Miracle-dz/UniFAR-FTUs huggingface dataset:
Molecular tools for functional genomic analyses of the stealth pathogenesis of wheat by Zymoseptoria tritici

2 List of Figures . 9 List of Tables and Equations . 11 Acknowledgements . 12 Abbreviations . 13 Chapter 1 General Introduction . 14 1.1 Global importance of plant pathogens . 15 1.2 An overview of microbial pathogenesis and plant defences . 16 1.3 Global importance of Mycosphaerella pathogens . 19 1.4 Wheat and Septoria tritici leaf blotch . 21 1.5 Biology of Z. tritici and its mode of pathogenesis . 24 1.5. 1 The Z. tritici genome . 24 1.5. 2 Taxonomy and growth morphologies . 26 1.5. 3 STB disease cycle . 27 1.5. 3.1 Disease initiation . 27 1.5. 3.2 Host penetration . 29 1.5. 3.3 Host colonisation . 31 1.5. 3.4 Host immune response . 32 1.5. 3.5 Suppression of host immune response by Z. tritici . 33 1.5. 3.6 Transition to the symptomatic phase of infection . 35 1.6 STB disease control . 38 1.7 Current status of functional genomics in Z. tritici . 41 1.8 Scope of the current study . 47 Chapter 2 Materials and methods . 49 4 2.1 Strains, databases and growth conditions . 50 2.1.1 Bioinformatics . 50 2.1.1 Growth media recipes . 50 2.1.2 Growth conditions . 53 2.2 Nucleic acid manipulations . 55 2.2.1 Z. tritici genomic DNA extraction . 55 2.2.2 RNA extraction and cDNA synthesis . 56 2.2.3 Restriction digestion using endonucleases . 57 2.2.4 Agarose gel electrophoresis . 57 2.2.4 Polymerase chain reaction . 58 2.2.5 Extraction of DNA from agarose gels . 58 2.3 Genetic cloning . 59 2.3.1 Blunt and sticky end ligation . 59 2.3.2 Yeast recombinational cloning using S. cerevisiae . 60 2.3.2.1 Transformation of S. cerevisiae . 60 2.3.2.2 Isolation of plasmid DNA from S. cerevisiae . 61 2.3.3 Gateway® recombination cloning . 62 2.3.4 Transformation of E. coli . 63 2.3.5 Extraction of plasmid DNA from E. coli . 64 2.4 Agrobacterium mediated transformation of Z. tritici . 65 2.4. 1 Preparation of A. tumefaciens competent cells . 65 2.4. 2 Transformation of A. tumefaciens . 65 2.4. 3 AMT of Z. tritici . 66 2.5 Southern blot analysis . 67 2.6 Virulence assay . 69 2.7 Phenotypic screen . 70 2.8 Microscopic analysis . 70 2.8. 1 Epifluorescence microscopy . 70 5 2.8. 2 Confocal microscopy . 71 Chapter 3 Exploitation of new drug resistance marker and non-homologous end joining mutants for functional analysis in Z. tritici . 73 Abstract . 75. 75 3.
Female performance in Euphorbia characias: effect of flower position on seed quantity and quality

Abstract Patterns of seed mass variation in the perennial spurge Euphorbia characias(L.) (Euphorbiaceae) in three populations from north-east Spain were examined. Mature inflorescences have a distinctive structure, with a distal umbrella of rays subtending dichotomously grown cyathia. Under the umbrella, cyathia are loosely arranged on rays growing from the bases of leaves. Seed characteristics were studied, especially in relation to position along the inflorescence. Maximum inflorescence height had no effect on seed set or seed mass. Seed set did not differ between populations. Flower position along the inflorescence had a marked effect on seed set and seed mass. Seed set was higher in the distal (upper) portion of the inflorescence. Seeds from the distal area had a greater mass than those from lower parts of the inflorescence. Seeds were planted in the field and observed under natural weather conditions. The bigger seeds from the higher position in the inflorescence produced seedlings with a greater percentage emergence, which, in addition, had an increased percentage establishment than seedlings originating from the smaller seeds from lower areas of the inflorescence. For the three populations considered together, seeds from the basal (lower) portion of the inflorescence were reduced in germination by 51% and establishment by 59%. No differences in seedling dry mass were observed. Seed dispersal-related structures (elaiosome and elaiosome/load ratio) did not vary in relation to position or population. Positional effects on female performance – seed quantity and quality – may be a very strong selective pressure for the peculiar flower disposition in the architecture of E. characias.
Performance of the Thermal Constant as an Indicator of the Time to Apply Cover Sprays for Codling Moth

Through a period of three years, 1928, 1929 and 1930, the thermal constant has been used for practical determination of the time when cover spraying should start for the first and for the second broods of codling moth and has seemed to be eminently successful for that purpose. It seems likely that the thermal constant can be used as a satisfactory practical determinator of the length of periods during which spray coatings must be maintained on fruit and foliage against entry by larvae of the first and of the second broods. When the average weekly minimum temperatures reach about 60o F pupation of summer larvae seems to cease and it is thought that these minimum temperatures are probably the agency limiting the number of codling moth broods.
On the mathematical formulation and parameter estimation of the Norwegian Sea plankton system

Abstract The mathematical description of the oceanic plankton system is often characterised by a simple structure where the major components of the system are governed by the dissolved nutrient concentration N, the phytoplankton biomass P, and the zooplankton biomass Z (also known as the NPZ model). The flows between the variables can be formulated in a variety of ways that, in general, alter the time development of the model. In this study we investigate how the numerical value of model parameters that are hard to determine experimentally can be estimated from in situ field observations. By that, we can assign parameter values to each model formulation such that they should follow a prescribed time development that is consistent with data. Accordingly, this gives us a tool to compare model formulations in a consistent way. The study emphasises the importance of analysing the model with respect to stability and multiple solutions. The study is exemplified using observations from Ocean Weather Station Mike (66°N, 2°E) in the Norwegian Sea, illustrating the need for a proper model formulation in order to reproduce measurements.
Portal absorption and hepatic uptake of amino acids in rainbow trout force-fed complete diets containing casein or crystalline amino acids

In order to study the dynamics of amino acid metabolism in rainbow trout, blood samples were collected from the hepatic vein, hepatic portal vein and caudal vein-artery complex at 0, 3, 6, 12, 24, 48 and 72h after force-feeding complete diets containing casein or corresponding crystal-line amino acids. In both dietary groups, a large proportion of free amino acids appeared in the portal blood within 3h and their level reached peaks by 12h at the latest and dropped to fasting levels by 24h. Most of the amino acids, including branched-chain amino acids, were taken up by the liver intensively during the absarptive period and less intensively but significantly even at 72h after food intake. Patterns of the portal absorption of and hepatic uptake of essential amino acids reflected the dietary profiles in both groups during the absorptive period. Postprandial changes in plasma free amino acids collected from all three regions showed similar patterns in both dietary groups.
Tropical Soil Biology and Fertility: A Handbook of Methods.

Based on the work of the Tropical Soil Biology and Fertility (TSBF) Programme, this is a handbook of recommended and validated methods for the characterization and analysis of tropical soils, with the aim of achieving sustainable use of soil resources. The objectives of the programme revolve around five main themes: synchrony of nutrient release and plant growth demands; management of soil organic matter; soil water balance; effects and management of soil fauna; and integration of biological processes into the maintenance of soil fertility. The methods given are endorsed by the International Soil Science Society and are part of the International Union of Biological Sciences and the UNESCO Man and the Biosphere Programme.
The Mitochondrial Antisense ncRNAs are Down-Regulated in Early Cervical Carcinoma

Background: Cervical cancer is the third most common disease and the fourth leading cause of death in female’s worldwide. Treatment of this disease is successful when detection is at early neoplasic stages. Hence, multiple efforts have been pursued for early detection of cervical neoplasia. The aim of this study was to analyze the differential expression of mitochondrial non-coding RNAs or ncRNA (sense and antisense) in normal and neoplastic cervical biopsies as a potential tool for diagnostic of cervical cancer. Methods: The expression pattern of the sense and the antisense mitochondrial ncRNAs in cervical biopsies was carried out by chromogenic in situ hybridization (ISH). We examined 17 normal cervical tissues, 108 early and late neoplasias and 24 invasive cervical carcinomas. The hybridization results were compared with the diagnostic of each specimen carried out by pathologists. Results: Like normal human keratinocytes, normal cervical epithelium expresses the sense and the antisense mitochondrial ncRNAs at the basal layer of the epithelium. Interestingly, ISH reveals that the antisense transcripts are always localized in the nucleus of basal cells in normal cervical epithelium. Early and late cervical intraepithelial neoplasia as well as invasive cervical carcinoma expresses the sense transcript. In contrast, the antisense transcripts are down-regulated in early and late neoplasia and in invasive cervical carcinoma. Conclusions: This pilot study indicates that down-regulation of the antisense mitochondrial transcripts at early stages of cervical neoplasia can be explored as a diagnostic tool for early cervical neoplasia.
Streptococcus pneumoniae vaccine, Prevenar, utilises Tregs to suppress Asthma (140.2)

Our recent finding that exposure to Streptococcus pneumoniae may suppress pro-asthmatic responses led us to investigate whether the current human S. pneumoniae vaccines may be used to suppress asthma using mouse models of ovalbumin-(OVA)-induced allergic airways disease (AAD). AAD was induced by intraperitoneal sensitisation and intranasal challenge with OVA. At the time of OVA sensitisation, Prevenar or Pneumovax were delivered intranasally either with or without CpG. Prevenar, but not Pneumovax, suppressed hallmark features of AAD, including eosinophil influx, OVA-specific T helper (Th) 2 cytokine release, mucus hypersecretion, total serum IgE and airways hyperresponsiveness. We then investigated whether regulatory T cells (Tregs) were important in the suppression of AAD. Prevenar increased the number of CD4+CD25+FoxP3+ expressing Tregs in the lungs, lymph nodes and spleens. The release of immuno-suppressive cytokines IL-10 and TGF-â from lymph nodes was reduced. However, Prevenar increased expression of CD103 and CTLA-4 on CD4+CD25+FoxP3+ cells. Proliferation assays demonstrated that Tregs suppressed allergic effector T cell proliferation regardless of Prevenar treatment. In conclusion, a currently available human vaccine increases the infiltration of Tregs and suppresses AAD, and may be useful as a novel therapy for asthma.
Distribution of benthic fauna in sediment grains and prop roots of a mangrove channel in south-eastern Brazil

We examined the benthic fauna in four areas along a mangrove tidal channel in south-eastern Brazil, between October 2008 and August 2009. The tested hypothesis is that the most abundant groups avoid competition as they occupy different types of substrata and that the longitudinal distance from the sea also affects the occurrence of benthic fauna along the channel. We also examined the prop root epibiont fauna to describe this different community. Polychaeta was the dominant group in the sediment whereas Isopoda and Tanaidacea were the dominant groups on the prop roots. We found a tendency for higher infauna species richness and diversity in the innermost channel area during the summer. Higher abundance of epibiont fauna was also found in summer with tidal movements allowing the colonization of the prop roots of the mangrove forest by some taxa. The polychaetes Ceratocephale sp. and Laeonereis acuta had indication of habitat partitioning, with the first occurring mainly in very fine sand sediment whereas the latter preferred medium sand sediment. The microcrustaceans Chelorchestia darwini and Tanaidacea sp. 1 occurred in high abundance colonizing the prop roots. Exosphaeroma sp. was found in high abundance in infauna and epibiont fauna. The tested hypothesis of spatial partitioning of the mangrove channel by the benthic fauna was confirmed with the most abundant species occupying the substrata with different grain fractions and prop roots in different stations.
In vitro and In vivo Evaluation of a Plant Origin Acari- cide and In vitro Evaluation of Plant Extracts Against Two-Spotted Spider Mite, Tetranychus urticae Koch

This study was performed at Sweida Research Center/GCSAR/ in Syria during 2016. The effect of garlic and soft wheat crude extracts as well as the effect of matrine (plant-based acaricide), jolly and sanmite (chemical-based acaricides) were tested under in vitro conditions on two-spotted spider mite, Tetranychus urticae Koch (TSSM). In addition, acaricides used were evaluated under in vivo conditions. Survival % of TSSM was calculated, neglog transformed and subjected to ANOVA analysis using Tukey HSD test. In vitro bioassay results revealed a significant effect of garlic and wheat extracts as well as matrine, jolly and sanmite. After 72 hours, no difference was observed between plant extracts, and among tested acaricides. In vivo bioassay results also showed a significant effect of acaricides used where jolly was the best and matrine and sanmite were comparable. These findings support the idea of using plant-based acaricides (including lectin-based acacicides) as an alternative strategy of using chemical-based acaricides. Taking into account the advantages of in vitro bioassays and based on the results of this study, we suggest predicting in vivo response from in vitro results although this issue needs to be tested first for the crude plant extracts to evaluate their stability under in vivo conditions.
Use of Azolla (Azolla pinnata) as Cattle Feed Supplement

Azolla (Azolla pinnata) has enormous potential as a livestock feed due to its high content of protein, essential amino acids, vitamins, growth promoter intermediaries and minerals. KVK, Ajmer pioneered the Azolla cultivation technique in Rajasthan and developed a prototype for its cultivation. This technology of cultivation of Azolla was transferred through conductance of demonstrations in five villages. Feeding of Azolla as livestock feed to milch animals resulted in increase in milk yield and fat content. Success of the technology led to its wide scale adoption and KVK Ajmer has so far established 523 Azolla cultivation units during the last five years in the district.
Factors Affecting Red Deer (Cervus elaphus) Population Density in Southeastern Poland

Augmentation inquietante des populations de C.e. au cours des dernieres annees (de 15,2% entre 1975 et 79), due a divers facteurs, notamment a des modifications recentes du mode d'exploitation forestiere. Presentation d'un modele de l'influence de l'habitat forestier sur les populations de C.e.
Association of Epstein-Barr virus (EBV) with Solid Tumors

The gamma-herpes Epstein-Barr virus (EBV) is a ubiquitous viral agent that causes persistent infection in more than 90% of the world adult population. EBV is associated with several lymphoproliferative disorders such as infectious mononucleosis, Burkitt's lymphoma, Hodgkin's disease, and post-transplant lymphoproliferative disease. The oncogenic role of EBV in tumors of lymphoid origin has been widely investigated. With respect to solid tumors, the role of EBV is well documented in nasopharyngeal carcinoma. However, new findings have shown that the spectrum of cellular infection of EBV is broader, having been detected in cells from other kinds of solid tumors, thus indicating its involvement in tumorigenesis of these tumors. The current article begins with a brief description of EBV biology and aims to provide a summary of new findings concerning the association between EBV and solid tumors, highlighting evidence of the viral role and characteristics of infections in each tissue.
Historical and present distribution of Zostera marina in the high north (Troms County, northern Norway) – a decline over the last century

Abstract Eelgrass meadows (Zostera marina) have been mapped in Troms (Norway), in the temperate northeast Atlantic, north of the polar circle, from 2008 to 2011. In this region, there is little knowledge of the distribution of the eelgrass meadows. Northern Norway has an extensive coastline with many pressures and stakeholders. Old records (back to 1900) have been revisited and new locations surveyed based on a combination of spatial modeling, using digital information on depth, slope, and wave exposure and stakeholder recommendations. The results showed that 42% of the previously mapped locations had disappeared. However, we found Z. marina meadows at seven locations where they had not previously been recorded. Most meadows (66%) were smaller than 10,000 m2. The largest meadow covered an area of 325,000 m2, and was located in Balsfjorden. The results clearly show that Z. marina is able to form actively growing stands even at ∼70°N. Three of the meadows were first registered over 100 years ago, indicating long-lived stands in stable conditions. This study cannot explain the causes for the observed decline, and only discusses possible relations. The eelgrass meadows are genetically isolated but yet diverse. Management at fjord range level is required to maintain healthy and stable stands of eelgrass meadows in this region.
Insights into the habitat and breeding biology of the federally endangered herbaceous plant, Thalictrum cooleyi Ahles

ENDANGERED HERBACEOUS PLANT, THALICTRUM COOLEYI AHLES A. Renée Fortner April, 2015 Director of Thesis: Dr. Claudia L. Jolls Major Department: Department of Biology Thalictrum cooleyi Ahles (Cooley’s meadowrue, Ranunculaceae) is a dioecious species, endemic to fire-dependent, wet pine savannas of the southeastern US. T. cooleyi was listed as federally endangered in 1989; knowledge of habitat and breeding biology are crucial to conservation. I studied NC populations of T. cooleyi and examined (1) woody species associates, (2) breeding system, (3) sex ratios, and (4) potential pollen limitation. I also assessed seed germination requirements and vegetative propagation potential for T. cooleyi. To document woody species associates of Thalictrum cooleyi, I sampled 104-3 m 2
Metabotropic Receptor Modulation of Kainate Receptors in the Hippocampus

viii LIST OF TABLES . xiv LIST OF FIGURES . xv LIST OF SYMBOLS . xvii LIST OF ABBREVIATIONS . xix CHAPTER 1 GENERAL INTRODUCTION . 1 1.1 SIGNIFICANCE . 1 1.2 THE HIPPOCAMPUS . 3 1.3 SYNAPTIC PLASTICITY.10 1.4 MUSCARINIC ACETYLCHOLINE RECEPTOR MODULATION OF GLUTAMATE RECEPTORS . 20 1.5 DOPAMINERGIC MODULATION OF GLUTAMATE RECEPTORS . 29 1.6 KAINATE RECEPTORS . 36 1.7 IMPLICATIONS FOR EPILEPSY . 47 1.8 IMPLICATIONS FOR EXERCISE . 50 1.9 SIGNIFICANCE REVISITED . 58
Filogenia y evolución local de la cabra montés (Capra pyrenaica) en el yacimiento Cuaternario de Chaves (Huesca, España) Phylogeny and local evolution of The Iberian Wild Goat (Capra pyrenaica) in the Quaternary site of Chaves (Huesca, Spain)

La cabra montesa iberica (Capra pyrenaica, Schinz 1838) es un endemismo de la Peninsula Iberica que en los ultimos siglos ha sufrido la perdida de dos de sus cuatro subespecies (C .pyrenaica pyrenaica y C. pyrenaica lusitanica, actualmente extintas, C. pyrenaica hispanica y C. pyrenaica victoriae). La taxonomia para esta especie, al igual que para el genero Capra, plantea un debate ya que la taxonomia habitualmente empleada se basa en caracteres morfologicos, tales como la morfologia de los cuernos o el pelaje, que muchos autores sugieren que no son suficientes para definir una especie o subespecie. Los distintos problemas de conservacion que plantea esta especie, asi como su valor anadido por ser la pieza de caza mayor mas importante de la Peninsula, hacen que la gestion de esta especie sea una prioridad tanto desde el punto de vista biologico como socioeconomico. En este trabajo, se aplican las tecnicas moleculares utilizadas en los estudios de ADN antiguo para investigar la historia paleo-genetica de la cabra montesa en el yacimiento de Chaves (Huesca). Con los datos obtenidos se pretende analizar las relaciones filogeneticas entre las distintas subespecies de la Peninsula asi como las fluctuaciones demograficas y cambios en diversidad genetica a traves del tiempo. Este tipo de estudio es importante ya que nos proporciona informacion sobre los cambios geneticos sufridos por esta especie a traves del tiempo y que han llevado a sus poblaciones a su situacion actual. Por ello, esta informacion puede ayudar a tomar decisiones mas fundamentadas para su gestion. El estudio consistio en la amplificacion y analisis de tres fragmentos del gen mitocondrial citocromo b de diecinueve muestras del yacimiento de Chaves de contextos neoliticos y paleoliticos. El analisis muestra, por un lado, una continuidad poblacional desde el Paleolitico hasta el presente en el yacimiento sin flujos geneticos externos y, por otro lado, una disminucion de la diversidad genetica desde el Paleolitico hasta el Neolitico sugiriendo que la reduccion de biodiversidad que termino con la extincion del bucardo ya estaba presente en el Neolitico. El estudio de las relaciones filogeneticas estimado por inferencia bayesiana agrupa en el mismo clado la cabra montesa y el ibice, apoyando este estudio la teoria de una sola ola de migracion del genero Capra en Europa seguido de una separacion geografica y especiacion.
A cost efficient model for minimizing energy consumption and processing time for IoT tasks in a Mobile Edge Computing environment

In a scenario with increasingly mobile devices connected to the Internet, data-intensive applications and energy consumption limited by battery capacity, we propose a cost minimization model for IoT devices in a Mobile Edge Computing (MEC) architecture with the main objective of reducing total energy consumption and total elapsed times from task creation to conclusion. The cost model is implemented using the TEMS (Time and Energy Minimization Scheduler) scheduling algorithm and validated with simulation. The results show that it is possible to reduce the energy consumed in the system by up to 51.61% and the total elapsed time by up to 86.65% in the simulated cases with the parameters and characteristics defined in each experiment.
A ring in graph theory

We call a point set in a complex K a 0-cell if it contains just one point of K, and a 1-cell if it is an open arc. A set L of 0-cells and 1-cells of K is called a linear graph on K if (i) no two members of L intersect, (ii) the union of all the members of L is K, (iii) each end-point of a 1-cell of L is a 0-cell of L and (iv) the number of 0-cells and 1-cells of L is finite and not 0.
Ring-necked pheasant population genetic structure

We investigated genetic variability in 34 ring-necked pheasants (Phasianus colchicus) from northeastern Iowa using randomly amplified polymorphic DNA (RAPD). We collected pheasants from 5 Conservation Reserve Program (CRP) habitats or longer-standing patches of overwintering and breeding habitats. Each habitat patch was separated from the others by 5-30 km of unsuitable breeding habitat. Significant genetic differentiation was found in 9 of the 10 possible inter-patch comparisons, the exception being 2 sites that were separated by only 5 km. This high level of genetic subdivision among closely neighboring patches suggests that populations are highly fragmented.