Exam 1 Flashcards
Describe the “Life Cycle”. Give emphasis on the most important steps (those shared by most groups of animals), and on how each stage influences the subsequent one.
The steps of the life cycle includes fertilization, cleavage, gastrulation, organogenesis, lrval stages and metamorohposis for some species, maturty and gametogenesis.
Immeditatly following fertilization rapid cleavage begins to form a blastula.
During gastrulation mitotic division slows down and gastrulation begins where the three germ layers are formed, the ectoderm, endoderm and mesoderm. The three germ layers are formed through invagination of the blastula. It’s during gastrulation the bilateral symetry is formed which seperates our motuh from our anus by the GI track.
Organogenesis is when the organs begin to develop from the three germ layers. Different organs generally develop from different germ layers such as ectoderm develops into skin and nerves, the endoderm the digestive track and the mesoderm muscles and bones etc.
Gametogenesis often doesn’t occur until species are matured and it’s when germ cells are seperated from the smatic cells often in gonads.
Select a model organism of choice: describe the advantages as well as the limitations in its use, and describe one relevant discovery that has been made possible with it
Pros: Drosophila are easy to breed, prolific, tolerant of diverse conditions, its genome is fully sequenced and annotated, cheap, no ethical restrictions, 60% of genome is homologous to humans.
Cons: The brain, cardiovascular, respiration anatomy of Drosophila Melanogaster is different from humans, less complex and adaptive immune system as in vertebrates, effects of drugs on the organism might differ strongly.
Drosophila melanogaster was used by Thomas Hunt Morgan for his discovery of genes and their placement on chromosomes (polytene chromosomes).
- Define what a stem cell is. Elaborate on the different types of stem cells you know, and give one example on how they can be used to treat human disease.
Stem cells is any cell in the body that can regenerate itself by continuant proliferation and that can give rise to more differentiated daughter cells with specialized functions. Stem cells can differ in their potency, the more powerful a stem cell is, the more potent it is. More potent stem cells produce less potent stem cells. The different types of potent stem cells are:
Totipotent – Give rise to any other cell type in the organism
Pluripotent – Give rise to the entire organism except the placenta
Multipotent – Organ/tissue-specific cells which can give rise to all cells in that organ/tissue
Oligopotent – Give rise to for example different lymphoid cells
Bipotent – Can only form 2 types of cells
Unipotent – Regenerating cells that only form one type of cell
Since stem cells are able to regenerate damaged tissues it can be used for various diseases. For example induced-pluripotent stem cells have been used to treat macular degeneration of the retina. Using stem cells as treatments they are patient specific
- What is cell “reprogramming”? Describe the experiment that proved its existence and the one that identified the “factors” involved.
Somatic cells, cells that are fully differentiated, can be reprogrammed into an embryonic-like state by the transfer of nuclear contents into oocytes or by fusion with embryonic stem cells (ES). There are factors that induce this somatic cell reprogramming and those factors are known as the Yamanaka factors, the factors are Oct3/4, Sox2, c-Myc, Klf4.
John B Gordon was the one that discovered that cell differentiation is reversible through nuclear transplantation. He replaced the immature cell nucleus in an egg of a xenopus with a mature intestinal cell, the xenopus egg would grow into in a normal xenopus, it showed that the DNA of a mature cell still had all the information needed to develop all cells in the xenopus. This technique is known as somatic cell nuclear transfer.
Shinya Yamanaka discovered how somatic mice cells could be reprogrammed into pluripotent
stem cells through the introduction of 4 genes. During his experiment there was 24 factors that was suspected of conducting pluripotency. What he did was that he used mice embryonic fibroblasts which are differentiated cells with no stem cell properties, he then took the 24 suspected pluripotency factors and induced it back into fibroblasts which resulted in growth of colonies on a petri dish, meaning they had become pluripotent. They then took this cocktail of 24 factors and removed 1 at a time eventually leading to the discovery that c-Myc, Klf4, Oct3/4 and Sox2 were the factors responsible for the pluripotent induction.
- Choose one signalling pathway and describe how its is executed. Provide an example of its requirement in development or tissue homeostasis, and a human disease in which it is involved.
WNT signalling is critically important during developmeant of the heart. Most of the time B-catenin levels are low because they are bound and regulated by a destruction complex that keeps the B-catenin degraded by the proteosome. When an extracellular signalling molecule binds to the frizzled receptor it will catalyze a reaction that leads to phosphorylation of LRP that will cause the destruction complex to bind to itself instead and it becomes deactivated. This leads to an increase of B-catenin in the cell which will bind to TCF in the nucleus which will cause transcription of WNT target genes that promotes growth and proliferation.
APC mutation leads to accumulation of beta-catenin causing colorectal cancer. The WNT signaling pathway is a critical mediator of tissue homeostasis and repair, and frequently co-opted during tumor development. Almost all colorectal cancers (CRC) demonstrate hyperactivation of the WNT pathway, which in many cases is believed to be the initiating and driving event. This occurs when there is a disruption in the APC tumor suppressor.
- What is Gastrulation? Describe why it is important.
During gastrulation the formation of the primitive streak occurs, cells will migrate to the midline of the gastrula and cause a thickening, this is what the primitive streak is. At the cranial end of the primitive streak the primitive pit is formed by epiblast cells forming a circular cavity, then migrating epiblast cells will join the primitive streak at the cranial end forming the primitive node, this is what becomes the primary tissue organizer where transcription factors (TGFB, Nodal, WNT, BMPs) further induce tissue formation in later stages.
Epiblast cells in the lateral edge of the epiblast layer will undergo epithelial to mesenchymal transition (EMT) to be able to migrate into the primitive streak. The first cells of epiblastic EMT to move into the primitive streak will transform into the endoderm. The second cells that do this will transform into the mesoderm. Multiple mesodermal structures such as the notochord (cells that pass through the primitive pit become notochord) will develop. The formation of the notochord is very important during embryonic development as it provides structural support, defining the midline of the embryo as well as providing chemical and physical interactions with the dorsal lying ectoderm to differentiate. It is the notochord that defines the anterior-posterior axis.
Important because: It primes the embryo for organogenesis by creating the three germ layers that are able to differentiate into tissues, it forms the body axis due to morphogenic gradients which allow for the correct position of the organs.
- What is “induction”, and how was it discovered?
Induction: close range interaction between two or more cells or tissues, in which one induces molecular/shape changes in the other. (Paracrine factors)
Induction, in embryology, process by which the presence of one tissue influences the development of others. In the 1920s, Spemann conducted a series of experiments on the embryos of newts. His research proved the existence of apparent “organizers” in the embryo (definite chemicals) that stimulate and direct development in neighboring tissues or parts. His work showed that, in the earliest stages of development, the fate of the embryonic parts has not been determined. If a piece of presumptive skin tissue is excised and transplanted into an area of presumptive nerve tissue, it will form nerve tissue, not skin. These findings illuminated not only the normal processes of development but also the origin of congenital defects. Spemann’s work indicated that the final role of cellular material in the developing embryo is not built into each cell, as early mechanistic biologists had supposed, but is determined by interactions among various parts of tissue in the embryo, with a special role played by “organization centers.”
- Enhancers are an important component of our genome. Describe what they are and suggest an approach to study them (How could you discover new enhancers and/or characterize theirs functions)
Enhancer sequences are regulatory DNA sequences that, when bound by specific proteins called transcription factors, enhance the transcription of an associated gene. Regulation of transcription is the most common form of gene control, and the activity of transcription factors allows genes to be specifically regulated during development and in different types of cells.
You can use ChIP (chromatin immunoprecipitation) to find new enhancers. ChIP identifies where proteins bind to DNA sequences. We start by cross-linking (covalently bound) DNA which allows us to “freeze” where a certain protein sits at a specific moment because it is covalently bound there. Now we can lyse the cell and extract the complex DNA proteins with for example restriction enzymes. Now we can now use an antibody that recognizes the specific protein and binds to it. These antibodies are bound to something that is “heavy” such as small balls of agarose or magnets, since it is heavy it will precipitate (by for example centrifugation) to the bottom of a tube and since the antibody is bound to the protein, which is bound to the DNA, the DNA will precipitate to the bottom as well. Now we can wash the sample which discards the supernatant leaving only the immunoprecipitation. Now we remove the protein by for example proteinases, and to reverse the crosslinking we can use high temperature to purify the DNA. Once the DNA is purified we can perform quantitative PCR and then DNA sequencing, we can map the position of the genome where this piece of DNA is along the genome. In this way we can find new regulatory DNA sequences (enhancers) which transcription factors induce.
- Describe eye development. Elaborate also on the evidence for a monophyletic versus a polyphyletic evolutionary origin of the eye.
The tissues of the vertebrate eye arises from different embryonic origins, the lens and cornea are derived from the surface ectoderm, the retina and the epithelial layers of the iris and ciliary body comes from the anterior neural plate. The activation by transcription factors and other inductive signals ensure correct development of the eye. The lens placode development is controlled by Pax6. The single eye field is separated into two, forming the optic vesicle and later (under influence of the lens placode) the optic cup. The lens develops from the lens placode (surface ectoderm) under influence of the underlying optic vesicle. Pax6 acts in this phase as master control gene, and genes encoding cytoskeletal proteins, structural proteins, or membrane proteins become activated. The cornea forms from the surface ectoderm, and cells from the periocular mesenchyme migrate into the cornea giving rise for the future cornea stroma. Similarly, the iris and ciliary body form from the optic cup. The outer layer of the optic cup becomes the retinal pigmented epithelium, and the main part of the inner layer of the optic cup forms later the neural retina with six different types of cells including the photoreceptors. The retinal ganglion cells grow toward the optic stalk forming the optic nerve.
Claudio lecture: page 546 (518) book
The development of the eye starts at about day 8.5 (in mice), the optic vesicle (OV) (an ectoderm derived protrusion of the encephalon) and presumptive lens ectoderm (PLE or surface head ectoderm), when these come in contact they start to exchange signals which leads to a thickening of PLE that forms what is known as a placode, the placode then invaginates to form a lens pit which follows the inward cell movements of the optic cap, on day 10-11 the lens pit pinches off from the surface head ectoderm and forms a small hollow ball of cells called the lens vesicle.
The development of the eye undergoes reciprocal induction.
The optical vessels is the inducer of the lens, only the surface head ectoderm is competent to respond. The optical vessel which is the inducer secretes paracrine factors BMP4 and FGF8, these molecules reach the surface head ectoderm/PLE which have receptors for them, these molecules activate a distinct transduction pathway within PLE which culminates in the activation of transcription factors in the lens cells, these transcription factors are Sox2 and L-Maf cooperate to turn on all genes that are required to make a lens. Pax6 is the master control gene controlling eye development. The Notch pathway is also important for this and becomes activated when cells come in contact when delta proteins are integral membrane proteins and cannot travel across the extracellular space. At this point the tissue layers (optic vesicle and PLE) are close and once the lens starts to form it starts secreting factors causes the optic vesicle to become the optic cup which differentiates into two layers the pigmented retina and the neural retina.
- Define the concept of “Lineage Tracing”, describing at least two technologies (ideally an “old time” and a modern example) that are/have been used to its realization.
Lineage tracing is the identification of all progeny of a single cell. Lineage tracing provides a powerful means of understanding tissue development, homeostasis, and disease, especially when it is combined with experimental manipulation of signals regulating cell-fate decisions. In lineage tracing, a single cell is marked in such a way that the mark is transmitted to the cell’s progeny, resulting in a set of labeled clones. Lineage tracing provides information about the number of progeny of the founder cell, their location, and their differentiation status.
There are different techniques to lineage tracing such as direct observation, vital dyes and genetic markers. Direct observation is the oldest technique of lineage tracing, it was done in 1905. They studied early cleavages by light microscopy. A more modern technique is the use genetic markers. A very common genetic marker is fluorescent proteins such as GFP, these are introduced by transfection or viral transduction. Genetic markers in comparison with vital dyes do not “spill over” to neighbouring cells.
- A recent report indicated that, despite the complete sequence of many genomes (that of humans and of many model organisms) is available, most of the genes remain understudied. Suggest an experimental approach to study a new gene (or new genes) of interest.
RNA sequencing, PCR, DNA sequencing, karyotyping, gene knockout
- What is the Spemann Organizer?
The Spemann-Mangold organizer, also known as the Spemann organizer, is a cluster of cells in the developing embryo of an amphibian that induces development of the central nervous system. This discovery also introduced the concept of induction in embryonic development, which is the process by which the identity of certain cells influences the developmental fate of surrounding cells.
Hans Spemann showed that by transplanting presumptive epidermis into an area of presumptive neural tissue the presumptive epidermis would develop into presumptive neural tissue and likewise when he transplanted presumptive neural tissue into presumptive epidermis. This gave rise to the idea that there were some type of organization center that was determined prior to embryonic development which also influenced differentiation of adjacent cells. He tested this hypothesis together Hilde Mangold resembled the previous experiment but now they used embryos from two different species Triturus taeniatus and Triturus cristatus. Teanitus is pigmented whilst cristatus is not which allowed for easier observation. They were able to see that a transplanted piece of the blastopore lip from the taeniatus into the cristatus and vice versa these developed normally. This experiment concluded that a piece of the upper blastopore lip can be transplanted into indifferent tissues and induce the host tissue into the formation of a secondary embryo, therefore implicating the transplanted tissue as an organization center.
- Describe the relevance of the Y chromosome in mammals and drosophila.
In mammals the Y-chromosome contain the master-switch gene for sex determination, called the sex-determining region Y or SRY in humans. In most normal cases, if a fertilized egg (zygote) has the SRY gene, the zygote develops into an embryo that has male sex traits.
In drosophila the Y-chromosome doesn’t determine sex, but it is important for forming sperm in adults.
- Explain the difference between homology and analogy. Provide one example for of the two.
Homology are features that overlap both morphologically and genetically which stem from a common ancestor are homologous structures. Analogy are features that are morphologically different but share a similar function and those do not stem from a common ancestor.
Bird wings and bat wings are an example of analogy.
The arm of a human and the leg of a dog are homologous.
- What is the HOX gene locus? Explain its importance in embryo patterning and our understanding of evolution.
The hox gene locus is a subset of homeobox genes that is highly conserved. HOX encodes homeobox transcription factors that are master regulators of embryonic development and continue to be expressed throughout postnatal life. In the embryonic development they encode for the specificity and characteristics of position, ensuring that the correct structures form in the correct places of the body.
There are 4 different clusters of HOX genes, A, B, C and D, each of these clusters contain genes 1-13 which reside at the extremities of the cluster.
HOX9 and HOX10 specify the limb region stylopod, HOX11 specified the zeugopod and HOX12 and HOX13 specified the autopod.
HOX-like genes have been discovered in cnidarians but they do not follow a clear anterior-posterior patterning or show any correlation with the bilateral HOX genes.
Homeobox genes can be divided into 11 subclasses and Hox belongs to the ANTP class. This class of genes also includes the closely related genes ParaHox and NK. NK genes are present in metazoans (sponges). Phylogenetic analyses of ANTP classes have shown that NK, ParaHox and Hox genes all arose prior to bilateral animals and it has been proposed that all of these three subclasses arose from the same hypothetical ancestral ANTP class gene which during evolution underwent mutations that ended up in three distinct clusters. This further “proves” how evolution
Sponges (metazoans) have several NK homeobox genes, Phylogenetic analyses
