Unpacking

IMG_3079
Putting together packaged furniture while the cats observe.

Unpacking boxes takes an awful lot of work.

My in-laws had come up just to help with the big furniture. After they left we were still left bunches of boxes to unpack.

Additionally, we hadn’t fully moved out of our old apartment. We have a lease that extends until the end of August. There are ways to get out of the lease, but moving somewhere else isn’t really one of them.

We have the option to sublease, but there are tons of people that want to sublease during the summer in Davis. We don’t even have the added benefit of offering a continuation of the lease past August because our apartment complex already found someone for that slot.

So why didn’t we wait until we’d finished the apartment lease before moving into a new home?

It’s mostly because the home is way bigger and a better place to live in. We thought about it prior to moving. Either way we end up paying the same amount of money. The apartment lease is for X amount of months whether we stay in it or not. The house we buy/bought will be Y amount of dollars whether we buy it in March or August.

So we’re not actually paying anymore money than if we’d stayed in the apartment until August. We have to pay MORE now, sure, but the total amount is the same.

I’ve got a decent amount saved up, so paying more now isn’t a huge inconvenience.

In exchange for paying more now we get to live in the house six months earlier. Woohoo!

Living in the new house includes many beneifts, most of which are related to choosing how our new house will be set up.

We get to decide where everything goes in our kitchen and the garage. We get to pick out plants to grow in the backyard. We get to pick out art to go on the walls or to present on shelves. We get to print out more pictures to put on our walls. We get to find places to put all the cat stuff. Stuff that never had a “place” at the old apartment (my wife’s shoes) get a whole new piece of furniture devoted to them.

All the new stuff is super great! And we get to blast music and stomp on the floor and not worry about offending our neighbors anymore. Nobody lives directly under or beside us.

Taking out the trash isn’t a huge trek across the parking lot (100 yards feels huge when you’re carrying 50+ pounds!). The laundry machines are much closer and I don’t have to hoard quarters like a lunatic anymore.

So many cool new things and this is only the beginning!

-GoCorral

My Master’s Project

All labwork is overseen by the disembodied head of Muppet lab assistant, Beaker.
All labwork is overseen by the disembodied head of Muppet lab assistant, Beaker.

I have begun my Master’s project in earnest and the goal is slightly different than what I’d been doing before.

First, I’ll repeat myself. I’m a biologist and I work with introns in C. elegans. C. elegans is a type of nematode worm that naturally lives in soil or on rotting vegetables. It is also one of the most widely used model organisms for biological research.

Worms! Ew! Gross!
Worms! Ew! Gross!

Introns are unused sections of genes. You’re probably aware that DNA is in our cells and contains the instructions for how an organism functions. The human genome contains around 25,000 genes and those genes are split into two parts, introns and exons.

Exons are the part of that gene that are actually used to produce things in your cells, while introns are spliced out and removed. So why are introns on there at all if they’re removed?

Well it turns out that some introns increase expression of the genes they’re in. My project looks at how placement of those enhancing introns affects expression.

Experiments in plants have shown that an enhancing intron works best when it is placed near the start of a gene. Experiments in C. elegans have suggested that, but no experiment has outright proved it. My project will hopefully do that.

I’m measuring the expression of genes according to how introns affect them, so I get to pick which gene to use. When picking a gene like this scientists often pick what are called reporter genes. The expression of these types of genes is easy to measure, often because they have produce light or fluorescence of some kind. The light tells you whether the gene is on, but also at what level it is turned on based on how bright the cell is.

Previously I was using a reporter gene called GUS. GUS is an enzyme that digests a specially prepared sugar, releasing a blue chemical that was attached to that sugar. The blue chemical is then visible to the naked eye.

There were a number of problems with that experiment though. First, adding the sugar chemical to the worms was a pain, taking about three days to set up and look at. Plus, the blue color was difficult to measure precisely because most of the machines in the lab are set up to measure red or green colors, not blue. Finally, GUS is traditionally a reporter gene for plants, not C. elegans. This could’ve been introducing other problems that we couldn’t easily identify. Thus the use of the GUS reporter gene has been scrapped in favor of another reporter gene.

I’ll be using Green Fluorescent Protein (GFP) as my reporter gene now. GFP is widely used in C. elegans and many other organisms. The protein created by the GFP gene glows green when you shine a red light on it. Very easy to see and measure. None of that three day procedure for GUS. I just pop the worms under the light and take a look.

Why weren’t we using this procedure before if it’s so easy? Two reasons!

Reason number one: C. elegans won’t express GFP without introns in the gene. So does that mean we proceed and hope one intron is enough or do we add the standard amount of introns to get expression? I’ve decided to see what the GFP looks like with the standard introns scientists put in it for C. elegans and without them. I’ll also be testing with an added intron. The whole thing is a little complicated so here’s a diagram to explain.

Here are the constructs I've been creating. The wide parts are exons and the thing parts are introns. The green bands are the GFP which will glow green in the worms. The white bands are a scaffold which allow the worms to express GFP
Here are the constructs I’ve been creating. The wide parts are exons and the thing parts are introns. The green bands are the GFP which will glow green in the worms. The white bands are a scaffold which allow the worms to express GFP.

There are eight different constructs I’m making. They are a combination of three different features that are present or not. Are there introns in the first GFP? Yes or no? The second GFP? And is the Unc54 intron there? This allows us to control for the positional effect the standard introns in C. elegans GFP.

Reason number two: Those eight constructs above? Those aren’t made yet! All the GUS constructs were made when I started the project. I’ve been working on making the new constructs for a few months. It could take a few more months to finish.

So my project is to make those constructs, put them into worms, and then see what the worms look like. As I perform these steps I’ll make more posts about what work I’m doing in lab and why its so cool.

-Mister Ed

Heroic Thaddius

The DREAM!
Misdirection. The DREAM!

Continuing in the series of posts about how to beat the Heroic bosses in Hearthstone’s Naxxramas adventure, here’s Thaddius!

Heroic Thaddius has two advantages over Normal Thaddius.

First, he’s got 15 more health than the Normal version.

Second, on his first turn he automatically summons his own Feugen and Stalagg.

While he may start with two immense monsters, the good news is that they can’t attack on the turn he summons them and they don’t trigger their own deathrattles.

Even better, Thaddius’ Feugen and Stalagg will trigger your own versions of those minions. So if his Feugen has died and your Stalagg dies, then Thaddius is summoned to your side of the field.

Thaddius starts with a big advantage and this is the deck I came up with to remove that advantage as quickly as possible:
Hunter’s Mark x2
Arcane Shot x2
Tracking x2
Webspinner x2
Explosive Trap x2
Freezing Trap x2
Misdirection x2
Mad Scientist x2
Nerubian Egg x2
Eaglehorn Bow
Animal Companion x2
Deadly Shot x2
Unleash the Hounds x2
Multishot x2
Feugen
Stalagg
Kel’Thuzad

The ideal hand includes a Misdirection or a Tracking. You go first and play the Tracking if you need to find a Misdirection.

Thaddius goes second and summons Feugen and Stalagg.

Your turn comes around again and you play Misdirection.

Thaddius goes. He plays a minion and then attacks with Feugen and Stalagg. The Misdirection triggers and you pray that the two beasties kill each other. It’s a 1/3 chance that they will.

And that’s it. The deck has a few other methods for removing Feugen and Stalagg. Then it stalls the game out with secrets until you can gain complete control with a big Unleash the Hounds combo or by playing your own Feugen and Stalagg and getting a huge Thaddius on your side.

Really once you’ve got a Thaddius on the board you’ve probably won.

Other things that work really well against Heroic Thaddius are Nerubian Egg, Dire Wolf Alpha, Raid Leader, and Stormwind Champion.

Thaddius’ Polarity Shift hero power will always trigger Nerubian Egg, making it a cheap 4/4.

The Polarity Shift also interacts strangely with buffs that the other three cards have. The buffed attack (or attack and defense for Stormwind) is switched to defense, creating a permanent gain in stats. Then the buff is applied to the attack once again. If it keeps switching then your minions keep getting more stats. Leokk from the Animal Companion spell also takes advantage of this effect.

Cards to avoid against Thaddius are ones with zero attack. The Shaman is pretty bad because his hero power will be close to useless. Flametongue Totem will have the same swapping power that Dire Wolf Alpha does, but it dies in the process.

Regardless, the Hunter deck works and isn’t too expensive to craft. Plus, secrets are always fun!

-Mister Ed

Naxxramas Construct Quarter

My Mage deck for taking down Heroic Patchwerk.
My Mage deck for taking down Heroic Patchwerk.

I did a Twitch stream on August 15th of the new Construct Quarter in Naxxramas. The stream will be available for a limited time on the GoCorral channel at Twitch if you want to watch.

I wasn’t able to finish all the bosses and class challenges this time. Mostly because the class challenges weren’t knock over easy anymore. I tried about a half dozen times on the Warrior challenge and had to end the stream defeated.

Later on I took a crack at the Heroic bosses and I took down Patchwerk on my first try with the deck pictured above.

If your eyes/computer can’t process pictures the decklist is:
Ice Lance x2
Mirror Image x2
Frostbolt x2
Mad Scientist x2
Murloc Tidehunter x2
Sunfury Protector x2
Arcane Intellect x2
Duplicate x2
Ice Barrier x2
Ice Block x2
Kirin Tor Mage x2
Fireball x2
Water Elemental x2
Sludge Belcher x2
Pyroblast x2

Patchwerk is the most unusual Naxxramas boss so far. He doesn’t have a deck.

All Patchwerk has is a weapon that he starts with and his hero power.

Patchwerk’s weapon, Hook, has a deathrattle effect that puts it back in his hand so he can play it again.

His hero power costs 4 and destroys one minion of Patchwerk’s choice. He’ll always pick a taunt minion or your strongest minion.

Patchwerk’s turn is easy to predict. If his Hook is in his hand he’ll play it. Next he uses his hero power if he has enough mana to do so to destroy the largest taunt minion you have or if there are no taunt minions, your largest minion without taunt. Finally, Patchwerk attacks your taunt minions or your face.

The only difference between the Normal and Heroic version of Patchwerk is the Hook. The Normal Hook has 5 attack and 8 durability. The Heroic Hook has 4 attack, 8 durability, and windfury so he can attack twice per turn.

So fiendish! So devilish! The Hook of Patchwerk!
So fiendish! So devilish! The Hook of Patchwerk!

A game against Patchwerk won’t take very long because his strategy focuses on hitting you in the face instead of clearing the board.

The deck I made is focused around freezing Patchwerk or stalling him with weak minions.

I won my first game against him by playing Mirror Image early, and then a Kirin Tor Mage to get a Duplicate secret down as well.

Patchwerk wiped out the Mirror Images, but the Duplicate put two more of them in my hand to stall him even further.

I used my Sunfury Protector, Murloc Tidehunter, and Sludge Belcher to stall further with other cheap taunt creatures while my Kirin Tor Mage hit Patchwerk for damage every turn.

Patchwerk hurt himself by using his Hook to take out my minions, but he was never smart enough to use his hero power to destroy the Kirin Tor Mage that was slowly murdering him.

I played two Ice Blocks to stall further and I had an Ice Barrier in hand to last another turn as well.

Another strategy of the deck is to get a Water Elemental down along with some taunts. The Water Elemental will keep Patchwerk frozen and unable to attack while the taunts will soak up the hero power instead of the Water Elemental. If you get that strategy going, you’re guaranteed a win.

Things I might change about this deck if you’re trying to build it or something similar include:
Taking out the Pyroblasts. The game ended on turn 9. Usually you won’t get a chance to use one.
Taking out Arcane Intellect maybe?
Adding Defender of Argus and Razorfen Hunter to have access to even more taunt creatures
Maybe adding cards like Dancing Swords and Coldlight Oracle to force Patchwerk to draw and hurt himself with fatigue damage.

I hope that helps you take down Patchwerk! I’ll be working on other decks to beat other Heroic bosses in the Construct Quarter soon.

-Mister Ed

My Lab Meeting

Here's a picture of one of my PowerPoint slides from today's lab presentation.
Here’s a picture of one of my PowerPoint slides from today’s lab presentation.

I presented the progress on my research at lab meeting today.

I haven’t gotten as far as I wanted to since my last lab meeting, but I did get as far as I expected to.

By the end of the summer I was expecting to have 5 of the 6 constructs successfully injected and integrated into C. elegans strains.

I’ve gotten 4 out of the 6 and the summer isn’t over yet. I’m on track to finish.

Otherwise, I’ve had a problem with the worms not staining like the ones of the person who used to work on this project.

His worms stained extremely dark. There’s so much blue color that the picture of them looks black.

My worms don’t look like that, but we aren’t sure why.

I’m going to tweak some things to try and make my strains look that way.

If the tweaks don’t work… I’ll have to check using a more complicated method to ensure that I injected the worms correctly.

That’s the gist of what I presented at the meeting.

The meeting went pretty well.

Today’s meeting was between my lab and the lab adjacent to us.

Our lab meetings are always joint meetings. The neighboring lab works on similar stuff. Both of us are small labs as well so it makes a lot of sense for us to meet together.

The professor from the other lab always asks the presenter tough questions.

I felt like I fielded everyone of his questions really well.

I felt prepared, I had answers to most of his questions.

I’m going to look for answers to the questions I don’t know in research papers.

I haven’t gotten around to describing more about what I do in lab, which might have made this post a little confusing.

I’ll try and upload a post that goes in more depth for my lab meeting presentation in the future.

That’s all for tonight.

-Mister Ed