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Author: Angry Scientist | Views: 615 | Comments: 0

I've been MIA for the last few months. It seems like everything's been piling up lately. I'm going to try to get back on schedule with a post per week. Don't hold me to that though!

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Author: Brian Krueger, PhD | Views: 1570 | Comments: 6
Last by Brian Krueger, PhD on Mar 23, 2012, 9:13am
A quick update on the side project since I'm procrastinating writing a short fellowship grant... About a month ago I realized why my sonications were not working. It turns out that when I moved to Florida from my Graduate work at Iowa, I didn't update my ChIP protocol to reflect a reagent change. At Iowa, we had been using 16% paraformaldehyde as our crosslinking agent. Unfortunately, I was throwing 37% formaldehyde in there instead meaning that I was way over crosslinking my samples which explains why I was having such a hard time shearing the DNA. I practically cemented all of the proteins in the cell together. Anyway, I had some more downtime this week waiting for a new batch of cells to grow for a massive timecourse experiment involving 3 timepoints and 10 different immunoprecipitations for cool proteins. I used this waiting period to optimize sonication conditions with the fancy programmable sonicator.

Misonix 4000, power 60, 30s on 1 min off. Numbers above lanes equals the number of cycles

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Author: Alchemystress | Views: 1731 | Comments: 11
Last by Alchemystress on Jun 08, 2011, 10:26pm
Hello gentle readers… or something. So I know I have been very, very quiet as of late, on twitter, on labspaces, etc. Well, I have had a rough few months, and sort of reclused myself from the world to deal with it all. I had to put everything else on hold and take care of business. My physical friends have seen very little of me as well, but I think I have everything under control now, and have time once again to delve into the world. So here is the low down on my insane life:

I’ve been having a hard time in my lab group. Miss Jade has been more help than I could ever say; I owe her huge thanks because she has been a great sounding board for advice, and I am happy to say I took it and am in a much better place because of it. So first, things in my lab group were getting rough. I know there is snide politics everywhere, but - I wasn’t shielded from any of it (to put it lightly). The work became rather uninteresting, and my capacity as PhD student rode on the line of technician. Plus, we did all research on one instrument and there were 5 of us vying for time on it. No data could be done except on that instrument, and each experiment run to set up etc. would take between 8-12 hours… I am sure at this point you are seeing some of the problems we were having.
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Author: Thomas Joseph | Views: 417 | Comments: 4
Last by JaySeeDub on May 12, 2011, 10:53pm
1. This is one way to get a few vacation days. I suppose. Or would this fall under sick leave?

2. A fool and his money are soon parted.

3. For those finding themselves affected by flooding, take extra precautions against bacterial disease. A study conducted in 2004 (PDF, 8 pages) after flooding in Haiti showed good results from using PuR water treatment systems, though boiling should achieve similar results.

4. You would think that, after the Nick Adenhart tragedy two seasons ago, MLB would get their act together involving DUI charges. Nope, not yet. There is simply no excuse for this.

5. Not a big fan of bed bugs. . . . More
Author: JaniceF | Views: 895 | Comments: 4
Last by Edward on May 21, 2011, 7:08am

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Author: JaniceF | Views: 780 | Comments: 0
Today Canadians go to the polls, in fact, those in Eastern Canada, probably already have voted.  And I am holding my breath.  I will be checking the interwebs frequently today to find out as much information as I can but there is a 73-year old law in Canada that prevents the media from presenting early election results.  Section 329 of the Canada Elections Act says that "no person shall transmit the results or purported result of the vote in an electoral district to the public or another electoral district before the close of all the polling stations in that other electoral district."  This provision essentially means that if I lived in Western Canada I couldn't use the election results of Eastern Canada to influence how I would vote .  This is because Eastern Canada's poll's (Newfoundland and Labrador) close 4 1/2 hrs ahead of Western Canada.

But because the provision was written prior to the invention of the internet and social media, it's unclear whether tweeting results is a transmission of results or simply communication between two individuals.  You can be fined up to $25,000 for transmission of results, but communication between two individuals is not illegal.  Is tweeting transmission?   Elections Canada says it is considered transmission of results i . . . More
Author: Thomas Joseph | Views: 206 | Comments: 0
I'm still around. I promise.

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Author: JaniceF | Views: 1091 | Comments: 2
Last by JaniceF on May 01, 2011, 4:18pm

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Author: JaniceF | Views: 928 | Comments: 2
Last by Brian Krueger, PhD on Apr 28, 2011, 6:40pm

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Author: Brian Krueger, PhD | Views: 1467 | Comments: 1
Last by Brian Krueger, PhD on Apr 24, 2011, 7:31pm
I've been working on this project on and off for a few months now. You may remember my previous post about attempting sonication trials. Unfortunately, things in lab have been busy trying to get a new graduate student started and troubleshooting problems with other experiments so I haven't had as much time to devote to this project as I would like. I've spent the past month or so trying to optimize my sonication conditions on a sonicator that's in my building, and I've gotten less than spectacular results (I've tested at least 10 different conditions on this machine ex: buffers, cell densities, sonication intensity, sonication duration). I'm looking to break my DNA up into short 100-300 base pair fragments and previously I was only able to get them down to about 600. I decided it was time to test other sonicators and here are the results.

Fisher 100 sonic dismembrator vs Misonix 4000 - 1/8" tapered tip.1 mL of RIPA buffer containing 1x107 cells. Numbers above the lanes indicate the number of cycles that were done (30 seconds on 1.5 minutes of rest between cycles)

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Author: JaniceF | Views: 1352 | Comments: 12
Last by JaniceF on Apr 15, 2011, 9:28am
I'm really excited to be joining Labspaces as a blogger. The idea of a social scientific network really appeals to me especially as someone who wants to have a space to discuss scientific concepts and ideas with researchers from very different backgrounds.

Let me introduce myself to you.

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Author: JaySeeDub | Views: 437 | Comments: 2
Last by JaySeeDub on Apr 07, 2011, 7:08pm
It's spring. A time of year that evokes confusing emotions for me. A two month window where I become manic about the weather. On the one hand, I suffer from terrible seasonal allergies and rant and rail about everything from wanting to claw my eyes out and rinse them with TRIS buffer to dreaming about slashing and burning every last plant on the planet. If you follow me on twitter, you may have seen recent rants on the matter. On the other hand, it is also a time where we start to see long stretches of dry weather in Northern California. The threat of constant rain starts to become a distant memory. As April gives way to May, the threat becomes a weirdly hazy memory. Something akin to a nightmare from two nights ago that your mind can no longer grasp or recall. This constant dry period lends itself well to one of those other passions in my life - tennis.

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Author: Thomas Joseph | Views: 493 | Comments: 8
Last by Genomic Repairman on Apr 01, 2011, 10:42pm
... it's time to bid adieu.

As people may have noticed, I haven't been blogging much lately. A lot of it has to do with work -- I'm slammed here writing papers and analyzing data -- but I also haven't been into the scene here at LabSpaces as much lately. There are a number of reasons for my feeling this way, but I don't think I really want to get into them because I do appreciate Brian giving me the opportunity to blog here. He allowed me to bring my backwater blog into the light and get some traffic, and for that I will always be grateful.

However, now it's time to turn over a new leaf. I hope not to bounce around too much (for fear of losing what little readership I have), so I hope that my next stop is my last before I eventually hang up my blogging shoes for good. With that, I'm happy to announce that I will be joining Scientopia!

See you on the flip side!

And when my new digs are ready, I'll come back and post a link.

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Author: Thomas Joseph | Views: 273 | Comments: 0
... in the meantime. The evolution of Apache.

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Author: Thomas Joseph | Views: 756 | Comments: 6
Last by Lavaland on Mar 15, 2011, 1:10pm
So I guess it's my turn to broadcast the results of this hockey pool. A pool that I was doing fairly well in, until Cath made me brag. This resulted in me being jinxed for the remainder of the season. Ok, so I was doing well maybe for the first two weeks of the pool, and the trend is clearly for me to stink it up. In my defense though ... this has always been a Canadian sport, and I'm a fan of the Islanders. Those two things mean I was fated to fail.

Anyways, onto the results.Here are the results for Week 23. dreamsandhope (Chall, correct?) ran away with the point total this week with 42. Richardipus trailed her by 7 to come in 2nd. Cath had 31 for 3rd, and a gaggle of us scored 30 points for the week (ScientistMother, Gerty, and myself) for fourth. Bob scored 28, and Lavaland brought up the rear with 27. Since this is all about me, I didn't really gain any ground this week (again), and tying with Gerty meant I'm still solidly in DFL.

The overall standings? Lavaland's poor showing this week allowed Richardipus to sneak within one point of the lead. Everything else stayed pretty much the same except Chall moved into a tie for 5th with . . . More
Author: Thomas Joseph | Views: 205 | Comments: 2
Last by Thomas Joseph on Mar 14, 2011, 9:16am
My bracket

Click to embiggen.

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Author: Lab Mom | Views: 703 | Comments: 4
Last by Lab Mom on Mar 17, 2011, 10:24pm
Is it just me or does one's affinity for science extend beyond the lab and office? I realized the other day, as I was browsing the bookstore for a new fiction book to read on a long plane ride, that my love of all things nerdy has permeated into my entire life. I don't know why it is, but I can't get enough.

I have mentioned before that of my favorite sitcoms is Big Bang Theory,and I am into [loosely] science-based programming like Mythbusters (controls? Who needs stinkin controls?), Mystery Diagnosis (I LOVE that show if I could just get past my hypochondria), House (I learned it is NEVER Lupus), E.R./Grey's Anatomy (where there is clearly a "sex appeal" screening before being hired as a physician), and Dr.G: Medical Examiner (which reminds us that "every body has a story.")

No, I am not so much a fan of science fiction (think space travel or robotics) but more medical thrillers and scientifi . . . More
Author: Thomas Joseph | Views: 185 | Comments: 1
Last by Suzy on Mar 12, 2011, 12:58pm

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Author: JaySeeDub | Views: 3997 | Comments: 4
Last by JaySeeDub on Mar 12, 2011, 9:40pm
So, I was reminded earlier by Jason Goldman that Monday* is Pi Day. And I mentioned that my favorite kind of pie is shepherd's pie. Added to the fact that Dr. G gave me his copies of Modernist Cuisine, I'm going to be distracted. The next part of Blurring The Lines will be delayed. So yeah. It's recipe time. By the way, these books are nearly 21kg total. People on BART were not happy with me when I brought them back.

Braised Short Ribs

6-8 trimmed short ribsSalt (kosher)Cracked pepper60mL olive oil2 medium onions chopped coarse1 whole celery (about 6 stalks), diced large2 carrots, get the biggest you can, diced large (same size as the celery)1 fennel bulb (remove the fronds and stalks), diced large (same as above)1 large leek (white only), diced large (same as above)5 cloves of garlic, finely minced1 bottle of Burgundy (or Pinot Noir)Fresh rosemary, thyme and 1 bay leaf6 cups beef stock, preferably homemade (can also use water)


Set your oven to 300F . . . More