Diversity of Bacteria

1. Proteobacteria constitute the majority of known bacteria of medical, industrial,

    and agricultural significance, and as a group what is their gram stain reaction?

2. Which species of Epsilonproteobacteria is responsible for causing peptic

     ulcers in humans?                                                                                        

3. The cytoplasmic membranes of mycoplasmas are unusual in that they contain

     what, which gives them the ability to resist osmotic lysis?   

4. What group of gram-positive bacteria are found in Swiss cheese?   

5. What species of gram-positive bacteria with filamentous morphology

     can synthesize antimicrobial metabolites?                                                    

Diversity of Archaea

6. Archaea found in hypersaline environments are know as what?   

7. The archael species Halobacterium salinarum can catalyze light-driven

     ATP synthesis using what protein which has a structural and functional

     similarity to rhodopsin, the visual pigment of the eye?   

8. What type of condition/environment is required methanogens to grow?

9. What is the highest temperature can one strain of Methanopyrus tolerate

     and grow?   

10. What enzyme is only found in hyperthermophiles which is responsible

       for DNA stability at high temperatures?   

15. In VNTR analysis, a conclusion that indicates “Inclusion” means which of the following: a. The profiles are different b. The profiles match c. No conclusion can be made d. The samples are from different sources

16. In RFLP profiling, DNA degradation can be detected using which of the following: a. Agarose gel electrophoresis b. Partial restriction digestion c. PCR analysis d. All of the above

17. This term refers to the deviation of the specificity of the cleavage site of a restriction enzyme: a. Point mutation b. Point degradation c. Partial stripping d. Star activity

18. In RFLP, this is caused by the substitution, deletion, or insertion of a single nucleotide a. Point mutation b. Point degradation c. Partial stripping d. Star activity

19. Which of the following loci was used by forensic DNA labs for amplified fragment length polymorphisms: a. D1S80 b. D1S99 c. T1S80 d. DS1980

20. Which of the following cases would be suitable for AFLP analysis: a. A cold case with a degraded sample b. A paternity case c. A case with mtDNA d. None of the above

Mesophilic organisms are organisms that prefer moderate temperatures (not too hot, not too cold). Their enzymes are similar to the potato enzymes, they work best at a range of 20-40 °C. What do you deduce is happening during the mesophilic stage? Why do the mesophilic organisms stop working at around 45°C?

2. Thermophilic organisms are organisms that survive best in hot temperatures (up to 70°C) What do you think is happening during the thermophilic stage of the compost pile?

3. Why does the curve peak (around 65°C) and not continue rising as temperature continues to increase?

4. Why do you think that, after some time, the curve begins to decline?

5. Does your data show any evidence that extreme heat has an effect on the ability of catalase to carry out its reaction, and if so, what is this evidence?
6. At what temperature did the potato enzyme work best?
7. What range of temperatures do you deduce are the best for potato catalase activity?

3. (10pt) Your colleague professor Stu Dentgenerated a genome-wide DNA methylation map for normal colon cells using MRE-seq (a restriction enzyme approach) and MeDIP-seq(an immunoprecipitation approach). In an intergenic region, he found an interesting locus. This locus is about 20kb. On one end of the locus, there is a 2kb CpG rich stretch that has both relatively lowMRE-seq and MeDIP-seq signals. The rest 18kb has high level of MeDIP-seq signals. (A) (3pt) Why might you suspect that this region encodes for a novel gene? (B) (4pt) You decide to look at histone modification patterns across this regionfor more evidence. There are several genome-wide datasets available for this cell type: H3K4me1, H3K4me3, H3K27me3, H3K9me3, H3K36me3, and H3K9Ac. Which histone mark would youinvestigatefor this locus and why? (C) (3pt) Suggestat least one other source of data (NOT annotation or bisulfide sequencing) that may help you confirm or refute your suspicion, and why you think it may help?

Case history: A 36-year-old Mediterranean man presents to your clinic with increased fatigue and weakness of 2 days duration. He was recently tested for tuberculosis exposure and was PPD positive with a normal chest x-ray film. He just started anti-TB prophylaxis medications the week before. On physical exam, he is tachycardic, appears jaundiced, and has mild splenomegaly. You order blood studies, which show low hemoglobin, low hematocrit, and precipitates in RBC. You begin to suspect that this patient suffers from an X-linked recessive disorder where an enzyme is deficient which is triggered by his current TB prophylaxis, and you decide to consult an infectious disease specialist about alternative regimens that will not cause his current symptoms.

Answer the following questions with the information from the case history:

a) Name the disorder.

Glucose-6-Phosphate Dehydrogenase Deficiency

b) Describe the pathogenesis of the disease. Incorporate the name the precipitates in RBC and their formation in your discussion.

c) List the precipitating factors for this disease.

PLEASE ANSWER B AND C

Case history: A 36-year-old Mediterranean man presents to your clinic with increased fatigue and weakness of 2 days duration. He was recently tested for tuberculosis exposure and was PPD positive with a normal chest x-ray film. He just started anti-TB prophylaxis medications the week before. On physical exam, he is tachycardic, appears jaundiced, and has mild splenomegaly. You order blood studies, which show low hemoglobin, low hematocrit, and precipitates in RBC. You begin to suspect that this patient suffers from an X-linked recessive disorder where an enzyme is deficient which is triggered by his current TB prophylaxis, and you decide to consult an infectious disease specialist about alternative regimens that will not cause his current symptoms.

Answer the following questions with the information from the case history:

a) Name the disorder.

Glucose-6-Phosphate Dehydrogenase Deficiency

b) Describe the pathogenesis of the disease. Incorporate the name the precipitates in RBC and their formation in your discussion.

c) List the precipitating factors for this disease.

PLEASE ANSWER B AND C

(Q001) Glucose-6-phosphate dehydrogenase deficiency (G6PD deficiency) is an inherited disorder where either the body has less of the G6PD enzyme than normal or the available G6PD is not functioning correctly. This deficiency affects red blood cell function and may result in anemia (the destruction of red blood cells) when people with the condition have infections, are taking certain medications, or eat certain foods. People with G6PD deficiency may have some protection from malaria because their abnormal red blood cells interfere with the reproduction of the malaria parasite in their bodies.

Consider the prevalence of G6PD deficiency estimated by the World Health Organization (WHO) as shown in the map on p. 247 of your lab manual. Compare the distribution of G6PD deficiency with the distributions of the sickle-cell trait and malaria shown in Figure 8.9 on p. 238 of your lab manual. What similarities between these distributions do you notice? What differences do you notice?

(Q002) Why might these similarities and differences exist? Be sure to consider the evolutionary context (including the natural environment, cultural practices, and interbreeding).

A production manager at a pottery factory has noticed that about 70 percent of defects result from impurities in raw materials, 15 percent result from human error, 10 percent from machine malfunctions, and 5 percent from a variety of other causes. This manager is most likely using a-
Select one:
a. cause-and-effect diagram.
b. scatter diagram.
c. quality loss function.
d. Pareto chart.
e. flowchart.

Suppose a politician proposes that we make college education free for all students. What impact would this proposal have on the level of human capital and the rate of growth in the country?

Several societies around the world make it very difficult for women and girls to become educated. What impact would this have on economic growth in these countries?

Suppose that the government decides to cut spending on research and development. What impact would this have on future economic growth?