Function and transmission of accessory chromosomes in Zymoseptoria tritici

Accessory chromosomes are non-essential genetic elements and defined by a presence/absence polymorphism within a population. During meiosis a number of fungal accessory chromosomes are transmitted in a non-Mendelian way. The involved exact processes are as yet unclear. The objectives of this PhD thesis are to improve our understanding of the function of the accessory chromosomes of the haploid fungus Zymoseptoria tritici and the mechanisms underlying their mitotic and meiotic transmission. This ascomycete fungus is an important pathogen of wheat causing a diphasic, hemibiotrophic infection. For the functional characterization, I used a forward genetics approach by generating isogenic whole chromosome deletion strains for each of the eight distinct accessory chromosome in the reference isolate IPO323. I could show that in contrast to other fungal accessory chromosomes, most accessory chromosomes in Z. tritici confer a fitness cost during infection of the host. Fitness costs should lead to rapid elimination of these chromosomes from the population. I therefore hypothesized that the continued maintenance of the accessory chromosomes is due to a transmission advantage during meiosis. I thus compared the meiotic transmission of the accessory chromosomes in the presence or absence of a homolog. My results revealed that unpaired accessory chromosomes of Z. tritici have a transmission advantage, as they are inherited by more than the expected 50% of the progeny. This effect is caused by the transmission of female-inherited unpaired chromosomes to all meiotic progeny instead of the expected half. This meiotic drive is most likely based on an additional DNA replication step that is restricted to the female-inherited unpaired chromosomes. This mechanism represents a completely novel aspect of meiosis and could have broader implications for the transmission of unpaired accessory chromosomes in general

Ago1 Affects the Virulence of the Fungal Plant Pathogen Zymoseptoria tritici

In host-pathogen interactions RNA interference (RNAi) has emerged as a pivotal mechanism to modify both, the immune responses of the host as well as the pathogenicity and virulence of the pathogen. In addition, in some fungi RNAi is also known to affect chromosome biology via its effect on chromatin conformation. Previous studies reported no effect of the RNAi machinery on the virulence of the fungal plant pathogen Zymoseptoria tritici however the role of RNAi is still poorly understood in this species. Herein, we elucidate whether the RNAi machinery is conserved within the genus Zymoseptoria. Moreover, we conduct functional analyses of Argonaute and Dicer-like proteins and test if the RNAi machinery affects chromosome stability. We show that the RNAi machinery is conserved among closely related Zymoseptoria species while an exceptional pattern of allelic diversity was possibly caused by introgression. The deletion of Ago1 reduced the ability of the fungus to produce asexual propagules in planta in a quantitative matter. Chromosome stability of the accessory chromosome of Z. tritici was not prominently affected by the RNAi machinery. These results indicate, in contrast to previous finding, a role of the RNAi pathway during host infection, but not in the stability of accessory chromosomes in Z. tritici

Design of a Flexible Component Gathering Algorithm for Converting Cell-based Models to Graph Representations for Use in Evolutionary Search

Background The ability of science to produce experimental data has outpaced the ability to effectively visualize and integrate the data into a conceptual framework that can further higher order understanding. Multidimensional and shape-based observational data of regenerative biology presents a particularly daunting challenge in this regard. Large amounts of data are available in regenerative biology, but little progress has been made in understanding how organisms such as planaria robustly achieve and maintain body form. An example of this kind of data can be found in a new repository (PlanformDB) that encodes descriptions of planaria experiments and morphological outcomes using a graph formalism. Results We are developing a model discovery framework that uses a cell-based modeling platform combined with evolutionary search to automatically search for and identify plausible mechanisms for the biological behavior described in PlanformDB. To automate the evolutionary search we developed a way to compare the output of the modeling platform to the morphological descriptions stored in PlanformDB. We used a flexible connected component algorithm to create a graph representation of the virtual worm from the robust, cell-based simulation data. These graphs can then be validated and compared with target data from PlanformDB using the well-known graph-edit distance calculation, which provides a quantitative metric of similarity between graphs. The graph edit distance calculation was integrated into a fitness function that was able to guide automated searches for unbiased models of planarian regeneration. We present a cell-based model of planarian that can regenerate anatomical regions following bisection of the organism, and show that the automated model discovery framework is capable of searching for and finding models of planarian regeneration that match experimental data stored in PlanformDB. Conclusion The work presented here, including our algorithm for converting cell-based models into graphs for comparison with data stored in an external data repository, has made feasible the automated development, training, and validation of computational models using morphology-based data. This work is part of an ongoing project to automate the search process, which will greatly expand our ability to identify, consider, and test biological mechanisms in the field of regenerative biology

The atmospheric charged kaon/pion ratio using seasonal variation methods

Observed since the 1950's, the seasonal effect on underground muons is a well studied phenomenon. The interaction height of incident cosmic rays changes as the temperature of the atmosphere changes, which affects the production height of mesons (mostly pions and kaons). The decay of these mesons produces muons that can be detected underground. The production of muons is dominated by pion decay, and previous work did not include the effect of kaons. In this work, the methods of Barrett and MACRO are extended to include the effect of kaons. These efforts give rise to a new method to measure the atmospheric K/$\pi$ ratio at energies beyond the reach of current fixed target experiments. These methods were applied to data from the MINOS far detector. A method is developed for making these measurements at other underground detectors, including OPERA, Super-K, IceCube, Baksan and the MINOS near detector.Comment: 15 pages, 4 figures, submitted to Astropart. Phy

Evidence for Allele-Specific Levels of Enhanced Susceptibility of Wheat mlo Mutants to the Hemibiotrophic Fungal Pathogen Magnaporthe oryzae pv. Triticum

Barley mlo mutants are well known for their profound resistance against powdery mildew disease. Recently, mlo mutant plants were generated in hexaploid bread wheat (Triticum aestivum) with the help of transgenic (transcription-activator-like nuclease, TALEN) and non-transgenic (targeted induced local lesions in genomes, TILLING) biotechnological approaches. While full-gene knockouts in the three wheat Mlo (TaMlo) homoeologs, created via TALEN, confer full resistance to the wheat powdery mildew pathogen (Blumeria graminis f.sp. tritici), the currently available TILLING-derived Tamlo missense mutants provide only partial protection against powdery mildew attack. Here, we studied the infection phenotypes of TALEN- and TILLING-derived Tamlo plants to the two hemibiotrophic pathogens Zymoseptoria tritici, causing Septoria leaf blotch in wheat, and Magnaporthe oryzae pv. Triticum (MoT), the causal agent of wheat blast disease. While Tamlo plants showed unaltered outcomes upon challenge with Z. tritici, we found evidence for allele-specific levels of enhanced susceptibility to MoT, with stronger powdery mildew resistance correlated with more invasive growth by the blast pathogen. Surprisingly, unlike barley mlo mutants, young wheat mlo mutant plants do not show undesired pleiotropic phenotypes such as spontaneous callose deposits in leaf mesophyll cells or signs of early leaf senescence. In conclusion, our study provides evidence for allele-specific levels of enhanced susceptibility of Tamlo plants to the hemibiotrophic wheat pathogen MoT

Effect of Education Level on Adequacy of Bowel Preparation Prior to Colonoscopy

Background Adequate bowel preparation is crucial for obtaining a high-quality colonoscopy. Inadequate preparation leads to impaired visualization, which can lower adenoma detection rate, increase the risk of complications and potentially necessitate repeating the procedure.1 Patients with higher health literacy and a higher level of education have been associated with better bowel preparation quality.2,3,4,

Toxicology in the Fast Lane: Application of High-Throughput Bioassays to Detect Modulation of Key Enzymes and Receptors

BackgroundLegislation at state, federal, and international levels is requiring rapid evaluation of the toxicity of numerous chemicals. Whole-animal toxicologic studies cannot yield the necessary throughput in a cost-effective fashion, leading to a critical need for a faster and more cost-effective toxicologic evaluation of xenobiotics.ObjectivesWe tested whether mechanistically based screening assays can rapidly provide information on the potential for compounds to affect key enzymes and receptor targets, thus identifying those compounds requiring further in-depth analysis.MethodsA library of 176 synthetic chemicals was prepared and examined in a high-throughput screening (HTS) manner using nine enzyme-based and five receptor-based bioassays.ResultsAll the assays have high Z' values, indicating good discrimination among compounds in a reliable fashion, and thus are suitable for HTS assays. On average, three positive hits were obtained per assay. Although we identified compounds that were previously shown to inhibit a particular enzyme class or receptor, we surprisingly discovered that triclosan, a microbiocide present in personal care products, inhibits carboxylesterases and that dichlone, a fungicide, strongly inhibits the ryanodine receptors.ConclusionsConsidering the need to rapidly screen tens of thousands of anthropogenic compounds, our study shows the feasibility of using combined HTS assays as a novel approach toward obtaining toxicologic data on numerous biological end points. The HTS assay approach is very useful to quickly identify potentially hazardous compounds and to prioritize them for further in-depth studies

Search for Nucleon Decays induced by GUT Magnetic Monopoles with the MACRO Experiment

The interaction of a Grand Unification Magnetic Monopole with a nucleon can lead to a barion-number violating process in which the nucleon decays into a lepton and one or more mesons (catalysis of nucleon decay). In this paper we report an experimental study of the effects of a catalysis process in the MACRO detector. Using a dedicated analysis we obtain new magnetic monopole (MM) flux upper limits at the level of $\sim 3\cdot 10^{-16} cm^{-2} s^{-1} sr^{-1}$ for $1.1\cdot 10^{-4} \le |\beta| \le 5\cdot 10^{-3}$, based on the search for catalysis events in the MACRO data. We also analyze the dependence of the MM flux limit on the catalysis cross section.Comment: 12 pages, Latex, 10 figures and 2 Table

A combined analysis technique for the search for fast magnetic monopoles with the MACRO detector

We describe a search method for fast moving ($\beta > 5 \times 10^{-3}$) magnetic monopoles using simultaneously the scintillator, streamer tube and track-etch subdetectors of the MACRO apparatus. The first two subdetectors are used primarily for the identification of candidates while the track-etch one is used as the final tool for their rejection or confirmation. Using this technique, a first sample of more than two years of data has been analyzed without any evidence of a magnetic monopole. We set a 90% CL upper limit to the local monopole flux of $1.5 \times 10^{-15} cm^{-2} s^{-1} sr^{-1}$ in the velocity range $5 \times 10^{-3} \le \beta \le 0.99$ and for nucleon decay catalysis cross section smaller than $\sim 1 mb$.Comment: 29 pages (12 figures). Accepted by Astroparticle Physic

Final results of magnetic monopole searches with the MACRO experiment

We present the final results obtained by the MACRO experiment in the search for GUT magnetic monopoles in the penetrating cosmic radiation, for the range $4\times 10^{-5}< \beta < 1$. Several searches with all the MACRO sub-detectors (i.e. scintillation counters, limited streamer tubes and nuclear track detectors) were performed, both in stand alone and combined ways. No candidates were detected and a 90% Confidence Level (C.L.) upper limit to the local magnetic monopole flux was set at the level of $1.4\times 10^{-16}$ cm$^{-2}$ s$^{-1}$ sr$^{-1}$. This result is the first experimental limit obtained in direct searches which is well below the Parker bound in the whole $\beta$ range in which GUT magnetic monopoles are expected.Comment: 12 pages, Latex, 9 figures and 2 Table