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2) Autoimmune polyendocrinopathy ectodermal dystrophy (APECED) is a combined autoimmune/immunodeficiency disorder triggered by defects in expression of the gene AIRE (for the autoimmune regulator). AIRE expression is believed to allow for the production of a ‘shadow self’ within the thymus, allowing for multiple tissue-specific antigens (e.g. insulin from the pancreas, or gonadotropin-releasing hormone from the hypothalamus) to be expressed at very low levels by thymic stromal cells. Thus, AIRE expression strongly correlates with the principle of ‘central tolerance’ whereby autoreactive T cells are deleted by negative self-selection in the thymus.

Read up on APECED, and pick two of the syndrome’s immunological problems. Explain or hypothesize how these defects arise from a failure of AIRE expression.  

(10 points, 5 points per condition)

Answer:

APECED or autoimmune polyendocrinopathy ectodermal dystrophy is an autoimmune disease that is caused by a defect in the AIRE protein. Under the normal functioning of the body, many T cells are produced which may react negatively with the antigens of the body itself, thus disrupting many important and core functions required for the normal functioning of the body (Gregory & Lionakis, 2019). The AIRE protein functions to identify and subdue these antibodies, and in case of any defect of AIRE, these T cells subsequently produced will cause autoimmune diseases.

Usually, in case the AIRE protein is malfunctioning, the effects in the form of autoimmune diseases are usually visible by early childhood. There are several diseases pertaining to this condition, three of the main ones are described as follows:

1. Chronic mucocutaneous candidiasis
2. Hypo para thyroidism
3. Adrenal gland insufficiency

At least two of the three aforementioned conditions must be present in a person at a given moment, who is suffering from some autoimmune disease.

Chronic mucocutaneous candidiasis

This is the first problem that usually appears when you happen to suffer from APECED. Its symptoms include infections on nails, mouth and basically anywhere else with a mucosal lining. These moist areas are usually attacked by the fungi of the candida family (e.g.: Candida Albicans) and these are called yeast infections that are more than often of severe and chronic nature. The person suffering often suffers from an infection in the oral cavity, esophagus and in cases of women, the vaginal cavity as well.

Hypo para thyroidism

The parathyroid glands are secreting hormones, mainly the parathyroid hormone that regulates calcium and phosphorus. The deficiency caused will lead to a tingling sensation in lips, muscle cramps, weakness, and fatigue as well. the severe cases will see muscular spasms and respiratory collapse.

Adrenal gland insufficiency

The adrenal glands are usually heavily effected and therefore will case several metabolic deficiencies in the body. Loss of appetite, short stature, yellowing of the skin, weight loss and slow blood pressure as well.

The hypothesis of how AIRE dysfunctionality occurs and its relation to the conditions above:

1. The first and foremost reason for the unavailability of AIRE, to help the normal functioning of the immune system is obviously a mutation in its genetic background. AIRE has its genes at position 22.3 on the long (q) arm of chromosome 21 with the exact co-ordinates of Cytogenetic Location: 21q22.3. an aberration in base pairs will definitely cause malfunctioning of sorts (reference, 2020).

Autoimmune polyglandular failure type 1 (APS1), is a recessive form of hypoparathyroidism which in turn is unvaryingly caused by Mutations of the autoimmune regulator gene (AIRE) gene this is also called autoimmune polyendocrinopathy candidiasis ectodermal dystrophy (APECED), which we have discussed in detail before (Ergun-Longmire & Maclaren, 2016).

Question 1. Cystic Fibrosis (CF) is an example of a protein mis-folding disorder since most of the mutations associated with CF lead to the improper folding and processing of the plasma membrane-localized Cystic Fibrosis Transmembrane Conductance Regulator ion channel (CFTR).

The CFTR protein initially enters the endomembrane system through the process of co-translational translocation into the endoplasmic reticulum (ER) and is inserted as a Type IV membrane protein. N-linked glycosylation of the CFTR protein then takes place in the ER and continues in the Golgi.

Name the four types of sequence signals in the CFTR protein required for its proper targeting and processing up to this point (the Golgi) and give an explanation for each.

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1) Scientists have observed temporary suppression of B cell development in bone marrow during infection with a number of viruses, including hepatitis A, B, and C, influenza, and parvovirus B19.

Given what you know about B cell development, provide 2 hypotheses to explain this phenomenon, one focusing on why the host might suppress B cell development, and the other focusing on why the virus might do this.  

Also, hypothesize why this sort of development suppression is seen with viral infections, but not with bacterial infections, even very severe bacterial blood infections.

(9 points, 3 per hypothesis)

Answer:

A Suppression of the immune system after contaminations or aggravation is a significant procedure that limits immune-mediated pathogenesis and autoimmunity. A few components of immune concealment have gotten a lot of consideration in the previous three decades. These incorporate components identified with suppressive cytokines, and changing development factor (TGF)- β and interleukin (IL)- 10, delivered by administrative cells, and instruments identified with apoptosis mediated by death-ligand

The immune system contains a huge swath of cell types and effectors specific to identify and demolish pathogenic microorganisms and the cells and tissues that harbor them. With this exceptionally lethal defensive capacity comes the requirement for tight guidelines so that once the risk of disease has passed, the system can come back to relative quiet and further harm can be stayed away from. This guideline is mediated by subsets of cells and immunosuppressive particles that are particular to effectively stifle the immune reaction. In a perfect world, immune concealment adjusts the ruinous powers of aggravation while permitting leeway of pathogenic irresistible operators.

General hypothesis why bacteria don’t factor the same response

The bacteria do not have the necessary DNA/RNA controlling abilities as our usually attributed to the viruses. The viruses have the ability to genetically alter the immunity of the victim that they attack, therefore, their effects are long-lasting and are often shown by the triggered immunodeficiency responses (Lundy, 2012). Bacterial infections do not have these characteristics.

Second Hypothesis

Viruses are obligate intracellular parasites. They are wired to take control of the biological machinery of the host. In this regard, it makes sense that their method of infecting is fundamentally different from those of bacterial infections. The bacteria are complete organisms in of themselves, whereas viruses are just proteins or genetic material encased in some protein covering (Laffin, 2001). This difference in their physiology explains why bacterial and viral infections are fundamentally different in their approaches.

Third Hypothesis

The third hypothesis answers the given question, in light of a different perspective. Viral-bacterial co-existence has been known to present for quite some time. Recently, it has been researched extensively, to see if it has any medically useful implications (Almand, Moore, & Jaykus, 2017). But we can take such an example, in order to see how bacteria and viruses are completely different entities and how they work in different spheres altogether. The viruses might even overtake the bacteria to get its own way into the cells of the host. These types of interactions show us the difference in viral and bacterial mechanisms.

How does each molecule of NADH generate 2.5 ATPs after electron transport and oxidative phosphorylation?

Why does FADH2 only generate 1.5?

Isle Royale SimBio lab model:

You have accepted a position with the U.S. Fish and Wildlife Service. You are asked to advise the U.S. Park Service on likely future population fluctuations in wolf and moose populations on Isle Royale. National Park Service policy is not to intervene in natural ecological processes unless absolutely necessary.

a) Based on your understanding of current ecological concepts, especially the importance of numerical and functional responses of wolves and moose (Krebs, pages 222-223) as well as both direct and indirect species interactions, list three alternatives for the Park Service regarding how to manage the predator population that is currently threatened by local extinction on Isle Royale. What sources did you use in developing your alternative suggestions?

b) Explain which of the three alternatives you would select if you were the Park Superintendent.

1. Which of the following statements is FALSE?

A. The amino acid pool is the body's total supply of amino acids in the body's proteins.

B. Fats and carbohydrates are oxidized directly to produce cellular energy.

C.Amino acids can be used to supply energy only after being converted to a citric acid cycle intermediate.

D. Excess carbohydrate and fat can be stored as such, whereas excess amino acids are oxidized for energy or converted to fat or glycogen for storage.

2. If you were to jog one kilometer a few hours after lunch, which stored fuel would you probably tap?

A. muscle proteins

B. blood proteins

C. fat stored in adipose tissue

D.liver glycogen and muscle glycogen

3.A fasting animal whose energy needs exceed those provided in its diet will draw on its stored resources in which order? (See slides 81-82 in the Exam 3 review PowerPoint.)

A.fat, then glycogen, then protein

B. glycogen, then protein, then fat

C. liver glycogen, then muscle glycogen, then fat

D. muscle glycogen, then fat, then liver glycogen

RECOMBINANT DNA REVIEW

1. How are genes cut into pieces, in preparation for recombinant DNA cloning?

2. What enzyme is used to securely paste a new piece of DNA into a recombinant DNA molecue? What other process is this enzyme used in?

3. How does recombinant DNA get into bacteria? Name the process and how it works.

1. Of the following events, which occurs last during meiosis and the preceding interphase in a male?

2.

Of the following events, which occurs first during meiosis and the preceding interphase in a male?

Question 10 options:

3.

An XYY individual could result from non-disjunction in

Question 11 options:

4.

An XXY individual could not result from non-disjunction in

Question 12 options:

List five foods from your culture or your family food traditions that are prepared using a microbial process. Describe the type of microbial process used to prepare the food item, any history of this product

In an epidemiologic context, define and explain the term confounding. Include in your description an example of confounding. Describe one approach that may be used to mitigate the effect of confounding in the study analysis phase.

INFECTIOUS DISEASE CASE STUDY 17- Gram - Coccobacilli Three-year-old Michael is brought to the emergency room of a large metropolitan hospital by his parents. What began about a week ago as a seemingly mild cold has turned into a severe cough. Michael has experienced several “fits” of coughing in the past 24 hours. Each seems to become more violent. During the latest, he seemed unable to get air and had begun to turn blue in the hands, feet, nose, and lips. Between coughs, he noisily gasps for air. After a quick examination, the doctor readily admits him in respiratory isolation. Laboratory Diagnosis A nasopharyngeal swab is obtained and quickly sent to the laboratory for culturing in Bordet-Gengou medium containing fresh blood. After five days of incubation, tiny glistening colonies with a pearl-luster appearance were visible. A narrow zone of hemolysis is present around the colonies. Immunofluorescent staining revealed tiny coccobacilli.

1. Which of these is the most likely cause of Michael’s symptoms? (1 point) - Diphtheria - Pertussis - Tuberculosis - Pneumocystis carnii

2. What is the name of the microorganism that causes this infection? Type answer as two words, using appropriate capitalization and separating each word with one space. (1 point)

3. What is the common name of this infection? Type answer as two words, separated by one space and using lowercase letters. (1 point)

4. Explain why this infection was given this common name. Type answer as 1 or 2 short sentences in your own words and using correct spelling, grammar and punctuation. Copied and pasted answers may receive 0 credit. (2 points)

5. Most cases of this infection occur in what population? (1 point) - Children under 5 and older adults - children 4 years of age and under - Immunocompromised individuals - teenagers to young adults

6. The route of transmission for this infection is primarily through _______________. - Feces - Respiratory droplets - Bodily fluids - Parenteral injection

7. During the catarrhal stage of this infection, which of the following symptoms occur? Mark all that apply. - Whoop sound upon inhalation - sneezing - Nasal drainage - nasal congestion - Hacking cough - occasional cough

8. During the paroxysmal stage of this infection, which of the following symptoms occur? Mark all that apply. - Whoop sound upon inhalation - sneezing - Nasal drainage - nasal congestion - Hacking cough - occasional cough

9. What standard “well baby” immunization procedure has Michael likely missed? Be specific please

10. Knowing the immunization for this infection was likely missed, for what other diseases is Michael at risk? Explain. Be specific.

11. What is the prescribed treatment for this infection?

1. a)List 6 concerns in opposition to the de-extinction research and reintroduction. For each concern, list the counterargument by proponents of the de-extinction argument.

b) What is the Theseus’ Paradox? How does it apply to de-extinction?

c) Do you think that de-extinction is a sound idea? If you do not, describe why? If you are for it, describe why?

List three places outside of Africa where sickle-cell anemia is fairly common in the indigenous population:

Why hasn't the sickle-cell trait died out?

What is the ultimate source of biological variation?

What is the difference between gene flow and genetic drift?