Redefining genera of cereal pathogens: Oculimacula, Rhynchosporium and Spermospora.

The taxonomy of Oculimacula, Rhynchosporium and Spermospora is re-evaluated, along with that of phylogenetically related genera. Isolates are identified using comparisons of DNA sequences of the internal transcribed spacer ribosomal RNA locus (ITS), partial translation elongation factor 1-alpha (tef1), actin (act), DNA-directed RNA polymerase II largest (rpb1) and second largest subunit (rpb2) genes, and the nuclear ribosomal large subunit (LSU), combined with their morphological characteristics. Oculimacula is restricted to two species, O. acuformis and O. yallundae, with O. aestiva placed in Cyphellophora, and O. anguioides accommodated in a new genus, Helgardiomyces. Rhynchosporium s. str. is restricted to species with 1-septate conidia and hooked apical beaks, while Rhynchobrunnera is introduced for species with 1-3-septate, straight conidia, lacking any apical beak. Rhynchosporium graminicola is proposed to replace the name R. commune applied to the barley scald pathogen based on nomenclatural priority. Spermospora is shown to be paraphyletic, representing Spermospora (type: S. subulata), with three new species, S. arrhenatheri, S. loliiphila and S. zeae, and Neospermospora gen. nov. (type: N. avenae). Ypsilina (type: Y. graminea), is shown to be monophyletic, but appears to be of minor importance on cereals. Finally, Vanderaaea gen. nov. (type: V. ammophilae), is introduced as a new coelomycetous fungus occurring on dead leaves of Ammophila arenaria. Citation: Crous PW, Braun U, McDonald BA, Lennox CL, Edwards J, Mann RC, Zaveri A, Linde CC, Dyer PS, Groenewald JZ (2020). Redefining genera of cereal pathogens: Oculimacula, Rhynchosporium and Spermospora. Fungal Systematics and Evolution 7: 67-98. doi: 10.3114/fuse.2021.07.04.

Learning algorithms for feedforward networks based on finite samples.

We present two classes of convergent algorithms for learning continuous functions and regressions that are approximated by feedforward networks. The first class of algorithms, applicable to networks with unknown weights located only in the output layer, is obtained by utilizing the potential function methods of Aizerman et al. (1970). The second class, applicable to general feedforward networks, is obtained by utilizing the classical Robbins-Monro style stochastic approximation methods (1951). Conditions relating the sample sizes to the error bounds are derived for both classes of algorithms using martingale-type inequalities. For concreteness, the discussion is presented in terms of neural networks, but the results are applicable to general feedforward networks, in particular to wavelet networks. The algorithms can be directly adapted to concept learning problems.

An artificial intelligence approach to DNA sequence feature recognition.

The ultimate goal of the Human Genome project is to extract the biologically relevant information recorded in the estimated 100,000 genes encoded by the 3 x 10(9) bases of the human genome. This necessitates development of reliable computer-based methods capable of analysing and correctly identifying genes in the vast amounts of DNA-sequence data generated. Such tools may save time and labour by simplifying, for example, screening of cDNA libraries. They may also facilitate the localization of human disease genes by identifying candidate genes in promising regions of anonymous DNA sequence.

Two-dimensional gel electrophoretic comparison of cytoplasmic proteins in C3H10T1/2 cells, a chemically transformed 10T1/2 line, and a transformation resistant C3H mouse ventral prostate cell line.

The cytoplasmic proteins from three cell lines derived from the C3H mouse were compared after treatment with benzo(a)pyrene by two-dimensional gel electrophoresis and computerized image analysis. The three C3H lines were the transformable 10T1/2, the transformation resistant CVP and the methylcholanthrene transformed 10T1/2Cl line. Specialized algorithms were used to analyze gel images to record and compare individual proteins in the three cytoplasmic preparations. Multiple replicate gels were used to construct a master image to insure all the proteins were represented in the analytical system. In studies designed to examine the efficacy of utilizing image analysis, benzo(a)pyrene treatment caused significant alteration in the expression of numerous proteins in all three cell lines. Comparative analysis between cell types also showed most of the induced and repressed proteins were unique to a given cell line and did not match the induced or repressed proteins in either of the other cell lines. These results suggest that the response to chemical carcinogen treatment may be somewhat cell-specific and result in a variable response to the cells ability to respond to the chemical insult.

Two-dimensional gel electrophoretic analysis of cytoplasmic proteins from Friend erythroleukemia cells chemically induced to undergo terminal erythroid differentiation.

The proerythroblastoid Friend erythroleukemia cell (FELC) line, clone TR 19-9, was treated with 4 mM hexamethylene bisacetamide (HMBA) over a 6-day period. Greater than 94% of the FELC reacted positively to the benzidine assay for hemoglobin by Day 4 of treatment. Protein accumulation during the final 4 days of treatment (from Days 2 to 6) was monitored by labeling for 24-h periods with a 14C-labeled amino acid mixture. At the end of each radiolabeling time point, cells were harvested and cytoplasmic proteins were isolated and subjected to two-dimensional gel electrophoresis in triplicate. Short-term fluorographic exposures were made in the linear X-ray film response range to monitor those polypeptides which were most rapidly accumulated. Fluorographs were digitized for computer image analysis and gel data comparison rationales were used to combine the polypeptides contained on the replicate fluorographs into a single cytoplasmic polypeptide profile or Master Image for each of the two experimental conditions, control and HMBA-treated FELC. These two images were merged into a single Master Composite Image containing a total of 211 polypeptides so that those polypeptides common to both and/or unique to each of the experimental conditions could be viewed graphically in the same plane. A total of 98 polypeptides in HMBA-treated FELC were shown to have large accumulation rate differences from the control FELC;32 of these polypeptides were present in the HMBA Master Image which were not detected in the Control Master Image and 66 polypeptides were present in the Control Master Image but not detected in the HMBA Master Image. Five polypeptides, found in both Master Images, were shown to vary quantitatively in the HMBA-treated FELC from the corresponding polypeptides in the control. These quantitative data measurements on the rates of accumulation of various common polypeptides offer a mode for simultaneously monitoring the kinetics of induction and repression of many gene products throughout an experimental time course.

On multiparameter data analysis in flow cytometry.

Increasing numbers of parameters that are accessible to simultaneous measurement in flow cytometric instruments, combined with the extremely large sample sizes common in flow cytometry, make it necessary to examine methods of multivariate statistics for their applicability to problems of visualization and quantitative analysis of flow cytometric data. This article describes some approaches to dimensionality reduction that appear well suited for data sets obtained by flow cytometry.

The effects of alerting tasks on caloric induced vestibular nystagmus.

The present study compared the effects of four different mental altering tasks on the speed of the nystagmic slow component during caloric testing in 40 young adults. Subjects were randomly divided into four groups (10/group) and stimulated twice in each ear in a counterbalanced manner according to test ear, irrigating temperature, and alerting task. Analysis of the data revealed significant differences between treatment effects on the magnitude of the slow phase velocity of nystagmus. Results suggest that passive listening does not sufficiently alert subjects to ensure the adequate release of nystagmus suppression during vestibular testing.

Use of multiparameter analysis to quantitate hematological damage from exposure to a chemical (ethylene oxide).

This study was designed to test the value of a multiparameter approach in evaluating perturbations in bone marrow and peripheral blood elements of mice exposed to ethylene oxide (EtO). Mice exposed to 255 ppm EtO for 5 h/d were removed for analysis after 1, 2, 8, and 14 d (sequential exposure) and 4, 6, 8, and 10 wk (5 d/wk). Prior to sacrifice, blood was removed from the orbital sinus for blood cell counts, hemoglobin determination, and hematocrit. A blood film was made for differential leukocyte counts. Bone marrow was flushed from femurs and tibias and counted, and aliquot were used for stem-cell assay (CFU-S) or flow cytometry (FCM) analysis. One aliquot of marrow was stained with propidium iodide for cell-cycle analysis and another was reacted with fluorescein-conjugated monoclonal antibody for B-cell analysis. The preparations were analyzed for forward and 90 degrees scatter and fluorescence on an Ortho 50H cytofluorograph. Perturbations of peripheral leukocytes occurred after one exposure. After multiple exposures, hematocrit, red-cell number, and hemoglobin were generally depressed, with transient compensatory bursts, and bone marrow cellularity and CFU-S were below normal. However, white-cell numbers fluctuated dramatically during the exposure period. There was a shift in differential toward granulocytes, at times resulting in severely depressed numbers of lymphocytes in the peripheral blood. The FCM analysis showed an early depletion of granulocytes in the bone marrow followed by replacement and a relative lymphocyte deficit, especially pronounced at 10 wk. The B-cell changes reflected general lymphocyte perturbations. Shifts in numbers of cells in S and G/M were observed, consistent with a moderate bone marrow response to cell loss.

Critical sample sizes for determining the statistical significance of mutation frequencies.

Based on the assumption that the numbers of mutations observed in an untreated and treated sample of individuals are binomial random variables, a method is presented to compute the probability of observing a specific number of mutations as a function of the sample sizes and the number of mutations in the untreated control sample. Knowledge of the true mutation frequencies is not required. The formalism is then used to compute critical sample sizes for testing hypotheses concerning mutation frequencies in the two populations.

Application of flow cytometry to detection and characterization of Legionella spp.

Flow cytometry, using fluorescein-bound specific antibodies and propidium iodide, was shown to be effective in detecting Legionella spp. in cooling tower waters. The procedure was quicker and less labor intensive than fluorescent microscopy. The use of these procedures also identified qualitative differences, perhaps related to infectivity, in Legionella populations.

The use of projections for dimensionality reduction of flow cytometric data.

In order to visualize multiparameter flow cytometric measurements it is desirable to reduce the dimensionality of the data to two while preserving important features of each data pattern. We describe a method that projects two-parameter data onto a straight line that forms an angle theta with one of the original parameter axis. The angle is selected interactively or by principal component analysis. The procedure is applied on-line or off-line to pairs of parameters of the original data set that has been collected in LIST mode.

The randomization test applied to flow cytometric histograms.

The randomization test is used to test the hypothesis that two groups of flow cytometric histograms consist of samples from the same probability density function. The hypothesis is tested channel-by-channel. This non-parametric method does not require any assumptions as to the probability density functions involved and is therefore applicable to histograms from many different biological systems. Moreover, it allows for very few histograms per group so that the hypothesis can be tested on the basis of a small number of experiments. The procedure is implemented in PASCAL on a mini computer which is connected to a flow cytometer.

Parametric analysis of histograms measured in flow cytometry.

Flow cytometric histograms frequently consist of several components that show various degrees of overlap. For many types of analysis it is of great importance to decompose the original histogram into its components. To that purpose, we investigated the maximum likelihood approach in detail. It is shown that the iterative method to solve the maximum likelihood equations is well behaved for a variety of initial values. Algorithms to obtain initial values are presented, and the performance of the method is tested when applied to the analysis of DNA measurements from heterogeneous cell populations that differ with respect to DNA content.

Slit-scan flow cytometry: separability properties of cell features.

A model is presented to compare the separability of cell populations described by features measured in low resolution slit-scanning flow systems with their separability when the features are extracted from high resolution digitized cell images. The results show that although the accuracy of the feature measurements deteriorates for increasing slit width, this is not necessarily true for the discriminatory power of the features. Depending on their original position in the high resolution feature space, the cell populations may be located even farther apart in the space of low resolution slit-scan features for reasonably small widths of the slit. The results presented with high resolution images of cells from gynecological specimens and simulated slit-scan measurements can be explained by the model. For the features nuclear DNA content and diameter the abnormal populations are shifted closer to the normal populations in the slit-scan simulations as compared to the high resolution measurements. The cell classifier errors rates are unacceptably high.

Base pairing in messenger RNA's for small peptides.

Longest runs of Watson-Crick pairing in hypothetical m-RNA's for a number of natural peptides were no greater than those in the hypothetical m-RNA's for a large number of randomized amino acid sequences from these peptides. This shown that even if base-pairing in m-RNA were a biological requirement, it would little constrain the amino acid sequence.