Archive for the ‘Biology’ Category

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9.5 Sunflowers vs. Daisies

December 16, 2010

Back in September, I took photographic proof as to why I get so confused when describing my sunflower/daisy patio quilt.

Here are what I believe are small sunflowers:

Notice the dark centers.

Now here are what I believe are daisies:

Notice the lighter centers.

Here are some other pictures of the two types of flowers.

And here is my quilt picture (again):

The darker centers seem to be showing more sunflowers, but the number of petals seem to be saying more daisy.

You see my dilemma now, don’t you.

I am not a botanist, however, so let’s do a little bit of research here.

Actually, when looking at the Kansas guide to Wildflowers and grasses, the flowers I was calling daisy appear to be closer to a Jerusalem Artichoke than anything. 

Photo from the Kansas grasses and wildflower site.

But it is also in the sunflower family, and there really are no daisies in the list of yellow native flowers of Kansas listed. 

A few other sunflower varieties from the website are equally good candidates for the flowers on my quilt, but now I don’t get to call it daisy anything. 

Perhaps sunflower artichoke patio?

I hope this little bit of sunny reminder is a welcome break to the dreariness outside. 

And if you’re not experiencing dreariness, hurray!

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4.7 Podcast 10 – It is in your DNA

March 2, 2010

Podcast Feed 

A long time coming, here is the tenth episode of the Scientific Quilter podcast.  I basically had to relearn some of Biology 101 to get this information, but the end result(s) are a cool and different quilt design.  

This is the Darla version of DNA.  Because I have a very basic understanding, this will be a very basic primer for a unique end result.  

This is still very “sciency”, so for the artsy types, scroll down to the middle to bottom of the post for the DNA design. 

The Science DNA Setup 

Every living thing has in their cells the instructions, the blueprint of life.  This is the DNA or deoxyribonucleic acid found in our cell nucleus.  

We hear about DNA on Court TV shows, crime scene shows, movies, books, your auntie June.  It’s hard to escape hearing about DNA.  

 

Image from Wikipedia 

DNA is made of a series of bases in a specific order.  Cells use DNA to create amino acids which in turn create proteins, which in turn create cells, which in turn create body parts (skipping a lot of steps and details here). 

The DNA is double helix shaped, which is a “twisted ladder” shape.  Each rung of the ladder is made of a series of two bases bonded together.   

DNA has four bases called: Adenine, Thymine, Cytosine, Guanine, which we shorten to A, T, C, G.  A always binds to T, C always binds to G.  

The way that these bases sit on each rung of the ladder determine the order they will code for proteins.  

The DNA will split apart when it is time to use the DNA for coding.  Each rung of the ladder is available to bind to other bases called RNA.  

The Thymine base is not found in RNA, but Uracil (known as U) takes its place.  An Adenine base will bond with a Uracil base on the RNA, otherwise the bases will bond the same as they do on the DNA ladder rings. 

 

Image courtesy of Munich RE 

As you can see from the website diagram from Munich RE, the DNA strand gets opened up, then copied, then coded to what they call codons.  

Codons are groups of three bases.  Then each codon codes for a specific amino acid.  The amino acids are linked together to form protein chains. 

For more information about this picture visit Munich RE 

For another simple picture recap: 

 

Image courtesy of Wikipedia 

   

Making Amino Acids with DNA 

So a set of three bases codes for an amino acid.  The three bases UGG is responsible for Tryptophane, the “sleepy amino acid” that is associated with turkey and thanksgiving.  (And ‘ugg’ is how I feel when I eat too much!) 

There are 20 amino acids and a sequence that starts a protein chain and a couple of sequences that stop a protein chain.  

There are more than 20 combinations of three letters in series (believe it or not) and so several DNA sequences code for the same amino acid. 

I could provide a boring table with all the information about the amino acids (yawn), or I could show you what I found on Munich RE website! 

The image below shows a pictorial way that you can find out which amino acids are created from three bases in order. 

 

Image courtesy of Munich RE 

The image works like this.  The innermost circle is the first base of the sequence, the second ring is the second base in the sequence, and the third ring is the third base in the sequence, with the names of the amino acids vertically coming out of the diagram. 

As you can see starting with A on the diagram, then going to U, then G, you see the word START.  

When this code is found in the DNA the protein knows “hey I need to start making amino acids now”.  Then the next three bases make the next amino acid, and so on, then eventually there is found a stop amino acid and the protein know to stop coding. 

For more detailed information about this diagram and the genetic code: 

Munich RE website about the Genetic Code 

Wikipedia has several DNA-related articles about DNA the Genetic Code, and Amino Acids

Translating DNA to Quilting 

 

The DNA has been translated to quilting by a scientific quilting visionary Beverly St. Clair.  Beverly St. Clair created and started Genome Quilts.  She shows how she represents each DNA base in the quilt on her site: 

Adenine A A quilt square
Cytosine C C quilt square
Guanine G G quilt square
Thymine T T quilt square

Thus, the base sequence,  

GATCGCCCTT 

becomes 

a single row of quilt squares 

So Beverly shows the diversity of the DNA sequence in a quilt. Beverly uses a dark and light contrast to determine the bases represented in the quilt.  For her code, the different corners of dark fabric represent the different bases in the sequence.  

Since the genes that Beverly works on are 600 – 900 bases in length this could become a crazy long process to obtain the quilt. 

Completeing half square triangles like these would be an easy task that could be completed while working on other projects if you use leaders and enders.  

Leaders and Enders from Bonnie Hunter of Quiltville is a technique where you work on one project before and after other projects.  

For such a long and simple piecing process, leaders and enders would help break up the monotony of half square triangles while working on piecing for another quilt.  

I learned about this technique from one of the ladies I have been starting to sew with and it looks like it works great – even though I haven’t been doing any piecing recently to test it out.  

The genetic design comes after the triangles are pieced and so one would only pay attention to light and dark sides when piecing, and how many pieces of each color.

On LabMom’s site, she highlighted the Genome Quilt and did an excellent job in explaining the quilting site. 

   

How do you find your DNA? 

Human DNA is very similar to each other.  We are over 99% conserved which means that a DNA sequence for one human will be very, very similar to the DNA sequence for another human.  

Since we have completed the human genome, there are public websites that hold the code for an entire human on the site.

There are complicated websites such as GenBank from NCBI (given to me by an old classmate of mine) and Ensembl (given to me by LabMom).   

With luck I was able to find part of a mouse gene on the GenBank site.  But I could not tell you how or where I accomplished this.  

A second attempt to find another gene had me running in circles.  I finally found another gene for Oryza sativa Japonica Group, but the I went so many places to get there I STILL don’t know what actually took me there.  

With LabMom’s help, I was able to find a DNA sequence (because she pointed me right to it) on the Ensembl site. This is for the Estrogen Receptor.  If it doesn’t show up in the link, click sequence on the left side.  

Only the letters in red are actually coded.  The rest is just “filler DNA”.  DNA that just takes up space. 

If you’re willing to pay National Geographic and be a part of a larger project, you can order a kit (runs about 100 dollars) and you just send off a cheek swab.  They’ll analyze your DNA (mitochondrial for the ladies and y chromosome for the gentlemen).  

Beverly St Clair says that the folks at National Geographic will provide you with a sequence and show how your sequence differs from the reference sequence and this is how Beverly obtains her DNA samples currently. 

 

If you want to go with other organisms besides humans and mice, here is a quilt from the hepatitis C gene that Beverly St Clair did.  You can see that with Beverly’s process color is part of the design.  

Beverly said that the Hepititus C quilt was for a nephew who was sequencing the Hepatitis C gene, so that is where she obtained the DNA sequence for that. 

This whole thing is so Madame Defarge.  Which is what makes it interesting to me. 

   

What’s next in Quilting (what did I do with it) 

Here’s where I was thinking about the next step.  What else could you do with a quilt?  I completely respect and appreciate the work and time done already by Beverly St Clair.  

But the Scientific Quilter likes to think about what else could be done. 

There was a very good article in the American Quilter magazine March 2010 issue. 

This magazine has an article that highlights Beverly St Clair, Marjorie Taylor who quilts brain scans, Karylee Doubiago who quilts with x-rays, and Maris Azevedo who quilted her CT scan of lung tissue.   

There is not any more description in this magazine about the DNA quilt than these medical quilts.   It also didn’t say more than Beverly’s own website. 

Being fairly squeamish, other than the DNA quilt, which is more academic and theoretical than the others, I will probably stick with the DNA idea over the other medically based quilts.  

If I went that one step further, from just DNA to Codons to Amino Acids, how would I do it? 

First I started with this other website that LabMom found that organizes your thoughts – a concept map bubble website called bubbl 

This was a direct response to the Munich RE image I saw earlier.  Even though there is a lot of customization on bubbl, I got started on my amino acid bubble and decided its best left to just use the Munich RE site image above. 

I couldn’t let that image sit all crooked and uneven like that.  I’m a quilter, for goodness sake.

Also this quilt idea would not code anything, but would provide the code for what I wanted to do next. 

However the bubbl website would be good for a flow chart of a genetic trait! (another quilty idea).  Fusible web or applique would be the way to go with bias bars traveling from one idea from another.  

In bubbl, you can chose to sign in and save your designs or just export them as is. 

The DNA Quilt Design

Then I was thinking about the codon/amino acid idea.  You could designate colors for each DNA or RNA base. 

 

And then you could create boxes (my original idea was flying geese, but this idea seems to have better continuity to it).  The boxes are broken up into three sections, one for each DNA base of the codon. 

 

Here is the completed design.  There are several key things about this design. 

  • There are lighter sections and darker sections.  The lighter sections represent a protien that is coded for.  
  • The first lighter block starts with AUG at the top and the last lighter block ends with UGA.  Starts with the start codon and ends with one of the stop codons. 
  • The darker sections are the filler design.  There is no start codon until the lighter section of the quilt. 
  • You could sash with dark or light fabrics.  
  • Each box actually has 6 sections, which would be good quilt as you go sections. 
  • The top three sections are the RNA side – the amino acid side which is actually the end result. 
  • The top of the box codes with Uracil not Thymine. 
  • The bottom half of each box is the DNA side, the original code which produced the RNA side.  
  • The bottom of the box codes with Thymine, not Uracil. 

 

Just how did I arrive at the final quilt? 

Warning:  I now believe that the following process does not have the correct translation (or maybe it’s transcription step).  So I left out a step here.  But I did get to a coded result anyway. 

If you’re taking my process as correct for any science project or homework assignment, just be warned that a) it’s not nice to plagarise, and b) you might not have the correct result. (end of Warning)

Before I arrived at the diagram I had to do a little science and reasoning. 

This is the original code I started with to create this quilt: 

TACCAAGCCCTGCGGAGCAAGGTACCTCACACTTCATGAGCGAGTTAAGATGGGTTTCAC 

AATTTTTCAAGCAAGGAAACGGGCTCGGAGGTCTTGAACACCTGCTACCCAATAGCAGAA 

But T bonds with A, C bonds with G, and U replaces T in the final product.  So for the RNA these letters need to be switched around.  I’ll replace T with A and C with G, G with C, and A with U. 

I found it helps to first replace these to a different letter such as X or Y when doing replace all in microsoft word.  

AUGGUUCGGGACGCCUCGUUCCAUGGAGUGUGAAGUACUCGCUCAAUUCUACCCAAAGUG 

UUAAAAAGUUCGUUCCUUUGCCCGAGCCUCCAGAACUUGUGGACGAUGGGUUAUCGUCUU 

Now breaking it up so I can see the codons better: 

  

AUG  GUU  CGG  GAC  GCC  UCG  UUC  CAU  GGA  GUG  UGA  AGU  ACU  CGC  UCA  AUU  CUA  CCC  AAA  GUG  

UUA  AAA  AGU  UCG  UUC  CUU  UGC  CCG  AGC  CUC  CAG  AAC  UUG  UGG  ACG  AUG  GGU  UAU  CGU  CUU 

   

I see two start codons and an end codon. The code in between is “filler DNA”.  There is more to the sequence but this is all I’m doing today folks. 

   

AUG  GUU  CGG  GAC  GCC  UCG  UUC  CAU  GGA  GUG  UGA  AGU  ACU  CGC  UCA  AUU  CUA  CCC  AAA  GUG UUA  AAA  AGU  UCG  UUC  CUU  UGC  CCG  AGC  CUC  CAG  AAC  UUG  UGG  ACG  AUG  GGU  UAU  CGU  CUU 

  

Reading the graph from Munich RE shows me exactly which amino acids are coded for.  You could quilt this information in each box. 

  

START – Valine – Argine – Aspartate – Alanine – Serine – Phenylalanine – Histidine – Glycine – Valine – STOP 

   

   

Here are a couple of in-progress pictures of me while I was creating the quilt design above: 

   

 

 

So what if I made a mistake?  Then as LabDad said to LabMom in her post, it’s like you introduced a mutation.  Genius! 

What gene exactly did I post?  First two lines of the gene from site: http://uswest.ensembl.org/Homo_sapiens/Gene/Sequence?g=ENSG00000139618 (clicked sequence on the side) 

Which I think is the Estrogen Recptor that LabMom sent me in an e-mail.  Thanks for your help LabMom. 

 

Where is the Gel Electrophoresis Quilt idea? 

Warning #2: This section may contain some errors due to a mix-up of understanding on protein gel electrophoresis and DNA gel electrophoresis. 

I never took BioChem and I am thinking it shows by my confusion here.  If you would like to explain the difference to me, please feel free to send me a (nice) e-mail. End of Warning.

Gel Electrophoresis is a technique where you take proteins, cut them up into sections, make them charged (usually negatively), and then electrify them in this gel.  

The electric charge pulls the large nonpolar molecules slowly across the gel, and pulls the small polar charged molecules quickly across the gel.  

Usually in the crime scene analysis Gel electrophoresis is a way to compare with a reference sample.  Say there is some crime scene DNA and you have suspect DNA and you run them both parallel in the gel electrophoresis plates at the same time.  

Then you stain the gel to see it and hold it under blacklight.  If the suspect DNA is broken up in similar patterns to the crime scene DNA then there is a higher chance that the suspect was at the crime scene. 

 

Image courtesy of Wikipedia 

Or you can see the types of proteins in a sample this way.  This would be a good quilt design as well. 

I have already designed a quilt that looks very similar to this – the Spectra Quilt idea.  

 

Since I don’t have any proteins to analyze, I would refer back to the website that shows your blog website as DNA for inspiration on this. 

If I would quilt any gel electrophoresis style of quilt, I would quilt this as my quilt.  Again I would use bias bars for the lines. 

 

 The idea of gel electrophoresis is very similar to color chromatography.  The idea of moving some particles faster than others, spreading particles out so you can see the differences. 

I found a nice website that shows how to make your own gel electrophoresis box and separate colors the same way as color chromotography. 

The New York Times posted this article, and I think you could translate this DNA research into quilting too, but I’m not attempting it.

Other fun sites 

Code Organ This synthesizes your website into music based on what you write about. 

Bubbl A great organizational tool for concept mapping

Customized Graph Paper A great tool for drawing your own quilt designs.

Check out my Quiltversary post, and my adding audio to podcast post.

Thanks go out to my commenters and correspondents

Lynn, LynnAnne, Jill, Michele, Irene, Colleen, Toni, LabMom, Allyson, Kelley, Ruthann, Brye, Beverly St Clair, and Robyn, Jennifer, Reeze, Valerie, Ingrid, Sarah

And thanks to Munich RE and Beverly St Clair for letting me use their images on my site.

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4.4 Podcast 10 Preview – It’s in your DNA

February 16, 2010

Finally.  I’ve finally given up on learning as much of this DNA thing as I am going to learn and so the next podcast – the big 1 – 0 here comes the Deoxyribonucleic acid.  (eek look at that big biology word!) 

I’ll present the original DNA quilt, talk (more) about the medicine magazine article that I finally received in the mail, and share another cool site. 

Then I’ll share some of my inspiration on creating the ‘next step’ of a DNA quilt with an ‘amino acid’ quilt. 

Does anyone out there in quilt-land have a DNA inspired quilt already?  Or a DNA inspired idea already?  If so, let me know, and I’ll put you up on the blog post. 

And yes I will highlight the Genome Quilt creator Beverly St Clair too.

Image from wikipedia

This coming week and weekend is a smattering of quilty commitments and playtimes and so I’ll try to get the podcast together and up shortly, but it may be posted by sometime mid next-week.  Thank you for your patience.

And I did get one response to “what happens to episodes 1-4 in iTunes”, and so thanks go out to Lynn.   I want to see if her experience is the same as others out there. 

If you’re a new listener and just started listening to my podcast recently if you enjoy what you’re listening to, can I ask that you check out and try to download episodes 1 – 4 on iTunes.  Then can you e-mail me (scientificquilter@gmail.com) and tell me what happened? (even if it DID work – that would be super helpful)

I’m getting some information from my hosting site on a FAQ written 2 years ago, but a different experience from my listener.  There are no forums for this hosting site (not wordpress) to ask questions, so I am using listener feedback to help me diagnose and decide what to do next.  Then I’ll stop asking about it – I promise.

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1.8 Podcast 3 Preview Color Chromatography & Crocheted Cells

November 24, 2009

What does a coffee filter or white fabric, markers, isopropanol, a bird drawing, have in common? 

Something I saw on Craftster from user: IamSusie  and the following post: Sharpie Dye Color Bursts gave me another experiment idea.  IamSusie got the idea from Happy Things and she saw it on Steve Spengler Science.  If you click on any of the links, you can see the Color Chromatography in action. 

Not to limit myself to finding one amazing science fiber art project on Craftster, I also found Sally Le Strange and her post about a Crochet Plant Cell Pillow who made her science craft for a school project and got an A+.  I like both of these projects enough to highlight them in my next podcast.  But first I have an idea about the chromatography one before I put it together.