Advanced Mycology

Topic outline

• General

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  • An-Najah National University

    Faculty of Science

    Department of Biotechnology

    Advanced Mycology

     

     

    Instructor Name: Dr.Ghadeer Ibraheem Omar

    Course Number: 424557

    Compulsory or Elective: Elective

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    Course Introduction :

    This course will give a comprehensive introduction to fungi in terms of their biology, physiology, genetics, biotechnological potential and pathogenity. This course will deal with an in-depth description of the biology, structure and physiology of fungi in which the structure, metabolism and growth of fungi will be introduced. Moreover, the genetics and life cycles of a number of representative fungi are described and the use of fungi for genetic analysis is outlined. During this course we will describe how genomics, transcriptomics and proteomics have increased our knowledge of fungi and made available new opportunities for exploiting fungi for the good of humanity. This course will introduce information about the fungal population’s diversity and speciation. This course will give an overview of how fungi are utilized for producing antibiotics, enzymes and a range of chemical products such as citric acid. The exploitation of fungi for the production of heterologous proteins and illustration how yeast can be used for the production of hepatitis B antigens will be introduced in this course. Introducing different fungal interactions with other organisms will be introduced. Description of plant pathogenic fungi and the human diseases caused by fungi will be studied. Plants and the impact of such pathogens on the global supply of food will be discussed.

     

    Intended Learning Outcomes (ILO):

    1. To understand the definition, characterization and classification of fungi.

    2. To study the features and growth of hyphae and mycelia formation.

    3. To know the fungi cell wall composition, structure and formation.

    4. To understand the fungal physiology in respect to nutrition, cellular biosynthesis, metabolism, growth and reproduction and understanding the fungal adaptations.

    5. To understand the fungal genetics and populations.

    6. To know the antibiotics, enzymes and chemical commodities production from fungi.

    7. To understand biotechnological exploitation in fungi.

    8. To understand the interactions of fungi with other organisms as symbiotic partners, plant pathogens and causing human diseases. 

        

       For full outline click here

     

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    Forum

    News forum
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    Assignment

    Fungal classification Assignment

• Topic 1

  Topic One : Introduction to Mycology.

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    Topic Introduction :

    General defenition of fungi will be introduced in this topic. The general features of fungi will be provided as are the basic characters upon on the fungi were classified as separate kingdom. in addition to that the characteristics of the fungi main goups will be introduced and the life cycle of each one of the major fungal division will be explained.

     

    Definition of fungi

    • A startling finding from comparisons of sequences of 18S rRNA—a component of the small subunit of ribosomes found in all organisms—was that some species, for example, the long-studied potato late blight fungus Phytophthora infestans , are quite distinct from other species of fungi. These species, termed the “pseudo fungi,” were given the status of kingdom named Straminipila (or Stramenopila) and distinguished from the “true fungi” placed in the kingdom Eumycota.

    • Other differences too came to light: the vegetative phase in Straminipila is predominantly diploid whereas in Eumycota it is haploid.

    • Moreover, Straminipila reproduce by means of motile biflagellate zoospores, suggesting that they evolved from an alga that lost chloroplasts. Their cell wall is composed of cellulose (cellulose-like β-1-4 glucan) and not of β-(1-3)-glucan or β-(1-3)- mannan and chitin as in Eumycota.
  • Topic Objectives :

    1. To understand fungal definition.

    2. To understand the general features of fungi.

    3. To understand the classification of fungi at the kingdom level and the division level.

    4. To discriminate between the features of each of the major fungal divisions.

    5. To understand the phylogenetiic relationship among the different fungal groups.

    6. To understand the general life cycle of fungi.

    7. To discriminate among the life cycles of each of the studied major fungal groups.

  • Topic Plan :

    First : Reed the following file for the lectures related to the introduction of mycology, defenition of fungi and general classification of fungi.

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    File

    advanced mycology lecture one File
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    Second :Show the associated video which related to the general information about fungi, their general features and classification.

     

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    Third :The second video is about the life cycle of an example for the basidiomycetes. 

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    Fourth :The third video is related to the life cycle of the ascomycetes.

     

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    Fifth: Do the following home work

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    Forum

    teaching mycology tools Forum

• Topic 2

  Topic Two : The Hyphal Mode of Life

  • Topic Introduction :

    The hyphal mode of life can be understood through the general features of hyphal growth. In addition to the different components of the fungal wall layers and the fuction of each one of them. The mechanism of the synthesis of the hyphal wall will be provided via understanding the enzymes involved in that process which is restricted to the hyphal tip where is a balance between the synthesis and lysis of the wall components.

     

    Topic Objective :

    1. To understand the general features of hyphae.

    2. To know and understand the different components of the fugal wall and their arrangment from outside to the inside of the hyphae.

    3. To know the function of each of the hyphal wall components.

    4. To understand the architecture of the hyphal wall and the chemical composition of each ot the wall layers.

    5. To know the variation in the hyphal wall layers composition among different main fungal divisions.

    6. To understand the mechanism and steps of the hyphal wall synthesis and the enzymes involed in that process and the wall precursors of each of the involed enzymes.

    7. To understand the concept hyphal wall maturation.

  • Topic Plan :

    First : Reed the following file  about the hyphal mode of life. as you will be provided by the general features of hyphae,  wall components and  wall assembly pathway. 

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    File

    second topic File

• Topic 3

  Topic Three :Hyphal Tip Growth, Hyphal Septation and Mycelium Formation

  • Topic Introduction :

    This topic will introduce to students how is the hyphal growth is achieved by the drown of the cytoplasm towards the tip region. In addition to that, providing an idea of the general growth of the fungal mycelium through the hyphal growth, branching, septation and union of hyphal tips.The synchronization among hyphal growth, branching and anastomosis will cause the overall fugus growth and morphogenesis.

     

    Topic Objective :

    1. To understand the hyphal tip growth and the mechanism of how is the cytoplasm drown towards to the hyphal tip.

    2. To understand the driven force for the hyphal branching and its mechanism.

    3. To understand and know the septa types in fungi, the function of each type, the cases in which each type is formed and the mechanism of septation in fungal hyphae.

    4. To understand the hyphal anastomosis and the sites of the fungal colony in which anastomosis occures and the reasons of its occurance.

    5. To know the different multihyphal structures which are formed in fungi clarifying the concept of morphogenesis

  • Topic Plan :

    First : Reed the following file  about hyphal tip growth, hyphal septation and mycelium formation .

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    File

    third week topic File

• Topic 4

  Topic Four :Fungal Nutrition .

  • Topic Introduction :

    This topic will provide information to students regarding the nutrition in filamentous and yeast form of fungi. Yeasts and fungi have relatively simple nutritional needs and most species would be able to survive quite well in aerobic conditions if supplied with glucose,ammonium salts, inorganic ions and a few growth factors. Macronutrients,supplied at millimolar concentrations, comprise sources of carbon, nitrogen,oxygen, sulphur, phosphorus, potassium and magnesium; and micronutrients, supplied at micromolar concentrations, comprise trace elements such as calcium, copper, iron, manganese and zinc that would be required for fungal cell growth. Some fungi are oligotrophic, apparently growing with very limited nutrient supply, surviving by scavenging minute quantities of volatile organic compounds from the atmosphere. The general mechanism of the uptaken of those nutrient requirements will be introduced in this topic. The form of such nutrient which can be absorbed by fungi will be explained. The degredation of the nutrient polymers into the simple form so to be absorbed by the fungi will be provided. 

     

    Topic Objective :

    1. To understand the nutrition concept in fungi.

    2. To know the different organic and inorganic requirements of fungi.

    3. To understand the mechanism of degredation of the polymeric substances by the different depolymerases enzymes to the simplest form of nutrients as to be absorbed by fungi.

    4. To understand the mechanism of upteken of such simple form of nutrient and understand how they are absorbed at the hyphal tip region in particular.

    5. To be introduced to the general terminology which are used to describe nutrition in fungi,  such as, heterotrophic,  oligotrophic, chemo-organotrophic, non-diazotrophic...etc.

    6. To know the available form of the fungal nutrients which can be absorbed by fungi.

  • Topic Plan :

    First : Reed the following file  about Fungal Nutrition.

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    File

    fourth topic File
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    Assignment

    Fungal nutrition and biotechnology Assignment

• Topic 5

  Topic Five :

  • Topic Introduction :

    Fungi have wide range of environmental conditions which they can tolerate or live in. Fungi can tolerate suboptimal environmental factor, but can not tolerate two of them as that may prevent their growth. Understanding the optimal environmental conditions of different fungi should be based on natural growth which is totally different as it is characterized by narrower range than the lab due to competition. The main limiting environmental factors for the fungi are, the temperature, the hydrogen concentration, water availability and light. Fungi show variable physiological and anatomical adaptations to those limiting factors.

     

     

    Topic Objective :

    1. To understand the different thermal growth limits of fungi and the different terminology regarding the different upper temperature limit, lower temperature limit and optimal temperature they live in.

    2. To understand the physiological adaptation to high and low temperatures.

    3. To understand the hydrogen concentration growth rang of different fungi and their physiological adaptation for such a factor.

    4. To know the water availability conditions in which fungi can live in and the physiological adaptations to water stress conditions and salinity stress.

    5. To understand and have a detailed idea about the response of fungi to light and what are the phenomenons which occur in fungi in relation to light.

     

  • Topic Plan :

    First :Reed the following file  about Environmental conditions for  fungal growth, and tolerance of extremes through physiological and morphological adaptations

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    File

    fifth week topic File
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    Second:Do the following homework .

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    Assignment

    Fungal physiological adaptations Assignment

• Topic 6

  Topic Six :Primary and Secondary Metabolites of Fungi.

  • Topic Introduction :

    Primary metabolites are those that are essential for growth to occur and include proteins, carbohydrates, nucleic acids and lipids. Indeed, the precursors of these primary products must be synthesized if they cannot be obtained from the growth medium. These primary metabolites have essential and obvious roles to play in the growth of the fungus. Typically, primary metabolites are associ- ated with the rapid initial growth phase of the organism and maximal produc- tion occurs near the end of this phase. Once the fungus enters the stationary phase of growth, however, primary metabolites may be further metabolized. Examples of primary metabolites produced in abundance include enzymes, fats, alcohol and organic acids. Economically speaking, primary metabolites are easily exploited as the biochemical pathways involved in their production are widespread throughout the fungal kingdom. This allows for the rapid screen- ing of classes of fungi for such products and the rapid development of produc- tion processes for their utilization.

    In contrast to the primary metabolites, secondary metabolites are not essential for vegetative growth and indeed may have little or no primary func- tion within the organism. Secondary metabolites are produced when the organ- ism enters the stationary phase, once the initial phase of rapid growth has declined. The metabolites produced in this phase are often associated with dif- ferentiation and sporulation and can have profound biological activities, which in some instances have been exploited economically. A number of distinct dif- ferences are apparent between primary and secondary metabolites. In the first instance they have been shown to possess an enormous variety of biosynthetic origins and structures that are not, in general, found among the primary metabo- lites. Second, their occurrence tends to be restricted to a small number of organ- isms and indeed can vary between individual strains of the same species. Finally, their production is characterized by the generation of groups of closely related compounds, which may have very different biological properties. Important examples of secondary metabolites include medically important compounds such as antibiotics, statins, cyclosporins and ergot alkaloids. 

    Fungal biotechnology has developed, to allow the utilization of the metabolic processes inherent to the organisms, in a commercially viable manner. In this chapter we will detail a number of the more important commercial commodi- ties produced by fungi and outline the production processes for them.

    Topic Objective :

    1. To understand the concept of primary and secondary fungal metabolites.

    2. To illustrate the types of primary and secondary metabolites in fungi.

    3. To understand the pathways of the biosynthesis of primary and secondary fungal metabolites.

    4. To explore the biotechnological application of the primary and secondary fungal metabolites. 

    Plan ;

    First :Study the following file about the primary and secondary metabolites and their biosynthesis in fungi.
    

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    File

    primary and secondary metabolites in fungi File
  • Second :Study the following file about the exploration of primary and secondary metabolites of fungi in biotechnology application

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    File

    biotechnology application of some primary and secondary metabolites of fungi File
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    Third:Study the following file then join the forum below

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    File

    biofuel assay in mushroom File
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    Forum

    biotechnological application in fungi Forum
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    Assignment

    Fungal metabolites Assignment

• Topic 7

  Topic Seven :Fungal Symbiosis

  • Topic Introduction :

    Symbioses are intimate associations involving two or more species. Fungi have evolved numerous symbioses involving diverse eukaryotes and prokaryotes. Traditionally, symbioses are categorized according to the relative benefit or harm that the partners experience (properly conceived in terms of fitness reproductive success) as a consequence of the interactions. In parasitism one partner benefits from the association, but the other partner is harmed. In mutualisms both symbionts benefit from the interaction. In commensalism, one partner benefits, but there is no (perceived) effect on the other partner. The categories given above are useful for conceptualizing the diversity of symbioses, but they oversimplify the nature of the interactions, especially mutualisms. It is now appreciated that even in the most benign associations there is a basic conflict of interest among the partners, both of which are trying to maximize their reproductive output at the expense of the other partner. Thus, many ecologists and evolutionary biologists now regard mutualisms and other symbioses as reciprocal parasitism. 
    

    Topic Objective :

    1. To understand the symbiosis concept in fungi.

    2. To illustrate the different types of symbiotic relationship between fungi and other organisms.

    3. To know all the scientific related terminology to symbiosis in fungi.

    4. To understand commensalism.

    5. To know the different types of mutualism.

    6. To understand the parasitism.

    7. To introduce different examples of symbiotic relationships in fungi and the mechanism by which this relationship is established.

  • Plan ;

    First :Study the following file about illustrating the different symbiotic relationship between fungi and other organisms. symbiosis in fungi 
    

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    File

    symbiosis in fungi File

• Topic 8

  Topic Eight :Fungi as Human Pathogen 

  • Topic Introduction :

    Humans come into contact with many hundreds of species of fungi every day and that in some cases humans have become potential sources of nutrients for some fungal species. For the most part, transient exposure to fungi or fungal colonization occurs without the knowledge of the affected individual. This is primarily due to the inherent low virulence of most fungi, especially when confronted with the full arsenal of the human immune system. However, some species of fungi are long established members of the human microflora (i.e. commensals), while under certain con- ditions some fungi can cause symptoms of disease and even death. As many as 200 fungal species have been associated with human infections (known as mycoses); however, fungi are far more important pathogens of plants and insects. Some of the most common infections in humans are associated with fungi (e.g. thrush, dandruff and ‘athlete’s foot’). These are superficial and relatively innocuous; however, fungi can also cause far more devastating diseases, such as invasive aspergillosis and systemic candidosis, both of which have very high associated mortality rates. The incidence of these latter infections has been increasing in recent years and this has fuelled an enhanced interest amongst the clinical and scientific communities in mycoses and the fungal species responsi- ble for them. Therefore, the purpose of this topic is to introduce the reader to these diseases and to their etiological agents.

    Topic Objective :

    1. To know the pathogenicity of fungi to human.

    2. To illustrate the clinical manifestation of mycoses.

    3. To understand the virulence of fungal diseases in human.

    4. To know the different criteria based on human diseases are diagnosed.

    5. To illustrate the main major human diseases caused by fungi by introducing the classification of mycoses.

    6. To know the infections routes of human fungal diseases.

  • Plan ;

    First :Study the following file about human diseses caused by fungi, their types, classification, diagnosis, route of infection and virulence.   human diseses caused by fungi, their types, classification, diagnosis, route of infection and virulence.

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    File

    fungi as human pathogen File

• Topic 9

• Topic 10