User talk:Kam D. Dahlquist

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== Answers to Student Questions Spring 2013 ==
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*Hey Dr.Dahlquist, I do not know how I chose 18 for that question on journal 12, I think it must have been a typo or I was overly tired when doing the assignment.  I changed it to 120. Also made correction on my answer to question 4 and shared my matrix and transpose with you on lionshare.
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Thanks*[[User:Kevin Matthew McKay|Kevin Matthew McKay]] 13:55, 18 April 2013 (EDT)
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Hi Dr. Dahlquist,
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Sorry I didn't post a question here, I misunderstood the directions.
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I've noticed that it is really hard to explain scientific idea to those not in the science field. After numerous discussions with my roommates, some of them still do not believe global warming is an issue being worsened by people. They also don't believe it is "as bad as scientists make it out to be". Is it an issue with scientists being unable to explain their knowledge to those not in the field, or is it just too hard to convince people that their long-held beliefs are wrong?
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Thanks! (also, I think I've made all the corrections you recommended to my page, but I'm still not sure if I'm doing the template right)
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[[User:Salman Ahmad|Salman Ahmad]] 20:18, 7 February 2013 (EST)
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Good afternoon,
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I responded to your feedback for my week 1 work on my talk page.  Have a good weekend!
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[[User:Elizabeth Polidan|Elizabeth Polidan]] 19:53, 2 February 2013 (EST)
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Hey Dr. Dahlquist, did you ever consider medical school?  What made you choose the research path?
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[[User:Kevin Matthew McKay|Kevin Matthew McKay]] 20:34, 17 January 2013 (EST)
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: I didn't consider medical school.  I'm actually pretty squeamish and have fainted at the sight of blood.  My parents instilled in me a love of science by giving me lots of educational opportunities when I was a kid.  I really loved my AP Biology class in high school, which inspired me to become a biology major.  I did undergraduate research in a plant physiology lab, which got me interested in research.  I also had always wanted to be a teacher because I loved my teachers and loved school when I was a kid.  This all came together to choose a profession as a biology professor where I could both teach and do research. 
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''— [[User:Kam D. Dahlquist|Kam D. Dahlquist]] 19:38, 21 January 2013 (EST)''
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Hi Dr. Dahlquist, I understand that you have a strong background in biology; what led you to have an interest in biomathematics? How has biomathematics helped you to become a better biologist? Thanks, [[User:Laura Terada|Laura Terada]] 15:31, 17 January 2013 (EST)
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: I got interested in biomathematics when I was a postdoc at the Gladstone Institute of Cardiovascular Disease/UCSF.  I was working on analyzing data from microarrays and it became really clear that I needed to learn statistics in order to analyze the data properly.  We were also working on visualizing the data on biological pathways.  I got started in modeling because I wanted to have a more quantitative model of the data we were visualizing on pathways.  The biomathematics has helped me become a better biologist because I am able to perform a more robust analysis of quantitative data.  I feel that I have a "leg up" on other biologists who do not do this type of analysis. 
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''— [[User:Kam D. Dahlquist|Kam D. Dahlquist]] 19:43, 21 January 2013 (EST)''
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----
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Hi Dr. Dahlquist, I was wondering what research projects your lab at LMU are currently working on?
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[[User:James P. McDonald|James P. McDonald]] 21:15, 21 January 2013 (EST)
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:I have three related research projects:
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# Understanding the transcriptional response to cold stress in yeast, ''Saccharomyces cerevisiae''.
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# Mathematical modeling of the above (which you guys will work on in this class).
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# Developing an open source program called [http://xmlpipedb.cs.lmu.edu/ XMLPipeDB] to create gene databases for analyzing microarray data.
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''— [[User:Kam D. Dahlquist|Kam D. Dahlquist]] 15:56, 22 January 2013 (EST)''
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Hi Dr. Dahlquist, I was wondering what your favorite subject in undergraduate biology was? Also, what is some of the research you did in college, and what are you currently working on? [[User:Kasey E. O'Connor|Kasey E. O'Connor]] 21:31, 21 January 2013 (EST)
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:I was always interested in how cells worked, so the classes that I took related to that were the equivalent of our Cell Function course, Genetics, and Biochemistry.  I knew that I was interested in molecular biology, but I didn't actually take a course specifically in that until graduate school
 +
 +
:In college, I worked in a plant physiology lab that was studying photosystem II in chloroplasts.  My advisor had discovered that some peripheral membrane proteins in photosystem II dissociated from the membrane during heat stress in wheat.  I was studying a strain of the ''Clorella pyrenoidosa'' algae that could survive at high temperatures to see whether these proteins stayed associated with the membrane.  My experiments suggested that they did, but we were not able to prove it definitively because we were having trouble purifying thylakoid membranes from the algae.
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:My current research projects are listed in the answer to James' question.
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''— [[User:Kam D. Dahlquist|Kam D. Dahlquist]] 19:27, 24 January 2013 (EST)''
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Hello Dr. Dahlquist,
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If you could be any celebrity for a day, who would you be and why?
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*'''[[User:Matthew E. Jurek|Matthew E. Jurek]] 23:01, 21 January 2013 (EST)''':
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: Wow, I've never been asked this before!  The first name that came to mind was Meryl Streep.  I really admire her as an actor and would love to be on one of her movie sets experiencing how she does such a great job doing characters like Julia Child or Margaret Thatcher.
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''— [[User:Kam D. Dahlquist|Kam D. Dahlquist]] 19:32, 24 January 2013 (EST)''
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My burning question
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Hello Professor Dahlquist,
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If you had to change careers, what would you choose?
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Thank you,
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[[User:Elizabeth Polidan|Elizabeth Polidan]] 22:33, 21 January 2013 (EST)
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:It's hard for me to imagine not doing something science-related.  One of my favorite jobs was when I worked at a book store in high school.  I was like a kid in a candy shop.  Sadly, that book store does not exist anymore; nor do many book stores.  I have become more and more interested in politics and government policy, so I could see myself as an investigative journalist, or working on government policy in some area.
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''— [[User:Kam D. Dahlquist|Kam D. Dahlquist]] 19:38, 24 January 2013 (EST)''
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Hi Dr. Dahlquist,  I was wondering what class you hated the most during undergraduate and why?  [[User:Anthony J. Wavrin|Anthony J. Wavrin]] 00:47, 22 January 2013 (EST)
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:I would have to say an Intro to Politics class that I took.  The class had a really great reading list, but all we seemed to do was sit around "bs-ing" during class and not really getting into the texts.  I distinctly remember one class where some of the students would say more and more outrageous things to see if the professor would call them out on it, but he never did.  Despite what looked like a great syllabus, I didn't feel like the class lived up to its potential.
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''— [[User:Kam D. Dahlquist|Kam D. Dahlquist]] 19:42, 24 January 2013 (EST)''
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Dr. Dahlquist:
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What is the most enjoyable research that you've done?
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Thanks,
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[[User:Ashley Rhoades|Ashley Rhoades]] 01:26, 22 January 2013 (EST)
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:I would have to say that my current research is the most enjoyable.  When I became a professor I was able to finally determine my research direction completely by myself (not influenced by my graduate or postdoc advisor).  That meant that I could finally choose what I was most interested in to work on.  My research projects are listed above in the answer to James' question.
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''— [[User:Kam D. Dahlquist|Kam D. Dahlquist]] 19:46, 24 January 2013 (EST)''
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Dr. Dahlquist,
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What are some of the different fields you have worked in within the area of biology? [[User:Paul Magnano|Paul Magnano]] 02:47, 22 January 2013 (EST)
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:* plant physiology (photosystem II in algae)
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:* RNA biochemistry (binding of translation initiation factor IF1 to A site of small subunit of the ribosome)
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:* bioinformatics (development of [http://www.genmapp.org GenMAPP] software; development of [http://xmlpipedb.cs.lmu.edu/ XMLPipeDB] software)
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:* genomics (global transcriptional response to cold shock in yeast)
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:* biomathematics (modeling of transcriptional network controlling the cold shock response in yeast)
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:* metagenomics (diversity of soil bacteria in the Ballona Wetlands)
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''— [[User:Kam D. Dahlquist|Kam D. Dahlquist]] 19:58, 24 January 2013 (EST)''
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Hi Dr. Dahlquist,
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What drew you back to Biology after studying Philosophy?
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[[User:Helena M. Olivieri|Helena M. Olivieri]] 01:10, 23 January 2013 (EST)
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:*I wouldn't say that I ever really left biology.  I got interested in the philosophy of science when I was in high school and just briefly considered majoring in philosophy in my first semester freshman year.  The biology major didn't start until the second semester and as soon as I took my first college biology class, I made my decision to major in biology and do some philosophy on the side.  I ended up taking a few extra courses in philosophy in college and was fortunate to be able to do a specialized tutorial in the philosophy of science when I studied abroad at Oxford my junior year.  I guess I thought I wanted to approach the philosophy of science from the point of view of a practicing scientist.
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''— [[User:Kam D. Dahlquist|Kam D. Dahlquist]] 20:03, 24 January 2013 (EST)''
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I am also having a difficult time understanding how to look at the maximum and minimum difference across subjects.  The instructions are a bit unclear
I am also having a difficult time understanding how to look at the maximum and minimum difference across subjects.  The instructions are a bit unclear
--[[User:Kristoffer T. Chin|Kristoffer T. Chin]] 00:19, 13 February 2010 (EST)
--[[User:Kristoffer T. Chin|Kristoffer T. Chin]] 00:19, 13 February 2010 (EST)
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I was wondering how you became so interested in Bioinformatics? [[User:Zeb Russo|Zeb Russo]] 18:04, 31 August 2011 (EDT)
I was wondering how you became so interested in Bioinformatics? [[User:Zeb Russo|Zeb Russo]] 18:04, 31 August 2011 (EDT)
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: I think my favorite experience when I was an undergraduate was studying abroad at Oxford University in England.  I joined a bunch of clubs and had a great time traveling around the country.  Two of my favorite classes were "Gender and Science", taught by a woman physics professor, and "Understanding the Earth: Feminist Perspectives", taugth by a woman geology professor.  ''&mdash; [[User:Kam D. Dahlquist|Kam D. Dahlquist]] 19:44, 31 August 2011 (EDT)''
: I think my favorite experience when I was an undergraduate was studying abroad at Oxford University in England.  I joined a bunch of clubs and had a great time traveling around the country.  Two of my favorite classes were "Gender and Science", taught by a woman physics professor, and "Understanding the Earth: Feminist Perspectives", taugth by a woman geology professor.  ''&mdash; [[User:Kam D. Dahlquist|Kam D. Dahlquist]] 19:44, 31 August 2011 (EDT)''
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Hey Dr. Dahlquist, I was wondering what recent scientific advancement are you most excited about for the future? [[User:Chris H. Rhodes|Chris H. Rhodes]] 14:13, 6 September 2011 (EDT)
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: I've been excited ever since the Human Genome Project was completed in 2000-2003.  That project enabled a whole suite of technologies (like DNA microarrays) that allow us to do high-throughput experiments and study cells at a systems level.  I'm very excited about the advancements in using this data to model a cell's activities.  I'm also excited for the prospect that soon it will be cheap enough to sequence individual genomes on a regular basis.  However, I think our ability to capture more and more data is outpacing our ability to understand it.  However, like I said in class, it's a really good time to be a biologist!  ''&mdash; [[User:Kam D. Dahlquist|Kam D. Dahlquist]] 11:31, 7 September 2011 (EDT)''
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Week 2 Journal Question
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* Hey Dr. Dahlquist, I had a quick question about the week 2 journal. Would it be alright if I incorporated the answers to the handout questions into my conclusion instead of sticking them in the results section? It seemed to me like a more natural way of presenting the information and I'm kind of having trouble with thinking what else would go into the conclusion. I already made the changes to the page if you wanted to look at it and see if it seems right.[[Chris_Rhodes_Week_2]] Thanks. [[User:Chris H. Rhodes|Chris H. Rhodes]] 19:44, 11 September 2011 (EDT)
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Dr. Dahlquist, I was wondering what part of bioninformatics you like working with the most? [[User:Alex A. Cardenas|Alex A. Cardenas]]
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: My favorite part of bioinformatics is really called "systems biology"; it involves studying the pathways and networks in the cell.  My favorite thing is to take DNA microarray data and use it to understand the gene regulatory networks in the cell.  I am involved in a modeling project that is trying to express the network interactions with differential equations.  ''&mdash; [[User:Kam D. Dahlquist|Kam D. Dahlquist]] 14:25, 14 September 2011 (EDT)''
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Hi Dr. Dahlquist, what was your favorite part of your graduate work? [[User:Robert W Arnold|Robert W Arnold]] 23:13, 20 September 2011 (EDT)
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: Hmmm.  I've never been asked that before.  I think my favorite part of my graduate work came out of my biggest frustration.  I was trying to reproduce the results in [http://www.sciencemag.org/content/277/5330/1262.abstract?ijkey=cc68074be3249ee57b012114d1e1268370ae2331&keytype2=tf_ipsecsha this ''Science'' paper], and I wasn't able to. Upon looking closer at the gel in the paper, I realized that they had done the proper controls and that if you accounted for that, my results were indeed similar to theirs.  From that, I made a hypothesis about the role of Initiation Factor 1 binding to the A site of the small subunit of the ribosome to provide kind of a "proofreading" function during translation initiation.  Coming up with that hypothesis was very satisfying after being frustrated for a long time.
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''&mdash; [[User:Kam D. Dahlquist|Kam D. Dahlquist]] 18:49, 21 September 2011 (EDT)''
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-->
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==week 12 paul magnano==
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I uploaded the genelist/GO for 5 clusters on the original assignment, im not sure why you were not able to access it on lionshare. I just re shared it with you please let me know if you cannot access it still. [[User:Paul Magnano|Paul Magnano]] 12:55, 18 April 2013 (EDT)

Revision as of 14:34, 19 April 2013

Answers to Student Questions Spring 2013

  • Hey Dr.Dahlquist, I do not know how I chose 18 for that question on journal 12, I think it must have been a typo or I was overly tired when doing the assignment. I changed it to 120. Also made correction on my answer to question 4 and shared my matrix and transpose with you on lionshare.

Thanks*Kevin Matthew McKay 13:55, 18 April 2013 (EDT)

Hi Dr. Dahlquist, Sorry I didn't post a question here, I misunderstood the directions. I've noticed that it is really hard to explain scientific idea to those not in the science field. After numerous discussions with my roommates, some of them still do not believe global warming is an issue being worsened by people. They also don't believe it is "as bad as scientists make it out to be". Is it an issue with scientists being unable to explain their knowledge to those not in the field, or is it just too hard to convince people that their long-held beliefs are wrong? Thanks! (also, I think I've made all the corrections you recommended to my page, but I'm still not sure if I'm doing the template right) Salman Ahmad 20:18, 7 February 2013 (EST)


Good afternoon, I responded to your feedback for my week 1 work on my talk page. Have a good weekend! Elizabeth Polidan 19:53, 2 February 2013 (EST)


Hey Dr. Dahlquist, did you ever consider medical school? What made you choose the research path? Kevin Matthew McKay 20:34, 17 January 2013 (EST)

I didn't consider medical school. I'm actually pretty squeamish and have fainted at the sight of blood. My parents instilled in me a love of science by giving me lots of educational opportunities when I was a kid. I really loved my AP Biology class in high school, which inspired me to become a biology major. I did undergraduate research in a plant physiology lab, which got me interested in research. I also had always wanted to be a teacher because I loved my teachers and loved school when I was a kid. This all came together to choose a profession as a biology professor where I could both teach and do research.

Kam D. Dahlquist 19:38, 21 January 2013 (EST)


Hi Dr. Dahlquist, I understand that you have a strong background in biology; what led you to have an interest in biomathematics? How has biomathematics helped you to become a better biologist? Thanks, Laura Terada 15:31, 17 January 2013 (EST)

I got interested in biomathematics when I was a postdoc at the Gladstone Institute of Cardiovascular Disease/UCSF. I was working on analyzing data from microarrays and it became really clear that I needed to learn statistics in order to analyze the data properly. We were also working on visualizing the data on biological pathways. I got started in modeling because I wanted to have a more quantitative model of the data we were visualizing on pathways. The biomathematics has helped me become a better biologist because I am able to perform a more robust analysis of quantitative data. I feel that I have a "leg up" on other biologists who do not do this type of analysis.

Kam D. Dahlquist 19:43, 21 January 2013 (EST)


Hi Dr. Dahlquist, I was wondering what research projects your lab at LMU are currently working on? James P. McDonald 21:15, 21 January 2013 (EST)

I have three related research projects:
  1. Understanding the transcriptional response to cold stress in yeast, Saccharomyces cerevisiae.
  2. Mathematical modeling of the above (which you guys will work on in this class).
  3. Developing an open source program called XMLPipeDB to create gene databases for analyzing microarray data.

Kam D. Dahlquist 15:56, 22 January 2013 (EST)


Hi Dr. Dahlquist, I was wondering what your favorite subject in undergraduate biology was? Also, what is some of the research you did in college, and what are you currently working on? Kasey E. O'Connor 21:31, 21 January 2013 (EST)

I was always interested in how cells worked, so the classes that I took related to that were the equivalent of our Cell Function course, Genetics, and Biochemistry. I knew that I was interested in molecular biology, but I didn't actually take a course specifically in that until graduate school
In college, I worked in a plant physiology lab that was studying photosystem II in chloroplasts. My advisor had discovered that some peripheral membrane proteins in photosystem II dissociated from the membrane during heat stress in wheat. I was studying a strain of the Clorella pyrenoidosa algae that could survive at high temperatures to see whether these proteins stayed associated with the membrane. My experiments suggested that they did, but we were not able to prove it definitively because we were having trouble purifying thylakoid membranes from the algae.
My current research projects are listed in the answer to James' question.

Kam D. Dahlquist 19:27, 24 January 2013 (EST)


Hello Dr. Dahlquist, If you could be any celebrity for a day, who would you be and why?

Wow, I've never been asked this before! The first name that came to mind was Meryl Streep. I really admire her as an actor and would love to be on one of her movie sets experiencing how she does such a great job doing characters like Julia Child or Margaret Thatcher.

Kam D. Dahlquist 19:32, 24 January 2013 (EST)


My burning question

Hello Professor Dahlquist,

If you had to change careers, what would you choose?

Thank you, Elizabeth Polidan 22:33, 21 January 2013 (EST)

It's hard for me to imagine not doing something science-related. One of my favorite jobs was when I worked at a book store in high school. I was like a kid in a candy shop. Sadly, that book store does not exist anymore; nor do many book stores. I have become more and more interested in politics and government policy, so I could see myself as an investigative journalist, or working on government policy in some area.

Kam D. Dahlquist 19:38, 24 January 2013 (EST)


Hi Dr. Dahlquist, I was wondering what class you hated the most during undergraduate and why? Anthony J. Wavrin 00:47, 22 January 2013 (EST)

I would have to say an Intro to Politics class that I took. The class had a really great reading list, but all we seemed to do was sit around "bs-ing" during class and not really getting into the texts. I distinctly remember one class where some of the students would say more and more outrageous things to see if the professor would call them out on it, but he never did. Despite what looked like a great syllabus, I didn't feel like the class lived up to its potential.

Kam D. Dahlquist 19:42, 24 January 2013 (EST)


Dr. Dahlquist: What is the most enjoyable research that you've done? Thanks, Ashley Rhoades 01:26, 22 January 2013 (EST)

I would have to say that my current research is the most enjoyable. When I became a professor I was able to finally determine my research direction completely by myself (not influenced by my graduate or postdoc advisor). That meant that I could finally choose what I was most interested in to work on. My research projects are listed above in the answer to James' question.

Kam D. Dahlquist 19:46, 24 January 2013 (EST)


Dr. Dahlquist,

What are some of the different fields you have worked in within the area of biology? Paul Magnano 02:47, 22 January 2013 (EST)

  • plant physiology (photosystem II in algae)
  • RNA biochemistry (binding of translation initiation factor IF1 to A site of small subunit of the ribosome)
  • bioinformatics (development of GenMAPP software; development of XMLPipeDB software)
  • genomics (global transcriptional response to cold shock in yeast)
  • biomathematics (modeling of transcriptional network controlling the cold shock response in yeast)
  • metagenomics (diversity of soil bacteria in the Ballona Wetlands)

Kam D. Dahlquist 19:58, 24 January 2013 (EST)


Hi Dr. Dahlquist, What drew you back to Biology after studying Philosophy? Helena M. Olivieri 01:10, 23 January 2013 (EST)

  • I wouldn't say that I ever really left biology. I got interested in the philosophy of science when I was in high school and just briefly considered majoring in philosophy in my first semester freshman year. The biology major didn't start until the second semester and as soon as I took my first college biology class, I made my decision to major in biology and do some philosophy on the side. I ended up taking a few extra courses in philosophy in college and was fortunate to be able to do a specialized tutorial in the philosophy of science when I studied abroad at Oxford my junior year. I guess I thought I wanted to approach the philosophy of science from the point of view of a practicing scientist.

Kam D. Dahlquist 20:03, 24 January 2013 (EST)


week 12 paul magnano

I uploaded the genelist/GO for 5 clusters on the original assignment, im not sure why you were not able to access it on lionshare. I just re shared it with you please let me know if you cannot access it still. Paul Magnano 12:55, 18 April 2013 (EDT)

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