Monday, December 15, 2014

Mindlin Undergraduate Mentored Researchers selected

Congratulations to Bich (Hien) Vu and Shawn Rupp for being selected as Mindlin Foundation Undergraduate Mentored Research awardees in the Wilson Sayres lab! From the Mindlin Foundation website:

This program is intended to support promising undergraduates in the sciences or engineering, in a mentored research project that introduces the student to academic research. 
The structure of the research plan should involve a mentored research experience, wherein the undergraduate student is responsible for addressing an appropriate self-contained question relevant to the mentor’s larger ongoing study.

I am thrilled to have the opportunity to mentor such wonderful undergraduate students! We are so thankful to the Mindlin Foundation for recognizing their potential, and for the value of their research contributions. 

Hien Vu, Senior
Dr. Wilson Sayres, faculty in the School of Life Sciences at Arizona State University, and Bich (Hien) Vu, a senior at Arizona State University majoring in Biological Sciences (Genetics, Cell and Developmental Biology), have been selected to receive Mindlin Foundation funding in support of their proposal, "Patterns of evolution across vertebrate sex determining genes."

Shawn Rupp, Junior
Dr. Wilson Sayres, faculty in the School of Life Sciences at Arizona State University, and Shawn Rupp, a junior majoring in Biological Sciences (Genetics, Cell and Developmental Biology), have been selected to receive Mindlin Foundation funding in support of their proposal, "Characterizing sex-biased gene expression in the green anole."

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. 

Friday, October 24, 2014

Open Access Week

The Arizona State University Library system has a series of interviews for Open Access week. I answered some questions for them about my experience with publishing in open access journals, and my thoughts about open access.

Check it out here:

What do you think about open access publishing?

Thursday, October 23, 2014

Funding 101: Mechanisms

Recently I attended a seminar giving an overview of different funding mechanisms for scientific research, and advice. This will be the first of two posts, talking about a variety of funding mechanisms. The next post will be advice from very successful researchers.

Traditional government funding 

111th US Senate class photo, Public Domain, via Wikimedia Commons
Do your homework
  • Understand the structure of the funding agency
    • what have they funded
    • what is their relationship with your home institution
    • what are you colleagues doing
    • be able to articulate what kind of research your colleagues are doing that is already funded by that agency
  • Identify who the appropriate program officer is
    • send an email with a paragraph in hand about the kind of research you do, and where you are moving. Is this the kind of research you are interested in funding? If not, can you point me in the right direction, and can I use your name?
    • Don't ask for information you could have gotten ahead of time online.
    • What concepts or priorities have already been approved? Look up the strategic plans. In particular those that are supported by the PO you are going to contact.
  • Look for requests for information, and respond with ideas in your area.

Establish relationships
  • There are no "cons" about talking with PO.
  • You cannot talk to PO about a submitted funding proposal that is in review.
  • You can (and should) ask, "Do you think this is something your funding agency is interested in in the future?" 
  • Diversify your support - don't go only to one PO or to only one funding agency.

Serve on review panels
  • The best experience you can get for preparing proposals.
  • Helps you to develop a good relationship with the PO.
  • You learn about what other panelists are expecting.
  • Hearing the way people critique, especially what can rule out a proposal.

Foundation, philanthropic, and business funding
Bill and Melinda Gates Foundation, photo by Adbar via Wikimedia Commons

  • Structured foundations (corporate and foundations group) generally follow the same rules as government funding agencies.
  • Unstructured foundations - do not accept proposals! How to get an "in"?
    • Have to make a personal connection with someone who sits on the board
    • Pitch your idea in email or on the phone
    • Quickly you will hear either: "Great! Send 1 page summary." or "Not interested"

Individuals philanthropists
  • You are immediately competing with colleagues at your Institution
  • How do you interact with rich people? Be social. Join the United Way committee. Join and attend one of the balls that support hospitals.
  • Be aggressive about getting out in the community.
  • If you are going to meet people with capacity, you need to make the time to do it. Probably difficult for early career scientists.
  • Talk with your Institutional office about possible philanthropist connections.
  • Check what the past history Institution with the organization-of-interest is.

Public versus private benefits for philanthropists
  • Public benefit - Interested in scholarship, research, public outcome of the gift.
  • Private benefit - Makes the philanthropist feel good. Seat saved in the front row.
    • Most people donate money for the private benefit. Figure out what their private benefit is (prestige, recognition, intellectual discussion, name on the wall), and target that.

Pitching your idea to businesses
  • Businesses are interested in partnerships - spinoffs
  • Talking to venture capitalists can seem like talking into a vacuum
  • Put up the money to start something yourself.
  • 10% of something is better than 100% of nothing.
  • Businesses/Corporations don't give much to start (average $25-30k), but this can improve
  • Underpromise and over-deliver
  • Business endeavors are designed to solve a specific problem

Crowd funding for science?
How to capture the interest of the crowd? Photo by brand via Wikimedia Commons

When I asked about crowd funding for research, I got the general sense that most people on this particular panel were not optimistic about crowd funding as a sustainable mechanism for scientific research. Here is the small summary:
  • On average crowd funding supports $5,000 grants, generally not hundreds of thousands or millions
  • Must utilize all of your networks - at least 12-15 primary people to expand to their larger networks.
  • Need a key statement, appeal, and to sell the research
  • Often a large time investment, with fairly low pay-off.

Tuesday, October 7, 2014

Bidstrup Undergraduate Fellow selected

Kara Schaffer, a junior at Arizona State University, majoring in Chemical Engineering was been selected as a Bidstrup Undergraduate Fellow for the 2014-2015 academic year to work in the Wilson Sayres lab. This award is a testament to her outstanding commitment to academic excellence, and is funded through the Barrett Honors College

Pretty Woman in academia.

Being in academia for good few years now, I've heard this said directly to me several times, most recently last week. The gist:
"It isn't fair, but people don't take a pretty woman in science seriously."
"Pretty woman" could easily be replaced with many different words describing minorities in science, rural/urban accents, people with disabilities. But why would a colleague say this to someone of such a group?

After some thought, I'm pretty sure these people must be referring to the 1990 classic movie, Pretty Woman. So, let's talk about academia in general, with some help from Pretty Woman.

Some days it feels like the academic pipeline is work, work, work:

And, whether it is stated out loud by a supervisor, a colleague, or in our heads, these voices exist, reminding us that we don't fit. 

And most days you can let it run off your back; you try to remember not to take it personally.

You do the right things, you cover your bases, you do your work, and you do it well.

But every now and then someone reminds you of the cost of just being *you*… reminds you of a time when you couldn't afford (through financial or personal or social capital) to be in the position you're in now.

Some days those little voices get louder and louder, bouncing in your head, and make you wonder if you belong.

Getting through it can take different forms. Maybe you remind yourself that it isn't all luck, that you have big dreams, and by dammit, you have worked hard for those dreams, and you deserve to want these things for yourself. 

Maybe you find a friend to commiserate with. Maybe you go to a mentor. Maybe you go to the source (either to the person, or to those dark parts of your mind) and tell those voices what's up, that the focus is on your work, your awesome work, not these petty distractions.

You deserve to be here. You deserve to be recognized for your work. And any voice that tells you otherwise is making a mistake.

Big Mistake. Big. Huge.

Thursday, October 2, 2014

Prepping for Class

The College of Liberal Arts and Sciences at Arizona State University is putting on (an excellent) series for new Assistant Professors (1st and 2nd years).

1. Advice from tenured professors for pre-tenure faculty

The second seminar I attended is about preparing for class. Some of the focus was about Arizona State University specifically, but much of the advice is applicable to anyone starting out teaching. The format was a panel discussion with three Assistant Professors (past their 3rd year review) and four Associate Professors. This group included winners of the Zebulon Pearce Award for teaching excellence, and one panelist who was invited to participate an an HHMI initiative to improve science education. The disciplines represented were wide, spanning across the Sciences and Humanities. You'll notice in my notes that there are some contradictory comments. Hey, they happens when a group of people talk about their teaching advice. Here we go:

Use the resources available to you
  • Ask to see syllabus and course notes from previous years.
  • Ask questions of those who taught before, what worked, what didn't.
  • You don't have to reinvent the wheel to prove yourself as an educator.
  • Be cautious: Just because a class has been taught before doesn't mean it was taught well.
Manage classroom time
  • Practice application of materials in class. If you expect students to do something (e.g., apply knowledge) on the exam, you need to teach them the critical thinking skills in class and in homework. They won't automatically know how to take it that extra step. 
  • Students may behave poorly. By not addressing problems, you enable them.
  • In large classes, walking around the classroom (and having TA's walk) can help keep students focused.
  • Prepare for misinformation that might be widely available about your topic.
  • Prepare for dissenting voices. Think about that one student who will antagonize you, and try to preemptively address it, or be prepared with a quick response if that voice speaks up.
Create an authentic model of authority
  • If you aren't an old white guy, don't act like an old white guy.
  • Some people command respect , but that isn't for everyone.
  • You can create a bond of respect that you are comfortable with.
Evaluate student learning and experience more than once
  • Leave a blank page at the end of each exam for students to tear off and leave anonymous comments about the class.
  • Evaluate at least once before or at the midpoint of the semester. For you. For your students. 
  • If using online technology, can run rolling quizzes. Put online at 8am Friday, and students have until 8am Monday to complete.
Interacting with students over email can require patience, and preparation
  • Wait (a day or two) to respond to emails that frustrate you.
  • Set the tone. Use a full salutation. Many students never learned how to write a proper letter.
  • Write a draft email that you can cut and paste in response to all of the similar questions you will get.
How do you stop obsessing and stressing about teaching? 
  • Assess whether it is true anxiety that affects you (if so, seek additional help). Or, check if it is care about student success and it is motivating you.
  • Allocate time for teaching. Allow yourself to stress out that day/time, and not the next.
  • Allow yourself to appreciate what you are doing right.
Structure your teaching so you don't spend all your time on it
  • Respect your prep time and respect your non-prep time. 
  • Put in your syllabus about when you will respond to questions about course materials (e.g., will not respond three hours before email).
  • Make a "need to respond" folder for student emails, then respond during your teaching time.
  • Don't waste your time trying to find "just the right picture." That picture is not going to substantially change the class.
  • Develop discussion questions.
Preparation time rules of thumb
  • 2 hours prep time to one hour of lecture
  • 4-5 hours of prep time to develop active learning activities for for each hour of class time.
  • 7 hours to prep for one completely online hour.
Manage Teaching Assistants (TAs)
  • Set up clear expectations, map out what the semester is going to look like, which weeks are busy and which are going to be lighter.
  • Require that the TAs teach.
  • Have a weekly meeting for the TAs.
  • Keep track of good students so you can ask them to be assistant TAs in future classes.
Use varied approaches to engage students in large lectures
  • Ask a lot of questions.
  • Work in pairs, upload answers to blackboard.
  • Lectures can be very boring
  • Make content into questions. Content will come out in the discussion.
  • Make nameplates for each student (they bring to class each session).
  • Cold call, but allow students to "phone a friend," asking for help from other students.
Teaching surprises (will vary from school to school) 
  • Diversity in background among the students.
  • That I liked teaching.
  • Students have many competing demands and responsibilities.
  • It is the exception that your students won't have a job (full or part); large veteran population.
  • How much students need mentoring. E.g., first generation college student.
  • Surprised and delighted by how you get to change a couple people's lives.
Things we learned the hard way so you don't have to 
  • Check the version of the book (especially if it includes a new ending and/or different material.
  • Cover the required amount of material.
  • Don't try to cover too much (especially packing slides too full).
  • Ask for feedback, but try to prepare yourself for the negative impressions.
General suggestions/thoughts
  • Design your course so that over-committed students can excel. Check in constantly. This doesn't mean cover less content, but it does mean hand-holding, mentoring, and taking a half-step back to reframe the contentt
  • It is generally not good to mirror your teaching expectations of students at your institution based on where you went to school. You will need to learn the dynamic at your new institution.
  • Have each student fill out a notecard with name, other classes, outside commitments. Even in a large class this can be useful for cold-calling.
  • Sometimes students don't read instructions. Make a difficult exam question, but within the  instructions state the answer, for example, "the answer is 'B'."
Whew! Alright, got all that? And we're just scratching the surface here. Please leave your comments and suggestions about teaching for new faculty. Happy teaching!

Friday, September 26, 2014

Fall 2014: Projects and people

Projects and people in the Wilson Sayres lab in Fall 2014. At the end of Spring 2015 we will check back in with all of our accomplishments, what we learned, and where we'll be heading.

Projects are listed alphabetically. Project members are listed first in ascending order of reported year in school, then alphabetically by last name. 

All the projects
Principal Investigator: Dr. Melissa Wilson Sayres


Comparative Fertility 
Investigating the evolution of genes involved in fertility.

Undergraduate: Brittany Hammis (freshman)


Lepidoptera life history and simulations
Investigating variations in genome evolution and life history, and investigating the effects of demographic history on estimates of mutation rates.

Undergraduate: Christopher Negrich (freshman)
Undergraduate: Samantha Daly (sophomore)

Undergraduate: Ashley Amidan  (junior)
Undergraduate: Melinda Jenner  (senior)


Mammary tissue evolution - Joint with Cartwright Lab
Investigating the evolution of pre-pregnancy mammary tissue development in humans.

Undergraduate: Caroline Erickson (sophomore) – Joint with Cartwright Lab
Undergraduate: Jaclyn Williams  (junior)


Proteome Evolution
Investigating positive selection in tissue-specific proteomes.

Undergraduate: David Barclay (junior)
Undergraduate: William Martelly (junior)


Pseudoautosomal region diversity
Investigating diversity in the pseudoautosomal region of the sex chromosomes.

Undergraduate: Danny Cotter (freshman)
Undergraduate: Sarah Brotman (sophomore)


Squamate sex determination
Investigating sex determination mechanisms and sex chromosome evolution in squamates.

Undergraduate: Shawn Rupp (junior)
Undergraduate: Hien Vu (junior)


Turner syndrome
Investigating parent-of-origin effects for the single X chromosome in people with Turner syndrome.

Undergraduate: Jada Wang (freshman)
Undergraduate: Marshall Styers (freshman)
Undergraduate: Kara Schaffer (junior)


X-Y recombination
Investigating the timing of X-Y recombination suppression.

Undergraduate: Alix Marinello (freshman)
Undergraduate: Reena Ygot (senior)