Tuesday, March 31, 2009

How the Living Organisms interact with the Environment

Living organisms and the physical environment have a close relationship. They interact with each other. The biosphere is the parts of Earth inhabited by living organisms. The biosphere consists of specific geographical areas known as biomes. A biome is a collection of different types of ecosystems. The ecosystems include grasslands, rain forests, streams, lakes, sea, deserts etc., with various types of organisms starting from bacteria, fungi, algae, and various other types of plants and animals. There are millions of known species of organisms and there are many millions to be discovered. Each organism lives in a specialized regional environment within the ecosystem known as the habitat. An organism can live in a specific habitat because it is adapted to live in that habitat. Deep-sea vent, bottom of sea, arctic rivers, and river banks, etc. are examples of habitat.

Organisms living in a specific environment interact with the environment and also with themselves in very different ways. There are big trees growing along the bank of the stream. Since the trees are very big, they make half of the stream a shady area, and this may make the temperature of the water a bit lower than that in the middle region. It is because the water at the bank side is not directly heated by the sun. Similarly, there are many algae floating in the water freely, and this may reduce the penetration of sunlight. So the light intensity under the water may be decreased. All the organisms living in an environment along with that physical environment form an ecosystem. The organisms living in a fresh water pond, along with the pond, form an aquatic ecosystem. All organisms on land along with their environment form the terrestrial ecosystem.

The energy flow in an ecosystem obeys the laws of thermodynamics. It is an open system. An open System allows the free flow or exchange of energy and matter such as water, carbon dioxide, nitrogen, food materials, and even the movement of organisms from one ecosystem to another. There are producers, consumers, and decomposers in ecosystems. The producers are the photosynthetic organisms or the autotrophs. The producers of the ecosystem take energy from sunlight and convert it into chemical energy. This energy is passed on to consumers and then to decomposers, which cycles back the materials to the environment. But the energy flows only in one direction and is not cycled back. Herbivorous animals consume the organic food synthesized by the producers, which form the primary consumers.

These herbivores form the food of carnivores, which are the secondary consumers. And finally the decomposers act on the dead remains of all these organisms including the producers. decompose the organic materials into inorganic materials, and thus cycle back the materials to the environment. This forms the food chain in the ecosystem. In each step of the food chain energy is also transferred. In each step a portion of the energy is lost in the form of heat. Thus, heat is flowing in one direction and is not cycled back. The energy enters the ecosystem from the sun through producers and leaves the ecosystem in all steps of the food chain in the form of metabolic heat.

The materials in the form of nutrients required for life are cycled between organisms and the environment. The materials are absorbed by the producers for synthesizing the nutrients and are cycled among the consumers and finally returned to the environment by the activity of saprophytes and other decomposers such as fungi and bacteria. Considering the flow of energy and nutrients in the ecosystem and in the biosphere, it can be considered a single living organism.

Tags: Bio Technology, Bio Genetics , Life Forms, organisms

Size & Complexity of Living Organisms

Living organisms greatly differ in size and complexity of their body. They range from minute unicellular bacteria to very big multicellular organisms such as blue whales and redwood trees. Primitive cell forms such as bacteria and blue-green algae are very simple in organization and function. The cells and organisms are very small and cannot be seen with the naked eye. A microscope is needed for observing these microorganisms. The multicellular organisms and their cells are very complex in organization and function. The body of higher plants and animals consists of billions of various types of specialized, structurally and functionally complex cells. Therefore, their body and its function is highly complicated.

Variations in the body size affect various other body measurements differently. This is because the volume of cells and so the volume of the entire organism increases much faster than the surface area. Entire single-celled organisms and most primitive multicellular organisms use their cell surfaces to acquire nutrients and dispose of wastes. But the amount of nutrients needed, and the quantity of wastes produced, is related to cell volume. Since the surface area to volume ratio of a cell decreases as its size increases, cells have an upper limit on how much volume they can sustain with a given surface area. Large organisms have less surface area relative to mass than do small organisms. This relationship affects the efficient exchange of material between the body and the environment. Allometric relationships describe the effect of body size on biological features. These relationships can reveal general patterns of how organisms function; for example, how much they sleep, their food requirements, and their brain size.

Allometric relationships also have practical applications, as in the proper determination of drug dosages for animals of differing body sizes. For multicellular organisms, increases in overall body size are mostly due to increases in cell number, not cell size. This is also because of surface area to volume ratio limitations on cells.

The evolution of complexity in multicellular organisms is driven by the specialization of cells. Multicellular complexity requires coordination among body cells. Internal communication mechanisms such as hormones and the nervous system help make this possible. Complexity also requires many body cells to give up reproduction in support of a relatively few cells that do reproduce.

Tags: Bio Technology, Bio Genetics , Life Forms, organisms

What are the Hierarchical Levels of Life Forms

Life on Earth is incredibly extensive and to make it easier to study, biologists have broken living systems up into generalized hierarchical levels as given below:

1) Molecules
2) Organelles
3) Cells
4) Tissues
5) Organs 6) Organisms
7) Populations
8) Communities
9) Ecosystems
10) Biosphere

The lowest level of the biological hierarchy begins with molecules. Examples include proteins, DNA, lipids, etc. Many such specialized molecules are organized into cells, the basic unit of life. There are single-celled organisms such as bacteria, amoeba, yeast, etc., in which the body consists of a single cell. When the body consists of more than one cell it is called multicellular. Multicellular organisms are collection of various types of specialized cells. A group of specialized cells carrying out a specific function is called a tissue. For example, muscle tissue, nervous tissue, connective tissue, etc. When different types of tissues are organized together to perform a common function it is called an organ. Examples include, liver, stomach, heart, etc. When a number of organs function together to accomplish a specific function of the body, it forms an organ system. For example, the stomach, liver, intestine, pancreas, salivary glands, etc. work together to form the digestive system. In an organism there are a number of organ systems that work in an associated way to form the organism and its life activities. Each individual organism is a member of a large population, which exists in a habitat.

A population is a group of organisms belonging to a species. A group of different species that live and interact in a particular area or environment is known as a community. The communities, along with the environment in which they exist, are known as ecosystems. An ecosystem consists of biomes, which are large geographical areas of the world. Each biome is a part of the biosphere, which includes the entire living population on the Earth along with its physical environment.

Tags: Bio Technology, Bio Genetics , Life Forms, organisms

Adaptation the special feature of Organisms

The existence of an organism in its environment or habitat is closely related to the special features of that organism or the adaptations. Adaptation is the special feature of an organism's morphology, anatomy, and physiology, which improves its interaction with its environment.

Adaptations usually have the following characteristics.
1) Special features are specially suited to a specific habitat.
2) These special features are often complex.
3) These special features help organisms to live in their environment and capture food, regulate the body's physiology, reproduce, disperse, and defend against enemies.

Adaptation is one of the important factors that drives the process of evolution. Adaptations are created through mutation and natural selection. Evolution requires genetic variation. In order for continuing evolution there must be mechanisms to increase or create genetic variation and mechanisms to decrease it. Mutation is a change in a gene. These changes are the source of new genetic variation. Natural selection operates on this variation. If these variations are suited to the changed environment that organism will outperform the others, which leads to the evolution of the population. If these new changes created through mutation are not suitable for existence in that environment, they will lead to extinction.Natural selection:Some types of organisms within a population leave more offspring than other Over time, the frequency of the more prolific type will increase. The difference ii reproductive capability is called natural selection. Natural selection is the only mechanism of adaptive evolution; it is defined as differential reproductive success of pre-existing classes of genetic variants in the gene pool.

The most common action of natural selection is to remove unfit variants as they arise via mutation. In other words, natural selection usually prevents new alleles from increasing in frequency. This led a famous evolutionist, George Williams, to say "Evolution proceeds in spite of natural selection."

Natural selection can maintain or deplete genetic variation depending on how it acts. When selection acts to weed out deleterious alleles, or causes an allele to sweep to fixation, it depletes genetic variation. When heterozygotes are more fit than either of the homozygotes, however, selection causes genetic variation to be maintained. (A heterozygote is an organism that has two different alleles at a locus; a homozygote is an organism that has two identical alleles at a locus.) This is called balancing selection. An example of this is the maintenance of sickle cell alleles in human populations subject to malaria. Variation at a single locus determines whether red blood cells are shaped normally or sickled. If a human has two alleles for sickle cell, he /she develops anemia-the shape of sickle cells precludes them from carrying normal levels of oxygen. However, heterozygotes who have one copy of the sickle cell allele coupled with one normal allele enjoy some resistance to malaria--the shape of sickle cells make it harder for the plasmodia (malariacausing agents) to enter the cell.

Thus, individual homozygous for the normal allele suffer more malaria than heterozygotes. Individual homozygous for the sickle cell are anemic. Heterozygotes have the highest fitness of these three types. Heterozygotes pass on both sickle cell and normal alleles to the next generation. Thus, neither allele can be eliminated from the gene pool. The sickle cell allele is at its highest frequency in regions of Africa, where malaria is most pervasive. Balancing selection involves opposing selection forces. An equilibrium results when two alleles selected in the homozygous state are retained because of the superiority of heterozygotes. Balancing selection is rare in natural populations.

Tags: Bio Technology, Bio Genetics , Adaptation of organisms

Know the Biodiversity of Life forms

Biodiversity is the occurrence of all life forms in the biosphere. The phenomenon of speciation increases biodiversity. Biodiversity can be for a specific region or geographical area and similarly can be within a species. Within a species there can be varieties or sub-species, strains, and types. This variation within a species constitutes the biodiversity within a species. It is directly linked to the stability of the ecosystem. The magnitude of the biodiversity is not completely studied. The total number of species collected, named, and classified in taxonomic groups is around 1.5 million. This number is only a small fraction, about 10% of all living organisms, in this biosphere. The remaining, more than 90%, remains to be identified and classified.

Out of this 1.5 million known species, 750,000 are insects. The remaining part includes 280,000 animal species and 250,000 numbers of plant species. There are approximately 69,000 fungi, 27,000 algae, 3,000 protozoans, and about 3,000 prokaryotes including eubacteria and archaebacteria. Among these known groups, some have been studied extensively and others have been studied very poorly. Biodiversity, which is created by speciation and evolution, has a direct impact on the stability of the ecosystem and the biosphere. Due to many man-made changes in the environment through deforestation and construction of big dams, there is disturbances in the habitat of the species, slowly leading to their mass extinction and destabilization. This loss of biodiversity is non-reversible unless we take special precautions. The phenomenon of extinction is opposite to that of speciation. Extinction is the ultimate fate of all species.

Reasons for Extinction : The reasons for extinction are numerous. A species can be competitively excluded by a closely related species, the habitat a species lives in can disappear, and/or the organisms that the species exploits could come up with an unbeatable defense. Some species enjoy a long tenure on the planet while others are short-lived. Some biologists believe species are programed to go extinct in a manner analogous to organisms being destined tc die. This is ordinary extinction. The majority, however, believe that if the environment stays fairly constant, a well-adapted species could continue to survive indefinitely.

Mass extinctions: Mass extinctions shape the overall pattern of macroevolution. If you view evolution as a branching tree, it's best to picture it as one that has been severely pruned a few times in its life. The history of life on this earth includes many episodes of mass extinction in which many groups of organisms were wiped off the face of the planet. Mass extinctions are followed by periods of radiation where new species evolve to fill the empty niches left behind. It is probable that surviving a mass extinction is largely a function of luck. Thus, contingency plays a large role in patterns of macroevolution.

Tags: Bio Technology, Bio Genetics , Genetic Variation

Understanding of Speciation

Speciation is the process of a single species becoming two or more species. Many biologists think Speciation is key to understanding evolution. According to biological species concept, species are groups of actually or potentially interbreeding natural populations, which are reproductively isolated from other such groups. Speciation is thus seen in terms of the evolution of isolating mechanisms and is said to be complete when reproductive barriers are sufficient to prevent gene flow between the two new species. The problem is that the capacity to interbreed cannot always be tested neither the potential for interbreeding. For asexually reproducing organisms and fossils, this concept does not apply.

Modes of Speciation
Biologists recognize two types of speciation: allopatric and sympatric speciation. The two differ in geographical distribution of the populations in question.

Allopatric speciation: is thought to be the most common form of speciation. It occurs when a population is split into two (or more) geographically isolated subdivisions that organisms cannot bridge. Eventually, the two populations gene pools change independently until they cannot interbreed even if they were brought back together. In other words, they have speciated.

Sympatric speciation: occurs when two sub-populations become reproductively isolated without first becoming geographically isolated. Insects that live on a single host plant provide a model for sympatric speciation. If a group of insects switched host plants they would not breed with other members of their species still living on their former host plant. The two sub-populations could diverge and speciate.

Tags: Bio Technology, Bio Genetics , Genetic Variation

Understanding of Genetic Variation

Evolution requires genetic variation. If there were no dark moths, the population could not have evolved from mostly light to mostly dark. In order for continuing evolution there must be mechanisms to increase or create genetic variation and mechanisms to decrease it. Mutation is a change in a gene. These changes are the source of new genetic variation. Natural selection operates on this variation.

Genetic variation has two components:
allelic diversity and non-random associations of alleles. Alleles are different versions of the same gene. For example, humans can have A, B, or O alleles that determine one aspect of their blood type. Most animals, including humans, are diploid-they contain two alleles for every gene at every locus, one inherited from their mother and one inherited from their father. Locus is the location of a gene on a chromosome. Humans can be AA, AB, AO, BB, 130, or 00 at the blood group locus. If the two alleles at a locus are of the same type (for instance two A alleles) the individual would be called homozygous. An individual with two different alleles at a locus (for example, an AB individual) is called heterozygous. At any locus there can be many different alleles in a population, more alleles than any single organism can possess. For example, no single human can have an A, B, and an 0 allele.

Allele frequency: The number of organisms in a population carrying a particular allele of gene determines the allele frequency. In population genetics the allele frequency is usually expressed as decimals. Thus, a frequency of 99% is represented as 0.99 and the 1% frequency would be 0.01, because the total population represents 100% or 1.0. In population genetics these are represented as:
p+q=1, where p - frequency of dominant allele & q - frequency of recessive allele.

Thus, in the above example total frequency is 0.99 + 0.01 = 1.0.

If we know the frequency of one allele (gene), the frequency of the other allele can be determined.

Non-random breeding: In most of the natural population, mating is nonrandom. But there are many structural and behavioral mechanisms that prevent the random mating. In populations where there is no random mating, fewer heterozygotes (an organism that has two different alleles at a locus) are found than would be predicted under random mating. A decrease in heterozygotes can be the result of mate choice, or simply the result of population sub-division. Most organisms have a limited dispersal capability, so their mate will be chosen from the local population.

Genetic Drift: The variation in allele frequencies can occur only by chance. This is called genetic drift. Drift is a binomial sampling error of the gene pool. What this means is, the alleles that form the next generation's gene pool are a sample of the alleles from the current generation. When sampled from a population, the frequency of alleles differs slightly due to chance alone. Alleles can increase or decrease in frequency due to drift.

Gene Flow: New organisms may enter a population by migration from another population. If they mate within the population, they can bring new alleles to the local gene pool. This is called gene flow. In some closely related species, fertile hybrids can result from interspecific matings. These hybrids can vector genes from species to species. Gene flow between more distantly related species occurs infrequently. This is called horizontal gene transfer.

Mutation: The cellular machinery that copies DNA sometimes makes mistakes. These mistakes alter the sequence of a gene. This is called a mutation. There are many kinds of mutations. A point mutation is a mutation in which one "letter" of the genetic code is changed to another. Lengths of DNA can also be deleted or inserted in a gene; these are also mutations. Finally, genes or parts of genes can become inverted or duplicated. Typical rates of mutation are between 10-1° and 10-1' mutations per base pair of DNA per generation. Most mutations are thought to be neutral with regards to fitness. Only a small portion of the genome of eukaryotes contains coding segments. And, although some non-coding DNA is involved in gene regulation or other cellular functions, it is probable that most base changes would have no fitness consequence.

Most mutations that have any phenotypic effect are deleterious. Mutations that result in amino acid substitutions can change the shape of a protein, potentially changing or eliminating its function. This can lead to inadequacies in biochemical pathways or interfere with the process of development. Organisms are sufficiently integrated that most random changes will not produce a fitness benefit. Only a very small percentage of mutations are beneficial. The ratio of neutral to deleterious to beneficial mutations is unknown and probably varies with respect to details of the locus in question and environment.

Genetic Load: The existence of disadvantageous alleles in heterozygous genotypes within the population is known as genetic load. The disadvantageous alleles when come as homozygous will affect the organism negatively for their phenotype and their existence. Such organisms may be eliminated from the population when these alleles (if they are deleterious in nature) occur in homozygous condition. If the allele is recessive, its effect won't be seen in any individual until a homozygote is formed. The eventual fate of the allele depends on whether it is neutral, deleterious, or beneficial.

Tags: Bio Technology, Bio Genetics , Genetic Variation

How Populations Evolve

Evolution is a change in the gene pool of a population over time. A gene is a hereditary unit that can be passed on unaltered for many generations. The gene pool is the set of all genes in a species or population. A population is a group of organisms of the same species usually found in a clearly defined geographical area.

The English moth or the peppered moth, biston betularia, is a frequently cited example of observed evolution. In this moth there are two color morphs, light and dark. Dr. Henry Bernard Davis Kettlewell, a British lepidopterist and medical doctor, is notable for his experiments on the peppered moth, most of which were done in Manchester, England. He found that dark moths constituted less than 2°,o of the population prior to 1848. The frequency of the dark morph increased in the years following. By 1898,95% of the moths in Manchester and other highly industrialized areas were of the dark type. Their frequency was less in rural areas. The moth population changed from mostly light colored moths to mostly dark colored moths. The moths' color was primarily determined by a single gene. So, the change in frequency of dark colored moths represented a change in the gene pool. This change was, by definition, evolution.
The increase in relative abundance of the dark type was due to natural selection. The late eighteenth century was the time of England's industrial revolution. Soot from factories darkened the birch trees the moths landed on. Against a sooty background, birds could see the lighter colored moths better and ate more of them. As a result, more dark moths survived until reproductive age and left offspring. The greater number of offspring left by dark moths is what caused their increase in frequency. This is an example of natural selection.

Populations evolve. In order to understand evolution, it is necessary to view populations as a collection of individuals, each harboring a different set of traits. A single organism is never typical of an entire population unless there is no variation within that population. Individual organisms do not evolve; they retain the same genes throughout their life. When a population is evolving, the ratio of different genetic types is changing-each individual organism within a population does not change. For example, in the previous example, the frequency of black moths increased; the moths did not turn from light gray to dark in concert. The process of evolution can be summarized in three sentences: Genes mutate. Individuals are selected. Populations evolve.

The word evolution has a variety of meanings. The fact that all organisms are linked via descent to a common ancestor is often called evolution. The theory of how the first living organisms appeared is often called evolution. This should be called abiogenesis. And frequently, people use the word evolution when they really mean natural selection-one of the many mechanisms of evolution. Phenotype is the morphological, physiological, biochemical, behavioral, and other properties exhibited by a living organism. Genotype is the genetic make up of an organism.
Evolution can occur without morphological change; and morphological change can occur without evolution. Humans are larger now than in the recent past, a result of better diet and medicine. Phenotypic changes like this, induced solely by changes in environment, do not count as evolution because they are not heritable; in other words, the change is not passed on to the organism's offspring. Most changes due to environment are fairly subtle, for example, size differences. Largescale phenotypic changes are obviously due to genetic changes, and therefore are evolution.

Tags: Bio Technology, Bio Genetics , Evolution

Formation of Tissues to become an Organ

Various types of tissues are associated together to carry out a specific function of the body and such structures are known as organs. In animals, stomach, heart, brain, etc., are specific organs carrying out specific functions due to the interaction of various tissues.

The heart is involved in the pumping of blood, which in turn is circulated to other organs and tissues by a network of arteries. Blood from various organs and tissues is brought back to the heart by another network of tubes called veins. Thus, forms an important system called the circulatory system. Kidneys are another example of organs. They are involved in the excretion of metabolic waste and other toxins produced in the body.

Similarly, there are a large number of organs such as stomach, intestine, liver, pancreas muscles, reproductive organs such as testes, ovaries, external genitalia, etc., that carry out specific functions in association with other organs. There are varieties of glandular organs, both ductless glands such as pituitary, thymus, adrenal, etc., and glands with ducts such as the salivary glands that execute their function primarily by secreting specific enzymes and hormones to carry out various metabolic activities.

Tags: Bio Technology Bio Genetics, Tissues Organs

Know the Plant Tissues

Vascular plants have distinctive cell types, all of which are surrounded by a cell wall of cellulose fibers and other molecules secreted by the cells. Just as in animals, cells are organized into tissues that perform different functions, but plants do not have organ systems like those of animals. The tissues of plants are grouped into three basic kinds: ground, vascular, and dermal. Meristem is a special embryonic tissue.

Plants differ from animals in that the tips of roots and stems, called apical meristem, remain embryonic and retain the ability to form new structures (e.g., leaves, stems, flowers, and roots). Hormones secreted by meristem cells are transported elsewhere in the plant; meristem is in part analogous to the endocrine system in animals.

Ground Tissues (Simple tissues):
Ground tissues or the simple tissues include parenchyma, collenchyma, and sclerenchyma. Thin-walled parenchyma cells have a variety of functions such as photosynthesis, starch storage, and secretion; they retain the capacity to divide and are important in repair of damage. They form the large part of the bulk of various organs such as stem, root, etc. In some parts they are modified to perform some special functions. For example:

This is a single-layered tissue that covers the whole plant body. It protects the internal part from infection and loss of water. This layer of cells has a waxy coating on the surface, which is secreted by the cells. This waxy layer is called cuticle, which helps to reduce the water loss.

These types of parenchyma cells are found in the leaves between the two epidermal layers. These are specialized for carrying out photosynthesis. Parenchyma cells containing chlorophyll are also known as chlorenchyma. If the cells of the mesophyll tissue are tightly packed without air space, they are known as palisade parenchyma or mesophyll; if a lot of air space is present it is called spongy parenchyma. Endodermis, pericycle, and companion cells, etc. are also an example of modified parenchyma cells.

These cells resemble parenchyma cells but are characterized by the presence of extra cellulose at the corners of the cells. Their walls are thickened and made strong with cellulose and pectin. Collenchyma cells help strengthen the plant parts in which they occur. Celery strings are an example.

Sclerenchyma cells have very thick secondary walls that are commonly impregnated with lignin, which makes them quite rigid. The lignified sclerenchyma of flax plants is made into linen threads for weaving, sewing, and paper making. Wood is made of lignified xylem cells. The hardness of a coconut shell or a peach pit is caused by lignified cells. Ground tissues are analogous to the supporting connective tissue and skeletal elements in animals. Sclerenchyma cells act as supporting elements in plants. Mature sclerenchyma cells can't elongate. The two types of sclerenchyma cells are fibers and sclereids. Fibers are long, slender, and tapered cells that occur in bundles. Sclereids are shorter than fibers and shaped irregularly. Nutshells and seed coats are composed of sclereids. Sclereids scattered among the soft parenchyma tissue of the pear give it a gritty texture.

Complex Tissues:

Complex tissues consist of more than one type of cells. Vascular tissues of plants include xylem and phloem; this is the plant's circulatory system. Xylem and phloem are the complex tissues.
Xylem consists of four types of cells-trachieds, vessel elements, parenchyma, and fibers. Trachieds are single cells that are elongated and lignified. At maturity, trachieds cells are dead and form interconnected tubes throughout the plant. Vessels are long, tubular structures formed by the fusion of several cells end to end in a row. They conduct water and dissolve nutrients that the plant absorbs from the soil; their thick, sclerified walls allow them to give mechanical support to the plant. Wood is made of xylem cells. Xylem parenchyma has thin cellulose cell walls and living contents similar to the typical parenchyma cells. Xylem fibers are shorter and thinner than trachieds and have much thicker walls.

Phloem consists of tubular cells modified for translocation. These tubular cells have interconnected cytoplasm and they conduct other solutes, chiefly nutrients (e.g., carbohydrates) from areas of food production such as leaves to areas of food storage such as tubers. There are five types of cells in phloem. They are sieve tube elements, companion cells, parenchyma, fibers, and schlerids. Sieve tubes are long tube-like structures formed by the end to end fusion of sieve tube elements. Adjacent to the sieve tube elements lie the companion cells with dense cytoplasm. Phloem parenchyma is similar to the ordinary parenchyma cells and the phloem fibers are like the sclerenchyma fibers.

Dermal tissues include epidermis and cuticle. The epidermis is a continuous layer of tightly packed cells. It is usually coated with a cuticle of waxes embedded in a fatty substance; this is analogous to keratinized outer layer of skin, including your own, in animals that live on land. Leaf epidermis is perforated by stomata for gas exchange between the photosynthetic mesophyll (parenchyma) and the surrounding atmosphere. Thus, leaves function in part like lungs. All these tissue types-both simple and complex tissues-are distributed all over the plant parts, but their position and orientations are different in different organs like stem, roots, leaves flowers, fruits, etc.

Tags: Bio Technology, Bio Genetics , Plant Tissues

Friday, March 27, 2009

Know the Animal Tissues

In animals, there are four basic types of tissues: epithelial or linings, connective or supporting, muscular, and nervous. An organ of the body may have all the four types of tissues. For example, the stomach, an organ of the digestive system has all the four types of tissues.

Epithelial Tissues:
The cells are arranged in single or multilayered sheets. They basically form the covering on the external and internal surfaces of the organs and body parts. Epithelial cells are not supplied with blood vessels. They protect the internal tissues from physical injury and infection. The free surface of the epithelial tissue may be of different types depending on its special function such as secretory, absorption, or excretory functions. Epithelial cells are basically classified according to their shapes.

There are three basic cell shapes in epithelial tissues: columnar, cubical, and squamous (scale-like).

The deep columnar cells often have a secretory function, and the nucleus is pushed to the bottom by the made and stored secretions near the surface from which they will exit (e.g., the cells lining the stomach, which secrete mucus). Cubical cells form the walls of small ducts as from salivary glands. Squamous cells are very flat, and the nucleus may form a bulge; they look something like a fried egg. The thinness permits diffusion of molecules across membranes (e.g., alveolar walls in lungs). Thick layers of cells (e.g., skin) prevent diffusion. In addition to the above three basic types there are some modified forms of these tissues. They are the following. Ciliated epithelium, the columnar cells with numerous cilia on their free surface, which lines the respiratory passage. Psudostratified epithelium, which forms a single layer of cells but on sectional view appears to be multilayered. The last one is the stratified epithelium, which are multilayered and form a very tough and impervious barrier.

The secretory or glandular cells may be present individually as in the case of goblet cells or in groups forming multicellular glands. An epithelial tissue having many goblet cells that secrete mucus is called mucus membrane. If the glandular cells or glands discharge their secretion on the surface of the cells or through a duct, they are called exocrine glands. But there are glands that discharge their secretion directly into the bloodstream and do not have any ducts. They are called the ductless glands.

Connective Tissues:
This includes the various types of supporting tissues in the body. Connective tissues are cells in a matrix. The matrix may be a fluid, semi-fluid, or a composite structure made up of secretory products of cells such as fibrous proteins. Blood is a connective tissue in which cells are embedded in a fluid matrix. In fibrous connective tissue cells are scattered among the collagen fibers (fibrous protein) they secrete. In bone and cartilage, cells are scattered throughout the hard or pliable matrix. In cartilage, the cells known as chondroblasts deposit in the matrix. The cell, along with the matrix, forms the chondrocytes. The cartilage is hard but flexible because the matrix is compressible and elastic. Bone is a calcified connective tissue. The cells are embedded in a hard matrix. The cells in the bone tissue are called osteoblasts, which are present in lacunae. Lacunae are present throughout the tissue. The main inorganic component of bone is hydroxyapatite.

Muscle Tissues:
These are made up of highly differentiated contractile cells or fibers held together by connective tissues. Muscle tissues are of three types. Striated muscle cells are large, multinucleate, and column-shaped cells; they are chiefly attached to the skeleton and are known as skeletal muscles or voluntary muscles. Voluntary muscles are under the control of the voluntary nervous system. They show powerful rapid contractions. They are attached to the bones in the trunk, limbs, and head. Smooth muscle cells are small and mononucleate; they are found in the walls of tubes such as blood vessels, glandular ducts, and the digestive system. They are also known as unstriated or involuntary muscles. The involuntary muscles are under the control of the autonomic nervous system and show sustained rhythmical contraction and relaxation movements. Cardiac muscle cells of the heart are small, striated, and branched. They are present only in the heart. They show rapid rhythmical contractions and relaxation movements with long refractory periods and do not show any fatigue.

Nervous Tissues:
Nervous tissues consist of nerve cells, the neurons and associated neuroglial cells. Neurons are capable of generating and transmitting electrical impulses. These cells also act as supporting connective tissue in the brain and spinal cord. The neurons transmit the stimuli from receptors such as skin to the effectors such as muscles and glands that then react to the stimuli.

Tags: Bio Technology, Bio Genetics , Animal Tissues

Wednesday, March 18, 2009

What are the Basic Cell Structure and their components

Cells are structural and functional units of life. According to the cell theory all living things are composed of one or more cells. One-celled organisms are called unicellular organisms and those with more than one cell are called multi-cellular organisms. Virus particles do not have any cells and therefore, are termed as acellular. No matter what type of cell we are considering, all cells have certain features in common: cell membrane, nucleic acids, cytoplasm, and ribosomes. Cells are small 'sacks' composed mostly of water. The 'sacks' are made from a phospholipid bilayer. The membrane is semi-permeable, allowing some things to pass in or out of the cell and blocking others. Microscopes make it possible to magnify small objects such as cells in order to see the details of their structure. Both light and electron microscopes are used to study cells. Study of cells with a microscope is called cytology. There are some fundamental activities, which are common for most of cell types from bacteria to the nerve cells in humans. The study of these basic cellular processes is called cell biology.

Cells are 90% fluid (cytoplasm), which consists of free amino acids proteins, glucose, and numerous other molecules. The cell environment (i.e., the contents of the cytoplasm, and the nucleus, as well as the way the DNA is packed) affects the gene expression/ regulations, and thus is very important part of inheritance.

Cells basically fall into two groups: prokaryotic cells and eukaryotic cells.

Prokaryotes, Eukaryotes and Viruses: Cells are classified as prokaryotes or eukaryotes based on their basic structure and the way by which they obtain energy. Cells are also classified according to their need for energy. Autotrophs are "self feeders" that use light or chemical energy to make food. Plants are an example of autotrophs. In contrast, heterotrophs ("other feeders") obtain energy from other autotrophs or heterotrophs. Many bacteria an( animals are heterotrophs.

Prokaryotic Cells: Prokaryotes include bacteria and blue-green algae (cyanobacteria). Simply stated, prokaryotes are molecules surrounded by a membrane and cell wall. Prokaryotic cells lack characteristic eukaryotic subcellular membrane-enclosed "organelles," but may contain membrane systems inside a cell wall as an extension or infoldings of the cell membrane. The nucleus is not well-organized and is without any membrane.

Prokaryotic cells may have photosynthetic pigments, such as is found in cyanobacteria ("blue-green algae"). Some prokaryotic cells have external whiplike flagella for locomotion or hair-like pili for adhesion. Prokaryotic cells come in multiple shapes: cocci (round), baccilli (rods), and spirilla or spirochetes (helical cells). All prokaryotes are unicellular organisms and eukaryotes include both unicellular and multicellular organisms.

Eukaryotes : Basic Structure:
The basic eukaryotic cell contains the following: 1) A Plasma membrane2) Nucleus3) Cytoplasm (semifluid)

Viruses : Basic Characteristics of Viruses:
Simply stated, viruses are merely genetic information surrounded by a protein coat. They may contain external structures and a membrane. Viruses are obligate intracellular parasites meaning that they require host cells to reproduce. In the viral life cycle, a virus infects a cell, allowing the viral genetic information to direct the synthesis of new virus particles by the cell. There are many kinds of viruses. Those infecting humans include polio, influenza, herpes, smallpox, chickenpox, and human immunodeficiency virus (HIV) causing AIDS.

Tags: Bio Technology, Bio Genetics , Cell Structure

Understanding of Cell Membranes

Characteristics of Cell Membranes are as under:
1) Cell membranes are selective barriers that separate individual cells and cellular compartments.

2) Membranes are assemblies of carbohydrates, proteins, and lipids held together by non-covalent forces. They regulate the transport of molecules, control information flow between cells, generate signals to alter cell behavior, contain molecules responsible for cell adhesion in the formation of tissues, and can separate charged molecules for cell signaling and energy generation.

3) Cell membranes are dynamic, constantly being formed and degraded. Membrane vesicles move between cell organelles and the cell surface. Inability to degrade membrane components can lead to lysosomal storage diseases.

4) Lipids of cell membranes include phospholipids composed of glycerol, fatty acids, phosphates, and a hydrophobic organic derivative such as choline or phosphoinositol. Cholesterol is a lipid component of cell membranes that regulates membrane fluidity and is a part of membrane signaling systems. The lipids of membranes create a hydrophobic barrier between aqueous compartments of a cell. The major structure of the lipid portion of the membrane is a lipid bilayer with hydrophobic cores made up predominately of fatty acid chains and hydrophilic surfaces.

5) Membrane proteins determine functions of cell membranes, including serving as pumps, gates, receptors, cell adhesion molecules, energy transducers, and enzymes. Peripheral membrane proteins are associated with the surfaces of membranes while integral membrane proteins are embedded in the membrane and may pass through the lipid bilayer one or more times.

6) Carbohydrates covalently linked to proteins (glycoproteins) or lipids (glycolipids) are also a part of cell membranes, and function as adhesion and address loci for cells.

7) The Fluid Mosaic Model describes membranes as a fluid lipid bilayer with floating proteins and carbohydrates.

8) Cell junctions are a special set of proteins that anchor cells together (desmosomes), occlude water passing between cells (tight junctions), and allow cell-to-cell direct communication (gap junctions).

Tags: Bio Technology, Bio Genetics , Cell Structure

Sunday, March 8, 2009

What are the Various Types of Proteomics

Even though proteomics can be defined as the study of the protein complement of the genome, the dynamic nature of the proteome made it difficult to study and understand. The total protein expression profile always changes with time and micro- and macro-environmental conditions. Only a small percentage of the total gene is expressed at a particular time. Information about the genome and gene structure can predict the structure and function of its protein complement to a limited extent because of the post-transcriptional modifications that the protein undergoes. These modifications are not represented in the respective gene. This is what makes proteomics difficult to study compared to genomics.

The following are the major types of proteomics:

Expression Proteomics:
This is the qualitative and quantitative study of the expression of total proteins under two different conditions. For example, expression proteomics of normal cells and diseased cells can be compared to understand the protein that is responsible for the diseased state or the protein that is expressed due to disease. Using this method disease-specific protein can be identified and characterized by comparing the protein-expression profile of the entire proteome or of the subproteome between the two samples.

For example, tumor tissue samples from a cancer patient and the same type of tissue from a normal person can be analyzed for differential protein expression. Using two-dimensional gel electrophoresis, mass spectrometry combined with chromatography and microarray techniques, additional proteins that are expressed in the cancer tissues or the proteins, which are absent, or those, which are over expressed and under-expressed can be identified and characterized. Identification of these proteins will give valuable information about the molecular biology of tumor formation.

Structural Proteomics:
Structural proteomics, as the name indicates, is about the structural aspects, including the three-dimensional shape and structural complexities, of functional proteins. This includes the structural prediction of a protein when its amino acid sequence is determined directly by sequencing or from the gene with a method called homology modeling. This can be carried out by doing a homology search and computational methods of protein structural studies and predictions.

Apart from this, structural proteomics can map out the structure and function of protein complexes present in a specific cellular organelle. It is possible to identify all the proteins present in a complex system such as ribosomes, membranes, or other cellular organelles and to characterize or predict all the proteins and protein interactions that can be possible between these proteins and protein complexes. Structural proteomics of a specific organelle or protein complex can give information regarding supra-molecular assemblies and their molecular architecture in cells, organelles, and in molecular complexes.

Functional Proteomics:
This is an assembly type of proteomic method to analyze and understand the properties of macromolecular networks involved in the life activities of a cell. With these methods it will be possible to identify specific protein molecules and their role in individual metabolic activities and their contribution to the metabolic network that operates in the system. This forms one of the major objectives of functional proteomics. For example, the recent elucidation of the protein network involved in the functioning of a nuclear pore complex has led to the identification of novel proteins involved in the translocation of macromolecules between the cytoplasm and nucleus through these complex pores.

Functional proteomics is yielding large databases of interacting proteins, and extensive pathway maps of these interactions are being scored and deciphered by novel high-throughput technologies. However, traditional methods of screening have not been very successful in identifying protein-protein interactions and their inhibitors. The identification and measurement of changes in the concentration of specific proteins that cells make as a result of their genetic response to specific toxicants, and how these proteins are related to each other and to the specific biological condition of the cell, also fall under functional proteomics.

Tags: Bio Technology, Bio Genetics , Proteomics

Understanding Genes in Relation to Proteins

Owing to concerted efforts by numerous state and commercial establishments, the human genome had completely been sequenced in 2000. All 24 human chromosomes are mapped, and the defects of hundreds of genes responsible for the development of hereditary diseases have been revealed.

A new medical concept has been advanced whereby all diseases can be divided into two major groups:

(a) Hereditary diseases : A consequence of transmission of defective genes from parents to their children.

(b) Non-heritable diseases: Or so called socially-significant diseases, which make up more than 95% of all human diseases and result from disturbances in normal genes' expression regulation. Thus, all human diseases, one way or another, are associated with the genome; the only difference is that the diseases of the former group are due to a defect(s) in gene's structure while those of the latter group are caused by disturbances in a gene expression's regulation. The cataloging of human genes is an achievement, which can hardly be overestimated: for many years to come this catalogization will serve as a basis for the development of basic biochemistry, molecular biology, and genome-associated applied sciences. The future of this area of research, called genomics, is even more brilliant. Currently, the emphasis has gone from sequencing the human genome to sequencing the genomes of animals and microorganisms, particularly pathogenic and plant genomes. This research promises enormous achievements in medicine, especially in the struggle against infectious diseases.

How is the informational structure (gene) connected with the actual working molecular machine (protein)?

To answer this question, we have to consider the results of those few works, where the expression map of mRNA was compared with the proteinous map in the same cellular system. It failed to reveal any strict correlation between the two maps. Thus, the informational knowledge cannot be directly converted into the knowledge of actually operating protein molecules. As a result, a new area of research has appeared, called proteomics, which deals with inventory of proteins. At first glance, this is an utterly impossible task. While the human genome map is the same for all human cells (24 chromosomes), in the proteomic map each cell is individual. Although the cell may have only 33,000 functional genes, the numerous modification reactions may increase the number of proteins in it up to several million. There are two definitions for proteomics: a narrow one (the so-called structural proteomics) and a broader one, encompassing both the structural and functional proteomics. In a narrow sense of the word, 'proteomics' is a science dealing with the cataloging of proteins based on a combination of several methods: two-dimensional electrophoresis, mass spectrometric analysis of molecular mass, and sequencing of electrophoretically separated proteinacious biological material with subsequent analysis of the results obtained, with the help of bioinformatical and computational methods.

In a broader sense, the terms 'proteome analysis' or 'proteomics' can be used not only for cataloging proteins of a biological subject but also for the monitoring of reversible post-translational modification of proteins by specific enzymes (i.e., phosphorylation, glycosylation, acylation, phrenylation, su1furization, etc). To date, more than 300 different types of post-translational modification have been characterized with the aid of proteomics. Another aspect of functional proteomics is to clarify the composition of functionally active complexes that constitute different metabolic chains and also, to determine the interactions between various proteins or subunits of oligomeric complexes by a combination of methods to isolate these complexes and subsequent mass-spectrometric analysis. Lately, structural proteomics is often called expressional proteomics while functional proteomics is also designated as cell-mapping proteomics, since it elucidates the interactions of proteins within metabolic pathways. Therefore, in short, the number of proteins and the number of genes are not equal and they are non-linear. The number of proteins easily outnumbers the number of genes.

Tags: Bio Technology, Bio Genetics , Proteins

Saturday, March 7, 2009

Understanding Proteomics

Proteomics permits genome-wide expression profiling providing a vital information required to describe how a cell functions, and gives an insight into the development of diseases.

Out of the two methods of genome-wide analysis, proteomics, the examination of the complete set of proteins synthesized by a cell under a given set of physiological or developmental conditions, should be most informative when making functional assignments. This is mainly due to the fact that the proteome is context-dependent and unlike mRNAs, proteins are functional entities within the cell. The proteome is the proteins expressed by a genome.

Proteomics involve the analysis of a large number of proteins with a combination of two-dimensional gel electrophoresis and mass spectrometry. Today, it includes both the identification of a large number of proteins expressed by a genome as well as the characterization of their functional and structural relationships. It was thought that a single gene would result in the formation of a single protein or polypeptide. But there are different stages in the process of transcription and translation, where the same process can take place but produces a different protein. These processes can take place just after the process of transcription-the post-transcriptional process that can result in different types of mRNAs with the control of splicing mechanisms. The second point where the alteration can occur is after the process of translation or protein synthesis. This is the post-translational modification which can also produce structurally and functionally different proteins from the same gene.

Proteomics also deals with the use of qualitative and quantitative protein-level measurements to characterize biological processes (e.g., diseases). By comparing the protein profiles from normal cells and diseased or metabolically aberrant cells, the reason for the diseased condition can be ascertained. Therefore, diseases can be treated at the protein level or even at the gene level because the proteins are the drug targets.

The Key Technologies in Proteomics
1) Reproducible Two-dimensional Gel Technology
2) Staining and Scanning Technology
3) Mass Spectrometry for Identification
4) Databases (protein and genome)
5) Database Searching Algorithms

The crude protein extracted from the tissue sample or cells or from individuals is separated in gel by two-dimensional electrophoresis comprising of IEF and SDS-PAGE. The gel is suitably stained and compared with that of the standard two-dimensional gel profile of protein from the same organisms grown under normal conditions (or healthy individuals). If the formation of any new protein is observed that spot can be excised from the gel along with the gel matrix and washed with sterile distilled water. This protein spot along with the gel can be digested with trypsin and then introduced into the mass spectrometer and (the MS fingerprint can be taken). The MS fingerprint can be used for the identification of the protein by database search or can proceed further to carry out amino acid sequencing by mass spectrometer. Thus, the protein purification and identification become very easy and simple. But the key challenge in proteome research is the automation and integration of these technologies.

Tags: Bio Technology, Bio Genetics , Proteomics

How to Improve the Nutritional Value of Cereals and legumes

In human nutrition, cereals and legumes provide a major part of the dietary protein requirement. The storage proteins of these seeds are a good source of essential amino acids. But some of these legumes and cereals create deficiency of some essential amino acids and therefore such cereals and legumes are considered to be poor in quality, even though they are rich sources of dietary protein. They cannot provide a balanced diet. In such cases the diet should be supplemented with other sources of essential amino acids. In some other cases certain rich sources of protein may not be suitable for human consumption because of toxicity, a bad quality such as bad smell, taste, etc. Thus, protein for human consumption should be safe and nutritious.

The major parameters for assessing the general effectiveness of a protein as a dietary protein are the Essential Amino Acids Profile (EAAP), Biological Value (BV), and Protein Efficiency Ratio (PER).

Essential Amino Acids :
Proteins are composed of 20 amino acids. Plants and microbes can synthesize all these amino acids, but animals cannot. Such amino acids have to be supplemented through the diet. Such amino acids are the essential amino acids. The presence of a high percentage of essential amino acids along with other amino acids increases the nutritive quality of protein for human consumption.

The nutritive quality of whey proteins is considered to be higher compared to other types of proteins. They are rich in branched chain amino acids-Ile, leu, val, lys and trp. The branched chain amino acid (BCAA) is needed for rapid energy metabolism for muscular activity. BCAA helps in the bio-availability of complex carbohydrates absorbed by muscle cells for anabolic muscle building activity. BCAA plays an important role in the production of metabolic energy during rapid muscular actions. During exercise BCAAs are released from the muscle cells. The carbon chain part of the molecule is used as fuel and the nitrogen part is used to synthesize alanine. Alanine is transported to the liver where it is turned into glucose to meet the energy requirements. So athletes are advised to take BCAA sources before and after exercises to protect their healthy body. Thus, BCAAs are very important for muscle growth and muscular activity.

Biological Value :
Biological value or BV is a measure of protein nitrogen retained by the body after consuming a particular amount of protein nitrogen. Among various types of dietary proteins whey protein showed the maximum BV compared to rice, soy, egg, and wheat proteins.

Protein Efficiency Ratio:
Protein efficiency ratio or PER is a measure of the efficiency of a protein on the rate of growth. It is the growth performance in terms of weight gain of an adult by consuming 1 gm of dietary protein. The order of PER for various dietary proteins is given below.

Wheat protein :
The quality of protein can be improved by the modem approach of protein engineering through recombinant DNA technology. The storage protein of cereals and legumes can be modified by introducing essential amino acids. These genes can be transferred to food plants to be expressed in the respective storage parts of the plants such as seeds, tubers, or grains. Modifications in proteins can be made by introducing new amino acids or by substituting the existing amino acids with new ones. Efforts are already being made to enhance the nutritive quality of protein genes in maize and other similar food grains. Scientists are on the look out for new types of dietary protein genes that are rich in essential amino acids, with which the nutritive quality of other plants can be increased.

Tags: Bio Technology, Bio Genetics ,Protein Designing

Art of Designing of Proteins

Protein design is important because it not only allows us to systematically investigate the forces that determine structure and stability but it also affords the possibility of creating proteins through novel and useful activities. The biotechnological industry is more interested in developing new types of enzymes, which are stable and more active under extreme working conditions such as high temperature and extreme pH such as acidic or alkaline pH.

Biochemists can now use a refinement of the genetic modification technique to redesign proteins. Once they have isolated the gene for a particular protein they can alter its code so that a change occurs in the protein's primary structure. They then incorporate the modified gene into a microorganism where it is decoded as before, but this time a new protein appears. Swapping one a-amino add in a protein can have a large effect on how the protein behaves. Biochemists have already used this protein engineering to modify human insulin in a way that makes it become absorbed more quickly after injection. Multiple changes are needed to 'humanize' antibodies.

Computer-modeling techniques allow protein chemists to make predictions about how proposed a-amino acid changes might change the structure and activity of a protein. Genetic and protein modification have enormous potential. Besides insulin, genetic modification can produce human growth hormone and the blood clotting factor VIII. Genetic engineering, thus, has provided a tool to produce designer proteins having special characteristics by changing the amino acid sequence. In addition, it is already possible to introduce into a plant new genes that enable it to produce its own protein insecticide or that make it resistant to disease. Hepatitis B vaccine, oil-digesting bacteria, and bacteria that produce biodegradable plastic are all recently developed products of protein engineering and genetic-modification techniques.

Creation of Novel Proteins: Vaccines are traditionally prepared from heat-inactivated microbes-bacteria or viruses or the surface proteins of these organisms to immunize against various infectious diseases. But in some cases it was frequently observed that some parts or components of the vaccines were creating some deleterious effects on people. It is known that proteins are the main candidates responsible for imparting the stimulus for immunity. Therefore, efforts have been made to design an altered protein molecule, which can produce only very little deleterious effects. There are some amino acid sequences, which are directly involved in the stimulation of immunity and that part of the protein or polypeptide is known as epitopes. A recombinant vaccine can be designed by involving only the essential epitopes in the immune response. Such vaccines will be very simple and will be safe without reducing their effectiveness. Safe vaccines against the hepatitis B virus and anthrax bacteria are under development.

Tags: Bio Technology, Bio Genetics ,Protein Designing