Monthly Archives: October 2016

Wolbachia PCR and Sequencing

We need a source of Wolbachia for injection into the mosquitoes. Using primers from Simōes et al. (2011) Áki and Maria were able to get these PCR products.


The gel is shown sideways with shorter fragments to the left. Our white[1] stock of Drosophila melanogaster is positive for Wolbachia infection. The Oregon-R stock appears to be uninfected. The Culex mosquitoes collected locally here on Oʻahu also appear to be infected and give a double band. We submitted them for sequencing and the Culex sequence came back very messy---consistent with possible super infection of multiple strains. However, the Drosophila w[1] sequence was clear enough to get a basepair sequence.


Here is the full sequence we recovered.


This appears to be a Group A Wolbachia and is consistent with wMel.

Simōes, P. M., Mialdea, G., Reiss, D., Sagot, M. F., & Charlat, S. (2011). Wolbachia detection: an assessment of standard PCR protocols. Molecular Ecology Resources, 11(3), 567–572.

SEM sponge imaging

Michael Wallstrom and Áki Láruson made some scanning electron microscope images of a new species of marine sponge we are working on (it is associated with invasive algal mats here in Hawai'i). I can't resist sharing a few of them here but I am saving the best for the publication we are working on.


Above is the surface of the sponge. If you look closely you can see the tiny ostia pores in the surface.


A closeup on the ostia, one is in cross section to the interior of the sponge.


Above, you can see two types of cells inside the sponge. The choanocytes use flagella (the threads) to move water through the sponge and filter food particles out of the seawater; amoebocytes crawl around and transport nutrients to other cells (among other functions).


In the above image, at the highest magnification for these images, you can see bacteria that are living in the sponge. The spiral objects are spirochaetes; some of these cause diseases in humans like Lyme disease, syphilis, relapsing fever, and leptospirosis.

New fly head phenotype


An undergrad, Angelina Holcomb, is working on a telomere-aging genetics project in the lab. While setting up crosses she noticed an odd eye phenotype. The two flies at the top of the image have smaller eyes and disrupted head development, along with some other more subtle phenotypes, compared to their sibling controls at the bottom of the image.

EM Algorithm Haikus

In a graduate "Ecology & Evolution" class I am co-teaching this semester I, on a lark, asked the students to write a Haiku on the Expectation-Maximization (EM) algorithm.

I introduced it in class to talk about finding maximum-likelihood answers to some complex problems using a simple approach. Earlier I gave them some homework problems to find answers to by writing EM algorithms in R. We had a midterm exam coming up and there is not enough time in-class for the students to program a new algorithm in R for an exam question. Rather, I asked them to write a Haiku about it to see what they would write and if this gave me any insight into their understanding of the method. I like the results so much I am posting them here.

Data and a guess
Update guess with each cycle
Find the true value.

Hey, start with a guess
then plug it in again and again
and again and again, yay!

Just a few short steps
Almost silly how simple
We find the answer

Find Expectation:
Calculate the Maximum.

Looping, elegant
Throw your guess into the loop
And see what comes out

We must use a guess
As the change becomes smaller
We approach the truth