gene|fish

Antibiotics are used in a wide range of techniques in molecular biology. My aim with this post is to provide an easy reference to some of the main antibiotics used in molecular biology, their mechanisms, range and working concentrations. I hope you will find it useful. If I have missed out an antibiotic that you use routinely in your work, please feel free to contact me or leave a comment and and I will add it to the table. (more…)

(via The Molecular Biology Blog)

OK, so I read this article last week: Rising Seas.  Basically, it says that the oceans will rise 3 feet or so in the next century, thus putting some populated places under water.  Towards the very end of the article, some dude from the U.S. Geological Survey Dept. place/thingy also says that the oceans have risen about a foot in the last 100 years.

Well, on Friday I was walking home after dropping some samples off at the sequencing facility (which is on the Elliot Bay water front) and I passed by an enormous cruise ship.  ENORMOUS! For anyone who hasn’t seen one of these in person, let me tell you.  They are enormous!  Like, 7 stories high and they are the length of like, 5 city blocks.  Do you know how big that is?  It’s, well, enormous!

Anyway, seeing the cruise liner got me thinking about how much water something like that displaces.  Then, that got me thinking about how much total water is currently being displaced by ALL of the boats/ships/tankers/barges that float around the globe along with their respective payloads…  Well, it’s gotta be a TON of water.  And, not a ton literally.  A ton like an enormous amount of water that only skilled mathematicians with patience larger than the Universe (and remember, the Universe is often believed to be infinite) could possibly even bother calculating.

And, when I was blathering on about this to Anne, she even pointed out the fact that there are also thousands of sunken ships that would need to be taken into account as well!  Yikes.  Of course, most of the sunken ships don’t have any air in them, so they wouldn’t be displacing nearly as much water as when they were on top of the ocean instead of the bottom, but still, that’s a lot of wood and metal and treasure chests displacing water down there.

So, what I’m getting at is, is it surprising that the oceans have risen approximately one foot in the last 100 years, which conveniently coincides with the beginning of the Industrial Revolution and the building of larger sea-faring vessels?

Well, that’s all.  I just wonder if “they’ve” (whoever that is?) thought about that aspect of rise in ocean volume over the past 100 years and if they haven’t, does that now throw off their predictions and models for the next 100?

Anyway, this has been Sam, your local “thinker”, saying keep on keepin’ on.

Sam

My PhD is rapidly becoming a distant memory. Before nostalgia completely obscures my recollections of this chapter of my career, I thought I’d jot down some pointers for prospective and current PhD students. These are mainly based on things I wish I had done during my PhD, or mistakes I have seen others make. I hope they’ll make your life easier! If you have any other suggestions, please feel free to chip in with a comment.

(more…)

(via The Molecular Biology Blog)

VIA - Nick at The Molecular Biology Blog: Bitesize Bio

1. You wash your hands before you go to the toilet
2. You tell your family to store the milk “at 4°C”
3. You cry when your cells die
4. you wonder what it would be like to experience ‘death by autoclave’
5. You suddenly realise you’ve been using sterile technique when opening a jar of mayo
6. You can tell the OD of your culture just by the smell
7. You can’t watch CSI without cursing at least one scientific inaccuracy
8. You’ve worked out that a trained chimp could probably do 90% of your job
9. You are strangely proud of the collection of junk you’ve stolen from vendors at trade shows
10. You can no longer spell normal words but have no trouble with spelling things like immunohistochemistry or deoxyribonucleic acid

Literally!! Walked into lab this morning and noticed the aroma of rotting flesh permeating both labs. No doubt this could only be related to the baby-eating spider. Obviously it claimed another victim over the weekend.

I’ll tell you what, though, that smell is disgusting! Trying to set up a bunch of PCR reactions while breathing only through your mouth or gagging periodically when you take a breath through you nose makes for an interesting morning. Luckily, it appears as though our resident baby-eating spider has been around for quite some time, as Ted (a long time professor in our building) suggested that pouring some water into the drains in the floor of our labs would eliminate the odor. Low and behold, it worked! Good thing, too, because I was to the point of rigging up a breathing apparatus whereby I would strap my shoe over my mouth and nose. Hey, that would have been WAY better than the smell of decay!

Before I get too into what’s happening this week, I’ll get back to last week. I know many of you out in cyberspace are dying to know what ended up happening with all the cloning craziness. Well, with the help of a virtual martian stress doll

as well as some different competent cells, everything ended up coming out perfectly! I still don’t know what the problem was before, but there are some suspects that I’ll be looking into this week. And, yes, Carmen Sandiego is indeed one of them. Where in the world can she be? I’ll have to look at my dosier on her and see what I can figure out. However, I think it’s going to be a lengthy search, seeing that she hasn’t been seen in public since I was in 3rd grade.

I also discovered last week that if your PCR reactions happen to evaporate leaving a viscous, un-pipettable goo in your tubes, just go ahead and reconstitute the samples with some water and you’re good to go! I guess this means we can probably throw away all of our sealing films and strip caps and save some dough!

Oh, I nearly forgot. I was alerted to the presence of some graffiti in our building last week. To document it in case I need to go across the street to talk to the po-po, I took a picture. Here it is:

Nice. A real weisenheimer. Vandal! Plus, I got clones at the end of the week anyway, so there! Again, Carmen Sandiego is a prime suspect. Additionally, I have a sneaking suspicion that my own boss may have had a role in it. Don’t believe it? I know, at first I was appalled at myself for even thinking it. But, when I showed it to him, the way he laughed about it for 5 minutes really got me thinking…

Anyway, this week, despite it’s literal nasty stench, is actually going quite well. We started the week off with a field trip, errr, I mean, research outing to Big Beef Creek. So, here are some pics from the day:

Hey, Steven, what’s up with the white boots, m’ man? It’s way after Labor Day. You gotta just let it go. Spring will be here soon enough. Oh, and for the readers, all the brown “rocks” that you see here are oysters!

We saw lots of hungry star fish, so that was pretty neat. After eating all those oysters and then once that salt water dries on you, your lips probably would get pretty dried out.

So, I offered up some Chapstick, but I think the star fish was probably in a tryptophan-induced coma-type thingy after devouring so many oysters because it didn’t even try to reach for the tube. Oh well, all I know is my lips weren’t dry and cracked!

For lunch, Steven went into the forest and, to my surprise and delight, emerged with a large, 10 point stag. Well, as you can see from the picture, we devoured that sucker! Nothing like a little venison to munch on for lunch. That fatty, Samwise Gamgee, would’ve been REAL jealous!

So, the week’s well under way. Going to work out the kinks on a few “problem” genes for cloning and then get some yeast co-transformations going as well. All in all, it’ll be a pretty productive week that should yield some good “stuff.”

Sam