Sometimes lab work is repetitive...

...like today, when I spent the entire day measuring 1 gram of powdered sample into each of these ~120 test tubes:

But now I'm done!! Also, thank goodness for internet radio to listen to in lab!

How to use an XRF machine!

The X-Ray Fluorescence (XRF) machine is super important to those of us doing research on heavy metals in soils. The XRF has a simple purpose: to measure, in a given sample, the concentrations of the various elements. It gives accurate concentration data on most elements in the periodic table. Plus, it's quick to use, requires little sample preparation, and doesn't modify or consume the sample it tests - so the same sample can be used again for subsequent unrelated tests and procedures.

The basic idea behind XRF is to bounce X-rays off of a sample at varying intensities and measure the fluorescence from the different elements present in the sample. The more fluorescence, the higher the concentration. It looks something like this: (credit to www.cat.ernet.in)

You start, as with any test, by prepping the samples. For XRF, it's easy! XRF can be a dry test, so all you need is some soil ground into a fine powder. It's definitely time-consuming, and a little dull, but it doesn't involve lots of careful solution-mixing or anything like that.

A few of our 70+ painstakingly ground soil samples

Once the samples are ready, you need to assemble the containers to hold the samples. The containers need to have transparent bottoms which will interfere minimally with the X-ray fluorescence. For this, we use a special kind of plastic wrap called prolene, which is extremely thin and pure. It's also very delicate and clingy, and you shouldn't touch the part that will actually hold the sample, so it can be tricky to work with.

The container comes in two parts: a tube and a ring. The ring snaps snugly around the bottom of the tube. The tube is placed upside-down in a hole in a small wood plank, which just makes the top of the tube more flush with the surrounding surface, and therefore the prolene film is easier to work with.

Upside--down tube on the left, and ring on the right.

Removing a section of prolene film (carefully!)

The prolene film is placed over the ring. The wooden plank gives it something to cling to so it's easier to work with and doesn't fly away.

Finally, the ring is snapped over the tube, stretching the film across its bottom. There should be no wrinkles or dust on the film.

Once the containers are assembled, labeled, and ready to go, fill the containers with approximately 5 grams of sample each.

Empty assembled containers 

A perfect measurement :)

Then load the samples into the special rack for the XRF machine. The rack spins during analysis to switch samples. Screw the rack into the XRF machine and close the lid tightly to shield from X-rays!

The rack filled with samples

Loaded into the machine

Finally, enter the names and masses of the samples into the XRF software and press "Start". Make sure the helium gas, which is used instead of air to minimize interference, is at the correct flow rate. Check it periodically, and come back in about two hours to remove the samples and get your data!

Here's what the full XRF setup looks like:

Machine on the left and computer/software window on the right. On the left of the screen, the circles on the rack change color from red to yellow to green, indicating (respectively) untested samples, the current sample, and finished samples. On the right of the screen are the names and masses of the samples and some other information about them.

Where are our samples from?

Wuhan, China!

Sam's here!

Today my official mentor Sam, a post-doc, officially arrived with the samples she collected in China. There were kilos and kilos of... well, dirt, and we're going to need to process it all.

The majority, but not all, of the samples Sam brought back

 First we're going to be looking at small cropland samples taken from 69 field sites around Wuhan, China. Each field site has a sample taken at the surface (0-2 cm deep) and one taken approximately 10 cm below the surface. We'll be processing the shallower samples first so that we can get some data as soon as possible.

The samples we're going to process first - deep & shallow samples from 69 field sites around Wuhan, China

 By "processing", I mean that we'll need to take each sample, dry it completely, grind it into a fine powder, and place it into a labeled 50-mL tube.

Large tubes where we'll put the powdered samples after we grind them

From there, we'll be able to use the powder in the XRF machine to get heavy metal concentration data, and we'll be able to perform acid extractions on the powder and run the ICP-MS machine like I did with Sarah to get lead isotope data.

Learning to graph our data in R

The past week has been pretty calm - I haven't been in the lab at all, and we've been waiting for our samples to run and then analyzing the data. Today we finally had our complete data set, so Sarah and I worked on processing some of it in R and graphing it. Hopefully early next week we'll be able to meet with Scott (the PI, or Primary (faculty) Investigator).

In the meantime, I learned how to do some simple data analysis, check correlations, run regressions, and plot some simple graphs! I've only taken one coding class (this past spring), but it was fun to apply some of what I learned there to a completely different kind of project. Here's some of what we worked on today:

Looking at the correlations of various ions

Plots of our calcium-treatment data before removing redundant variables (you can tell there are a lot because many of the plots are straight-looking)

The lithium data had less obvious correlation

Our final calcium plot: the concentration of calcium is shown on the bottom, and the amounts of calcium and arsenic (red) sorbed onto the clay are shown on the y-axis. We had to throw out our last sample, so we don't know what it would look like at equilibrium.

Our final barium plot looks good!

Our final lithium plot shows that lithium probably doesn't help arsenic sorb onto the clay much.

Why clays? A background on my mini-project with Sarah

In order to get clean water, you have to play around in the dirt.

Many people are aware of the horrific rates of arsenic poisoning through drinking water in Southeast Asia. Professor Scott Fendorf and his team have studied this contamination process extensively in Bangladesh and Cambodia. Now my preliminary mentor Sarah is working under Scott studying a similar process closer to home,  in the Orange County Water District. Don't worry - arsenic levels in Southern California are only a tiny, tiny fraction of the levels in Bangladesh. However, a new plant in Orange County uses cleaned and purified wastewater to recharge subterranean aquifers (see the video and diagram below), and water district officials there need to be sure that the recharging process won't bring dissolved arsenic levels above the California standard maximum concentration.

Original video site here

Once wastewater is cleaned and purified, it re-enters the aquifers through two channels: infiltration basins (below, left side) and deep injection (below, right side). The infiltration basins simply allow the water to seep through the ground and into the higher-level aquifer. Below this first aquifer, however, lies a 'confining layer' made up of much less porous materials, particularly our phyllosilicate clays. 

A diagram of the different modes of the aquifer recharge process showing infiltration basins for subsurface aquifer recharge and deep injection for aquifer recharge past the denser confining layer and into the deeper aquifer.

Water must be injected through this confining layer, but the injection process has been shown to liberate some of the arsenic bound to the soil into the groundwater. Scientists at the Orange County Water Department, in collaboration with researchers like Sarah, have cleverly realized that the presence of certain ions in the injected water hampers the dissolution of arsenic into the water during recharge. In other words, if the optimal concentration of ions can be found, those ions can be put into the water during the purification process and the water can essentially shield itself against arsenic as it is injected through the clays.

The current hypothesis Sarah is working with is that positively-charged ions in the water bind weakly to the permanent negative charge on the clays (see this post of mine). This creates a "bridge" by which the negatively-charged arsenic compounds can bind weakly to the clays (called sorption).

Our project now is to figure out which ions are best at creating these bridges. We currently believe that divalent cations, i.e. alkaline earth metals (below - important because they have a 2+ charge rather than 1+) with high charge density (thus, smaller radii) will be best at helping the arsenic to sorb onto the clays and stay out of the water. When we get our data, hopefully we'll have a clue if we're right!

The periodic table helps us to think that beryllium, magnesium, and calcium will help the most at keeping arsenic out of the water.

Figure 1 & 2 Source: Fakhreddine S., Dittmar J., Phipps D., Dadakis J. and Fendorf, S. 2014. “Influence of Calcium and Magnesium on Arsenic Sorption to Phyllosilicate Clays,” In Proceedings of Goldschmidt Annual Meeting, Sacramento, CA.