x inactivation

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ScienceAlert on Instagram: “ Calico cats are actually super interesting from a genetic point of view. Girl cats have two X chromosomes, and one will inactivate a few days after conception. It inactivates randomly, leaving blotches of fur coded with one X chromosome, and the remaining fur coded with the other! “ 

tsukinopen  asked:

What about Kaneki being associated with the sterile male calico cat? Eto might be sterile too considering the length she is going to create half-ghouls. Maybe the Washuu provide genetic material because half-ghouls are sterile and cannot mate with each other?

I haven’t heard of Kaneki being associated with the sterile male calico cat tbh. 
This association, genetically, is false. 

I will be using some scientific terms in the following which meanings can be found fully explained on here [x]

  • From what we know so far, the ghoul phenotype is not due to a sex genotype ie the gene(s) responsible for ghoulification are not found on the X and Y chromosomes. If ghoulification was associated with XY chromosomes, we would have seen different phenotypes.
  • Calico cats’s fur phenotype is due to a sex genotype, ie the gene responsible for fur color is present on a sex chromosome, the X chromosome. Humans and Cats are similar in that females have XX, while males have XY sex chromosomes. Because the gene for fur color is only present on the X chromosome, males have only one copy of the gene, while females have 2 copies. Many alleles exist for fur color, including Black and Orange. Because males only have one gene, and hence one allele, they are either black or orange. Females, however, can have both colors if they have an orange allele on one X and a black allele on the other X chromosome. 
  • Fur color is not a co-dominant character ie if the alleles were on different chromosomes, the female calico cat will not be both orange and black. The reason why female calico cats have both colors is X-inactivation, a complex mechanism present in all females whereby certain tissues inactivate one copy of X while the other tissues inactivate the second copy of X. Hence the tissue that inactivated the black allele on X1 will have an orange color, while the tissue that inactivated the orange allele on X2 will have a black color. This can be generalized to all genes and their alleles on the X chromosomes. Hence, although females have 2 Xs: XX genotype, their phenotype is due to all genes present on the X chromosome that was not deactivated.
    You can read more about X-inactivation on here [x] or ask me about it since I taught the concept to sophomore students at the university I am working at.
  • The only reason you will get a male calico cat is an abnormality. A male calico cat has XXY as sex chromosomes rather than XY. The male is sterile not because he’s patched (has black and orange color), but because he has 3 copies of sex chromosomes rather than 2, and so reproduction is not successful. Humans born with XXY suffer from  Klinefelter syndrome and they are sterile. 

Because Kaneki does not have any ghoul genes in his germ-line cells, he can reproduce normally as a human. See explanation at the end of this post [x] Nonetheless, since genetics is more complex than just partitioning of genes, Kaneki may be sterile for other reasons, and this may depend on who he is mating with [human, half-ghoul, ghoul].

Eto, on the other hand, is a natural-born half-ghoul. Her system is different than Kaneki’s, so are her genes and their behavior. Although I partitioned all possible offspring outcomes for the possible mating between ghouls, half-ghouls and humans, again in this post [x], natural-born half ghouls may be sterile. Indeed, the issue that you are raising is worth thinking about. It is odd that Eto did not try to have her own children. 

If we need to use an animal model as an example, calico cats are a bad choice, however mules are a good one. Mules are the offspring of a female horse and a male donkey. They are viable, but almost all of them are sterile. Sterility here is different from the sterility we know of. Mules do give birth but their offsprings die. Hence, a hybrid, the mule, is only viable in the first generation, while the offsprings of the second generation do not survive. This is also common to other animals. 
Here, the sterility is not due to having XXY chromosomes or less than 2 sex chromosomes. It is due to the fact that Horses and Donkeys are 2 different species with different sets of chromosomes and characters. One of the famous definitions for speciation or a species is: a population of organisms that can mate with one another and produce offsprings. Two organisms are no longer from the same species when their offsprings are non-viable. 
Humans and ghouls are different species. If Eto is indeed sterile, then this just confirms this conclusion. 

Eto obviously incorporated her kagune into many other ghouls. This incorporation is not mediated by mating, and it worked well. It was repeated with Kanou’s experiments using Kuzen and Rize. The CCG may be doing the same thing.

In very limited conditions, even if we assume Eto is sterile, some combination of genes and alleles may be just right to produce a single viable offspring. We are yet to see if this will ever happen. 

YouTube Videos on Genetics

I went apprehensively to my first genetics lecture this morning; some acquaintances who had taken the course before said they hadn’t gotten much out of this particular professor’s lectures. But then an amazing thing happened! The professor announced that the course was going to be  different this year. 

Apparently, last year he noticed that a particular student was doing very well on the exams, despite never attending lecture. He pulled her aside and asked her where she was getting her information, since she wasn’t coming to class.

The answer? YouTube, of course! 

The professor has thoroughly embraced the idea, and now the syllabus is full of videos for us to watch before lecture. I love studying by watching YouTube videos (preferably at 1.5x or 2x speed) so this made me super happy.

And here, for your enjoyment (and so I’ve got an easily clickable list for my own use), are the videos on my professor’s syllabus for intro to genetics. I’ve listed them in the following format: “Channel Name: Video Subject (video length).”

I. Basic Mendelian Genetics

  1. Useful Genetics: Introduction to genetic analysis (5:58)
  2. Useful Genetics: Genetic nomenclature (19:29)
  3. Useful Genetics: Mendelian genetics (20:57)
  4. Useful Genetics: How to do genetic analysis (30:44)
  5. Bozeman Science: Punnett Squares (12:14)
  6. Bozeman Science: Chi square test (11:52)
  7. Useful Genetics: Chi square test (25:03)
  8. Todd Nickle: Branch diagram Mendelian genetics problem (12:59)
  9. DNAunion: Branch diagram method for trihybrid cross (2:52) [NB: Watch this one on mute. The audio is just really annoying music, unrelated to the video content.]
  10. StatisticsLectures.com: Non-genetic chi square example (4:00)
  11. StatisticsLectures.com: Another non-genetic chi square example (3:53)

II. The Physical Basis of Mendelian Principles

  1. Biology / Medicine Animations HD: Mitosis animation (6:20)
  2. Useful Genetics: Mitosis (20:19)
  3. Crash Course Biology: Mitosis (10:47)
  4. MrAac007: Meiosis (2:57)
  5. Biology / Medicine Animations HD: Meiosis and Crossing Over (6:45)
  6. Crash Course Biology: Meiosis (11:42)
  7. Useful Genetics: Sexual Life Cycles (12:03)
  8. Useful Genetics: Sex Chromosomes in Meiosis (11:44)
  9. Useful Genetics: Crossing Over (20:51)
  10. Useful Genetics: Following genotypes through meiosis (16:24)

III. Sex-chromosome linkage

  1. Useful Genetics: Sex linkage (19:47)
  2. Useful Genetics: Sex determination (10:06)
  3. Biology / Medicine Animations HD: X inactivation (1:47)
  4. Useful Genetics: X-linked gene expression in females (15:21)
  5. Useful Genetics: X-linked gene expression in males (12:28)

IV. Pedigree Analysis

  1. Juliana Agostino: Karyotyping (10:17)
  2. Suman Bhattacharjee: Pedigree analysis (15:29)
  3. Biologybyme: How to do pedigree analysis (8:42)
  4. Biologybyme: Autosomal dominant pedigree (6:48)
  5. Biologybyme: X-linked recessive pedigree (7:11)
  6. Biologybyme: Autosomal recessive pedigree (8:00)
  7. Biologybyme: X-linked dominant pedigree (11:16)

V. Extensions of Mendelian Genetics

  1. Bozeman Science: Chromosomal Genetics (14:22)
  2. Useful Genetics: Extensions of Mendelian Analysis and Linkage (23:11)
  3. John Munro: Biochemical Pathways (1:12)
  4. Biology Rangitoto: Types of biochemical pathways (8:14)
  5. Useful Genetics: Gene interaction in biochemical pathways (14:11)

VI. Mutation and Mutational Analysis

  1. Useful Genetics: Central Dogma of Molecular Biology (19:55)
  2. Biology / Medicine Animations HD: Transduction (1:08)
  3. Anirban Basu: Bacterial Conjugation (3:11)
  4. John Munro: Bacterial Transformation (1:15)
  5. The Petersson Lab: Doing bacterial transformation in a molecular biology lab (8:27)
  6. Life Technologies: Invitrogen (6:57)

VII. Control of Gene Expression in Bacteria and Bacteriophage

  1. iBiology: Gene Regulation Part One (31:28)
  2. iBiology: Gene Regulation Part Two (41:20)
Mary Lyon

Born in 1925, Mary Lyon is an English geneticist who is best known for her discovery of X-chromosome inactivation (also known as lyonization), which is the process by which one of the two copies of the X chromosome present in female mammals is randomly inactivated.

During WWII, Mary pursued her studies at Girton College at the University of Cambridge, where she studied zoology, physiology, organic chemistry and biochemistry, with zoology as her main subject. During that time she became interested in embryology. She went on to do her PhD with R A Fisher, who was Professor of Genetics in Cambridge, where she characterized a mutant mice strain.

After her PhD, Mary joined the group of Conrad Hal Waddington, funded by the Medical Research Council to investigate mutagenesis and the genetic risks of radiation. She has published many papers on radiation and chemical mutagenesis and on studies of mutant genes. She was head of the Genetics Section of the MRC Radiology Unit at Harwell from 1962 to 1987. She retired from active research in 1990.

In 1961, while working on radiation hazards, Mary Lyon proposed the random inactivation of one female X chromosome to explain the mottled phenotype of female mice heterozygous for coat color genes. The Lyon hypothesis also accounted for the findings that one copy of the X chromosome in female cells was highly condensed, and that mice with only one copy of the X chromosome developed as infertile females. Examples of X chromosome deactivation are calico fur patterns in female cats and Duchenne muscular dystrophy in human males. 

youtube

A nice video on Lyonization, or X-Inactivation. It is the process by which one of the two copies of the X chromosome present in female mammals is inactivated. The inactive X chromosome is silenced by its being packaged in such a way that it has a transcriptionally inactive structure called heterochromatin - another example of epigenetics!

OB Science Time: X Inactivation and Clones

This is a topic I have discussed in passing before, but it is super interesting, so I thought it warranted a Science Time!! Yay for science!!

So in humans there are two main variations of sex chromosomes (I say this because there are some intersex people whose sex chromosome composition is different from the two common types): there is XX and XY. The X chromosome is a full-length chromosome encoding numerous genes, and all people have at least one copy of it. The Y chromosome is a small, almost partial chromosome that encodes for only some of the same genes as the X chromosome and a few unique genes.

Now, for all other chromosomes, we all have two copies, and they are roughly identical: they encode for all the same genes unless there are deletions, but they may have different alleles for the genes. For every gene not on the sex chromosomes, we express two copies of it: the allele from one parent and the allele from the other parent.

In the case of people with XY chromosomes, they pretty much only have one copy of all the genes on the X chromosome. Therefore, they are only expressing a single dose of these genes. To equal out the dosage discrepancy for people with XX chromosomes, one X chromosome in every cell gets inactivated so only one copy of every gene on that chromosome is expressed in the cell. The inactivated chromosome gets turned into a tightly wound bunch of heterochromatin that can no longer be accessed for gene expression, known as the Barr Body.

The pattern of X inactivation is completely random, so not every cell in the body has the same chromosome inactivated. In most people, the result is about 50/50 so there is roughly equal expression of the alleles of each gene from both parents. A good visual for this process is coat color on cats. The gene for coat color is on the X chromosome, and if the cat has an allele for black fur from one parent and an allele for white fur from the other parent, then some cells will cause the fur to be black and others will cause the fur to be white, depending on which chromosome is inactivated in each cell. This results in a patchwork coat, with areas of black and areas of white fur.

Now let’s think about this in terms of the Leda clones. They all start out with the same two X chromosomes, but during development they begin to inactivate in a random process. No two clones are going to inactivate the X chromosomes in the exact same pattern. Now for any genes in which the clones have the same allele on both chromosome, this won’t make a difference, but if there are two different alleles for any gene, then the clones will all vary in their expression of these alleles. This would make them not exactly identical, as far as gene expression is concerned.

There are thousands of genes encoded on the X chromosome, not all of which are known, so it’s hard to say what exactly would vary among the clones due to their differences in X inactivation. But, it is safe to say that this is another area of their genetics (along with their epigenome) that will differ amongst each of them. Pretty cool, right?!

As always, if you have any questions, comments, concerns, don’t be afraid to hit me up so we can discuss all the science!!! And for more OB Science Time click here :D