Showing posts with label microorganisms. Show all posts
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1:34 AM
Algae
Algae
Algae comprise a diverse group of (with few exceptions) photosynthetic oxygen-producing organisms, ranging in size from microscopic single cells to gigantic seaweeds.

The study of algae is known as phycology (in Greek, phycos means "algae"). Currently, most authors place eukaryotic algae in the kingdom Protista (domain Eukarya) and prokaryotic algae in the domain Bacteria.

In the past algae were considered to be lower plants because some forms look like plants. As in plants, the primary photosynthetic pigment in algae is chlorophyll a, and oxygen is produced during photosynthesis.

What Are Algae?

Algae can be found nearly everywhere on earth: oceans, rivers, lakes, in the snow of mountaintops, on forest and desert soils, on rocks, on plants and animals (such as within the hollow hair of the polar bear), or even on other algae. They are involved in diverse interactions with other organisms, including symbiosis, parasitism, and epiphytism.


Lichens are symbiotic associations between algae (blue-green algae, or cyanobacteria) and fungi. Atmospheric nitrogen-fixing cyanobacteria occur in symbiotic associations with plants such as bryophytes, water ferns, gymnosperms (such as cycads), and the angiosperms.

The aquatic fern Azolla, commonly used as a biofertilizer in rice fields in Asian countries, harbors the symbiotic cyanobacterium Anabaena azollae. Gunnera, the only flowering plant to house symbiotic cyanobacterium Nostoc, is widely distributed in the tropics.

Symbiotic dinoflagellates known as zooxanthellae livewithin the tissues of corals. Corals get their colors and obtain energy from their photosynthetic symbionts. About 15 percent of red algae occur as parasites of other red algae. Parasitic algae may even transfer nuclei into host cells and transform them.

After transformation, the reproductive cells of the host algae carry the parasite’s genes. Various algae live on the surfaces of plants and other algae as epiphytes. Sometimes algae can be found in strange places—the pink color of flamingos originates, for example, comes from a pigment in the algae consumed by these birds.

Algal Structure and Properties

Algal cells are bounded by a cell wall. Algal cells are either prokaryotic or eukaryotic. All prokaryotic algae belong to Cyanophyta (cyanobacteria) and lack both a nucleus and complex membrane-bound organelles, such as chloroplasts and mitochondria.

Photosynthesis occurs in cyanobacteria in thylakoid membranes similar to those of plants. However, there is no double membrane surrounding the thylakoids of cyanobacteria.

All other algal groups are eukaryotic. Eukaryotic algae differ from cyanobacteria in that they possess chloroplasts and flagella with associated structures and in their cellwall composition. According to the endosymbiont hypothesis, some eukaryotic algae (red and green algae) obtained their chloroplasts by acquiring symbiotic prokaryotic cyanobacteria. This is known as primary endosymbiosis.

types of alga
types of alga

Other eukaryotic algae probably obtained their chloroplasts by taking up eukaryotic endosymbiotic algae, a process known as secondary endosymbiosis. The existence of secondary endosymbiosis is indicated by the occurrence of more than two membranes around the chloroplasts of some algae, such as haptophytes, euglenophytes, dinoflagellates, and cryptomonads.

Pigments found in algae include chlorophylls, phycobilins, and carotenoids. All algae contain chlorophyll a. Accessory pigments vary among different algal groups.

Photoautotrophy is the principal mode of nutrition in algae; in other words, they are "self-feeders", using light energy and a photosynthetic apparatus to produce their own food (organic carbon) from carbon dioxide and water. The majority of algal groups contain heterotrophic species, which obtain their organic food molecules by consuming other organisms.

Numerous algae are mixotrophs; that is, they use different modes of nutrition (such as autotrophy and heterotrophy), depending on the availability of resources. The molecules used as food reserves differ among and are characteristic for algal groups. Food reserve molecules are polymers of glucose with different links between monomers.

Many algae are capable of movement. Movement is accomplished by means of flagellar action and by extrusion of mucilage. There are also peristaltic and amoeba-like algal movement. Within algal cells, movement of the cytoplasm, plastids, and nucleus also occurs.

Advantages conferred by mobility include achieving optimal light conditions for photosynthesis, avoiding damage caused by excess light, and obtaining inorganic nutrients.

Algal Reproduction and Life Cycles

Algae may reproduce either asexually or sexually. Asexual reproduction among algae includes production of unicellular spores that germinate without fusing with other cells, fragmentation of filamentous forms, and cell division by splitting.

In sexual reproduction, parent cells release gametes, which then fuse to form a zygote. Zygotes may either develop into new filaments or produce haploid spores by meiotic division.

Algae exhibit different types of life cycles. Some algal life cycles are characterized by an alteration of generations similar to that of plants. Two phases occur: sporophyte (usually diploid) and gametophyte (usually haploid).

The sporophyte produces haploid spores through meiosis, and the haploid gametophyte produces male or female gametes by mitosis. Gametophyte and sporophyte may be structurally identical or dissimilar, depending on the algal group.

Roles of Algae

Algae have played significant roles in the earth’s ecosystems since the origin of cyanobacteria (also known as blue-green algae)more than three billion years ago. Early cyanobacteria were responsible for the development of significant amounts of free oxygen in the atmosphere, which then made aerobic respiration possible.

More than 70 percent of all photosynthetic activity on earth is carried out by phytoplankton—floating microscopic algae—rather than plants. Phytoplankton recharge the atmosphere with oxygen and simultaneously absorb carbon dioxide, helping to support the complex web of aquatic biota.

Algae are also very important in the global cycling of other elements, such as carbon, nitrogen, phosphorus, and silicon. Several algal groups—such as cyanobacteria, green algae, red algae, and the haptophyte algae—are able to generate calcium carbonate.

Sedimented algae are the major contributors to deep-sea carbonate deposits (sand), which cover about half of the world’s ocean floor. Calcified coralline red algae contribute to coral reefs in tropical waters. Silica sediments in oceans (sand) are based on abundant growth of another algal group, the diatoms, which contain silica in their cell walls.

Some algae (cyanobacteria) are able to fix atmospheric nitrogen and convert it to ammonia. Ammonia, in turn, can be a nitrogen source for plants and animals. On the other hand, high levels of nitrogen and phosphorus in rivers and lakes owing to pollution can cause the rapid and uncontrollable growth of algae, known as algal blooms.

A bloom of algae is a threat to human and marine health, both directly and indirectly. It clogs fishes’ gills, interferes with water filters, and ruins recreation sites. More than 50 percent of algal blooms produce toxins.

Cases of human respiratory, skin, and gastrointestinal disorders associated with algal toxins have been reported. Certain blooms of algae are called red tides. The water appears to be red or brown because of the color of algal bodies, mainly dinoflagellates that contain the pigment xanthophyll.

Technological Applications

Algae can be grown and turned into biofuel - an ethanol that can power homes and cars.
Technological Applications

Algae have been used as food, medicine, and fertilizer for centuries. The earliest known reference to the use of algae as food occurs in Chinese poetic literature dated about 600 b.c.e. More recently, algae have begun to play important roles in certain biotechnological processes.

Several algae, including reds, browns, greens, and cyanobacteria, are used for food in Pacific and Asian countries, especially Japan. The annual harvest of the red alga Porphyra worldwide is worth several billion dollars. Porphyra (Japanese nori, Chinese zicai) is used as a wrapper for sushi or may be eaten alone. Another edible alga with a high iodine content is the brown alga Laminaria (Japanese kombu). The cyanobacterium Spirulina, with a protein level of 50 to 70 percent, was cultivated for centuries by indigenous Central Americans at Lake Texcoco near modern-day Mexico City for use as human food.

Several gelling agents are produced from red and brown algae. Agar from red algae is used as a medium for culturing microorganisms including algae, as a food gel, and in pharmaceutical capsules. Red algal carrageenan is used in toothpaste, cosmetics, and food such as ice creamand chocolate milk.

Alginates from brown algae have extensive applications in the cosmetics, soap, and detergent industries. Sources of alginates are Laminaria, some Fucus species, and the giant kelp Macrocystis,which can grow to more than 60 meters long. Algae are also used as feed in the culture of commercially important fish and shrimp.

Mass cultivation of algae (microalgae)—in open ponds and photobioreactors for production of fuels (such as biomass) and biochemicals (such as carotenoids, amino acids, and carbohydrates) and for water purification—is a rapidly developing area based on the use of solar energy as energy source. The green alga Dunaliella is used in the industrial production of carotene. In wastewater treatment plants, algae are used to remove nutrients and heavy metals and to add oxygen to the water.

Algae are used worldwide as indicators (biomonitors) of water quality, helping to detect the presence of toxic compounds in water samples. Several fast-growing algae are used, including the green alga Selenastrum capricornutum.

Many algae are widely employed as research tools because they are easy to culture and manipulate. Danish biologist Joachim Hammerling’s experiments with the green alga Acetabularia identified the nucleus as the likely storage site of hereditary information.

Diversity

Taxonomists believe that there are between thirty-six thousand and tenmillion species of algae. Molecular comparisons using nucleotide sequences in ribosomal RNA (ribonucleic acid) suggest that algae do not fall within a single group linked by a common ancestor but that they evolved independently.

The algae are divided into ninemajor phyla, which differ in their photosynthetic pigments, food reserves, cell structure, and reproduction. These groups include euglenoids, cryptomonads, dinoflagellates, haptophytes, and red algae.

Phylum Euglenophyta contains mostly unicellular formswith one or two flagella. Only one-third of this group possess chlorophyll-containing chloroplasts. Other euglenoids are strictly heterotrophic.

The phylum contains more than nine hundred, mostly freshwater, species. The food reserve is the carbohydrate paramylon, a polymer of glucose. Euglenophytes have chlorophyll a and b as well as carotenoids as their photosynthetic pigments. There is no cell wall.

Cells have several small chloroplasts; each is surrounded by three membranes. A close relative of euglenophytes is the protozoan Trypanosoma, which causes the human disease African sleeping sickness. Reproduction in the euglenophytes occurs by division of cells. Sexual reproduction is unknown.

Phylum Cryptophyta includes unicellular biflagellates. In addition to chlorophyll a, chloroplasts can contain chlorophyll c, carotenoids, and phycobilins. The carotenoid pigment alloxanthin is unique to Cryptophyta. Four membranes surround each chloroplast.

Chloroplast endoplasmic reticulum borders the chloroplasts. The principal food reserve is starch. Instead of a typical cell wall, a periplast composed of protein plates occurs beneath the cell membrane. There are about two hundred freshwater and marine species. Reproduction is primarily asexual.

Members of the phylum Dinophyta, or dinoflagellates, have unicellular forms with two different flagella. There are between two thousand and four thousand marine species and about two hundred freshwater forms. Many have chlorophylls a and c as well as the unique carotenoid peridinin. Some members of Dinophyta have fucoxanthin.

Chloroplasts have three closely associated membranes. The primary food reserve is starch, but lipids are also important storage molecules. A dinoflagellate cell is not surrounded by a cell wall but has a theca (a sort of armor) made of cellulose. Dinoflagellates can reproduce asexually and sexually.

Phylum Haptophyta includes primarily marine unicellular biflagellated algae. A haptophyte cell also has a flagellum-like haptonema, used to capture food. There are about three hundred species. The photosynthetic pigments include chlorophyll a and accessory pigments chlorophyll c and the carotenoid fucoxanthin.

Each chloroplast has four membranes. The food reserve is chrysolaminarin, which is a polymer of glucose. Several layers of scales, or coccoliths, composed primarily of calcium carbonate may cover the haptophyte cell. Asexual and sexual reproduction is widespread.

Phylum Rhodophyta, or the red algae, has between four thousand and six thousand species. Red algae lack any flagellated stages. The photosynthetic pigments include chlorophyll a as well as accessory phycobilins and carotenoids. Two membranes surround each chloroplast.

The food reserve is a floridean starch. A red algal cell is encircled by a wall composed of cellulose. Asexual and sexual re production, as well as alteration of generations, are widespread among Rhodophyta. A triphasic life cycle is unique for this group of algae.
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9:00 AM
Anaerobes
Anaerobes
The first organisms to evolve on the earth are thought to have been heterotrophs and anerobes. Heterotrophs are organisms that cannot produce their own food but must fill their energy requirements by consuming organic molecules produced by other processes or organisms. Anaerobes are organisms that do not require free oxygen gas in order to survive; for some anaerobes, free oxygen may be poisonous.

Heterotrophs include many familiar organisms (such as animals) whose existence is tied to primary producers, those organisms that create energy-storing molecules, such as photosynthesizing plants. Anaerobes also are common, though less apparent. Typically, they are microscopic organisms restricted to living in a few surface environments where oxygen is absent.

It may seem strange, then, that these organisms were perhaps the first organisms to have evolved on the earth. Yet the combination of the heterotrophic lifestyle and the anaerobic life requirement is consistent with what is known about the conditions of the early earth’s surface environment.

The earliest anaerobic heterotrophs laid the biochemical foundations for the evolution of photosynthesis, free oxygen in the atmosphere, and the rise of complex organisms. All those events had the adverse impact of limiting the range of environments available to the anaerobes.


The world’s first organism evolved in what has been called a "prebiotic soup" of energy-rich organic molecules. Heterotrophic organisms would exploit this environment by absorbing the molecules. A continuing supply of energy-rich molecules depended on the absence of free oxygen in the early atmosphere and the functioning of the abiotic synthesis.

Fermentation

The energy-richmolecules of the soupwere converted to energy by a series of biochemical reactions. One of the simplest, and therefore perhaps one of the oldest, types of energy conversion reactions is anaerobic fermentation.

During anaerobic fermentation, an energy-rich molecule, such as the simple sugar glucose, is dismantled to release energy and waste by-products. Several lines of evidence suggest that this form of energy conversion was utilized by the early heterotrophs.

One indicator that fermentation is a very ancient biochemical process is that the reaction used to release energy from the glucose molecule is very common among modern organisms. The ability to utilize the fermentation reaction is evident in the anaerobic reaction of yeast using sugar and releasing ethyl alcohol.

Although it is not the primary energy-releasing reaction for most organisms, fermentation’s widespread availability suggests that it is very old and perhaps inherited from an early, simpler ancestor.

The fermentation reaction is not very efficient. For example, it releases two units of energy for every glucose molecule, whereas oxidation of the same glucose molecule releases more than thirty energy units.

Such an inefficient reaction for energy release could not be tolerated by an advanced organism with many energy demands. Alternatively, single-celled heterotrophs surrounded by, and absorbing, energy-rich molecules such as glucose (which is unlikely to decompose in an anoxic environment) do not expend much energy in gathering their food.

The Earliest Organisms

Thus, two very different types of evidence—that which points to an anoxic early atmosphere and evidence for the ancient ancestry of the glucose fermentation reaction—suggest that the earliest organism was a single-celled heterotroph that absorbed energy-rich molecules from the surrounding anaerobic environment.

Modern analogues for such an organism exist. Single-celled bacteria, called obligate anaerobes, exist in a few anoxic environments today.

It is likely that the modern obligate anaerobes have not changed significantly (especially in their morphology, or shape and size) from their Precambrian ancestors. Given this much information, paleontologists know that their search for early Precambrian fossils, the petrified remains of organisms, is not easy.


The process of fossilization—that is, the preservation of the shape of an organism in rock—is best at preserving the details of hard body parts. Hard skeletons and shells or their impressions are easier to preserve than are soft body parts. In the case of early Precambrian fossils, the most likely organisms (bacteria) not only are small but also contain no hard body parts.

Despite these barriers to preservation and despite the very poorly preserved Precambrian rock record, some early Precambrian fossil remains have been found and described. The fossils are usually found preserved in rock called chert, which probably began as a gelatinous material. Microscopic remains of organisms embedded in this gelatin were delicately preserved when the chert lost some of its water and solidified.

The oldest fossil remains identified have been found in cherts from southern Africa. These cherts, part of what is called the Fig Tree Formation, are more than three billion years old. The fossils consist of the wispy, spherical remains of what may have been a type of alga and the rod-shaped remains of a possible heterotrophic bacterium.
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8:51 PM
Aleuria aurantia. The Orange Peel Fungus is a widespread ascomycete fungus in the order Pezizales. The brilliant orange, cup-shaped ascocarps often resemble orange peels strewn on the ground, giving this species its common name.
Ascomycetes

The ascomycetes are fungi (phylum Ascomycota or Ascomycotina) that produce sexual spores in a specialized cell called an ascus. These diverse fungi, with more than thirty thousand species, can be found in almost every ecosystem worldwide. One of the most famous members of the ascomycetes is the truffle.

Ascomycetes, one of the four phyla of the fungus kingdom, by definition possess an ascus, a single cell inside of which sexual spores are produced.

The reproductive process has been well documented and occurs when the dikaryotic mycelium (the mass of hyphae forming the body) undergoes changes that precede the formation of the ascus. Dikaryotic is the genetic state in which two haploid nuclei are present in the cell. One nucleus is donated by each parent.


The first change occurs when the end cell of a hyphal strand begins to form a small bend. The cell divides into three cells; the outer two cells are haploid, and the middle cell is dikaryotic. The middle cell then elongates, and the nuclei migrate into its center.

The two haploid nuclei then fuse to form a single diploid nucleus, which undergoes mitosis and meiosis to form eight haploid nuclei. Cell walls form around the nuclei producing eight haploid ascospores. The ascospores are then liberated from the ascus.

The ascus wall determines the kind of dispersal of the spores. Some asci have a thin, single-layer wall, which breaks down to liberate spores. Unitunicate asci have a multilayer cell wall with a pore at the end of the ascus. Spore release is active through the pore.

Chlorociboria aeruginascens. Fieldstack from a beautifully colored ascomycete (Cup fungus) growing on a rotten log (Alnus) in a wet swampy forest. The wood, although not clearly visible in this shot, is also deeply stained with this bluish-green.
beautifully colored ascomycete

Bitunicate asci have multilayer cell walls, and release of spores is by the separation of the layers of the cell wall, with the inner layer inflating to several times its normal size and then lifting off of the ascus, allowing the spores to be released.

The spores are released into the environment, where they germinate and produce haploid hyphae. The haploid hyphae fuse with compatible haploid hyphae, forming dikaryotic hyphae, and the process begins to repeat itself.

There are five different ways in which asci are formed in nature. First, asci can be produced by exposure to the environment, as are the asci of yeasts or the ascus of the peach leaf-curl pathogen Taphrina deformans. With these fungi, the ascospores are released by the breakdown of the ascus wall.

The other four ways of production of asci all take place inside structures made from mycelium, called ascocarps. These structures range from totally closed to open, like a cup. The totally closed ascocarps are called cleistothecia. Within these, the asci are scattered, and the spores are released by breakdown and decomposition of the fungal tissue.

Ascomycetes as Pathogens

Ascomycetes as Pathogens
Ascomycetes as Pathogens
Some members of the ascomycetes are very important plant and animal pathogens, causing serious diseases. One of the more impressive plant pathogens is the ergot fungus (Claviceps purpurea). This fungus colonizes the ovaries of grains, such as rye (Secale cereale).

It produces a mass of mycelium, called a sclerotium, which is hard and has a density similar to that of a seed. Because of this, the sclerotia are often found in the threshed grain. Sclerotia contain an accumulation of alkaloids and other secondary metabolites.

When the sclerotia are ground into flower and baked into bread, many of these secondary metabolites are passed into the bread. During the Middle Ages this fungus was responsible for a human disease called St. Anthony’s Fire. Today, this fungus is used for the natural production of a coagulant which is used in medicine.

Another group of plant pathogens are the powdery mildews. There are several hundred species of these fungi, which produce a powdery spore mass on the outer surfaces of plant leaves. If a leaf is infected before it has expanded, it will remain small and puckered andmay drop from the plant.

The powdery mildews are superficial and send hyphae through the leaf cuticle into the epidermis. The fungus then grows over the surface of leaf, giving it a powdery appearance. During the winter, the fungus produces cleistothecia on the surface of the leaf. Powdery mildew can occur on most plant species and can be very damaging to crop and ornamental plants.

Economic Uses

Truffle
Truffle
Truffle is a generic term for fungi that form mycorrhizae (a symbiotic association) with the roots of various trees. The fungus grows into the roots and helps the plant tolerate stress, providing the plant with increased absorption of phosphorus from the soil.

In return, the plant gives the fungus metabolites that it needs for growth. These fungi then produce fruiting bodies, either in the soil or upon the surface of the soil. The truffles are produced in the soil up to a depth of 1 foot.

Truffles can be located in the soil using a trained sowor dog that is able to sniff out the volatile chemicals that are produced. However, it is important to note that edible fungi such as truffles can often be mistaken for highly toxic fungi and should never be gathered or eaten without expert identification.

Truffles are used as condiments and are able to impart unique aromas and sensations to food. They are shaped like small balls, varying in size from that of a pea to that of a golf ball. Truffles are only produced in nature and therefore fetch high prices.

The price of truffles depends on the species, size, and freshness. Prices of the famous French Black Périgord truffle (Tuber melanosporum) can reach into thousands of dollars per kilogram (2.2 pounds). In the United States, the Oregon white truffle is quite appealing and can be found in the Pacific North-west.

Morels (Morchella) are another choice edible ascomycete. Shaped like a little hat sitting upon a stalk, they are brown in color and have an appealing aroma. They add flavor to any food and are a favorite of many wild animals.

Scientific Uses

Some members of the ascomycetes are used for genetic studies. Such is the case for Neurospora, a common fungus found growing on soil and organic matter and one of the first organisms to be found in an area after a fire. A swith all ascomycetes, there are two compatible mating types, which makes for easy genetic study.

Using spore characteristics of shape, color, and texture, it is possible to see how mitosis and meiosis occur in the ascus by determining the placement of the spores. The fungus is readily mutated, which further enhances genetic study.
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6:17 PM
Bacterial Genetics
Bacterial Genetics
Bacterial genetics is the study of the genetic material of bacterial DNA, which can provide valuable insights into the process of mutation because of bacteria’s rapid rate of reproduction.

Plants were the original candidates for genetic studies, which began in the late 1800’s. Studies with animals soon followed; bacteria did not become candidates for such study until the mid-1940’s, when adequate technology for handling bacteria developed. Bacteria have become extremely useful organisms for genetic studies since the early 1950’s.

Two major features of bacteria make them desirable subjects. First, bacterial cells typically divide every twenty minutes. Their rapid rate of reproduction allows a very large number of bacteria to be produced in a short time. This, in turn, provides the researcher with more opportunity to detect the "rare genetic events" of mutation or recombination.

Even more important, unlike all other organisms, bacteria have a single chromosome with a single set of genes. Thus, genetic modifications are more likely to result in immediately observable changes. In organisms that have multiple chromosomes, a change in a single gene may go undetected because its effect is masked by genes on other chromosomes.


Bacterial DNA

All bacteria have a single circular chromosome, composed of deoxyribonucleic acid (DNA). The DNA is subdivided into specific message areas known as genes, and the chromosome carries from four thousand to five thousand individual genes. For many bacteria, this constitutes the entirety of its genetic information.

A number of bacteria, however, have additional DNA in the form of plasmids. A plasmid is a small additional circular piece of DNA, independent of the chromosome,which can hold an additional twenty to one hundred genes. Plasmid-containing cells often have several plasmids.

Many researchers have described the plasmid genes as nonessential to the normal activities of bacteria. Under certain circumstances, however, those genes might provide a survival advantage to the possessor. For example, genes for antibiotic resistance are often carried on a plasmid.

Normally, antibiotics are not present in the bacteria’s environment; such resistance genes would therefore be unnecessary. If the bacteria later were to come into contact with antibiotics, however, having antibiotic- resistant genes would be to their distinct advantage.

Two major types of plasmids exist: F plasmids, or fertility plasmids, and R plasmids, or resistance plasmids. Both types can carry resistance genes. Only the F plasmids, however, are able to control the formation of a special cytoplasmic tube known as the sex pilus. Cells with the F plasmids are known as F+, or donor cells. Cells without the F plasmids are called F-, or recipient cells.

Conjugation

Conjugation
Conjugation

The plasmid is a prerequisite to one type of genetic exchange, conjugation. During conjugation, the donor cell copies its plasmids and transfers them to a recipient cell to which it has attached itself by means of a sex pilus.

The recipient cell can now take advantage of whatever additional genes it has received. If, in the process, it received an F plasmid, it has also become a potential donor cell.Whenever bacterial cells undergo cell division, any plasmids they possess are typically passed on to their progeny.

Originally it was thought that conjugation could occur only between members of the same species, but that is not always true. For example, it is now known that some strains of the bacteria responsible for causing gonorrhea, Neisseria gonorrhoeae, have received antibiotic-resistant genes from unrelated species of bacteria.

There is one other type of donor cell, the Hfr+, or high-frequency recombinant, cell. Instead of the plasmid remaining independent of the cell’s chromosome, it inserts itself into the chromosome. When that plasmid gets ready to copy itself, the chromosomal genes are the first to be copied.

Unless the donor and recipient cells are able to maintain direct contact for a fairly long period of time, which almost never occurs, the recipient cell will not receive the plasmid. It will, however, receive numerous chromosomal genes from the donor. Those genes may later be incorporated into the chromosome of the recipient, causing gene replacement.

Not all species of bacteria participate in conjugation. Some rely on transduction as a means of receiving new genetic information. This is how Staphylococcus aureus has developed resistance to many antibiotics.

Transduction

Transduction
Transduction
There are two types of transduction: generalized and specialized. In both cases, a donor cell becomes infected with a bacteriophage, a virus that attacks bacteria. Upon the death of that donor cell, fragments of donor DNA are transferred as the escaping bacteriophage infects another bacterium.

In generalized transduction, a bacteriophage infects a bacterial cell. Shortly after infection, the bacterial chromosome becomes fragmented, and viral components are produced. Later the viral components are assembled to form a complete virus particle.

Occasionally during this assembly process, a particle becomes contaminated with fragments of the bacterial chromosome or plasmids. After assembly is completed, the bacterial cell ruptures, allowing the escape of all virus particles.

Eventually these virus particles will invade other bacterial cells. Any cells that are invaded by contaminated bacteriophage particles are said to be transduced, because they have received DNA from another bacterium. The DNA received in this manner is strictly random.

Specialized transduction involves what is known as a latent bacteriophage. After the initial invasion of a bacterium, the bacteriophage inserts itself into a specific region of that cell’s chromosome. At some later time, the bacteriophage removes itself from the chromosome and accidentally takes a few bacterial genes located near its original insertion point.

When the bacterial cell finally begins making new bacteriophage components, it behaves as if those particular genes are part of the bacteriophage and replicates them as such. Therefore, all the newly formed bacteriophage particles will contain those bacterial genes. Transduction then occurs when these bacteriophage particles invade other bacterial cells.

Transformation

Transformation
Transformation
The final method of genetic transfer is transformation. An extensively utilized organism for such investigation has been Streptococcus pneumoniae. The most famous studies involved converting nondisease-causing strains of Streptococcus pneumoniae intodisease-causing strains.

Transformation also occurs in a wide variety of other bacteria. The process of transformation requires that a population of actively reproducing bacteria come into contact with DNA fragments, often from closely related dead bacteria. These DNA fragments are referred to as either naked or cell-free DNA.

Genetic Modification

A small portion of that DNA can be absorbed and utilized by the growing bacteria. These recipients can then take advantage of any usable genes that the fragments might contain, incorporating them into their chromosome in place of their own copies of these genes by the process of recombination.

Conjugation, transduction, and transformation are all mechanisms of genetic change within a bacterial population. These mechanisms allow a specific characteristic to be spread throughout the population within a few hours.

A wide number of bacterial genes have been found to be transferred by these methods, including genes that control a bacterium’s ability to cause disease, to produce toxins, and to develop resistance to antibiotics and other drugs as well as genes that control a number of other characteristics.

The purpose of these mechanisms, as far as the bacteria are concerned, is to enable the bacteria to adapt to changing environmental conditions so that their survival is ensured. Scientists, however, have found ways to adapt some of these mechanisms for human benefit.

Scientists have used the mechanisms of genetic transfer along with new technology from DNA research to perform genetic engineering on bacteria. They can use genes and specially engineered plasmids, called plasmid vectors, to make recombinant DNA in the laboratory.

Recombinant plasmids can then be used to transform bacteria such as Escherichia coli (E. coli). The bacteria will treat these recombinant plasmids just like ordinary plasmids, replicating them and, for expression vectors, expressing any genes included in them.

In this manner, bacteria can be used to produce a wide variety of products for medicine, agriculture, and industry. Genetic engineering and the products that result from it would not be possible without the knowledge of genetic transfer gained from studies of bacterial conjugation, transduction, and transformation.
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6:56 AM
Bacteriophages
Bacteriophages
Viruses that attack bacterial cells are known as bacteriophages. Many results gained from studying bacteriophages have universal implications.

For example, the physical properties of DNA and RNA are remarkably identical in all organisms, and these are perhaps easiest to study in bacteriophage systems.

Bacteriophages, or phages for short, are viruses that parasitize bacteria. Viruses are an extra ordinarily diverse group of ultramicroscopic particles, distinct from all other organisms because of their noncellular organization.

Composed of an inert outer protein shell, or capsid, and an inner core of nucleic acid—either deoxyribonucleic acid (DNA) or ribonucleic acid (RNA) but never both—viruses are obligate intracellular parasites, depending to a great extent on host cell functions for the production of new viral particles.


There is considerable variation in size and complexity among viruses. Some have fewer than ten genes and depend almost entirely on host functions. Others are known to contain from thirty to one hundred genes and rely more on proteins encoded by their own DNA.

Even the largest viruses are too small to be seen under the light microscope, so studies on viral structure rely heavily on observation with the transmission electron microscope.

The Study of Bacteriophages

Because scientists know more about the molecular and cell biology of the common bacterium Escherichia coli than about any other cell or organism, it is perhaps not surprising that the best-known phages are those that require E. coli as a host (coliphage).

It is not possible to observe phage growth directly (as bacterial growth can be detected by the appearance of colonies on an agar plate), but phage growth can be indirectly observed by the formation of plaques, small clear areas in an otherwise continous lawn of host bacteria growing on a solid growth mediumin a petri dish.

Reproductive Cycles

Bacteriophages can multiply by two different mechanisms, termed the lytic cycle and the lysogenic cycle. Some phages are capable only of lytic growth, while others retain the ability to reproduce by either lytic growth or entry into the lysogenic cycle. In the lytic cycle, phages first attach themselves to specific receptor sites on the host cell wall.

Reproductive Cycles
Reproductive Cycles

The phage nucleic acid (DNAor RNA) is injected inside the host, while the protein capsid of the infecting particle remains outside of the host cell at all times. Once the DNA or RNA is inside, transcription of phage genes begins, and phage-encoded proteins begin to be made.

Some of these proteins serve to inactivate and destroy the host cell DNA, ensuring that the cell’s energy resources will be directed exclusively toward the production of phage proteins and the replication of phage nucleic acid. Phage DNA or RNA replication ensues quickly and is followed by the packaging of this genetic material into the newly synthesized capsids of the progeny phage particles.

The final step is host cell lysis—the bursting of the host cell to release the completed and infective phage progeny. The number of phages released in each burst varies with growth conditions and species, but ideal conditions often result in a burst size of one hundred to two hundred per host cell.

For temperate bacteriophages, those capable of entering the lysogenic cycle, infection of the host cell only rarely causes lysis. Injection of the phage DNA into the host is followed by a brief period of messenger RNA (mRNA) synthesis, necessary to direct the production of a phage repressor protein, which inhibits the production of phage proteins involved with lytic functions.

A DNA-insertion enzyme is also made, allowing the phage DNA to be physically inserted into the DNA of the host. The cell then can continue to grow and multiply, and new copies of the phage genes are replicated every cell generation as part of the bacterial chromosome.

The host cell is said to be lysogenic, for it retains the potential to be lysed if the prophage pops out of the host DNA and enters the lytic cycle. The integrated prophage does confer a useful property on the host cell, however, for the cell will now be immune to further infection from the same phage species.

T4 Coliphage

One of the best-known lytic phages, which is often used in genetic studies, is the coliphage T4. Its protein capsid consists of three major sections—the head, the tail, and the tail fibers.

The double-stranded circular DNA molecule of T4 is packaged into the icosahedral-shaped head, and during the infection process it is forced through the hollow core of the cylindrical tail and then directly into the host cell. Contact with the cell is established and maintained throughout the infection process by the tail fibers.

Self-assembly of progeny phages occurs in at least three distinct cellular locations, as complete heads, tails, and tail fibers are first assembled separately and then pieced together in one of the last phases of the infection cycle.

Packaging of the replicated T4 DNA is an integral part of the head assembly process. Each of the three subassemblies involves a reasonably complex and highly regulated sequence of assembly steps.

For example, head assembly is known to require the activity of eighteen genes, even though only eleven different proteins are found as structural components of mature heads. Identification of the number and sequence of genes involved with each subassembly process has been facilitated by the analysis of artificial lysates from t8 mutants.

For those temperate phages capable of entering the lysogenic cycle, many additional strategies for genetic control and regulation have evolved. The most thoroughly studied of the temperate coliphages is phage lambda (λ).

Genes controlling phage DNA integration, excision, and recombination, and those involved with repressor functions, have been identified in phage λ as well as structural genes involved with lytic functions that are similar to those studied in T4.

Research Tool

One of the most important conclusions to be drawn from studies on bacteriophages, and viral genetics in general, is that many of the results have universal implications. For example, the physical properties of DNA and RNA are remarkably identical in all organisms, and these are perhaps easiest to study in bacteriophage systems. The experiment that provided the final proof that DNA was the genetic material was performed using a coliphage very similar to T4.

Studies on the origin of spontaneous mutations, first performed in phage, have extended to higher forms of life as well. Some of the most basic questions concerning protein-DNA interactions are best addressed in viral systems, and the principles that emerge seem to hold for all other experimental systems.

There is every reason to believe that many basic questions in cell and molecular biology will continue to be best studied in viruses such as bacteriophages, and that some of these investigations will spawn applications that can directly benefit humankind.

It is certain that advances in molecular biology that have revolutionized the understanding of cell biology and the molecular architecture of cells will continue to expand the frontiers of knowledge in the study of viral genetics. Applications in human medicine, veterinary medicine, and plant breeding are sure to follow, as scientists continue to unravel the complexities of these simplest of organisms.
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2:52 AM
Basidioporic Fungi
Basidioporic Fungi
Basidiosporic fungi (also known as the Basidiomycota or Basidiomycotina) are fungi that produce sexual spores on a specialized cell called a basidium.

The basidiosporic fungi are the most diverse phylum of the fungi world, with more than 22,300 species described. Some of the fungi in this phylum are microscopic, while the larger members of this group produce fruiting structures that are basketball-sized and weigh in excess of 10 pounds.

This phylum contains fungi that fall into three classes: mushroom, rusts, and smuts—and range widely in appearance, from the common mushroom to weblike fungi with an odor that can be detected at several feet.

Taxonomy

The basidiosporic fungi are divided into three classes: Basidiomycetes (mushrooms); Teliomycetes (rusts); and Ustomycetes (smuts). The Basidiomycetes are the higher basidiosporic fungi, which are normally fleshy. They produce true basidiocarps, and the only spore formed is the basidiospore.


The other two classes both have more than one spore form and do not have extensive mycelium. The Teliomycetes are commonly called rusts and are serious biotrophic parasites of plants. The rusts are able to complete their life cycle only in the presence of living plant host tissue.

The Ustomycetes are commonly called smuts and are mostly minor pathogens of plants, especially monocots. Some smuts have been cultured in axenic culture, where they form a "yeastlike" phase. The yeastlike phase has no true mycelium but rather individual cells.

Basidium

The basidium is a single cell on which basidiospores are produced externally. The basidium forms either as the terminal cell of a dikaryotic mycelium or from a resting spore that initially is dikaryotic.

basidium
basidium
The dikaryotic mycelium or spore contains two haploid nuclei, one donated by each of the parent strains. As the basidium begins to form, the two nuclei migrate into the center of the cell and fuse, forming a diploid nucleus.

This nucleus then undergoes meiosis, forming four haploidnuclei. As this is occurring, the cell wall of the basidium begins to produce little extensions called sterigmata, upon which the basidiospores will form. The tips of the sterigmata then inflate, and one nucleus migrates into each forming basidiospore.

The basidiospore is haploid and has a very thin cell wall. The spore is normally transmitted in air currents. Upon germination, the basidiospore produces a haploid mycelium which will fuse with a compatible hyphae, producing a dikaryotic mycelium.

Spore release from the basidiumcan be either active or passive. Passive release occurs when the junction of the sterigma and basidiospore separates, releasing the spore. Active release is more specialized. When the basidiospore is forming, a small segment of the spore wall at the junction with the sterigma loosens and fills with either gas or liquid.

At the time of release, the fluid or gas escapes, propelling the basidiospore away from the basidium. The distance traveled is not great, just enough to make sure that the basidiospore is able to enter into air currents for dissemination.

Hyphal Structure

The hyphae of the Basidiomycetes are septate and have special modifications at the septa. When a cell divides, a cross wall forms between the two daughter cells. With the dikaryotic hyphae of the Basidiomycetes, as the cell divides, the nuclei migrate toward the apex of the hyphae.

The nuclei then undergo mitosis, with one of the nuclei migrating into a small outgrowth of the hyphae and the other migrating backward. Septa form, creating a new dikaryotic cell near the apex and two haploid cells, one in line and the other as the outgrowth.

The outgrowth then turns and fuses with the haploid cell, and the nucleus migrates back to form a dikaryotic cell. The outgrowth remains visible with a microscope and is called a clamp connection.

The reproductive structure of the Ustomycetes is called a sorus. The sorus is a mass of dikaryotic spores that are normally dark brown or black in color. The sorus is formed in meristematic regions of the plants. The spores are called probasidia, because they form basidia when they germinate.

With the Teliomycetes, there are up to five distinct spore forms. The basidiospore lands on a susceptible plant and germinates, producing a haploid mycelium that infects the plant. The infection results in the formation of a haploid spermagonium that produces both spermatia and receptive hyphae.

When a compatible spermatia and receptive hypha combine, a dikaryotic hypha is produced, which initiates formation of an aecium. The aecium produces dikaryotic spores that are transmitted by air currents and infect another plant.

The resultant infection produces a subcuticular or subepidermalmass of thin-walled spores. These dikaryotic spores are called urediniospores and are formed in the uredinium. The urediniospores are blown by air currents and produce reinfection of the same species of plant.

At the end of the growing season, infections by urediniospores will result in the formation of a subcuticular or subepidermal mass of thick-walled spores called teliospores which are formed in the telium. These spores are initially dikaryotic but then become diploid and finally germinate by formation of the basidium.

Basidiocarps

basidiocarp
basidiocarp
The basidiocarp is the fruiting body of the higher Basidiomycetes. This structure is multicellular and composed of hyphae. The basidiocarp resembles the familiar image of the mushroom. The mushroom consists of a stalk (stipe) which has a cap (pileus)on top.

The stipe can be as tall as a meter (40 inches), and the pileus as long as ameter in diameter. Alternatively, both parts could be less than a centimeter in size. The pileus has pores or gills on the underside, where the basidia are produced. The layer of basidia is called a hymenium or "fertile layer."

Other kinds of basidiocarpsmay be found in nature. Some are totally enclosed and remain on the ground, looking much like a golf ball. These are called puffballs. As the puffball matures, the other layers begin to crack at the apex.

When drops of rain fall, the force of the impact causes spores to puff out of the opening. Another kind of puffball is the earthstar. In these unique fungi, the outer layers pull away from central part of the puffball and form a starlike pattern on the ground.

Ecological Importance

The basidiosporic fungi all play important roles in ecosystems. The rusts and the smuts are impor- tant plant pathogens, capable of great destruction of crops. These fungi have been known for thou- sands of years and are some of the most devastating fungi around.

The mushrooms are part of the natural cycle of decay. They are found on the ground or on wood and are the later stages of decay of organic matter. Some mushrooms are found on living plants, where they can be serious pathogens. Others are edible and are excellent sources of digestible protein. Still others are toxic or poisonous and can be fatal when eaten.

Stinkhorns and the bird’s nest fungi are unique basidiosporic fungi. The stinkhorns are basidiocarps that form on the soil and produce the basidia in a mass of putrid cells.The stench from the cells draws flies, which walk over the spores and then disseminate them. These can be found in wooded areas and can be detected by smell at distances of up to several meters.

The bird’s nest fungi look like small birds’ nests. The outer part of the basidiocarp resembles a small nest, up to an inch in diameter. On the inside, several small puffball-like structures can be found, with basidia on the inside. These look like small eggs.

When a drop of water enters the nest, the force thrusts the “egg” upward and extends a small cord from the back. The small cord catches hold of a plant and suspends the egg in the air. As the egg dries, it turns into a powdery mass, which is blown about by the wind.
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9:37 PM
Biological Weapons
Biological Weapons
Biological weapons are biological agents that can be used to destroy living organisms. This general definition includes the use of virtually any kind of microorganism (bacterium or fungus) or biological agent (mycoplasma like organism, virus, viroid, or prion) to destroy any biologically important plant or animal.

There are two basic ways of using biological weapons against humanity. The first is to attack the food or water supply. This would produce hardship and the possible death from starvation of many individuals. In developed countries such as the United States, total devastation due to such an attack would likely be avoided, as there are considerable stores of food, in dispersed locations, that would mitigate against crop failure of moderate proportions.

In addition, most experts agree that the amount of biological contaminant required to overcome the effects of dilution and time in most water reservoirs makes poisoning of water supplies impractical, although not impossible.

The other way of using biological weapons against humanity is to attack individuals directly, using pathogens. Numerous known pathogens could be used, but the most effective biological weapons would creep upon the population with stealth. Naturally occurring agents that have promise as biological weapons are pathogens, which can infect and colonize a host. A pathogen causes disease, an alteration in the metabolism of a host.


In order for disease to occur, it is necessary to have a virulent pathogen, that is, one that is capable of causing disease; a susceptible host, able to be infected; and an environment that is favorable to both the host and the pathogen. When these occur together, disease occurs.

For the disease cycle to begin, it is necessary for propagules of the pathogen to come in contact with the susceptible host. Propagules include those that cause initial infections, called the primary inoculum.

As the disease cycle progresses, the host may release other propagules, considered the secondary inoculum. When only one progression of disease occurs during a prolonged span of time, the disease is termed monocyclic. When more than one cycle of disease takes place in a growing season, the disease is called polycyclic.

Monocyclic Diseases

An example of the monocyclic disease cycle occurs with corn smut. The primary inoculum is released in the spring, as the tassel and silk of the corn appear. Infection occurs, symptoms of large black galls develop on the ears, and new inoculumis produced for the following growing season.

This kind of disease produces a single cycle during a growing season. The potential for problems depends on the amount of inoculum present at the beginning of the disease cycle. In order to use corn smut as a biological weapon, the initial amount of inoculum must be sufficient to reach all of the plants that are targeted.

This is the same general case as with anthrax. Anthrax is a disease of animals that is caused by the bacterium Bacillus anthracis. The bacterium is able to survive in nature as small spores that are able to resist extremes of climate and time.

These microscopic spores are produced at any time when environmental conditions are unfavorable for growth of the bacterium. The spores are less than 2 microns in diameter, and if they become suspended in the air, they will hang indefinitely. Such small particles are called PM 10 (particulate matter less than 10 microns in size).

These particles are of extreme importance, as they are not filtered out by common filters and must be removed by HEPA (high-efficiency particulate-arresting) filters, which can remove particles smaller than a micron. When these particles are inhaled, they cause disease of the lung tissue, which will result in destruction of the lungs and the resultant death of the host.

The reasons that Bacillus anthracis could be a biological weapon are that it is easily concealed and disseminates quickly as an invisible, airborne powder. The small particle size allows it to be inhaled, after which it lodges in the lungs and begins the process of infection. The infection begins like that of a common chest cold.

By the time the host determines that anthrax might have been contracted, the condition is normally fatal. One of the features of anthrax as a biological weapon is that it is not contagious. Spores are not produced until the host is dead, at which time the spores are not placed back into the air currents. This permits anthrax to be used against a specific target.

Polycyclic Diseases

Some kinds of biological weapons can be termed weapons of mass destruction. These biological weapons are able to self-perpetuate and thereby create great amounts of destruction. They are polycyclic in nature.

A plant-based example of this is the epidemic of potato late blight,which caused the Irish Potato Famine of the mid-1840’s. Most of the people living in Ireland at that time depended on their own harvests for food. During a two-year period, the climate became especially cool and damp, conditions favorable for the spread of potato late blight.

Because potatoes are planted from vegetative parts, there was genetic uniformity of the crop, which was highly susceptible. The pathogen is extremely virulent, with the capacity to destroy a single plant overnight. Total crop failure resulted in the reduction of Ireland’s population from about six million to about two million people.

About one-third of the people emigrated to other lands, and about one-third of the population died from starvation. All of this destruction could have started from a single fungal propagule that infected a plant and then spread. This fungus is still problematic world wide. However, regular sprays with fungicide reduce the risk of crop destruction.

Pathogens that occur at low levels in any given area are called endemic and may, when conditions are favorable, produce a widespread surge of disease in that area. This is called an epidemic. Epidemics that occur over wide geographic ranges, such as two or more continents, are called pandemics. The endemic potato late blight fungus caused an epidemic, and because it also spread into Europe and North America, the situation could be called a pandemic.

A similar concern is expressed with regard to the disease smallpox. Smallpox is caused by a virus that is easily passed from an infected individual to a healthy one. The smallpox virus no longer occurs in nature (is not endemic) anywhere in the world. The last reported case of smallpox in nature occurred in the late 1970’s. As a result of a concerted vaccination effort among many nations, this normally fatal disease was eradicated.

The last stores of smallpox virus are housed at the Centers for Disease Control (CDC) in Atlanta, the U.S. Army Biological Weapons Research Unit in Fort Detrick, Maryland, and the Russian Academy of Sciences in Moscow. Some people fear some of the inoculum from one of these storehouses could be transported into unconfined areas of the outside world.As such, small pox would become a very formidable biological weapon.

Smallpox is highly contagious and spreads easily from person to person. Should an infected person walk the streets of a highly populated urban area, it would be possible to infect millions of people within the span of a week or two. Within several weeks, especially in this age of global travel, the infection could spread around the world.

Vectors

One method of spreading disease is through the use of vectors.Vectors are arthropods or other invertebrates that have the ability to transmit a pathogen from one host to another. The most famous vector is the mosquito, which can transmit malaria, dengue fever, West Nile virus, and many other diseases.

The corresponding vector in plants is the aphid, which can transmit a host of viruses and mycoplasmas (bacteria that lack cell walls). In order for transmission to occur, it is necessary for a vector to first come in contact with an infected host, feed upon that host, and then pass the pathogen to an uninfected host.

The most notable vector-borne disease is plague, which is passed from infected animals to humans by fleas. This disease, which was once responsible for hundreds of thousands of deaths, is now readily controlled by the use of insecticides to kill off the vector.

Designer Weapons

With twentieth century advances in technology, the manipulation of the genetics of a pathogen to make it a "super pathogen" is possible. The creation of a genetic code which could be pathogenic is also possible. So-called designer weapons are those that may be envisioned by someone who feels he or she has a need to make a more destructive or more "targeted" weapon. These weapons could then be used on a specific population or area.

The creator of the designer weapon would have an advantage, as he or she would also be able to create a vaccine against the designer weapon, which could be administered to a specific group of individuals. Designer weapons, like all biological weapons, work best when there is an abundant supply of susceptible hosts and when the genetics of these hosts do not vary greatly.

Pathogen Dispersal

There is considerable opportunity for the use of any pathogen as a biological weapon. Most pathogens can be cultured with standard laboratory equipment; however, the difficulty is in creating a system of dispersal that will effectively spread the inoculum over an area of susceptible hosts.

There are innumerable systems that could be used; these include spraying particles into the air, mailing them in an envelope, or placing them into a bomb. One of the less sophisticated methods of dissemination is the use of aircraft that are used for agricultural spraying. These aircraft could spray inoculum over large areas, with the potential of infecting large populations.
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