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A Genetics Riddle

Along with his brothers, a soldier goes off to war leaving behind his wife and two sons. Six years later he returns to his family after losing both his brothers in action. Something is different though. His wife suspects something, but can’t put her finger on it. She just knows that something is different about her husband. Over the next two years, the family grows by twins (a boy and a girl) and then another girl. Then, in an auto accident, the husband dies and his widow decides that she can now investigate a hunch she has had for some time without upsetting her husband.

That month, she takes all of her children in for their annual checkup and vaccines, and also asks the doctor to check her blood type along with all of the children.

The results, mailed to her (see below) later that week, give her a start as she realizes her hunch was correct.

What was her hunch? How did she arrive at her conclusion?

Screen Shot 2016-03-27 at 3.16.30 PM.png

 

 
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Posted by on March 27, 2016 in Uncategorized

 

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Stephen King’s Carrie and the problem of genetics in an horror story

carrieIn the novel, Carrie, Stephen king attempts to explain telekinetic ability in terms of a real genetically inherited trait. OK, this is fiction, I have no problem with Carrie’s telekinetic ability … where would this story be without it after all?
Explaining this ability in terms of science was a mistake for two reasons. For one thing, it undermines the very idea of ‘supernatural’ that the reader has already bought into. This was exactly the problem that fans of Star Wars had with the prequel trilogy’s explanation of ‘The Force’ in terms of sub-cellular microorganisms. The second reason he shouldn’t have done this is because he didn’t understand it well himself.

Characters:
Carrie White – The protagonist, who possesses telekinetic (TK) ability
Margaret Brigham – Carrie’s mother
Ralph White – Carrie’s father

From Stephen King’s Carrie (please don’t sue me Mr. King)

It is now generally agreed that the TK phenomenon is a genetic-
recessive occurrence-but the opposite of a disease like hemophilia,
which becomes overt only in males. In that disease, once called “King’s
Evil,” the gene is recessive in the female and is carried harmlessly.
Male offspring, however, are “bleeders.” This disease is generated only
if an afflicted male marries a woman carrying the recessive gene. If the
offspring of such union is male, the result will be a hemophiliac son. If
the offspring is female, the result will he a daughter who is a carrier. It
should be emphasized that the hemophilia gene may be carried
recessively in the male as a part of his genetic make-up. But if he
marries a woman with the same outlaw gene, the result will be
hemophilia if the offspring is male.

In the case of royal families, where intermarriage was common, the
chance of the gene reproducing once it entered the family tree were
high-thus the name King’s Evil. Hemophilia also showed up in
significant quantities in Appalachia during the earlier part of this
century, and is commonly noticed in those cultures where incest and
the marriage of first cousins is common.

With the TK phenomenon, the male appears to be the carrier; the
TK gene may be recessive in the female, but dominates only in the
female. It appears that Ralph White carried the gene. Margaret
Brigham, by purest chance, also carried the outlaw gene sign, but we
may be fairly confident that it was recessive, as no information has ever
been found to indicate that she had telekinetic powers resembling her
daughter’s. Investigations are now being conducted into the life of
Margaret Brigham’s grandmother, Sadie Cochran-for, if the dominant/recessive
pattern obtains with TK as it does with hemophilia,
Mrs. Cochran may have been TK dominant.

If the issue of the White marriage had been male, the result would
have been another carrier. Chances that the mutation would have died
with him would have been excellent, as neither side of the Ralph
White-Margaret Brigham alliance had cousins of a comparable age for
the theoretical male ottspring to marry. And the chances of meeting and
marrying another woman with the TK gene at random would be small.
None of the teams working on the problem have yet isolated the gene.

Surely no one can doubt, in light of the Maine holocaust, that
isolating this gene must become one of medicine’s number-one
priorities. The hemophiliac, or H gene, produces male issue with a lack
of blood platelets. The telekinetic, or TK gene, produces female
Typhoid Marys capable of destroying almost at will….

Questions

Stephen King’s explanation of the genetics of hemophilia is not quite right.

1. How is hemophilia actually inherited? Explain in terms of dominant / recessive inheritance.
2. King suggests that hemophilia is inherited from two carrier parents. Is this correct? Describe, in genetic terms, how a boy can be born with disease.
3. Is it possible for a female child to inherit the disease?

Queen_Victoria

 
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Posted by on July 20, 2015 in Uncategorized

 

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Looking Glass Genetics : Gene Mapping

The Mad Hatter and March Hair setting up a breeding experiment in a teacup

The Mad Hatter and March Hair setting up a breeding experiment in a teapot

In addition to Genetic Counseling for the cards, your lab has been investigating the genetics of the Dormouse.

Dormice have either the ability to Speak (S) – or are Mute(s).

Additionally, they are either Cruel or Kind.

You wish to map the distance between the Speech and Disposition genes and determine whether Cruelty or Kindness is dominant. (Here, not a metaphysical question)

You begin by obtaining true-breeding animals:

  1. A Speaking , Kind Male
  2. A Mute, Cruel Female

(oh, the cries of misogyny!)

Once bred, this coupling gives rise to a litter of six offspring. All six can speak and are unfailingly kind.

These offspring are then bred to true-breeding homozygous recessive mates. The results of these matings are:

      #                     Phenotype

35                   Speaking, Kind

15                   Speaking, Cruel

15                   Mute, Kind

35                   Mute, Cruel

  1. What can you determine from these results?

In similar experiments, Cruel, Longhair and Kind,Shorthair animals were examined. Both parentals were true breeding and the F1 litter consistend entirely of Kind, Longhair animals. These F1 were then crossed with homoztgous recessives for both traits, resulting in:

    #                     Phenotype

20                   Kind, Longhair

80                   Kind, Shorthair

80                   Cruel, Longhair

20                   Cruel, Shorthair

What do these data add to your understanding of Dormouse genetics? Can you map the three genes to one Chromosome? What experiment do you want to do next?

 
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Posted by on November 8, 2014 in Uncategorized

 

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The first hand : Mendel in Wonderland

In wonderland, much depends upon the suit and rank of a card. In the time of Alice, the Hearts held power, but since then, the Queen of Hearts has been imprisoned and the Kind of Spades now rules the land.

Families now strive to have children of high suits in order to give them the best chance at a good life.

Suit values are as follows:

Clubs < Diamonds < Hearts < Spades

illustration-card-soldier-three-clubs-alice-wonderland-lewis-carrol-29829263

Conveniently, the inheritance of the suits follows the same order. That is Spades are dominant over all suits, Hearts are dominant over Diamonds and Clubs, and Diamonds are dominant over Clubs.

SC < SD < SH < SS

Two cards come into your clinic to get genetic counseling. They want to know what chance they have of having a Hearts or Spades baby.

Mom is the Three of Hearts

Dad is the Five of Diamonds

They already have three children: a Two of Hearts, a Seven of Clubs, and a Jack of Clubs.

cards

From the information provided above, what do you know?

Is it possible that they can have a Hearts Baby?

 
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Posted by on November 7, 2014 in Uncategorized

 

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Blood and Genetics

Blood type is a fun and easy way to get to know genetics and learn some practical applications. In the simplest of ways, the three basic blood types are A, B and O.

A good place to brush up on blood type genetics is wikipedia, which has an excellent article on the topic.

Once you’ve reviewed this material (if you need to), then go to nobelprize.org to play a game about blood transfusions (all based on simple blood type genetics).

While you’re on the site, read a little about Alfred Nobel and why it was so important to him to have a lasting positive legacy.

 
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Posted by on November 3, 2014 in Uncategorized

 

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Bane of the Garden Gnomes

Last week, we discussed the use of the Hardy Weinberg equations to estimate the rate of change in population under conditions of extreme selection, i.e. total elimination of one phenotype. This is essentially the goal of any sort of eugenics program. As an example of a way that this kind of policy could creep into culture, we watched GATTACA. Besides, it’s just a good film.

The purpose of the Hardy Weinberg equations is to model conditions under which allele frequencies can NOT change from one generation to the next. Therefore, it is evident that these are exactly those conditions that are responsible for allele frequency changes.

These conditions are:

  1. No Mutation
  2. No Selection (survival)
  3. No Sexual Selection
  4. No Genetic Drift –due to occasional fluctuations occurring by chance
  5. No Gene Flow – immigration / emigration

In order to prevent the random changes in allele populations stipulated in #4, we also need a sufficiently large population, where sufficient is likely definable by someone with better probability-computing skills than my own. (I feel like going off half-cocked on notions of probability and finite vs infinite time, but I’ll spare you).

Anyway, if we know something about the population, we might be able to work out the allele frequencies and then compute our theoretical proportions for the next generation from the equations…

p+q = 1,

where p and q are the frequencies of the (only) two alleles we are calculating.

and

p2+2pq+q2 = 1

where each unit above represents the proportion of that genotype.

Mathematically, these equations provide insight into how rapidly the rate of an allele in a population could be eliminated if reproduction was prevented in a specific group. (This sounds completely esoteric without using an example, so let’s come up with one…)

A Healthy Gnome Couple

A Healthy Gnome Couple

Imagine a population of fictional creatures – Garden Gnomes.

These gnomes have a recessive allele that makes them susceptible to a fungal disease. We’ll call the two alleles for this trait H – hearty (resistant) and h– weak (susceptible)

There was recently a new law passed amongst the gnomes forbidding susceptible gnomes from breeding (let’s imagine that the H allele is apparent by a normal complexion and the h allele is apparent by a jaundiced complexion. Like susceptibility to disease, jaundice only appears in the homozygous recessive (hh) gnomes.)

Imagine a population starting with equal allele frequencies, p=q=0.5.

p2+2pq+q2 = 1

will give us genotype frequencies of:

25% HH   + 50% Hh + 25%hh = 1

for the present generation.

Now, if we start our draconian, anti-jaundiced gnome policy and prevent breeding of these individuals, then this generation‘s breeding population only consists of the HH and Hh gnomes, where only the heterozygotes will contribute the h allele to the next generation.

If we call the next generation q1, we can estimate the new proportion of the q allele in the population as the frequency of the heterozygote over the total population excluding the hh gnomes:

No wonder they want to get rid of these guys

No wonder they want to get rid of these guys

After one generation, the frequency of the H allele is now 67%.

Since the same process would occur generation after generation (as long as the law was in place – and followed), we can determine the frequency of q at any generation, where n is the generation number.

  1. From this information, try calculating the frequency of both alleles after the policy has been in place for 5 generations.
  2. How long will it take to completely eliminate the h allele?
  3. How would this change if the susceptible (h) allele is dominant?

 
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Posted by on April 28, 2014 in Education, Uncategorized

 

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A Pointer to My Post After Watching GATTACA

ImageToday’s post about the film, GATTACA, is just as much a movie review as it is a discussion of eugenics, so I thought I’d post that on my other blog instead. Go on over and check that out. That and my thoughts on an ungodly number of bad movies that I watch all the time. 

 
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Posted by on April 24, 2014 in Uncategorized

 

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Eugenics in film: GATTACA

Tomorrow in class, where we have recently been discussing Mendelian Genetics and its twisted perversion,Eugenics; we will be watching the dystopian film, GATTACA. The story is good enough, but what I find compelling is the way that society has become the way it is. The population has been recently ‘improved’ by the production (?) of ‘designer babies‘. The method seems very much like one that I can honestly imagine working its way into present society. These children aren’t fabricated, they’re yours. Only – just the best parts of you.

Society fell for Eugenics once – and not just Hitler. I know that’s where your mind is going. But there were plenty of Eugenics believers here in the USA as well. Just ask this happy family:

Image

They’re smiling because they’ve just won the ‘medium family size’ medal for fittest family at the 1927 Kansas Free Fair.

It was a time when Mendelian genetics was coming to be understood in principle by a wider audience following the work’s ‘rediscovery’ by Hugo de Vries and Carl Correns in 1900. The main idea behind Eugenics was that better people could be made through selective breeding of only the right kinds of folks. The term Eugenics was coined by Sir Frances Galton, who actually a great thinker contributing several key ideas in the field of statistics and inventing the sciences of meteorology and psychometrics. His books, Hereditary Genius (1869) and Essays on Eugenics (1909) lay the groundwork for thinking about which traits are inherited and which are learned in humans. In exploring the idea of hereditary greatness, he also explores the hereditary of less desirable genes. 

What he concluded was that great, geniuses like himself simply aren’t having enough children while the lowly dregs of humanity were breeding like bunnies. Well, there’s a couple of ways to put an end to that nonsense. 

Here is an excerpt from a Scientific American editorial of the time (1911) lauding Galton’s ideas: 

ADA JUKE is known to anthropologists as the “mother of criminals.” From her there were directly descended one thousand two hundred persons. Of these, one thousand were criminals, paupers, inebriates, insane, or on the streets. That heritage of crime, disease, inefficiency and immorality cost the State of New York about a million and a quarter dollars for maintenance directly. What the indirect loss was in property stolen, in injury to life and limb, no one can estimate.

Suppose that Ada Juke or her immediate children had been prevented from perpetuating the Juke family. Not only would the State have been spared the necessity of supporting one thousand defective persons, morally and physically incapable of performing the functions of citizenship, but American manhood would have been considerably better off, and society would have been free from one taint at least.

The Free Kansas Fair of 1927 had more than just pretty families. It also proposed just how even prettier families could show up in the years to come:

Image

 

Why is Blind in quotes? Is that, perhaps, a suggestion? Or is it just poor grammar?

Image

 

Do you suppose ‘Pauperism’ is dominant or recessive? Either way, it’s bad. How can they go around having no money like that? Have they no shame?

 
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Posted by on April 23, 2014 in Uncategorized

 

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More on the Lac Operon

A while ago I wrote two posts about the Lac Operon here. The first pointed to an animation by McGraw Hill Publishers that did a pretty good job illustrating how the operon works. In the second post, I highlighted the notion of polycistronic messages (more than one gene per mRNA molecule) and how this allows for control of a number of related genes at once – a trait not shared by eukaryotic cells. In that second post, I also finished with a graph of how cells grow in the presence of glucose and lactose.

image002

Cell Growth in the presence of glucose + lactose – As glucose is depleted, cells adjust to lactose digestion

One feature of that graph (reproduced here) that is notable is a little bump in the growth rate as glucose runs out and the cell converts to lactose digestion. A second important feature is that the rate of growth slows when the cell is burning lactose as its primary fuel.

 

Together, these features suggest that the cell is regulating lactose digestion very closely. In fact, there are two primary mechanisms of this regulation to appreciate. The first is that the lactose-digesting enzymes are controlled together on an operon that is regulated by lactose itself (or at least we can assume so for simplicity’s sake). In the absence of lactose, no lactase enzymes are made and no lactose is used as fuel. The reason for this is obvious when you look at the slope of cell growth under glucose metabolism (left) and lactose metabolism (right). Clearly, growth is SLOWER when lactose is used as fuel.

Therefore, so long as there is glucose, it is pointless to digest lactose at the same time. So it is best to only turn on the lac operon in the ABSENCE of glucose – regardless of whether lactose is present of not.

If glucose is absent and lactose is absent, turning on lactase enzymes is still useless. However, slow growth is better than no growth. So we should have a mechanism to turn on the operon when there is lactose in the environment.

Here’s a matrix of ideal regulation:

Screen Shot 2014-03-31 at 2.18.05 PM

How can a little, mindless bacteria achieve this exquisite control?

Simple: By using two regulators. One for glucose and one for lactose. Only when both conditions (glucose-, lactose+) are met do we make lactase.

Structure of the Lac Operon

operon1

First, lactose itself serves as an inducer. In the absence of lactose, a regulator protein binds to a DNA site between the polymerase binding site (the promoter) and the structural genes (the enzymes). When the regulator binds, its presence physically prevents the progress of RNA Polymerase.

When lactose is present, it binds the repressor protein in a way that causes its shape to change in a way that can no longer bind the DNA. The repressor then drifts away from its binding site allowing RNA Polymerase a clear shot to the structural genes.

operon2

However, RNA Polymerase is not always parked on the promoter waiting for the repressor to be removed. Its binding requires another protein to help stabilize its interaction with the DNA. This second protein is the CAP protein. The Catabolite Activated Protein. However, CAP alone will not bind either. It requires a signaling molecule called cyclic AMP (cAMP). cAMP is readily broken down when glucose is in the cell, so it only accumulates when glucose is absent. In that case, cAMP accumulates and binds to the CAP protein, which then binds to the CAP site. This site is located adjacent to the promoter, but on the side away from the structural genes. When CAP binds, it assists in recruiting the RNA polymerase to the promoter.

operon3

Therefore, if only one condition is met, it is insufficient to promote gene transcription. Only when the CAP+ cAMP protein is bound will the Polymerase be recruited. And only when lactose is present, will the repressor protein let the Polymerase pass.

operon4

In terms of the matrix we set forth above, we can see that these molecular interactions result in exactly the regulation that is optimal:

post-operon

 

 
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Posted by on March 31, 2014 in Uncategorized

 

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BLyS Sequence Analysis

I’ve been playing with some sequence analysis and phylogentic tree construction programs recently because I would like to introduce these sorts of data analysis into my biology classes. As a sample protein, I decided to use BLyS / BAFF, a protein important in regulating B Cell numbers. I’ve always wondered about the origin of this kind of molecule, since working on it in grad school, and this seemed like a decent way to get some ideas about where it might come from.

The first thing I did was go to the NIH’s National Library of Medicine website: http://www.ncbi.nlm.nih.gov

It’s easy to search for any protein / gene / whole genome you are interested in examining. Knowing that BLyS is vital in humans and mice, I chose to start with the human sequence. I retrieved it as the following:

>gi|20196464|dbj|BAB90856.1| BLyS [Homo sapiens]
MDDSTEREQSRLTSCLKKREEMKLKECVSILPRKESPSVRSSKDGKLLAATLLLALLSCCLTVVSFYQVA
ALQGDLASLRAELQGHHAEKLPAGAGAPKAGLEEAPAVTAGLKIFEPPAPGEGNSSQNSRNKRAV

The easiest tool to find similar proteins in other animals is the Basic Local Alignment Search Tool for proteins, or BLASTp. Just using default settings, I pasted the sequence in the search field and hit go. (note, I actually just used the accession number, not the whole sequence)

Image

This retrieved tons of proteins with similar sequences from the vast database of sequence information, from which I chose several model species. One thing I wanted to do was to include several primates as a sort of internal calibration (assuming that they would all have very similar sequences compared to more distantly related species). I also wanted to get a few animals’ sequences who are quite distantly related to humans (frog and ground tit fir that bill)

Once I had a list, I put them all into a single text file and then used that in a second program. This time, I decided that the best ‘multiple alignment tool’ would be CLUSTALX. It’s been around for a while and can create data in a number of different forms. Besides, it’s free and versions are available for both mac and PC.

Again, for starters, I just accepted the default parameters and did a quick alignment:

Image

Obviously, there’s something odd about the canid familiars (dog) sequence, but before I did anything about that, I just wanted to see what a phylogenetic tree looked like. This is another thing that Clustal does well, it will export your sequence alignment as tree data in a number of formats, then I could plug that data into one final program. This last is a web based program that I access through a french site (but you can probably find it in a number of places). The program is called DRAWGRAM. It accepts alignment data and outputs a graphical tree representation of the alignment.

This is an important logical step… What I’m doing is asking for a family tree of sorts to be displayed that represents the relationship of the sequences I provided. We might want to assume that this also tells us how related the organisms that have these proteins are – and that’s not wrong, but it’s also not thorough as we’re only using ONE protein to make that assumption.

Here’s my first tree:

Image

Note how isolated Canis is on this representation.

Finally, I went back and truncated the Canis sequence to a place where I suspect the protein actually starts – my sequence from the NCBI gave me a string of Amino Acids at the front of the protein that I think are probably not there, but just got added by some computer algorithm without proper human oversight.

Once I did that Canis (by the way, I remained the sequence ‘DOG’ so I was sure it was the new one) fell in line with a sequence more similar to that seen in cats (felis):

ImageThat’s it for now. Although I expect that I will dig a little deeper with more animals to see if I can come closer to an ‘original BLyS’.

 References:

  1. Dereeper A., Audic S., Claverie J.M., Blanc G. BLAST-EXPLORER helps you building datasets for phylogenetic analysis. BMC Evol Biol. 2010 Jan 12;10:8. (PubMed)
  2. Dereeper A.*, Guignon V.*, Blanc G., Audic S., Buffet S., Chevenet F., Dufayard J.F., Guindon S., Lefort V., Lescot M., Claverie J.M., Gascuel O. Phylogeny.fr: robust phylogenetic analysis for the non-specialist. Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W465-9. Epub 2008 Apr 19. (PubMed) *: joint first authors
  3. Felsenstein J. PHYLIP – Phylogeny Inference Package (Version 3.2). 1989, Cladistics 5: 164-166
  4. Larkin,M.A., Blackshields, G., Brown, N.P., Chenna, R., McGettigan, P.A., McWilliam, H., Valentin, F., Wallace, I.M., Wilm, A., Lopez, R., Thompson, J.D., Gibson, T.J., Higgins, D.G. (2007) Clustal W and Clustal X version 2.0. Bioinformatics, 23:2947-2948.
  5. Thompson,J.D., Gibson,T.J., Plewniak,F., Jeanmougin,F. and Higgins,D.G. (1997) The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Research, 25:4876-4882.
 
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Posted by on March 7, 2014 in Uncategorized

 

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