Quiz 4 Review - Biotech

Piwi-interacting (piRNA)

Silences transposons in eukaryotes

CRISPR (crRNA)

Prokaryote defense vs foreign RNA/DNA. Involves Clustered Regularly Interspaced Short Palindromic Repeats and viral sequences in the genome, an RNA, and a nuclease.

Riboswitch

Regulation of transcription, translation, or splicing of attached molecule, by small effector molecule metabolites or temperature. All organisms, but rare in eukaryotes, common in bacteria.

snRNA (Small Nuclear RNA)

RNA splicing as a snRNP component; Eukaryotes/Archaea

DNAzyme

Enzymes not seen in organisms, but made in the lab to carry out a variety of reactions targeting nucleic acids

siRNA (small-interfering)

Short, initially double-stranded defense vs foreign RNA/DNA; e.g. anti-virus in plants and mammals; a type of RNAi

Ribosomal (rRNA)

Helps carry out peptide bond formation, for protein synthesis.

Present in all organisms

Xist RNA

X chromosome inactivation in eukaryotes

Telomerase

Templates repeat sequences at chromosome ends to prevent chromosome shortening and cell death with rounds of replication in eukaryotes

Ribozyme

Function as enzymes in all organisms including tetrahymena, fungi, plants, algae, viruses, and viroids. Used medically to suppress virus or cancer genes by cleavage.

miRNA (micro)

Initiate as hair pins, short, and regulate protein expression at the level of mRNA degradation or translation in eukaryotes. A type of RNAi.

Antisense RNA

Genetic regulation: translation, splicing in all organisms, single-stranded.

Templated from coding (sense) strand

RNAi

General term for cellular system of inhibitory double-stranded RNAs involving RISC

What is significant about Ashanti DaSilva is that she was the first patient to be treated with...?

gene therapy

3 multiple choice options

The fruit that has been used extensively for edible vaccines against a variety of pathogens is?

banana

3 multiple choice options

For what type of genetic defect is gene therapy a most viable option?

single-gene

3 multiple choice options

Of the gene editing or targeting methodologies available for gene therapy, some relatively recent and promising ones involved use of...

CRISPR and Base Editors

3 multiple choice options

Gene targeting and gene therapy technologies have been advanced since COVID-19 due to the coming together of approaches for...

A. stabilizing RNA

B. gene delivery in lipid nanoparticles

C. targeting cells by attachment of molecules to nanoparticles

What type of gene(s) do you have to transfect into adult fibroblasts to convert them into iPS cells?

gene regulatory proteins i.e. transcription factors

Of the following types of stem cells, which are pluripotent?

A. embryonic

B. fetal

D. induced (iPS)

Modification of antisense oligonucleotides involves making them resistant to which of the following?

nucleases

3 multiple choice options

What are two ways what to deliver antisense (or RNAi) to cells?

1. Lipids sphere

2. Nanoparticles like carbon nanotubes

3. A vector like bacteria

List three methods of sampling or genetic analysis used in genetic counseling.

1. Amniocentesis - the testing/treatment of amniotic fluid

2. Chorionic Villus sampling

3. FISH

What are two important considerations when picking a virus to deliver gene therapy?

1. What you are targeting

2. If it's going to integrate into the host genome

Why is it notable that many recombinant DNA protein pharmaceuticals are not directed against infectious pathogens? (How it relates to causes of death worldwide not including covid)

Many diseases not infectious

What are "designer pharmaceuticals"?

Drugs designed for that specific person used to target whatever disease they have

State the coolest thing you've learned about nanoparticles and list three additional uses of nanoparticles or nanocrystals

Coolest:

1. That earthquakes can make nanocrystals

2. Carbon nanotubes can be made of diamond

3. That they can come in a variety of shapes forms and materials

Uses:

1. How they can target just unhealthy cells

2. The gene gun in biolistics shooting those particles

3. The fact that can be magnetized

Simply put how do "immune checkpoint inhibitor" drugs promote responses against a tumor?

(BONUS for names of 2018 Nobel winners and the specific molecules they targeted)

They can block the negative responses tumors give to T cells so the T cells can stay activated and destroy the tumor cells.

Jim Allison - like CTLA-4

Tasuki Honjo - PD-1/PDL1

What are CAR T-cells (describe the CAR and "accessories") and for what type of malignancy did they initially show promise?

CAR T-cells are modified T cells with a Chimeric Antigen Receptor that helps them target cancer. The CAR includes an antigen-binding domain, a transmembrane part, and signaling domains, plus co-stimulatory elements to boost function. They first showed promise in B-cell lymphoma.

What is Xenotransplantation and why has there been interest in getting it to work?

What organism has shown promise for xenotransplantation and why?

(BONUS: State the recent news in xenotransplantation out of Boston - Mass General Hospital)

Xenotransplantation is transferring organs or tissues between species, like from pigs to humans, to help with organ shortages. Pigs are promising due to organ size and ease of genetic modification. BONUS: Mass General Hospital recently transplanted a pig kidney into a human—a major breakthrough.

List three specific "stem cell niches" that we discussed?

1. gut

2. testes

3. bone marrow

Explain the basic idea behind a CRISPR gene drive.

What is its benefit over normal inheritance of an altered gene?

Spreads the edited gene plus the CRISPR system to the other chromosome so it spreads more quickly through a population (like in the wild); quicker than normal inheritance

T/F: Somatic cell nuclear transfer may be used to generate stem cells for therapeutic cloning, potentially for cloning whole organs and organoids, and for cloning whole organisms. Additional pathways (E.G. for cysteine and wool production in sheep) can also be engineered into the cloned animals. While race horses, cattle, pets, other animals, and endangered species can be cloned, there are regulations to prevent cloning of humans. An egg cell nucleus and a somatic cell with its own nucleus destroyed, is required.

False; "An somatic cell nucleus and a egg cell with its own nucleus destroyed, is required."

T/F: "Mighty Mouse" is aggressive and lacks a transcription factor in the brain

False; "Is aggressive due to the overexpression of a transcription factor in the brain, not the lack of one."

T/F: Rat somatotropin (growth hormone) transgene expression in mice gave 2x reduced size mice. Chinook salmon growth hormone gene has been used to make triploid sterile females that grow slowly increasing time to market.

False; "...gave larger size mice." and "...that grow faster decreasing time to market."

T/F: In classic mouse knockout production, chimeric mice resulting from blastocyst injected with ES cells containing the knockout allele (by homologous recombination) are bred to a single (blastocyst) color mouse to obtain the color of the ES cell strain and thus potentially containing the knockout allele in their germ cells allowing subsequent breeding.

True

T/F: Transgenic livestock has been made to express therapeutic proteins in their milk

True

T/F: Wikipedia describes Position-effect variegation as "a variegation caused by the silencing of a gene in some cells through its abnormal juxtaposition with heterochromatin via rearrangement or transposition. It is also associated with changes in chromatin confirmation." This and other effects of nearby regulatory sequences can be prevented by a surrounding transgene with "insulators."

True

T/F: Tetracycline and other inducible gene expression systems and cell type-specific promoters can be used to allow control of a transgene when constant expression in every cell would negatively impact animal development or where tissue-specific expression is desired.

True

T/F: Knockout flies are created using drosophila P elements and vectors and coding a transposase and knockout cassette.

False; "Transgenic flies...and transgene cassette."

T/F: Fluorescent silkworm silk has been made and strengthened with spider silk modification.

True

T/F: Transgenic pigs that reduce need for phosphate supplementation in feed, transgenic chickens that resist bird flu, cattle, goats, or pigs that express lysozyme, vaccines, and other pharmaceuticals in their milk, or carry nutrients or resist allergens, genetically modified mosquitoes that prevent parasite and virus transmission, and transgenic zebrafish that sense environmental xenoestrogens, have all been developed.

True

State if following is associated with interactives/videos.

1. Targeting, Binding, Cleavage, DNA repair

C-I

State if following is associated with interactives/videos.

2. Dicer, RISC, and flower pigment patterns

R-I

State if following is associated with interactives/videos.

3. Retinitis Pigmentosa, rare mutation, reduced tRNA function

M-I

State if following is associated with interactives/videos.

4. Bring Me A Gene

MC-V

State if following is associated with interactives/videos.

5. Guide RNA, CAS9, PAM

C-I

State if following is associated with interactives/videos.

6. Science is a serendipitous endeavor (Jennifer Doudna)

C-I

State if following is associated with interactives/videos.

7. Creation of mutant zebrafish with vision issues

M-I

State if following is associated with interactives/videos.

8. Butterfly color pattern disruption

C-I

State if following is associated with interactives/videos.

9. Swiss army knife of the genome

C-I

State if following is associated with interactives/videos.

10. Knockout all genes in a melanoma cell line to find genes that help the tumor evade T lymphocytes

C-I

State if following is associated with interactives/videos.

11. Who would have thought, the bacteria that cause flesh-eating disease

MC-V

State if following is associated with interactives/videos.

12. Studies of Duchenne Muscular Dystrophy involving rescue of dystrophin function in mice

C-I

Regarding the PCR research exp. for isolation of SCN1B sodium channel regulatory subunit cDNAs from different species that we started working on Monday...

5. How many PCR reactions did each person or group do? (How many in each strip?)

We have 4 tubes: RXC, Class, PS, and Control

Regarding the PCR research exp. for isolation of SCN1B sodium channel regulatory subunit cDNAs from different species that we started working on Monday...

6. What were the samples in each of the PCR tubes in their correct order?

1. RT RXN

2. Class

3. PS

4. Control - filled with water

How did Gleevec and subsequent similar drugs act to help treat CML (Chronic Myeloid Leukemia)? (Where do they bind in the BCR-Abl protein?)

Gleevec and similar drugs treat CML by targeting the BCR-Abl fusion protein. They bind to the ATP-binding site of the Abl kinase domain, blocking phosphorylation and stopping leukemia cell growth. Newer drugs like d.a.s.a.t.i.n.i.b and n.i.l.o.t.i.n.i.b target resistant BCR-Abl mutations.

What is the genetic cause of overactivation of BCR-Abl protein kinase expression in CML? (Hint: Philadelphia chromosome)

A translocation between chromosomes 9 and 22, known as the Philadelphia chromosome, fuses the BCR and ABL genes, leading to overactivation of the BCR-Abl protein kinase in CML.

What issue with Gleevec led to second generation (and now additional) versions of BCL-Abl inhibitors?

Some patients developed resistance to Gleevec due to mutations in the BCR-Abl kinase domain, like T315I. Second-generation drugs like dasatinib and nilotinib were made to target these mutations, and later drugs like ponatinib addressed even more resistant forms

List a disease in which gene therapy or editing is in use, noted in the central dogma and genetic medicine interactive.

Sickle cell disease is treated with gene therapy, including CRISPR-Cas9 and gene addition, to fix or replace the defective HBB gene and restore normal hemoglobin function.

T/F: Gene therapy can act at the level of gene expression, RNA splicing, or translation

True