Wednesday, July 27, 2011

Cat Whiskers

I'd thought I'd remain far from the realm of animal research here in crystallography land. I don't oppose it, but don't have the constitution for some of it. Today I discovered that we need cat whiskers for a couple specific techniques. I was thinking for a while they were some kind of plastic filament, but no. Actual whiskers off a cat.  After being traumatized about this for a bit, I learned from my lab mate that the whiskers are reusable (unlike everything else in this field, but that's a different rant). Also he harvests them from his own cat, who tends to leave them on the bed while sleeping.


Preparing a dilution series of the seed stock makes it more quantitative, but by far the easiest and fastest method for seed transfer is streak seeding. This method uses an animal whisker (usually cat or rabbit) as a seeding wand, which is touched or stroked over the surface of the parent crystal to dislodge and trap the nuclei.  The whisker is then drawn through the new drop, depositing the seeds in a streak line. Although seeding wands have been made from thin glass rods, platinum-wire inoculation loops, and acupuncture needles, animal whiskers or hairs offer a definite advantage. The overlapping cuticles capture the seeds effectively. Here we would like to bring attention to an animal source of material for making seeding wands which, at least to our knowledge, has not been exploited much by the crystallization community.  Horse tail hair is much more abundant than most animal whiskers, which makes it useful when organizing large scale laboratory sessions.  In addition, horse tail hairs maintain the same thickness throughout their length (which is why violin bow makers use it), and this property may be useful in its own right for reproducibility in seed transfer. On the other hand, a cat whicker can be cut into three or four segments to obtain wands of different thickness.  We use both horse tail hairs and cat whiskers because of their complementary properties. We find that rabbit whiskers, being thinner than both horse hair and cat whiskers, are too flexible.

--Therese Bergfors. Seeds to crystals. Journal of Structural Biology, 2003.

Tuesday, July 19, 2011

Learning from your mistakes, directly

Checked my first crystallization plates today. Lots of precipitant; 70% methanol was not the answer (only 1/4 of wells down, no biggie). No crystals in most of the other wells yet, except one. One that I messed up.

That particular well I didn't seal very well, so it dehydrated. This concentrates the protein, inducing crystallization as the solution grow saturated. These might be usable for microseeding future trials.

The other wells may still form crystals, given some time. The other answer may be to poke holes in the seals and let them dehydrate too. The real answer is do it all over again and use a higher concentration.

Being science, will try all of them, as only one really needs to work.



Monday, July 18, 2011

The happiest place on earth

Today I head up to get my badge to the happiest place on earth, the synchrotron. Many shouts or eureka! And no small number of mumbled "that's funny"'s.

Saturday, July 16, 2011

Milestone: Potato is Sequenced

In amusing science news, scientists have sequenced the potato!

  • 884 megabases, or roughly 1/4 of the human genome, at 86% completion.
  • 40k predicted genes, which is a bit higher than that originally predicted for humans, and twice what is currently accepted for humans. This number was confirmed by RNA-Seq, meaning these genes were actually expressed as mRNA, so are likely real.
  • About 25% of genes are alternatively spiced, compared to 50% of human genes.
  • two genome duplications
  • autotetraploid, so have 4 copies of each chromosome, leading to some difficulties with breeding
  • 3k genes which define the potato family 
  • "acute inbreeding depression", meaning it's suffering intense problems like disease susceptibility because of how long we've been mono-farming the original few strains imported to Europe from South America.
  • >62.2% of the genome is repetitive and will likely make the remaining 14% of the genome hard to sequence.

There are of course many other bewildering things about the plant, as seems to be the case in general in plant biology. Mendel was very lucky to study the particular traits in a particular species that managed to behave according to simple (Mendelian) genetics.  Many other plant quirks take some getting used to.

Friday, July 15, 2011

The experiments begin

Yesterday I started pipetting! First time in 4-5 years. So far I've managed to acquire most of the basic instruments, have a bench and fridge space, pulled a few chemicals out, and started mixing. Spent a lot of quality time with the micro pH machine getting my samples titrated. I spent even more time figuring out how to recalculate pH from several conditions, and eventually got it down well enough to write some code to do it for me. Now I need to go back to the pH meter and see how close I got. Monday I get to throw it all in crystal trays and the the real test will happen, though no results for a week or so. This is a slow feedback loop. Nothing else too exciting today, but hopefully good times this weekend.

Location:7th Ave,Oakland,United States

Wednesday, July 13, 2011

So many stupid questions

For the past couple days I've been struggling with noob questions. This is to be expected, but not questioning your whole understanding of acid/base chemistry. I found several protocols for crystalizing my protein, all fortunately starting with just ordering it from the Internet, as my protein is readily available. (usually there is weeks to months of ramp up time depending on what you can borrow from other scientists.)

The next steps are to dissolve the lyopholized protein powder in distilled water, then adjust the pH to 5.5 using NaOH, also known as sodium hydroxide or lye. A strong base... pH 14 at 1M concentration, for those who forget how pH works. Now, normal water starts at pH 7, so how am I going to add 14 to 7 and get 5.5?

I thought I had the answer as I'm also supposed to mix in 50% methanol. pH is only well defined in water, so I spent hours looking up how organic solvents affected "apparent" pH and doing a deep literature search and generally questioning my sophomore chemisty.

Finally, team leader reads the methods, laughs at me, and points out that proteins are quite acidic and I had to compensate that. I had briefly considered this, but naively assumed that they wouldn't be THAT acidic. Shows what I know.

Er, trust me, I'm a professional.

Better Living Through Chemistry

Welcome. I should begin in the grand tradition of first posts by laying out my grand vision of what you'll find in these pixels.  Really, it'd be as much to my benefit as to you. I'm curious to see what comes of it, or if it lasts more than a month.  I have a personal homework assignment of posting at least once a week, which definitely is to my benefit.

Last week I started a postdoc with [prestigious lab] at [even more prestigious university]. Astute readers will likely be able to sort out these details. I'll preserve my anonymity beyond that as I was raised in the internet age. This is going to be a professional blog and shouldn't contain anything incriminating or indiscrete.  But you never know when your coworkers will take offense at you pointing out their foibles to an audience of at least...ones of your friends.

Back to the prestigious university part, if you can't figure out who I am, you can at least trust that I am very good at what I do, even if I don't know much about what I'll be doing yet. I'm also very good at figuring things out. That's half the fun. So my opinions on the matters at blog will be at least reasonably well informed or annotated for speculation. At least in regards to science.
"I believe that a scientist looking at nonscientific problems is just as dumb as the next guy."  -  Richard P Feynman
Back to the vision, I'm going with three parts:

  1. Talk about my daily experience with science, especially adapting the the new position and relearning my field.
  2. Talk about science in general, and what's cool in the world.
  3. Talk about the sociology of science: how it's done, how it's perceived, and whether it works.
There are innumerable blogs on these topics already, you are by no means obliged to care about this one.


Adios,
-Alex