Anatomy, The human eyeball, the organ responsible for the sense of sight, is a very complex structure. We use our vision in almost every activity, so the eye is one of the most important organs in the body.
How it works Sight begins when light rays from an object enter the eye through the cornea, the clear front “window” of the eyeball. The cornea is actually responsible for about sixty percent of the eyeball’s light-ray-bending capability. The cornea’s refractive power bends the light rays in such a way that they pass freely through the pupil, the size-changing hole in the iris.
The iris, the structure that gives the eye color, works like a shutter in a camera. It has the ability to enlarge and shrink, depending on how much light the environment is sending into the eye. After passing through the iris, the light rays strike the eye’s crystalline lens. This clear, flexible structure works much like the lens in a camera – shortening and lengthening its width in order to focus light rays properly.
In a normal eye, after exiting the back of the lens, the light rays pass through the vitreous -- a clear, jelly-like substance that fills the globe of the eyeball. The vitreous humor helps the eye hold its spherical shape.
Finally, the light rays land and come to a sharp focusing point on the retina. Continuing with our “camera” analogy, the retina’s function is much like the film in a camera. It is responsible for capturing all of the light rays, processing them into light impulses through millions of tiny nerve endings, then sending these light impulses through over a million nerve fibers to the optic nerve.
Saturday, December 13, 2008
indian human rights (women)
The year 2000 marked the fifth anniversary of the U.N.'s Fourth World Conference on Women in Beijing, China, an event that heralded respect for women's human rights as a central part of any and all efforts to improve women's status around the globe. Five years later, what gains did women see in government efforts to protect their rights? Activists welcomed important signs of progress, including greater awareness of abuses of women's human rights; stronger international standards for prosecuting violence against women, particularly in conflict situations; and some initial efforts by governments and international actors to implement programs to support women's rights. Still, these steps forward seemed few and far between, especially when contrasted with the scale and scope of ongoing violations of women's most fundamental human rights.
One of the most striking developments in the past year-evident in June 2000 in the negotiations at the special sessions of the U.N. General Assembly for the Beijing + 5 Review (Beijing + 5) to assess progress in improving women's status-was how actively some governments were willing to work to thwart recent gains in protecting women's human rights. They set out to master the language of women's human rights while they at the same time sought to undermine the power of the idea and the movement. Perhaps a sign that they had started taking women's rights activists seriously, governments' resistance to further progress on women's human rights took several forms, although most of the obstructionist tactics at the U.N. meeting and elsewhere relied on the age-old strategy of divide and conquer.
First, and perhaps most threatening, was the refusal of governments to accept that for women to truly enjoy their human rights, they must be treated with dignity in all aspects of their lives. Instead, government actions reflected the belief that women are not entitled to full enjoyment of their human rights. Hence, while governments condemned some forms of violence against women, they readily excused others and defended laws
that denied women their legal rights. In Morocco, for example, a reformist government pledged to pursue programs to measure and respond to violence against women, but allowed proposed reforms to the country's family code-which continues to subject female decision-making to male authority-to languish. In other countries, laws that recognized men as the legal heads of households remained in place, denying women's rights to decide for themselves, freely, whether and whom to marry, whether to work outside the home, or even when to seek medical attention. Laws requiring female obedience or subservience were often key to making women dependent on men and tied to abusive relationships.
One of the most striking developments in the past year-evident in June 2000 in the negotiations at the special sessions of the U.N. General Assembly for the Beijing + 5 Review (Beijing + 5) to assess progress in improving women's status-was how actively some governments were willing to work to thwart recent gains in protecting women's human rights. They set out to master the language of women's human rights while they at the same time sought to undermine the power of the idea and the movement. Perhaps a sign that they had started taking women's rights activists seriously, governments' resistance to further progress on women's human rights took several forms, although most of the obstructionist tactics at the U.N. meeting and elsewhere relied on the age-old strategy of divide and conquer.
First, and perhaps most threatening, was the refusal of governments to accept that for women to truly enjoy their human rights, they must be treated with dignity in all aspects of their lives. Instead, government actions reflected the belief that women are not entitled to full enjoyment of their human rights. Hence, while governments condemned some forms of violence against women, they readily excused others and defended laws
that denied women their legal rights. In Morocco, for example, a reformist government pledged to pursue programs to measure and respond to violence against women, but allowed proposed reforms to the country's family code-which continues to subject female decision-making to male authority-to languish. In other countries, laws that recognized men as the legal heads of households remained in place, denying women's rights to decide for themselves, freely, whether and whom to marry, whether to work outside the home, or even when to seek medical attention. Laws requiring female obedience or subservience were often key to making women dependent on men and tied to abusive relationships.
Types of tobacco
Flue-cured is also known as "Bright" and "Virginia" by the world trade. It is used almost entirely in cigarette blends. Some of the heavier leaves may be used in mixtures for pipe smoking. Some English cigarettes are 100% flue-cured.Flue-cured leaf is characterized by a high sugar: nitrogen ratio. This ratio is enhanced by the picking of the leaf in an advanced stage of ripeness, and by the unique curing process which allows certain chemical changes to occur in the leaf.
Cured leaves vary from lemon to orange to mahogany in color. The leaves are relatively large with the largest at midstalk. A well grown plant will be topped at a height of 39 to 51 inches with 18-22 harvestable leaves. Yields average around 2200 lbs/A with some in excess of 3000 lbs/A. The leaves are harvested as they mature from the ground up.Flue-cured tobacco is grown in approximately 75 countries from New Zealand to Germany. Major producers in the world are: China, USA, Brazil, India and Zimbabwe. The major exporters are the U.S., Brazil, India and Zimbabwe.
Flue-cured is grown in six states in the U.S. - Virginia, North Carolina, South Carolina, Georgia and Florida. A very small amount is in Alabama.Burley is light air-cured type derived from the White Burley which arose as a mutant on a farm in Ohio in 1864. Burley is used primarily in cigarette blends. Some of the heavier leaf is sued in pipe blends and also for chewing.Cured burley leaf is characterized by low sugar content and a very low sugar to nitrogen ratio (high nicotine). This is enhanced by high N. fertilizer, harvesting at an early stage of senescence, and the air curing process which allows oxidation of any sugars which may have occurred. Burley has a tremendous capacity to absorb flavorings (25% of its own weight vs. 7-8% for flue-cured).Cured leaves vary in color from light tan to reddish and brown. The leaf should be without yellow patches or fringes.
Crops in the field are light green in color. This is particularly true for the midrib and stalk which are creamy- white. The leaves are slightly larger than flue-cured and the plants are generally taller. A typical plant is topped at 20-30 leaves. Average yields are 2500-3000 lbs/a and the plants are stalk cut. The leaves are stripped after curing.
Burley is produced in around 55 countries but only a small amounts in over 1/2 of these. The main producers and trades are the U.S., Italy, Korea, Brazil, and Mexico. In the U.S. production is in Kentucky, Tennessee, Ohio, Virginia, North Carolina, West Virginia and Missouri
Cured leaves vary from lemon to orange to mahogany in color. The leaves are relatively large with the largest at midstalk. A well grown plant will be topped at a height of 39 to 51 inches with 18-22 harvestable leaves. Yields average around 2200 lbs/A with some in excess of 3000 lbs/A. The leaves are harvested as they mature from the ground up.Flue-cured tobacco is grown in approximately 75 countries from New Zealand to Germany. Major producers in the world are: China, USA, Brazil, India and Zimbabwe. The major exporters are the U.S., Brazil, India and Zimbabwe.
Flue-cured is grown in six states in the U.S. - Virginia, North Carolina, South Carolina, Georgia and Florida. A very small amount is in Alabama.Burley is light air-cured type derived from the White Burley which arose as a mutant on a farm in Ohio in 1864. Burley is used primarily in cigarette blends. Some of the heavier leaf is sued in pipe blends and also for chewing.Cured burley leaf is characterized by low sugar content and a very low sugar to nitrogen ratio (high nicotine). This is enhanced by high N. fertilizer, harvesting at an early stage of senescence, and the air curing process which allows oxidation of any sugars which may have occurred. Burley has a tremendous capacity to absorb flavorings (25% of its own weight vs. 7-8% for flue-cured).Cured leaves vary in color from light tan to reddish and brown. The leaf should be without yellow patches or fringes.
Crops in the field are light green in color. This is particularly true for the midrib and stalk which are creamy- white. The leaves are slightly larger than flue-cured and the plants are generally taller. A typical plant is topped at 20-30 leaves. Average yields are 2500-3000 lbs/a and the plants are stalk cut. The leaves are stripped after curing.
Burley is produced in around 55 countries but only a small amounts in over 1/2 of these. The main producers and trades are the U.S., Italy, Korea, Brazil, and Mexico. In the U.S. production is in Kentucky, Tennessee, Ohio, Virginia, North Carolina, West Virginia and Missouri
china river
After the celebrations over reopening border trade at Nathu La, a distinct dampener is the news that China is building a hydroelectric power station in western Tibet.The project involves storing the waters of the Sutlej River as it flows into Himachal Pradesh.China says building of the hydroelectric station on the Sutlej River in Tibet and this will not affect flows to India. But experts in India warn that with the Himalayan lakes drying up, India cannot afford to allow China to dam upstream rivers.
"In future it would be much more critical because most of the lakes, streams are in the upper reaches and any construction in this area would have implications for India's security in the long run," China specialist Srikanth Kondapalli said.The hydro power station has been under construction over the last three years in Zenda in Tibet, which is directly opposite Ladakh and Himachal Pradesh.
Experts say China has built as many as 13 barrages in the area over the last many years.But the concern is that in the long term, as the demand for water increases in China and India, these barrages could interfere with the flow of waters into India It is not clear if India has taken up the issue with China as the foreign office is refusing to clarify. But experts say it is not too late to do something even now.
The 1984 Peace and Tranquility Agreement and the 1986 Confidence Building Agreement are very comprehensive in terms of both sides abiding by norms and regulations. So it is possible for India to push through some kind of understanding over the Sutlej," says Srikanth Kondapalli.China is also reported to be building similar barrages that would dam the Brahmaputra before it enters India in Assam.
"In future it would be much more critical because most of the lakes, streams are in the upper reaches and any construction in this area would have implications for India's security in the long run," China specialist Srikanth Kondapalli said.The hydro power station has been under construction over the last three years in Zenda in Tibet, which is directly opposite Ladakh and Himachal Pradesh.
Experts say China has built as many as 13 barrages in the area over the last many years.But the concern is that in the long term, as the demand for water increases in China and India, these barrages could interfere with the flow of waters into India It is not clear if India has taken up the issue with China as the foreign office is refusing to clarify. But experts say it is not too late to do something even now.
The 1984 Peace and Tranquility Agreement and the 1986 Confidence Building Agreement are very comprehensive in terms of both sides abiding by norms and regulations. So it is possible for India to push through some kind of understanding over the Sutlej," says Srikanth Kondapalli.China is also reported to be building similar barrages that would dam the Brahmaputra before it enters India in Assam.
Blood alcohol
Blood alcohol (or blood alcohol concentration), often abbreviated BAC, is the concentration of alcohol in blood, measured, by volume, as a percentage. For example, a BAC rating of 0.20 means 1 part per 500 in an individual's blood is alcohol. In many countries, the BAC is measured and reported as milligrams of alcohol per 100 milliliters of blood (mg/100ml).
Number of drinks consumed is a poor measure of intoxication, because of variation according to body weight. One drink (unit of alcohol) will increase the average person's BAC to roughly 0.04, but there is much variation according to body weight, gender and body fat percentage. Furthermore, neither BAC nor the number of drinks consumed are necessarily accurate indicators of the level of impairment. Individual alcohol tolerance varies, and can be affected by genetic or nutritional factors, drugs, other degrees of impairment, and long-term heavy drinking.
Alcohol content in blood can be directly measured by a hospital laboratory. More commonly, for law enforcement purposes, BAC is estimated from breath ethanol content measured with a machine commonly referred to as a Breathalyzer (even though that is just the trademark of one manufacturer of the devices). For purposes of law enforcement, BAC is used to define intoxication and provides a rough measure of impairment. Although degree of impairment may vary among individuals with the same BAC, the BAC has the advantage of being simpler to measure objectively, and therefore harder to contest, than impairment of driving.
Most countries disallow operation of motor vehicles and heavy machinery at prescribed levels of BAC, which vary both by country and by situation. In Sweden, driving with a BAC rate of over 0.02 is illegal. By contrast, the policies of the United States have historically been more liberal; however as of 2004, 47 States and the District of Columbia had adopted a BAC of .08. As of 2005, all states in the US have adopted a BAC of 0.08. In some states, drivers under 21 (the American drinking age) are considered legally impaired at lower levels (perhaps 0.02, or even a mere trace) as part of a zero tolerance policy.
Unless a person has developed a high tolerance, a BAC rating of 0.20 represents very serious intoxication (most first-time drinkers would be passed out by about 0.15), and 0.35 represents potentially fatal alcohol poisoning. 0.40 is the accepted LD50, or lethal dose for 50% of adult humans. For a long-time, heavy drinker, those numbers can at least double. In extreme cases, individuals have survived BAC ratings as high as 0.914, but only with medical attention.
Number of drinks consumed is a poor measure of intoxication, because of variation according to body weight. One drink (unit of alcohol) will increase the average person's BAC to roughly 0.04, but there is much variation according to body weight, gender and body fat percentage. Furthermore, neither BAC nor the number of drinks consumed are necessarily accurate indicators of the level of impairment. Individual alcohol tolerance varies, and can be affected by genetic or nutritional factors, drugs, other degrees of impairment, and long-term heavy drinking.
Alcohol content in blood can be directly measured by a hospital laboratory. More commonly, for law enforcement purposes, BAC is estimated from breath ethanol content measured with a machine commonly referred to as a Breathalyzer (even though that is just the trademark of one manufacturer of the devices). For purposes of law enforcement, BAC is used to define intoxication and provides a rough measure of impairment. Although degree of impairment may vary among individuals with the same BAC, the BAC has the advantage of being simpler to measure objectively, and therefore harder to contest, than impairment of driving.
Most countries disallow operation of motor vehicles and heavy machinery at prescribed levels of BAC, which vary both by country and by situation. In Sweden, driving with a BAC rate of over 0.02 is illegal. By contrast, the policies of the United States have historically been more liberal; however as of 2004, 47 States and the District of Columbia had adopted a BAC of .08. As of 2005, all states in the US have adopted a BAC of 0.08. In some states, drivers under 21 (the American drinking age) are considered legally impaired at lower levels (perhaps 0.02, or even a mere trace) as part of a zero tolerance policy.
Unless a person has developed a high tolerance, a BAC rating of 0.20 represents very serious intoxication (most first-time drinkers would be passed out by about 0.15), and 0.35 represents potentially fatal alcohol poisoning. 0.40 is the accepted LD50, or lethal dose for 50% of adult humans. For a long-time, heavy drinker, those numbers can at least double. In extreme cases, individuals have survived BAC ratings as high as 0.914, but only with medical attention.
arts and crafts
Arts and crafts comprise a whole host of activities and hobbies that are related to making things with one's own hands and skill. These can be sub-divided into handicrafts or "traditional crafts" (doing things the old way) and "the rest". Some crafts have been practised for centuries, while others are modern inventions, or popularisations of crafts which were originally practised in a very small geographic area.
Most crafts require a combination of skill, speed, and patience, but they can also be learnt on a more basic level by virtually anyone. Many community centres and schools run evening or day classes and workshops offering to teach basic craft skills in a short period of time. Many of these crafts become extremely popular for brief periods of time (a few months, or a few years), spreading rapidly among the crafting population as everyone emulates the first examples, then their popularity wanes until a later resurgence.
Arts and crafts also refers to the Arts and Crafts movement, a late 19th century design reform and social movement. Its proponents were motivated by the ideals of William Morris and John Ruskin, who proposed that in pre-industrial societies, such as the European Middle Ages, people had achieved fulfillment through the creative process of handicrafts. This was held up in contrast to what was perceived to be the alienating effects of industrial labour.
These activities are called crafts because originally many of them were professions under the guild system. Adolescents were apprenticed to a master-craftsman, and they refined their skills over a period of years in exchange for low wages. By the time their training was complete, they were well-equipped to set up in trade for themselves, earning their living with the skill that could be traded directly within the community, often for goods and services. The Industrial Revolution and the increasing mechanisation of production processes gradually reduced or eliminated many of the roles professional craftspeople played, and today "crafts" are most commonly seen as a form of hobby or art.
Most crafts require a combination of skill, speed, and patience, but they can also be learnt on a more basic level by virtually anyone. Many community centres and schools run evening or day classes and workshops offering to teach basic craft skills in a short period of time. Many of these crafts become extremely popular for brief periods of time (a few months, or a few years), spreading rapidly among the crafting population as everyone emulates the first examples, then their popularity wanes until a later resurgence.
Arts and crafts also refers to the Arts and Crafts movement, a late 19th century design reform and social movement. Its proponents were motivated by the ideals of William Morris and John Ruskin, who proposed that in pre-industrial societies, such as the European Middle Ages, people had achieved fulfillment through the creative process of handicrafts. This was held up in contrast to what was perceived to be the alienating effects of industrial labour.
These activities are called crafts because originally many of them were professions under the guild system. Adolescents were apprenticed to a master-craftsman, and they refined their skills over a period of years in exchange for low wages. By the time their training was complete, they were well-equipped to set up in trade for themselves, earning their living with the skill that could be traded directly within the community, often for goods and services. The Industrial Revolution and the increasing mechanisation of production processes gradually reduced or eliminated many of the roles professional craftspeople played, and today "crafts" are most commonly seen as a form of hobby or art.
phylogenetic tree
A phylogenetic tree is a graphical representation of the evolutionary relationship between taxonomic groups. The term phylogeny refers to the evolution or historical development of a plant or animal species, or even a human tribe or similar group. Taxonomy is the system of classifying plants and animals by grouping them into categories according to their similarities. A phylogenetic tree is a specific type of cladogram where the branch lengths are proportional to the predicted or hypothetical evolutionary time between organisms or sequences.
Cladograms are branched diagrams, similar in appearance to family trees, that illustrate patterns of relatedness where the branch lengths are not necessarily proportional to the evolutionary time between related organisms or sequences. Bioinformaticians produce cladograms representing relationships between sequences, either DNA sequences or amino acid sequences. However, cladograms can rely on many types of data to show the relatedness of species. In addition to sequence homology information, comparative embryology, fossil records and comparative anatomy are all examples of the types of data used to classify species into phylogenic taxa. So, it is important to understand that the cladograms generated by bioinformatics tools are primarily based on sequence data alone. Given that, it is also true that sequence relatedness can be very powerful as a predictor of the relatedness of species.
Cladograms cannot be considered completely true and accurate descriptions of the evolutionary history of organisms, because in any cladogram there are a number of possible evolutionary pathways that could produce the pattern of relatedness illustrated in the cladogram. The cladogram only illustrates the probability that two organisms, or sequences, are more closely related to each other than to a third organism, it does not necessarily clarify the pathway that created the existing relationships. However, the cladogram can be used in the formulation of new hypotheses and to cast new light on existing data. One of the most ambitious cladograms produced to date can be viewed at the tree of life website, originated by david and wason at the University of Arizona
(1) . Please take a moment to view the "Root of the Tree" link on the Tree of Life web site. In this phylogenetic tree, the root is at the far left, termed the root of the cladogram because it is at the base of the cladogram, opposite the branches. Return to the home page and click on the link entitled "Popular Pages", then select "Mammals". At the right side of this cladogram are the terminal nodes, located at the tip of the branches in any cladogram.In the Mammalia cladogram illustrated here, there are six terminal nodes, labeled Triconodonts, Monotremata, Multituberculata, Marsupialia, Palaeoryctoids, and Eutheria.An internal node is a hypothetical common ancestor. The branching points between the root and the terminal nodes are internal nodes. Each internal node is also at the base of a clade, which includes the common ancestral node plus all its descendents. Sample a few more links on the Tree of Life. Be sure to read Darwin's quote on the home page and ponder how difficult it would be to get published in a scientific journal today, if it were necessary to write this beautifully in order to succeed.The Tree of Life is an example of a cladogram illustrating the relationships between taxa, based on the collective evidence from many different fields of biology and bioscience. In contrast, the subject of this tutorial is the construction of cladograms through bioinformatics tools, where the cladograms are based on sequence data. First, use the billogy workbench
(2) 2) to build a simple unrooted cladogram. The Workbench will require a password (it's free), but it will grant entrance immediately upon registration of a password. Enter the site, and scroll down the page until the five menu buttons are visible.The "Session Tools" button allows the naming of a session, so that different jobs in progress can be saved under distinct sessions. Select "Session Tools", then select "Start New Session" and click on "Run" to change the name of "Default Session" to a new name. Once the workbench has been exited, the session will remain. Subsequently, clicking on the dot to the left of the session name under the "Session Tools" menu, and then selecting "Resume Session", will recall the session. The Workbench policy at the time of this writing is that old jobs are deleted only when an account has not been accessed for 6 months.
Next, select "Protein Tools" from the menu buttons, highlight "Ndjinn Multiple Database Search", and click "Run". In the query box to the right of the term "Contains", type HSP70, for the molecular chaperone, heat shock protein 70 kDa. Scroll down the database list and check the box to the left of the database entitled "PDBFINDER" before hitting the "Search" button. Among the results, find 2BUP, chaperone, and check the box to the left. Then select the menu button entitled "Import sequence(s)". This will import the sequence in fastA format into the open session. Now, under the box of session options, there should be a listing for the 2BUP sequence, with a small box to the left. Notice that the main menu under "Protein Tools" allows more options such as "Delete Protein Sequence", "Copy Protein Sequence" and "Add New Protein Sequences".
For now, select the "Ndjinn Multiple Database Search" again. Search the PDBFINDER Database again by scrolling down the page and selecting it, but this time, just search using the PDB ID codes 1HKB, 1ATN and 1DKG for hexokinase, actin and the molecular chaperone DnaK (use the OR operator between each PDB ID code to search for all three in the same search). Import all three sequences simultaneously by checking the box to the left of the PDB ID codes used in the query and clicking on "Import sequence(s)". 1DKG will return three chains, A, B and D. Only chain D is the molecular chaperone, chains A and B are nucleotide exchange factors that co-crystallized with DnaK. Delete chains A and B by checking the box to the left of 1DKG_A and 1DKG_B, highlighting "Delete Protein Sequence", and clicking on "Run". Actin (1ATN) returns two chains, but chain A is the actin, chain D should be deleted in the same manner.
Hexokinase (also called phosphotransferase) will return two chains as well. They are both hexokinase, but two identical sequences are not desirable in the cladogram, so delete chain B. Four sequences should remain, 1DKG_D, 1ATN_A, 1HKB_A, and 2BUP_A; check the boxes to the left of each of these. Scroll down the protein tools menu and highlight "CLUSTALW - Multiple Sequence Alignment", then click "Run". The default parameters will be sufficient for our purposes, just select "Submit". When the sequence alignment is returned, scroll down the page and view the multiple alignment. The Workbench automatically returns an unrooted tree with the alignment.
Cladograms are branched diagrams, similar in appearance to family trees, that illustrate patterns of relatedness where the branch lengths are not necessarily proportional to the evolutionary time between related organisms or sequences. Bioinformaticians produce cladograms representing relationships between sequences, either DNA sequences or amino acid sequences. However, cladograms can rely on many types of data to show the relatedness of species. In addition to sequence homology information, comparative embryology, fossil records and comparative anatomy are all examples of the types of data used to classify species into phylogenic taxa. So, it is important to understand that the cladograms generated by bioinformatics tools are primarily based on sequence data alone. Given that, it is also true that sequence relatedness can be very powerful as a predictor of the relatedness of species.
Cladograms cannot be considered completely true and accurate descriptions of the evolutionary history of organisms, because in any cladogram there are a number of possible evolutionary pathways that could produce the pattern of relatedness illustrated in the cladogram. The cladogram only illustrates the probability that two organisms, or sequences, are more closely related to each other than to a third organism, it does not necessarily clarify the pathway that created the existing relationships. However, the cladogram can be used in the formulation of new hypotheses and to cast new light on existing data. One of the most ambitious cladograms produced to date can be viewed at the tree of life website, originated by david and wason at the University of Arizona
(1) . Please take a moment to view the "Root of the Tree" link on the Tree of Life web site. In this phylogenetic tree, the root is at the far left, termed the root of the cladogram because it is at the base of the cladogram, opposite the branches. Return to the home page and click on the link entitled "Popular Pages", then select "Mammals". At the right side of this cladogram are the terminal nodes, located at the tip of the branches in any cladogram.In the Mammalia cladogram illustrated here, there are six terminal nodes, labeled Triconodonts, Monotremata, Multituberculata, Marsupialia, Palaeoryctoids, and Eutheria.An internal node is a hypothetical common ancestor. The branching points between the root and the terminal nodes are internal nodes. Each internal node is also at the base of a clade, which includes the common ancestral node plus all its descendents. Sample a few more links on the Tree of Life. Be sure to read Darwin's quote on the home page and ponder how difficult it would be to get published in a scientific journal today, if it were necessary to write this beautifully in order to succeed.The Tree of Life is an example of a cladogram illustrating the relationships between taxa, based on the collective evidence from many different fields of biology and bioscience. In contrast, the subject of this tutorial is the construction of cladograms through bioinformatics tools, where the cladograms are based on sequence data. First, use the billogy workbench
(2) 2) to build a simple unrooted cladogram. The Workbench will require a password (it's free), but it will grant entrance immediately upon registration of a password. Enter the site, and scroll down the page until the five menu buttons are visible.The "Session Tools" button allows the naming of a session, so that different jobs in progress can be saved under distinct sessions. Select "Session Tools", then select "Start New Session" and click on "Run" to change the name of "Default Session" to a new name. Once the workbench has been exited, the session will remain. Subsequently, clicking on the dot to the left of the session name under the "Session Tools" menu, and then selecting "Resume Session", will recall the session. The Workbench policy at the time of this writing is that old jobs are deleted only when an account has not been accessed for 6 months.
Next, select "Protein Tools" from the menu buttons, highlight "Ndjinn Multiple Database Search", and click "Run". In the query box to the right of the term "Contains", type HSP70, for the molecular chaperone, heat shock protein 70 kDa. Scroll down the database list and check the box to the left of the database entitled "PDBFINDER" before hitting the "Search" button. Among the results, find 2BUP, chaperone, and check the box to the left. Then select the menu button entitled "Import sequence(s)". This will import the sequence in fastA format into the open session. Now, under the box of session options, there should be a listing for the 2BUP sequence, with a small box to the left. Notice that the main menu under "Protein Tools" allows more options such as "Delete Protein Sequence", "Copy Protein Sequence" and "Add New Protein Sequences".
For now, select the "Ndjinn Multiple Database Search" again. Search the PDBFINDER Database again by scrolling down the page and selecting it, but this time, just search using the PDB ID codes 1HKB, 1ATN and 1DKG for hexokinase, actin and the molecular chaperone DnaK (use the OR operator between each PDB ID code to search for all three in the same search). Import all three sequences simultaneously by checking the box to the left of the PDB ID codes used in the query and clicking on "Import sequence(s)". 1DKG will return three chains, A, B and D. Only chain D is the molecular chaperone, chains A and B are nucleotide exchange factors that co-crystallized with DnaK. Delete chains A and B by checking the box to the left of 1DKG_A and 1DKG_B, highlighting "Delete Protein Sequence", and clicking on "Run". Actin (1ATN) returns two chains, but chain A is the actin, chain D should be deleted in the same manner.
Hexokinase (also called phosphotransferase) will return two chains as well. They are both hexokinase, but two identical sequences are not desirable in the cladogram, so delete chain B. Four sequences should remain, 1DKG_D, 1ATN_A, 1HKB_A, and 2BUP_A; check the boxes to the left of each of these. Scroll down the protein tools menu and highlight "CLUSTALW - Multiple Sequence Alignment", then click "Run". The default parameters will be sufficient for our purposes, just select "Submit". When the sequence alignment is returned, scroll down the page and view the multiple alignment. The Workbench automatically returns an unrooted tree with the alignment.
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