Mycelial Ascomycotina

Mycelial Ascomycotina

The remainder of the Ascomycota are the mycelial Ascomycota. These species have septate, mycelium and produce asci and ascospores that are borne in an ascocarp. There are four types of ascocarps recognized; cleistothecium, perithecium, apothecium and ascostroma. The latter is a acavity that has been produced in a stroma to accomodate the asci and ascospores.

The development of the various types of ascocarp is very variable, but certain events are consistently present in most types of ascocarps. We will use Pyronema domesticum, an apothecium forming species as an example of ascocarp development.

Asexual reproduction, when present, occurs by conidia. Asexual spores borne in sporangia do not occur in this division. The mycelial Ascomycota can also be divided into two ascus types. Species that produce cleistothecia, perithecia and apothecia have unitunicate asci while . those that produce ascostroma have bitunicate asci (Fig. 1). The bitunicate ascus may be distinguished from the unitunicate in that the inner layer of the ascus, the endoascus, is flexible and will become considerably extended, prior to spore release, and will separate from the rigid outer layer of the ascus, the exoascus, and grow through its apical pore. In the unitunicate ascus, separation of  endo- and exoascus does not occur.
 

Fig. 1: Bitunicate Ascus of  Leptosphaerulina. The flexible endoascus has grown through the rigid exoascus.

 

Because of the tremendous variations that exist in this group of fungi, we will divide the mycelial Ascomycota into four series, based on the type of ascocarps produced. This classification scheme was once used to divide the division into classes. Although this system proved to be artificial and a continual gradation can be seen to exist from the typical cleistothecium, perithecium and apothecium, it continues to be used. However, usage today is no longer as an official taxon, but as a series, which is in the context that we are using this scheme, and does not have any taxonomic significance. In this classification scheme, Ascomycota producing cleisotothecia are in the Plectomycetes, those producing perithecia are in the Pyrenomycetes and apothecial producing members are in the Discomycetes. The ascostroma group is in a different line of evolution and is in the Loculoascomycetes.

Series I: Plectomycetes (=Cleistothecial Ascomycota)

This series is characterized by the formation of an ascocarp called a cleistothecium. This ascocarp type is entirely closed and have asci that are scattered, randomly, throughout the interior, i.e. a hymenium is absent (Fig. 2). Paraphyses do not occur in this series. There is not an obvious means of ascospore release other than through break-down of the cleistothecium and disintegration of asci.
 

	Figure 2: Cleistothecium. An ascocarp that is entirely closed, with scattered asci, i.e. not in an hymenium and without sterile filaments, e.g. paraphyses.

The order Eurotiales will be used as a representative of cleistothecial Ascomycota. In addition, because many species of Ascomycota have both sexual and asexual stages in their life cycles, we will also go introduce the concept of anamorphs and telomorphs as we go over the representative life cycle of the Eurotiales.

The Eurotiales includes some very familiar genera of fungi, such as Penicillium and Aspergillus. However, in the strict sense, these genera do not belong in the Ascomycota. In order to explain this contradiction, let us go over the life cycle of Emericella variecolor, a species belonging to the Eurotiales. This species produces rather distinct, star-shaped ascospores, in globose asci with phalanges (Figs. 3-4). E. variecolor, is said to be the telomorph or sexual stage of the life cycle. Figure 3 shows mostly stellate (=star-shaped) ascospores with a few asci that are similar in appearance due to the phalanges that emanate from the asci. Figure 4 is a closeup showing several ascospores. Ascospores on right are magnified to show characteristic stellate appearance.
 

	Figure 3: Asci and Ascospores: Ascospores are stellate (=star-shaped). Asci are similar in appearance because of the phalanges that are present on the asci surface. However, they are larger. Two asci are present in center of this figure.
	Figure 4: Many stellate ascospores, with an ascus in the center. Compare the size of ascospores with the ascus.

During asexual reproduction, conidia are produced on conidophores that terminates in a globose, vesicle on which phialide, bearing conidia (Fig. 5) are produced. At the base of the conidiophore is a foot cell (Fig. 6). Although the asexual stage is part of the same life cycle as the Emericella stage discussed above, the asexual stage has a different name, Aspergillus, which is the anamorph part of the life cycle. The genus Aspergillus, as well as many other genera, are referable only to fungi that are known only by their asexual stage. A special division, the Deuteromycota, was erected to accomodate these fungi, with the understanding that should the sexual stage be discovered, the asexual name would be dropped and only the sexual stage would be the correct name? (more will be said about the Deuteromycota later)   So, what happened? Why do we continue to maintain two names for a single species even though both the sexual and asexual stage is known? The main reason is a practical one. Most fungi that have an asexual and sexual stage rarely are seen in their sexual stage and are better known by their asexual stage and are most often referred to in the literature by their asexual stage. Thus, it was decided that both names would be retained andd the concept of concept of telomorph and anamorph arose.
 

	Figure 5: Aspergillus variecolor, the anamorph of Emericella variecolor. The anamorph produces upright conidiophores, that swells apically into a vesicle where phialides produce conidia in chains.
	Figure 6: A lower magnification of A. variecolor, showing the entire conidiophore with the characteristic foot cell at the base of the conidiophore. The foot cell and the rest of the conidiophore can readily be recognized by the thicker cell wall.

Series: Pyrenomycetes

The series Pyrenomycetes is characterized by the formation of an ascocarp called a perithecium. This ascocarp type may be variously shaped, but is typically flasked-shaped or globose with a small ostiole through which the ascospores are released. Asci are unitunicate and are arranged, in a single fertile layer throughout the base of the perithecium or in a fascicle. Such a fertile layer is a hymenium. Sterile filaments called paraphyses may also be present among the asci. Such filaments are absent in the Plectomycetes. As the paraphyses grow into the central cavity, it becomes enlarged and provides a space where the asci and ascospores will develop. Ascospores are often forcibly ejected from the ascus and perithecium when mature. Species in this series may produce perithecia directly on their substrate or in a stroma. A stroma is a compact mass of mycelium or mycelium with host tissue, on or in which sporulating structures may be produced.

Order: Sordariales

The perithecia produced in this order ar usually dark or pallid, with asci produced in fascicles and paraphyses are absent when ascospores are mature.

Sordaria fimicola: This is an example of a species that does not produce a stroma. In nature, this species grows on dung. Such species are said to be coprophilous. The perithecia are small, black, flask-shaped ascocarps with an ostiole (Fig. 7). Asci and ascospores are borne within without paraphyses (Fig. 8).
 

	Figure 7: Black, flask-shaped perithecium of Sordaria fimicola. Ostiole is not visible.
	Figure 8: Ascospores are dark brown, in asci on right. Asci are difficult to see, but their outlines are readily visible.

Order Xylariales

This order includes a very large and diverse group of Pyrenomycetes that typically produce their perithecia in stromata. The shape of stroma are very variable. We will look at two examples:

Xylaria sp. and Penzigia globosum (Figs. 9-12): These are examples of species that produce perithecia in stromata. Their stromata are externally black, and can be seen to be mostly white in section. The perithecia are entirely immersed in the stromata with only the ostioles opened to the surface. The stromata of Xylaria are long and tapering (Fig. 9) while those of P. globosum are hemisphaerical to globose that usually occur in clusters (Fig. 10). These taxa are the most conspicuous members of the stroma producing Pyrenomycetes in Hawaii.
 

	Figure 9: Stromata of Xylaria. Stromata, on left, have white conidia covering the tips, giving it a white appearance. Stromata, on right, have swollen areas due to the perithecia pushig upward on the stroma.
	Figure 10: Stromata of Penzigia globosum. Sectioned stroma, on left, shows white interior and black perithecia lining periphery of stroma.

A prepared slide of a longitudinal section through a Xylaria stroma (Figs. 11-12) clearly shows the perithecia and ostiole breaking through the surface of the stroma.  figure is a longitudinal section through stroma with several perithecia.
 

	Figure 11: Prepared slide of longitudinal section of Xylaria.  Perithecia line the periphery of the stroma and so are able to produce ostioles on the stroma surface, through which ascospores will be dispersed.
	Figure 12: Prepared slide of longitudinal section of Xylaria, at a higher magnification.

Series: Discomycetes

The series Discomycetes is characterized by the formation of an ascocarp called an apothecium. Typically an apothecium is cup-shaped (Fig. 13) which is why Discomycetes are sometimes called "cup fung". However, the shape of the apothecium is quite variable (Figs 14-17). Whatever their shape may be, the asci form a hymenium that is usually, entirely exposed at maturity. The asci are unitunicate and forcibly eject the ascospores. Paraphyses are generally present in apothecia.

Variations in Apothecium Configuration

From left to right: Morchella esculenta, a species in which the apothecium has now formed depressions that are fertile with sterile ridges in between; Leotia lubrica, a species in which the "cup" of the apothecium is interpreted as being folded back, i.e. the hymenium is on top, giving it a mushroom-like appearance; Gyromitra californica, a species in which the apothecium is said to be "saddle-shaped", and the interpretation here is similar to the previous species, but now the cup has been folded in half.
 

	Figure 13: Sarcoscypha coccinea, a typical cup-shaped apothecium.
	Figure 14: Sarcoscypha mesocyatha is more flattened and has a dish or saucer-shaped apothecium. This species was recently (1997) described as new, from Hawai‘i.
	Figure 15: The morphology of Morchella esculenta, as well as other species of morels, is far different than the two examples above. The ridges that can be seen on the surface are sterile. Asci and ascospores are found only in the sunken areas of this apotheciuim.
	Figure 16: The morphology of the Leotia lubrica apothecium superficially looks like a mushroom. However, the "cap" of this  species is actually the apothecial surface. The apothecium is interpreted a being folden back.
	Figure 17: The morphology of the Gyromitra californica is said to be saddle-shaped for obvious reason. This apothecium is interpreted as being folded back, as well, but in this species it is specifically folded back and in half.

Series: Loculoascomycetes

The series Loculoascomycetes is characterized by producing their asci in ascostroma. An ascostroma is a locule that forms in a stroma where the asci are borne. This differs from a perithecium that is formed within a stroma in that a perithecial wall is formed by the perithecium that delimits it from the stroma. Such a wall layer is absent in the Loculoascomycetes. Asci in this series are said to be bitunicate (Fig 1). This differs from a unitunicate ascus in that the endoascus will grow through the outer layer, the exoascus, and extends beyond it through the open pore at the tip of the exoascus. This type of ascus has also been referred to as the jack-in-the-box ascus. Paraphyses may also occur in this series.

The example that we will examine in lab is the genus Leptosphaerulina. The ascostroma in this genus is very difficult to distinguish from perithecial species of Pyrenomycetes because it is a uniloculate ascostroma (Fig. 18). However, if examined,  microscopically, this genus can be observed to have a bitunicate ascus, a characteristic of the Loculoascomycetes series of Ascomycota.
 

	Figure 18: Leptosphaerulina sp.: An example of a uniloculate ascostroma. In this type of stroma it would be very difficult to   distinguish if it is a perithecium rather than an ascostroma. However, the characteristic of the bitunicate ascus is a reliable feature in determining that this fungus is a Loculoascomycetes.

 

Ascomycotina

Ascomycotina The division is a large and very diverse group that has historically been difficult to characterize. However, the one unifying characteristic is that all members produce ascospores inside of a sac-like cell called an ascus (pl.= asci) and during sexual reproduction (Fig. 1). There are typically eight ascospores produces per ascus. However, the number can vary from one to over a thousand. As does the ascus, which may be globose to cylindrical.
 

	Figure 1: Cylindrical asci of Ascobolus stercorarius, with eight ascospores in each ascus.

Other characteristics are variable. The thallus is often mycelium that is septate. However, there are also many species that form a yeast thallus and some species have both and are said to be dimorphic. Most species produce asci and ascospores in an ascocarp, which is a complex fruiting body made up of tightly interwoven mycelium, but some produce "naked" asci, i.e. an ascocarp is not produced.
Based on recent molecular data, concepts concerning the phylogeny of this division has undergone major changes. Characteristics that have been traditionally used to classify the Ascomycota, such as thallus type, ascocarp type and development and ascus types, now appear to be less useful as indicators of phylogeny.
We will cover the Ascomycota by dividing them into two artificial groups, based on thallus type: Yeast and mycelial species.
Yeast and Yeast-like Ascomycota
The yeast and yeast-like fungi of the Ascomycota are structurally simple fungi. Many species are unicellular and reproduce asexually by budding (Fig. 2, 4)or fission (Fig. 3, 7). The process of budding begins in a mature yeast cell at predetermined areas of its cell wall. In Saccharomyces cerevisiae, for example, budding takes place at the poles of the cell. In these areas when budding is about to take place, the cell wall is softened and is "blown out" to form the so-called "bud", which will become the new cell. As the bud enlarges, mitosis of the nucleus occurs, with one of the nuclei moving into the newly formed cell. When the cell reaches the approximate size of the original cell, cell wall material is laid down in the passage between the two cells, which will then shortly separate.
 

	Figure 2: Asexual reproduction of a budding yeast. Formation of new cell begins with blowing out of a new cell, at the pole of the cell. Mitosis follows with migration of one nucleus to the new cell. New wall
material is then laid down in the passage between the two cells and separation of the cells will occur.

Fission is a simpler process. In Schizosaccharomyces, during fission mitosis of the nucleus occurs, followed elongation of cell and the laying down of a cell wall that divides the cell in half, separating the two nuceli.
 

	Figure 3: Asexual reproduction of a fission yeast. Mitosis of the nucleus occurs, followed by elongation of the cell and formation of a cell wall that divides the cell in half, separating the two nuclei.

We will describe the life cycle examples of a budding and a fission yeast. The representatives that are typically used are Saccharomyces cerevisiae, the brewer's yeast and Schizosaccharomyces octosporus, respectively. The two species were formerly placed in the class Hemiascomycetes, in one of the more conservative classifications. This was the class in which all the yeast and yeast-like members of the Ascomycota were placed. However, recent molecular evidence indicates that there are two distinct group of yeast, based primarily on DNA sequence analysis. The two representatives that we are using are now recognized to be in these two distinct lines. The S. cerevisiae is placed in the order Saccharomycetales, which usually is no longer placed in a class and S. octosporus is in the order Schizosaccharomycetales and in some classification schemes in the class Archiascomycetes. However, it should be noted that reference to fungi having yeast thalli has long been considered an artificial category in classifying fungi. In the Ascomycota, there are apparently two phylogenetic lines of yeast fungi. In addition, the next division that we will study, the Basidiomycota, will also have several phylogenetic lines that form yeast thalli. Thus, the term yeast should be and is here used only as a means of describing a thallus type.
 
 
Saccharomyces cerevisiae (Brewer's Yeast) is probably the most studied species of fungi because of its economic importance in the beer and wine industry. It is an example of a budding yeast.
Saccharomyces cerevisiae
Saccharomyces cerevisiae is a heterothallic species and require the presence of two mating strains of yeast cells that have been designated as "a" and "a". Fusion of the two mating strains will produce the zygote. Unlike other species of fungi, the life cycle of this species is not zygotic. The diploid cell does not undergo meiosis and will assimilate food and reproduce asexually for a time. Thus, there is a true alternation of generations and this species has a sporic life cycle. The life cycle is completed when meiosis occurs in the diploid yeast cells and each of the four nuclei becomes an ascospore (Fig. 5). Two will be of the "a" and the other two will be of the "a" mating strains. The original cell wall of the diploid yeast cell is the ascus.
Figures 4-5: Saccharomyces cerevisiae.  Figure 4 (left) shows several yeast cells reproducing asexually by budding.  Figure 5 (right) shows an ascus, approximately in the middle of the figure, with four ascospores. Both micrographs were stained in phloxine and taken under phase contrast optics, which gives the images their dark reddish appearance.
Schizosaccharomyces octosporus
Schizosaccharomyces octosporus is an example of a fission yeast, which also readily produce asci and ascospores in vitro. This differs from S. cerevisiae, however, in that it is homothallic and has a zygotic life cycle, which is typical of most fungi. Thus, any two yeast cells of this species can fuse to produce a zygote. Once the zygote is formed, it immediately undergoes meiosis. this is followed by a mitotic division, with each nucleus becoming an ascospore. The old zygote cell wall becomes the ascus (.
Figure 6-7:  Schizosaccharomyces octosporus. Figure 6, on left, shows two cells that are dividing by fission and Fig. 7, on right, shows at least three asci with ascospores.
Although many species in the order Saccharomycetales may be unicellular, some have short, septate, hyphal growth. Extensive mycelial growth does not occur. In these species, asci and ascospores are still borne naked and are not produced in an ascocarp. An example of a species with short hyphal growth is Dipodascopsis uninucleatus.
Dipodascopsis uninucleatus
Dipodascus uninucleatusis an example of a species in which limited hyphal growth occurs. This species is homothallic and sexual reproduction occurs when the septum separating adjacent gametangial cells disintegrates. Karyogamy occurs immediately, followed by formation of the ascus and numerous mitotic divisions. Thus, the mature ascus is filled with numerous ascospores (Figure 8). Students that follow the derivation of the Ascomycota from the Zygomycotina believe the multispored ascus of Dipodascopsis to be homologous to the zygosporangium of the Zygomycotina. However, recent molecular evidence does not indicate this to be the case. Asexual reproduction apparently does not occur in this species.
Figure 8. Mature ascus (center) of Dipodascopsis uninucleatus with numerous ascospores. The ascospores are released, passively, through the apical pore of the ascus. Note that there is only limited hyphal growth present.

Cell Walls of Algae

Cell Walls of Algae

Algae are the plants with the simplest organization.

Many of them are single-celled, some have no cell wall, others do though its composition and structure differ strongly from that of higher plants. 

They are good specimen for tracing back the evolution of the cell wall. Primitive cell walls do not fulfil the same requirements as that of higher plants.

It seems quite likely that a structure like that of the cell wall has developed several times in the course of evolution. 

All archaebacteria, eubacteria and blue-green algae (cyanobacteria or blue-green algae) have complex walls with an energetically rather costly biosynthesis. 

Neither in composition nor in biosynthesis do they have any common ground with the cell walls of plants.

Although the evolution of plants from early eucaryotic cells is not known in detail, is it commonly agreed on that primitive algae are flagellates closely related to the non-green flagellates. Many, though not all species of this stage of evolution, among which the euglenophyta are typical green representatives, have no cell wall. It is not only a simple membrane, but by a pellicle of already quite complex organization, that separates them from the surrounding. It consists mainly of glycoproteins organized in regular patterns the way two-dimensional crystals are. Helical ribs wind round the cell's surface.

Most single-celled algae like the Volvocales possess real cell walls. The most-studied species is Chlamydomonas reinhardii. Its wall lacks long, fibrillary carbohydrates. Most of it is made up by glycoproteins, and even here can an extensin-like protein rich in hydroxyproline be found. Among the identified sugar residues are arabinosyl-, galactosyl- and mannosyl residues. In the electron microscope does it seem as if the wall consisted of seven layers. The middle layer contains an extensive grid-shaped framework of polygonal plates consisting mainly of the mentioned glycoproteins, while the layers above and below display fibre-like structures. The thickness of the outer layer varies since it includes components that the cell takes up from its surrounding.

This indicates a main function of the cell wall of simple, single-celled algae: it mediates between the cell and its surrounding. It protects not only the cell but serves, too, communication with cells of the same or other types. It has to be permeable for metabolites and regulators and / or to carry receptor molecules with which it may contact other cells. The diversity of these functions (and their specificity) caused the evolution of a variety of differently structured cell walls.

In many-celled plants is the communication via the whole cell surface largely restricted. Contact with neighbouring cells develops in the course of tissue formation. Strength is in this respect a decisive and limiting criteria. The exchange of compounds between cells occurs via specific openings in the wall (pits, plasmodesmata). The functions originally performed by one structure are now distributed onto two different structures.

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Structural Components of The Cell Walls of Algae - Molecular Classes and Conformations of the Molecules

The main structural elements of all plant cells are polysaccharides. Differences in their chemical composition cause fundamentally different physical properties. No plant cell wall consists only of one class of molecules. The interactions of the different molecules produce properties that allow to distinguish the cell walls of certain classes.

In many classes of algae is cellulose already the main structural element of the wall, though remarkable variations of the fibrillary structure exist. Reliable X-ray analytical data prove that is mostly crystalline in cells of algae, too. Differences in the type of the flexor reflexes hint at the fact that cellulose could aggregate in many more or less uniform crystalline structures. Such reflexes are a measure for periodic distances at the molecular level, which may differ considerably from species to species and are specially large in Rhodophyta

In some classes of algae exist only disperse textures, while others (specially many Chlorophyta-species) have a higher degree of organization (layers of parallel microfibrils). Such layers do usually alternate with layers of an amorphous material. No clear difference between primary and secondary cell wall exists in most algae. Where such a distinction is possible, differ the causes usually from that in higher plants.

Mannanes In a number of marine green algae (Codium, Dasycladus, acetabularia, etc.) as well as in the walls of some red algae porphyra Bangia) constitute mannanes the main structural elements. They are linear and the mannosyl residues are 1 > 4 glycosidically linked. Hydrogen bonds that are (just like in cellulose) the cause of the partially crystalline organization of microfibrils may develop. In Codium the carbohydrates are tightly associated with protein

Xylanes are polymers where the beta-D-xylosyl residues are linked via 1 > 3 and 1 > 4 glycosidic bonds. In contrast to the polymers discussed until now, are xylans partially ramified. In species with xylan-containing walls exists nevertheless a layered structure and an orientation of the microfilaments. They contain mostly linear polymers.

Alginic Acid: alginic acid and its salts, the alginates are important components of the walls of phaeophyta They are singular in many respects. They consist exclusively of uronic acids: mannuronic acid and beta-L-glucuronic acid in changing ratios and of small amounts of beta-D-glucuronic acid.

Beside homopolymers exist also heteropolymers in many algal groups, partially exist species specific differences, an indicator of the fact that the single species contain different sets of enzymes.

The alginates of brown algae exist both within the cell wall and in the intercellular substance. Their part in the cell wall may be as high as 40 per cent of the dry matter. They have a high affinity for divalent cations (calcium, strontium, barium, magnesium) and the tendency to gel. The main portion of the magnesium ions isolated from brown algae stem from the alginic acid fraction.

Sulfonated Polysaccharides: polysaccharides: polysaccharides whose monomers are esterized to sulfuric acid residues and are moreover partially methylated have been detected in nearly all marine algae. They occur partially in the cell wall itself and partially in the intercellular substance. Sulfonated galactanes are typical for many red algae, depending on their origin are they called agarose, carrageenan, porphyran, furcelleran and funoran.

L- and D-galactose, which are linked by beta 1 > 3 or alpha 1 > 4 glycosidic bonds form the basic pattern of agarose and porphyran, in the latter alternate L- and D-galactosyl residues. Carrageenan and furcelleran contain exclusively D-compounds. Just like in alginates is the formation of gelatine one of the most important physical properties of this family of molecules. Agar, whose basic unit is agarose, is yielded mainly from Gelidium and Gracillaria, both genera of red algae.

The extraordinary binding types of agarose and carrageenan lead to specific tertiary structures.

Further Cell Wall Compounds. A number of algae contain mineral cell wall components. Silicon, for example, is the main component of the diatom shell, though it occurs also in the cell walls of other groups of algae. Silicon-containing scales enclosed the chrysophyt Synura. In some brown algae and in the green algae Hydrodictyon  is silicon a cell wall component. Diatoms take silicon up as silicate. The process is dependent on oxygen and temperature, it consumes energy and it is dependent on the presence of divalent sulphur.

Sporopollenin is an isoprene derivative. It is a component of pollen cell walls, but was also detected in the walls of some green algae (Chlorella, Scenedesmus, etc.).

Calcium: calcium encrustations of cell walls have on several occasions be described. They seem to be especially common in species of tropical, marine waters. Some species participate in reef formation. Calcium is always deposited as calcium carbonate. Calcium carbonate occurs in two different crystalline states: calcite and argonite. Calcite is produced in the walls of some groups of red algae and in charophycea, while argonite is produced by some green (Acetabularia, etc.), brown and red algae. Both states do not occur simultaneously in one species.

Binomial Nomenclature

Carolus Linnaeus

Linnaeus (1707-1778), a Swedish physician and botanist, was the founder of modern systematics. He originated the system of binomial nomenclature used for naming plants and animals and grouping similar organisms into increasingly general categories. Today, biologists still use this basic system of classification, but advances in the fields of genetics and evolutionary theory has resulted in some of Linnaeus’ original categories being changed to better reflect the relationships among organisms.

Binomial Nomenclature

Also called binary nomenclature, this formal system of naming organisms consists of two Latinized names, the genus and the species. All living things, and even some viruses, have a scientific name.

The binomial aspect of this system means that each organism is given two names, a ‘generic name,’ which is called the genus (pl. genera) and a ‘specific name,’ the species. Having a universal system of binomial nomenclature allows scientists to, in essence, speak the same language when referring to living things, and avoids the confusion of multiple common names that may differ based on region, culture or native language.

When written, a scientific name is always either italicized, or if hand-written, underlined. The genus is capitalized and the species name is lower case. For example, the proper format for the scientific name of humans is Homo sapiens.

What Is a Genus?

In biology, ‘genus’ is the taxonomic classification lower than ‘family’ and higher than ‘species’. In other words, genus is a more general taxonomic category than is species. For example, the Grey Wolf, or Timber Wolf (Canis lupus) belongs to the same genus as the domestic dog (Canis domesticus). Although in the same biological family (Canidae) as wolves and dogs, foxes belong to a different genus (Vulpes). This reflects a closer evolutionary relationship between the wolf and the domestic dog than between either and the fox.

What is a Species?

The species name, also called specific epithet, is the second part of a scientific name, and refers to one species within a genus. A species is a group of organisms that typically have similar anatomical characteristics and that can successfully interbreed to produce viable offspring. A mule, for example, is not a distinct species. It is an infertile hybrid of a male donkey (Equus asinus) and a female horse (Equus caballus).

What is Nanotechnology?

What is Nanotechnology? A basic definition: Nanotechnology is the engineering of functional systems at the molecular scale. This covers both current work and concepts that are more advanced. In its original sense, 'nanotechnology' refers to the projected ability to construct items from the bottom up, using techniques and tools being developed today to make complete, high performance products.

Zygomycotina

 Division: Zygomycotina
 The Zygomycotina is thought to be the most primitive of the terrestrial fungi. This division has coenocytic mycelium, and asexual spores (=sporangiospores) that are produced in sporangia borne on stalks (=sporangiophores). These characteristics are shared with the divisions of flagellated fungi that were just studied. For this reason the Zygomycotina were once thought to be closely related to the aquatic fungi. However, cell wall composition is chitin-chitosan and flagellated spores and gametes are absent in this division as well as in the remaining taxa of terrestrial fungi. Sexual reproduction occurs with the fusion of undifferentiated isogametangia or anisogametangia to produce a zygote. The zygote later develops into a thick-walled zygospore, the diagnostic feature of this division. Two classes are recognized in this division; the Trichomycetes and Zygomycetes. Only the Zygomycetes will be studied.

Class: Zygomycetes

Characteristics of the class is the same as those of the division.

Rhizopus stolonifer:

Asexual Reproduction: A typical sporangium (Fig. 1) is produced on a sporangiophore, singularly or in clusters, where rhizoids have formed and grown in the substrate. Within the sporangium proper are sporangiospores and a columella.

	Figure 1: Rhizopus stolonifer: Root-like rhizoids giving rise to three sporangia on sporangiophores.

Variations in asexual reproductive structures

There is a great deal of variation that occurs in the sporangia of the Zygomycotina

. Below are a few of the more common variations:

		Figure 2-3: Syncephalastrum racemosum: Cylindrical sporangia (=Merosporangia) with spores produced in a single column. Merosporangia are borne on a swollen vesicle on top of the sporangiophore.

			Figures 4-6: Cunninghamella echinulata: This species of Zygomycotina	is apparently one of the most common in Hawai‘i. Micrograph of this species were taken
through phase optics. Micrograph on left shows immature vesicles that have not yet developed sporangioles. Middle micrograph shows three, young vesicles with immature sporangioles starting to develop, on short stalks. At maturity, right micrograph, superficially resembles S. racemosum. However, single-spored, sporangioles are produced rather than the cylindrical merosporangia. The individual sporangioles are difficult to observe in mature specimens.

Sexual Reproduction

Sexual reproduction occurs when opposite mating strains, designated as "+" and "-", grow towards one another. As the opposite mating strains near one another a hormone, trisporic acid, induces formation of progametangia which meet to initiate sexual development. Nuclei migrate into the apex of the progametangia where septa will form. The terminal cells are the isogametangia and the remainder of what was the progametangia are the suspensors. Fusion of gametangia will take place, followed by plasmogamy and karyogamy, and zygote formation. A dark, thick cell wall then forms around the zygote which may now be referred to as a zygospore. The formation of the zygospore is the unifying characteristic of the fungi inthis division. Life cycle images of Rhizopus stolonifer from Dr. Tom Volks.
 

	Figure 7: Pair of progametangia of different mating strains: "+" and "-" grow towards each other. Migration of nuclei will occur in the tips of both progametangia where gametangia will form.
	Figure 8: Septa are laid down at the apex of the progametangia to form isogametangia. The outside, larger cells are the suspensors that support the gametangia.
	Figure 9: Plasmogamy occurs following fusion of the gametangia. Karyogamyimmediately follows to form a multinucleate zygote.
	Figure 10: The zygote will form a thick, pitted wall around itself to form the zygospore. Further development will not develop until after it has gone through a period of dormancy.

Functions of the cell wall

The cell wall possesses catalytic activity

But the cell wall is even more than just polysaccharide relatives. A critical component of cell walls is protein that provides catalytic activity for the cell wall region. Enzymes that polymerize wall monomers, enzymes that cross-link polymers, enzymes that cleave polymers, these and others permit the cell wall region to be a dynamically-sculpted element for a living cell.

The cell wall provides for turgor pressure

Far from being a barrier, the wall is partially for the structural support of a multicellular, multidimensional plant body, but has a critical function in providing a means to survive in a dilute solution of solutes. Soil water is a hypotonic medium and the wall provides a means to avoid cell expansion that would otherwise exceed the bursting strength of the cell membrane. It permits the development of turgor pressure which can be a structural and functional factor in support and movement.

The cell membrane is more than phospholipids

The cell membrane, generally just inside of the cell wall and tightly apressed against it because of turgor pressure, is the exchange regulator for the cell and its environment. Indeed the oligosaccharide subunits and wall-sculpting enzymes are passed from the interior of the cell through this membrane: by exocytosis. Water, minerals, sometimes organic particles, pass from the environment through this membrane to the cell's interior: endocytosis. While "goodies" are allowed to pass through the membrane, other substances are kept outside. The cell membrane is shown below.

The phosopholipids provide barrier functions

The main barrier function is provided by the phospholipid bilayer. This bilayer is composed of amphipathic phospholipid molecules. Two C14-C24 fatty acids, one saturated (no double bonds) and the other at least mono-unsaturated (one double bond), comprise the hydrophobic "tails" that make passage of charged and polar molecules into and out of the cell all but impossible. These are linked by a glycerol (3C-sugar) to a very polar and hydrophilic phosphate-small-organic-group "head." Thus polar solutes might pass into the "heads" part of the membrane, but cannot pass through the non-polar "tails." Similarly non-polar molecules would pass easily through the "tails" part of the membrane, but cannot approach that because of the polar "heads" layer.

Phospholipids spontaneously form bilayers with the polar "heads" facing the aqueous extra-cellular fluids and the aqueous cytosol. Between these layers of "heads" the hydrophobic "tails" inter-mingle. The double-layer of "tails" thus provides a the barrier functions for many biologically-interesting ions and molecules.

An individual phospholipid in the bilayer is free to move about in the plane of the bilayer. Contributing to this fluidity of movement, or stabilizing this fluidity depending on temperature are various steroids that are often a part of the membrane. In plants the steroid components include wide range of distinct molecules.

The cell membrane proteins provide catalytic functions

But a cell membrane that is a great barrier is not good for the cell per se. In fact a barrier is only as good as its doors and windows. The mark of a good barrier is that it allows for exchange of positive elements while providing only exit and never entrance of negative elements. This lesson, hopefully recalling the Iron Curtain, is pointing to the proteins of a cell membrane.

The phospholipid bilayer is traversed by integral proteins. These proteins have two hydrophilic zones separated by a hydrophobic zone of suitable dimensions to become trans-membrane transport proteins. These may permit facilitated diffusion of suitably small charged molecules or elements, or perhaps even active transport of essential components. Active transport of course involves the conversion of ATP into ADP and Pi or AMP, with the released energy from the cleavage of the phosphate bond driving the movement of the component through the membrane.

The membrane is also a site of catalytic activity. In addition to integral proteins, there may also be peripheral proteins attached to one side or the other of the bilayer. The attachments may involve simple hydrophobic and hydrophilic domains of the protein, but might also involve linkage of the protein to fatty acids or other hydrophobic attachments that anchor them within the bilayer and leaving the protein facing the aqueous environment. These proteins likely serve various catalytic or electronic functions. Depending on which face of the bilayer we are examining, we might find ATP synthases or electron transfer proteins here. We might also find enzymes, such as succinate dehydrogenase, that catalyze steps associated with pathways in one compartment or another adjacent to that surface of the bilayer. The many proteins in a membrane may constitute 40% of that membrane! To simply call a membrane a "phospholipid barrier" would be a gross over-simplification.

The cytosol is more than just water

Inside the cell wall and membrane we have the fluid compartment of the cell. Indeed this compartment is mostly water...and water has some very important roles to play in the life of a cell...but this fluid is much more than just water!

Saying "just water" is really an injustice to this critical molecule for life! We will get into that later in the course in some detail. Let's remember it as the medium for the creation of life, as a UV screen until the ozone layer helped out, and as more than 90% of the weight of metabolically active cells.

This region was called cytoplasm (literally cell fluid) back in the days when light microscopy was a cutting-edge technology. When electron microscopy was developed, we learned that this cytoplasm was not just fluid...it contained previously-invisible structures that are not simply fluid. So we use cytoplasm generally to mean the fluid and all of these contained organelles together. A newer word, cytosol (literally cell solvent), is used to mean only the fluid in which the organelles are suspended.

The cytosol hosts tremendous catalytic activity

The cytosol contains dissolved minerals, gases, and organic molecules. These provide for the many catalytic functions of the cytosol. Dissolved proteins, often called soluble enzymes, are responsible for a range of biochemical sytheses and degradations that characterize a living cell. The cytosol is host to a range of entire pathways of regulated biochemistry! Examples include glycolysis, fermentation, and (from a certain perspective) translation!

In addition to these functions, the cytosol serves as a hydraulic fluid for organismal support, as a medium for diffusion, and as a compartment for osmosis. It provides thermal buffering capacity and as a transparent medium for light penetration. The differential solubility of oxygen gas and carbon-dioxide gas provides for a medium in which photosynthesis can occur. Dissolved pigments may provide protection in times of excessive light irradiation.

The nucleus is more than just a DNA container

The nucleus is an organelle of the cell that is not considered part of the term cytoplasm. It was obvious in the early days of microscopy. Various staining procedures revealed that it contained nucleic acids (DNA and RNA) well before the hereditary roles of these molecules was known. But early tests also indicated the presence of proteins.

The nuclear envelope is composed of two bilayer membranes

The outer membrane and inner membrane of the nuclear envelope are separated by a perinuclear space. The bilayer facing the cytosol is perhaps very much like that of the endoplasmic reticulum and often hosts polyribosomes. The bilayer facing the nucleoplasm is coated with the nuclear lamina...a layer of intermediate filaments. During mitosis the envelope is dispersed as small vesicles that coalesce after mitoses.

The nuclear envelope has "pores" for the passage of large materials

The nuclear pore complex is a formation of structural and functional proteins that permit the movement of molecules, macromolecules, and even the subunits of ribosomes through the envelope. The pore complex is depicted below. A key element of this complex is the transporter protein, which can be regulated to permit or prohibit movement through the envelope.

DNA in the nucleus is found in chromosomes

The hereditary molecule, DNA, is amazingly long. Each molecule, called a chromosome, is composed of many shorter lengths of DNA, called genes, that are linked end to end. The sequence of nucleotides in each gene constitute the instructions for the synthesis of a single protein. For various portions at one time or another, and for the whole chromosome at the start of mitosis, the chromosome is condensed in a process shown below.

Histone proteins are a primitive feature of most eukaryotic organisms. The amino acid sequence of these proteins is exceedingly conservative among plants, animals, and fungi. The DNA molecule is wrapped around histones in the form of nucleosomes. These are cross-linked by other histones, and coiled and looped in repeatable ways to ultimately produce the familiar X-shaped chromosomes we observe during mitosis. Because the set of n chromosomes, as a group, represent one entire genome, and two such sets are present in most plant nuclei, it is no surprise that most of the DNA in any particular cell is not being expressed (used) at any point in time. When one considers that each cell contains two complete sets of instructions for a whole organism, it is clear that most of the DNA must not be "active."

The nucleus often demonstrates a nucleolus

Early light microscope preparations were stained and even in interphase, when the chromosomes are NOT condensed, one or more intensely-staining zones were observed in the nucleus. These were called nucleoli. RNA-specific stains and probes reveal that the nucleolus is a region with much RNA compared to the rest of the nucleus. The nucleoli are considered to represent the location of genes coding for ribosomal and transfer RNAs. In metabolically active interphase cells, many ribosomes and transfer RNAs are needed to maintain the protein pools needed for active metabolism. These genes, then, are being transcribed at a very high rate and the RNA products are locally abundant, explaining the intense local staining.

Protein stains also highlight the nucleolus. Proteins are translated in the cytosol and those destined for the nucleus pass through the pore complex into the nucleoplasm. Some of these are enzymes are involved in replication and transcription, including DNA and RNA polymerase. Other proteins arriving are the components that must join ribosomal RNA to form ribosome subunits. The two ribosome subunits, the large and small subunits, are assembled in the nucleolus region explaining the protein stain results. The ribosome subunits are transported out of the nucleoplasm through the pore complex separately. They join only after arrival in the cytosol and in the presence of messenger RNA and transfer RNAs.

The nucleus is the site of mRNA transcription

In addition to the production of rRNA and tRNA, the nucleus is responsible for producing messenger RNA. This process is called transcription. Regions of the "active" genes in the genome possess nucleotide sequences which are called the promoter. This region is recognized by RNA polymerase (a protein) as a site for binding to the DNA. The RNA polymerase slides down the length of the gene and catalyzes the formation of a single-stranded RNA transcript. If this gene codes for a protein, the RNA transcript is called messenger RNA. The processes of transcription and translation are depicted below.

The messenger RNA will be modified (introns removed, etc.) and shipped out of the nucleus through the pore complex. In the cytosol, it will join to the small and large subunits of a ribosome and through the interaction of the ribosome with transfer RNAs, a protein will be synthesized.

The ribosome is the site of protein translation

The ribosome subunits attach to the mRNA and together slide along the RNA. As the subunits pass along the RNA, transfer RNAs deliver amino acids as coded by the sequence of nucleotides in the RNA. The ribosome proteins and ribozymes catalyze the formation of the peptide bond between the amino acids to provide the primary structure of the developing polypeptide.

Ribosomes can be found freely in the cytosol and produce "soluble" proteins that are used locally in the cytosol. Other ribosomes are associated with the endoplasmic reticulum. These are attahed to mRNAs that code for a hydrophobic signal sequence of 18-30 amino acids in the developing polypeptide. These sequences bind to a signal recognition particle which facilitates the attachment of the ribosome to the bilayer of the endoplasmic reticulum and the penetration of the developing polypeptide into the lumen of the ER. Once inside the lumen, the polypeptide is processed in various ways to attach a particular oligosaccharide to the polypeptide. This "label" facilitates the sorting, packaging, and transport of the polypeptides to ensure their delivery to the correct intracellular or extracellular location.

The difference between rough ER and smooth ER is both structural and functional. Areas where the ER is associated with ribosomes (rough ER) the main functions are translation of export proteins. Areas where the ER is not associated with ribosomes (smooth ER) carry out synthesis of lipids and other membrane components. ER located near the nucleus is often rough ER; areas of the cell remote from the nucleus are more likely to be smooth ER.

The endoplasmic reticulum processes and transports materials across the cell

The endoplasmic reticulum is a network of connected membrane sacs and tubules. Materials crossing into the lumen from the cytosol are transported from one region of the cell to another. Precisely how the ER accomplishes the movements is apparently unknown.

Ultimately proteins that require packaging and export arrive through the network near an ending close to a Golgi apparatus. Here the ER produces a vesicle that contains the protein and carries it across the cytosol toward the Golgi.

The Golgi (dictyosome) has two faces

The Golgi apparatus is very much like a specialized stack of ER; it is depicted. The layers of the stack which are closest to the ER are called the cis face; the layers which are closer to the cell membrane are called the trans face. Each layer in the stack is called a cisternum.

The cisternae of the cis face of the Golgi receive the vesicles from the ER with their contents. Within the cisternae, the oligosaccharides at the end of the protein are modified again prior to export. Cisternae on the trans face either produce secretory vesicles or disintegrate into large populations of export vesicles. In the latter case, new cisternae are produced on the cis face to replace those breaking up on the trans face. Which of these two mechanisms, or some combination, is reality has not been determined precisely.

The secretion vesicles can migrate to the cell membrane and participate in exocytosis.

One type of vesicle that is critical for plants is a secretory vesicle that releases cell wall oligosaccharides and wall-enzymes by exocytosis into the cell wall environment. Another vesicle, found in storage cells, are coated with clathrin and contain proteins and other materials for digestion. These transport materials to special vacuoles for intracellular digestion. There are also means for lysosomes to participate in this process.

We will continue with Basic Cytology in the next lecture.