Rapid improvements in sequencing and array-based platforms are resulting in a flood of diverse genome-wide data, including data from exome and whole-genome sequencing, epigenetic surveys, expression profiling of coding and noncoding RNAs, single nucleotide polymorphism (SNP) and copy number profiling, and functional assays. Analysis of these large, diverse data sets holds the promise of a more comprehensive understanding of the genome and its relation to human disease. Experienced and knowledgeable human review is an essential component of this process, complementing computational approaches. This calls for efficient and intuitive visualization tools able to scale to very large data sets and to flexibly integrate multiple data types, including clinical data. However, the sheer volume and scope of data pose a significant challenge to the development of such tools.

Integrative Genomics Viewer

(1991). Applied Linear Regression Models. Journal of Quality Technology: Vol. 23, No. 1, pp. 76-77.

Applied Linear Regression Models

Arbuscular mycorrhiza (AM), a symbiosis between plants and members of an ancient phylum of fungi, the Glomeromycota, improves the supply of water and nutrients, such as phosphate and nitrogen, to the host plant. In return, up to 20% of plant-fixed carbon is transferred to the fungus. Nutrient transport occurs through symbiotic structures inside plant root cells known as arbuscules. AM development is accompanied by an exchange of signalling molecules between the symbionts. A novel class of plant hormones known as strigolactones are exuded by the plant roots. On the one hand, strigolactones stimulate fungal metabolism and branching. On the other hand, they also trigger seed germination of parasitic plants. Fungi release signalling molecules, in the form of 'Myc factors' that trigger symbiotic root responses. Plant genes required for AM development have been characterized. During evolution, the genetic programme for AM has been recruited for other plant root symbioses: functional adaptation of a plant receptor kinase that is essential for AM symbiosis paved the way for nitrogen-fixing bacteria to form intracellular symbioses with plant cells.

Arbuscular mycorrhiza: the mother of plant root endosymbioses.

Biocontrol fungi (BCF) are agents that control plant diseases. These include the well-known Trichoderma spp. and the recently described Sebacinales spp. They have the ability to control numerous foliar, root, and fruit pathogens and even invertebrates such as nematodes. However, this is only a subset of their abilities. We now know that they also have the ability to ameliorate a wide range of abiotic stresses, and some of them can also alleviate physiological stresses such as seed aging. They can also enhance nutrient uptake in plants and can substantially increase nitrogen use efficiency in crops. These abilities may be more important to agriculture than disease control. Some strains also have abilities to improve photosynthetic efficiency and probably respiratory activities of plants. All of these capabilities are a consequence of their abilities to reprogram plant gene expression, probably through activation of a limited number of general plant pathways.

/pdf/induced-systemic-resistance-and-plant-responses-to-fungal-1iv7dpy3wl.pdf

Induced Systemic Resistance and Plant Responses to Fungal Biocontrol Agents

Filamentous fungi are unique organisms-rivaled only by actinomycetes and plants-in producing a wide range of natural products called secondary metabolites. These compounds are very diverse in structure and perform functions that are not always known. However, most secondary metabolites are produced after the fungus has completed its initial growth phase and is beginning a stage of development represented by the formation of spores. In this review, we describe secondary metabolites produced by fungi that act as sporogenic factors to influence fungal development, are required for spore viability, or are produced at a time in the life cycle that coincides with development. We describe environmental and genetic factors that can influence the production of secondary metabolites. In the case of the filamentous fungus Aspergillus nidulans, we review the only described work that genetically links the sporulation of this fungus to the production of the mycotoxin sterigmatocystin through a shared G-protein signaling pathway.

/pdf/relationship-between-secondary-metabolism-and-fungal-2kcz9g7ogb.pdf

Relationship between Secondary Metabolism and Fungal Development

Infection structures of phytopathogenic fungi are modified hyphae specialized for the invasion of plant tissues. Initial events are adhesion to the cuticle and directed growth of the germ tube on the plant surface. At the site of penetration, appressoria are often formed that may have melanized walls and develop high turgor pressure to support the penetration process. The penetration hypha accumulates components of the cytoskeleton in the tip and secretes a variety of cell wall‐degrading enzymes in a highly regulated fashion in order to penetrate the cuticle and the plant cell wall. This article reviews recent papers on the cytology, physiology, and molecular biology of the penetration process.

/pdf/morphogenesis-and-mechanisms-of-penetration-by-plant-4a74p0yaon.pdf

Morphogenesis and mechanisms of penetration by plant pathogenic fungi

When and how to kill a plant cell: infection strategies of plant pathogenic fungi.

Many plant pathogenic fungi, such as the cereal pathogen Colletotrichum graminicola, differentiate highly specialized infection structures called appressoria, which send a penetration peg into the underlying plant cell. Appressoria have been shown to generate enormous turgor pressure, but direct evidence for mechanical infection of plants by fungi is lacking. A microscopic method was developed that uses elastic optical waveguides to visualize and measure forces locally exerted by single appressoria. By this method, the force exerted by appressoria of C. graminicola was found to be about 17 micronewtons.

/pdf/optical-measurements-of-invasive-forces-exerted-by-8bfbe0mpj1.pdf

Optical Measurements of Invasive Forces Exerted by Appressoria of a Plant Pathogenic Fungus

Summary
• Conversion of surface-exposed chitin to chitosan in cell walls of in vitro - and in vivo -differentiated infection structures of two rust fungi, the wheat stem rust fungus Puccinia graminis f. sp. tritici and the broad bean rust fungus Uromyces fabae , and of the causal agent of maize anthracnose, Colletotrichum graminicola , were studied.
• Epi-fluorescence microscopy with the fluorescence-labeled lectin wheat germ agglutinin (WGA) revealed that surfaces of infection structures formed on the plant cuticle expose chitin, whereas surfaces of structures formed after invading the host do not.
• To identify chitin modification by de- N -acetylation, we raised polyclonal antibodies specifically recognizing de- N -acetylated chitosan. These antibodies labeled only those infection structures that differentiate inside the plant, indicating that chitosan is exposed on cell wall surfaces post penetration.
• Surface modification of the fungal cell walls by chitin de- N -acetylation is discussed as a fungal strategy to protect cell walls of pathogenic hyphae from enzymatic hydrolysis by host chitinases, and to avoid generation of an auto-catalytic defense response system in the invaded host tissue.

Developmentally regulated conversion of surface‐exposed chitin to chitosan in cell walls of plant pathogenic fungi

SUMMARY
Many fungi differentiate specific infection structures in order to infect the host plant. The spore attaches to the host surface, the cuticle, and the germ tube may recognize suitable penetration sites, over which an appressorium is formed. Additional wall layers in appressoria of many fungi suggest that this structure supports increasing pressure during the penetration process. During appressorium formation, synthesis of polymer-degrading enzymes is often initiated. Cutinases, cellulases and pectin-degrading enzymes can be formed in a developmentally controlled or adaptive, i.e. substrate-dependent, fashion. The penetration hypha develops below the appressorium. This hypha has a new wall structure and exhibits features which serve to breach the plant cell wall. However, at present it is not clear whether penetration hyphae arising from appressoria are more efficient in penetration or induce less damage than hyphae which penetrate without detectable special adaptations. The infection hypha differentiates within the host. During differentiation a characteristic set of enzymes is synthesized to enable successful establishment of the host-pathogen relationship. If, as in most cases, multiple forms of cell wall-degrading enzymes are formed by the pathogen, mutagenesis or deletion of a gene encoding one of these enzymes very often has no effect on pathogenicity or even virulence. Proof is missing very often that an enzyme is needed at the right time and at the right site of infection.

Events occurring during differentiation of fungal infection structures are reviewed with special emphasis on Magnaporthe grisea, Colletotrichum spp., and rust fungi, and common features which may be of importance to the success of infection are discussed.

/pdf/infection-structures-of-fungal-plant-pathogens-a-cytological-39dvgy5c82.pdf

Holger B. Deising

Papers

Morphogenesis and mechanisms of penetration by plant pathogenic fungi

When and how to kill a plant cell: infection strategies of plant pathogenic fungi.

Optical Measurements of Invasive Forces Exerted by Appressoria of a Plant Pathogenic Fungus

Developmentally regulated conversion of surface‐exposed chitin to chitosan in cell walls of plant pathogenic fungi

Infection structures of fungal plant pathogens – a cytological and physiological evaluation