Genome papers published: Brachybacterium muris UCD-AY4 and Microbacterium sp UCD-TDU

When we first started this genome sequencing project in Jan 2012 we had hopes of wrapping up the project by Spring and getting the papers out that summer.   Turns out it was a bit more complicated than we thought.   The first two papers, by Jonathon and Zach, came out today.  The other 4 are in various stages of processing (waiting on GenBank).

Congrats guys!


Advice on asking for letters of recommendation (updated May 2013)

This is based off an e-mail I sent recently to a student and someone suggested I post it here:

Asking for letters of recommendation

In general I, and others are happy to write letters of recommendation for people… it’s part of our jobs after all.  However, there are some tips I would offer anyone soliciting letters at any stage of their career.

1)  Don’t ask me for a letter only a few days before it’s due.  This seems like such a simple concept but one that is violated so often.

2)  If you ask me for a letter, you need to send a copy of your CV.  No matter how long I’ve worked with you, there’s probably still information in there I didn’t know and this helps me write a letter that doesn’t sound like a form letter.

3) Send me a description of the program you’re applying for and why.  Again, this helps me write a better letter and doesn’t force me to have to trawl the internet for information

4) Make it as easy as possible for me to write the letter!  This is especially critical with professors.  If the letter needs to be mailed, you should hand me a stamped, already addressed envelope so all I have to do is drop in a letter and throw it in the outgoing mail.  If it’s an electronic form provide me with detailed instructions and links.

5) Don’t attempt to bribe me.  I’m not kidding… for example once I got a handwritten request for a letter of recommendation along with $50.  This is not a good idea!

(Updated with two more in May 2013)

6) Before asking a post-doc or a project scientist for a letter of recommendation make sure that you don’t actually need one from the professor.

7) Don’t list me as a reference for anything without at least asking first.

Water Chemistry Sampling: Our kit list

A couple of people have requested that I post information on the various kits and probes being used to assay water chemistry for our aquarium study.  Here’s the list, divided by type with a link to each item on Amazon.  Also various user complaints.


pH  (worked fine, held calibration well)

Salinity (worked fine, held calibration well)

Temperature (annoying, a bit fiddly, I wouldn’t do this one again)

Titration-based kits:

Hardness, Alkalinity, Chloride, and Sulfide were all measured using this combo package  It also includes an iron assay that we didn’t use.  All of these kits are prone to error since they’re titration based.   But used very carefully (takes time!) they seemed to produce okay results.  I recommend using glass flasks instead of the plastic beakers supplied.

Colorimetric scanners:

Dissolved oxygen (this kit requires that you have a glass container capable of holding exactly 60 mls of water.. they don’t tell you this until you read the instructions.  Otherwise worked fine.  A bit hard to use but conversely you’ll learn new vocabulary from reading the instructions)

Ammonia (worked fine, but you have to be very careful to follow the instructions and mix between adding reagents or you’ll get a false high reading)

Nitrate (worked fine)

Nitrite (this one is pretty annoying; it’s hard to get the reagents into the tiny vial and these handheld meters turn themselves off after only 2 minute so if you get distracted you have to start over)

Phosphorus (see nitrite, but even worse.  As far as we can tell it’s not even possible to follow the instructions for this since it turns itself off before you finish mixing the reagents)

Water Chemistry 10 Commandments

So for this aquarium project we have been doing a ton of water chemistry (over 50 hours so far).  Along the way we’ve learned a number of lessons the hard way and so have written up a set of “Water Chemistry 10 Commandments”.  I’m posting them here for both the current students or for anyone else doing water chemistry analysis.

1. Wear gloves! (seriously… reagents include mercury, corrosives, and carcinogens)

2. Double-check all reagents!!! For example “sulfuric acid” ≠ “sulfamic acid”.  Likewise “phosphorus” ≠ “phosphate”.

3. Be sure your measurement is within the range of the test.

4. Be sure to keep track of “ppm” versus “ppb”!

5. Replace the cap of each solution immediately! Spills are expensive, hazardous, and annoying.

6. Rinse all glassware with the sample to be measured before conducting an assay

7. Always rinse everything between measurements and assays.   The pH meter should be rinsed in tapwater, everything else should be rinsed in DI water.

8. Dilutions should be performed with DI water.  Be sure to measure the concentration of whatever you’re testing in the DI water first so that you can subtract the background.  The blank needs to be of the diluted solution as well!

9. Keep cuvettes clean!  Clean before each use… wipe with a Kimwipe immediately before placing in detector.

10. If you get an anomalous measurement: do it again twice more.  Sometimes things really do change but if you’ve been getting ammonia measurements between .5ppm and 1ppm for days and then all of a sudden you see 25ppm… it’s worth making absolutely sure!

Preliminary Nitrite/Nitrate data just for fun

Since we’ve been collecting all this water chemistry data I thought it’d be nice to share a bit of it.   Here you can see the nitrate and nitrate levels in Coral Pond #1 over a couple of weeks.  Levels start out low, then rise in the newly established system right up until inoculation with an stable microbial community.  At that point the nitrites head back down quickly and the nitrates continue to rise.  So question for the undergrads on the project:  Is this what we expect or not?   Why would we see this pattern?


A tale of two stoppers (one of which is a rip-off)

For the water filtration we’ve been using Supor PES membrane filters (.1um), supported using a fancy filter holder from Millipore. (both recommended by Laura Sauder from the University of Waterloo).  So far this setup has worked pretty well, although obviously a bit slow when there’s a lot of sediment in the water.   However, last night the rubber stopper that holds the thing together cracked and got sucked into the vacuum flask.  Which is pretty much a one-way trip… It’ll probably stay there forever.   So I looked at the Millipore website and they want $100 + shipping for a replacement stopper!   It’s a piece of rubber (well silicone actually) with a hole in it.  Sheesh.

So after consulting with Russell in our lab, he directed me to Central Services on campus where I bought a rubber stopper for $1.05 and they drilled the hole for free.   As a bonus, it actually fits better and is easier to use than the one that costs one hundred times as much from Millipore.

Follow the pH meter on Twitter

As part of the environmental monitoring of the coral ponds that we’re going to undertake Russell has agreed to loan us his famous tweeting pH meter.   Right now it’s just practicing in a freshwater tank at the facility but soon it will go into the first coral pond and we’ll get a continuous record of pH over the course of the project.   Follow along on Twitter @RussellspHMeter