Biology 3401 Module 2 Exam

Cumulina and Dolly were cloned using different approaches. What was a key step in the method that produced Dolly. A) Using quiescent donor cells (G0) B) Using female cells C) Using fresh cells taken from an ovary D) Using a surrogate mother with a different phenotype E) Using both an egg donor AND a surrogate mother with a different phenotype

A) Using quiescent donor cells (G0)

In intestinal cancer, all tumor cells expressed Dclk1 (marked blue). This shows Dclk1 must be expressed_____. A) in all cells, including cancer stem cells B) in all differentiated cells C) in all rapidly dividing tumor cells

A) in all cells, including cancer stem cells

What is unique about the heredity of Hutchinson-Gilford progeria syndrome?

It is a dominant disease but not genetic because in every case, it is a new mutation.

If a planarian is bisected what happens? A) Two planaria are generated B) The head end regenerates C) A new new limb forms

A) Two planaria are generated

Describe the steps of a gene drive:

1) The gene drive encodes both the gRNA and Cas9. 2) It targets the second allele. 3) By HDR it will be inserted and both alleles have the gene drive.

What is unique about the niche in which HSCs are found?

MSCs are a part of the niche as well

What was found when MSCs were studied in vivo?

MSCs give rise to bone, cartilage and fat

What is encapsulation?

Modifying the surfaces on the beta cells invisible to the immune system.

Is the shape of the liver reformed after being regenerated?

No.

Describe the process of genetically modifying HSCs for gene therapy:

1) Purify the HSCs from the patient 2) Correct the gene defect 3) Transplant cells back into the patient

What cells LACK telomerase?

1) Somatic cells

In each case of the MLD and WAS study the normal gene was transduced into hematopoetic stem cells using a ___________. (Note the answer is two words.)

Lentiviral Vector

Do young plasma injections help to reverse the effect of Alzheimer's disease?

No. The subjects only performed slightly better at daily tasks and did not do better on cognitive tests.

What is the function of the Enteroendocrine cell (of intestine)?

Produce hormones

What do beta cells trigger once sugar is introduced into the bloodstream?

Production of insulin which makes use of and stores blood sugar.

What other type of proliferative cells are there in the blood system other than HSCs?

Progenitors. CLP cells give rise to lymphoid cells CMP cells give rise to myeloid cells

What is a known way to extend the life of an individual?

Reduce calorie intake (15%). This was studied in yeast, worms, flies, rodents, dogs and monkeys. It was found that after two years, the diet group had lower metabolism and used energy more efficiently than the control group.

What is an important component in age-related morbidity?

Reduction in the number and function of old stem cells

What are essential to yielding pluripotent stem cells from somatic adult stem cells?

Reprogramming factor such as Yamanaka factors

Transplant of a single neoblast from a donor strain results in growth and the __________________.

Restored capacity for regeneration.

What is a limitation of the SCNT method of cloning?

The lengths of the telomeres can limit the longevity of the clone. This is directly correlated to the age of the organism from which the donor cells derive.

Of all body organs in the human body, which has the greatest capacity to regenerate?

The liver. It can grow after a 70% partial hepatectomy.

What is dedifferentiation?

The loss of differentiated characteristics and return to a more progenitor-like phenotype

Which organs of the body regenerate themselves too poorly after serious injury or degenerative disease?

The nervous system, pancreas and the heart

What was an important takeaway from the zebrafish heart regeneration experiment?

The newly generated cardiomyocytes had derived from cardiomyocytes in the injured heart tissue that had dedifferentiated, rather than from unlabeled stem cells.

Why are maternal diseases passed through the maternal line?

The egg has the mitochondria in it... the sperm have very few mitochondria.

What is gastrulation?

The first major morphogenetic event and leads to the formation of the germ layers, including the gut, which is from the endoderm.

What is the specific component that unwinds the double helix during CRISPR?

The guide RNA. Which matches and binds to a particular sequence of the DNA.

How was Cas9 founded?

The idea of viral DNA integration into bacterial DNA was used. During this process, part of the viral DNA is added to the bacterial genome and thus, the bacteria can recognize future viral infections. The same idea of cutting the viral DNA exists.

What does the outer layer of the blastocyst go on to become?

The placenta

What state can the ICM cells be said to be at in terms of differentiation?

Undifferentiated

Define totipotent

can give rise to all cell types (eg. zygote)

Define pluripotent

can give rise to many cell types (eg. ICM cell, ES cell)

Define multipotent

can give rise to many cell types in a lineage (eg. adult stem cell)

What is the 14 day rule?

no research can be done after the embryo has developed for 14 days

What are chromosomes composed of?

proteins (hisones) and DNA. Together these make chromatin

The niche (TME) may be controlling what?

The development of stem cells.

List the ways that genome damage can occur:

1) Cell dysfunction 2) apoptosis 3) cancer

What was the first organism to ever be cloned?

A carrot

Where are the crypts found?

At the bases of the villi of the intestines

What is a major challenge for ES cells?

To direct them to the cell type you want

What two types of cell categories are generated from intestinal stem cells?

1) Absorptive cell 2 Secretory cell- a. goblet cell b. enteroendocrine cell c. paneth cell

What is the function of the absorptive cell (of intestine)?

1) secrete enzymes to fully digest food from stomach 2) absorb nutrients

What does apoptosis do aside from simply shedding off cells?

1) shapes tissues 2) molecular sequence of events to degrade cellular contents

Facts about the epithelial lining of the intestine:

1) Absorbs food coming from the stomach. 2) Secretes enzymes for digestion along with enzymes from the liver and pancreas. 3) Maintains a barrier against: a) lethal microorganisms b) carinogens 4) Contents of gut lumen are harsh and induce cell death in the epithelium. (up to 10^11 cells die each day in the gut... self renewal is essential)

What are the types of bone marrow transplants?

1) Autologous- donor is the patient 2) Allogeneic- the donor stem cells are taken from a genetically matched donor --usually sibling... you would have 1/4 chance of matching --rarely a parent --unrelated donors can be found through national bone marrow registries

Which three stem cell therapies are established and safe?

1) Bone marrow 2) Skin 3) Cornea

What four properties should a neural stem cell have?

1) Capable of extended proliferation 2) Capable of self renewal 3) Capable of generating multiple differentiated cell types 4) Migration to regions of injury or requirement

What are the 3 sources of human ES cells?

1) Cell lines that already exist 2) Spare embryos left over from fertility treatment 3) Custom-made embryos created by SCNT

What are the hallmarks of aging?

1) Cellular damage that accumulates with age (DNA, proteins, telomeres, epigenetic changes) 2) Cell responses that are altered with age. (altered nutrient sensing, mitochondrial dysfunction, cell senescence- cant divide) 3) Stem cell exhaustion (decrease function in HSC, MSC, satellite cells, IESCS)

What factors influence the aging of stem cells?

1) Changes in the stem cells themselves, altering their normal functions 2) Aging of the stem cell niche 3) Systemic influences (coming from body of animal) 4) External influences from the environment

What were some specific examples of what CRISPR-Cas can be used for?

1) Creating Malaria free mosquitos 2) Maintaining pest of 'environmentally' resistant wheat 3) Removing HIV from blood

What are some obstacles to overcome when using human ES cells for therapy?

1) Culture media for human embryos produced by IVF were suboptimal. 2) Species-specific differences between humans and mice present practical issues when using human ES cells. - ES cell lines from two non-human primates in the 1990's offered close models to humans.

Outline the simple process of aging at the molecular level:

1) Damage. (DNA replications mutagens, translation errors) 2) Targets. (Mitochondria, DNA, proteins, lipids, telomeres) 3) Outcomes. (Apoptosis, senescence, cancer, altered physiology)

What are the symptoms of Wiskott Aldridge Syndrome (WAS)?

1) Eczema 2) Thrombocytopenia (low plts) 3) Immune deficiency

What cells HAVE telomerase?

1) Embryonic cells 2) Stem cells 3) Cancer cells 4) Germline cells

What are the ideas for a genetic basis for aging?

1) Extrinsic mortality- it is so dangerous in the wild that no genes specific to aging have evolved. 2) Mutation accumulation theory: Lack of selection later in life means that deleterious mutations can accumulate. 3) Pleiotropy theory: genes that are good for the young will be selected even if they are bad for the old. 4) Disposable soma theory: using metabolic resources for maintaining the body beyond a certain point is not selected for because life in the wild is short.

Name the three uses of cloning in biology:

1) Gene cloning 2) Therapeutic cloning 3) Reproductive cloning

What is unique about old HSCs in terms of how it is different from a young HSC?

1) Greater distance from the endosteum. 2) Decreased regenerative capacity. 3) Skewing of differentiation towards myeloid progenitors. 4) Increased self-renewal capacity. 5) Increased mobilization.

Outline what Yamanaka did in his experiment:

1) He took an MEF (mouse embryonic fibroblast) and then introduced 24 factores that are involved in pluripotency (known from studies of ES cells and embryos). 2) They then used a virus to get the factor cDNAs into the MEF. The only cells that survived in the experiment were the iPS cells.

What are the two types of stem cell types that the bone marrow has?

1) Hematopoetic stem cells (HSC) 2) Mesenchymal stem cells (MSC)

What are the three ways that sexual life cycles can introduce genetic diversity?

1) Independent assortment (in meiosis) 2) Crossing over (in meiosis) 3) Random fertilization of eggs by sperm

Aside from the parabiosis experiment, what also showed the same effect in improving effects of aging?

1) Injecting the animal with a protein called growth differentiation factor 11 2) Plasma injections

What diseases are bone marrow transplants used to treat?

1) Leukemias 2) Severe aplastic anemia 3) Lymphomas 4) Multiple myeloma 5) Immune deficiency disorders 6) Some solid-tumor cancers

Outline the process of the zebrafish heart regeneration:

1) Lower part of heart is dissected 2) Blood clot formation occurs 3) The epicardium is activated 4) Cell proliferation and migration occurs 5) New blood vessels form 6) Heart muscle regeneration

What are the products of all three germ layers?

1) Mesoderm: immature cartilage 2) Endoderm: gastrointestinal lining cells/glands 3) Ectoderm: epidermis with keratin

What are the major epigenetic modifications?

1) Methylation of DNA and histones 2) Acetylation of histones

Name two ways that the CRISPR-Cas9 system can be used:

1) Nonhomologous end joining (NHEJ) -gene disruption by small insertions or deletions (mutations to inactivate the gene) 2) Homology-directed repair (HDR) -gene correction or insertion by assisted recombination (repairing mutant genes or making 'designer' changes.

What are the 3 main problems associated with Animal Cloning?

1) Nuclear transplantation has a very low frequency of live births 2) Large offspring syndrome 3) Possible telomere defects

What research is currently prohibited with federal funding?

1) the creation of a human embryo for research purposes 2) research in which a human embryo or embryos are destroyed, discarded, or knowingly subjected to risk of injury or death greater than that allowed for research on fetuses in utero.

What are potential problems with deriving cultures from normal embryonic stem cells?

1) Numbers of pluripotent cells in an embryo could be small 2) The time when embryos were competent to produce such cells could be short 3) The cultured cells may be 'too good' at differentiation and lose pluripotency and the ability to grow in culture

What type of stem cells are possible in regeneration?

1) Pluripotent stem cell 2) Tissue-specific stem cell

What two types of cells are cancerous tumors known to be comprised of?

1) Rapidly dividing cells 2) Differentiated cells

Outline the process of cloning a mammoth:

1) Sequence woolly mammoth genome. 2) Find differences with the closest relative. 3) Use CRISPR-Cas9 to edit elephant genes into the mammoth version in elephant fibroblasts. 4) Induce iPS cells from 'mammophant' cells 5) Examine differentiation of different cell types 6) Generate embryo from iPS cells 7) Raise 'mammophant' in artificial uterus

Describe the process of obtaining iPS cells:

1) Somatic cells are obtained from adult organism. 2) The reprogramming factors are introduced into the cultured somatic cells. 3) The cells are grown under ES cells conditions. After 2-3 weeks, iPS cells emerge. 4) These induced pluripotent stem cells may be differentiated into various cell types for regenerative medicine applications

What are the two arguments as to where a tumor arises from?

1) Some scientists say that they arise from slowly dividing cancer stem cells which produce the rapidly dividing cells and thus the differentiated cells of the tumor. 2) Others say that the cells that are fueling the tumor are derived from the rapidly dividing cells and that there are no cancer stem cells.

Outline the consequences of the Obokata case:

1) The reputation of scientists was impacted due to mistrust of the public. 2) Patients were disappointed because they may have thought that they could have had a cheap and simple solution that has now been lost. 3) It was a waste of resources for other scientists trying to replicate the experiment

Why is the idea that cancer stem cells exist a controversial issue among scientists?

1) They are rare. 2) They are hard to distinguish from normal stem cells. -a marker needs to be found to distinguish between them!

When do people need a bone marrow transplant?

1) To replace diseased or nonfunctioning bone marrow. 2) To regenerate a new immune system. 3) Replace the BM and restore its normal function after high doses of chemotherapy and/or radiation are given to treat malignancy. 4) Replace BM with genetically healthy functioning BM to prevent further damage form genetic disease.

How can we avoid iPS cells from giving rise to tumors?

1) Use iPS cells without the Myc retrovirus 2) Non-viral delivery methods -plasmids 3)DNA-free delivery methods -mRNA -Protein

What are the arguments supporting that the blastocyst stage has the same moral status as the baby?

1) We shouldn't judge the blastocyst by what it is, but by what it can become 2) We protect the most vulnerable humans and the embryo is very vulnerable 3) The only type of research that should be done is to protect the embryo itself

What are the differences between the Dolly method (Roslin technique) and the mouse method (Honolulu technique)

1) With Roslin technique, the udder cells were grown in culture and were not used right away. The donor cell was also in G0. The entire donor cell was also used, not just the nucleus. Electric shock was used. 2) The nucleus was removed from the cumulus cell in the Honolulu technique and then injected into an egg cell (from which the nucleus was removed). This is different from the Roslin technique because the entire donor cell was not fused (or injected) to the egg cell. The donor cell was in G1 and the donor nucleus was injected into the egg. Chemical activation was used. The success rate was better for the mouse experiment.

Outline the ultimate consequences of the response to repair a damaged muscle in an aged animal:

1) aging of the stem cell- weaker response 2) aging of the niche- weaker signal 3) aging of the animal- reduced support for the response

Describe the two methods to cell labeling and sorting with HSCs:

1) cells are treated with an antibody, coupled to iron particles, that recognizes a surface antigen (CD34 usually). A magnet can then collect the cells. -this can collect a lot of cells. BUT many other cells could contaminate the pool. 2) Cells can be treated with fluorescent antibodies which recognize surface antigens. They are subjected to FACS. A laser can detect the color of the signal and can direct cells of each color into a pool. - multiple markers can be used BUT it is a small scale technique (not many cells obtained)

What important insights were gained after the frog cloning experiment?

1) cloning potential decreases with donor age 2) reprogramming a donor nucleus involves reversing effects of differentiation (epigenetic changes)

List four age associated diseases:

1) cognitive 2) neoplastic 3) immunologic 4) metabolic

What are the different types of stem cells?

1) embryonic stem cells 2) adult stem cells 3) induced pluripotent stem cells

What is unique about young HSCs in terms of how it is different from an aged HSC?

1) increased homing to the bone marrow 2) increased proximity to the endosteum. 3) increased regenerative capacity.

What are two classes of mutations that occur with cancer development?

1) loss-of-function tumor suppressor genes 2) gain-of-function mutations in oncogenes

What is the function of the paneth cell (of intestine)?

1) part of the niche to support stem cells 2) To supply growth factors 3) Secretes antimicrobials and lysozyme

What occurs after 14 days?

1) the germ layers begin to form. The CNS is formed, leading to consciousness and sensory feeling. 2) Twinning can't occur-- embryo is an individual! 3) Implantation occurs. ( beginning of mother/child relationship)

What are the arguments supporting that there is no moral status at the blastocyst stage? It is not a human but just a ball of cells because...

1) there are no bodily characteristics 2) can't feel 3) can't survive on its own 4) not implanted (mother would not even know she was pregnant 5) not a single individual because it can still split and become twins -it is our moral obligation to do research which involves the end to human suffering -there should be restrictions later in development when some human characteristics are apparent

What was found about 3D culture growth vs 2D culture growth?

3D cultures are more like the real tissue from an animal (in vivo) than a flat 2D culture.

What is the life span of a red blood cell, white blood cell and platelet?

120 days- RBC 1 day- WBC 6 days- Plt

How many active sites does Cas9 have?

2

Cloning is very difficult and it took ___ (write the number in numerals) attempts to clone Dolly.

277

What is necessary for Cas9 to promote silencing of certain genes?

A KRAB domain can fuse to Cas9 and inactivates transcription by recruiting more factors that can physically block the desired gene.

Describe the Mosaic model

A cell with a given nuclear factor will develop into a specific type

What is Bicoid RNA?

A cytoplasmic determinant that controls development of anterior patterning in Drosophila (forms the head).

How is the 2018 cloning of the first primate different than the cloning of Dolly?

A fetal fibroblast was fused with a enucleated oocyte from an oocyte donor. Kdm4D was then introduced to promote development and the oocyte was transferred to a surrogate mother.

What was the first animal to be cloned?

A frog

What is Dclk1?

A protein that was thought to mark normal stem cells. BUT it was found in cancerous cells of the intestine as well.

How can the stem cells from intestinal crypts be utilized?

A small biopsy can be obtained and the harvested stem cells can be ran over a cell sorter machine to isolate the stem cells.

What is a stem cell?

A stem cell has the capacity to self renew and give rise to differentiated cells. They should also maintain proliferative capacity for the life time of the organism.

What is the enzyme part of CRISPR-Cas that cuts the DNA? A) Cas B) RNA

A) Cas

When a nucleus from a differentiated cell is injected into an egg, factors in the egg reprogram the nucleus so that it can support development of the embryo. This procedure is called ______. A) Cloning B) DNA sequencing C) iPS cell induction D) parthenogenesis

A) Cloning

By which process do cells take on their specialized structure and function? A) Differentiation B) Determination C) Pattern formation D) Morphogenesis E) Germ layer formation

A) Differentiation

Past attempts in making beta cells resulted in cells called polyhormonal cells (PH cells), which got their name because they secrete additional hormones such as glucagon. Figure 1 B-D illustrates another defect in PH cells. These are the data that show, unlike SC-beta cells and primary cells (adult 1° beta cells), the PH cells A) Do not perform glucose-stimulated insulin secretion B) Have high insulin levels C) Are more similar to adult 1° beta cells than SC-beta cells D) Have low glucose levels

A) Do not perform glucose-stimulated insulin secretion

The researchers made a gene that combined the Fbx15 gene and resistance to the drug G418 (called Fbx^bgeo, Fig 1A). Now any cell that expresses Fbx15 will be resistant to the drug (and survive). Which of the following is true? A) Factors that induce pluripotency in somatic cells will cause expression of the Fbxbgeo gene and the cells will survive in G418 B) Factors that induce pluripotency in somatic cells will cause expression of the Fbxbgeo gene and the cells will die in G418

A) Factors that induce pluripotency in somatic cells will cause expression of the Fbxbgeo gene and the cells will survive in G418

The first animal to be cloned was a.... A) Frog B) Mouse C) Sheep D) Pig E) Carrot

A) Frog

Which scientist is working on this project (saving the woolly mammoth)? A) George Church B) Shinya Yamanaka C) Martin Evans D) Ben Mezrich

A) George Church

What personal interest does the leader of the study (Dr. Melton) have in diabetes? A) He has two children with type 1 diabetes B) He has type 2 diabetes C) He is head of the Harvard Stem Cell Institute D) He has scientists in his lab who are interested in disease

A) He has two children with type 1 diabetes

Young blood restores muscle and liver tissue in older mice. What was one effect of the young blood? A) Increased stem cell division B) Increased longevity C) Increased blood clotting D) Increased appetite

A) Increased stem cell division

Where is the mouse Fbx15 gene expressed and is it required for maintenance of pluripotency? A) It is expressed in embryos and ES cells, but it is not required for pluripotency B) It is expressed in embryos and ES cells, and it is required for pluripotency C) It is only expressed in embryos, but it is not required for pluripotency D) It is only expressed in embryos, and it is required for pluripotency

A) It is expressed in embryos and ES cells, but it is not required for pluripotency

What key observation proved the stress-induced stem cells (STAP cells) must be 'fakes'? A) They had a different genetic background than the body cells they were supposed to be derived from B) Some captions did not describe what was in the scientific figures C) Stomach cells are exposed to acid but they do not become pluripotent

A) They had a different genetic background than the body cells they were supposed to be derived from

All organs have stem cells. A) True B) False

A) True

Cancer stem cells may not be affected by therapies (chemotherapy and radiation) because they divide slowly. A) True B) False

A) True

Somatic cells do not normally express Fbx15, but if they are induced to become pluripotent, the Fbx15 gene will be expressed. A) True B) False

A) True

The researchers found Dlck1 is expressed in cancer stem cells, not normal stem cells. This means killing Dlck1-expressing cells will______ A) kill both the tumor and surrounding normal tissue, but not normal stem cells, which will allow regrowth of normal tissue B) not be an effective treatment C) kill the tumor without affecting normal tissue

A) kill both the tumor and surrounding normal tissue, but not normal stem cells, which will allow regrowth of normal tissue

The stem cell (form intestinal stem cell LGS) must have the following properties. Select all that apply. A) last for the life time of the animal B) make all cell types in the embryo (pluripotent) C) make all the cell types in the tissue (multipotent) D) live for 4 days

A) last for the life time of the animal C) make all the cell types in the tissue (multipotent)

Wiskott-Aldrich syndrome (WAS) is a/an ___________ disease trait. (Additional fact, boys are more often affected than girls.) A) sex-linked recessive trait B) sex-linked dominant trait C) autosomal recessive trait D) autosomal dominant trait

A) sex-linked recessive trait

Using the cell marker Lgr5, the researchers were able to isolate single stem cells. Under the correct culture conditions these stem cells could generate a 'mini gut'. These organoids were used A) to repair the intestine in a mouse B) prove the existence of a pluripotent stem cell in the gut C) generate mice with villi marked with different fluorescent colors D) treat humans with ulcers

A) to repair the intestine in a mouse

What do changes in stem cells ultimately cause?

Ability to self-renew and the ability to produce daughters that differentiate the full range of cell types diminishes.

Where are MSCs found?

On blood vessels in the bone marrow

What would be observed if a stem cell contained Dclk1?

All of the cells would express Dclk1 and the blue color would persist.

Video 2 part 3 discusses adult (somatic/tissue) stem cells. What are the advantages of ES cells when compared to these adult stem cells? 1) ES cells are easier to grow in culture 2) ES cells grow indefinitely in culture 3) Adult stem cells only give rise to particular lineages (like blood and gut epithelium) All the above 1 and 2

All the above

What could human ES cells potentially be used for? 1) A source of cells for wound healing 2) A source of cells for replacing damaged organs 3) To cure diabetes All the above 1 and 2

All the above

What does Matrigel do?

Allows stem cells to grow in a 3D environment for organoid formation.

What is cancer classified at the DNA level?

At least one active oncogene and the mutation of several tumor-suppressor genes.

During pattern formation the major body ______ form.

Axes

How could CRISPR-Cas be used for controlling malaria? A) By disabling the malaria virus B) By gene editing in mosquitos C) By removing HIV from blood cells

B) By gene editing in mosquitos

Cloning experiments are carefully designed so that the clone is genetically related only to the.... A) Egg donor B) Donor cell C) Surrogate mother

B) Donor cell

What gene is expressed in inner cells of the early embryo? A) CDX 2 B) OCT 3/4

B) OCT 3/4

24 genes were selected as candidates for encoding factors that induce pluripotency in somatic cells. Why were these genes selected? A) All the genes are upregulated in tumors B) Other evidence suggested they might play roles in maintaining ES cell pluripotency C) The genes are known to be mutated in teratomas D) These genes are expressed in females prior to ovulation

B) Other evidence suggested they might play roles in maintaining ES cell pluripotency

What is the specificity (guide) component of CRISPR-Cas that targets the molecular scissors to the matching DNA sequence? A) Cas B) RNA

B) RNA

What steps will the journal Nature (that published the papers) take to make sure fake data are not included in papers? A) Give all authors lie detector tests B) Scan papers for manipulated data C) Reduce the number of papers published D) Only publish papers from well-known scientists

B) Scan papers for manipulated data

Use these search terms (Zhong-Zhong clone) and find the latest member to join the menagerie of cloned animals. What is it about Zhong-Zhong that makes the result exciting and most relevant to human cloning? A) She is a monkey B) She is a primate C) She is a macaque D) She is a mammal

B) She is a primate

Why is understanding development critical for learning how to induce stem cells to differentiate into pancreatic beta cells in a culture dish (also called in vitro)? A) In practice, studying development is not essential because trial and error testing of different factors in vitro is more efficient B) The genes required for normal development of beta cells must be identified first C) Once scientists know how the pancreas develops, they will be able to use stem cells for diseases involving other organs, like brain and liver

B) The genes required for normal development of beta cells must be identified first

How do cells communicate during development? A) With intrinsic cell signals B) With extrinsic cell signals C) Through the process of morphogenesis D) By cell proliferation E) By differentiation

B) With extrinsic cell signals

In normal tissue, the scientists found expression of Dclk1 (marked by blue color) in A) all cells B) differentiated cells C) stem cells

B) differentiated cells

The surgical procedure that links the blood supplies of two animals is called ______. A) splicing B) parabiosis C) cojoining D) heart transplanation

B) parabiosis

Planarian stem cells are called neoblasts. Given the potential for planaria to regenerate, which of the following is most likely to be true. Neoblasts are A) multipotent B) pluripotent C) unipotent

B) pluripotent

What happens to the beta cells in type 2 diabetes?

Beta cells become dysfunctional and cannot create enough insulin.

What are teratocarcinomas?

Bizarre tumors containing multiple tissue types, including fully differentiated structures, such as teeth and hair. Can form all three germ layers.

What types of cells do hematopoetic stem cells give rise to?

Blood cells

What types of cells do mesenchymal stem cells give rise to?

Bone, cartilage, fat

What was found to be happening to cancer patients who were being treated with chemotherapy or radiation therapy?

Both cancerous and normal dividing cells were targeted and damaged. A way to replenish the normal cells was needed. This lead to the Till and McCulloch experiments.

How are tumors supported?

By a tumor microenvironment (TME) much like a stem cell is supported by it's niche.

What is the origin of ES cells in development? Choose the most closely related cell type. A) Morula (early embryo) cells B) Cells of the zygote C) Inner cell mass cells D) Cell culture cells

C) Inner cell mass cells

How are allogeneic transplants matched?

By human leukocyte antigen (HLA) complex type

How can the number of different combinations of chromosomes in a gamete be calculated?

By taking the number of chromosomes in the haploid set (n) and applying it to the following equation 2^n= number of combinations.

In what organisms does CRISPR-Cas provide an adaptive immune system? Choose all the correct answers. A) Mosquitos B) Humans C) Bacteria D) Viruses E) Archaea

C & E

What is the definition of a stem cell? A) An immortal cell that can produce all embryonic and adult cell types B) A pluripotent or multipotent cell C) A cell that can produce more stem cells and specialized cells D) A cell in an early embryo E) A cell that can replace other body cells, such as, a blood stem cell

C) A cell that can produce more stem cells and specialized cells

Alkahest, a biotech company initiated a clinical trial based on the mouse results. What disease did they analyze in the study? A) haemophilia B) cancer C) Alzheimer's D) heart disease

C) Alzheimer's. Which showed little improvement.

How might the project also 'save the world'? (Choose the answer that was mentioned in the video, which is a scientific driving force for the project in addition to the merit of resurrecting an extinct animal.) A) By proving de-extinction of species is possible B) By providing a sustainable source of ivory and taking some of the pressure off elephant poaching C) By reversing effects of climate change D) By inspiring a new movie that will be a big box-office draw

C) By reversing effects of climate change

The papers showing that various stresses (including acid exposure and squeezing) could cause somatic (body) cells to change into pluripotent cells (stress-induced stem cells) have been retracted. The cells are also known as Stimulus-triggered acquisition of pluripotency cells (STAP cells). Other scientists could not repeat the procedures to make stress-induced stem cells and fraudulent data was found. In one claim the stress-induced stem cells were reported to make a tissue that even ES cells do not differentiate into. This tissue is: A) Brain B) Skin C) Placenta D) Liver

C) Placenta

The main experimental approach in the paper (about beta cells and diabetes) is A) Curing diabetic mice with embryonic stem cells B) Developing a way to ensure the immune system cannot detect beta cells C) Using systematic testing of factors, and the order in which they need to be used, to induce human pluripotent stem cells to differentiate into beta cells D) Comparing the function of in vitro produced beta cells with pancreatic cells taken from a cadaver E) Conducting electron microscopy

C) Using systematic testing of factors, and the order in which they need to be used, to induce human pluripotent stem cells to differentiate into beta cells

Metachromatic Leukodystophy (MLD) is a/an ___________ disease trait. A) sex-linked recessive trait B) sex-linked dominant trait C) autosomal recessive trait D) autosomal dominant trait

C) autosomal recessive trait

In newt limb regeneration, what occurs first? A) blastema formation B) outgrowth of new digits C) wound healing

C) wound healing

What genes are expressed in the morula (mass of 8 cells during early development)?

Cdx 2 and Oct 3/4

What occurs with the expression of Cdx 2 and Oct 3/4 as the cellular division occurs beyond the morula?

Cdx 2 is downregulated in the innermost cells while Oct 3/4 remains expressed throughout.

The outer layer of the blastocyst is made up entirely of cells that express ______________.

Cdx2

Who is the Ohio State cancer researcher who was forced to resign after falsifying data, funded by Pelotonia and the Stefanie Spielman cancer fund?

Ching-Shih Chen

The stem cell, which expresses Lgr5, is found in the _________.

Crypt

What are the stem cell-containing areas of the intestines called?

Crypts

Which of the following is a multipotent stem cell? A) Embryonic stem cell B) White blood cell C) Red blood cell D) Adult blood stem cell E) iPS cell

D) Adult blood stem cell

Studying mammoths may also help in understanding another disease that is very rare in elephants (a close relative of mammoths). The disease is _____. A) Diabetes B) Liver disease C) Heart disease D) Cancer

D) Cancer

The major goal of the study ('Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors') was to __________ . A) Discover a new method for cloning B) Compare ES and iPS cells C) Create ES cells from embryos D) Identify factors that can induce pluripotency in somatic cells

D) Identify factors that can induce pluripotency in somatic cells

What cellular process does not occur in limb regeneration? A) dedifferentation B) differentiation C) cell division D) gametogenesis

D) gametogenesis

One study showed that _______ was sufficient to see improved function in the older animals. A) linkage to a similar age anmal B) one week of a joined blood supply C) haematopoetic stem cells (HSCs) alone D) plasma alone

D) plasma alone

What happens with time in a confetti mouse?

Daughter cells of one stem cell become resident stem cell (random). They give rise to all cells in the crypt and the crypt becomes one color.

What is an extrinsic development?

Development due to information coming from surrounding cells (cell-to-cell)

What is an intrinsic development?

Development due to information inherited and passed on from the mother cell

What results in the loss of functional B-cells?

Diabetes

A somatic cell nucleus transplanted into an egg by SCNT has the epigenetic marks of the _________________

Donor cell. These reflect a differentiated cell not a zygote.

What does Cas9 do once the guide RNA has found its matching sequence?

Each nuclease domains of the Cas9 programs makes a cut, leading to a double stranded break in the DNA.

What are the three germ layers?

Ectoderm, Mesoderm, Endoderm

What is a way to derive human embryonic stem cells?

Embryo cloning by use of Somatic Cell Nuclear Transfer

When the ICM cells are isolated, they can grow indefinitely in a plastic petri dish. What is produced in the dish?

Embryonic stem cells (ES Cells). They maintain the state of being undifferentiated and can produce all cell lineages.

How quick do stem cells of your gut renew?

Every 4 days

Which gene and drug was important in Yamanaka's experiment in order to obtain only pluripotent stem cells?

Fbx15 locus is only turned on in pluripotent cells and thus express B-geo. In the presence of G418, only cells expressing B-geo survived.

What does FACS stand for?

Fluorescent activated cell sorting

What do acetylated histones promote?

Gene expression

How do cells become differentiated and what does it mean to be differentiated?

Gene expression will initiate a program of differential gene expression so that cells can differentiate with a specific structure and function (eg. muscle and eye).

What do the ES grown in culture during the Evans experiment do when injected into mice?

Generate teratomas.

What happens when ES cells grown in vitro are combined with a blastocyst?

Generates chimaeric offspring carrying teratomas.

What happens when ES cells grown in vitro are injected into an adult mouse?

Generates teratomas.

What does pattern formation do?

Generates the body plan

What does HLA typing look at?

Genes clustered on chromosome 6. It helps the immune system distinguish 'self' from 'non-self'.

What happens when ES cells grown in vitro are combined with a endoderm tissue?

Growth of teratomas on the tissue.

Dr. Clevers decided to isolate stem cells from an organ he thought would have the 'champion' of stem cells because cells are replaced every 4 days. This organ is the ______.

Gut

Who is the Japanese researcher who is being investigated for misconduct with the STAP method of creating pluripotent cells?

Haruko Obokata

Figure 6 shows that transplanted SC-beta cells alleviate defects in blood glucose levels in diabetic mice. The figure also shows the mice secrete ______ insulin, which demonstrates the origin is from the donor cells and not the recipient.

Human

What was injected into monkeys with spinal cord injuries and what was the result?

Human neural progenitor cells and not only did the cells survive, but they produce hundreds of thousands of human axons and synapses which ultimately helped to improve the forelimb function in monkeys.

Describe induction and the Spemann-Mangold experiments

Induction involves signals from one cell to another to influence their development. The experiment found that embryonic cells can be isolated and transplanted into another embryo, leading to the transplanted cells being able to induce the host cells to make an additional body axis

Where are 80% of HSCs located?

In a ring close to the bone. The other 20% are found in the region approaching the central vein.

Where are adult stem cells found?

In a stem cell niche

Where do most people lie in terms of use of embryos in research?

In between. They: 1) recognize the human need 2) think an early human embryo is more than just a cluster of nameless cells --it is an ethical dilema

Where are the stem cells found in the gut?

In the crypts (small indentations on the sides of the villus)

What is the normal life span and cause of death of someone suffering from Hutchinson-Gilford progeria syndrome?

In their teens (average of 12 years old). They usually suffer from a heart attack or a stroke.

Where has neurogenesis been confirmed in the nervous system?

In two regions of the adult brain: 1) subventricular zone of the anterior lateral ventricles 2) dentate gyrus of the hippocampus

How can the liver be used to create liver organoids for therapy?

Isolate bi-potential progenitor cells from human bile ducts and grow into organoids. Then, they can be differentiated into hepatocytes and duct cells.

What was found about a NSCs ability to proliferate in vitro culture?

It can generate all neural cell types

What exactly is a stem cell's niche composed of?

It is an anatomical structure including cells and other components required to maintain stem cell function. The environment must support it's long term survival, self-renewal and production of other cell types. Cells and factors together supply support and other information to the stem cells.

What is the process for isolating HSCs like?

It is very difficult because they are rare. 1/10,000 cells in the BM and 1/100,000 cells in the PB. Cell markers must be used to enrich for HSCs.

What happened when pancreatic human beta-cells were implanted into the kidneys of diabetic mice?

It treated their diabetes by secreting more insulin.

What does the cell try to do once the break of DNA occurs due to Cas9?

It tries to fix it; however, the fix is error prone and often introduces mutations which can knock out the effectiveness of entire genes. This is essentially what CRISPR aims to do. However, we can introduce specific DNA sequences to target a change we wish to see in the genome instead of allowing the cell to fix it on its own (making it a very selective.... and thus accurate.... process.

What does the egg cell often try to do to the nucleus in an SCNT?

It tries to reprogram the nucleus and most of the time the nucleus resists. -Not a change in the genome, but how it is modified by epigenetic changes

What does the host egg try to do to the epigenetic marks of the donor cell?

It tries to reprogram them but the molecular process is often faulty.

Outline the first de-extinction attempt:

It was performed on the last Pyrenian ibex. The cells were preserved by freezing and the clone was made by using a goat egg and surrogate (domestic goat). Died at birth with lung problems.

Do state and private funds have more or less strict laws in regards to embryonic research?

Less strict (generally)

Which cancers have been found to contain cancer stem cells?

Leukemia, Breast cancer, colon cancer and pancreas cancer.

What is the "molecular flag" needed to see the production of gut stem cells?

Lgr5

What do the normal stem cells of the intestine express?

Lgr5 and give rise to all cell types. The Dclk1- expressing cell only gives rise to one cell type.

What do the tumor stem cells express?

Lgr5 as well and Dclk1 and give rise to all cells in the tumor.

How did the iPS cells look in the Yamanaka experiment after they were generated?

Like ES cells, not MEFs from which they derived.

What do methylated histones do?

Lower transcription as a result of condensed chromatin

Match the disease to the gene disease: MLD WAS gene: ARSA WASP

MLD, ARSA WAS, WASP

Name some misconceptions with mesenchymal stem cells in terms of bad biology leading to misconceptions:

MSCs were apparently found to be easily purified from many different sources (they were found in several different tissues) and give rise to many different cell types and germ layers. This would be biologically impossible because the germ layers are very different lineages.

What was found when MSCs were studied in vitro?

Many different cell types were induced chemically.

What did the experiment which tested the presence of Dclk1 entail?

Mice were designed whose cells turned blue when Dclk1 was present and they induced this color only for a short period of time to track what happens to the cells (using this, they can track where the cell came from and what cells it produced.

What was used to narrow down which factors were contributing to producing the iPS cells in the Yamanaka experiment?

Microarrays which could show how similar the use of each factor was to actual ES cells.

What is epigenetics?

Modification that leads to a change in gene expression that does not alter DNA sequence

What is needed for a full-fledged cancer?

Multiple mutations. Thus, incidence increases with age.

What potency do adult stem cells have? What does this mean?

Multipotent. They can differentiate into a few different cell types that make up the tissue.

What has been found to extend life span in worms, flies and mice?

Mutations in genes affecting energy pathways.

How can CRISPR-Cas9 be used in mice to model colon cancer?

Mutations which are found in colon cancer can be introduced into a mouse to be used for further study.

What was discovered in the CNS of rodents and humans?

Neurogenesis... dividing cells. It was previously thought that all cells did not divide and were all post mitotic. This provides possibility that the nervous system can be repaired.

What gene does the ICM express?

Oct 3/4

What are the Yamanaka factors?

Oct 3/4, Sox2, Klf4 and c-Myc

What can CRISPR be used for?

Of particular interest to 3401: 1) organoids 2) hESCs 3) iPSCs

How is a cell's fate determined and what does it mean to be determined?

Once a cell's fate is determined, it is irreversibly committed to a certain fate. It's fate is often determined through the expression of various master genes (such as MyoD for muscle cells or Pax6 for eyes).

In what environment do the villi of your gut live in?

One of the harshest biological environments. ( your gut is full of bacteria, toxins, all sorts of chemicals)

What would be observed if a differentiated cell contained Dclk1?

Only those differentiated cells would be blue since they are not dividing. The color would not persist because they do not divide and would die off.

Describe the problem of CSCs:

Other tumor cells can become CSCs due to the plasticity in stem cells.

What would be true if pluripotency was achieved from acid treatment?

Our bodies would have a lot of problems. We have many acidic sites in our bodies and pluripotent cells are generally not found in these sites.

What can be said about the mortality of our germline cells and somatic cells?

Our germline is immortal and somatic cells are mortal.

What was found (in terms of Dclk1 expression) in a mouse that spontaneously developed intestinal cancer?

Over time, more and more of the tumors (cells) turned blue. The color persisted and thus suggested that the stem cells were the cause of the cancer. Since the normal tissue around the tumor was not blue after a long period of time, this means that there are some kind of cancer specific stem cells.

What is the target site known as on the genome?

PAM. This is the site where the Cas9 protein binds.

What is a specific retrovirus that would need to be removed from pig cells to be used in human transplants?

PERVs (porcine endogenous retroviruses)

What potency do ES cells have?

Pluripotency

What type of potency do the cells of the ICM have?

Pluripotency. They can give rise to all cell lineages.

What type of cells are the neoblasts of a planarian?

Pluripotent somatic stem cell.

What mechanism is occurring in the regeneration with planaria?

Pluripotent stem cells called neoblasts are responsible for regeneration.

What are satellite cells?

Precursor cells to skeletal muscle cells.

What type of cells do teratocarcinomas (teratomas) include?

Proliferative undifferentiated cells, called embryonal carcinoma (EC) cells

Where are the neoblasts found in the planaria?

Scattered throughout the body, but restricted to behind the eyes and absent from the pharynx.

What is the function of the goblet cell (of intestine)?

Secrete mucus (for lubrication)

What was studied that can help to improve stem cell function in old mice?

Sharing blood supply (parabiosis) or blood factors from a young mouse.

What technique is used in reproductive cloning?

Somatic-cell nuclear transfer (SCNT)

Scientists are doing what with MSC research and clinical trials?

Some scientists are pushing clinical trials with little or no evidence of safety or efficacy. They say that MSCs can help to treat patients with defects of cells in a completely different lineage. MSCs are somatic stem cells so can only help with bone, cartilage or fat cell disorders! Patients are desperate so they go ahead with certain therapies that may end up doing nothing.

How did bone marrow/hematopoietic stem cell (HSC) transplants begin?

Soon after the bombings in Hiroshima and Nagasaki. It was discovered (using mice) that a mouse subject to whole body irradiation could be rescued by injection of bone marrow. Transplants have been used since 1959.

What is RNA interference?

Specific targeting and knock-down of gene function by cleaving the mRNA.

What causes the extension of telomeres?

Telomerase

How are progenitors different from stem cells?

Stem cells can self renew OR differentiate. Progenitors can proliferate AND differentiate.

What does the multistep protocol of differentiating human pancreatic beta-cells from human pluripotent cells involve?

Subjecting the cells to multiple different factors over a period of 14 days.

What was found when the iPS cells derived from MEFs in the Yamanaka experiment were introduced into neural and muscle tissue?

Teratoma assays produced differentiated cells from all three germ layers.

What occurred when human NT-ESCs were injected into SCID (severe combined immune deficiency) mice?

Teratomas were generated

What did all of the information about the Dclk1 research reveal?

That Dclk1 may be a marker of intestinal cancer stem cells and NOT normal stem cells. With this, killing the Dclk1 cells, the tumor should be able to be completely killed without harming the normal tissue.

What was a conceptual breakthrough on the road to ES cells?

That ES cell differentiation was not abnormal, disorganized, random or stochastic but rather followed the normal pathways of early embryonic development.

What did the Till and McCulloch experiment reveal?

That in vivo quantitative assay, a linear relationship was observed between the number of bone marrow cells injected and the number of colonies (spleen colonies) that developed. A lethal dose for the host was given that destroyed its own bone marrow. However, this dosage was sub lethal for transplanted bone marrow, but enough to induce chromosome abnormality.

What would most likely occur after the CSC's and subsequent cells are eliminated from an "ideal therapy"?

The CSC's niche would likely signal to regenerate the tumor. Thus, it would be necessary to alter the signals influencing the CSCs niche (TME) and how the CSCs are generated in the first place.

What is the Cas9 complex composed of?

The Cas9 protein and single guide RNA.

How can scientists engineer any desired mutation?

The ES cells can be combined with methods of genetic modification such as homologous recombination and CRISPR/ Cas 9

From where can ES cells be taken from?

The ICM

Which type of cells does chemotherapy kill?

The cells that divide rapidly and in return the differentiated cells since they could not be replenished by the dividing cells. BUT chemotherapy would not do a good job at killing cancer stem cells since they divide slowly-- they would resist.

Explain an experiment that supported the Mosaic model

The damage experiment showed that when destroying (not removing) one cell from a 2-cell frog embryo results in the development of only one-half of the embryo.

What was unique about the second paper's results which we read about from the article "Papers on 'stress-induced' stem cells are retracted".

The data showed that the STAP (Stimulus-triggered acquisition of pluripotency) process created cells that could differentiate into placenta cells. This is something that no other cell (ES cell, iPS, etc) was known to be able to do.

What is a problem with using CRISPR for wiping out unwanted species mutations or traits?

The traits would not be entirely wiped out. They would be diluted but there would still be some of the trait left in offspring.

What were the genetic discoveries from the primate cloning experiments?

The two primates nuclear DNA matches that of the donor cell from which the nucleus was taken. The mitochondrial DNA matched that of their respective egg donor.

What is the purpose of using bioreactor in generating an organoid?

There comes a point in the matrigel where it lacks nutrients. The bioreactor increases the nutrients able to be used by the organoid for growth.

What is essential for Cas9 to be able to cut the DNA?

There must be a complementary sequence to the guide RNA on the DNA molecule. (could be other essentials as well)

What is a problem with the EC (embryonal carcinoma) cells?

They are derived from a tumor and have an abnormal karyotype.

What are gene drives?

They are designed to eliminate unwanted traits in insects and animals to push out genetic modifications until we have created a species free of unwanted mutations and genetic traits.

What happens to the beta cells in type 1 diabetes?

They are destroyed by the bodies immune system

What is true about an aged HSC when they are transplanted?

They are not good at regeneration though they have increased self renewal.

What is true about the niches in the brain where stem cells reside?

They are often more complex and specific to the region within the brain.

What is unique about neural stem cells?

They are often quiescent (not dividing/dormant) for long periods of time.

What happens to villus cells when they reach the tip of the villus?

They are shed and undergo apoptosis

What is done to grow ES cells in culture?

They are taken from the ICM. Then, they are then chemically deactivated by chemical irradiation (yet alive); however, they do not proliferate. Then, an MEF (mouse embryonic fibroblasts) feeder layer which provides growth factors is added to encourage growth.

What can be done with isolated stem cells ( in respect to the intestinal stem cells)?

They can be used to grow mini-guts. They can be transplanted into an organism and the living organoids can land and treat a targeted disease.

What is a practical use of the production of 'mini brains'?

They can be used to model various human brain diseases.

What is the problem with iPS derived organisms?

They can develop tumors. -With mice, one of the factors, c-Myc, is an oncogene. -Viruses are used to insert the factor genes and can cause mutations (including those that cause cancer)

What was found when tail tip fibroblasts were implanted into host blastocyst?

They differentiated into many tissues in an embryo. BUT they didnt get progeny mice from the chimeras which suggested that the cells did not become a part of the germline.

What was ultimately discovered in the Dclk1 mouse experiment?

They found that the cells that turned blue were the ones which were differentiated. Thus, the blue color (due to Dclk1 presence) did not persist. This means that in normal tissue, the Dclk1 was not present in stem cells.

What was found about Dolly's chromosomes?

They had shorter than normal telomere lengths and this meant that Dolly's cells were aging faster than the cells from a normal sheep.

What has been done with pigs so far in research to remove PERV?

They have been edited using CRISPR-Cas9 to get rid of the unwanted retrovirus. PERV-free piglets were then produced by somatic cell nuclear transfer (SCNT).

What is a large takeaway from the amphibian tail regeneration experiment?

Tissues only regenerate the same tissue.

What is a more outside-the-box idea for using Cas9?

To attach fluorescent proteins to the Cas9 complex in order to find out where certain DNA sequences are found in the cell, thus giving a 3D architecture of the genome or to follow the position of a chromosome in the nucleus.

What would be the ideal cancer therapy for a cancer originating from cancer stem cells?

To obtain a combined therapy with which the use of current chemotherapy to eliminate the dividing cells and new therapy to target the stem cells would be used. But there is more.... the niche would need to be targeted as well.

What was the method of the first paper which we read about from the article "Papers on 'stress-induced' stem cells are retracted".

To use acid exposure or physical pressure to convert spleen cells from newborn mice into pluripotent cells.

What else can Cas9 be used for?

Transcription activation by deactivating the nuclease components but still use the gene targeting mechanism to bring other activities to genes and DNA regions.

What components are necessary to add to Cas9 in order to promote transcription factors to bind and thus transcribe DNA?

Transcription activators to which RNA polymerase and other factors to the target and increasing transcription of a certain gene.

What type of pluripotent cells are being manipulated now in order to get around the problem of using embryonic stem cells?

Using somatic stem cells and reprogramming them to become pluripotent. (induced pluripotent stem cells)

What are progerias?

Very rare diseases that cause accelerated aging.

How can we edit pig cells to use them for transplants into humans?

We can use CRISPR-Cas9 to edit the cells so they'd be safer for human use. (Immunological compatibility).

What is a major issue that needs addressed when using beta cells in human patients?

We need to make sure that the immune system does not attack the beta-cells.

What would happen if we did not have stem cells?

We would die much much earlier in life.

Describe regulation in an isolation experiment

When one cell of a 2-cell embryo is separated, both embryos will develop into smaller, but normal, organisms

What was found about a NSCs ability to proliferate in vivo culture?

With rats, adult neurogenesis was found in the dentate gyrus

The_______cell type is abnormal or missing in diabetes. These cells respond to high blood glucose by secreting _________.

beta, insulin

What is morphogenesis?

formation of tissues, organs which must allow various structures to take on their shapes