Efficacy of chemical and fluorescent protein markers in studying plant colonization by endophytic non-pathogenic <Emphasis Type="Italic">Fusarium oxysporum</Emphasis> isolates

In studying plant colonization by inoculated Fusarium oxysporum endophytes, it is important to be able to distinguish inoculated isolates from saprophytic strains. In the current study, F. oxysporum isolates were transformed with the green (GFP) and red fluorescent protein (DsRed) genes, and benomyl- and chlorate-resistant mutant isolates were also developed. The benomyl- and chlorate-resistant mutants, and the fluorescently labelled transformants, were able to grow on potato dextrose agar amended with 20 mg Benlate^® l^?1, 30 g chlorate l^?1 and 150 μg hygromycin ml^?1, respectively. Single spores of all mutants remained stable after several transfers on non-selective media. Most mutants and transformants produced colony diameters that did not differ significantly from that of their wild-type progenitors after 7 days of growth on non-selective media. Few mutants, however, had growth rates that were either slower or faster than for their wild-types. Plant colonization studies showed that root and rhizome tissue colonization by most benomyl- and chlorate-resistant mutants was similar to that of their wild-type isolates. Unlike GFP transformants, DsRed transformants were difficult to visualize in planta. Both the mutants and transformants can be used for future studies to investigate colonization, distribution and survival of biocontrol F. oxysporum endophytes in banana plants.     

Systematic placement of the basidiomycetous yeastCystofilobasidium lari-marini comb. nov. as predicted by rRNA nucleotide sequence analysis

Based on similarities in basidial morphology and nucleotide sequences of the V3 variable region in the large sub-unit ribosomal RNA, the yeastLeucosporidium lari-marini is considered phylogenetically related to the genusCystofilobasidium. Therefore the new combinationCystofilobasidium lari-marini is proposed.     

Über die einwirkung von Röntgenstrahlen auf Amphibienlarven

Ohne Zusammenfassung Mit 22 Textabbildungen.     

Intermediates in the oxidative pathway from torulene to torularhodin in the red yeasts Cystofilobasidium infirmominiatum and C. capitatum (Heterobasidiomycetes, Fungi)

Two red Cystofilobasidium spp. isolated from spring sap-flows of Betula pendula were analysed for their carotenoid content. In Cystofilobasidium infirmominiatum, three unusual pigments were detected and identified by structure elucidation as oxidised torulene derivatives. These included 16'-hydroxytorulene and torularhodinaldehyde, two carotenoids known so far only from chemical synthesis or as postulated biosynthetic intermediates en route to torularhodin. Unprecedented formation of beta-apo-2'-carotenal was also observed. The production of these pigments in pure culture was dependent on enhanced oxidative stress caused by cultivation in well-aerated (indented) flasks with or without 2% ethanol (16'-hydroxytorulene), or with 100 microM duroquinone (torularhodinaldehyde and beta-apo-2'-carotenal). Among these three pigments, only 16'-hydroxytorulene was detected in C. capitatum. Torularhodin, a common end product of carotenoid oxidation in red yeasts, was not produced by either species under any incubation conditions. Biosynthetic aspects of incomplete oxidation of torulene by these Cystofilobasidium spp. are discussed.     

FogBank: a single cell segmentation across multiple cell lines and image modalities

Background

Many cell lines currently used in medical research, such as cancer cells or stem cells, grow in confluent sheets or colonies. The biology of individual cells provide valuable information, thus the separation of touching cells in these microscopy images is critical for counting, identification and measurement of individual cells. Over-segmentation of single cells continues to be a major problem for methods based on morphological watershed due to the high level of noise in microscopy cell images. There is a need for a new segmentation method that is robust over a wide variety of biological images and can accurately separate individual cells even in challenging datasets such as confluent sheets or colonies.

Results

We present a new automated segmentation method called FogBank that accurately separates cells when confluent and touching each other. This technique is successfully applied to phase contrast, bright field, fluorescence microscopy and binary images. The method is based on morphological watershed principles with two new features to improve accuracy and minimize over-segmentation.First, FogBank uses histogram binning to quantize pixel intensities which minimizes the image noise that causes over-segmentation. Second, FogBank uses a geodesic distance mask derived from raw images to detect the shapes of individual cells, in contrast to the more linear cell edges that other watershed-like algorithms produce.We evaluated the segmentation accuracy against manually segmented datasets using two metrics. FogBank achieved segmentation accuracy on the order of 0.75 (1 being a perfect match). We compared our method with other available segmentation techniques in term of achieved performance over the reference data sets. FogBank outperformed all related algorithms. The accuracy has also been visually verified on data sets with 14 cell lines across 3 imaging modalities leading to 876 segmentation evaluation images.

Conclusions

FogBank produces single cell segmentation from confluent cell sheets with high accuracy. It can be applied to microscopy images of multiple cell lines and a variety of imaging modalities. The code for the segmentation method is available as open-source and includes a Graphical User Interface for user friendly execution.

Electronic supplementary material

The online version of this article (doi:10.1186/s12859-014-0431-x) contains supplementary material, which is available to authorized users.     

Photoprotective pigment as an adaptive strategy in the antarctic moss Ceratodon purpureus

Summary Variation in leaf pigmentation from green to ginger is observed for Ceratodon purpureus (Hedw.) Brid. in Antarctica. Electron microscopy of ginger and green leaves reveals less thylakoid stacking, a response to greater light exposure, in the ginger leaves. In extremely exposed sites C. purpureus has low chlorophyll a/b ratios which correlate with decreased 77K chlorophyll fluorescence, indicating damage to chlorophyll a. Pigment analysis of ginger moss shows that even when the chlorophyll a/b ratio has not decreased the pigment composition differs from green moss. The increase in anthocyanin and decrease in chlorophyll concentrations largely account for the visual change from green to ginger. The ratio of total carotenoid to chlorophyll varies from 0.35 in green moss to 0.55 in the ginger moss, with violaxanthin increased preferentially. Since these changes in pigmentation are consistent with photoprotection and they are linked to light dependent variations in chloroplast structure, it appears that photoprotective pigments are a useful adaptation for the bright Antarctic environment.     

Dendritic cells: driving the differentiation programme of T cells in viral infections

Protective immunity against viral pathogens depends on the generation and maintenance of a small population of memory CD8(+) T cells. Successful memory cell generation begins with early interactions between na?ve T cell and dendritic cells (DCs) within the inflammatory milieu of the secondary lymphoid tissues. Recent insights into the role of different populations of DCs, and kinetics of antigen presentation, during viral infections have helped to understand how DCs can shape the immune response. Here, we review the recent progress that has been made towards defining how specific DC subsets drive effector CD8(+) T-cell expansion and differentiation into memory cells. Further, we endeavour to examine how the molecular signals imparted by DCs coordinate to generate protective CD8(+) T-cell immunity.     

Genetic control of wheat quality: interactions between chromosomal regions determining protein content and composition, dough rheology, and sponge and dough baking properties

While the genetic control of wheat processing characteristics such as dough rheology is well understood, limited information is available concerning the genetic control of baking parameters, particularly sponge and dough (S&D) baking. In this study, a quantitative trait loci (QTL) analysis was performed using a population of doubled haploid lines derived from a cross between Australian cultivars Kukri × Janz grown at sites across different Australian wheat production zones (Queensland in 2001 and 2002 and Southern and Northern New South Wales in 2003) in order to examine the genetic control of protein content, protein expression, dough rheology and sponge and dough baking performance. The study highlighted the inconsistent genetic control of protein content across the test sites, with only two loci (3A and 7A) showing QTL at three of the five sites. Dough rheology QTL were highly consistent across the 5 sites, with major effects associated with the Glu-B1 and Glu-D1 loci. The Glu-D1 5 + 10 allele had consistent effects on S&D properties across sites; however, there was no evidence for a positive effect of the high dough strength Glu-B1-al allele at Glu-B1. A second locus on 5D had positive effects on S&D baking at three of five sites. This study demonstrated that dough rheology measurements were poor predictors of S&D quality. In the absence of robust predictive tests, high heritability values for S&D demonstrate that direct selection is the current best option for achieving genetic gain in this product category. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.