacking V-ATPase activity (Deltavma) are viable when grown at low pH, suggesting alternative methods of organellar acidification. This was confirmed by directly measuring the vacuolar pH by ratio fluorescence imaging. When Deltavma yeasts were cultured and tested in the acidic conditions required for growth of V-ATPase-deficient mutants, the vacuolar pH was 5.9. Fluid-phase pinocytosis of acidic extracellular medium cannot account for these observations, because the V-ATPase-independent vacuolar acidification was unaffected in mutants deficient in endocytosis. Similarly, internalization of the plasmalemmal H(+)-ATPase (Pma1p) was ruled out, because overexpression of Pma1p failed to complement the Deltavma phenotype and did not potentiate the vacuolar acidification. To test whether weak electrolytes present in the culture medium could ferry acid equivalents to the vacuole, wild-type and the Deltavma yeasts were subjected to sudden changes in extracellular pH. In both cell types, the vacuoles rapidly alkalinized when external pH was raised from 5.5 (the approximate pH of the culture medium) to 7.5 and re-acidified when the yeasts were returned to a medium of pH 5.5. Importantly, these rapid pH changes were only observed when NH(4)(+), routinely added as a nitrogen source, was present. The NH(4)(+)-dependent acidification was not due to efflux of NH(3) from the vacuole, as cells equilibrated to pH 7.5 in the absence of weak electrolytes rapidly acidified when challenged with an acidic medium containing NH(4)(+). These findings suggest that although NH(3) can act as a cell-permeant proton scavenger, NH(4)(+) may function as a protonophore, facilitating equilibration of the pH across the plasma and vacuolar membranes of yeast. The high concentration of NH(4)(+) frequently added as a nitrogen source to yeast culture media together with effective NH(4)(+) transporters thereby facilitate vacuolar acidification when cells are suspended in acidic solutions.     

Simple detection method for distinguishing dead and living yeast colonies

A rapid and simple assay was developed for detection of yeast colonies containing dying or dead cells. Methylene blue, phloxin B, rose bengal and trypan blue at concentrations of 5-10 micromol l(-1) were shown to stain non-viable cells in colonies of Saccharomyces cerevisiae, Schizosaccharomyces pombe, Candida albicans and Filobasidium capsuligenum without staining or affecting the viability of living cells of the colonies.     

A new deep learning method for image deblurring in optical microscopic systems

Deconvolution is the most commonly used image processing method in optical imaging systems to remove the blur caused by the point‐spread function (PSF). While this method has been successful in deblurring, it suffers from several disadvantages, such as slow processing time due to multiple iterations required to deblur and suboptimal in cases where the experimental operator chosen to represent PSF is not optimal. In this paper, we present a deep‐learning‐based deblurring method that is fast and applicable to optical microscopic imaging systems. We tested the robustness of proposed deblurring method on the publicly available data, simulated data and experimental data (including 2D optical microscopic data and 3D photoacoustic microscopic data), which all showed much improved deblurred results compared to deconvolution. We compared our results against several existing deconvolution methods. Our results are better than conventional techniques and do not require multiple iterations or pre‐determined experimental operator. Our method has several advantages including simple operation, short time to compute, good deblur results and wide application in all types of optical microscopic imaging systems. The deep learning approach opens up a new path for deblurring and can be applied in various biomedical imaging fields.