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The end is near September 3, 2007

Posted by Sacha in Blogging, Research, School.
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No, I have not subscribed to a new apocalyptic cult, I have applied for graduation!  Assuming I can complete six more classes in the next nine months, I will graduate in June.  It’s been a long road, so it feels great to know I won’t be an undergrad all my life. 

The reason I haven’t been blogging here lately is not for lack of things to talk about, but because I’ve had way too much going on.  I went to North Carolina for a workshop at the Statistics and Applied Math Sciences Institute, received a scholarship to participate in the Summer Institute in Statistical Genetics in Seattle and received a grant from NASA to continue my microRNA research this summer.  These were all fantastic opportunities and I need to do some reflective blogging on them before I forget everything. 


Straight from the Nucleus: miR-29b January 13, 2007

Posted by Sacha in Genetics, microRNA, News, Research, Science.
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Another paper on microRNA.  This one is about miR-29 was published in Science‘s Jan. 5, 2007 edition.  It’s titled “A Hexanucleotide Element Directs MicroRNA Nuclear Import.” 

This is basically a note to myself to read it later.  

2 miRs and Cancer January 13, 2007

Posted by Sacha in Genetics, microRNA, News, Research, Science.
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During all this kurfuffle of winter storms and sick kitties I failed to update you on an important microRNA breakthrough.  At Ohio State University, Yuri Pekarsky’s team has found two microRNA (miRs) that regulate the most common human leukemia:  B-cell chronic lymphocytic, or just B-CLL for short.  These two microRNA are miR-29 and miR-181. 

microRNA can function as reverse regulators of disease.  So, when certain microRNA have low levels of expression, their targets genes are not surpressed and aggressive cancer can result.  What the researchers found was that there was an inverse relationship between expression levels of miR-29 and miR-181 and Tcl1, the ocncogene associated with B-CLL. 

The Ohio State team’s paper was titled “Tcl1 Expression in Chronic Lymphocytic Leukemia Is Regulated by miR-29 and miR-181″ and published in the December 15, 2006 edition of Cancer Research.  According to the paper, “Because miR-29 and miR-181 are natural Tcl1 inhibitors, these miRs may be candidates for therapeutic agents in B-CLL-overexpressing Tcl1. ” 

To read the original paper click here.  To read an excellent, non-technical summary from the American Association for Cancer Research click here

New Paper: Human microRNAs transcribed by polymerase III November 14, 2006

Posted by Sacha in Evolution, Genetics, microRNA, Research, Science.
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A new paper out this week in Nature Structural and Molecular Biology presents evidence that Polymerase III is associated with miRNA genomic sequence and sufficient for transcription.  This is as opposed to the privious view that Pol II was required in mammals for expression.  The miRNAs they analyzed (miR-515-1, 517a, 517c, 519a-1) were interspersed among the Alu repeats, which are transcribed through Pol III recruitment.

Now, I had to ask myself after I read the abstract for this article, “What are Alu repeats?” and “Why do I care if they hang out on the chain with miRs?”  If Wikipedia is accurate, and I hope it is, the Alu family is a family of polymorphisms in the human genome, about 300 bp long.  Their repetitive sequences are the most abundant mobile units on the human genome and have been implemented in diseases, such as cancer.  As for the second question, this connection suggests that repetitive elements play an important role in human miRNA origin and expression, according to this new paper.

Genetics of Celiac Disease July 25, 2006

Posted by Sacha in Genetics, Research, Science.
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I was recently diagnosed with gluten intolerance via a blood test.  While my doctor told me this doesn’t necessarily mean I have celiac disease (a disease characterized by intolerance to the proteins of wheat and other cereals), other people have argued with me that all people with gluten intolerance have celiac disease (CD).  Apparently the definition isn’t clear enough.  So, anyway, I decided to research this disease a bit. 

While I’m not sure my original question was answered, what I found that was interesting while reading about CD were the genetic factors.  According to this paper published in Human Immunology, 95% of patients carry the HLA-DQ2 molecule and of the other 5%, most carry HLA-DQ8.  However, CD develops in only a minority of HLA-DQ2 positive people.  In other words, although CD patients have a gene for it, not many with that gene have CD.  Scientists speculate that other genes and environmental factors affect whether or not a person actually develops CD.

If you want to read more about CD, I recommend the above article or this article from Gastroenterology on the prevalence, incidence, and progression of CD if you have access to journals, or this consensus statement from the NIH if you don’t. 

The Research Proposal May 18, 2006

Posted by Sacha in Research.
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Where have I been????  I was so excited to finally have a blog and I have so many things I want to post, but finding the time lately has not been easy.  Besides trying to get over my worst sinus infection yet, I was writing my very first research proposal. 

From an undergraduate perspective this is both harder and easier than it sounds.  It is more difficult because I'm trying to explain computational genetics concepts and techniques that are extremely new to me, without having a single genetics class under my belt (into biology courses don't count).  It is easier in some ways than more advanced researchers deal with, because I have the help of my research advisor and hopefully, those on the committee understand that I'm still learning and they only ask for a mere 3000 words. 

The strangest thing to me was the organization of the paper.  I was really good at writing essays for English teachers, but with research papers/proposals you get to have headings, lists of hypotheses, and even figures (fancy!).  I think this is actually much easier to read than the traditional essay.  It's very easy to get the point across.  English teachers probably consider it cheating.   

I was surprised at the number of applicants for this particular research award, since it is specifically for undergraduates at my university who have completed at least three quarters of research already.  I don't know hardly any other undergraduate researchers, besides the few I met through my fellowship last summer.  Did any of you do undergraduate research (science or other fields)?