Researchers identify genetic mutation for rare cancer

Researchers identify genetic mutation for rare cancer

Summary
In Michigan, researchers studied the DNA of a patient with rare solitary fibrous tumor (cancer). They have been unable to find the mutation that led to this cancer until just recently. Using a new program called MIONCOSEQ that makes finding new mutations possible, they sequenced the genome. Researchers discovered that two genes, NAB2 and STAT6 had fused together. This advanced technology is unlike all previous sequencers, because it recognizes new mutations and identifies them without them being familiar, and seen before. Researchers then sequenced 51 other cancerous solitary fibrous tumors and found this same mutation in every single one. With this new information, researchers can now work on treatments and drugs that correlate directly to this mutation, because as of now there is very little available for patients.

Connection
This article relates to our studies because it emphasizes the importance of genetic sequencing. Sequencing genes and genomes is something we did on a lower scale and this technology is being used in the real world too. It's still improving and will potentially save lives, by locating the mutations among other patients with unknown cancers and more. The discovery of the mutation is also something we learned about, specifically fusing together.

Link: http://www.uofmhealth.org/news/archive/201301/researchers-identify-genetic-mutation-rare-cancer
Author: Yi-Mi Wu
Published: 13 January 2013

Keelin McCarthy

Evolution of Humans

Summary: Humans have evolved very quickly over their lifespan on Earth. The rate of natural selection was very quickly increasing 50,000 to around 10,000 years ago, but then it slowed.Throughout there years there has been an increased rate of selection that has occurred for two reasons. One is the increased population leaves more room for mutation, and the other was the need to adapt to different diseases and climates. One reason why the rate may have slowed is because now humans may create barrier to protect themselves from disease and the environment.

Relevance: This relates to our unit because it talks about natural selection in humans and how we tried to slow the rate of natural selection. We adapted to the new environments, but for a while, it was survival of the fittest, and only the humans with the proper skills could survive.

Article: Selection Spurred Recent Evolution, Researchers Say
Published: December 11, 2007
Link: http://www.nytimes.com/2007/12/11/science/11gene.html?_r=0

Wrist bones distinguish Hobbits

    

     Summary: Scientists have discovered three new wrist bones of hobbits in Indonesia that may show that hobbits belong to the Homo floresiensis species. The structure of the wrists also show that the hobbits' wrist would limit their ability to make or use stone tools, but they would still be able to primitively use them. It also shows that the hobbit wrist differ very much from that of a human. These wrists also show that hobbits were descended from a member of the human evolutionary species, branching off about one million years ago. 

     Relevance: In class, we discussed how the anatomy of an individual can be used to determine how closely it is related to another individual. In this case, the hobbit wrists are being used to determine how closely related hobbits are to humans. It is also an example of homologous structures, where the wrists of hobbits were used to use tools, similar to humans. 

Article: News in Brief: Wrist bones said to distinguish hobbits
Published: January 9, 2013

http://www.sciencenews.org/view/generic/id/347436/description/News_in_Brief_Wrist_bones_said_to_distinguish_hobbits

Epigenetics Posited as Important for Success of Invasive Species

Summary:

     Some ecologists are beginning to believe that epigenetics is one of the reason why invasive species do so well in certain environments. Epigenetics is an idea in which environmental factors leave a genome intact, but somehow modify certain genes. It is really difficult for ecologists to prove this theory though because the genomes of many wild organisms haven't been sequenced, so it is almost impossible to see which genes have been modified due to epigenetics. One strong piece of evidence supporting the idea of epigenetics is Japanese knotweed. Christina Richards, an ecologist, discovered that although Japanese knotweed is genetically identical, different knotweed had varying leaves and heights depending on their environment, Hopefully, Richards and her team will be able to prove or disprove their idea soon.

Relevance:

     This is relevant to our studies because although we learned that overtime, organisms can adapt to their environments, this idea of epigenetics puts a bit of a twist on that. Epigenetics is similar to natural selection because during natural selection, organisms with characteristics best adapted to a certain environment will reproduce and tend to do better than organisms that lack these characteristics. The phenotype of species that go through natural selection tends to change. This is the same with epigenetics. In epigenetics, there is no selection, however, genes seem to be modified, and this changes an organism's phenotype. Both of these changes in phenotype are beneficial to the species, and it helps them survive.

Article Title: Epigenetics Posited as Important for Success of Invasive Species

Authors: Sujata Gupta, Nature magazine

Date published: January 10, 2013

Link: http://www.scientificamerican.com/article.cfm?id=epigenetics-posited-as-important-for-success-of-invasive-species

Humans = Perfect Running Machines

 A link, for your convenience:  http://news.nationalgeographic.com/news/2004/11/1117_041117_running_humans_2.html

Summary:  A new study suggests that natural selection has designed humans as ideal distance runners.  The co-author of the job, Dennis Bramble, has researchers studying a variety of human traits.  From the traits they look at, they conclude that through these adaptations, the human species were better suited to compete with other predators for food.  It is theorized that apes evolved to be able to walk, and eventually run.  Eventually distance running was mastered, and humans used this skill to run down and tire out their prey.  Some humans have been known to be able to outrun other animals such as horses.  One adaptation involves the Achilles tendon.  Its springy qualities reserve energy and so prolong the distance a human can run.  Another case of an energy saving adaptation is the springy, high-arched feet of humans.  Scientist say that longer legs have increased humans' speed.  Larger joints absorb shock better and reduce stress on the body.  Also an assortment of adaptations to balance the body include broad shoulders, shorter forearms, and a larger buttocks.  We have a more streamlined and balanced face, with a smaller nose and teeth than our ancestors.  Scientist suggest that our skill for distance running was used to exhaust prey before we had advanced hunting tools.  Some Southern Africans use this same strategy today in order to hunt antelope.

Relevance:  The article describes many human adaptations that have helped our species compete for food and therefore survival.  This is a clear example of natural selection.  There was a variation of traits among primitive humans.  Some traits were better suited for survival than other traits.  As a result, the percentage of individuals with the most effective traits increased as they were producing more offspring than those without the ideal traits.  In short, this is how the human species evolved from apes into long distance hunters.  This is also a basic description of how evolution occurs.  Natural selection evolves a species to help them compete with similar species of a similar niche.

First Fossil Bird With Teeth Specialized for Tough Diet

Summary:
          Scientists have found a new prehistoric bird, Enantiornithine ,with teeth that can break through the hard exoskeletons of organisms such as insects and crabs. They had hard teeth with grooves on the inside surface for extra strength. This is very unique because teeth weren't the main structure evolving most in other species, but the Enantiornithine teeth kept evolving into their diverse dental patterns until they became extinct. at the end of the Cretaceous period.

Connection:
         This is relevant because we have been studying evolution in biology. These prehistoric birds evolved into having a great diversity in their teeth unlike any other species at the time. Also, these birds are very much like Darwin's finches because, like the beaks of the finches, the Enantiornithine birds' teeth had to be adapted to fit their new food sources. The birds with the strongest teeth survived, while the less-tough-toothed birds died off.

Article: First Fossilized Bird With Teeth Specialized For Tough Diet
Published: January 7th, 2013
Link: http://www.sciencedaily.com/releases/2013/01/130107082602.htm

Scientists Use Light To ‘Tag and Track’ Genetic Processes

Author: Amanda Seigfried

August 13, 2012

http://www.utdallas.edu/news/2012/8/13-19101_Scientists-Use-Light-To-Tag-and-Track-Genetic-Proc_article-wide.html

Summary: UT Dallas researchers recently found a way to use fluorescent molecules to 'tag' DNA and monitor DNA looping, a biological mechanism that rearranges genetic material in some cells. This helps them begin to understand the biophysics of the process, because before this discovery, only bits of information was known about DNA looping. In DNA looping, proteins attach to the DNA molecule at two specific points, then bring those two points together. The loop is snipped off and the loose ends are connected. DNA looping is seen mainly in organisms with circular DNA. The scientists used a specific protein commonly used to delete genes from laboratory animals using DNA looping, and in the points where the DNA connects with that protein, added a molecule that fluoresces when exposed to certain wavelengths of light. The scientists then are able to monitor the steps of the loop formation. This method could lead to more efficient potential drug screening for anti-HIV activity, as it would allow them to see how HIV inserts itself into its host's genome and test drugs made to interfere with the the insertion. Fluorescence based methods like this could be up to 10000  times more efficient than current methods. 

Connection: DNA looping helps viruses integrate themselves into the human genome and disrupts it, creating mutated proteins. This is like the process of insertion, which we have spoken about in class. The process would help the scientists monitor other virus' integration into DNA and use the information to produce drugs that would interfere with the process and possibly undo it, which ties into the subject of biotechnology because it is part of the DNA technology branch. another topic we have spoken about.  

The Secret of Wrinkly Fingers!

Article: Wrinkly Fingers are Evolutionary Superpower!

Author: Sourcefed.

Link: Here

Published: 1/9/13.

This video covers the reason behind your skin wrinkling upon becoming wet. The reason is that when your fingers becoming wet, blood vessels contract and pull the skin along with it, leaving a wrinkled finger. The body has actually evolved for this to happen. The reason is that wrinkly hands allow us to better grip things when we’re wet. This allowed gathering and hunting in bodies water more practical, providing more food and resources, thus giving a survival benefit. Natural selection caused for it to be a trait of humans. Also, when on slippery surfaces, we run better with wrinkled feet, so our feet do the same.

This relates to our science class this term because it relates to the process of natural selection and how traits that give a survival benefit pass on, such as how being able to grip things and move better in water due to wrinkling provides humans an advantage, and therefore it is passed on throughout the human species.

Editing Genomes with High Precision

Summary:
Scientists are finding new ways to alter genomes by inserting or deleting genes. The altered genomes create new organisms that are helpful in studying diseases. This technique originated from genetically adding small pieces of DNA to cells. Now the insertion of genes is being adapted to include homologous recombination. This takes place when an inserted gene is surrounded by genes similar to the original DNA strand so that they do not disrupt the rest of the DNA. Additionally, complexes can cut genes at specific targeted locations which the nuclease Cas9 recognizes. Cas9 can target different sequences so that multiple genes can be altered. One specific disease that the insertion and deletion of genes will influence is Huntington's Disease.  Huntington's Disease is caused by a single, abnormal gene. If this gene can be cut out and replaced then the disease has potential of being cured.

Connection:
In class we studied the uses of biotechnology and the manner in which organisms are manipulated so that they can perform tasks for humans. Specifically we mentioned recombinant DNA technology which combines genes from different sources. Additionally, we discussed how the enzymes such as Cas9 act as restriction enzymes and cut genes out of a long DNA molecule. Genes are inserted into plasmids and from there can genetically modify a plant or animal so that the species reaches its maximum potential. This is similar to the new organisms which have been genetically modified so that they can be used in research. Lastly, we learned how restriction enzymes are used to cut up DNA so that there can be easily seen bands during gel electrophoresis.

Article: Editing the Genome with High Precision
Author: MIT
Published: January 3rd, 2013
Link: http://www.biologynews.net/archives/2013/01/03/editing_the_genome_with_high_precision.html

'Severe abnormalities' found in Fukushima butterflies

Summary: Two months after radioactive materials released from the Fukushima Daiichi nuclear power plant, scientists have found mutations in pale grass blue butterflies that inhabited the surrounding areas. The mutations consisted of smaller wings and irregularly developed eyes. After collecting and breeding the butterflies, researchers were able to find that the following generations of butterflies developed new mutations. Malformed antennae were found, and in insects, antennae are used to find mates and explore their environment. These butterflies are very useful in the experiments of finding impacts of exposure to radioactive contaminants because it shows the long-term results of exposure. Even though the contamination of food has decreased, the mutation rate has not lowered because it has been passed from each generation's genetic material to the next.

Relevance: The findings of the mutations in butterflies is relevant to our studies because we learned what mutations are and how they affect genes; mutations are changes to the nucleotide sequence of the DNA. This is a real life situation to how changes in the environment can cause mutations in organisms living there.

Source:
http://www.bbc.co.uk/news/science-environment-19245818
by Nick Crumpton. 13 August 2012.

A Snapshot of Pupfish Evolution.

Jan. 10, 2013

 

Summary:

 

As a graduate student, Chris Martin has bred more than 3,000 hybrid fish in his time in subjects of  evolution and ecology at UC Davis.   He made one of the most inclusive snapshots of natural selection and demonstrated an important point in evolutionary biology. "The adaptive landscape is very important for evolutionary biology, but rarely measured," said Martin.  It takes variable traits in an animal or plant, spreads them over a surface, and exposes points of success (what evolutionary scientists call fitness) where those traits become effective, or adaptive.  Martin studied species that he found only in a few lakes on the island of San Salvador in the Bahamas, where some of the fish have evolved in different-shaped jaws which allow them to feed on hard-shelled prey like snails or, in one case, to snatch scales off other fish.  "In a paper published in 2011, Martin showed that these San Salvadoran fish are evolving at an explosively faster rate than other pupfish."  Martin breed those fishes that he found with different types of jaws.  Then he studied and made measurements on the hybrids.  when he was done with his studies, he released those fishes in to the stream of their grandparents.  It was seen that most of the surviving fish were on an isolated peak adapted to a general style of feeding, with fish adapted for eating hard-shelled prey. Competition between the fish had eliminated the fish, in which whose jaws put them in the valleys between those peaks. The scale-eating fish did not survive, and eventually population decreased.  Scientists are still interested in how those ones that couldn't survive can't make it to the peak.  Martin concluded and said "The results explain why most pupfish species in America have pretty much the same diets."  he also said "An early burst of variation, when fish entered a new environment with little competition could have allowed the shell-eaters and scale-eaters to evolve on San Salvador."

 

Connection:

 

This article's concept is what we are learning that some kind of evolution has happened in the past, about millions of years ago.  These unique fish (scale-eating and hard-shell eating) had competition over food.  Eventually, one group of population survived and the other population decreased.  This was an example of natural selection.  Adaptation also played and important role in some fish to survive and reproduce in a particular environment.  Just like Darwin, Martin went to Bahamas instead of Galapagos islands, and studied to fish instead of finches. 

 

References:

 

http://www.sciencedaily.com/releases/2013/01/130110142043.htm

 

by Christopher H. Martin, Peter C. Wainwright.

01/8/2013

 

 

 

An Organic Veiw of Human Evolution

http://www.nytimes.com/2012/08/09/science/new-fossils-indicate-offshoots-in-human-family-tree.html?ref=evolution

 Author: John Noble WIlford

New York TImes

Published Aug. 9th 2012

 



                  According to a recent article on the evolution of humanity, the evolution of the human being is not very linear, according to Susan C. Anton. The Koobi Fora association has sponsored the excavation of African remains to determine their relationship to modern humans. The specific remains found display a human-like head with appropiate skull structre, yet no lower jaw. Therefore, the effect of ones ability to consume a variety of food is shown as a positive trait; this particular characteristic did not proliferate succesfully.  Ms. Anton speculates that the remains display the final peice of re-affirming evidence that a variety of sub-species of Homo Erectus have lead to the modern species. Africa is also shown as a highly important base for the evolution of the modern human's early evoltuion, before the line of the early representatives of the Genus ventured further. COnclusively, the article, (because it was not written well,) alludes to the notion that these various groups of semi/primal humans branched, mated with other sub-sets, and became extinct.

 

 

                 This article speaks to various example of factors that lead to the development of a species. FOr exaple, natural selection is specifically displayed in the unfavorable nature of the jaw, because it is not visible within the modern. The concept of speciation is shown in a peculiar fashion, although there are noticeable sub-species of human, they did not survive along with the Homo Sapiens. it can be surmised that behavorial selection could also have been determinent to this development, as certain physical profiles could have been sexually favored. 

How bacteria evolve resistance to antibiotics

Summary:
Scientists at Rockefeller University for the first time ever have been able to observe the process of how bacteria adapts to become resistant to antibiotics. By collecting and isolated the bacteria in the blood of a patient with heart disease, the scientists were able to trace how a common strain of bacteria adapted its genes to try to kill it the antibiotics, until it became fully resistant to the antibiotics. This new information may be able to get scientists one step closer to creating an antibiotic that kills the adapted bacteria.

Relevance:
We have recently been learning about the adaptation of species to become better fit for their environment. The bacteria in this article has become resistant to the antibiotics that were once able to kill it. over time the bacteria changes and produces generations that gradually become more and more resistant to the drugs.

Article: How bacteria evolve resistance to antibiotics
Author: Not Given
Published: June 6th, 2007

http://www.itqb.unl.pt/news/how-bacteria-evolve-resistance-to-antibiotics

Virus Caught in the Act of Infecting a Cell

Summary:
     In this article, scientists see for the first time, a virus infecting an E. coli bacterium. Scientists have finally seen the details of the changes in a virus' structure while it infects the bacterium. Before infecting a cell, the virus extends feeler-like structures from its head. These feelers essentially locate an optimum cell to infect. When the virus arrives at it's chosen host cell, it moves along the membrane searching for a good spot to infect from. When it chooses a good spot, it then injects some of its own proteins to make a bridge or tunnel for the DNA to travel through. After the DNA has been fully transmitted, the protein "bridge" breaks apart and the virus unattatches itself. This greatly changed the ideas of many scientists.

Relevance:
     In Biology class, we have studied phages before in the beginning of the previous unit. We studied how they reproduced and how we didn't classify them as living due to their lack of cells. In the first chapter of that unit we read a little bit about how the phages infected bacteria.

Article: Virus Caught in the Act of Infecting a Cell
Published: January 10, 2013
Link: http://www.sciencedaily.com/releases/2013/01/130110152628.htm

Spanish Scientist Puts Genetics to Work to Find Missing Children

Summary: This article is about a scientist named Dr. José A. Lorente, and how he used and is using DNA sequencing to link found children to their parents. His idea is to form a database with the DNA of all the parents with missing children, so it can be matched even if the child is found years later. His foundation, named DNA-Prokids has reportedly reunited "about 550 children with their families, most of them in Guatemala and Peru." This has been done with free DNA tests for parents and DNA collection kits. The foundation has also helped stop over 200 illegal adoptions, in which the people selling the child are not actually the parents. Lorente thinks that all adoptions should have DNA tests before selling. Lorente has worked on big cases like identifying the DNA of Columbus, but for him, he feels much better in finding missing children for distressed parents.

Relevance: In term 2, we discussed DNA sequencing and how you can compare DNA sequences to find similarities. Dr. Lorento is using DNA sequencing and comparison for a different purpose than relationships in evolution, finding missing children.

Article: Putting Genetics to Work to Find Missing Children
Author: Suzanne Daley
Published: August 3, 2012
Link: http://www.nytimes.com/2012/08/04/world/europe/spanish-scientist-puts-genetics-to-work-to-find-missing-children.html?pagewanted=all  

Human Hands Evolved For Fighting, Not Just Dexterity

Summary:
A study run by the university of Utah is now suggesting that hands evolved not only for the dexterity needed to use tools, but for fighting as well. David Carrier, a senior author in the study, says "the role aggression has played in our revolution has not been adequately appreciated." What Carrier means by this is that the aggressive nature of humans has played a role into how we as a species have evolved. Compared to chimpanzee hands, humans have shorter palms and fingers, and a longer, stronger, more flexible thumb. This combination not only allows for humans to use and operate tools, but allows humans to make a clenched fist; something apes cannot do with their long fingers and palms.  When a human makes a fist, it protects fragile hand bones, muscles, and ligaments during hand-to-hand combat. As our ancestors evolved, those that could protect themselves and fend off attackers and hit harder without injuring themselves were more likely to survive, and reproduce with mates. Fights could also be over food, water, shelter, and even "pride" in some cases. The hand "is arguably our most important anatomical weapon," says Carrier once again. The hand not only evolved for the ability to grip things more easily, use tools, but evolved as a weapon to attack enemies and protect themselves.

Relevance:
We have learned about Darwin's idea of Natural Selection, and this is a prime example. Humans that could hit harder to defend themselves to get mates were more likely to reproduce. The humans with the larger hands would not be able to get a mate, and therefore would die, bringing the long, larger hand trait with them. When humans left the trees where they used their long fingers to climb, they no longer needed it on the ground. Selection then favored smaller hands for manipulation because humans did not need to climb the trees anymore, and they could use it for using tools. This also shows how humans evolved and adapted their hands to their new environment.

Author not posted
January 10, 2012
http://www.sciencedaily.com/releases/2012/12/121219223158.htm

Synthetic Heredity Molecules Emulate DNA

Summary:
Philipp Holliger and a team of scientists have created synthetic molecules called XNA (xenonucleic acid) that can evolve and pass information like DNA. There are six forms of XNA molecules with substitutions for deoxyribose in their backbone. XNA still requires DNA to make copies, along with the help of engineered enzymes that can read XNA and create a complementary strand of DNA. Scientists have also created enzymes that can do the opposite to make XNA. The molecules can also evolve, and the scientists selected one of the molecules, called HNA, to be able to attach to target molecules. At first, most of the HNA molecules were not very effective. Scientists used DNA to replicate those that attached well. After a few generations, the molecules were much more effective. XNA can be more stable than DNA and can withstand acidic environments better. Also, molecules that damage DNA will not recognize XNA, and not have the same effect. All of this makes it likely that XNA could be used instead of DNA in drugs and vaccines, as well as a tool in biotechnology.

Relevance:
This new molecule is a product of biotechnology, which we studied. It is designed to function much like DNA, and we learned about nucleic acids. Our past few units have been focused on genes and heredity, and this molecule could serve as a form of genetic material. Also, XNA evolves through artificial selection, which we have studied.

Article by Rachel Ehrenberg
Posted April 19, 2012
http://www.sciencenews.org/view/generic/id/340076/description/Synthetic_heredity_molecules_emulate_DNA

Skin Wrinkles in Water for Grip

Summary:
     After a long time in water, vessels in our palms and fingers contract, which creates temporary wrinkles in the skin there. For a long time, it was commonly thought that the skin on the fingertips absorbed water and increased in size, creating the wrinkles. However; this was also doubted because of the fact that people with nerve damage didn't exhibit this trait. After careful observations, it was deemed that the blood vessels contracted, and the skin stayed the same size.
     A biologist named Tom Smulders recently concluded that this was an adaptation that helps humans handle objects when they are wet. He experimented by having 20 people who started out with dry hands move a total of 45 submerged objects (45 for each person) to another container. He then repeated the same test, but instead having the test subjects soak their hands in water for 30 minutes prior to the test. Both tests were timed.
     In his results, he found that on average, people took 15 seconds longer to pick up submerged objects when their hands were unwrinkled, compared to when they had wrinkles in the skin of their hands. Mr. Smulders speculates that this adaptation came into play to help humans with things such as keeping their footing in water, or holding on to wet tools during the rain, fishing, or even uprooting sea plants to eat.

Relevance:
     In Unit 7, we learn about evolution, natural selection, and adaptations. Wrinkling skin is an adaptation, because it helped hominids grip wet objects such as food and tools, which in turn affected their ability to survive. Because it affected their ability to survive to reproduction, it is related to natural selection, adaptations, and (biological) fitness.


Link to Article: http://www.guardian.co.uk/science/2013/jan/09/skin-wrinkle-water-grip

Nanomaterial Graphene May Reduce the Time and Cost of Sequencing DNA

Summary: Engineers at the University of Texas at Dallas have used advanced techniques to shrink the material graphene, graphite that has been changed into a strong sheet of bonded carbon atoms, small enough so that it could read DNA. Making the size of this graphene pore smaller to less than a nanometer makes it possible to be used as low-cost tool to sequence DNA. Being able to sequence DNA cheaper would allow scientists and doctors to better predict and diagnose disease and specifically construct a drug to an individual's genetic code. It was first established in 2004 that graphite could be turned in to graphene, and to this day graphene is believed to be the strongest material ever measured. Because it is thin and strong engineers have spent a long time trying to control the size of its pores. Now that scientists know pore size can be controlled, the next step to drive their research is to build a prototype device. Dr. Moon Kim and his team shrunk the nanopore by using an electron beam from an advanced electron microscope and simultaneously heating the nanopore to 1200˚ Celsius. According to Kim, "We used high temperature heating and electron beam simultaneously, one technique without the other doesn’t work."

Relevance: This article is relevant to our curriculum since we studied DNA in our unit on molecular genetics. We learned about the human genome project and that it took a lot of money and time to actually sequence the human genome. By enlarging the size of these graphene pores, it is possible to sequence DNA faster and cheaper by just pulling a strand through the pore. However, to make that happen, the next step is to build a prototype. 

Research Shows Graphene Nanopores Can Be Controlled
By: LaKisha Ladson
October 2, 2012
http://www.utdallas.edu/news/2012/10/2-19931_Research-Shows-Graphene-Nanopores-Can-Be-Controlle_article-wide.html

Wrinkled Fingers and Toes

Summary:
When fingers and toes get wet after a while they become wrinkled. It was recently discovered that these wrinkles have a purpose. They help humans pick up wet objects. This came about when human would gather things from streams and other wet areas. It is much harder to pick up wet objects with unwrinkled hands. The humans with this trait would get more food most likely making them more fit. These humans would therefore produce more offspring and so forth natural selection would take place. There is not a definite idea as to why fingers and toes don't stay wrinkled but one hypothesis is “Our initial thoughts are that this could diminish the sensitivity in our fingertips or could increase the risk of damage through catching on objects."
Relevance:
This article connects to natural selection and evolution which are both topics we have studied in class.

http://www.scientificamerican.com/article.cfm?id=why-do-our-fingers-and-toes-wrinkle-during-a-bath
Author: Becky Summers and Nature Magezine
Published on January 9, 2013

Scientists Create GM Cow to Cut Milk Allergies in Children

Summary
Beta-lactoglobulin is a milk protein that is not present in human milk, but triggers allergies in some young children causing a variety of symptoms. In developed countries between 2-3% of infants are allergic to this milk protein. For that reason scientists have created a genetically modified cow that makes milk with less than 2% of normal levels of beta-lactoglubin. The milk also is richer than usual in other kinds of milk proteins, and believed to contain higher concentrations of calcium than ordinary milk. However the calf that had been cloned and genetically engineered with a piece of genetic material to turn off the gene for producing beta-lactoglobulin was born without a tail. Scientists hypothesize that this rare congenial abnormality was caused by the cloning process rather than the GM technique used to lower levels of the milk protein.

Relevance
This article relates to what we have learned, because it has to do with genetically modifying animals for  human benefits. We learned in class about transgenic animals and producing genetically modified animals. The cow in this article is transgenic because it was cloned and then genetically modified with an extra piece of generic material. Also we recently learned about the  advantages and disadvantages of genetic engineering and the cow losing it's tail is an example of that.

This article is from The Independent and written by Steve Connor. Published October 2, 2012.

Once- Extinct Toads Reintroduced to Wild

Summary:
      About 2,000 Kihansi spray toads, once extinct in the wild, have been released and are now living next to  artificial sprinklers in their native habitats. It is the first time an amphibian species that had once been declared extinct in the wild to be reintroduced to the wild. These gold-colored toads with pale white skin that seem translucent so that their abdomen can be seen, are part of a unique group of amphibians that give birth to live young and then carry their newborns on their backs.After being first discovered in Tanzania in 1996, the construction of a hydroelectric dam on the river, that now supplies Tanzania with one fourth of its energy, severely reduced the number of Kihansi spray toads in the wild until five hundred were saved and taken to New York's Bronx Zoo. Still, the numbers continued to decline in the wild until the species was declared extinct in 2009. Then, about fifty of the toads were sent to the Toledo Zoo in Ohio where they were capable of reproducing in captivity. About a hundred of these toads were then sent back to Tanzania where they continued to reproduce until finally being released back into the wild.

Relevance:
     This article is relevant to the term two curriculum because of its connection to the topics of extinction and genetic bottlenecks. These toads could not be found in the wild making them extinct in one sense, but some were taken and kept captive so that they were able to reproduce and be released again. Due to being extinct into being reintroduced, this caused a genetic bottleneck. A bottleneck can reduce a species genetic variation significantly. From thousands in number of the Kihansi spray toads into five hundred, and then reproducing just the remaining toads narrows the amount of genetic variation that had possibly once existed when having the thousands of toads.

http://www.scientificamerican.com/article.cfm?id=once-extinct-toads-reintroduced-to-wild
Author: Douglas Main
Date: December 13, 2012

Major Source of Evolutionary Differences Among Species Uncovered

Summary

Some species, like humans and chimps, have almost identical sets of genes, but still behave and appear very different from each other. Scientists have recently discovered an explanation that could account for the significant differences between humans and other genetically similar vertebrate species, and why humans are more likely to get some diseases than other vertebrates. A group of scientists from the University of Toronto sequenced and compared thousands of genetic messages in the brain, heart, and liver organs of 10 different species like humans and frogs. They discovered that a process called alternative splicing,which can cause a single gene to control several proteins. It may have changed how genetic messages were sent during vertebrate evolution, creating fundamental differences between species. Also, alternative splicing could help scientists figure out why humans are more susceptible to diseases like Alzheimer's and certain types of cancer and develop more effective methods for treating these diseases. It could show how humans are unique from other closely related vertebrates.

 

Relevance

This article connects to what we have learned about genetics and evolution. In genetics, we have learned about the One Gene, One Polypeptide concept, and this shows how sometimes one gene can control the production of multiple proteins instead of one. Also, this article relates to evolution since we have been discussing how mutations in DNA create variation among a population. In the article, alternative splicing causes mutatations that can be passed to offspring. Eventually, the population can evolve into two different species, like humans and chimps.

 

Source

http://www.sciencedaily.com/releases/2012/12/121220144124.htm

Will My Son Develop Cancer? The Promise (and Pitfalls) of Sequencing Children’s Genomes

Summary: This article from the Time Magazine website is on sequencing children’s' genomes. It talks about the possible benefits and the possible nightmares for parents. As the cost of sequencing entire genomes is spiraling down (from $2.7 billion to only $7500), genetic sequencing is become available in ways other than helping people with mysterious illnesses. The possible future is that genetic sequencing will be used in all newborns. Not only that, but it could even be available in drugstores. With this possible future looming, it can be possible to know the future of every newborn, what diseases they will have and possible disorders. This knowledge brings up a possible dilemma for parents. Is it worth knowing you child’s future? Most parents want to know as much information as possible about their kids. But would they want to know that their child will have a debilitating disease. If they know that their child will have a disease, they have the most time to prepare and possibly even prevent the disease from happening. But no parent wants to know that their child will have a disease is "x" number of years. How will parents react to being notified that their child is at risk for something? Another question brought up in this article is how much of the information gained by parents from sequencing their child should be shared to that child? What if a child was told that he/she would get cancer later on in their life? How would they react? And how would a parent manage knowing this without telling their child? All of these questions result from the knowledge gained from genetic sequencing. But some researchers believe that sequencing newborns is much bigger than the individual itself. They believe that it can help identify certain genetic changes that can be addressed early in life, and learning what causes diseases hill help everyone. Knowing what conditions we are predisposed to can lead us to taking preventive steps, and researchers believe that the best place to start is at birth. In the end this article is about what knowledge genetic sequencing gives us, and with the availability of sequencing genomes becoming more available and cheaper; would you want to know your child’s future knowing that there may be something bad in it? It ponders how humans will react and what types of decisions they will make regarding their children.

Relavence:

We have talked in class about the use of technology in genetics, and we have learned about the human genome project and sequencing DNA. This article revolves around this topic of genetic sequencing. It talks about how when the Human genome project cost 2.7 billion dollars and how now it only costs 7500 dollars to sequence a genome. We can see the progression in how far genetic sequencing has come. We have also learned about the link between genes and mutations, cancers, disorders, and diseases. This article talks about how through genetic sequencing, we can know the future of possible mutations, cancers, disorders, and diseases.

http://healthland.time.com/2012/10/22/will-my-son-develop-cancer-the-promise-and-pitfalls-of-sequencing-childrens-genomes/
Bonnie Rochman
10/22/2012

Scientists breed big-brained guppies to demonstrate evolution's trade-offs

Summary

Scientists have come up with a hypothesis known as the "Expensive-Tissue Hypothesis" which is "the idea that there's a trade-off between the demands of the brain and the demands of other organs". In humans, the brain takes up 20% of the overall amount of energy a human has, and less energy is set aside for other organs, such as the organs involved in the digestive system.

Recently, a Swedish team of scientists selected and bred a common species of guppies with the goal of producing fish with bigger brains. What they discovered is that these new fish tended to have smaller guts and produced 19% less offspring than the smaller-brained fish. The results from the experiment support the hypothesis explained above.

The results also seem to show that these big-brained fish have a low fitness level, as they do not produce as many offspring compared to the small-brained fish, but this cannot be concluded because the experiment did not show how well the new fish would do versus the small-brained fish in natural situations (ex. avoiding predators, finding food...). If the new fish survived in higher numbers, it would show that they have a trait with advantages, increasing their overall fitness despite the offspring number setback. 

Relevance

This article ties in with the most recent unit, evolution. The scientists who have found a way to breed bigger-brained guppies have used the method referred to as selective breeding; they select animals with desirable traits, and breed them for a higher chance of offspring with that trait. This article also taps into the realm of fitness and evolution. Fitness is "the contribution that an individual makes to the gene pool of the next generation compared to the contributions of other individuals" (Campbell). These big-brained fish seem to have a lower fitness, as they do not produce as many offspring, but their increased brain could help the survive, and therefore they would live to contribute to the gene pool. 

Source

http://cosmiclog.nbcnews.com/_news/2013/01/03/16325592-scientists-breed-big-brained-guppies-to-demonstrate-evolutions-trade-offs?lite 

by Alan Boyle 

1/3/13

Carl Woese Dies at 84; Discovered Life’s ‘Third Domain’

During his work at the University of Illinois, Woese along with some of his colleagues discovered a single-celled microbe called archaea.  After finding this microbe he started studying the origin of it.  In this article, it is mentioned that there are three evolutionary groups all of which are derived from the same ancestor.  The fact that all three groups came from the same ancestor was first proved by Woese.  Archaea happens to be the third group.  Woese also discovered that not only do archaea live in extreme environments such as volcanic vents, but they also were found inside many organisms such as humans and plankton.   He also said that there are "far more of the living protoplasm on earth than all humans, animals and plants combined" (Woese).  He mentions this to show how little we pay attention to something that is far more prominent on Earth just because of its size in comparison to the size of the plants and animals that we know much more about.
     This connects to our unit on evolution and how all animals share a common ancestor.  Woese discovers different groups of species and is able to prove that although they have almost nothing in common, they all evolved from one species.  This is difficult enough for some of us to understand how humans and baboons might be related which is something we went over in class, therefore it is nearly impossible for some of us to imagine how archaea and humans might be related as Woese says.
http://www.nytimes.com/2013/01/01/science/carl-woese-dies-discovered-lifes-third-domain.html?ref=evolution&_r=0

DNA Directly Photographed For First Time

Summary:
Italian scientist Enzo Di Fabrizio has taken a photo of DNA with an electron microscope. Di Fabrizio teaches physics at an Italian university. DNA is hard to directly photograph, so Di Fabrizio and his collegues built a "nanoscopic landscape" made of silicon pillars, which repel water. They then added a water-based solution with DNA in it, and the water evaporated. The DNA was left on the silicon pillars, and the scientists used electron beams to visualize and photograph the DNA. This is different from the technique developed by Rosalind Franklin, who used x-rays bouncing off of the DNA to identify the double helix shape. The pictures actually show several strands of DNA that were woven together, because a single double helix would've been destroyed by the high-powered electrons used to visualize the DNA. Technological advances may enable double helices to be individually photographed someday. This discovery may allow people to see how DNA strands interact with each other and other genetic materials. 

Relevance: 
We learned about DNA in class during our genetics unit, and how x-ray crystallography was used by Watson and Crick to discover the double helix shape. We also talked briefly about Rosalind Franklin, her work, and how it was used in the future. Hopefully, this technology will improve and become more widely available, so schools could use it in Biology classes.

Source:
http://news.yahoo.com/dna-directly-photographed-first-time-193138553.html
11/30/12 - Taken from NanoLetters; written by Eli MacKinnon

Heart Telltale: Engineered Cardiac Cells Flash When They Beat

Heart Telltale: Engineered Cardiac Cells Flash When They Beat
By Tina Hesman Saey
http://www.sciencenews.org/view/generic/id/347159/description/Heart_telltale
December 17, 2012


Summary: Researchers "borrowed" a protein from Dead Sea microbes and re-engineered it to make heart cells light up with every contraction. The flashing cells can offer a way to predict whether new drugs will cause heart problems in people. A protein that helps a Dead Sea microorganism harvest energy from sunlight was taken by Adam Cohen and his colleagues, and they broke the molecule so it would give off instead of absorb light under certain conditions. When the protein- called archaerhodopsin 3, or Arch for short- was placed in heart cells, it flashed dim red light when heart cells got an electrical signal to beat. When calcium enters the cell or is released from storage place inside the cell to trigger heart muscle contractions, a different version of the Arch protein blinks blue. A new field of research known as optogenetics, in which researchers use flashes of light to control the activity of nerve cells, gave way to the idea for the flashing cells. The researchers placed the red and blue twinkling proteins into human skin cells that had been reprogrammed to make stem cells, and then were altered into heart muscle cells. The cells beat in time with each other. Reprogrammed cells could be created from skin cells of people with genetic heart problems to learn more about how their condition affects heart cell function in the future. Cohen envisions using his flashing cells to screen out drugs that could cause heart problems before they go into clinical trials, because applying drugs that affect heart rate on the cells changes the way the cells beat and alters the pattern of flashes from the monitoring proteins. People someday could be able convert their own skin cells into dishes of heart cells to test how they might respond to certain drugs. Cohen and his team also engineered the monitoring proteins into the hearts of zebra fish, which are partially transparent, allowing the researchers to see how the heart cells work in an actual organism. To test for any toxic effects on the heart, drugs can be added to the water the fish swim in. Simon Atkinson, a cell biologist at the Indiana University School of Medicine in Indianapolis, said putting the proteins into zebra fish is a good way to see how cells work together in a tissue.

Relevance: This relates to our study of molecular biology, as the researchers reengineered the protein so it would give off light. We learned about biotechnology, the use of organisms to perform practical tasks for humans. The branch of biotechnology that analyzes and manipulates the genomes of organisms at the molecular level is called DNA technology. The researchers manipulated the Dead Sea microorganism's proteins so they could see it flash. This experiment could lead to discoveries in drugs, which will help humans test their responce to them . We also learned from our textbook that stem cells have the potential to differentiate into various types of cells. Skin cells were reprogrammed to make stem cells, which could become heart muscle cells.
  

Sex-Reversal of Male Mice

Summary:
         Recent studies at the Institute of Molecular Biology (IMB) have shown that with just the deletion of one gene, the gender of a male mice can be completely reversed. This doesn't mean that the mouse's Y chromosome will convert into an X chromosome, (in fact, the Y chromosome will remain there) but rather that this specific gene, called Gadd45g, is necessary for the development of male sex organs. Gadd45g regulates signals that control Sry, a master regulator of male sex development. For male sex organs to develop properly, it is necessary for an abundance of Sry, but without Gadd45g, there will be a lack of Sry as well.    
         Research done at IMB by Professor Christof Niehrs has shown that with the deletion of this gene and a lack of Sry, the external genitalia of the mouse will be altered to be identical to that of a female mouse. With the deletion of Gadd45g, there is also a change in the internal reproductive organs within the mouse, making them those of a female mouse as well. While completing his experiment, Niehrs was puzzled why he got only females after breeding Gadd45g mutant mice, until he discovered that in some of the female mice, a Y chromosome was still present. From his observations, he was able to conclude that this gene is essential for the development of male sex organs. His research has since then been published in the  journal: Developmental Cell.

Relevance: 
          This news article is relevant to our current studies because it relates to our unit on genetics. We discussed how mutations in genes can have very disastrous effects or no effect at all. One of the mutations we have talked about is deletions. This article shows how the deletion of one gene, Gadd45g, can result in a very extreme change. This article also portrays how one gene can control another gene by helping it function. This story also has a relation to our unit on heredity because in this case, Gadd45g is a male gene inherited on the Y chromosome from father to son, but with the deletion of this gene, which could occur from a mishap in meiosis, a mouse's gender can be completely reversed.

November 29, 2012  - Research by Christof Niehrs of the Institute of Molecular Biology
http://www.medicalnewstoday.com/releases/253293.php

Quarter 2 Biomedia Report Due Dates

Due Dates and Topics for Quarter 2
Due Dates:
- Post Media, Summary, and Relevance by 1/10.
- Questions of Classmates made in comments by 1/18. THIS LINK may help.
- FOR EXTRA Credit: Answers to Questions posted in comments by 1/21.
The topics for term 1 are Heredity, Genetics, and Evolution.