Bottlenecking Events

Submitted by robynfarrell on Mon, 04/24/2017 - 12:20

Bottleneck events reduce the genetic variation in a population. For example, take the species of elephant seals. Elephant seals used to be really common. They bred on islands, but have now shifted their breeding area to be shore lines. When examining their allelic composition, you would think to find a great diversity in alleles, but you find out there is a lot of homozygous diversity, which in the scientific community is not great. This is actually due to human hunting, due to them being hunted for their oils. At one point this species was down to only a few hundred, so rather than stopping hunting on them museums decided to step in. They thought that by taking dozens of these elephant seals that they would help maintain their safety. That actually drastically dropped their population in the wild to only 35. Throughout the last few decades their population has risen in the wild to around 100,000 but due to the incredible bottleneck their gene pool has dramatically shrunk. They have such a small gene pool that there are barely any mutations occurring, so their genetic diversity is slim.

Journal #34--Naked Mole Rat

Submitted by skhall on Mon, 04/24/2017 - 10:31

   This week while looking through biological news, I found an article discussing the “bizarre biology of the naked mole rat.” It begins talking about the species as a whole and their amazing features. From withstanding cancer, pain and surviving 18 minutes without oxygen, there is much to learn about this animal. Scientists are discovering even more about this “super rodent.” The animal lives in large colonies that  an reach up to 280 animals…wow. They are found in Africa, living in underground tunnels in the desert where there is a very low oxygen supply. In humans, such a lack of oxygen would cause hyperventilating and acid build up in our tissues causing brain damage and even death. However, for the naked mole rat, lack of oxygen is the least of their worries. In order for scientists to test the real ability of this animal and its lack of desire for oxygen, they created a controlled environment that is essentially a tube that seals off all oxygen. When oxygen levels were dropped to even 5% the rats were fine for five hours. Mice on the other hand only lasted approximately 15 minutes before suffocating. The big question is how the rats do it. The naked mole rat switches to using fructose in the body so its levels are higher to help the vital organs survive. Scientists have not determined where the fructose levels are rising in the body, but that is for further research.

Immunology

Submitted by amprovost on Mon, 04/24/2017 - 10:30

The human body is under attack every minute of every day; fungi, virions, bacteria, and other infectious agents are constantly present in every environment. When faced with such exensive threats, the human body must have a system designed to handle these attacks. The system designed for this is referred to as the immune system, a system with multiple cell types interacting with one another to defend the body. The human immune response is one of the most intricate systems in human biology.

When an infection is spread, it is initally responded to by macrophages, which are also known as guard cells. These huge cells are the first to respond to an infection, and operate by using phagocytosis to ingest enemy organisms. These cells are very large, and on average can ingest about 100 bacteria per cell. Once ingested, these invaders are stored in a membrane until they can be degraded by enzymes from the macrophage. Macrophages also cause an influx of water from the bloodstream, which results in the swelling that we see around an infection. If the macrophages are unable to destroy the infection alone, they release messanger signals into the blood stream calling for backup. The next line of defense is the neutrophil. These cells are so deadly that they are saved for serious infection, as their attacks are somewhat indiscriminate that they also damage host cells. These cells also only have a lifespan of 5 days, as if they accumulate they can cause serious damage to the host. 

Dendedritc cells are then used to find particles of the invader and then bring in then to the lymphatic system. These cells are made to be very specific, as they are designed around the piece of invader that is presented to them. These super specific cells are difficult to produce correctly, and many of them never make it to te "battlefield", as they are not perfect matches for the invader. Once a cell that is a perfect match is found, it replicate rapidly in an attempt to destroy the invader.

Warburg effect

Submitted by abnguyen on Sun, 04/23/2017 - 21:40

The warburg effect is the observation that most cancer cells mainly produce energy through glycolysis followed by lactic acid fermentation in the cytosol.  This differs from normal cells where there is a low rate of glycolysis and oxidation of pyruvates in the mitochondria.  A possible explanation for the warburg effect is that mitochondria was damaged during the process of tumor proliferation and a new means of energy production is required.  Another possible explanation is that glycolysis provides most of the building blocks for cell proliferation and used even in the presence of oxygen.  As such, glycolysis in the presence of oxygen is highly inefficient in energy production but makes up for it in the proliferation factor.

Script draft 2

Submitted by abnguyen on Sun, 04/23/2017 - 21:40

 

Slide 1

           Hello everybody and welcome to our Biochem 275 final presentation.  The focus of our presentation is Huntington’s disease.

 

Slide 2

           Like we just said, our project is on the Huntington’s disease.  This is a neurodegenerative disorder that is inherited dominantly on autosomal chromosomes.  Some symptoms of the disease are behavioral changes, involuntary movement, and intellectual disabilities.  However, there is no guaranteed way to predict when the symptoms will appear.  As shown by the bar graph, the most common age of Huntington’s onset ranges from 30-50 years old.  There is no treatment that currently detects the age a person will develop the disease, only an estimate from previous data.

 

Slide 3

           Currently, there are no treatments that can 100% cure huntington’s.  On the bright side, there are hundreds of scientists testing and trying to develop a cure.  There are 2 ongoing treatments that have a high chance of helping HTT patients.  The first is AUTEN-99.  This drug is a potent neuroprotective candidate for preventing and treating neurodegenerative disorder.  AUTEN-99 works to degrade excess detrimental material in the cytoplasm.  This will clear up cell space and provide room and nutrients for functioning proteins.  This has been tested in flies and has been shown to slow/stop neurodegeneration.  AUTEN-99 has been known to work for other diseases such as alzheimer's and parkinson's.   

 

Slide 4 (I think we should break up the treatment slide, we can add pictures of the drug, molecule or pathway and it will prevent the powerpoint slide from looking like a block of text.)

    Another treatment for Huntington’s is the regulation of HSF1.  This works to control protein quality.  Possible ways to regulate this transcription can lead to cures for huntington’s.  Some ways that this can be regulated are to inject more HSF1 TF directly into the patient or we can use CRISPR technology.  With CRISPR we can look for the gene that creates HSF1 and upregulate that promoter.     

    Alternatively, with CRISPR we can have it attach itself to parts of the CAG codon to prevent it from transcribing and creating proteins.  This method might help reduce the about of repetitions and restore normal function within the body.

 

Slides 5-7 (new 7)

    The Huntington’s gene is located on chromosome 4 for humans.  The nucleotide is 13,498 base pairs long and it codes for roughly 3144 amino acids.  The main protein produced is characterized by a single codon repetition.  The CAG codon, also known as the glutamine codon, is repeated 40-120 times.  A normal human will have between 10-35 repetitions.  An individual with 35-39 repetitions may not develop the disease while someone with 40+ repeated glutamine proteins will almost always develop huntington's.  The protein created from this string of codons are associated with the nervous system and interact with the neurons within the brain.  The exact function of this protein is not fully understood.  However, what we do know about this protein is that it undergoes alternative splicing.  The splice variants are not related to the disease; the disease is caused by a different mutation.

 

Slide 7:

The HTT gene, as you can tell is relatively huge, but even so, we must amplify it to be able to study it better. First, we heat up the environment so that the hydrogen bonds between the two strands break and allow for the strands to separate. Next, we cool the DNA strands to allow the PCR primers to anneal to the 3’ ends of the gene segment on each strand. If you look in the middle, here, you can see that these two are our left and right primers. Now that the primers are annealed, this allows us to have our heat-withstanding Taq polymerase to start at the primers and elongate the complementary strands. More DNA copies are being made, so when this process repeats, our gene gets amplified enough to study.

 

Slide 8: Now we move onto cloning, expressing, and purifying the HTT gene, and you may be wondering why we would want to clone the gene. Well, cloning the gene allows us to study the gene’s function and determine how mutating it causes Huntington’s Disease. It can allow the specific HTT gene to be studied and the protein to be produced. Many variables affecting the gene and protein expression can be tested, as well as comparing proteins with the mutations to those without.

Slide 9: With that in mind, we must first chemically cut the open reading frame of the HTT gene from the strand of a DNA sample. Then, attach the cut gene in between the restriction enzymes Not1 and Sbf1, in the multiple cloning sequence for the plasmid. Next, insert the plasmid into the BL21 derivative NEB Express™ host strain of E. Coli. Using IPTG as a promoter, the gene can be expressed in the bacterial cells. A chaotrope is used to destabilize and collect the proteins. The specific protein can be purified by affinity chromatography and further analyzed by gel electrophoresis on an SDS PAGE gel.

Journal #33 - Bottleneck

Submitted by robynfarrell on Sun, 04/23/2017 - 19:35

I had always heard about the term bottleneck, but was always confused as to what it was and what it meant for a population. Bottleneck events actually reduce the genetic variation in a population. For example, take the animal, elephant seals. Elephant seals used to be really common. They bred on islands, but it has now shifted to shores. When examining their allelic composition, you would think to find a great diversity in alleles, but you find out there is a lot of homozygous diversity, which in the scientific community is not great diversity. This is actually due to human hunting, since we hunt these beautiful animals for their oil. At one point this species was down to only a few hundred, so rather than stopping hunting on them museums decided to step in. They thought that by taken dozens of these elephant seals that they would help them maintain safety, dropping the population in the wild to only 35. Throughout the last few decades their population has risen in the wild to around 100,000 but due to the incredible bottleneck their gene pool has dramatically shrunk. They have such a small gene pool that there are barely any mutations, so their genetic diversity is slim.

Brainstem PP

Submitted by maurabenson on Sun, 04/23/2017 - 18:42

The brain stem is an essential part of our central nervous sysem connecting the  cerebrum, cerebellum, and spinal cord. There are three different parts of the brainstem: the medulla, pons and the mid brain. The medulla regulates unconscious actions such as breathing, heartbeat, and blood pressure. The midbrain deals with the auditory and visual processing and sends the information to the prospective cortexes. The pons is important in regualting the sleep wake cycle and arousal. Like the spinal cord, white matter is on the outside of the brainstem and gray matter is on the inside. The brainstem also contains long tracts which as long axons that all go together to the same place, including upper motor neurons and somatosensory tracts. Without the brainstem receiving important information and sending it to the correct portion of the brain, neccesary functions for life would nto be possible. 

The Brain Stem

Submitted by maurabenson on Sun, 04/23/2017 - 18:35

The brain stem is an essential part of our central nervous sysem connecting the  cerebrum, ccerebellum, and spinal cord as well as all the cranial nerves. There are three different parts of the brainstem: the medulla, pons and the mid brain. The medulla regulates unconscious actions such as breathing, heartbeat, and blood pressure. The midbrain deals with the auditory and visual processing and sends the information to the prospective cortexes. Like the spinal cord, white matter is on the outside of the brainstem and gray matter is on the inside. The brainstem also contains long tracts which as long axons that all go together to the same place, including upper motor neurons and somatosensory tracts. 

Journal #32 – Resistance to Pesticides

Submitted by robynfarrell on Sun, 04/23/2017 - 18:21

In one of my classes we learned about the resistance to pesticides. Insects pests, such as scale insect, were a lot to deal with so people in the scientific community tried to come up with something to deal with it. The scale insect is a tiny insect, around .5mm, and has a tube mouth that drinks plant fluid. It grows scales all over itself so nothing can get into it, sort of as a defense mechanism. They realized that if you sprayed it with lime and sulfur it killed this insect, but as time passed on a resistance built up. After few years they saw that some populations in certain areas didn’t succumb to this resistance mechanism, due to genetics. They then turned to the fact that maybe diesel oil would be another solution. Though scientists did warn farmers that if you use it too much the insect will build up a resistance to it and the same pattern would occur again, but the farmers did not listen. A trend was found that resistance started evolving to their mechanisms 5 years after it was sprayed, and after 10 to 20 years it became ineffective. This process still continues on to this day.

The same trend was found with gypsy worms. In order to make silk it requires a lot of intensive, long labor if you get it from silk worms. So some person decided to come back to his home location and use gypsy moths to do the same thing. Sadly, the population he was breeding escaped and in a few years there was an outbreak of gypsy moths. These gypsy moths started creeping up in bad places such as apple crops and ruining them. Scientists realized that if you sprayed the apple trees with arsenic and lead it was very effective in killing these gypsy moths. But the consequence of this is that now you’re eating apples with lead arsenic in it, which is really unhealthy, as it does not break down into anything and is toxic. This is seen in the soil in Worcester currently. Now farmers have to leave a big chunk of their land free of pesticides, it ranges from 30-50% depending on the crop you’re growing. These big areas that are left untreated will have a good percent of insects that have a decent percentage of insects that are nonresistant

pp

Submitted by jiadam on Sun, 04/23/2017 - 16:54

DNA structure

DNA is known to have a double helix structure, but it is not common knowledge that it normally has a right handed spiral and contains major and minor grooves. The major grooves for DNA are where the sequence-specific DNA binding proteins bind and have access to the nucleotides which for allows for post translational modifications. The minor groove is where non-specific DNA binding proteins have access to the DNA, but more specifically to the sugar-phosphate backbone. DNA is made up of nucleotides and each nucleotide has a phosphate group, a 5 carbon deoxyribose sugar and nitrogenous bases. Each strand of DNA is a polymer because it is a chain of nucleotide monomers. The strands run antiparallel and form hydrogen bonds between each other. CG has 3 hydrogen bonds whereas AT only has 2. If they ran parallel, the bases would not form hydrogen bonds. Chargaff’s rule states that adenine binds with thymine and cytosine binds with guanine.

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