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

/pdf/fumonisins-from-aspergillus-niger-in-grapes-and-derived-31z0bh8hbn.pdf

Fumonisins from Aspergillus niger in grapes and derived products

Natural Occurrence oftheMycotoxin Fusarochromanone, a Metabolite ofFusarium equiseti, inCereal FeedAssociated with Tibial Dyschondroplasia

Classical procedures for identification of fungi at species level are based on observation of morphological characters, in some cases supported by visual detection of pigmentation. For mushrooms and other fleshy fungi tasting and sniffing to the specimen are also used. The fungal taxonomy which is the base for identification keys is mainly based on morphological characters. However, morphology is only part of the extrovert differentiation. Another part is a chemical fingerprint of biological active compounds such as antibiotics, exoenzymes, volatiles, toxic compounds, pigments a.o. The chemical characters should be regarded just as important in taxonomy as morphological characters. Similar to morphological structures production of secondary metabolites are based on expressions of hundreds of genes. The profile of biological active chemicals is very important for survival of an organism in nature. The need of multidisciplinary data within fungal taxonomy is now accepted among many mycologists which is reflected by an increasing number of publications on fungal systematics using a holistic approach.

Ulf Thrane

Papers

Fumonisins from Aspergillus niger in grapes and derived products

Natural Occurrence oftheMycotoxin Fusarochromanone, a Metabolite ofFusarium equiseti, inCereal FeedAssociated with Tibial Dyschondroplasia

Identification of Fungi by Secondary Metabolites