Characterization and potential evolutionary impact of transposable elements in the genome of Cochliobolus heterostrophus

Background

Cochliobolus heterostrophus is a dothideomycete that causes Southern Corn Leaf Blight disease. There are two races, race O and race T that differ by the absence (race O) and presence (race T) of ~ 1.2-Mb of DNA encoding genes responsible for the production of T-toxin, which makes race T much more virulent than race O. The presence of repetitive elements in fungal genomes is considered to be an important source of genetic variability between different species.

Results

A detailed analysis of class I and II TEs identified in the near complete genome sequence of race O was performed. In total in race O, 12 new families of transposons were identified. In silico evidence of recent activity was found for many of the transposons and analyses of expressed sequence tags (ESTs) demonstrated that these elements were actively transcribed. Various potentially active TEs were found near coding regions and may modify the expression and structure of these genes by acting as ectopic recombination sites. Transposons were found on scaffolds carrying polyketide synthase encoding genes, responsible for production of T-toxin in race T. Strong evidence of ectopic recombination was found, demonstrating that TEs can play an important role in the modulation of genome architecture of this species. The Repeat Induced Point mutation (RIP) silencing mechanism was shown to have high specificity in C. heterostrophus, acting only on transposons near coding regions.

Conclusions

New families of transposons were identified. In C. heterostrophus, the RIP silencing mechanism is efficient and selective. The co-localization of effector genes and TEs, therefore, exposes those genes to high rates of point mutations. This may accelerate the rate of evolution of these genes, providing a potential advantage for the host. Additionally, it was shown that ectopic recombination promoted by TEs appears to be the major event in the genome reorganization of this species and that a large number of elements are still potentially active. So, this study provides information about the potential impact of TEs on the evolution of C. heterostrophus.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-536) contains supplementary material, which is available to authorized users.     

Physiological responses of free-swimming adult coho salmon to simulated predator and fisheries encounters

The responses of free-swimming adult coho salmon (Oncorhynchus kisutch) to simulated predator and fisheries encounters were assessed by monitoring heart rate (f(H)) with implanted data loggers and periodically taking caudal blood samples. A 10- or 30-min corralling treatment was conducted to simulate conspecifics being cornered by a predator or corralled by fisheries gear without physical contact. Corralling rapidly doubled f(H) from ～31 beats min(-1) to a maximum of ～60 beats min(-1), regardless of the duration of the corralling. However, recovery of f(H) to precorralling levels was significantly faster after the 10-min corralling (7.6 h) than after the 30-min corralling (11.5 h). An exhaustive-exercise treatment (chasing for 3 min, with physical contact) to simulate a predator chasing a fish to exhaustion or a fish becoming exhausted after encountering fisheries gear resulted in increased f(H) (to 60 beats min(-1)), plasma lactate, glucose, sodium, osmolality, and cortisol (males only) and a significant decrease in mean corpuscular hemoglobin concentration. Recovery of f(H) and most blood variables was complete about 16 h after exhaustive exercise and handling. The results illustrate a clear relationship between the intensity of exercise and the duration required for recovery of f(H). Changes in f(H) were significantly correlated with those in plasma lactate, chloride, and sodium at 1 h after the exercise treatment protocols. Thus, measurements of f(H) may provide an accurate indication of the general physiological response of salmonids to exhaustive exercise in the natural environment.     

Effects of evaporative cooling on reproductive performance and milk production of dairy cows in hot wet conditions

Fourteen animals of second and third lactation of Thai Friesian crossbred cows (87.5% Friesian × 12.5% Bos indicus) located at Sakol Nakhon Research and Breeding Centre, Department of Livestock Development, Ministry of Agriculture and Cooperatives, were divided randomly into two groups of seven each to evaluate the effects of evaporative cooling on reproductive and physiological traits under hot, humid conditions. Results indicated that installation of evaporating cooling in the open shed gave a further improvement in ameliorating heat stress in dairy cows in hot-wet environments by utilising the low humidity conditions that naturally occur during the day. The cows housed in an evaporatively cooled environment had both a rectal temperature and respiration rate (39.09°C, 61.39 breaths/min, respectively) significantly lower than that of the non-cooled cows (41.21°C; 86.87 breaths/min). The former group also had higher milk yield and more efficient reproductive performance (pregnancy rate and reduced days open) than the latter group. It is suggested that the non-evaporatively cooled cows did not gain benefit from the naturally lower heat stress during night time.     

Array2BIO: from microarray expression data to functional annotation of co-regulated genes

Background  

There are several isolated tools for partial analysis of microarray expression data. To provide an integrative, easy-to-use and automated toolkit for the analysis of Affymetrix microarray expression data we have developed Array2BIO, an application that couples several analytical methods into a single web based utility.     

Swimming patterns and behaviour of upriver-migrating adult pink (Oncorhynchus gorbuscha) and sockeye (O. nerka) salmon as assessed by EMG telemetry in the Fraser River,British Columbia,Canada

Little is known about the behaviour patterns and swimming speed strategies of anadromous upriver migrating fish. We used electromyogram telemetry to estimate instantaneous swimming speeds for individual sockeye (Oncorhynchus nerka) and pink salmon (O. gorbuscha) during their spawning migrations through reaches which spanned a gradient in river hydraulic features in the Fraser River, British Columbia. Our main objectives were to describe patterns of individual-specific swim speeds and behaviours, identify swimming speed strategies and contrast these between sexes, species and reaches. Although mean swimming speeds did not differ between pink salmon (2.21 BL s^–1) and sockeye salmon (1.60 BL s^–1), sockeye salmon were over twice as variable (mean CV; 54.78) in swimming speeds as pink salmon (mean CV; 22.54). Using laboratory-derived criteria, we classified swimming speeds as sustained (<2.5 BL s^–1), prolonged (2.5–3.2 BL s^–1), or burst (>3.2 BL s^–1). We found no differences between sexes or species in the proportion of total time swimming in these categories – sustained (0.76), prolonged (0.18), burst (0.06); numbers are based on species and sexes combined. Reaches with relatively complex hydraulics and fast surface currents had migrants with relatively high levels of swimming speed variation (e.g., high swimming speed CV, reduced proportions of sustained speeds, elevated proportions of burst speeds, and high rates of bursts) and high frequency of river crossings. We speculate that complex current patterns generated by river constrictions created confusing migration cues, which impeded a salmon's ability to locate appropriate pathways.     

Response ofZea mays roots to infection withPhytophthora cinnamomi

Summary Zea mays is a non-host ofPhytophthora cinnamomi; plants survive contact with this fungus both in the field and in pot trials. TheZ. mays-P. cinnamomi interaction has been studied by light and electron microscopy. In the epidermal layer, fungal hyphae grow intercellularly through the middle lamella. This is always the case for the first hyphal contact with any cell. Hyphae making second or subsequent contacts with a cell grow preferentially between the cell wall and plasma membrane of the infected cell rather than through the middle lamella.Papillae (callose deposits) are formed in response to some, but not all, regions of contact between the plant cell and the hypha. They do not completely encase the hypha and do not stop hyphal growth. The plasma membrane-cell wall interface of the host cell must be intact for effective papilla formation, as papillae are rarely formed when the hyphae grow between the plasma membrane and the cell wall.     

The microbiology of pine bark composting: An Electron-microscope and physiological study

An electron microscope study was conducted on samples of pine bark taken from stacks during consecutive stages of composting. It was found using scanning electron microscopy (SEM) that bacteria, actinomycetes and fungi were present in relatively low numbers on the bark surface before composting was initiated. After addition of urea and water to bark heaps, microbial numbers rose, particularly the bacterial fraction. A large number of actinomycetes were seen below the surface of the bark as composting progressed. Transmission electron microscopy (TEM) of bark in the late stages of composting demonstrated the presence of a variety of microbes within the bark cells. The microorganisms were seen, using SEM, to be degrading the surface of the bark chips, and, using TEM, to be attached to the lignified cell walls. Physiological studies on bacteria isolated at different stages of composting showed they had a number of enzymes such as carboxymethyl cellulase that could aid in the degradation of pine bark. The isolates consisted of Gram-negative and Gram-positive strains, some of which were spore formers. Most of the isolates, including some Gram-negative non-sporing bacteria, were able to grow over a wide range of temperatures from 30 to 60°C, and, in some cases, 70°C.     

Diversity of free-living ‘naked’ amoeboid organisms

Amoeboid organisms are phylogenetically diverse, some being more closely related to plants or metazoans than to each other. Amoeboid organisms are ecologically successful, having been isolated on all continents, including Antarctica, as well as being the main predators controlling bacterial populations in soil. The classification of these organisms has historically relied upon morphological characteristics. The application of electron microscopy, comparison of enzymic profiles after electrophoretic separation, and analysis of nucleic acid fractions have provided reliable bases for classifying amoeboid organisms. The extent of diversity of these organisms has been recognized, as methods to detect, culture, characterize and identify them has increased. It is reasonable to anticipate that the current 40 000 species of protists will increase substantially as amoeboid organisms are cultivated from poorly accessible niches and from extreme environs.