Monday, November 10, 2014

Fall 2014 Lightning Journal Club - Part 1

We have a variety of formats for lab meeting. One of them is a lightening journal club, where each person shares one paper from an assigned journal, including one question and one comment about the paper. This allows us to get a snapshot of research that is interesting to people in the lab. By posting it here, we can also allow the space for continued discussion. I have not edited the Comments or Questions that were sent to me by the members of the lab. The "Lab Thoughts" are our brief comments from lab meeting in response to the paper/question. This is the first group of papers we discussed at lab meeting last week:

"Big data and other challenges in the quest for orthologs"
Sonnhammer et al., 2014
It does seem, that until the computational capacities catch up to the demand that a viable temporary solution is analyzing smaller, easily-managed sets of data and compiling the results. However, this would result in a decreased confidence in the determined relationships. 
To work around computational demands in sequence analysis the Similarity Matrix of Protein project (SIMAP) utilized user-volunteered computing. They have used this method for the past 10 years, but are now returning to ‘in-house’ computations; what changed that would warrant this shift? There are still high computational demands, so after 10 years what are the drawbacks of user-volunteered computing that would cause them to return to in-house computations? (pg. 2994)
Lab Thoughts:
Perhaps the computing is taking up more RAM than it was in the past. So, previously user-volunteered computers would be sufficient for the analysis, but now there is need for higher-RAM processors.

BMC Bioinformatics
"MoTeX-II: Structured MoTif extraction from large-scale datasets"
Pissis, 2014
Comment:I find it impressive that this tool is able to speed up current motif extraction by about 7 times. 
Question: How well would this program run on a normal computer? Could it be run efficiently using the cloud?
Lab Thoughts:From the paper, "We implemented MoTeX-II in three flavors: a standard CPU version; an OpenMP version; and an MPI version. " Thus, it seems like the program can definitely run on the CPU capacity of a desktop, but there are also versions that require more computing power.

British Journal of Cancer
"Notch-induced transcription factors are predictive of survival and 5-fluorouracil response in colorectal cancer patients"
Candy et al., 2014
It was interesting that atypical Notch signaling seems to be a factor in chemotherapy treatment resistance. 
What is "Notch" in Notch-induced transcription factors?
Lab Thoughts: Notch refers to the phenotype that was observed when mutations in this pathway were originally detected (notches in the wings of fruit flies). More about Notch signaling pathway here:

"A Discovery Resource of Rare Copy Number Variations in Individuals with Autism Spectrum Disorder"
Prasad et al., 2014
Many of the mutations in the genes came from the mother which would explain the higher prevalence of ASD in males, some were deletions and others were additions, there were similar findings paternally at a lesser degree. 
Which genes overlap between females and males with ASD?
Lab Thoughts:
This paper doesn't analyze differences in risk between males and females. There is a sex-bias in risk for autism, and the paper even analyzes drastically different numbers of male and female patients (571 males and 125 females). Understanding the sex-bias in autism may help inform on potential mechanisms.

"Bayesian inference of shared recombination hotspots between humans and chimpanzees"
Wang and Rannala, 2014
The article concludes that there are areas on different chromosomes in both humans and chimpanzees that regularly undergo recombination – “hotspots”. Although these hotspots aren’t universal, there are many shared hotspots between the two. This relates directly to our research on X-Y recombination, as we analyze many different organisms (including humans and chimpanzees) for shared recombination areas, and this tells us that one group has already found links that we can verify. 
What is the Baseyian method?
Lab Thoughts:
Bayesian refers to a type of statistical modeling. Statistics can usually take three major forms: Frequentists, Bayesians, and Likelihoodists (although some argue this is just a flavor of Bayesian statistics).  A brief discussion of the difference between Bayesian and Frequentist statisticians by Hochester: And, an XKCD cartoon:

Wednesday, November 5, 2014

Lab meeting: first semester

A few months ago we had a great discussion on twitter about the best and worst practices for lab meetings (Storified here). Please feel free to comment here if you find something missing from that discussion.

This is my first semester as head of the lab (also called PI, for Principal Investigator). Right now, the lab is composed solely of undergraduate students (a brief overview of projects). That has actually made it slightly easier to plan lab meetings. We meet weekly, and are using it almost as a lab-training course. Here is our schedule:

Sept 10: Lab introductions, expectations, and getting comfortable in the terminal 
Sept 17: Course credit, Lab paperwork; Post-graduation options; Introduction to command line (Start here: 
Sept 24: How to read and understand a scientific paper (read this) 
Oct 1: Command line continued (Install datasciencetoolbox) 
Oct 8: ASHG practice talk 
Oct 15: Tutorial on VPN and SSH 
Oct 22: NO LAB MEETING - ASHG Conference 
Oct 29: Presentation from visiting researcher - Laurent Frantz 
Nov 5: Journal Club 
Nov 12: Summary of ASHG meeting 
Nov 19: TBD 
Nov 26: NO LAB MEETING - Happy Thanksgiving! 
Dec 3: Student project Updates And End of Semester Wrap Up 
Dec 10: NO LAB MEETING - Good Luck on Finals!

The students gave me great feedback on my ASHG talk that I think really improved it.

They've also been wonderfully interactive with me and with the invited speaker. 

I decided that once a semester I want to have a journal club. In this case, it might be better to call it a journal survey club. Each student is assigned one journal, and asked to read through the most recent issue (or most recent few issues if they want) to find one article that they find interesting. Prior to lab meeting, each student will send me the link to the article, a comment about the article, and a question about the article. I will compile these links, questions, and comments on the blog, and we will discuss them at lab meeting. We might push things around a little, because with 18 students, we may need a couple lab meetings to make it through all the papers!

Tuesday, November 4, 2014

Delicious sex chromosomes.

Plants have sex? Yes, they totally do.

A brief overview: 
Plants have female reproductive organs (carpels) and male reproductive organs (stamens), but several different ways of determining sex. There are two main groups of seed-producing plants.

Gymnosperms are plants without covered seeds, and include those that produce cones. Gymnosperms and are split with about 75% exhibiting monoecy (having male and female sex organs on the same plant), and 25% exhibiting dioecy (having separate male plants and female plants).

Photo by Muhammad Mahdi Karim, via Wikimedia Commons
Alternatively,  Angiosperms, the flowering plants, have only a small subgroup that exhibit either separate male and female flowers or separate male and female plants, and instead most angiosperms are hermaphrodites, meaning all of their flowers contain both male and female sex organs.

Photo by Derek Ramsey, at Chanticleer Garden, via Wikimedia Commons
One thing that is fairly common among vertebrates (found in mammals, birds, frogs, reptiles, and fish), but rare among plants is sex chromosomes. But, as we look more and more, we are finding sex chromosomes in the most delicious places. All of the following plants have sex chromosomes:

A Y-chromosome–encoded small RNA acts as a sex determinant in persimmons
Takashi Akagi1,2,  Isabelle M. Henry1,  Ryutaro Tao2,*,  Luca Comai1,*

Photo by Σ64, via Wikimedia Commons
Identification of molecular markers for selection of supermale (YY) asparagus plants.
Gebler P, Wolko Ł, Knaflewski M.

Photo by Rasbak, via Wikimedia Commons
Wild strawberry
Sex-determining chromosomes and sexual dimorphism: insights from genetic mapping of sex expression in a natural hybrid Fragaria × ananassa subsp. cuneifolia.
Govindarajulu R, Liston A, Ashman TL.

Photo via Walter Siegmund, via Wikimedia Commons
Accumulation of interspersed and sex-specific repeats in the non-recombining region of papaya sex chromosomes.
Na JK, Wang J, Ming R.

Photo by Sakurai Midori, via Wikimedia Commons
Wild grapes
A small XY chromosomal region explains sex determination in wild dioecious V. vinifera and the reversal to hermaphroditism in domesticated grapevines.
Picq S, Santoni S, Lacombe T, Latreille M, Weber A, Ardisson M, Ivorra S, Maghradze D, Arroyo-Garcia R, Chatelet P, This P, Terral JF, Bacilieri R.

Photo by Bangin, via Wikimedia Commons

So, yes, plants have sex, and some even have sex chromosomes. Just something to keep in mind as you work towards fulfilling your daily servings of fruits and veggies.