抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

The nuclear ribosomal internal transcribed spacer (ITS) region is the formal fungal barcode and in most cases the marker of choice for the exploration of fungal diversity in environmental samples. Two problems are particularly acute in the pursuit of satisfactory taxonomic assignment of newly generated ITS sequences: (i) the lack of an inclusive, reliable public reference data set and (ii) the lack of means to refer to fungal species, for which no Latin name is available in a standardized stable way. Here, we report on progress in these regards through further development of the UNITE database (http://unite.ut.ee) for molecular identification of fungi. All fungal species represented by at least two ITS sequences in the international nucleotide sequence databases are now given a unique, stable name of the accession number type (e.g. Hymenoscyphus pseudoalbidus|GU586904|SH133781.05FU), and their taxonomic and ecological annotations were corrected as far as possible through a distributed, third-party annotation effort. We introduce the term ‘species hypothesis’ (SH) for the taxa discovered in clustering on different similarity thresholds (97–99%). An automatically or manually designated sequence is chosen to represent each such SH. These reference sequences are released (http://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and in the QIIME pipeline. The system and the data will be updated automatically as the number of public fungal ITS sequences grows. We invite everybody in the position to improve the annotation or metadata associated with their particular fungal lineages of expertise to do so through the new Web-based sequence management system in UNITE.

http://web.stanford.edu/~kpeay/papers/Koljalg_2013_MEC.pdf

Towards a unified paradigm for sequence-based identification of fungi

https://cbs.umn.edu/sites/cbs.umn.edu/files/public/downloads/Nguyenetal2015b.pdf

FUNGuild: An open annotation tool for parsing fungal community datasets by ecological guild

EVidenceModeler (EVM) is presented as an automated eukaryotic gene structure annotation tool that reports eukaryotic gene structures as a weighted consensus of all available evidence. EVM, when combined with the Program to Assemble Spliced Alignments (PASA), yields a comprehensive, configurable annotation system that predicts protein-coding genes and alternatively spliced isoforms. Our experiments on both rice and human genome sequences demonstrate that EVM produces automated gene structure annotation approaching the quality of manual curation.

/pdf/automated-eukaryotic-gene-structure-annotation-using-3fo28wpira.pdf

Automated Eukaryotic Gene Structure Annotation Using EVidenceModeler and the Program to Assemble Spliced Alignments

This review addresses recent developments in non-equilibrium statistical physics. Focusing on phase transitions from fluctuating phases into absorbing states, the universality class of directed percolation is investigated in detail. The survey gives a general introduction to various lattice models of directed percolation and studies their scaling properties, field-theoretic aspects, numerical techniques, as well as possible experimental realizations. In addition, several examples of absorbing-state transitions which do not belong to the directed percolation universality class will be discussed. As a closely related technique, we investigate the concept of damage spreading. It is shown that this technique is ambiguous to some extent, making it impossible to define chaotic and regular phases in stochastic non-equilibrium systems. Finally, we discuss various classes of depinning transitions in models for interface growth which are related to phase transitions into absorbing states.

Non-equilibrium critical phenomena and phase transitions into absorbing states

Methods for the screening of fungal cultures for toxic secondary metabolites are reviewed. Thin layer Chromatography (TLC) and high-performance liquid Chromatography (HPLC) are good general analytical methods for secondary metabolites in unpurified extracts. The combination of normal phase TLC using different chemical spray reagents with reversed phase HPLC, using alkylphenone retention indices and diode array detection, is a powerful technique for identifying the individual mycotoxins detected. The results of the screening methods are very dependent of the growth media and incubation conditions and a general method for the detection ofPenicillium, Aspergillus, Fusarium, Alternaria andCladosporium toxins is suggested.

Analysis and screening for mycotoxins and other secondary metabolites in fungal cultures by thin-layer chromatography and high-performance liquid chromatography

In the literature and in our own experience, significant variations occur in morphological characteristics and production of secondary metabolites by cultures grown on YES (2% yeast extract and 15% sucrose) agar, a substrate which is often used in screening for mycotoxins in moulds In this investigation we have demonstrated a very significant influence of yeast extract brand (Difco, Sigma Y4000 and Y0325, Oxoid, Merck, Lab M and Gibco) on the production of mycotoxins in YES by some important Penicillia Using a TLC screening method the variation in mycotoxin production due to the use of different brands of yeast extract ranged between detection in 5 days and none detected in 4 weeks The difference in mycotoxin production was often accompanied by differences in several other characteristics like pH changes of the substrate, sporulation, colony diameter and reverse colour We have been unable to find which components in the yeast extracts were responsible for the observed changes, but the addition of MgSO4 appeared to be a satisfactory compensation in most respects So it is suggested that this compound in general is added to the YES formula, along with previously suggested compounds like ZnSO4 and CuSO4, thus making this substrate a very valuable and reliable tool in screening for production of secondary metabolites and in mould taxonomy Further it is suggested to use pH registration monitoring in the cultures parallel to screening for secondary metabolites, since pH differences proved to be a useful indication of significant changes in the detected profiles

The significance of yeast extract composition on metabolite production in Penicillium.

Forty-four Trichoderma strains from water-damaged building materials or indoor dust were classified with chromatographic image analysis on full chromatographic matrices obtained by high performance liquid chromatography with UV detection of culture extracts. The classes were compared with morphological identification and rDNA sequence data, and for each class all strains were of the same identity. With all three techniques each strain – except one – was identified as the same species. These strains belonged to Trichoderma atroviride (nine strains), Trichoderma viride (three strains), Trichoderma harzianum (10 strains), Trichoderma citrinoviride (12 strains), and Trichoderma longibrachiatum (nine strains). The odd strain was identified as Trichoderma hamatum by morphology and rDNA sequencing, but not by image analysis as no reference strains of this species were included. It is concluded that the secondary metabolite profile contains sufficient information for classification and species identification.

Identification of Trichoderma strains by image analysis of HPLC chromatograms

A simple screening method was used to investigate mycotoxin production among 114 Fusarium isolates. Zearalenone, T‐2 toxin, HT‐2 toxin, diacetoxyscirpenol, neosolaniol, deoxynivalenol, nivalenol, fusarenon‐X, butenolide, moniliformin and equisetin were detected. The importance of the use of a range of different substrates for mycotoxin production was proved.

Detection of toxigenic Fusarium isolates by thin layer chromatography

The variation in the photostability among the currently authorized natural pigments limits their application span to a certain type of food system, and more robust alternatives are being sought after to overcome this problem. In the present study, the photostability of an orange-red and a yellow fungal pigment extract produced by ascomycetous fungi belonging to the genera Penicillium and Epicoccum , respectively, were studied in a soft drink model medium and in citrate buffer at low and neutral pH. The quantitative and qualitative color change pattern of the fungal pigment extracts indicated an enhanced photostability of fungal pigment extracts compared to the commercially available natural colorants Monascus Red and turmeric used as controls. Yellow components of the orange-red fungal pigment extract were more photostable than the red components. Chemistry of the photodegradation of the orange-red pigment extract was studied by high-performance liquid chromatography-diode array detection-mass spectrometry (HPLC-DAD-MS), and a light-induced formation of a structural analogue of sequoiamonascin C, a Monascus -like polyketide pigment discovered in the extract of Penicillium aculeatum IBT 14263 on yeast extract sucrose (YES) medium, was confirmed in the soft drink medium at pH 7.

Ulf Thrane

Papers

Analysis and screening for mycotoxins and other secondary metabolites in fungal cultures by thin-layer chromatography and high-performance liquid chromatography

The significance of yeast extract composition on metabolite production in Penicillium.

Identification of Trichoderma strains by image analysis of HPLC chromatograms

Detection of toxigenic Fusarium isolates by thin layer chromatography

Photostability of natural orange-red and yellow fungal pigments in liquid food model systems.