Tuesday, November 10, 2009
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Welcome to YOUR AP Biology Blog
This Blog is designed for you! A place where you can find information to help you be successful in AP Biology. Help on specific assignments, labs, or even quiz preparation will be provided here.
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Helpful Reads
- "The Seven Daughters of Eve" Brian Sykes
- "The Hot Zone" Richard Preston
- "What is Evolution" Ernst Mayr
- "The Monk in the Garden" Robin Henig
- Anything by Richard Dawkins
- Anything by Stephen Jay Gould
- "The Third Chimpanzee: The Evolution and Future of the Human Animal" Jared Diamond
- "Silent Spring" Rachel Carson
- "Origin of Species" Charles Darwin
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Stressed-Out DNA Turns Mousy Brown Hair Grey
ReplyDeletehttp://www.sciencenews.org/view/generic/id/44610/title/Stressed_Out_DNA_turns_mousy_brown_hair_gray
Gray hair color is usually a result of damaged DNA that then causes stem cells for hair color cells to lose their stemness. Causing the hair color to change. The data collected from the research may provide scientists with a new pathway to the effects of aging related to stem cells and damaged DNA over time of a person's life.
Melanocyte stem cells are what produce the color of the hair through it's splitting into two new cells. When the cells divides into two new ones, the daughter cell created is what creates the pigment in the hair. The other cell created replaces itself. Different tests were conducted and it was found that there are different types of stress on DNA that affect the stem cells. In mice, radiation greatly increased the effect on color, as well as hydrogen peroxide. It was discovered that the when the cells have collected a large amount of DNA they lose their ability to replace themselves or produce melanocyte.
Article: "Nanoparticles' indirect threat to DNA"
ReplyDeletehttp://www.sciencenews.org/view/generic/id/49191/title/Nanoparticles_indirect_threat_to_DNA
UK scientists, in a test to see how nanoparticles affect cells, found out that they can, in fact, kill a cell. The test, in which nanoparticles separated metal from cells, which were protected by either a plastic wall or other cells, determined that the nanoparticles, when in direct contact with the cell, will causes DNA damage, which is, in turn, relayed to neighbor cells, which causes further damage.
The scientists warn that the nanoparticle concentrations were ungodly high, and that the cells used were not human. However, this shows that, in some cases, nanoparticles could be toxic.
Genome 10k: A New Ark
ReplyDeleteBy:Janet Raloff
DNA tells biologists a lot about how a species may have evolved by comparing them to other related or unrelated species. But large investments are required to find these pieces of DNA that proves this. Earlier this year, the Genome 10K project started to collect tissues or cells from at least 10000 vertebrates to catalog DNA sequences from about every genus. Species have a lot of identical long stretches of DNA and giant differences in appearance may be due to only 2 percent difference in their genes. Scientists are looking for when the traits split to approximate the exact time the genes mutated. It's like watching evolution happen. This project may answer many questions like how shark's cant get cancer (tight) or how monkeys are resistant to AIDS (whoa? no idea). The Genome 10K project may not last long since test samples cost $50000-$100000. In a couple of years, the project may cost to be around $50 million. But the true challenge is collecting the specimens properly and legally transported to the centers that can sequence the DNA. Zoos' contain many species but ancient samples may be hard to get. Also, biologist must prevent from wasting time collecting data from samples that were stored improperly so that its genetic material has degraded. In order to make mass sequencing of the samples cost effective, assembly line tactics must be taken. But DNA is also not the main focus, since DNA codes for proteins which make tissues, and signals that orchestrate the timing of processes within the cells. So Proteins are what the biologists in the Genome project truly care for. When the genome 10K project starts there will be Petabytes (oh snap) of information collected, analyzed and stored, which is very costly.
Summarized by,
Yours Truly,
Son Phan
New View Reveals How DNA Fits Into Cell
ReplyDeleteby: Laura Sanders
A new 3D view of the human genome, may help to solve a long-standing biological mystery and lead to a deeper understanding of how genes operate and are compacted so neatly in the cell.
Researches have been curious as to how cells could pack the DNA, which is organized into 23 pairs of chromosomes inside the nucleus, so tightly without it becoming tangled and therefore useless.
“This paper is truly outstanding because it solves a problem that’s been around for a long time,” comments physicist and polymer expert Gene Stanley of Boston University. “It’s the question any child would ask — how does all of this DNA fit into the cell?”
The simple lack of appropriate tools has delayed answering the mystery. Earlier studies focused on the shape of small pieces of DNA that had been chopped out, removing them from their larger context. In the new study, Erez Lieberman-Aiden of Harvard University and MIT, Nynke L. van Berkum of University of Massachusetts Medical School in Worcester and colleagues developed a trick to lock pieces of neighboring DNA to each other while they were still in the nucleus. After removing the pieces and sequencing them, the researchers could calculate how close each and every piece of DNA had been to the other pieces and could reconstruct the 3-D shape of the genome.
“Our technology allows us to ask really fundamental questions about chromosomes,” says study coauthor and molecular biologist Job Dekker of the University of Massachusetts Medical School in Worcester. “It really is a radical improvement over the previous technology. It’s truly genome wide and unbiased.”
Researchers discovered that each genome is highly organized. DNA pieces fold into globs, which leads to a chain reaction of glob-forming. The researchers report that this chain reaction is fractal, it's the same pattern no matter how closely viewed. This fractal shape is “super-dense, but has no knots,” says Lieberman-Aiden.
Earlier studies by Alexander Grosberg, a theoretical physicist at New York University, first predicted the fractal structure of packed DNA. “Now this paper delivers beautiful confirmation of that prediction,” he says.
The new analysis discovered that the genome is made of two compartments: One is made of active DNA sections, the other inactive DNA, and is placed aside for storage, Lieberman-Aiden says. “The chromosomes are kind of weaving back and forth between those compartments,” he says.
Future comprehensive sequencing may allow researchers to discern individual genes. One of the reasons for this research is because that genes can be turned on and off by far-flung DNA elements, brought together by folding. By understanding the distance between genes in the pack, researchers may thoroughly understand gene regulation. For example, misfolding on the large scale may disrupt proper gene regulation, which could lead to cancer, Dekker says.
“Now that we know the structure, we can ask questions like, why does it look like this?” Dekker also wants to understand how a gene and a regulatory element find each other a glob. As of now, “We simply don’t know,” he says.
Scientists also don’t whether or not this folding pattern holds true across different cells. Dekker says that there may be “a tremendous amount of variation.”
"New view reveals how DNA fits into cell"
ReplyDeleteBy Laura Sanders November 7th, 2009; Vol.176 #10 (p. 14)
Cells are tidy packers, cramming DNA into nuclei to create a tangle-free, dense ball with pieces that are still accessible. The findings, based on a new three-dimensional view of the whole human genome, solve a long-standing biological mystery and may lead to a deeper understanding of how genes operate.
a human cell’s two meters of DNA is jammed into an area about a hundredth of a millimeter wide. But researchers had been puzzled by how cells could pack the DNA, which is organized into 23 pairs of chromosomes inside the nucleus, so tightly without hopelessly tangling it and making it impossible to use.
“how does all of this DNA fit into the cell?”
One of the reasons that DNA packing remained such a mystery is that scientists lacked the tools required to assess the shape of the entire genome. Earlier studies focused on the shape of small pieces of DNA that had been chopped out, removing them from their larger context. A trick was developed to lock pieces of neighboring DNA to each other while they were still in the nucleus. After removing the pieces and sequencing them, the researchers could calculate how close each and every piece of DNA had been to the other pieces and could reconstruct the 3-D shape of the genome.
Applying the method to human cells, researchers found that the genome has a highly organized structure. Small pieces of DNA fold into globs, and those globs fold into larger globs and so on. The researchers report that this “globule of globules of globules” is fractal, meaning it is organized in such a way that it has the same pattern no matter how far you zoom in. This fractal shape is “super-dense, but has no knots,”
The new analysis also found that the genome separates into two clear compartments: One is made up of stretches of DNA known to be active and working, and the other is made up of inactive DNA, set aside for storage, Lieberman-Aiden says. “The chromosomes are kind of weaving back and forth between those compartments,”
Part of the reason scientists are so intent on understanding the shape of packed DNA is that genes can be turned on and off by far-flung DNA elements, brought together by folding. By knowing which pieces of DNA are close to each other in the pack, researchers may be able to understand more thoroughly how genes are regulated. For example, misfolding on the large scale may disrupt proper gene regulation, which could lead to cancer, Dekker says.
Scientists also don’t yet know whether this folding pattern holds true across different cells.
Article:
ReplyDelete"A Gene Critical for Speech"
By Tina Hesman Saey
Recently researchers have discovered a gene that may be linked to the correct development of human speech, which they have dubbed as "tospeak". In an Australian family with a speaking disorder, it was found that many women had deep husky voices, while men could not speak much above a whisper. Raymond Clark of University of New South Wales’ St. George Hospital in Kogarah, Australia, studied further this strange disorder with his colleagues. Together, they traced it to a region of chromosome 8. The "tospeak" region has been rearranged in a way that reveals a break within it. Because the production of the RNA located on the region seem to be important for development of the larynx, defects in it have affected the way that this family can speak.
Members of the family also reveal signs of bone fusion in the carpals and tarsals. This is due to the fact that located next to the "tospeak" region is the gene GDF6, which helps to monitor eye and bone development. Other discoveries have shown that GDF6 may also lead to the joining of the neck vertabrae, in turn causing problems when trying to stretch the vocal cords. Interference with the "tospeak" region will also affect the GDF6 gene.
The "tospeak" gene first showed up in primates, but was not as well-developed as to be found in humans. This causes humans to have a stronger and more flexible voice than these creatures. This advantage may be the reason to human development in language. Although there have been arguments toward this theory, it is true that brain changes could not lead to language without the aid of human speech.
Janna Vo
MITOCHONDRIAL DNA REPLACEMENT SUCCESSFUL IN RHESUS MONKEYS
ReplyDeleteBy Laura Sanders
http://www.sciencenews.org/view/generic/id/46732/title/Mitochondrial_DNA_replacement_successful_in_Rhesus_monkeys
Mitochondria, the power-house of the cell, contains many DNA different from the DNAs made in the nuclei. Found recently in these DNAs are many mutations or diseases that can be transfered from mother to child, which can cause serious and debilitating diseases. although not commonly looked upon, 1 out of every 6000 humans suffer from these mutilations, therefore, if successful, these hereditary diseases and be prevented. First tested on Rhesus monkeys, the researchers took the mother’s mitochondrial DNA completely out of the picture. Then the researchers identified nuclear DNA in a mother’s egg cell by the DNA’s attachment to structures called spindles. The Researchers next removed the nuclear DNA (leaving the original mitochondrial DNA behind) and then put it into different egg cells lacking nuclear DNA but replete with healthy donor mitochondrial DNA. With the help of an inactive virus, the nuclear DNA fused into the donor cells. These modified egg cells were fertilized with donor sperm and implanted into Rhesus females to develop. As their Theory held true, the offspring's of the female monkeys DNA from the mitochondria, resulted in fine health, this still does not ensure the procedures complete safety. The FDA still has to work out a few kinks in order for this procedure to ever be tested and used on humans. Hoping for a new break through, scientist still have to solidify this procedures reaction towards humans.
PENGUIN DNA EVOLVING FASTER THAN THOUGHT
ReplyDeleteBy Tina Hesman Saey
http://www.sciencenews.org/view/generic/id/49671/title/Penguin_DNA_evolving_faster_than_thought
A recent study on a species of penguins brings the possibility that the calculations scientists have made could be incorrect. Researchers collected some mitochondrial DNA from penguins living in Antarctica as well as from the bones of the same species from 44,000 years ago. When they studied this genetic material they found that the previous theory of genetic aging and shift in penguins was off by about two times. The method the researchers use for indicating approximately how long away the is simple, they essentially count the number of changes that have occurred in the mitochondrial DNA. This can be done because the only evolutionary changes that occur in mitochondrial DNA are very small because any substantial change in the DNA is likely to "throw a wrench" in the processes in energy production.
The most general idea to date is that the rate of evolution is the same in all organisms. Due to this discovery many have begun to question the rates in other organisms.
Previously the only part of the mitochondrial DNA that was mapped was an area called the "Hypervariable" but new studies have mapped the entire gene.
The rate of evolution in the circle of DNA found in the penguins is not all uniform, though. Some evolve and change at extreme rates whereas others are standard and hold true to older ideas.
These results have even brought up questions about the origin of man and the age of the human race.