Responsive material could be the 'golden ticket' of sensing

Source: University of Cambridge
Date: January 7, 2015
Website: sciencedaily.com
Author: University of Cambridge
URL: http://www.sciencedaily.com/releases/2015/01/150107082221.htm

Summary:
Short DNA strands attach synthetic lipid spheres, called vesicles, together to form a new substance that researchers of the University of Cambridge created. It is self-assembled and can intensify small differences in temperature and concentration of biomolecules when it changes its shape. This makes them easier to detect. Also, it can support a new type of biosensors and a new type of system for delivering drugs into the body. The material actually shrinks when exposed to high temperatures, which is caused by the interaction between the lipid spheres and the DNA strands. Researchers are able to make materials self-assemble into different shapes because they can customize DNA's sticky ends to only be able to compliment in base pairs with particular corresponding DNA sequences. On one end of each DNA strand is a sticky end. On the other end is a cholesterol anchor. The vesicles can be easily disfigured, which makes the material even more flexible. When the DNA strands spread out or rearrange, the material undergoes huge change in shape. The porosity of the material is affected by temperature. It is also affected by change in the concentration of the material's DNA chains.

Relevance:
The article is related to what we have learned in class. As the article says, the reason why the researchers are able to change the shape of this material into whatever they want is because the researchers can manipulate the sticky ends of the DNA strands in the material to go together with DNA that has a specific sequence of base pairs. In class, we learned that biologists are able to use restriction enzymes to make incisions in different locations in DNA sequences to get sticky ends with base pairs that will only match with sequences containing complementary base pairs. Because of the DNA's ability to be customized, the material's shape can be manipulated.

Why humans are right handed.

Matthew Clabault P2

Title: Evolution: Why are most of us right handed
Website: BBC
Author: Jason G Goldman
Date: December 16 2014
http://www.bbc.com/future/story/20141215-why-are-most-of-us-right-handed

Summary

85% of humans are right handed, an overwhelming amount assuming that it would be a 50/50 chance to be left or right handed. But what if there was another factor involved? Scientists have researched our distant ancestors and at around 1.5 million years ago it seems like the right hand was emerging to be dominant. Around 600,000 years ago there is a clear preference of the right hand. This is shown by examining the teeth of ancient remains which shows evidence that the right hand was used to bring food to mouth. Scientists believe that we are mostly right handed because of the wiring of our brain, the left side controlling the right side of the body but also being in charge of language. So because the left side was language controlling the right side of the body, the right hand became dominant as a side effect. Scientists are still trying to find evidence to what gave right handed people an advantage over left handed people.

Connection

This connects to what we are learning because while studying evolution we learned about natural selection while learning about Charles Darwin. And from the fossil record it seems like being right handed gave humans a distinct advantage at some point due to the large amount of people who are right handed. Or it might just be a coincidence, an example of genetic drift. Most likely there was a change in the environment that gave an advantage to the right handed people, thus killing off most of the left handed people. According to Darwin's theory the best fit to survive will repopulate the gene pool thus making it mostly right handed people.

New Antibiotic Stirs Hope Against Resistant Bacteria

Author: Denise Grady
Publication Date: January 7, 2015
URL: http://www.nytimes.com/2015/01/08/health/from-a-pile-of-dirt-hope-for-a-powerful-new-antibiotic.html?ref=health

Summary: A new method of producing antibiotics has reaped a potential new drug: teixobactin. The unusual process extracts drugs from bacteria that live in dirt. This method has the potential to unlock natural compounds that fight infections and cancer. So far, the drug has been tested on mice and "easily cured severe infections", without side effects. In addition, the drug works in a way that makes it unlikely that bacteria will become resistant to it. However, it has not been tested in humans, and will most likely not be tested in them for two years, so its safety and effectiveness are questionable. These tests will take several years, so if it is approved and becomes available, it will be in five to six years. It will probably have to be injected.

The search is in response the urgent global problem of a rise in infections that resist treatment with commonly used drugs. According to the Center for Disease Control and Prevention, drug-resistant bacteria infect at least two million people a year in the US, and kill 23,000. Additionally, the World Health Organization warned that such infections are occurring all over the world, and that drug resistant strains of many diseases are emerging faster than new antibiotics can be made to fight them. The fact that companies prefer developing more profitable types of drugs exacerbates the problem.

Previously, the natural compounds in teixobactin were unable to be studied because the microbes that produce them could not be grown in the laboratory. In order to grow them, scientists diluted a soil sample, placed it on specialized equipment, then put the equipment into a box of the natural soil, tricking the bacteria into growing.

Relevance: This article relates to what we've learned in two ways. First, when we were studying genetic modification, we studied how to use plasmids so that E. coli changes color and has bacteria resistance. Although teixobactin is still in the early stages of development and also is different from most antibiotics, the process of creating a drug for humans may involve some techniques involving plasmids. Second, the research of the development of teixobactin is in response to antibiotic resistance, which we are currently studying. Antibiotic resistance evolves by natural selection; the few strains of bacteria that happen to be resistant are more likely to reproduce, thus changing the gene pool and making the resistance allele more frequent.

Tobacco plant may be key to Ebola drugs

Varun Aysola

Author:Madeleine Stix

Date of Publication: October 3, 2014

Link: http://www.cnn.com/2014/10/03/health/ebola-tobacco-plant/

Summary:
     Over 3,000 people have died in West Africa and many American patients diagnosed with the deadly Ebola virus and , and the world is in desperate need of a cure. Two diagnosed American patients have recovered from the disease when treated with the ZMapp drug, however, it is not clear whether or not the drug was the cause of the recovery. Even if it was the cause, the process is very time-consuming and expensive, and an alternate method is preferred. A effective, fast, inexpensive technique is using genetically modified tobacco plants. Some companies implementing this technique include Kentucky BioProcessing, Caliber Therapeutics, Medicago, PlantForm, and University of Louisville's Owensboro Cancer Research Program in Kentucky. All of these are possible contenders for producing the GM tobacco-based Ebola vaccine.

Relevance: 
     This relates to the Honors Bio curriculum, as the scientists have utilized the tobacco-based drugs. These drugs were made using GM tobacco, which we studied in the molecular genetics unit. Similar to how we inserted an ampicillin resistance gene and a glowing gene to a plasmids in the E.coli in class, the scientists added certain genes to the DNA of a tobacco plant cell to make it contain the desired ingredients. Furthermore, the purpose of the drug was to cure the symptoms of Ebola, which is a virus. We talked briefly about viruses in the molecular genetics unit, when Hershey and Chase used them to observe where the genetic material was contained.

'Tasty': How Flavor Helped Make Us Human.

Jan 12, 2015
Title: 'Tasty': How Flavor Helped Make Us Human.
Author: NPR Staff
Website: http://www.npr.org/blogs/thesalt/2015/01/08/375932038/tasty-how-flavor-helped-makes-us-human
Date of Article's Publication: January 11, 2015



Summary: 
 It is true that in today's society, there seems to be an obsession with food. The term "foodie" is a popular term coined to describe all the food lovers out there. In a new book, The Art and Science of What We Eat, written by John McQuaid, the author describes how in an evolutionary standpoint, flavor has helped define who we are as a species. Billions of years ago when primitive life forms were roaming around the earth, and of course with the means of evolution, they had to compete with other primitive life forms in order to survive. To outcompete your fellow primitive creatures, you had to have sharper senses. If you had those sharper senses, that meant you would need a bigger, smarter brain for you to process those senses. For humans, bigger brains evolved after the beginnings of raw meat consumption, because raw meat had much more calories and fat opposed to fruits, nuts, veggies that were the main staples of their diet. It is an idea that the nutrients in the meat helped grow the brain. Another big part of the growth of the brain was cooking the meat, which allowed calories more easily available due to the meat being easier to chew and digest. As human's brains grew, so did their appreciation for food, therefore improving the taste of their food.

Analysis:
This article connects with our current study of evolution. This article discusses the hand in hand correspondence between the taste of food and human evolution. Along with that, came the evolution of food as well. As we humans began eating more complex foods, such as meat, it allowed our brains to grow supposedly. This allowed us to outcompete our competitors and also slowly change our diets, therefore the evolution of human diet. The "fittest" of the humans who are able to grow their brains and able to consume more calories are the ones who are able to pass on their "bigger brains" to offspring. This can get much more complex because once humans start eating meat, there is a new predator to animals, therefore more ways an animal can also evolve are introduced. My conclusion is that since we are a new predator, animals will now find ways to protect themselves and adapt to their new environment involving humans. Now the fittest for humans and animals and even plants will now survive. An example for plants are that plants can evolve to become more poisonous to fend from humans.

Devil is in the detail: Evolution of color in plants and animals

Full URL for the website- http://www.sciencedaily.com/releases/2015/01/150109093727.htm 

Author's name/source- Monash University

Date of the publication- January 9, 2015

Summary

Researches looked at some species of fish to help them answer a mysterious question. Their question was based on how populations come in different color variants: Why doesn't one color variant replace another color variant of a population. Also, researches wondered about why some variants of the same animal exist in nature. Color variants of the same species are huge examples of biological variation, but what adaptive significance and which evolutionary processes maintain them is still unknown. Researches decided to look at a species of fish called the red devil cichlid. This species comes in either a grey color with dark patterns, or a gold color with traces of red. The gold colored fish is genetically dominant. However, the darker colored fish is more common than the gold colored fish. The researches then took both types of the red devil cichlid and filmed them over some dark and light surfaces. They found out that the darker colored fish could change its brightness so it could match and blend to the surface it was on. The gold fish however could not do so. This means that the darker colored fish can blend in with its environment better, helping it hide from predators. 

Relevance 

This article is relevant to our biology class because it relates and refers to a lot of things we learned in chapter 14. Chapter 14 is all about evolution, which is what this article is relating to. The article refers to adaptation, which improves an organism’s ability to survive and reproduce in a particular environment. The article talks about how the dark colored fish is more common because it is able to adapt better to the environment and blend in with it. This prevents it from being eaten from a predator, which leads it to produce more offspring. This idea also related to natural selection because the offspring that the dark colored fish would produce would have the inherited characteristics to blend in with the environment and survive. Also, the article reveals a lot about variation, which refers to differences among members of the same species. The researches looked at two fish of the same species with a different variations to help them answer a question of how those variants are maintained, 

Orangutans crack consonants and vowels to shed new light on the evolution of human speech

Source: Phys.org
Date 1/09/15
URL: http://phys.org/news/2015-01-orangutans-consonants-vowels-evolution-human.html

Summary: For a long time it has been a mystery how humans evolved the capacity for the complex languages we have today but recent studies in orangutans have shed light on how this occurred. Ever since darwin first proposed his theory of evolution the origin of language in humans has been a question asked by critics of his theory. And now after all these years we have a parallel in the great apes, the orangutans. Research has shown the orangutans ability to create new calls displaying similarities to human consonants and vowels. These calls were produced by rapidly opening and closing of the lips, much like humans do. Prior to this discovery the ridged use of calls amongst the great apes was a huge roadblock to understanding the origin of human language. Their apparent lack of a capacity to modify of learn new calls stood in stark contrast to humans, causing us to wonder about the origin of our complex languages. However this new finding allows us to see similarities between humans and great apes.

Relevance: In this chapter we are learning about Darwin's theory of evolution, the selection of beneficial traits through natural selection of random mutations. This article talks about the evolution of the capacity to learn complex languages in humans. We already know that we evolved from great apes but the lack an early form of a this capacity and the rigidity of most great apes calls was odd given the complex languages we have evolved to be able to use. But the appearance of this trait in orangutans shows that it is possible for it to arise through natural selection showing how it is possible for us to have evolved our languages from great apes.

The Evolution of Several Species of Insects

Elizabeth Hora
1/12/15
Websites:
#1 http://www.the-scientist.com/?articles.view/articleNo/41396/title/Genetic-Data-Clarify-Insect-Evolution/
#2 http://www.livescience.com/48663-insect-family-tree-evolution.html

Summary:
People have often wondered about the history of insects, and how they became  what they are now. A new study has looked into the evolution of insect species and how they differentiated into the many species that we see today. The research team from around the world was able to construct a family tree from an evolutionary standpoint called a phylogenetic tree. The researchers compared 1,478 protein-coding genes and compared them with insects today and fossils. Due to the technology available to sequence transcriptomes, or a set of all RNA molecules, the research team was able to compare 144 insect genuses of insects that exist today. They found out that remipedia, a type of crustacean, is the closest living relative to insects. Fossils have provided evidence that insects started to evolve 412 million years ago. Even though the results and dates are not confirmed, researchers believe that insects began to colonize land around 479 million years ago. The researchers also believe that insects started flying around 406 million years ago, which was before the fossil record started having many fossilized flying insects. The study also looks in the evolution of lice and claims that the parasites started off with the feathery dinosaurs and later went to mammals and birds. The research team also believes that the insects we see today look relatively similar to the prehistoric insect species.

Connection:
This article relates closely to what we are learning about in class. First, it talks about speciation, how a common ancestor can lead to the differentiation of species, in this case insects. The study also mapped out 1,478 protein-coding genes. Our last unit in class was about molecular genetics. We learned all about RNA and all of its different forms such as: tRNA, mRNA, and rRNA, which is what the study was able to sequence. We also learned about the structure of RNA and how each of the different types function. We also have learned about the fossil record. We know that based on where fossils are situated in the rock strata, we have a good idea of when the fossil specimens lived. This is how the research team who authored the paper was able to figure out when the insects started to differentiate from one another. Finally, the whole study was about the evolution of insects. We have learned about Darwin and his observations, and the process he followed to reach a conclusion that is accepted by scientists. Evolution describes how an original species can divide into many other species.

Natural Selection is Furthering Mutations That are Making Skin Paler

Source: (Science Daily), University of the Basque Country
Link: http://www.sciencedaily.com/releases/2014/12/141205100058.htm
Date: January 9, 2015

Summary:

     Human skin color varies according to the latitude and, therefore, according to the intensity of ultraviolet light. Individuals living at low latitudes generally have darker skin, whereas those living at high latitudes have paler skin. It has been determined that evolution is furthering mutations that are lightening the skin, probably owing to the need to synthesize vitamin D at latitudes where there is reduced solar irradiation. However, in turn, this increases the probability of developing melanoma or other types of skin cancer. Natural selection furthers certain mutations so that individuals can have paler skin, since at certain latitudes having a skin with a dark pigmentation prevents the synthesis of adequate levels of vitamin D, essential for survival. Vitamin D can be obtained through the diet, but also in an indirect way as UV light passes through the skin. Dark skin contains the pigment melanin, which acts as a barrier and prevents UV rays from penetrating. At high latitudes where the intensity of UV light is very low, this is a problem, as insufficient quantities of vitamin D are synthesized.

     Why does natural selection further a mutation that causes cancer? Vitamin D is essential for skeletal mineralization and development, and the lack of this vitamin can lead to various problems in children's health. Yet the skin cancer melanoma is a cancer that tends to appear in adult life, following the reproductive phase. Theoretically, as these adult individuals have by now produced offspring, they are no longer important in evolution. 

Relevance: 

     

     This topic relates to what we are learning about evolution in Chapter 14. This article relates to natural selection, the process whereby organisms better adapted to their environment tend to survive and produce more offspring, which we have talked about in class. Darwin's theory of "Descent with Modification" presented in Chapter 14 states that over time and generations, traits providing reproductive advantage become more common within a population. This directly relates to my article, in which over time, human skin depigmentation has occurred due to the need to synthesize vitamin D. This has occurred due to the process of natural selection, in which individuals who carry the trait for paler skin have a higher chance of surviving and passing on this trait to their offspring at higher latitudes, where there is less solar irradiation. 

There's More Than One Way to Silence a Cricket: Co-evolution of Crickets Who Lost Their Chirp

Source: Cell Press
Date: May 29, 2014
http://www.sciencedaily.com/releases/2014/05/140529142442.htm

Summary

Crickets, usually most recognizable from their distinct chirping sounds males make with their wings to attract females, have gone silent on the islands of Hawaii. The silence is an adaptation for the quiet males to use to avoid parasitoid flies, which are attracted the the cricket song. The fly larvae burrow into the cricket, and kill the cricket within a week or so. These quiet crickets are able to avoid the flies, and still manage to mate with female crickets by positioning themselves near male crickets that are able to produce the cricket song and attract female mates.

At first, scientists had thought that a group of these silent crickets had traveled or migrated from one island in Hawaii to another. After further research, scientists have noticed obvious differences in the wings of the silent crickets from the different islands Oahu and Kauai. The silent wing mutation was traced back to a sex-linked gene. Another scientist performed a genome-wide scan which showed that the genes responsible for the traits were linked to different genetic markers for the two silent cricket populations. This has led scientists to believe that the trait for the silent crickets rose in two different islands independently, but at the same time. This is an example of convergent evolution.

Relevance

This relates to our topic about evolution. If the flies were not present, the normal chirping crickets would possess traits that would be more favorable to the environment, as the crickets would be able to find mates more easily than the silent ones.With the presence of the flies, the silent crickets are more likely to survive, so they will be able to reproduce and pass on the gene. But, since the silent crickets depend on the song-producing crickets, each new generation of crickets must have a few chirping crickets for both different types of crickets to survive.

This also relates to our study of genetics. Crickets do not have Y chromosomes to determine sex. Two X chromosomes (XX) would be a female, and one X chromosome would be a male. Because this mutation is sex-linked, it would explain why the trait for silent-wings spread rapidly. It would only require one copy of the silent wing gene to be displayed in the cricket's phenotype.

Scientists identify new gene that drives triple-negative breast cancer

Author: Honor Whiteman

Date Published: January 11, 2015

URL: http://www.medicalnewstoday.com/articles/287788.php

Summary: Scientists in the United Kingdom have been researching a cure for breast cancer and have found a gene called BCL11A. This gene causes triple-negative breast cancer - an aggressive form of the disease that accounts for 10-20% of breast cancers. This gene does not react to hormone therapy. Therefore hormone therapy is rendered useless for treatment of cancer when someone has triple-negative cancer.   Dr. Walid Khaled of the Welcome Trust Sanger Institute and the University of Cambridge in the UK has noted that a lot of research has been put into curing triple-negative cancer. Scientists have been trying to find the gene that cause this form of the disease for years. To find the BCL11A gene, scientists had to take a different approach where they looked at genes that influence the actions of stem cells and developing tissue cells. When they reduced the BCL11A gene they saw a decrease in cancer activity. In a study of 3,000 patients, the BCL11A gene was found to be increased and was associated with the cause of aggressive tumors. In later tests when the gene was decreased cancer activity was greatly decreased and tumor growth stalled until the gene was allowed to be used again.

Relevance: This is relevant to class because we have recently studied how depending on your genes you could have some sort of disease. We had learned about trisomy 21 where if you have three 21st chromosomes instead of two you could have a serious mental handicap. We also learned about mutations in genes, how they could affect the persons appearance or mental capabilities. Cancer is a mutation that can be passed on from your parents to you and if your parents had a mutation in their genes there is a good chance that you could receive it. We also learned that you can genetically modify organisms in our GMO lab and our debates. In the article it discussed how humans were able to deactivate and/or decrease the number of BCL11A genes in humans and in mice which lowered the amount of cancer activity. 

Bowhead Whales are the longest lived mammals. How do they do it?

Title: Bowhead whales may unlock the secrets to a long, healthy life

Website: sciencenews.org

Author: Kate Baggaley

Date of Publication: January 6, 2015

URL: https://www.sciencenews.org/article/bowhead-whales-may-unlock-secrets-long-healthy-life?mode=topic&context=76&tgt=nr

Summary
        Bowhead whales, the longest lived mammals, can live more than 200 years as they are not prone to many cancerous diseases and aging issues. By running tests to map out the genome, scientists reveal that though bowhead whales contain approximately a thousand times more cells than humans, their risk for cancer is low due to an almost zero percentage chance of uncontrollably dividing cells. In addition, whales can repair their DNA better than humans. Whales do not allow any damaged DNA to accumulate to such an extent where they may receive cancer or any aging type diseases. Within their DNA, the nitrogenous bases code for certain characteristics which prevent the accumulation of many cancerous cells. A gerontologist at the University of Liverpool named João Pedro de Magalhães suggests that by identifying those genes and manipulating human genes so that cancer and other aging diseases decrease may be the next step for humans to live a longer, healthier life.

Connection
      This article connects to our unit of Molecular Genetics in many different ways. First, when DNA is replicated, there are few errors due to enzymes self-checking the process. Although the human DNA is extremely thorough, there are many things that can go wrong such as a mutation in large regions of a chromosome or a single nucleotide pair. However, in whales, the self-checking process is more detailed so nothing can go wrong. Of course, there are some exceptions, but the percentages for mutations are higher in humans. In addition, cancer is created through uncontrollable cell reproduction caused by a mechanism that normally controls the cell cycle. A possibility is that this mechanism can be turned off by a restriction enzyme which unlocks a repressor protein from controlling cellular production. Finally, artificial, desirable genes from the whale for the cancer "resistance" can be added to a plasmid in a human's cell, which may answer Magalhães theory of humans living longer, healthier lives.
        

Evolution: Why are most of us right-handed?

Madison Hora
Website: http://www.bbc.com/future/story/20141215-why-are-most-of-us-right-handed
Author: Jason G Goldman
Date: 12/16/14

Summary:
This article tries to answer the question of why there is such a dominant right-handed society today. It says that for humans about 85% of us are right-handed, and they think that there has never been a society of humans that were predominantly left-handed. They think that this started in the brain. Since the left side of the brain controls the right side of the body and some major physical tasks they think this could be a reason for it. They even think that some of our ancient ancestors were right-handed by looking at the tools that they made. But there is little evidence for this, and it would be very difficult to prove. They looked at the chimpanzee to see if they also were dominantly right-handed, but there didn't appear to be any favor over either hand between them. The article also explored the idea of language first developing in the left side of the brain which for some reason intensified the preference for the right hand as a side effect. They also accept that it might be just a coincidence that humans passed down the preference of the right hand.

Relevance: 
This relates to what we are learning because the article is about the evolution of human's preference to use the right hand. They suggest that early humans used their right hand purely by chance or because of the way that the brain developed. In class we have talked about evolution and the passing down of traits and genes. This article says that the preference for the right hand is genetic and has been passed down from our ancient ancestors. We have also talked about genetic traits and habits being passed down. The preference for the right hand also relates to evolution since as the brain developed language, it became associated with the left side of the brain. This side controls the right hand, so maybe this is why people started writing and drawing with their right hand.

Using GMOs for Biofuel

Title: Biofuel breakthrough: scientists use GMO yeast to produce fuel

Website: ScienceNordic.com

Author: Kristian Sjøgren

Date of Publication: October 10, 2014

URL: http://sciencenordic.com/biofuel-breakthrough-scientists-use-gmo-yeast-produce-fuel

Summary: Two studies done at the Technical University of Denmark and at the Massachusetts Institute of Technology (MIT) have found ways to genetically modify yeast to make a more efficient way to produce cheaper biofuel.  One of the problems with yeast is that it is not very tolerant to the ethanol that its cells produce themselves.  The genetic engineering done at MIT has made the yeast more tolerant to its produced ethanol, meaning that the yeast doesn’t die when the ethanol concentration gets higher.  These studies found that their genetic engineering led to an eighty percent increase in the production of biofuel from the yeast.  Another problem with regular yeast is that it can only function at certain temperatures and yeast stops working at about 35°F.  The Danish study’s genetic engineering has made yeast able to withstand temperatures up to 45°F instead.  The studies found that a major difference was made when they added potassium chloride and potassium hydroxide.  This made the yeast cells able to withstand the ethanol that they produce making the production of biofuels cheaper and faster.  This biofuel is also looked at as a possible alternative to fossil fuels.

Connection: This article connects to our fifth unit where we looked at molecular biology.  In this unit we looked specifically at genetically modified organisms (GMOs).  We studied modern uses of genetically modified organisms and we specifically looked into the process of genetic engineering to give useful characteristics to different types of organisms.  However, we mostly looked into the use of GMOs to give farmers more profit or to make farming easier for themselves in examples such as pesticide resistance.  This article takes the use of GMOs outside the farm and looks at the benefit that they can bring to the energy industry.  However it does connect to farming as it does provide a cheaper alternative to using traditional crops, like in the case with farming.  This also connects to our first unit where we looked at different cycles, specifically the carbon cycle.  One of the main contributors of carbon emissions is the burning of fossil fuels.  Using genetically modified yeast to produce biofuel works as an alternative to using the limited source of fossil fuels.    

Heritable Variation Discovered in Trout Behavior

Source: University of Eastern Finland 
Date of Publication: March 13, 2014
Link: http://www.sciencedaily.com/releases/2014/03/140313092219.htm

Summary: 
Recently, researchers have noticed that endangered salmonids' catches have decreased. Previous research has shown that certain behavioral traits explain individual differences in how fish survive in the wild. A new Finnish study conducted on brown trout now shows that there are predictable individual differences in behavioral traits, like tendency to explore new surroundings, activity, and stress tolerance. Certain individual differences were observed to contain heritable components. A study was carried out in the Finnish Game and Fisheries Institute's Kainuu Fisheries Research Station in Paltamo: they discovered that the behavioral traits examined were individually repeatable. Fish showed personality. Furthermore, certain behaviors related to stress tolerance, such as freezing, showed statistical heritability at a level of 14%. This means that it is not random that mortality related to stress tolerance both in fish farms and in the wild can modify the heritable traits of fish populations and lead to changes that are difficult to reverse. This is bad for humans, because these changes might weaken the ability of fish to avoid predators and decrease the fisheries' catches unless mitigated by acknowledging the potential selection acting on fish personality.


Relevance: This article is relevant to what we are doing in class for 2 main reasons. Firstly, in chapter 9.5, we talked about how meiosis functions in sexual reproduction, and in a sexually reproducing species inherits a unique combination of genes from its two parents. So for example: people resemble the other members of their family more than they resemble a stranger, but they do not look exactly like their parents or siblings. In this article, mother fish can pass some of it's hereditary material onto it's off springs (14%), and that fish don't look or act, exactly like each other. Secondly, in chapter 14.1, after Darwin went on the HMS Beagle, and collected evidence from geology, he published his theory- the first of two main points Darwin presented was "Descent with Modification": descendants from earlier organisms spread into various habitats over millions of years. And in these habitats, they accumulate different modification or adaptations to diverse the ways of life. It is the same thing with the fish in my article, they have live in the same habitat, but they certainly do have different  traits that they have adapted, they would make the fish population have more diversity. 

Transgenic American Chestnuts

Author: Chau Tu
Date: article published Dec. 22 2014
Website: Science Friday
Link: http://www.sciencefriday.com/blogs/12/22/2014/picture-of-the-week-transgenic-american-chestnuts.html

Summary:

For almost 100 years, the American chestnut has been “spiraling towards extinction,” according to Charles Maynard, a professor at SUNY College of Environmental Science and Forestry (ESF). At the turn of the 20th century an exotic fungus called Cryphonectria parasitica, which originated from imported Japanese chestnut trees that were resistant to the parasite, destroyed the American chestnuts. The fungus spread across its natural range in less than 50 years, infecting close to 100% of the population. Researchers at SUNY-ESF have been developing a blight-resistant chestnut tree. They needed to find a blight-resistant gene that could be incorporated into the American chestnut tree genome. William A. Powell’s lab discovered a gene from wheat that makes an enzyme that detoxifies oxalic acid, breaking it down into hydrogen peroxide and carbon dioxide—both chemicals that chestnut trees can use to fight the fungus. Another lab has focused on incorporating this gene into American chestnut tree embryos derived from the plant's somatic cells. These embryos are regenerated into whole plants. Earlier in the year, the American Chestnut Restoration Project team announced that it was successful in developing a blight-resistant chestnut. So far 18 lines of trees, have demonstrated good blight resistance, says Powell. After the researchers funnel the trials to find the most successful plants, they will apply for approval from the FDA, the USDA, and the EPA. Powell estimates that the process will take about five years, after which they will distribute the trees to the public. 

Explanation: 
This article referred to two units we have studied so far: the unit on heredity, and the first unit on biomes and the environment. The American chestnut trees are transgenic. Transgenic describes an organism whose genome has been altered through the addition of a foreign gene from a completely different species. The researchers are have added a gene from wheat into chestnut trees, in order to make them resistant to the fungus. We learned that invasive species are organisms that are not native to the land that they are 'invading' and that they have a negative impact on the species around them. This fungus was actually brought along by imported Japanese chestnut trees that were resistant. The Japanese trees can be called an invasive species, because they caused a harmful fungus to spread thus causing a decrease in the population of the American chestnut trees. These trees were obviously not native to North America and did not grow in a similar environment. 

Making Evolution Makes Microbes Make Products

Author: Cynthia Graber

Date Published: January 8, 2015

Website: Scientific American

Link: http://www.scientificamerican.com/podcast/episode/making-evolution-make-microbes-make-products/

Summary:

          Genetically engineered bacteria has proved its worth, by producing products specifically of biomedical importance, such as insulin. But the variety of products made is limited due to inefficiencies within the genetically engineered bacteria. Researchers at Harvard’s Wyss Institute for Biologically Inspired Engineering have shed light on a new solution that could potentially broaden the variety of products made while reducing the number of environmentally harmful byproducts made using other production methods. Using a few of Darwin’s principles, researchers created a system of bacteria in which they mutated specific genes related to the production of the desired molecule. Then they altered the properties of the bacteria by making the antibiotic resistant genes “turn on” only once the bacteria had made a specific amount of the desired product. Once the system of bacteria is ready, the antibiotics are added. The bacteria that are able to produce more than the required limit survive, those who cannot manufacture the required limit are killed, reducing the number of unproductive bacteria each time. This process is repeated numerous times and is referred to by the researchers as the cycle of evolution. By putting the bacteria through the “cycle of evolution”, the researchers are able to create the desired chemicals a thousand times faster than other current production systems and are able to synthesize the desired chemical with 30 times the output of those production systems. Within time, this new method may induce genetically engineered bacteria as the main manufacturers of commercial chemicals.

Connection:

         This article connects to both of our units on Molecular genetics and our current unit on Evolution. Within our unit on Molecular Genetics we learned about the process of transformation within bacteria. In this unit we closely examined insulin, and how it was once extracted from animals and then entered into patients. Now, scientists are able to use restriction enzymes to cut a desired trait and then add it to a plasmid and then transfer the plasmid into a cell to make the desired molecule. This article explains the same process but has edited this process to make the production rates more efficient. Although the basics remain the same, scientists have applied Darwin’s theory of Natural selection to the process. Although it may appear artificial selection is going on as well, scientists say that “Because artificial selection tends to amplify unproductive cheaters, we devised a negative selection scheme to eliminate cheaters while preserving library diversity.” This being said, natural selection is present because when the bacterium is in the environment filled with antibiotics, only the highest producers survive. Here we see that the survival of the fittest is applied. Then as the survivors reproduce asexually, their offspring have an identical set of DNA and are also able to produce the desired chemicals at a high production rate. The bacterium that produce the chemicals insufficiently die out and do not reproduce therefore, only those who can produce a good quantity of the desired chemical survive on to the next cycle.The part in which the antibiotic resistant genes “turn on ” closely resembles our study of gene regulation. Similar to the lac Operon within E, coli, the microbes’ antibiotic resistant gene is turned off until the microbe has produced the required amount of the desired chemical.

Gene Editing Will Change The World

Author: Harry Glorikian

Date Published: January 2, 2015

Link:http://www.genengnews.com/insight-and-intelligence/gene-editing-will-change-everything-just-not-all-at-one-time/77900351/?kwrd=GMO

Summary:
First, the article talks about gene editing, where scientists use site-specific endonucleases to identify a double-stranded break in the genome of an organism, and fix that gene by disrupting it or rewriting its sequence. The author then cites four ways of gene editing using meganucleases, zinc finger nucleases (ZFNs), transcription activator-like effector nucleases , and clustered regularly interspersed short palindromic repeats. According to the article, Sangamo Biosciences is the only company to utilize the ZFNs technology at clinical trials for human therapeutics.

Secondly, gene editing has agricultural applications. Glorikian mentions that the human population is expected to rise by 2 billion people by 2050, and that it will be accompanied by rising food prices, famines caused by natural and political events, and by the overdevelopment of crop-suited land. Nevertheless, gene edited crops, can help with this anticipated disaster in that the crops can be edited to have higher yields, withstand droughts, and have more essential nutrients. In addition, genetically edited genes are more socially acceptable than genetically modified organisms because scientists edit the original/native genes of an organism while modifying an organism involves taking foreign genes, a process that has not been widely appealed to.

Connection:
This article primarily connects to our unit on molecular genetics. Relating to molecular genetics, the article describes how gene editing involves biological structures that make up genes, such as DNA, and edits them by disrupting or rewriting sequences that are “written” in nitrogenous bases. Additionally, this article relates to our debate on GMOs. Harry Glorikian brings up the level of social acceptance of GMOs, and how they’re not well supported, stating how they’re “politically controversial”, because of the addition of foreign genes. 

Lastly, this article briefly states a concept related to our study of evolution. The article states that the human population will grow from 7 million to 9 million people, and that the world currently doesn’t have the necessary resources to support that many people. The author is linking to an idea brought up by Thomas Robert Malthus in that a production of more individuals than the environment can support leads to struggle for existence.

Scientists Tap Tree Genomes to Discover Adaptation Strategies

Source: Virginia Tech
Date of Publication: January 5, 2015
Links: http://www.sciencedaily.com/releases/2015/01/150105092922.htm

Summary:
After decades of extrapolation about gene function in trees based on gene function from a tiny, less complex plant, a team of scientists has finally sequenced whole genomes from 544 unrelated trees of the same species. This accomplishment makes it easier for the scientists to understand the significance of gene variation for the environmental adaptations of trees. For example, the scientists identified two related genes from Populus, a type of deciduous flowering tree species that lives in northern hemisphere. This type of tree contains FT 1 gene and FT 2 gene. The FT 1 gene was known to regulate the transition to flowering and FT 2 gene is important for controlling fall growth cessation and bud set. This gene variation helps the tree to survive because they control the timing of both dormancy transitions in spring and fall. They are like an alarm clock, they tell the trees when to bloom and when to sleep. This gene variation is also an example of adaptation because the area where the Populus grow has four seasons. Therefore, Populus adapted to the environment genetically. Unfortunately, according to Professor Brunner, this example is just a notable exception. It is going to take a while for scientists to derive more conclusions. She said, "The challenge is that we have identified all these genes but don't yet have a good idea of their function." Currently, most of the knowledge of what genes are important for environmental adaptation of trees has been evidentiary guessing that built upon the model plants. Brunner also stated that they need to do more in the actual tree system rather than relying solely on extrapolating from model herbaceous plants.

Relevance:
This article is related to what we have learned in Chapter 14, Evolution: A history and a process. Specifically, in Concept 14.1, we learned that adaptation is an inherited characteristic that improves an organism's ability to survive and reproduce in a particular environment. In this case, genetic variation played a key role in the adaptation of Populus tree. If there is only FT 1 gene, the trees could die because they cannot adjust to fall and winter. In turn, if the FT 2 gene is missing, the trees would not bloom in spring. And based on the concept of the artificial and natural selection, the trees that do not bloom may have some issue with the next generation because they cannot spread their seeds as easily as other plants do. And humans might cut down those kind of trees because people might think they are useless according to their plain-looking. Additionally, in the article, it also mentioned that Poopulus is a type of deciduous tree. According to Concept 34.3, the temperature deciduous region tend to be very cold in winter and quite hot in summer. So this genetic variation is extremely important for the trees like Populus to adapt to such environment.

Cell Analysis Reveals Complex Variations In Stem Cells

By: Cherry Jia

Author: Kat J. McAlpine

Publication Date: December 4, 2014

Website: Wyss Institute

URL: http://wyss.harvard.edu/viewpressrelease/182

Summary:

Stem cells, which can multiply indefinitely, have the potential to to differentiate and develop into any kind of human cell and bodily tissue. Recently, scientists at the Wyss Institute for Biology Inspired Engineering at Harvard University discovered that stem cell colonies actually contain a lot of variability between individual cells. They learned that there are small fluctuations in the state of a stem cell’s pluripotency that can influence the development path that the cell eventually follows. The researchers have captured a detailed molecular profile of the different states of stem cells. The Broad Institute provided them with the new technologies used for studying individual cells. The researchers learned about stem cell development through these technologies by perturbing the cells with variants such as different chemicals, culture environments, and genetic knockouts. They then analyzed the individual genetic makeup of each cell to find that there were microfluctuations in each stem cell’s state of pluripotency. The scientists observed small differences in the way the stem cells were influenced by internal, chemical, and environmental cues. This led to the discovery of a complex “decision making” circuit of developmental regulators. Since, the scientists now understood the causes and consequences of differences between individual stem cells and how the balance of key regulators within a cell can affect that cell’s developmental outcome, they realized that there must be a “code” that relates patterns of dynamic behavior in stem cell regulatory circuits to the developmental  path a cell ends up taking. By using that code, they hope to dial in precisely to specific individual cell states. They also hope to use this new technology for purposes such as making better regenerative medicines by making stem cell engineering more predictable. Scientists are already able to precisely classify cells, identify the regulatory circuits that control their cell states, and balance the key regulators within a cell that can affect a cell’s developmental outcome. So all they need to do is apply this. If this is successful, they hope to use stem cells to overcome a wide range of diseases and injuries in the future.

Relevance:

During our unit on the applications of DNA technology and molecular biology, we learned that stem cell clusters present after birth are no longer capable of making the full range of new tissues with the ease that embryonic stem cells (before birth) can. We also learned that because of laboratory experiments, scientists can develop bone marrow stem cells into nerve cells under the right conditions. However, this procedure did not have a good success rate as it was mostly trial and error. This connects to the article because now that scientists have a much better understanding of stem cells and how they operate by the “code,” they can dial in precisely to specific individual cell states and be able to grow stem cells in the way that works with the stem cell’s regulatory circuits. This will boost the success rate of stem cell development, whereas before, this kind of technology was much less predictable and controllable.

Modern Human Bone Density Drop Tied to Lifestyle Shift

Title: Modern Human Bone Density Drop Tied to Lifestyle Shift
Website: Discovery News
Author: Charles Choi
Date: December 29, 2014
http://news.discovery.com/human/evolution/modern-human-bone-density-drop-tied-to-lifestyle-shift-1412291.htm

Summary:
Scientist have observed that modern day humans' bones are much less dense than our ancestors. Originally, they figured that modern-day humans' bones would just be less dense than those of Neanderthals and our primate ancestors, but upon more in-depth research, they have found that our bone density also differs with the modern humans from before the current Holocene Epoch, which started around 12,000 years ago; they also had denser bones than us. The lesser dense bones in recent modern humans explain the rise of some bone conditions such as osteoporosis.

As for an explanation as to why this shift occurred, there are two main hypotheses. One is simply that the modern humans have fallen into bad dietary habits and have been consuming less calcium than our ancestors. The other hypothesis is that physical activity has changed. To support this, a group of paleontologists compared the hip bones in groups of old humans- groups of agriculturalists and groups of mobile-foragers. They found that these mobile-forager groups, who would be more physically active, had the stronger hip bones, suggesting that physical activity was a factor in the bone density of humans.

Relevance:
This relates to ideas of evolution and natural selection that we talked about in class. Stronger bones in the mobile-forager groups is an adaptation that would be genetically advantageous for these humans, given that the groups would have to move a lot, so the denser, stronger hip bones would be of advantage to them. These humans may have been more likely to survive to reproductive age and support the population growth, as the weaker-boned mobile-foragers would not be as fit to survive the lifestyle. Thus, natural selection would occur and the population would eventually be made up of denser-boned mobile-foragers.

As for the explanation of the differences in bone density in humans today, this evolution occurred partially because of genetic drift, and partially because of natural selection. As humans transitioned from hunter-gatherer nomads to more permanent living arrangements, there may no longer be a benefit for the denser bones, which relates to the idea of adaptation. As we talked about, Darwin's findings contradicted the once-believed idea that species remained unchanged. But Darwin said that species could adapt to their environments, and also that these adaptations could evolve as well as they became more or less useful to the species. This relates to the bone density research because of the change in bone density after the adaptation became less useful. Genetic drift comes into play here, because thousands of years ago, perhaps it was by chance whether the thinner or denser bone genes were inherited from the gene pool . But it could also be do to natural selection, because the denser bones may actually have been slightly detrimental. When they no longer needed the bones to walk long distances, it is possible that the denser, heavier bones actually decreased mobility, causing natural selection to play out, with evolution favoring the humans with lesser dense bones. Either way, it is clear that some evolutionary change has caused this shift in human bone density over time, similar to ideas we have discussed in class about Darwin's finches and other evolutionary phenomena.






Hannah Gearan

8,000-year-old mutation key to human life at high altitudes: Study identifies genetic basis for Tibetan adaptation

       

Date published: August 17, 2014

Source: University of Utah Health Sciences 
http://www.sciencedaily.com/releases/2014/08/140817215846.htm

Summary:

A study led by University of Utah scientists have found a genetic cause for an adaptation that caused Tibetans to thrive at high altitudes of the Tibetan Plateau where the air is thin and oxygen is scarce. After a strong reluctance by the Tibetan people to provide samples for research the team finally obtained and analysed blood from the people to achieve astounding results. They found that a gene specifically notated as EGLN1 had been mutated in a single base pair 8000 years ago and was the cause for this adaptation. They also found that about 88% of all Tibetans had it and that the mutation was absent in closely related Asians that lived in the lowlands. They have also identified the advantages that this mutation provides for carriers like the Tibetans in the particular habitat. At high altitudes where oxygen is scarce, blood normally thickens with oxygen carrying blood cells that cause long term effects like heart failure.  The Tibetans are protected as the mutation gives them a decreased response to the low amount of oxygen. Further research that is being done on this mutation can result in treatments for various diseases.

Relevance:

This is relevant to what we learnt in class about how in evolution, mutation changes gene pools by adding new traits(characteristics) that then undergo natural selection, how mutations  affect phenotype and also how the mutation is passed on through generations. The Tibetan people would have originated from the lowland areas which they were normally adapted to. They probably did not survive very well at high altitude environment which they were not adapted to, but through natural selection the few people with the gene mutation would be able to withstand the conditions of scarce oxygen and reproduce successfully in the new environment. The particular environment favoured this essential trait and so its frequency increased very quickly and made it common to most people living there. The mutation affected the gene in the gametes of people who had the mutation that then caused future offspring to inherit it. This also shows how a single mutation in the genotype can greatly change an organism’s phenotype. 

Forget the selfish gene: Evolution of life is driven by the selfish ribosome, research suggests

Author: Aarhus University
Publication Date: January 7, 2015
URL: http://www.sciencedaily.com/releases/2015/01/150107101405.htm

Summary:
    Many scientists accept the "selfish gene" theory to explain the origins of life; it states that DNA came first in the evolution of life and coded for the synthesis of the proteins and nucleic acids found throughout the cell. However, Dr. Meredith Root-Bernstein and her father, Dr. Robert Root-Bernstein, have found evidence that suggests that the ribosome was the original structure that self-replicated and led to DNA. Molecules can change form when provided with energy, but they all have a natural resting position, the form that the molecule returns to. In this way, the resting position could be considered the molecule's "desired" form. While DNA rests in coils, "not wanting" to replicate or translate, ribosomes rest in a position than can readily translate DNA. This led the Root-Bernsteins to hypothesize that ribosomes were once capable of replication and protein synthesis. Upon close examination of the ribosomes of E Coli, they discovered that the ribosomal RNA contained structures that resembled ribosomal protein-encoding sequences, messenger RNA, and transfer RNA-encoding sequences. Thus, ribosomes may have originally been able to self-replicate, possibly before DNA could.

Relevance:
    This article relates directly to our unit on molecular genetics. The basis of the Root-Bernsteins' proposal is the structure of DNA and ribosomes. One of their pieces of evidence came from how DNA is found in coils for most of the cell's life. They also further explorer the structure of the ribosome. The ribosome had previously been thought to have a purely structural function; its two subunits are positioned well for tanslation, but the Root-Bernsteins examined the rRNA more closely. They were able to find indications about the existence of three types of RNA in the ribosome: the rRNA itself, mRNA sequences folded into the subunits, and coding regions for tRNA. In class, we learned about these types of RNA and their key roles in protein synthesis. Additionally, the article relates to evolution in the sense that the ribosome may have coded for the first forms of organisms. From the indication of the organelle's ability to self-replicate and code for the production of nucleic acids, the idea that organisms coded by ribosomes evolved into those coded by DNA is now a possibility.

Coming soon: Genetically edited 'super bananas' and other fruit?

Title: Coming soon: Genetically edited 'super bananas' and other fruit?
Website: Science Daily
Author: Not Stated
Date: August 13, 2014
http://www.sciencedaily.com/releases/2014/08/140813131044.htm

Summary:
     The recent advances in biotechnology now allow scientists to genetically "edit" bananas' and other fruits' genomes. This will allow scientists to genetically improve these fruits without having to introduce foreign genes to them. Avoiding the transgenic aspect of genetic modification makes the process a lot more natural and takes away the scare for a lot of anti-GMO people. The slight changes in the fruit genome would allow us to increase and decrease how much of a natural ingredient they would make. For example, increasing the amount a vitamin A made in bananas. This is made possible by the use of new tools CRISPR and TALEN. Also, the knowledge of the fruit genome allows us to pinpoint the areas that require change in genetic editing. Once the area of the genome is pinpointed, the scientists can insert, delete or alter the order of this specific part of the genome. Fruits are only the start to this new process, and as the genomes of more foods become more well-known the process will be able to become more widespread. So say good bye to GMOs, and say hello to the more natural GEOs.

Relevance:
     This article relates to our curriculum of the past term because it relates to biotechnology and how plants are genetically modified. The article describes a new, more natural way genetically modify fruits. We had a GMO vs. Non-GMO debate and this new tactic would have been a good tactic for the GMO side as all the people who are Anti-GMO because is "unnatural,"can be answered with this new more natural way tactic to genetic modification. Also, the article mentioned that the genomes were to be edited by the processes of insertion, deletion, and reordering. Insertion and Deletion were two things that we studied that could naturally occur in the genome, and often had a negative effect. These processes are now slightly different as they are not natural and have a positive outcome but share the same idea as the processes we studied.

Genetically Modified Organisms (GMO): Profit, Power and Geopolitics

Genetically Modified Organisms (GMO): Profit, Power and Geopolitics

Written By Colin Todhunter

Date Published: December 15, 2014

http://www.globalresearch.ca/genetically-modified-organisms-gmo-profit-power-and-geopolitics/5419873

Summary:

The use of genetic modification has turned into a political business. The larger corporations such as Monsanto are playing a monopoly on poor farmers in third world countries who are struggling to feed their families. These giant companies are able to do so via royalties, and in essence, force farmers to purchase specific seeds that they cannot afford. This greatly impacts the economies of second and third world countries as farming and agriculture are the staple industries there. These large companies claim that genetically modified crops and the usage of their specific chemicals will produce an increased yield, therefore benefitting the farmers who buy it. However true that might be, they have not included the toll on the environment and the cost of human health. These chemicals may seem more beneficial for increasing marginal profits. The reason for why these chemicals and crops are being sold in the third world countries is because the people in these countries want to represent first world countries. It has become the norm in first world countries to consume food that is not naturally grown, so naturally, second and third world countries would like to follow in suit. However, as the article warns, these chemicals will bring to the destruction of our planet and health. First world countries must take the lead and stop using these genetically modified organisms in order to save our planet. 

How this relates to class:
We learned about the science behind using genetically modified food and actually conducted an experiment where we tested whether or not a common food that was sold in major supermarkets was genetically modified. From this lab, we found that much of the staple crops-corn and soy-were genetically modified. This showed that many of the major biotech companies have a major monopoly over the market and can force their products into the lives of their people. We also learned about how the dangers of using genetically modified organisms, especially to the health of the people. In addition, when we had the genetically modified organism debate, in which we learned both the positive and negative impacts of genetic modification. This is how the article connects to what we have learned in class. 

Genetic Mutation Studies Shed New Light on Schizophrenia

Title: Genetic Mutation Studies Shed New Light on Schizophrenia
Website: Reuters
Author: Kate Kelland
Date: January 22, 2014
http://www.reuters.com/article/2014/01/22/health-schizophrenia-genes-idUSL5N0KW1IY20140122

Summary: 1 in 100 people worldwide have the psychiatric illness known as schizophrenia. People diagnosed with schizophrenia have genetic mutations in specific proteins, key to the workings and the development of the brain. These gene mutations are found in the people affected, however, they are not found in either of the parents. Scientists can conclude that these gene mutations are not inherited. Researchers also found that the causes of schizophrenia are similar to the causes of other brain disorders like autism and intellectual disabilities. Scientists do not know for sure what brings on this illness, but they believe it is the combinations of genetic predisposition and environmental factors. Researchers examined DNA blood samples from 623 schizophrenia patients and their parents at the Icahn School of Medicine at Mount Sinai, New York, the Broad Institute of the Massachusetts Institute of Technology, from Harvard, and from Britain's Cambridge University. In another study, the gene sequences of more than 2,500 people with schizophrenia were analyzed. They found that genetic mutations contribute to triggering schizophrenia and that these mutations are clustered in proteins that are involved in modulating the strength of connections between the nerve cells, and they are a part of brain development, learning, memory, and cognition.

Relevance: This article is relevant to what we have been learning about this term because it talks about genetic mutations, inheritance, DNA blood sampling, and proteins. The genetic mutations found near the proteins of people with schizophrenia, fail to code for certain proteins or enzymes that are key to the regular workings of the brain. In this term we have talked about how the sequence of bases in genes code for proteins. If there is a gene mutation, like chromosomal mutations or mutations in the sequence of bases, it can affect the whole outcome and it can cause a failure to produce a functioning protein. From inheritance we learned that in order for the parents to pass down these gene mutations, they have to have been in gametes. However, these mutations are not inherited, and they are located in mostly brain cells. Also, this article talks about DNA blood sampling in order to conduct research about what these mutations are affecting in the brain. Scientists had to retrieve DNA from people with this illness in order to see where the mutations are located. They still do not yet know what genes are affected even with the DNA blood sampling and the sequencing of each person’s genes. 

A clear, molecular view of how human color vision evolved

Author: Carol Clark
Title: A clear, molecular view of how human color vision evolved

Source: Emory Health Sciences

Date: December 18 2014

URL: http://www.sciencedaily.com/releases/2014/12/141218210100.htm

The Summary 

Many genetic mutations occurred in visual pigments over the past millions of years. These mutations were required for humans to evolve and change from a primitive mammal with a dim, and not clear view of the world into a a  larger ape/chimpanzee able to see all of the colors in the spectrum of light. In todays world, after extensive amounts of research done by Emory Health Sciences, scientists have produced a vivid picture of the evolution of human color vision over the past millions of years. PLOS Genetics published the process for how humans switched from ultraviolet vision to violet vision (ability to see blue light). Shozo Yokoyama who is a leading author of the publications explains that they, at Emory Health Sciences have traced the evolutionary pathways going back over 90 million years. Yokoyama and various other scientists have been studying adaptive evolution of vision in humans and other vertebrates by studying ancestral molecules. Firstly scientists have to estimate and synthesize proteins and pigments of an ancestral species. After this the scientists then conduct experiments on them by combining microbiology with theoretical computation, biophysics, quantum chemistry and genetic engineering. Five classes of opsin genes encode visual pigments for dim-light and color vision. Bits and pieces of the opsin genes change and vision adapts as the environment of a species changes. Around 90 million years ago our ancestors had UV-sensitive and red-sensitive color but 30 million years ago, they evolved four classes of opsin genes, allowing them to see the full-color spectrum of visible light. For the PLOS genetic papers researchers focused on the seven genetic mutations involved in losing UV vision and achieving the current function of a blue-sensitive pigment. They traced the progression from 90-30 million years ago. 5,040 possible pathways for the amino acid were discovered for changes required to bring about the genetic changes. Experiments were  carried out for each of these 5,040 possible pathways. Scientists discovered that of the 7 genetic changes needed, each of them individually has no effect. It was only when several of the changes were combine in a particular order that the evolutionary pathway could be completed. Thus just as an animal's environment drives natural selection, so do changes in the animal's molecular environment. About 80 percent of the 5,040 pathways the researchers traced stopped in the middle, because a protein became non-functional. The other 20 percent remained possible pathways. Yokoyama described how our ancestors only used one of these paths and he discovered this path. The three specific amino acid changes that led to human ancestors developing a green-sensitive pigment were uncovered. Yokoyama tried to construct an extensive evolutionary tree for dim-light vision. At specific branches of the tree, his lab engineered ancestral gene functions, in order to connect changes in the living environment to the molecular changes.

 Description of its Relevance 

This article is relevant to the current unit we are studying as it concerns the study of evolution. Specifically the evolution from humans ultraviolet vision to violet vision (ability to see blue light). The article discusses molecular genetics, and how as well as an animal's environment driving natural selection, so does changes in the animals molecular environment. The article discusses genetic mutations.  It describes how many genetic mutations in visual pigments, spread over millions of years, were required for humans to evolve from a primitive mammal with a dim, shadowy view of the world into a greater ape able to see all the colors in a rainbow. A genetic mutation, as we learned in the last chapter is a mutation is a permanent change of the nucleotide sequence of the genome of an organism.