CSB329 Midterm Questions and Answers 2025.
1. Fill in the blanks: Complete the following sentences by filling in the blank in the
sentence with one of the words provided below. Record the word choices on this test
paper. In each case choose the BEST option from the list provided. Note that you may
not use all of the words, and you may use a word more than once.
a) Cell therapy using embryonic stem cells as the source of cells will always be allogenic.
a. Explanation:
i. Allogenic therapy refers to cell therapy where the cells come from a
genetically distinct donor. Human ESCs are derived from donated
embryos, which means they come from a different genetic background
than the patient receiving the therapy. Because of this, hESC therapy
requires immunosuppression to prevent the patient’s immune system from
rejecting the transplanted cells. (e.g. Macular Degeneration)
ii. In contrast, autologous therapy involves using the patient’s own cells,
often modified, such as in induced pluripotent stem cell (iPSC) therapy.
(e.g. Retinis Pigmentosa – RP)
b) To affect only the secondary/ping-pong piRNA production pathway you would delete the
Argonaute3 (Ago3) gene.
a. Explanation:
i. The piRNA (PIWI-interacting RNA) pathway is a mechanism that protects
genome integrity by silencing transposons.
ii. 2 piRNA pathways:
1. Primary pathway: Produces antisense piRNAs that bind to PIWI or
Aubergine proteins
2. Secondary (ping-pong) pathway: Amplifies piRNAs and targets
transposon RNAs using Argonaute3 (Ago3) and Aubergine (Aub).
a. Deleting Ago3 would only disrupt the ping-pong cycle
because Ago3 binds sense piRNAs and helps amplify the
piRNA population.
b. Without Ago3, the primary pathway would still function,
but transposon repression would be weaker.
c) The fate of the outside layer of cells in the mouse morula is placenta cells.
a. Explanation:
i. In early mammalian development, the morula is a solid ball of cells before
it forms the blastocyst.
ii. Cells in the outer layer of the morula will contribute to the inner cell mass
(ICM), which gives rise to the embryo.
iii. The ability to form both placental and embryonic tissues is what makes a
zygote totipotent.
iv. Trophectoderm = extraembryonic structures (yolk sac, placenta, etc.)
, d) In fibroblast cells, most of the enhancers for pluripotency genes are located in
heterochromatic regions.
a. Explanation:
i. Heterochromatin is tightly packed DNA, making genes and regulatory
elements less accessible for transcription.
ii. In differentiated cells like fibroblasts, enhancers for pluripotency genes
(Oct4, Sox2, Nanog) are silenced and stored in heterochromatin.
iii. During induced pluripotency (iPSC reprogramming), these regions
undergo chromatin remodeling to become euchromatic (open and
transcriptionally active).
iv. Key Epigenetic Mechanisms:
1. Histone acetylation: Loosens chromatin and activates transcription.
2. DNA demethylation: Removes inhibitory methyl groups, allowing
gene expression
v. Example: When reprogramming fibroblasts into iPSCs, chromatin
modifications allow pluripotency enhancers to become active again
e) Sense piRNA transcripts are bound primarily by Argonaute3.
a. Explanation:
i. The piRNA pathway functions to silence transposable elements and
protect genome stability, especially in germline cells.
ii. There are two types of piRNAs:
1. Antisense piRNAs: Produced in the primary pathway and bound
by PIWI/Aubergine proteins.
2. Sense piRNAs: Generated in the secondary (ping-pong) pathway
and bound to Argonaute3 (Ago3).
iii. Ago3 binds sense piRNAs and is critical for the ping-ping amplification
cycle.
iv. Without Ago3, fewer antisense piRNAs would be produced, weakening
transposon repression.
1. Fill in the blanks: Complete the following sentences by filling in the blank in the
sentence with one of the words provided below. Record the word choices on this test
paper. In each case choose the BEST option from the list provided. Note that you may
not use all of the words, and you may use a word more than once.
a) Cell therapy using embryonic stem cells as the source of cells will always be allogenic.
a. Explanation:
i. Allogenic therapy refers to cell therapy where the cells come from a
genetically distinct donor. Human ESCs are derived from donated
embryos, which means they come from a different genetic background
than the patient receiving the therapy. Because of this, hESC therapy
requires immunosuppression to prevent the patient’s immune system from
rejecting the transplanted cells. (e.g. Macular Degeneration)
ii. In contrast, autologous therapy involves using the patient’s own cells,
often modified, such as in induced pluripotent stem cell (iPSC) therapy.
(e.g. Retinis Pigmentosa – RP)
b) To affect only the secondary/ping-pong piRNA production pathway you would delete the
Argonaute3 (Ago3) gene.
a. Explanation:
i. The piRNA (PIWI-interacting RNA) pathway is a mechanism that protects
genome integrity by silencing transposons.
ii. 2 piRNA pathways:
1. Primary pathway: Produces antisense piRNAs that bind to PIWI or
Aubergine proteins
2. Secondary (ping-pong) pathway: Amplifies piRNAs and targets
transposon RNAs using Argonaute3 (Ago3) and Aubergine (Aub).
a. Deleting Ago3 would only disrupt the ping-pong cycle
because Ago3 binds sense piRNAs and helps amplify the
piRNA population.
b. Without Ago3, the primary pathway would still function,
but transposon repression would be weaker.
c) The fate of the outside layer of cells in the mouse morula is placenta cells.
a. Explanation:
i. In early mammalian development, the morula is a solid ball of cells before
it forms the blastocyst.
ii. Cells in the outer layer of the morula will contribute to the inner cell mass
(ICM), which gives rise to the embryo.
iii. The ability to form both placental and embryonic tissues is what makes a
zygote totipotent.
iv. Trophectoderm = extraembryonic structures (yolk sac, placenta, etc.)
, d) In fibroblast cells, most of the enhancers for pluripotency genes are located in
heterochromatic regions.
a. Explanation:
i. Heterochromatin is tightly packed DNA, making genes and regulatory
elements less accessible for transcription.
ii. In differentiated cells like fibroblasts, enhancers for pluripotency genes
(Oct4, Sox2, Nanog) are silenced and stored in heterochromatin.
iii. During induced pluripotency (iPSC reprogramming), these regions
undergo chromatin remodeling to become euchromatic (open and
transcriptionally active).
iv. Key Epigenetic Mechanisms:
1. Histone acetylation: Loosens chromatin and activates transcription.
2. DNA demethylation: Removes inhibitory methyl groups, allowing
gene expression
v. Example: When reprogramming fibroblasts into iPSCs, chromatin
modifications allow pluripotency enhancers to become active again
e) Sense piRNA transcripts are bound primarily by Argonaute3.
a. Explanation:
i. The piRNA pathway functions to silence transposable elements and
protect genome stability, especially in germline cells.
ii. There are two types of piRNAs:
1. Antisense piRNAs: Produced in the primary pathway and bound
by PIWI/Aubergine proteins.
2. Sense piRNAs: Generated in the secondary (ping-pong) pathway
and bound to Argonaute3 (Ago3).
iii. Ago3 binds sense piRNAs and is critical for the ping-ping amplification
cycle.
iv. Without Ago3, fewer antisense piRNAs would be produced, weakening
transposon repression.
