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Rare Piebald Deer on Orcas Island (Washington State) September 4, 2007

Posted by Sacha in Genetics, News, Science.
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I had the good furtune to see a piebald deer while visiting the Spring Bay Inn on Orcas Island in Washington state a few weeks ago.  Isn’t it pretty?

thesmallest

My father-in-law, a geneticist, says it is not a result of inbreeding, as one fellow inn guest had told me, but simply a genetic difference.  I am having trouble finding reliable information on this variation.  Does anyone have a scientifically sound source of information about it?

A new quarter… already??? March 26, 2007

Posted by Sacha in Genetics, Programming.
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That was the shortest spring break yet!  It was just over a week and I barely made a dent in my to-do list.  Oh well, spring quarter has begun and I have my first genetics class!  It’s called “Genome Informatics,” so it’s right in my area of interest.  That is pretty exciting.  I’m a little bummed that the only math class I have this quarter is mathematical reasoning, beacause I’m not sure how much math will really be involved.  I was really starting to enjoy linear analysis by the end of last quarter and was wishing we were on semester classes so we could get a bit more indepth with the Laplace stuff.  I’ll have to see what else I can take in that area of study another quarter. 

I have a ton of updating to do on the journal articles side that I was hoping to do over the break.  I’ll see if I can get on top of it now.  I like to feel like I’m keeping up on all the latest research, but I have to prioritize classes and my own research.  Hopefully some interesting news on my own research to share in the next week, but I’ll have to keep my mouth shut for a few more days. 

Are microRNA required for ovarian stem cells? February 20, 2007

Posted by Sacha in Genetics, microRNA, Science.
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A report was published this weekend in the journal Current Biology titled “Dcr-1 Maintains Drosophila Ovarian Stem Cells.”  The authors were Zhigang Jin, Ph.D, and Ting Xie, Ph.D, from Stowers Institute for Medical Research (Missouri) and the Department of Anatomy and Cell Biology (U of Kansas), respectively. 

According to this paper, the ovaries of Drosophila (a type of small fly) contain three types of adult stem cells: 
Germline stem cells (GSCs)
Escort stem cells (ESCs) and
Somatic stem cells (SSCs)

The authors go into much detail about GSCs and SSCs and the role of Dicer-1(Dcr-1) ribonuclease to maintain them in the Drosophila ovary.

So what is this review doing on an miRNA blog?  In the last paragraph of the article, Xie and Jin state “Because Dcr-1 is an essential component of the miRNA pathway in Drosophila, we further propose that miRNAs processed by Dcr-1 are essential for controlling self-renewal of GSCs and SSCs.”  They go on to explain the problems associated with the absence of miRNA generated by Dcr-1, such as depletion of stem cells.

An article on Biology News Net quoted Dr. Xie on the importance of the role of miRNA:

“We are in the process of identifying the microRNAs that are important for stem cell self-renewal,” said Dr. Xie. “Understanding the mechanisms controlling stem cell self-renewal will be crucial to our developing the ability to expand stem cell populations for performing tissue repair.”

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. 

Another complete mapping of the genome May 25, 2006

Posted by Sacha in Genetics.
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I was just catching up on my latest favorite finds in the blogosphere, Genetics Health and DNA Direct Talk.  They reported that on the 17th, scientists published the sequence of the last of the human chromosomes (chrom 1).  I think this is about the third time we've "completed" the genome, but it does get better every time. 

There is an excellent article titled "Human genome completed (again)" at news@nature.com that talks about the details and history in lay terms (unfortunately you need a subscription to view).  And something new I didn't know about, they have a link to a blog where you can discuss the article.  Pretty neat, although only 2 people have commented.