Thursday, February 2, 2012

BLAST (Basic Local Alignment Search Tool) Genes

HTT huntingtin [ Homo sapiens ] (Gene 1)

Huntingtin is a disease gene linked to Huntington's disease, a neurodegenerative disorder characterized by loss of striatal neurons. This is thought to be caused by an expanded, unstable trinucleotide repeat in the huntingtin gene, which translates as a polyglutamine repeat in the protein product. A fairly broad range in the number of trinucleotide repeats has been identified in normal controls, and repeat numbers in excess of 40 have been described as pathological. The huntingtin locus is large, spanning 180 kb and consisting of 67 exons. The huntingtin gene is widely expressed and is required for normal development. It is expressed as 2 alternatively polyadenylated forms displaying different relative abundance in various fetal and adult tissues. The larger transcript is approximately 13.7 kb and is expressed predominantly in adult and fetal brain whereas the smaller transcript of approximately 10.3 kb is more widely expressed. The genetic defect leading to Huntington's disease may not necessarily eliminate transcription, but may confer a new property on the mRNA or alter the function of the protein. One candidate is the huntingtin-associated protein-1, highly expressed in brain, which has increased affinity for huntingtin protein with expanded polyglutamine repeats. This gene contains an upstream open reading frame in the 5' UTR that inhibits expression of the huntingtin gene product through translational repression. [provided by RefSeq, Jul 2008]

ELN elastin [ Homo sapiens ] (Gene 2)

This gene encodes a protein that is one of the two components of elastic fibers. The encoded protein is rich in hydrophobic amino acids such as glycine and proline, which form mobile hydrophobic regions bounded by crosslinks between lysine residues. Deletions and mutations in this gene are associated with supravalvular aortic stenosis (SVAS) and autosomal dominant cutis laxa. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

FBN1 fibrillin 1 [ Homo sapiens ] (Gene 5)

This gene encodes a member of the fibrillin family. The encoded protein is a large, extracellular matrix glycoprotein that serve as a structural component of 10-12 nm calcium-binding microfibrils. These microfibrils provide force bearing structural support in elastic and nonelastic connective tissue throughout the body. Mutations in this gene are associated with Marfan syndrome, isolated ectopia lentis, autosomal dominant Weill-Marchesani syndrome, MASS syndrome, and Shprintzen-Goldberg craniosynostosis syndrome. [provided by RefSeq, Jul 2008]

DMD dystrophin [ Homo sapiens ] (Gene 7)

he dystrophin gene is the largest gene found in nature, measuring 2.4 Mb. The gene was identified through a positional cloning approach, targeted at the isolation of the gene responsible for Duchenne (DMD) and Becker (BMD) Muscular Dystrophies. DMD is a recessive, fatal, X-linked disorder occurring at a frequency of about 1 in 3,500 new-born males. BMD is a milder allelic form. In general, DMD patients carry mutations which cause premature translation termination (nonsense or frame shift mutations), while in BMD patients dystrophin is reduced either in molecular weight (derived from in-frame deletions) or in expression level. The dystrophin gene is highly complex, containing at least eight independent, tissue-specific promoters and two polyA-addition sites. Furthermore, dystrophin RNA is differentially spliced, producing a range of different transcripts, encoding a large set of protein isoforms. Dystrophin (as encoded by the Dp427 transcripts) is a large, rod-like cytoskeletal protein which is found at the inner surface of muscle fibers. Dystrophin is part of the dystrophin-glycoprotein complex (DGC), which bridges the inner cytoskeleton (F-actin) and the extra-cellular matrix. [provided by RefSeq, Jul 2008]

Wednesday, December 21, 2011

Osmosis Jones

Similarities: 
  • Both the Immune System and the movie, Osmosis Jones, have cells with specific jobs. The white blood cells, in this case, Osmosis Jones, kill any dangerous substance.
  • Like the Immune System, whenever a disease appears, white blood cells such as Osmosis Jones as sent to neutralize the disease.
  • Diseases, in both real life and the movie, cause harm to the body which causes the immune system to respond.
 Differences:
  • The most obvious example would be that the cells in the movie are anthropomorphic, that is they contain human characteristics and unique personalities.
  • Another difference is Drix's ability to fight the disease, Thrax, when real-life cold pills only subdue the symptoms of a cold.
  • There is also the abundance of technology in the body, such as cars and various machines that help the cells in their various jobs.

Virtual Epidemic

Using the Epidemic Stimulation, one can determine the effects of a contagious disease over a population.
The factors, distribution, contagion, and deadliness, all have a factor in this.

Out of the three, contagion appears to have the largest impact, followed by distribution and then deadliness.

Using the following:        Results in:(5th Pass)                Distribution:

H>C:80                         Healthy:291
C>S:40                         Carrier:49
S>D:30                         Sick:39                                   Towards the middle of the
S>I:20                          Dead:16                                  population
I>H:5                            Immune:5

H>C:60                         Healthy:321
C>S:50                         Carrier:24
S>D:30                         Sick:40                                    Towards the middle
S>I:20                          Dead:9

I>H:5                            Immune:6

H>C:60                         Healthy:333
C>S:40                         Carrier:28
S>D:40                         Sick:28                                     Towards the middle
S>I:20                          Dead:9 
I>H:5                            Immune:2

H>C:80                         Healthy:349
C>S:40                         Carrier:18
S>D:30                         Sick:17                                    Touching the Edge
S>I:20                          Dead:8 
I>H:5                            Immune:8

As the data displays, the position of the original carrier matters greatly as it determines how many people the carrier will come in contact with.

(The more people come in contact with the carrier, then there are more chances the disease spreads to more people) 
After the contact, how contagious the disease is will determine to how many people it spreads to.

(Likewise, the more people the disease spreads to, then there is a larger amount of chances the disease has to kill)
Finally the rate of death decides how many of the people die.

5 nutrients for your body


Proteins: 
Proteins are used for a variety of functions. They are essential for creating hormones or enzymes and help build and repair body tissues.


Carbohydrates:
The main source of energy, carbohydrates are used not because they are efficient in harnessing all potential energy, but because they provide quick, immediate energy.


Lipids (Fats):
Lipids are mainly used to store energy. They may also carry fat-soluble vitamins, such as vitamin A and D.


Vitamins:
Vitamins, due to the many kinds, have a variety of functions ranging from bodily growth to metabolic regulation.


Minerals:
Like vitamins, minerals have a variety of uses due to the different  kinds. Minerals such as potassium, shown above, help regulate body functions, while iron, another mineral, helps form hemoglobin which is used by red blood cells to carry oxygen.

Monday, December 19, 2011

Fermentation in sour pickles



Sour picklesSOUR PICKLES

These are a favorite of many and a lot of people miss them when going on a Paleo diet, but the naturally lacto-fermented kind if perfectly healthy, crunchy and sour. This version is flavored with garlic and dill. Your garlic too will lacto-ferment and can be enjoyed afterwards as it will be packed with flavor.

Ingredients

  • 3.7854 liters pickling cucumbers, unwaxed;
  • 2 bunches fresh dill
  • 16 cloves garlic, whole and peeled
  • 3 tbsp pickling spices (peppercorns, mustard seeds, bay leaves, cloves, …)
  • 5 or 6 tbsp sea salt

Preparation

  1. Soak the cucumbers in cold water for a few hours then scrub them thoroughly to to prevent any mold from forming during the fermentation process.
  2. Place the cucumbers, dill, garlic and spices in your fermentation jar and sprinkle a bit of sea salt as you go along.
  3. Prepare a brine of 5 tablespoons sea salt to 1.9 cups water, making sure to stir well to dissolve the salt and fill the fermentation jar with the brine so it covers the cucumbers.
  4. Cover the jar place it in a warm spot in your kitchen and allow the cucumbers to ferment for 5 to 10 days.
  5. A good way to know when it’s ready is to taste it during the fermentation process. It’s ready when you’re satisfied with the taste.


  The fermentation helps cooks the pickles through a certain process.

Lactic acid is produced from the fermentation (Lactic Acid Fermentation) which makes the liquid acidic. The salt then encourages good bacteria to come, while simultaneously driving away the bad bacteria. This makes the liquid even more acidic. Once the acidity dips below 4.6 Ph, most bacteria is killed leaving the food safe to consume.