Showing posts with label genetics. Show all posts
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12:48 AM
Water lilies, a kind of adaptations
Water lilies, a kind of adaptations

The results of natural selection in which succeeding generations of organisms become better able to live in their environments are called adaptations. Many of the features that are most interesting and beautiful in biology are adaptations. Specialized structures, physiological processes, and behaviors are all adaptations when they allow organisms to cope successfully with the special features of their environments.

Adaptations ensure that individuals in populations will reproduce and leave well-adapted offspring, thus ensuring the survival of the species. Adaptations arise through mutations—inheritable changes in an organism’s genetic material.

These rare events are usually harmful, but occasionally they give specific survival advantages to the mutated organism and its offspring. When certain individuals in a population possess advantageous mutations, they are better able to cope with their specific environmental conditions and, as a result, will contribute more offspring to future generations than those individuals that lack the mutation.


Over time, the number of individuals that have the advantageous mutation will increase in the population at the expense of those that do not have it. Individuals with an advantageous mutation are said to have a higher fitness than those without it, because they tend to have comparatively higher survival and reproductive rates. This is natural selection.

Natural Selection

Growing on poisonous environtment
Growing on poisonous environtment

Over very long periods of time, evolution by natural selection results in increasingly better adaptations to environmental circumstances. Natural selection is the primary mechanism of evolutionary change, and it is the force that either favors or selects against mutations.

Although natural selection acts on individuals, a population gradually changes as those with adaptations become better represented in the total population. Most flowering plants, for example, are unable to grow in soil containing high concentrations of certain elements (for example, heavy metals) commonly found in mine tailings.

Therefore, an adaptation that conferred resistance to these elements would open up a whole new habitat where competition with other plants would be minimal. Natural selection would favor the mutations, which confer specific survival advantages to those that carry them and impose limitations on individuals lacking these advantages.

Thus, plants with special adaptations for resistance to the poisonous effects of heavy metals would have a competitive advantage over those that find heavy metals toxic. These attributes would be passed to their more numerous offspring and, in evolutionary time, resistance to heavy metals would increase in the population.

Types of Adaptations

Although natural selection serves as the instrument of change in shaping organisms to very specific environmental features, highly specific adaptations may ultimately be a disadvantage. Adaptations that are specialized may not allow sufficient flexibility (generalization) for survival in changing environmental conditions.

The degree of adaptative specialization is ultimately controlled by the nature of the environment. Environments, such as the tropics, that have predictable, uniform climates and have had long, uninterrupted periods of climatic stability are biologically complex and have high species diversity.

Tropical rain forest
Tropical rain forest, complex competition for resources
and intense predator-prey relationships

Scientists generally believe that this diversity results, in part, from complex competition for resources and from intense predator-prey relationships. Because of these factors, many narrowly specialized adaptations have evolved when environmental stability and predictability prevail.

By contrast, harsh physical environments with unpredictable or erratic climates seem to favor organisms with general adaptations, or adaptations that allow flexibility. Regardless of the environment type, organisms with both general and specific adaptations exist because both types of adaptation enhance survival under different environmental circumstances.

Metabolism is the sum of all chemical reactions taking place in an organism, whereas physiology consists of the processes involved in an organism carrying out its function. Physiological adaptations are changes in the metabolism or physiology of organisms, giving them specific advantages for a given set of environmental circumstances.

harsh physical environments, enhance survival under different environmental circumstances
harsh environments, enhance survival under different environmental circumstances

Because organisms must cope with the rigors of their physical environments, physiological adaptations for temperature regulation, water conservation, varying metabolic rate, and dormancy allow organisms to adjust to the physical environment or respond to changing environmental conditions.

Adaptations and Environment

Desert environments, for example, pose a special set of problems for organisms. Hot, dry environments require physiological mechanisms that enable organisms to conserve water and resist prolonged periods of high temperature.

Evolution has favored a specialized form of photosynthesis in cacti and other succulents inhabiting arid regions. Crassulacean acid metabolism (CAM) photosynthesis allows plants with this physiological adaptation to absorb carbon dioxide at night, when relative humidity is comparatively high and air temperatures relatively low.

✯ A Beavertail cactus in Henderson Canyon - CA
Adaptations and Environment

Taking in carbon dioxide during the day would dehydrate plants, because opening the pores through which gas exchange takes place allows water to escape from the plant. CAM photosynthesis, therefore, allows these plants to exchange the atmospheric gases essential for their metabolism at night, when the danger of dehydration is minimized.

Because organisms must also respond and adapt to an environment filled with other organisms— including potential predators and competitors— adaptations that minimize the negative effects of biological interactions are favored by natural selection. Often the interaction among species is so close that each species strongly influences the others and serves as the selective force causing change.

Under these circumstances, species evolve together in a process called coevolution. The adaptations resulting from coevolution have a common survival value to all the species involved in the interaction. The coevolution of flowers and their pollinators is a classic example of these tight associations and their resulting adaptations.

Speciation

Adaptations can be general or highly specific. General adaptations define broad groups of organisms whose lifestyles are similar. At the species level, however, adaptations are more specific and give narrow definition to those organisms that are more closely related to one another.

Slight variations in a single characteristic, such as bill size in the seed-eating Galapágos finches, are adaptive in that they enhance the survival of several closely related species. An understanding of how adaptations function to make species distinct also furthers the knowledge of how species are related to one another.

Why so many species exist is one of the most intriguing questions of biology. The study of adaptations offers biologists an explanation. Because there are many ways to cope with the environment, and because natural selection has guided the course of evolutionary change for billions of years, the vast variety of species existing on the earth today is simply an extremely complicated variation on the theme of survival.
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11:07 PM
In adaptive radiation, numerous species evolve from a common ancestor introduced into an environment with diverse ecological niches. The progeny evolve genetically into customized variations of themselves, each adapting to survive in a particular niche.

In 1898 Henry F. Osborn identified and developed the evolutionary phenomenon known as adaptive radiation, whereby different forms of a species evolve, quickly in evolutionary terms, from a common ancestor.

According to the principles of natural selection, organisms that are the best adapted (most fit) to compete will live to reproduce and pass their successful traits on to their offspring. The process of adaptive radiation illustrates one way in which natural selection can operate when members of one population of a species are cut off or migrate to a different environment that is isolated from the first.

Such isolation can occur from one patch of plantings to another, from one mountain top or hillside to another, from pond to pond, or from island to island. Faced with different environments, the group will diverge from the original population and in time become different enough to form a new species.


Genetic Changes

In a divergent population, the relative numbers of one form of allele (characteristic) decrease, while the relative numbers of a different allele increase. New environmental pressures will select for favorable alleles that may not have been favored in the old environment.

Over successive generations, therefore, a new gene created by random mutation (change) may replace the original form of the gene if, for example, the trait encoded by that gene allows the divergent group to cope better with environmental factors, such as food sources, predators, or temperature.

The result in the long term is that deoxyribonucleic acid (DNA) changes sufficiently through the growth of divergent populations to allow new generations to become significantly different from the original population. In time, they are unable to reproduce with members of the original species and become a new species.

Galápagos Islands Case Study

Adaptive radiation occurs dramatically when a species migrates from one landmass to another. This may occur between islands or between continents and islands. A classic example of adaptive radiation is the evolution of finches noted by Charles Darwin during his trips to the Galápagos Islands off the west coast of South America.

Several species of plants and animals had migrated to these islands from the South American mainland by means of flight, wind, ocean debris, or other means of transport. Finches from the mainland—perhaps aided by winds—settled on fifteen of the islands in the Galápagos group and began to adapt to the various unoccupied ecological niches on those islands, which differed.

Over several generations, natural selection favored a variety of finch species with beaks adapted for the different types of foods available on the different islands. As a result, several species of different finches evolved, roughly simultaneously, on these islands.

Hawaiian Silversword Alliance

Although plants seem unable to "migrate" as birds and other animals do, adaptive radiation occurs in the plant world as well. In the Hawaiian Islands, for example, twenty-eight species of the Asteraceae family are known together as the Hawaiian silversword alliance. The entire group appears to be traceable to one ancestor, thought to have arrived on the island of Kauai from western North America.

The silverswords—which compose three genera, Argyroxiphium, Dubautia, and Wilkesia— have since evolved into twenty-eight species, and this speciation came about due to major ecological shifts. These plants are therefore prime examples of adaptive radiation.

Within the silversword alliance, different species have adapted to widely varying ecosystems found throughout the islands. Argyroxiphium sandwicense, for example, is endemic to the island of Maui and grows at high elevations from 6,890 to 9,843 feet (2,100 - 3,000 meters) on the dry, alpine slopes of the volcano Haleakala.

This species has succulent leaves covered with silver hairs. It is thought that the hairs lessen the pace of evaporative moisture loss and protect the leaves from the sun. In contrast, species of the genus Dubautia that grow in wet, shady forests have large leaves that lack hairs.

Despite their "customized" physiologies, the silverswords that have evolved in Hawaii are all closely related to one another, so much so that any two can hybridize. Studies of the silverswords have provided what geneticist Michael Purugganan called a "genetic snapshot of plant evolution". Adaptive radiation is one window into how new plant structures arise.
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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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7:44 AM
Biotechnology
Biotechnology
Biotechnology is the use of living organisms, or substances obtained from those organisms, to produce processes or products of value to humanity, such as foods, high-yield crops, and medicines.

Modern biotechnological advances have provided the ability to tap into a natural resource, theworld gene pool,with such great potential that its full magnitude is only beginning to be appreciated.

Theoretically, it should be possible to transfer one or more genes from any organism in the world into any other organism. Because genes ultimately control how any organism functions, gene transfer can have a dramatic impact on agricultural resources and human health in the future.

History of Biotechnology

Although the term “biotechnology” is relatively new, the practice of biotechnology is at least as old as civilization. Civilization did not evolve until humankind learned to produce food crops and domestic livestock through the controlled breeding of selected plants and animals. Eventually humans began to utilize microorganisms in the production of foods such as cheese and alcoholic beverages.


During the twentieth century, the pace of modification of various organisms accelerated. Through carefully controlled breeding programs, plant architecture and fruit characteristics of crops have been modified to facilitate mechanical harvesting. Plants have been developed to produce specific drugs or spices, andmicroorganisms have been selected to produce antibiotics and other medicinal or food products.

Developments in Biotechnology

Since the mid-twentieth century, the ability to utilize artificial media to propagate plants has led to the development of a technology called tissue culture. The earliest formof tissue culture involved using the culture of meristem tissue to produce numerous tiny shoots that can be grown into full-size plants, referred to as clones because each plant is genetically identical.

Developments in Biotechnology
Developments in Biotechnology
More than one thousand plant species have been propagated by tissue culture techniques. Plants have been propagated via the culture of other tissues, including the stems and roots. In some of these techniques, the plant tissue is treated with hormones to produce callus tissue, masses of undifferentiated cells.

The callus tissue can be separated into single cells to establish a cell suspension culture. Callus tissue and cell suspensions can be used to produce specific drugs and other chemicals. Entire plants can also be generated from the callus tissue or from single cells by addition of specific combinations of hormones.

Afar more complex method of cloning of plants and animals from the deoxyribonucleic acid (DNA) of a single cell is amore recent development. Proponents of this method of producing copies of organisms have suggested that cloning technology might be used to improve agricultural stock and to regenerate endangered species.

These ideas have had their detractors, however, as critics have noted the potential dangers of narrowing a species’ gene pool. The July, 1996, birth in Scotland of Dolly, a sheep cloned and raised to adulthood, demonstrated that the cloning of animals had left the realm of science fiction and become a matter of scientific fact.

Recombinant DNA Technology

In practice, recombinant DNA methodology is complex, but in concept, it is fairly easy to comprehend. The genes in all living cells are composed of the same chemical, DNA. The DNA of all cells, whether from bacteria, plants, or animals including humans, is very similar. When DNA from a foreign species is transferred into a different cell, it functions exactly as the native DNA functions; that is, it "codes" for protein.

The easiestway to manipulate genes is using bacterial cells (most often Escherichia coli) and a vector, an agent that can be used to pass the gene fromone cell to another. Plasmids, small extra circular DNA molecules found in many bacterial cells, are commonly used for this purpose. Plasmids are replicated along with the bacterial cell’s own DNA every time the cell reproduces. Plasmids can be easily isolated from bacterial cells.

Recombinant DNA Technology
Recombinant DNA Technology
When a specific gene has been isolated, it can be fused, using restriction endonucleases, with a plasmid to produce a recombinant plasmid. These recombinant plasmids can then be put into bacterial cells by a process called transformation. Special plasmids called expression vectors allow expression of inserted genes once they are inside a bacterial cell.

Although expressing foreign genes in bacterial cells is relatively simple, inserting theminto plants and getting them expressed is more complicated. The Ti plasmid is a widely used vector that works well in dicots but has never worked for monocots. Consequently, the first successful transgenic plants were dicots, while success with the most important food crops, monocots such as rice and corn, took more time and effort.

Many alternative methods for inserting genes into plant cells have been developed that work on both monocots and dicots. Microinjection can be used to insert a gene into individual cells. A less laborious method is called biolistic, for biological ballistic, where millions of copies of the gene are attached to tiny projectiles that are then fired into groups of plant cells. Using these and other methods, genetic modification of plants is becoming more routine.

Future of Biotechnology in Agriculture

This new technology could have a tremendous impact on agriculture. As the human population grows, biotechnology will most likely play an important role in producing an increase in food production. Such an increase will require developments such as crop plants that will produce higher yields under normal conditions and crops that will produce higher yieldswhen grown inmarginal environments.

Biotechnology provides a means of developing higher-yielding crops in much less time than it takes to develop them though traditional plant-breeding programs. Genes for the desired characteristics can be inserted directly into the plant without having to go through repeated controlled selection and breeding cycles to establish the trait.

There are also economic advantages in diversifying agriculture production in a given area. A producer might wish to grow a particular high-value cash crop in an area where soil or climate conditions would prevent such a crop from thriving. Biotechnology can help solve these types of problems. For example, high value crops can be developed to grow in areas that heretofore would not have supported such crops.

Plants also can be developed to produce new products such as antibiotics, drugs, hormones, and other pharmaceuticals. Crop plants bioengineered to produce novel products mean that pharmaceuticals and other valuable products could be grown in farm environments rather than in laboratories.

While there will be a growing pressure for agriculture to produce more food in the future, there will also be pressure for crop production to be more friendly to the environment. Biotechnology has the potential to play a major role in the development of a long-term, sustainable, environmentally friendly agricultural system. For example, the development of crop varieties with improved resistance to pests will reduce the reliance on pesticides.

Methods of crop production and harvestwith less environmental impact will also have to be developed. Because agriculture will continue to have an impact on the environment, the need to remediate polluting agents will continue to exist. Hence biotechnology will play an important role in the development of bioremediation systems for agriculture as well as other industrial pollutants.

Ownership Issues

There will be many difficult ethical and economic issues surrounding the use of this new biotechnology. One of the major questions concerns ownership. Patent laws in the United States read that ownership over an organism can be granted if the organism has been intentionally genetically modified through the use of recombinant DNA techniques.

In addition, processes that utilize genetically modified organisms can be patented. Therefore one biotechnology firm may own the patent to an engineered organism, but another firm may own the rights to the process used to produce it.
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3:15 AM
Chloroplast DNA
Chloroplast DNA
Plants are unique among higher organisms in that they meet their energy needs through photosynthesis. The specific location for photosynthesis in plant cells is the chloroplast, which also contains a single, circular chromosome composed of DNA. Chloroplast DNA contains many of the genes necessary for proper chloroplast functioning.

A better understanding of the genes in chloroplast deoxyribonucleic acid (cpDNA) has improved the understanding of photosynthesis, and analysis of the deoxyribonucleic acid (DNA) sequence of these genes has been useful in studying the evolutionary history of plants.

Discovery of Chloroplast Genes

The work of nineteenth century Austrian botanist Gregor Mendel showed that the inheritance of genetic traits follows a predictable pattern and that the traits of offspring are determined by the traits of the parents.

For example, if the pollen from a tall pea plant is used to pollinate the flowers of a short pea plant, all the offspring are tall. If one of these tall offspring is allowed to self-pollinate, it produces a mixture of tall and short offspring, three-quarters of them tall and one-quarter of them short.


Similar patterns are observed for large numbers of traits from pea plants to oak trees. Because of the widespread application of Mendel’s work, the study of genetic traits by controlled mating is often referred to as Mendelian genetics.

In 1909 German botanist Karl Erich Correns discovered a trait in the four-o’clock plants (Mirabilis jalapa) that appeared to be inconsistent with Mendelian inheritance patterns.

He discovered that four-o’clock plants had a mixture of leaf colors on the same plant: Some were all green, many were partly green and partly white (variegated), and some were all white.

If he took pollen from a flower on a branch with all-green leaves and used it to pollinate a flower on a branch with all-white leaves, all the resulting seeds developed into plants with white leaves.

Likewise, if he took pollen from a flower on a branch with all-white leaves and used it to pollinate a flower on a branch with all-green leaves, all the resulting seeds developed into plants with green leaves.

Repeated pollen transfers in any combination always resulted in offspring whose leaves resembled those on the branch containing the flower that received the pollen, that is, the maternal parent. These results could not be explained by Mendelian genetics.

Since Correns’s discovery, many other such traits have been discovered. It is now known that the reason these traits do not follow Mendelian inheritance patterns is that their genes are not on the chromosomes in the nucleus of the cell where most genes are located. Instead, the gene for the four o’clock leaf color trait is located on the single, circular chromosome found in chloroplasts.

Because chloroplasts are specialized for photosynthesis, many of the genes on the single chromosome produce proteins or ribonucleic acid (RNA) that either directly or indirectly affect synthesis of chlorophyll, the pigment primarily responsible for trapping energy from light.

Because chlorophyll is green and because mutations in many chloroplast genes cause chloroplasts to be unable to make chlorophyll, most mutations result in partially or completely white or yellow leaves.

Identity of Chloroplast Genes

Advances in molecular genetics have allowed scientists to take a much closer look at the chloroplast genome. The size of the genome has been determined for a number of plants and algae and ranges from 85 to 292 kilobase pairs (one kb equals one thousand base pairs), with most being between 120 kb and 160 kb. The complete DNA sequences for several different chloroplast genomes of plants and algae have been determined.

Although a simple sequence does not necessarily identify the role of each gene, it has allowed the identity of a number of genes to be determined, and it has allowed scientists to estimate the total number of genes. In terms of genome size, chloroplast genomes are relatively small and contain slightly more than one hundred genes.

Roughly half of the chloroplast genes produce either RNA molecules or polypeptides that are important for protein synthesis. Some of the RNA genes occur twice in the chloroplast genomes of almost all land plants and some groups of algae.

The products of these genes represent all the ingredients needed for chloroplasts to carry out transcription and translation of their own genes. Half of the remaining genes produce polypeptides directly required for the biochemical reactions of photosynthesis.

What is unusual about these genes is that their products represent only a portion of the polypeptides required for photosynthesis. For example, the very important enzyme ATPase, the enzyme that uses proton gradient energy to produce the important energy molecule adenosine triphosphate (ATP), comprises nine different polypeptides.

Six of these polypeptides are products of chloroplast genes, but the other three are products of nuclear genes that must be transported into the chloroplast to join with the other six polypeptides to make active ATPase.

Another notable example is the enzyme ribulose biphosphate carboxylase (RuBP carboxylase), which is composed of two polypeptides. The larger polypeptide, called rbcL, is a product of a chloroplast gene, whereas the smaller polypeptide is the product of a nuclear gene.

The last thirty or so genes remain unidentified. Their presence is inferred because they have DNA sequences that contain all the components found in active genes. These kinds of genes are often called “open reading frames” (ORFs) until the functions of their polypeptide products are identified.

Impact and Applications

The discovery that chloroplasts have their own DNA and the further elucidation of their genes have had some impact on horticulture and agriculture.

Several unusual, variegated leaf patterns and certain mysterious genetic diseases of plants are now better understood. The discovery of some of the genes that code for polypeptides required for photosynthesis has helped increase understanding of the biochemistry of photosynthesis.

The discovery that certain key chloroplast proteins, such as ATPase and RuBP carboxylase, are composed of a combination of polypeptides coded by chloroplast and nuclear genes also raises some as yet unanswered questions.

For example, why would an important plant structure like the chloroplast have only part of the genes it needs to function? Moreover, if chloroplasts, as evolutionary theory suggests, were once free-living bacteria-like cells, which must have had all the genes needed for photosynthesis, why and how did they transfer some of their genes into the nuclei of the cells in which they are now found?

Of greater importance has been the discovery that the DNA sequences of many chloroplast genes are highly conserved; that is, they have changed very little during their evolutionary history. This fact has led to the use of chloroplast gene DNA sequences for reconstructing the evolutionary history of various groups of plants.

Traditionally, plant systematists (scientists who study the classification and evolutionary history of plants) have used structural traits of plants, such as leaf shape and flower anatomy, to try to trace the evolutionary history of plants.

Unfortunately, there are a limited number of structural traits, and many of them are uninformative or even misleading when used in evolutionary studies. These limitations are overcome when gene DNA sequences are used.

A DNA sequence of a few hundred base pairs in length provides the equivalent of several hundred traits, many more than the limited number of structural traits available (typically much fewer than one hundred).

One of the most widely used sequences is the rbcL gene. It is one of the most conserved genes in the chloroplast genome, which in evolutionary terms means that even distantly related plants will have a similar base sequence.

Therefore, rbcL can be used to retrace the evolutionary history of groups of plants that are very divergent from one another. The rbcL gene, along with a few other very conservative chloroplast genes, has already been used in attempts to answer some basic plant evolution questions about the origins of some of the major flowering plant groups.

Less conservative genes and ORFs show too much evolutionary change to be used at higher classification levels but are extremely useful in answering questions about the origins of closely related species, genera, or even families. As analytical techniques are improved, chloroplast genes show promise of providing even better insights into plant evolution.

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11:34 AM
Chromatin
Chromatin
Chromatin is an inclusive term referring to DNA and the proteins that bind to it, located in the nuclei of eukaryotic cells. The huge quantity of DNA present in each cell must be organized and highly condensed in order to fit into the discrete units of genetic material known as chromosomes. Gene expression can be regulated by the nature and extent of this DNA packaging in the chromosome, and errors in the packaging process can lead to genetic disease.

Scientists have known for many years that the hereditary information within plants and other organisms is encrypted in molecules of deoxyribonucleic acid (DNA) that are themselves organized into discrete hereditary units called genes and that these genes are organized into larger subcellular structures called chromosomes.

James Watson and Francis Crick elucidated the basic chemical structure of the DNA molecule in 1952, and much has been learned since that time concerning its replication and expression.

At the molecular level, DNA is composed of two parallel chains of building blocks called nucleotides, and these chains are coiled around a central axis to form the well-known double helix.


Each nucleotide on each chain attracts and pairs with a complementary nucleotide on the opposite chain, so a DNA molecule can be described as consisting of a certain number of these nucleotide base pairs.

The entire human genome consists of more than six billion base pairs of DNA, which, if completely unraveled, would extend for more than 2 meters. It is a remarkable feat of engineering that in each human cell this much DNA is condensed, compacted, and tightly packaged into chromosomes within a nucleus that is less than 10–5 meters in diameter.

Plants typically have larger genomes than humans; for example, wheat has fifteen billion base pairs of DNA. By contrast, the most widely studied plant among current scientists is Arabidopsis. The species Arabidopsis thaliana was selected as a model organism in plant research because of its comparatively simple structure: Its 26,000 genes make up “only” 125 million base pairs.

Chromatin
Chromatin
What is even more astounding is the frequency and fidelity with which this DNA must be condensed and relaxed, packaged and unpackaged, for replication and expression in each individual cell at the appropriate time and place during both development and adult life. The essential processes of DNA replication or gene expression (transcription) cannot occur unless the DNA is in an open or relaxed configuration.

Chemical analysis of mammalian chromosomes reveals that they consist of DNA and two distinct classes of proteins, known as histone and nonhistone proteins. This nucleoprotein complex is called chromatin, and each chromosome consists of one linear, unbroken, double-stranded DNA molecule that is surrounded in predictable ways by these histone and nonhistone proteins.

The histones are relatively small, basic proteins (having a net positive charge), and their function is to bind directly to the negatively charged DNA molecule in the chromosome.

Five major varieties of histone proteins are found in chromosomes, and these are known as H1, H2A, H2B, H3, and H4. Chromatin contains about equal amounts of histones and DNA, and the amount and proportion of histone proteins are constant from cell to cell in all higher organisms, including the higher plants.

In fact, the histones as a class are among themost highly conserved of all known proteins. For example, for histone H3, which is a protein consisting of 135 amino acid “building blocks,” there is only a single amino acid difference in the protein found in sea urchins as compared with the one found in cattle.

This is compelling evidence that histones play the same essential role in chromatin packaging in all higher organisms and that evolution has been quite intolerant of even minor sequence variations between vastly different species.

Nonhistones as a class of proteins are much more heterogeneous than the histones. They are usually acidic (carrying a net negative charge), so they will most readily attract and bind with the positively charged histones rather than the negatively charged DNA.

Each cell has many different kinds of nonhistone proteins, some of which play a structural role in chromosome organization and some of which are more directly involved with the regulation of gene expression. Weight for weight, there is often as much nonhistone protein present in chromatin as histone protein and DNA combined.

Nucleosomes and Solenoids

The fundamental structural subunit of chromatin is an association of DNA and histone proteins called a nucleosome. First discovered in the 1970’s, each nucleosome consists of a core of eight histone proteins: two each of the histones H2A, H2B, H3, and H4.

Around this histone octamer is wound 146 base pairs of DNA in one and three-quarters turns (approximately eighty base pairs per turn). The overall shape of each nucleosome is similar to that of a lemon or a football.

Nucleosomes and Solenoids
Nucleosomes

Each nucleosome is separated from its adjacent neighbor by about fifty-five base pairs of linker DNA, so that in its most unraveled state they appear under the electron microscope to look like tiny beads on a string. Portions of each core histone protein protrude outside the wound DNA and interact with the DNA that links adjacent nucleosomes.

The next level of chromatin packaging involves a coiling and stacking of nucleosomes into a ribbonlike arrangement, which is twisted to form a chromatin fiber about 30 nanometers in diameter, commonly called a solenoid.

Formation of solenoid fibers requires the interaction of histone H1, which binds to the linker DNA between nucleosomes. Each turn of the chromatin fiber contains about twelve hundred base pairs (six nucleosomes), and the DNA has now been compacted by about a factor of fifty.

The coiled solenoid fiber is organized into large domains of 40,000 to 100,000 base pairs, and these domains are separated by attached nonhistone proteins that serve both to organize and to control their packaging and unpackaging.

Loops and Scaffolding

Physical studies using the techniques of X-ray crystallography and neutron diffraction have suggested that solenoid fibers may be further organized into giant supercoiled loops.

The extent of this additional looping, coiling, and stacking of solenoid fibers varies, depending on the cell cycle. The most relaxed and extended chromosomes are found at interphase, the period of time between cell divisions.

Interphase chromosomes typically have a diameter of about 300 nanometers. Chromosomes that are getting ready to divide (metaphase chromosomes) have the most highly condensed chromatin, and these structures may have a diameter of up to 700 nanometers.

One major study on the structure of metaphase chromosomes has shown that a skeleton of nonhistone proteins in the shape of the metaphase chromosome remains even after all of the histone proteins and the DNA have been removed by enzymatic digestion. If the DNA is not digested, it remains in long loops (10 to 90 kilobase pairs) anchored to this nonhistone protein scaffolding.

Impact and Applications

Studies on chromatin packaging continue to reveal the details of the precise chromosomal architecture that results from the progressive coiling of the single DNA molecule into increasingly compact structures. Evidence suggests that the regulation of this coiling and packaging within the chromosome has a significant effect on the properties of the genes themselves.

In fact, errors in DNA packaging can lead to inappropriate gene expression and developmental abnormalities. In humans, the blood disease thalassemia, several neuromuscular diseases, and even male sex determination can all be explained by the altered assembly of chromosomal structures.

The unifying lesson to be learned from these examples of DNA packaging and disease is that DNA sequencing studies and the construction of genetic maps will not by themselves provide all the answers to questions concerning genetic variation and genetic disease.

An understanding of genetics at the molecular level depends not only on the primary DNA sequence but also on the three dimensional organization of that DNA within the chromosome. Compelling genetic and biochemical evidence has left no doubt that the packaging process is an essential component of regulated gene expression.
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9:34 AM
Chromosomes
Chromosomes

Chromosomes contain the genetic information of cells. Replication of chromosomes assures that genetic information is correctly maintained as cells divide.

The genome of an organism is the sum total of all the genetic information of that organism. In eukaryotic cells, this information is contained in the cell’s nucleus and organelles, such as mitochondria and plastids. In prokaryotic organisms (bacteria and archaea), which have no nucleus, the genomic information resides in a region of the cell called the nucleoid.

A chromosome is a discrete unit of the genome that carries many genes, or sets of instructions for inherited traits. Genes, the blueprints of cells, are specific sequences of deoxyribonucleic acid (DNA) that code for messenger ribonucleic acids (monas), which in turn direct the synthesis of proteins.

Each eukaryotic chromosome contains a single long DNA molecule that is coiled, folded, and compacted by its interaction with chromosomal proteins called histone. This complex of DNA with chromosomal proteins and chromosomal RNAs is chromatin.


DNA of higher eukaryotes is organized into loops of chromatin by attachment to a nuclear scaffold. The loops function in the structural organization of DNA and may increase transcription of certain genes by making the chromatin more accessible.

To maintain the genetic information of a cell, it is essential that chromosomes correctly replicate and divide as a cell divides. After DNA replication, chromosomes separate in a process called mitosis.

During this process, the nuclear envelope breaks down and chromosomes condense into compact structures. A cellular structure known as the mitotic spindle forms, pulling pairs of replicated chromosomes apart so that the two cells receive identical sets of chromosomes.

Chromosomes are readily visualized when they condense during cell division. All the chromosomes of a cell visualized during mitosis constitute that cell’s karyotype.

Each chromosome has a centromere—a constricted area of the condensed chromosome where the mitotic or meiotic spindle attaches to assure correct distribution of chromosomes during cell division—and a telomere, the end or tip of a chromosome, which contains tandem repeats of a short DNA sequence.

The number of chromosomes in a gamete (either egg or sperm) is the haploid number, n. The haploid number of chromosomes in humans is 23; in corn, 10; in peas, 7; in Arabidopsis (the model organism used in much botanical research), 4.

Some carp and some ferns have more than 50 chromosomes in the haploid genome. Pollen grains of some plants, such as pear, contain three haploid cells: One directs the growth of the pollen tube down the style to the ovary; the other two are sperm.

In flowering plants (angiosperms), there is a unique double fertilization where by one sperm nucleus fuses with the egg nucleus to form the diploid (2n) zygote, and the other sperm nucleus fuses with two polar nuclei to form the triploid nutritive tissue, or endosperm, which will nourish the embryo in the seed.

The zygote then increases in cell number by mitosis, a type of cell division during which chromosomes in a nucleus are replicated and then separated to form two genetically identical daughter nuclei.

schematic of chromosome
schematic of  a chromosome

This is followed by cytokinesis, the process of cytoplasmic division, which results in two daughter cells, each having the same number of chromosomes and genetic composition as the parent cell. The mature 2n plant forms the haploid (n) gametes by meiosis, a type of cell division that reduces the number of chromosomes to the haploid number.

A distinctive feature of plant cell division is the plant cell has three genomes (the nuclear, mitochondrial, and plastid genome) to replicate and divide. The chromosomes of eukaryotes consist of unique genes among a complex pattern of repeated DNA sequences. Arabidopsis has only 4 chromosomes containing about 120 million base pairs.

There are typically between twenty and one hundred copies of the mitochondrial genome per mitochondrion, ranging in size from two hundred to twenty-four hundred kilobase pairs (or kb; one kilobase pair equals one thousand base pairs).

Plant mitochondrial genomes are much larger than the mitochondrial genomes of yeast or animals. Chloroplast genomes range in size from 130 to 150 kb, with 50 to 150 copies of that genome per plastid.

In cell division in plant cells, the two daughter nuclei are partitioned to form two separate cells by a cell plate that grows at the equator of the mother cell. In animal cells, this separation involves the constriction of the cell at a central contractile ring. DNA replication is strictly controlled during the cell cycle.

DNA synthesis occurs in the synthesis (S) phase, beginning at origins of replication distributed around the genome, occurring on average every 66 kb in dicotyledonous plants and on average every 47 kb in monocotyledonous plants.

Heterochromatin is the term for regions of chromosomes that are permanently in a highly condensed state, are not transcribed, and are late-replicating.

chromosomes made out of
chromosomes made out of

Heterochromatin contains highly repeated DNA sequences. Euchromatin is the rest of the chromosomes that is extended, accessible to RNA polymerase, and at least partially transcribed.

Some plants and animals have extra chromosomes that do not seem to be essential. These are called accessory or supernumerary chromosomes. They have been most studied in corn where these extra chromosomes are called B-chromosomes. B-chromosomes are usually highly condensed heterochromatin that may or may not be present in an individual of that species.

An increase in the copy number of the genome is common in plants and animals, occurring during the development of individuals. Polyploids have three or more complete sets of chromosomes in their nuclei instead of the two sets found in diploids. For example, in Arabidopsis, tissues of increasing age have an increase in polyploidy, reaching up to sixteen duplications.
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