Rat Coat Genetics Part 4

4. Color locus

Often people think of this as the most confusing locus, and it can be, because there are so many alleles and each relates to the others somewhat differently.

Because this is the first locus in the series with more than two alleles, we have to use superscripts to denote the different alleles. C, wild-type, is a capital letter. c, albino, was discovered first of the alleles and thus gets a lowercase c. The other alleles came afterward, and so they are denoted with a superscript. But sometimes our text-editors don’t have superscript capabilities. In this case we might use a carat or drop it altogether.

Here are a few ways to write the marten allele:

• c^m where on the blog this would have a superscript
• c^m the carat denotes that we are “raising” the m up
• cm for speed, especially when we know we’re discussing the C locus.

Typically when we write an allele pair, we don’t use spaces: cc for instance.

However with superscripts it can be a little difficult to read chch or c^hc^h. So you could add a space c^h c^h or ch ch, OR you could use a slash: c^h/c^h, ch / ch.

This works for albino too: c / c.

Just try to be consistent about loci. We’ll see this throughout the blog. For this entry, I’ll switch between the terms so that you get practice with each.

C: wild-type, or no effect. This is completely dominant to all other alleles. If a copy of C is present, none of the other alleles can express themselves. We typically don’t say anything about the C locus then.

c^t: Tonkinese. Points appear, but the rat is overall a dark chocolate type of color (at least, when the Agouti locus shows only black). Tonkinese is simply recessive to C, completely dominant to Siamese and albino, and incomplete dominant to marten. This means that c^tc^t, c^tc^h, and c^tc all look identical, and are called Tonkinese.

c^m: Marten. Phaeomelanin is reduced, the eyes become red, but black pigment (eumelanin) stays relatively dark. Lightening may occur over the lifetime. Marten is incompletely dominant to Tonkinese and Siamese, simply recessive to C, and completely dominant over albino. c^m c^m and c^m c are called Marten, c^m c^h are called pointed marten, and c^m c^t are called Tonkinese marten.

c^h: Siamese. Melanin production becomes more sensitive to heat. On the extremities, pigment remains dark, but on the body it is not produced as well. Siamese is simply recessive to Tonkinese and wild type C, and incompletely dominant to marten and albino. c^h/c^h is called Siamese, c^h/c is called Himalayan, and c^m/c^h (or c^h/c^m, the order doesn’t matter) is called pointed marten. The c^h allele doesn’t change eye color.

c: Albino. Melanin production completely ceases and eyes become red. Albino is simply recessive to everything except Siamese. chc is called Himalayan, and cc is called an albino. (However, it is possible to have a pink-eyed white rat that is not albino).

Even with all of this information, it can be kind of hard to keep track of what each allele in the C locus does and how it interacts with the others. I find it helpful to make a flowchart.

Rat Coat Genetics Part 3

3. Simple recessive traits

Last time we talked about the Agouti locus. The wild-type is completely dominant over the recessive black allele or gene. We also talked about types of dominance. When the trait we care about is recessive and the other allele is completely dominant, we tend to call our recessive trait “simply recessive.” For this portion I’m going to talk about simple recessive traits, but I’m going to concentrate on loci where there are only two alleles (variations of the gene) on the locus. This will give you some practice with completely dominant genes.

It’s now worth talking a little bit about variety names. Rat fanciers exist all over the world, and there are many different gene pools. New alleles and genes are discovered in multiple places, or may only exist in one place. So the name of the variety may vary. I’m using the Rat Variety Guide‘s names for colors, because I’m not affiliated with any particular fancy or club, and the Rat Variety Guide is a great compendium.

• Agouti: A. As discussed last time, affects the striping on the hair. a, the recessive allele, removes striping. aa gives a black rat.

• Brown (Chocolate): B. The recessive allele, b, dilutes eumelanin so that it appears to be brown instead of black.
• Dilute (Russian Blue): D. The recessive allele, d, dilutes all melanin production to a lighter color. Why is it the D locus? Because this gene also exists in other animals, including dogs, horses, and cats. Russian Blue may come from the cat breed the Russian Blue, which is well-known for this color.

• Blue: G. Slightly different type of dilution of melanin from D locus, but the same idea. The quality of the color is different. Keep in mind that in some part of the worlds this may be called “Russian Blue” and the D locus “Blue”. Double check what your standard is.
• Pink Eye Dilution: P. The recessive allele p creates pink eyes and dilutes eumelanin more significantly than phaeomelanin. Also called PED.
• Red/Ruby Eye Dilution: R. The recessive allele r creates ruby eyes and dilutes eumelanin more significantly than phaeomelanin. Slightly darker than pink eyed dilutes on the coat. Also called RED.
• Mock mink: Mo. The recessive allele mo is another kind of dilution.
• Mink: M. The recessive allele m is another kind of dilution.

Other non-colors are also simple recessive:

• Dumbo: Du. This gene affects ear placement. Du is normal ears, du dictates that ears be set lower on the head.
• Dwarf: Dw. This affects growth speed. With two recessive alleles dw, the rat will stop growing and remain small after about 6 weeks.

Some interesting notes about pink and red-eye dilution:

• It seems that if a rat has the genotype pp rr (i.e., it has instructions telling it to produce melanin in a way consistent with both pink-eye and red-eye dilutes), the rat will actually appear to have pink eyes.

Rat Coat Genetics Part 2

2. Dominance and shorthand

I mentioned last time that dominant alleles have “stronger” instructions than recessive ones. Think of them as the person who shouts louder, so it’s easier to be heard. Or who speaks more persuasively. However, there are a few different ways to be dominant:

• complete dominance: alleles like this steamroll over the other alleles (variants of the gene) on the locus and what they say goes. The recessive allele has no expression here.
• incomplete dominance: alleles like this manage to express some of their characteristics, but not all of them, and the recessive allele can shine through a little. One example would be rex fur. One copy of the Re allele will give rex fur; slightly wavy compared to standard fur. (Genotype Re/re), while two copies will give much wavier fur (Re/Re).
• codominance: while I’m not aware of this being in rats, this is like a “compromise” between the alleles. One significant example are Mendel’s pink flowers.
• Recessive alleles need “back-up” to be expressed, so you need two copies.

Dominance types in genetics

Keep in mind that dominance only works if you have at least two alleles to compare! It’s like being taller. You can’t just be “taller”, you have to be taller than something! You might be tall compared to me (5’5″) but short compared to my husband (6’3″). You might be short compared to both of us, or tall compared to both of us.

We tend to use shorthand for the loci, genes, and alleles, using letters and superscripts instead of writing out all the genes. This is because there are so many genes that make up coat color, markings, etc. Let’s take the example of the Agouti locus.

The Agouti locus controls the striping of eumelanin and phaeomelanin on the hair shaft. If you look closely at a hair, you’ll see stripes of red and black running all the way up and down the hair shaft.

In rats, there are two alleles present at this locus (that we know of). The wild-type, A, is completely dominant over the pure black allele, a.

You can remember this shorthand by thinking of “A for agouti. Sewer rats are agoutis, so the agouti type is a capital letter A, and black is the recessive lowercase a.”

Small typo: a is recessive to A in the image, but I wrote a is recessive to a by accident.

Recap:

• What kinds of dominance are there? If you had to have a conversation with each type of allele, how would you characterize them as a person?
• What does a rat with Aa look like? (Think about what kind of dominant the A allele is).
• Breeders often talk about rats having a black-based color or an agouti-based color. If I told you “Russian Blue” is a black-based color, what would the genetics on the Agouti (A) locus look like?

Rat Coat Genetics Part 1

The beginning of a series (of unknown size) on rat genetics. I’ll try to link to all of them at the beginning of this post, or have a table of contents later.

1. Some basic information about pigments and genetics

Rats, as with all mammals I am aware of, have two pigments that are responsible for all of their coat coloration. This is called melanin, and it comes in two types, or “colors”.

• eumelanin (black)
• phaeomelanin (red) (may also be called pheomelanin)

Coat color genes modify the way these pigments are produced, either in terms of their tone (saturation, hue), location on the hair shaft (striped throughout, all over, only on the tip), or existence (say, no eumelanin (black) is produced, or no melanin is produced at all.)

Keep in mind that while eumelanin is “black” and phaeomelanin is “red”, the way they may appear on the rat actually ranges over a spectrum of black to brown to bluish gray for eumelanin, and dark red to orange to light yellow to cream to dusty brown for phaeomelanin. This may sound confusing, but it’s what is responsible for all the beautiful colors we see in the fancy!

Some other important terms before we start: (will modify this for more details)

• chromosome: structure that contains DNA. Mammals have one from each parent (simply said). So in the body, an animal will have multiple pairs of chromosomes. Rats have 21 pairs, one half of each pair from each parent.
• locus (loci): a location on a chromosome where a gene lives (basically a storehouse for some instructions regarding one particular thing)
• genes: a unit of information or instructions that tell the body how to do something (say, make pigment)
• allele: a variant of a gene, basically slightly different instructions for what the body should do (make the pigment THIS way instead of THAT way)

(Note that gene and allele are sometimes used interchangeably)

Depiction of a chrosome, locus, alleles, and how they fit together.

• homozygous: two copies of the same allele on the same locus on each chromosome of the pair (so one chromosome’s locus has one copy, the other chromosome’s locus has another copy of the same allele).
• heterozygous: two different alleles on the same locus on each chromosome.
• dominant: the instructions from an allele are “stronger” than the instructions from any other allele on the locus, and thus are expressed. However there are a few types of dominance, which we’ll get into later.
• recessive: the instructions from an allele are “weaker” than the instructions from another allele on the locus, and thus are NOT expressed unless two copies are present.

Depiction of homozygote and heterozygotes, dominant and recessivve alleles.

Recap:

• Rats have two types of pigments that are responsible for all of their coloration. What are they?
• Color genes in rats can affect the expression of those pigments. What are some of the ways they do that?
• What does it mean to be homozygous?
• What does it mean to be heterozygous?

PCT Day 15 Ziua 15

We are at the laundromat waiting for our laundry to finish being washed. It is a race against time as when we first came in they had no electricity and no idea when it would come back. It is going to be really got today, about 110 to 115 Fahrenheit. So there are 20 minutes left and we are praying there is enough electricity for drying as well.

Suntem la spălătorie așteptând să ni se termine hainele de spălat. Când am ajuns, nu aveau electricitate și ne gândeam serios dacă sa așteptăm sau nu, pentru că se încălzește și vor fi vreo 42 de grade. Teoretic. Deci așteptăm să se termine rufele și ai sperăm să fie destul și pentru uscat.

The first two weeks were okay. The first day was definitely the worst as we were recovering from diarrhea given to us by Derek’s family. Then at the end of that, after I had what I now realize was some kind of anxiety attack, the blisters started, as did the potentially 40 mile stretch without water. The 17 pounds of water we carried up and down hills gave me a lot of foot aches and we were walking at only a mile per hour at one point as I began limping. Derek took the tent and some of my water and I was left with 2 liters while he carried ten. For the first time on the trip, we were evenly matched and I was feeling better, while he started getting some blisters.

Primele două săptămâni au fost ok. Prima zi a fost cea mai rea din cauză că aveam diarrhe de la familia lui Derek. După aceea eu am avut un fel de atac de anxietate, cum spun americanii, și am începe o bucată de 64 de kilometri unde nu este apă naturală. Am carat fiecare 8 litri de apă, adică opt kilograme pe lângă mâncare și haine, și au început să mă doară picioarele îngrozitor, și din cauza bașicilor dar și din cauza mușchilor și oaselor. La un moment dat mergeam la mai puțin de doi kilometri pe oră și Derek a luat cortul și apa mea. Ca urmare el mergea cu 10 litri iar eu doar cu doi. Pentru prima dată în această excursie, mergeam la aproape același ritm. Eu mă simțeam mai bine, iar el era obosit și făcea bășici.

Thankfully the forty mile stretch turned into a 20 mile stretch. Trail angels stock easily accessible locations with up to fifty gallons of water. We’re at the tail end of the season so caches are not being resupplied as often and the water is running out. Its slightly stressful but we’re doing our best to catch up.

Din fericire, cei 64 de kilometri fără apa au fost doar 32. Îngeri de drum, cum li se spune, vin cu mașina la locuri mai ușor accesibile și lasă aproape 200 de litri de apă în sticle. Suntem la sfârșitul sezonului ca urmare “ascunzătorile” de apă se termină și nu mai este așa de multă apă. Este puțin stresant dar încercăm să prindem din urmă.

We have been doing about 15 miles a day in the past week. Every day we wake up and say today will be the 20 mile day but it hasn’t happened yet. Maybe tomorrow- since we’re getting a late start because of the laundromat it will be difficult to get 20 miles.

În ultima săptămână facem vreo 24 kilometri pe zi. În fiecare dimineață ne sculăm și zicem că azi va fi ziua în care mergem 32 de kilometri. Dar încă nu sa întâmplat. Ne trebuiesc 32 de kilometri pe zi ca să terminăm înaintea zăpezii din Washington. Poate mâine. Din cauza rufelor va fi greu să facem 32 de kilometri.

We have done 179 miles.

(There was a fire closure from 5 years ago so we hitched into town for the last 30 miles.)

Pana acum am mers 286 kilometri.

(A fost închisă o parte din drum din cauza unui foc acum cinci ani, deci am stat pe marginea drumului și ne-a luat o femeie foarte drăguță până în Idyllwild pentru ultimii 48 de kilometri.)

Edits and Sophomore Year

It’s almost halfway through the sophomore fall semester at Colgate, and there’s a lot of new updates:

• The Tapestry first draft is finished, edits are going forward.
• I’m going to Wales in Spring 2016
• I’m now officially a mathematics and computer science double major.
• I’m planning a new novel.

The Tapestry

A writer friend read through the entire book and gave me some great critiques for fixing the ending. The book will be ready for beta readers by the beginning of November, then I’ll hopefully have final edits and perhaps another beta finished by February, when I’m hoping to actually publish. But we’ll see. I was going to finish the book completely so many times before this.

The new book

The new book is only just now being planned. It’s based on a Blackfoot Indian legend, and the setting is based in the Arctic. This is actually for a class, and I am outlining the entire novel (or at least creating some type of query package) by the end of the semester.

College

Number theory is fascinating, calculus 2 is boring me, and my other classes range in levels of fascination. More to come, if I feel like it.

Schedules and Procrastination

The good news is that I’m at 55k in The Tapestry. I finished Ivanhoe (you can read my woefully short review by clicking). And The Cherry Orchard by Anton Chekhov. (Unfortunately this one’s review is even shorter). I’m getting up in the morning and exercising about five mornings out of seven. I am making progress in math. My professor recommended The Beginner’s Guide to Mathematical Logic by Raymond M. Smullyan. I am enjoying it thus far—but I move very slowly through it.

About this slowness anyway—when did it start taking me a week to finish a 100 page play? Or a month to get through a 500 page novel that I would have devoured at 15? I was certainly writing much less five years ago, but the gist of it is that I did not have a smartphone, I did not use websites that stream or social media (e.g. Facebook or Snapchat). I did not have friends to message (this may be crucial), and I certainly did not watch YouTube videos. I was also motivated. That may be because schoolwork was boring at the age of fifteen. (Was it?) It may be because I had a greater capacity to focus. It may be because I had fewer distractions. (Scratch that. It’s definitely because I had fewer distractions. And more motivation.)

I still have a great capacity to focus. If it’s something I like, I’ll look up once in two hours. Just last semester I did one particular math problem three times, trying to figure out where 1) my drawing had gone wrong, if it had, 2) where my calculations had gone wrong, if they had. I ended up going to the professor’s office, having basically memorized the problem. I can no longer remember the solution, but I do remember the pure exhaustion after, I kid you not, almost three hours of trying to finish that problem, and when that failed, to move on to another. Unfortunately, I was still very fixated on that problem and it took time to focus on the rest of my homework. It’s obvious that when I want to, I can still focus very well.

The trouble is that typically, I don’t want to start work. I will—and this is embarrassing, but not as much as it should be—look at my computer, know that I’ll be very happy and proud of myself if I finish Chapter 21 of The Tapestry today, and then pass over that in order to—*cough* read a romance novel. (Another good thing? Monday I’m quitting those. For permanent.) Then I beat myself up for the rest of the day for not responding to my professor’s e-mail about “Smullyan’s Problem 6” (Chapter 2, in case anyone is wondering), with a question about “Smullyan’s Problem 10” (Chapter 2 again). When do I get excited about doing work? At about 5pm, when the work day is almost over. In college, my workday will be over by 5pm.

So this has to be fixed—I’m instituting an absolutely no-work rule between the hours of 6pm and 8am. I’m also trying to cut that back to 5pm, and to not work at all on Sundays. 

I’ve tried this before. Then I don’t do any work, to call my own bluff—I resist for about three days, then I cave. Now I’m not going to cave. It’s my grades or working before 5pm. Quitting romance novels will help with that—my schoolwork is going to be fascinating (I’ll make that the subject of another post, perhaps), I have friends that I can talk to at college, and I’ll be finishing the novel. If at any point I’m bored, I have ballroom and belly dancing, and if that isn’t enough, there’s doing more math with the guidance of the math professor via e-mail. Plus minor procrastination. I dislike procrastination. I’m trying to figure out how to ruthlessly curtail it to Sundays, when it’s allowed, and to evenings… when it’s allowed. Will this be hard? Yes, quite.

The plan:

* On Monday, when my SelfControl thing runs out, peruse the list of websites and add more time-wasters to it. Migrate the ones I never want to visit again in my life to the hosts file on my computer. <— This will probably include Netflix

* Stop checking e-mail or reading the news before lunch. <— this morning I spent about 10 minutes longer than needed upstairs because I was reading about Cecil the Lion and trying not to cry.

* Have to-do lists (I’ll make a post at some point about how I use Habitica)

* Have a flexible schedule for the day-to-day. I’ve realized that while I love scheduling things ahead of time, I also really like spontaneity. That may be why I really like Mark Forster’s Final Version (when I actually get around to it). The trouble is when I don’t have enough to populate it with, though I’m certain I could if I went through a trigger list of things I want to do.

* Happy thoughts! This one is a big deal. It works when I’m running on the elliptical*, it should also work for writing.

* I never quite understood this thing called a runner’s high until I ran on an elliptical. I like the quantification I get, and the fact that I don’t have to depend on the weather or people staring. I’ll get over the staring part soon, though.

That’s the plan—tomorrow I start work by 7:30am (I’m preparing for college when distances between buildings are larger—starting earlier while at home means that travel time impacts me less. I hope.)

Trouble with The Tapestry

The alliteration in the title of this post frustrates me a little… partially because I feel as if there should be no alliteration in a grown-up post. But there you go.

I’m rewriting The Tapestry… which is something of a process. I planned out the entire novel (in its entirety! THE WHOLE THING!) in January, in little things called incidents. Which, if you look at the idea, is something like this:

Explanation of Incidents

If Emeli wants to take X action…

A determined/sad/desperate/ridiculously-happy Emeli, after/before/at some period of time, attempts some Big Thing (or small thing, it’s really your choice), and experiences a setback.

^ That thing leads into another incident, either another action incident or… a dilemma incident!

If Yazmeen is deliberating on X problem…

After/before/at some period of time, a perplexed/frustrated/dying-of-hunger Yazmeen needs to make a decision between X and Y thing. After a ridiculous amount of deliberation, a yak butts Yazmeen in the head/some action happens to force him to make a decision.

And onward to another incident!

So that’s the gist of it. Please note that I did not invent it. Rather, Ruv Draba off Scribophile did—or at least, that’s where I got the technique.  I wrote 150 of those little incidents instead of the 50 I’d planned on writing in December, because the book kept expanding (and scaring me). Now I’m faced with actually writing those scenes. I’ve written up to the 42 incident mark… which according to my guesstimations means that the book itself will total about 120,000 words. < This is a scary number. I would have loved this number when I was 15. Now it just tells me it’s a bit too long.

However, even that marvelous discovery does not solve my current problem—the fact that I am now entering the scary middle part of the book, where Emeli, Yazmeen, Margya, and Lizzi (and Nakong!) all have interesting things going on at the same time. I don’t know what I was thinking when I decided to have six adults living in close quarters. I don’t think I’m yet skilled enough to keep them all happy with the amount of screen time they’re getting, nor do I feel as if I know what two-thirds of them are doing at any given time. It may be a writer myth that we’re supposed to know that… because I certainly do not.

The next book will feature fewer mandatory characters.

In any case, the trouble currently is that Emeli has one thing that she needs to prepare, Yazmeen has talks and errands to run, Margya is beginning to get out of the house, Lizzi and Nakong also each have their own deal that must be resolved and is rather a big thing for the rest of the book. And I’m not certain any longer how to fit it into however many chapters I have left.

But! I suppose that probably just requires a small piece of white paper so that I can hammer details out of how I want the next three chapters to go. Thankfully the true hard work was done in January.

Updates

It has been a long time since I posted… hence a few updates before I (try to) post here on a more regular schedule.

College I started (and finished) my first year of college. Soon I’ll declare a mathematics major, and afterward either a computer science major or minor. We’ll see. Thus far I’ve learned Python, first-semester single-variable calculus, and first-semester multivariable calculus. I’m rather annoyed with my math department for not offering a second semester of multivariable calculus, but that’s what studying abroad is for.

Writing Still working on editing Perfume, which I retitled The Tapestry. I’m currently doing a rewrite of the whole book. The entirety has been planned out and I am currently at Chapter 11, at about 29k.

Reading If I had a schedule I’d be behind. As I don’t have a schedule, I can consider that instead I’m woefully unread this year. Currently fighting through Ivanhoe, which would be interesting if I had the patience to sit down and read it in one or two sittings.

Hair I’m growing my hair out and trying to figure out things that make it happy. This includes styles, washing methods, what ingredients work well with it, etc. It’s about 25″ long right now, which puts it at about midback level. Or, according to the LHC’s (and other’s) length markers, about one inch below Bra-Strap Level (BSL). Typically I practice benign neglect with my hair, so I fully anticipate that once the semester starts I’ll forget about it completely.

Languages According to the Parisian language school I went to for two weeks this summer, I’m now at a B2 level in French. I’ll be taking FREN 202 this fall and hopefully that will be at a good level for me… if I’m slightly above where I should be for the class I’m planning on taking Italian. (I’d take Russian or Arabic, honest, but the language will be my fifth course on top of a busy dancing and tutoring schedule, so I’m going for something that will be easier to learn.)

Ballroom Dancing I’m part of the Ballroom Club at Colgate University and am planning to lead it with a good friend by junior year, and just with myself and my dance partner by senior year. So I suppose I ought to start coming up with ideas about now. Thus far I’ve learned enough dances to make it into the auditioned dances.

 

 

Les Trois Mousquetaires en francais, jours 1 et 2 (English)

So! I’ve decided this is the end of the second day’s post, because I have nothing else to do right now.

We were driving in the car today, and for most of it I either slept or read a romance novel, which probably explains the fact that in two days I’ve reached 10%, rather than the 20% I was aiming for.

But, no problem. On the first day, September 7th, it took me about 4 hours and 8 minutes to read 5% of the book. On September 8th, today, it took me 2 hours and 14 minutes to read 5% of the book. The fact that I almost gave up on looking up words in the dictionary may have contributed to this, but I figure it’s also the random French phrases popping around up in my head.

The interesting thing about reading in French is that I have no idea what’s being said. I get the gist of it though, and I know almost exactly what’s happening at any one moment. I just cannot explain to you, word for word, as I could Much Ado About Nothing, what’s going on. Soon, I will, though. When I first read Much Ado About Nothing I thought it was okay. (Now, of course, it’s the best play ever.)