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Draft #5, week 15, whole exome sequencing

Submitted by vvikhrev on Thu, 05/03/2018 - 22:02

This is just a paragraph on why one would use whole exome sequencing instead of whole genome sequencing to find a variant of Leber's congenital amaurosis. Leber's congenital amaurosis is characterized by atrophic macular lesions, pale optic disk, reduction of retinal blood vessels, pigment disruption, and scattered pigment clumping in the peripheral retina. It is an inherited retinal disorder and the most common variants are at the gene NMNAT1. Why would you use whole exome sequencing to find a variant in a family that has been affected by this disease?
exome: part of the genome formed by exons, coding portions of genes,
- because most known mutations that cause disease occur in exons,
- cheaper than whole-genome tests,
- in this example, good for testing already present mutations, proven to be successful
- most alleles known to underlie Mendelian disorders disrupt protein-coding sequences
- a lot of rare, protein-altering variants (missense, non-sense single-base substitutions, INDELs) are predicted to have functional
consequences and/or be deleterious
- the exome presents a highly enriched subset of the genome in which to search for variants w/ large effect sizes

Type 2 diabetes and protein

Submitted by lgiron on Wed, 05/02/2018 - 14:06

            One source found state that Whey protein can potentially be the treatment for type 2 diabetes. The main reasoning behind this statement is that it can manipulate the gut function in order to secret incretin and reduce gastric emptying which are key components for type 2 diabetes. Whey protein stimulates beta cells to secrete these gut peptides, to include incretin, which then leads to the slower metabolizing and slower gastric emptying once an individual has consumed their meal, this is because it suppresses appetite and effects the gut-brain axis and hypothalamus, which is responsible for controlling hunger and homeostasis, which includes these peptides (Mignone et al. 2015). In addition, in a clinical trial in which men with type 2 diabetes were given 15g of Whey protein, the consumption of this protein was proven to improve glycaemia after means were consumed, increase secretion of insulin. This trial proves the suggestions made by Mignone through its evidence and direct relevance of the valid conclusions made (King et al. 2018).

Protein and Renal problems

Submitted by lgiron on Wed, 05/02/2018 - 13:59

            A study on a healthy 27-year-old patients who has taken a reportedly safe concentration of Whey protein was found to have a profound case of jaundice due to his protein and creatine intake, therefore linking back to a kidney malfunction. The laboratory tests had concluded elevated bilirubin concentrations in his liver which is the yellow pigmentation due to the breakdown of hemoglobin. The individual had been using Whey protein 4 weeks and creatine 9 weeks, prior to the arrival of the symptoms. They concluded that the supplements were the cause of his kidney malfunction. I do not believe this case study has sufficient evidence or relevance in the represented topic. One reason being that it is a single subject which leaves error to be great. Another reason being that he had been taking other supplements that could have caused his profound case of jaundice. Their assumption is not fully backed by a vast trial but rather a single case (Whitt et al. 2008).

Chemo and Protein

Submitted by lgiron on Wed, 05/02/2018 - 13:58

Another source set out to prove the improvements in health in cancer patients receiving chemotherapy. A scientific trial conducted stated that cancer patients receiving chemotherapy have side effects such as a weakened immune system and malnutrition. In the study, 42 cancer patients who received chemotherapy were blindly split into an experimental, 23 patients, and control group, 19 patients. It was shown that the experimental group that was given 42g of Whey protein every day for 12 weeks, had improved nutritional status and a boosted immune system than the control group which did not receive it. I believe that this piece of evidence is relevant and representative for the benefits of Whey protein, and even though the size of the trial groups were not large, they had enough data to give a conclusion. The assumptions based on the evidence, and clinical trials are valid because the conclusion of the trial showed the physical improvements of these individuals when compared to those who did not get treated with the Whey protein (Bumrungpert et al. 2018).

P. hydrobothynus

Submitted by brettconnoll on Wed, 05/02/2018 - 12:39

Like most species of otters when the pride is together they spend most of their time playing and frolicking in the water. This species is incredibly rambunctious and has been known to mess with boats traveling through the territory. There is one case of a few females boarding a small canoe and stealing the belongings of the person on board.

social and reproduction behaviors of P. hydrobothynus

Submitted by brettconnoll on Wed, 05/02/2018 - 12:39

The females will typically be pregnant for 65-80 days. The young are born fully covered in fur and are able to open their eyes after just a week. The pups are able to walk around and swim just after they are able to open their eyes. This rapid development is supported by the constant support and protection of the pup by the pride. When they are young male and female pups look morphologically similar. It isn’t until they reach eight months old that the males begin to develop secondary sex characteristics. Their pectoral girdle starts to get larger and a small brown mane begins to form. The young males will begin to forage with the dominant male when they are a year old and are first taught to hunt for insects. It isn’t until they have been foraging for a month that the dominant males will allow the young males to begin hunting for A. galactonotus. After a few months of eating the frogs the color of the young males’ mane changes from dark brown to hues of bright red, orange and yellow. It has been observed that the primary color of frog that the males eat will determine the proportions of red, orange, and yellow in their mane. The amount of frogs that the male eats also determines how bright his mane will be. Males that are not able to eat many frogs may have a dull colored mane, or it may not be colored at all. The males that are the best at foraging and have the best territory will have the biggest and brightest manes. The female’s preference for the amount of each color they like in the male's mane has yet to be explored, however, it has been observed that they do prefer males with very large manes. 

social behavior of P. hydrobothynus

Submitted by brettconnoll on Wed, 05/02/2018 - 12:38

Unlike the males, the female stellar river otters are much more docile and spend most of their days working together hunting and taking care of the young. They only rely on the male to construct and maintain the dens and to defend the territory. The females of this species have a very different social structure than the males of this species. Females of neighboring territories are capable of coexisting and leaving one another alone. This allows there to be many rafts of females throughout a single river system and makes it easy for young females to easily find a new raft if they so desire. 

497 final - genetic testing tech

Submitted by liamharvey on Wed, 05/02/2018 - 11:36

I used AncestryDNA for my genetic testing. To have your DNA tested, you send a saliva sample to their labs and results are posted several weeks later. They test your DNA using microarray-based autosomal DNA testing. A microarray is basically a grid of many known DNA segments which then are used to test and map out the DNA sample in question. The microarray used by Ancestry surveys your DNA at 700,000 locations to help find your heritage.

AncestryDNA has an extremely large database not only for DNA testing, but of public records. Here Ancestry can help you create a family tree by using things like U.S. Census records and marriage certificates to link your ancestors. This service can tell you about generations of ancestors, showing you what they did, where they lived and much more. You can start by simply putting you parents and grandparents names into a tree that you create. By adding their name, birth/death dates and birth place, Ancestry will search its database for records of these family members and provide you with a “hint”. By using the hints that Ancestry finds for you, it can help you find older generations like great grandparents. You may also add a family member to your tree that is on someone else’s tree and then you can be linked to their tree which will show much more family members. Using the resource Promethease, I was able to take the raw genomic DNA provided by Ancestry and get a report of what my DNA indicates. Promethease uses my DNA genotypes and compares it with findings that are cited from scientific studies in the website SNPedia.

poster - introduction

Submitted by jonathanrubi on Tue, 05/01/2018 - 17:44

In this experiment, we sought to understand the effects of tree management techniques by the University of Massachusetts - Amherst compared with the surrounding town of Amherst on tree health, ecological diversity, and safety hazards. UMASS-Amherst characterizes the tree management needs as a strategy for the removal of hazardous conditions and improving the overall wellbeing of the trees including, ruining, irrigation, fertilization, cabling and other programs on an “as need” basis. In abandoned, unmanaged areas, research has shown that species diversity is increased particularly those that are dependent on tree coverage. Tree management also been shown to have a positive effect on invasive species and a negative effect on native species. By observing trees in the jurisdiction of the university and those in the surrounding area, we were able to identify differences in factors related to overall tree health, safety hazards and ecological diversity.


Methods - poster

Submitted by jonathanrubi on Tue, 05/01/2018 - 17:44

Effects of tree management techniques were gathered by randomly selecting trees on the University of Massachusetts - Amherst campus and the surrounding area. Factors identified were

- Number of tree cavities: characterized as a semi-enfolded hallow that naturally has occurred within the trunk or branch of a tree.

- number of branches: counted from the main trunk of the observed tree

- understory diversity: characterized as the underlying layer of vegetation and measured at a maximum of 4 feet from the root of the trunk. Understory diversity also includes nests and species inhibited on the trunk or branches of the tree.

- human infrastructure: characterized as the distance from an area of the tree to the closest man-made structure. These structures included roads, pavement, cable wires, storm drains and buildings.


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