QUESTIONS NICOSIA

11/2/2014
1) Which of the following statements is WRONG about cloning by homologous recombination:
a. Requires the use of special bacterial strains
b. May require sub-cloning in smaller plasmids
c. And completely independent of the presence of restriction sites
d. Allows splicing in seq frames. About DNA
e. Requires the presence of RecBC mitation
2) Which of the following statements is WRONG about cloning for "Recombeneering":
a. Requires inducible expression of exo, bet and gam genes of the Lambda bacteriophage
b. Allows you to replace or delete any DNA sequence through insertion and deletion
steps of selection boxes
c. Can be used to clone or modify entire eukaryotic genes
d. It is often used to generate transgenic mice through the use of BAC constructs with
extensive homology regions.
e. With the "gap cloning" technique it allows to inactivate a gene in the bacterial
chromosome to study its function
3) Which of the following statements is WRONG about BAC:
a. They can be used for the construction of genotheques
b. They are artificial DNA vectors based on the E. Coli F plasmid.
c. They are present in multiple copies in bacterial cells
d. They are artificial vectors suitable for cloning large inserts
E. They contain seq SopA,B,C responsible for the breakdown of the plasmid into
daughter cells
4) Which of the following statements is FALSE:
a. Plasmids can be used as vectors
b. DNA viruses can be used as vectors
c. RNA viruses can be used as vectors
d. RNA amplicons can be used as vectors
e. All the above are true

5) Which of the following statements regarding plasmid vectors is

WEDDING BAND:
a. Plasmid vectors cannot be readministered
b. Plasmid vectors do not induce an immune response against
Vector itself
c. Plasmid vectors are produced in mammalian cells
d. Plasmid vectors cannot be used in mammalian cells
e. Plasmid vectors have a high transduction capacity
7) Which region is maintained in the genome of a retroviral vector
defective for replication?
a. The region coding the gag protein
 b. The protein-coding region of the envelope
c. The region coding for the pol protein
d. The two LTRs and the packaging sequence (cis-elements)
e. None of the above
8) The main reason for the use of "split genome" methods is
"complementing cell line" for the production of a retroviral vector
defective for replication is:
a. Modification of tropism
b. Increased expression of the gene transduced by the vector
c. Need to reduce the risk of replicative virus generation
d. Increased carrier productivity
e. None of the above
9) What is the difference between adenoviral vectors defective for
First generation replication and "helper dependent"
a. Different tropism
b. Ability to infect different cells
c. Helper dependent must be produced in a cell
complementant, the first generation vector does not
d. In helper dependent, most of the genome has been eliminated
leaving only the ITR and the packaging signal, while in the vector of
first generation only the E1 region has been eliminated
e. There are no significant differences between the two.
10. What are the advantages of a first generation adenoviral vector?
a.They are safe (do not integrate into the genome)
b. They induce a powerful immune response against the
codified interest
c. They have a broad tropism d. They are obtained with high titer.
e. All the above
11. What is the best use of a vector Modified Vaccinia Ankara (MVA)
a. Construction of stable cell lines for protein expression
Recombinant.... Genetics
b. RIGHT ANSWER:b
12. (It doesn't read well) A vector Helper Virus....
RIGHT ANSWER: d
13.What characteristics must a preclinical model have to be more predictive for a cancer vaccine
a. Not having MHC-I
b. Be immunologically tolerant to antigen
c. Spontaneously develop a tumor
d. Both a and b
e. Both 1 and 3
14.Tumor antigens are
a. Tumor cell DNA fragments
b. microRNAs expressed by the tumor and released into the circulation
c. proteins predominantly expressed by the tumor
d. proteins expressed exclusively by the tumor and not by normal tissues
e. Are the D ed responses true?
15. The phenotype of two different cell types... mammal is due to:
a. Differential gene expression
b. Different number of genes
c. Different number of chromosomes
d. Different genotype
e. None of the above
16. The different relative concentration of two transcription factors with equal activation and
dimerization domains, but with DNA recognition domains of different specificity can give rise
to:
a. Different concentration of the resulting dimers
b. Differential transcription of c. genes. Different cell phenotype
d. Regulation of gene expression during development
e. All precedes
17.Which of the following statements regarding transposition is FALSE:
a. La transposition is a specific form of genetic recombination that moves certain genetic
elements from one site to another.
b. A donor site and an acceptor site c are involved in the transposition. Recombination is
a specific site at a defined site: transposition site
d. The recombinase responsible for this process is transposase
e. As in the other recombination processes, in the transposition there is homology
between the sequence of the donor site and acceptor
18. The different classes of transposons are:
a. DNA transposons
b. Virus/retrovirus type transposons(i.e. transposons that move via RNA intermediate)
c. Poly-A retrotransposons
d. None of the classes listed and.
e. classes listed
19. To limit the risk of mutations due to integrations in the host genome as
vectors/methodologies it is necessary to use:
a. Viral vectors
b. Transposition mediated by the SB system
c. Lentiviral vectors
d. Site-specific recombinant nucleases and
e. false
20) Genome editing is:
a. A type of genetic engineering that allows you to modify a genome by INSERTING
seq. Of DNA by means of recombinant site-specific nucleases
b. A type of genetic engineering that allows you to modify a genome by
SUBSTITUTING seq. DNA by means of Recombinant Nucleases
sitespecific
c. A type of genetic engineering that allows you to edit a genome by REMOVING seq.
DNA by means of site-specific recombinant nucleases
d. A type of genetic engineering that allows you to modify a genome INSERTING,
REPLACING BY REMOVING eg. DNA by means of site-specific recombinant
nucleases
e. answers are all false
11/07/14
1. Which of the following statements is WRONG about cloning by homologous recombination:
f. Requires the use of special bacterial strains
g. May require sub-cloning in smaller plasmids
h. And completely independent of the presence of restriction sites
i. Allows seq frame splicing. About DNA
j. Requires the presence of RecBC mitation
2. Homologous recombination
a. It is a technique used for cloning large DNA fragments
b. Can be used by the cell to generate new genes
c. It can only occur in particular bacterial strains that have mutations in specific genes
d. It occurs only in prokaryotic cells that express the gene
e. Does not require DNA synthesis
3. The genes of the "red" operon of the Lambda bacteriophage:
a. They are generally constitutively expressed in E. coli and used to induce homologous
recombination.
b. They code, among other things, for bGalactosidase, which is necessary for the
selection of recombinant colonies because it generates blue colonies in the presence of
Xgal
c. Contain a selection box that can give the bacterium selective growth in certain culture
media
d. They can be expressed in E. Coli by a defective prophage integrated in the bacterial
chromosome
e. They are expressed in the presence of the sbcA mutation (mutation that depresses Rec
E/T)

4) Quale delle seguenti affermazioni è FALSA:

f. I plasmidi possono essere usati come vettori
g. I virus a DNA possono essere usati come vettori
h. I virus a RNA possono essere usati come vettori
i. Gli ampliconi a RNA possono essere usati come vettori
j. Tutte le precedenti sono vere

5) Non-replicative viral vectors are obtained:

a. Encoding the TetR repressor in the viral vector to interfere with replication
b. Increasing transduction efficiency to compensate for replication defect
c. Modifying the tropism of the viral vector
d. Increasing the expression of the gene encoded to compensate for the replicative defect
e. Mutating or deleting genes encoding exsensory functions for replication
6) Non-replicative viral vectors are produced in:
a. Bacterial cells
b. Bacterial cells that produce the TetR repressor
c.Cells complementing the replicative vector defect
d. Mammalian cells
e. Mammalian cells that produce the TetR repressor
7) What is the best use of a first generation adenoviral vector
 a. Construction of stable cell lines for protein expression
Recombinant
b. Genetic vaccination
c. Genome editing
d. Gene therapy
e. All the above

8) What is the difference between adenoviral vectors defective for first generation replication
and "helper dependent"
a. Different tropism
b. Ability to infect different cells
c. The helper dependent must be produced in a complementary cell, the first generation
vector must not
d. In the helper dependent most of the genome was eliminated leaving only the ITR and
the packaging signal, while in the first generation vector only the E1 region was
eliminated
e. There are no significant differences between the two.
9) What is the problem with the use of human adenovirus of serotype 5 (ADS) for genetic
vaccination in humans:
a. Presence of neutralising antibodies against Ad5 in the human population
b. Low cellular response induction efficiency
c. Low efficiency of induction of humoral response
d. High toxicity
e. Risks of integration into the DNA of the infected cell
10) An oncolytic virus is:
a. A virus that only infects cancer cells
b. A virus capable of infecting all cells
c. A virus that is capable of causing lysis of cancer cells
d. A virus that has been modified to infect a particular type of cell
e. None of the above
11)A re-directed Herpes virus (HSV) vector is:
a. A vector that no longer infects cells using its natural receptors
b. A carrier that infects cells expressing a particular c-receptor. A vector that infects all
cells
d. A vector that no longer infects cells using its natural receptors and that infects cells
expressing a particular receptor of interest
e. None of the above

12) What characteristics must a preclinical model have to be more predictive for a cancer
vaccine
a. Do not have MHC-1
b. Be immunologically tolerant to antigen
c. Spontaneously develop a tumor
d. Both to b
 e. Both b and c
13. The phenotype of two different cell types... mammal is due to:
a. Gen differential expression
b. Different number of genes
c. Different number of chromosomes
d. Different genotype
e. None of the above
14) Which of the following statements regarding transcriptional control of gene expression is
CORRECT:
a. Each differentially regulated gene is activated by a specific transcription factor
b. All differentially regulated genes are subject to alternative splicing
c. Genes differentially regulated at the transcriptional level are controlled by a set of
transcription factors present in specific concentrations
d. Each differentially regulated gene is repressed by a specific transcription factor
e. Differentially regulated genes at the transcriptional level are found in regions of poorly
condensed chromatin
15. The different relative concentration of two transcription factors with equal activation and
dimerization domains, but with DNA recognition domains of different specificity may give rise
to:
a. Different concentration of the resulting dimers
b. Differential transcription of genes
c. Different cell phenotype
d. Regulation of gene expression during development
e. All previous

16) To limit the risk of mutations due to integrations in the

Host genome Which vectors/methodologies should be used:
a. Viral vectors
b. Transposition mediated by the SB system
c. Lentiviral vectors
d. Site-specific recombinant nucleases
e. All false
17) Genome editing is:
a. A type of genetic engineering that allows you to modify a genome by INSERTING
seq. DNA by means of site-specific recombinant nucleases
b. A type of genetic engineering that allows you to modify a genome by
SUBSTITUTING seq. DNA by means of site-specific Recombinant Nucleases
c. A type of genetic engineering which allows the modification of a
Genome REMOVING seq. DNA by means of recombinant site nucleases
Specific
d. A type of genetic engineering that allows a genome to be modified
INSERTING, REPLACING OR REMOVING seq. Of DNA by means of nucleases
Recombinant Site Specifications
e. The answers are all false
18. Which of the following statements concerning transposable elements (
TRANSPOSONS) is FALSE:
 a. Transposable elements are genetic elements that move from a
site to another
b. Transposons can move within a single cell
from one position of the chromosome to another
c. Transposable elements can be moved within a
single cell from one chromosome to one plasmid and vice versa
d. Transposable elements are present both in the genome of prokaryotes
than eukaryotes
e. Transposable elements do not require the presence of sites
specific for recombination.
19. Which of the following statements concerning transposition is FALSE:
a. Transposition is a specific form of recombination
genetics that move certain genetic elements from one site to another
b. A donor site and an acceptor site are involved in the transposition
c. Recombination is a specific site at a defined site: transposition site
d. The recombinase responsible for this process is transposase
e. As in the other recombination processes, in the transposition there is homology
between the sequence of the donor site and acceptor
20) The different classes of transposons are:
a. DNA transposons
b. Virus/retrovirus type transposons (i.e. transposons that move via RNA intermediate)
c. Poly-A retrotransposons
d. None of the classes listed
e. All classes listed

Nicosia:
1. ERRATA on cloning by homologous recombination: It is completely independent of the
presence of restriction sites

2. Il cloning for recombeeniring: does not require the use of restriction enzymes.

3. ERRATA on recombeeniring: -It can only occur in particular bacterial strains that have
mutations in specific genes; -With the technique of "gapeloning" allows to inactivate a gene in
the bacterial chromosome to study the function

4. FALSE on transposition: As in the other recombination processes, in the transposition

there is homology between donor site and acceptor.

5. FALSE, which of the following applications concerning the transduction of nucleic acids
is false: All previous applications are realized by transduction of nucleic acids.
(expression of recombinant proteins, gene therapy, gene expression studies,
genetic vaccination)

6. FALSE, Which of the following statements regarding transposable elements is false:

Transposable elements do not require the presence of specific sites for recombination.
 7. FALSE on the enzyme transposase: It recognizes the sequence of the target site and
produces a single-stranded cut.

8. FALSE on the production of a non-replicative viral vector: No expression of the gene

encoded in the producing cell.

9. FALSE on Zing Finger Nucleases (ZFNs): They consist of a single domain

10. INCORRECT on TALEN (transcription activator like effector nuclease): The DNA
binding domain recognizes and binds a DNA sequence of 4 bp.

11. FALSE on genome editing systems ZFN nuclease, TALEN, CRISP/CAS9: All three
systems are able to simultaneously bind several target sequences

12. ERRATA on BAC: they are present in multiple copics.

13. Which of the following is FALSE? NONE (in fact it is true that plasmids, DNA
viruses but na amplicans can be used as vectors)
And
14. TRUE on plasma vectors you say: Do not induce an immune response against the
vector
same
15. Which region is maintained in the genome of a defective retroviral vector for
replication: The two LTRs and the packaging sequence (psi)

16. The main reason for the use of split genome and complementing cells line methods
for the production of a defective retroviral vector for replication is: Need to reduce the risk of
replicativist virus generation

17. Differences between adenoviral vectors of 1st generation: In the Helpere Dependent,
most of the genome was eliminated, leaving only the LTRs and the psi packaging signal (in the
adenviral), In the 1st generation vector only the E1 region was eliminated.

18. Adenoviral benefits: Do not integrate into the genome, Broad tropism, High levels,
Powerful immune response. (ALL)

19. Adenoassociated Benefits: They are not pathogenic to humans, They are stable, Wide
tropism, Prolonged transgene expression in vivo. (ALL)

20. Better use of MVA vectors: genetic vaccination

21. Better use of a 1st generation adenoviral vector: Genetic vaccination.

22. Which vector is most suitable for gene therapy: adenoassociated.

 23. What is the best vector for the generation of stable cell lines for the expression of
recombinant proteins (monoclonal Ab): Retrovirus.

24. Transposon classes: DNA transposons, virus/retrovirus type transposons, polyA

retrotransposons (ALL)

25. Genome edititing: A type of genetic engineering that allows you to modify a genome,
inserting, replacing, or removing DNA sequences, using site-specific recombinant nucleases.

26. Homologous recombination: It can be used by the cell to generate new genes

27. The homologous recombination pathway RecBCD dependent: Requires the action of
the RuvABC complex for migration and resolution of solid joints

28. 1 RED operon genes of the lambda bacteriophage: They can be expressed in E.Coli
by a defective prophage integrated in the bacterial chromosome

29. A selection box: It is a sequence that contains genes that can give bacteria the ability
to grow or not on specific selective culture media.

30. An advantage of VIRAL vectors over PLASMID vectors: Higher translation

efficiency.

31. Non-replicative viral vectors are produced in: cells complimenting the replicative
defect of the vector

32. The modification of the tropism of a retro viral vector is obtained: By removing the
coding region for the envelope protein from the vector and co-transfecting an expression plasmid
encoding a protein of the "envelope" of a different virus.

33. A pseudo typical virus is: a virus that has been modified to infect a particular type of
cell.
34. An oncolytic virus is a virus capable of causing lysis of cancer cells.

35. A Herpes Simplex vector: it is a vector that does not infect.

36. Which administration regimen is best suited to increase the immune response of a
genetic vaccination: Prime boost heteroloo with MVA al prime

37. What is the problem with the use of human adenovirus of serotype 5 (Ad5) for enetic
vaccination in humans: Presence of neutralizing antibodies against Ad5 in the population
Human

38. What characteristics must a preclinical model have to be more predictive for a cancer
vaccine: -be immunologically tolerant to Ag. -Spontaneously developing a tumor (B and C are
correct)
 39. To limit the risk of mutations due to integrations in the host genome, which
vectors/methodologies should be used? Site specific recombinant nucleases.

40. Which of the following statements is correct about transcriptional control of gene
expression: Genes differentially regulated at the transcriptional level are controlled by a set of
transcription factors present in specific concentrations.

41. During the development of Drosophila the cellular differentiation of the

anteroposterior axis: depends on the formation of concentration gradients of activators and
transcriptional repressors.

42. A re-directed Herpes Virus (HSV) vector is: A vector that no longer infects cells
using its natural receptors and that infects cells expressing a particular receptor of interest.

43. The phenotype of two different cell types of a mammal is due to: differential
expression of genes

44. The different relative concentration of two transcription factors with equal activation
and dimerization domains, but with DNA recognition domains of different specificity can give
rise: ALL PHENOMENA (-different concentrations of dimer results, different cell phenotypes,-
regulation of gene expression during development)

45. The homologous recombination pathway RecE dependent. It is active if the

SbcA mutation

46. The RecE pathway needs : RecT

47. Cloning by recombeeniring requires the use of restriction enzymes

48. The encapsulation of an RNA amplicone in lipid nanoparticles serves to protect

against degradation.

49. Which of the following disadvantages can be attributed to viral vectors: ALL (-limits
in the size of cloneable DNA in the viral genome, -need for cell lynx for -Induction of immune
reactions in vivo, production (comlementant cells). Risk of insertional mutagenesis (for those
that integrate randomly into the genome)

50. The combination of two transcription factors, with equal activation domains
Dimerization but with DNA recognition domains of different specificity, allows to bind the
following dimer of different sequences: THREE

51. Which of the following statements regarding simple transposons (sequences 15)
CORRECT: The insertion sequence IS is a small bacterial transposon that encodes all the
proteins necessary for its transposition.
 52. On which of the following statements depends the activity of the SB system for Gene
Delivery ALL TRUE (-From the length of the transposon and the sequences of the ITRs,-From
the distance between the IR terminations of the transposon (the lower the distance, the more the
transposition efficiency increases), -From the relationship between transposon transposases.

53. What are the processes of repair of DSBs by the cell: -Homologous recombination
processes "Non Homologus End Joining" processes, NHEJ. (AeB
are correct).

54. Which transposition mechanism does the Sleeping Beauty (SB) system belong to:
The SB system is of the cut & paste type.

55. The main classes of recombinant site specifications are: ALL CLASSES LISTED,
(ZFNs, TALENS, CRISPR)