Term
| What are the overall anabolic and catabolic pathways involved in nucleotide metabolism? |
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Definition
Anabolic:
Purine/Pyrimidine De Novo synthesis
Purine/Pyrimidine Salvage Pathways
Catabolic:
Purine/Pyrimidine Degradation |
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Term
| What major difference is there between purine and pyrimidine synthesis in terms of when and how the ring is added? Both purine and pyrimidine synthesis involve what common molecule? |
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Definition
Purine Synthesis: PRPP is the precursor on which the ring is added
Pyrimidine Synthesis: The ring is made first, then PRPP is added.
The molecule in common is: PRPP |
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Term
| What molecule is utilized in the start of the purine synthesis pathway? What molecule is formed by the purine synthesis pathway? What is the name of the enzyme that catalyzes the addition of the first component of the purine ring? What nitrogen-containing amino acid donates this first part of the ring? |
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Definition
a. Ribose-5 phosphate
b. IMP (common precursor for AMP & GMP)
c. glutamine PRPP amidotransferase
d. glutamine |
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Term
| How many enzymatic steps are required to synthesize IMP from PRPP in humans? What is the cellular localization of all the enzymes that carry out these steps? |
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Definition
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Term
| What carrier is utilized in two different steps to add to the ring? What vitamin is it derived from? What atom does it donate? |
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Definition
a. N10-formyl tetrahydrafolate
b. It is derived from folate.
c. It donates carbon atoms. |
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Term
| What is the name of the enzyme required to turn folate into the form used in purine synthesis? How many steps are required for this enzyme to carry out its job? What exactly does the enzyme do? Where in purine and pyrimidine metabolism does inhibition of this enzyme have an effect? |
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Definition
a. Dihydrofolate Reductase
b. 2 steps
c. The enzyme converts double bonds into single bonds.
d. Inhibition of DHFR would effect addition of the formyl group on the purine ring. (Not sure how it would effect pyrimidine synthesis) |
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Term
| The pathway that is most affected by sulfa drugs is? |
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Definition
| G. Prokaryotic Purine Synthesis |
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Term
| What nucleotides are formed from IMP? |
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Definition
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Term
| What is the only enzyme that is known to be regulated in the steps of forming IMP from PRPP? What are the allosteric activators of this enzyme? What are the allosteric inhibitors of this enzyme? |
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Definition
Glutamine PRPP Amidotransferase
Activators: PRPP
Inhibitors: IMP,GMP,AMP |
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Term
| What is the allosteric inhibitor of adenylosuccinate synthetase? What is the allosteric inhibitor of IMP dehydrogenase? |
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Definition
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Term
| What is the difference in mechanism between the inhibition by thio-IMP of 1)glutamine-PRPP amidotransferase and 2) adenylosuccinate synthetase and IMP dehydrogenase? |
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Definition
1.) Inhibited via allosteric negative feedback inhibition
2.) Inhibited via competitive inhibition |
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Term
| Can 6-mercaptopurine be incorporated into DNA and if so, what is the effect? |
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Definition
| It can be incorporated into DNA and it results in the arrest of de novo synthesis of DNA. |
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Term
| What do the acronyms "HGPRT" and "APRT" stand for and what do they do? What disease arises as a result of HGPRT deficiency? What are its symptoms? What is the reason for the increase in uric acid levels of the HGPRT deficient patient? What is their usual cause of death? |
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Definition
a. HGPRT - hypoxanthine-guanine phosphoribosyltransferase
APRT - adenine phosphoribosyltransferase
hypoxanthine + PRPP --hgprt--> IMP + PPi
guanine + PRPP --hgprt----> GMP + PPi
adenine + PRPP ---aprt----> AMP + PPi
b. Lesch Nyhan Syndrome
c. Symptoms: mental retardation, spasticity, self-mutilation
d. No HGPRT means increased levels of PRPP, so de novo synthesis of nucleotides occurs. Without regulation, this excess gets degraded resulting in an increase in uric acid.
e. Kidney failure is the cause of death. |
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Term
| If there were no salvage pathways in purine metabolism, would 6-mercaptopurine be effective as a cancer chemotherapeutic? |
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Definition
| It would still be effective because it arrests the de novo synthesis of DNA. |
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Term
| 6-mercaptopurine itself doesn't inhibit enzymes, but is the precursor to what molecule that is an inhibitor? |
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Definition
| 6-thioinosine monophosphate (thio-IMP) |
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Term
| How many enzymatic steps are required to synthesize OMP from glutamine and PRPP in humans? What is the cellular localization of all but one of the enzymes that carry out these steps? |
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Definition
a. 6 steps
b. The enzymes are located in the cytosol except Dihydoorotate Dehydrogenase which is in the mitochondria. |
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Term
| What cytosolic enzyme that catalyzes an ATP-requiring step of pyrimidine synthesis has an analogous mitochondrial enzyme that participates in the urea cycle? What is the enzyme that catalyzes the first step of pyrimidine synthesis? What are the important differences between the cytosolic and mitochondrial enzymes? What is an enzyme of pyrimidine synthesis that is only found in the mitochondria? Why is it advantageous that it is a mitochondrial enzyme? |
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Definition
a.carbamoyl phosphate synthase II (CPS II)
b.CPS II
c.
d.Dihydroorotate Dehydrogenase
e. |
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Term
| Why does excess ammonia lead to elevated levels of orotic acid in the urine (orotic aciduria)? And why does this primarily involve the liver? |
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Definition
a. With increased ammonia, CPS-I synthesizes carbamoyl phosphate. This gets converted to orotate. Orotate is also synthesized via a pathway which involves CPS-II. The combined effect of the two pathways results in increased levels of orotate which is then excreted in the urine.
b. This involves the liver because this is where excess ammonia and CPS-I interact to synthesize the carbamoyl phosphate. CPS-I is not tightly regulated in the liver. |
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Term
| What enzyme is present at low levels in E.coli lab strains, and accounts for the relative safety of these strains for use in recombinant DNA work? What does the low enzyme expression mean for the ability of the bacterium to survive in the wild? |
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Definition
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Term
| What are the sources of carbon and nitrogen atoms in the pyrimidine ring? |
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Definition
Glutamine and Aspartate are sources of Nitrogen atoms.
Bicarbonate and Aspartate are sources of Carbon atoms. |
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Term
| What molecule is formed by the pyrimidine synthesis pathway? |
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Definition
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Term
| How is the pyrimidine synthesis pathway like a salvage pathway? |
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Definition
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Term
| Are other pyrimidine bases than orotate salvaged? Why are salvage pathways useful? |
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Definition
| Orotate, Uracil, and Thymidine are salvaged. Cytosine is not directly salvaged, but it is indirectly salvaged. |
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Term
| What purine triphosphate activates pyrimidine synthesis? |
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Definition
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Term
| How is cytidine monophosphate (CMP) formed? |
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Definition
| UMP is phosphorylated to UTP. UTP is converted to CTP via CTP synthase, which uses glutamine as an amino group donor. CTP is then converted to CMP via dephosphorylation. |
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Term
| What purine triphosphate allosterically activates pyrimidine synthesis? |
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Definition
| ATP (same question as #24)? |
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Term
| How is thymidine monophosphate (TMP) formed? |
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Definition
| Deoxy UMP (dUMP) is converted to TMP via thymidylate synthase. |
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Term
| What carrier donates a carbon to form TMP from dUMP? What is the enzyme that catalyzes the reaction? |
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Definition
a. N5,N10-methylene THF
b. Thymidylate Synthase |
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Term
| If there were no salvage pathways in pyrimidine metabolism, would 5-fluorouracil be effective as a cancer chemotherapeutic? |
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Definition
| 5-FU is converted to fDUMP which inhibits thymydilate synthase. This inhibits dTMP formation. dTMP is converted to dTTP which serves as a substrate for DNA synthesis...so it would be effective. |
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Term
| 5-Fluorouracil itself doesn't inhibit enzymes, but is the precursor to what molecule that is an inhibitor? |
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Definition
| fDUMP which inhibits Thymidylate Synthase |
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Term
| What type of inhibition does fluoro-dexoyuridine monophosphate have on thymidylate synthase? |
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Definition
| fDUMP provides suicide inhibition of T.S. which is irreversible. |
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Term
| Can 5-fluorouracil be incorporated into DNA and if so, what is the effect? |
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Definition
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Term
| What are some of the strategies cancer tumor cells have been observed to employ to exhibit resistance to methotrexate? |
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Definition
Resistance to MTX is
1. due to alterations in folate transporters
2. marked amplification of dihydrofolate reductase gene
3. generation of mutant DHFR, that is insensitive to MTX
4. synthesis of MDR1 or MRP...these are proteins that are pumps that remove drugs from cells.
5. Decreased uptake of DHFR
6. Decreased degradation of DHFR |
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Term
| What is the mechanism of ICID 1694? Considering that it could be said that ICID 1694 resembles methotrexate, would it be expected to cause teh same, or fewer, or more side effects as methotrexate? |
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Definition
ICID 1694 inhibits N5,N10-methylene THF. It is a specific inhibitor of T.S. formation of TMP. TMP goes into the DNA.
Fewer side effects? |
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Term
| How is the use of leucovorin with methotrexate different from the use of leucovorin with 5-fluorouracil? |
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Definition
Leucovorin causes MTX not to work. It bypasses the steps MTX inhibits to form N5,N10-methylene THF. Leucovorin is a form of N5-formyl THF which is introconvertible with N5,N10-methylene THF. "Antidote to methotrexate."
Leucovorin enhances the activity of 5-FU. |
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Term
| What do nucleotide kinases? What do nucleoside diphosphate kinases do? This can also be done for what nucleotide by glycolysis or oxidative phosphorylation? |
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Definition
Nucleotide Kinases?
Nucleotide Diphosphate Kinases are used to synthesize dNTPs from dNDPs. |
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Term
| What is the name of the enzyme that converts ribonucleotides to deoxyribonucleotides? What molecule does the reducing power come from originally? What form are the ribonucleotides in before they are converted? |
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Definition
a. Ribonucleotide Reductase
b. Thioredoxin
c. base + ribose molecule + 2 phosphate groups |
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Term
| What class of enzyme breaks nucleic acids down into nucleotides? What class of enzyme removes phosphates from nucleotides (converting them to nucleosides)? What class of enzyme breaks nucleosides into bases and sugars? |
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Definition
a. nucleases
b. nucleotidases
c. nucleoside phosphorylase (PNP) |
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Term
| What muscular enzyme deaminates adenine nucleotide (in skeletal muscle)? What enzyme in other tissues deaminates adenosine nucleoside? What is the difference in terms of the order in which the phosphate and the amino group are removed? |
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Definition
a. AMP Deaminase
b. Adenosine Deaminase
c. ?
Not sure about the answers for this one. The answers from Inverse LOG were the same for a and b, and it was AMP deaminase. |
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Term
| What is the enzyme that is defective in most patients with SCID? What are the two enzymes of purine degradation that may be defective in SCID? Which of these two enzymes of purine degradation is defective in more patients with SCID that the other? |
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Definition
a. interleukin 2 receptor gamma chain
b. adenosine deaminase and purine nucleoside phosphorylase (PNP)
c. Adenosine Deaminase is more defective than PNP
Not sure about the answer for the first question. |
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Term
| What is the most common therapy for SCID due to defects of purine metabolism? Why does this work? What is a drawback to this therapy? What is an alternative therapy for SCID due to one of these defects? What are drawbacks to this therapy? Why is this therapy not available for SCID due to the other defect? Why does enzyme replacement therapy for SCID utilize the enzyme conjugated to PEG rather than the enzyme alone? |
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Definition
a. enzyme replacement therapy: PEG-ADA
b. It works because it maintains adenosine deaminase levels which are low in patients with SCID.
c. Drawback? (Maybe because it doesn't do anything to impact a PNP defect?)
d. ADA gene therapy
e. Drawback: only cured some patients
f. ?
g. It utilizes the enzyme conjugated to PEG because PEG reduces degradation and reduces immunogenicity of bovine ADA. |
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Term
| There was an attempt made to replace what enzyme in the first gene therapy trial designed to cure or partially cure a patient? Was a cure achieved? Why is SCID a "good" disease for early attempts at gene therapy? |
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Definition
a. Attempted to replace adenosine deaminase (ADA)
b. Cure was achieved in some patients.
c. "Good" Disease for Gene Therapy:
1) single gene defect that could be treated by introducing a functional expression of the gene
2) defect was in an organ that was accessible
3) disease is severe enough to make extreme measures worthwhile and ethical |
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Term
| What is the name of the heterogenous base attached to IMP? |
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Definition
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Term
| What is the nitrogenous product of purine degradation that is excreted? What is it converted from? By what enzyme? |
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Definition
a. Uric acid
b. Xanthine
c. Xanthine oxidase |
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Term
| What is gout? What are some of the underlying causes of gout? What are the symptoms and what explains them? |
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Definition
a. Gout is due to high levels of uric acid.
b. It is caused by underexcretion of uric acid by the kidneys or a purine metabolism problem in which there is overproduction of uric acid.
c. Symptoms include big toe pain, joint pain in extremities, and kidney (renal failure.) Sodium urate crystals deposit in joints of extremities causing arthritis. Renal failure is due to accumulation of uric acid crystals in the tubules. |
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Term
| What do allopurinol and rasburicase do? In what way is rasburicase superior? What are the drawbacks of rasburicase, and what is it about the drug that leads to these drawbacks? How do the drawbacks explain why allopurinol is preferred for treatment of gout, and rasburicase is used in conjunction with treatment for cancer? |
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Definition
a. Allopurinol (similar to hypoxanthine) inhibits xanthine oxidase thereby inhibiting uric acid production. Rasburicase is found in bacteria and breaks down uric acid. It is given via IV and it is expensive. It is pharmacologically superior to Allopurinol.
Not sure about the rest of the questions. This is all the information Campbell gave on these two. |
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Term
| The degradation of cytosine, uracil, and thymine have what two degradation products in common? What other degradation end product results from catabolism of cytosine and uracil? what other degradation end product results from catabolism of thymine? |
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Definition
a. CO2 and NH4+
b. Beta Alanine
c. Beta Aminoisobutyrate |
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Term
| Tetrahydrobiopterin synthesis involves what nucleotide? NAD+ synthesis involves what two nucleotides? FMN synthesis involves what vitamin? FAD+ synthesis involves what two nucleotides? Coenzyme A synthesis inovles what amino acid? Coenzyme A inovles what nucleotide? |
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Definition
a. GTP
b. NMP and ATP
c. vitamin B2 (riboflavin)
d. FMN and ATP
e. Cysteine
f. ATP
Double check the answer to b. |
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Term
| What is the effect of AZT on a cell? Does it require a salvage pathway to become active? |
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Definition
AZT gets incorporated into the DNA. It is involved in DNA elongation and inhibits viral DNA polymerases.
I don't think it requires a salvage pathway to become active...but double check this. |
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Term
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Definition
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Term
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Definition
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Term
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Definition
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Term
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Definition
A
(pretty sure about this answer...but might want to double check) |
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