DNA-RNA MAKEUP

Heinrich Roder lab - Protein Folding Picture protein folding pictures

Leading genomics researchers site.

        Including: C. Ventor, H. Smith, F. Collins, H. Morris, 

         A. Slovine, ....


Genome/DNA BASICS

            Also: Bio-medecine and Bio-medecine mutations explained 


FEED | After Darwin: Seven Ways of Looking at a Protein 

Atlas of Protein Side-Chain Interactions

Picture It -- Biochemistry visual histone 3D graphics

BERC Publications:

        A few words about DNA, Histone Code and chromatin A-G-C-T

        Genome structure 


Bio-Animation: cells - tissue - human body

Genetic Material

NIGMS -- Inside the Cell

BBC News | SCI/TECH | 'The end of the beginning'

Gene Gives Clues to Melanoma

Thinking Local About GM Foods

FEED | Science - Living Language --- CellaML & GEML



UCSC grad student puts genome browser on the Web

                     (2/13/2001)


NEW: Genome Browser

Pufferfish Genes Are People, Too (comparative genomics)

Gene Map: Help or Hype? Feb. 10,2002


     With Just a few days before the complete human genome map is to be
     published, we learn that there are less than 35,000 genes in humans,
     when it is known that there are more than > 50,000 genes in a simple
     Pufferfish?
     This whole project MUST be some kind of joke!

     Now they are finding that the gene decoder chip they used, was missing
     sensors for certain sequences:

More on gene chip technology

And yet more .....

New Scientist: Chip chop ( A flaw in a widely used

            "gene chip" stops some research projects dead )
 


********************************************************************** 


Researchers Cut Gene Estimate (we have the same amount of genes 
                 as a head of corn) scientists are bewildered!

DNA Junkyard Yielding Gold

Human Mutations: Blame Men

Interesting Facts:  Cool Facts - 


          Most living cells contain a nucleus, a semi-enclosed
          compartment where the cell's DNA (genetic material)
          is stored, but bacteria just have a single,
          looped DNA molecule, tangled into a mass called
          the nucleoid.

          There are over 62,000 miles (99,780 kilometers) of veins,
          arteries, and capillaries inside of each of us.

          The Smallest Genome --> A bacterium of the genus Mycoplasma
          has the smallest number of genes of any known
          self-reproducing organism. (Some viruses have fewer genes,
          but they need to use another cell's DNA machinery to
          reproduce.)


DNA Extraction from Cheek Cells

How to Extract DNA From Human Cheek Cells
From your Biology Guide

Lab method for extracting DNA from human cheek cells. 

Difficulty Level: Easy   Time Required: 15 minutes
Here's How:

1) Gather together sodium chloride, liquid soap, 2 glass beakers, 
   bottled and distilled water, 2 test tubes, test tube stoppers, 
   glass rod, a plastic cup and rubbing alcohol.
2) Place 8 grams of sodium chloride in one of the beakers and dissolve 
   with 92 milliliters of distilled water.
3) In a second beaker, combine 25 milliliters of liquid soap with 75 
   milliliters of distilled water.
4) Pour 1 milliliter of the sodium chloride solution into a large test 
   tube.
5) Pour 10 milliliters of the bottled water into a plastic cup and swirl 
   the water in your mouth for 30 seconds.
6) Spit the water back into the cup and pour the contents into the test 
   tube containing the sodium chloride solution.
7) Add 1 milliliter of liquid soap to the test tube.
8) Cover the top of the test tube with a stopper and gently mix the 
   contents by turning the test tube upside down and right side up.
9) Add 5 milliliters of the rubbing alcohol to the test tube making 
   sure to pour it at an angle down the side of the test tube.
10) Wait for about 5 minutes and watch as the DNA floats to the surface.
11) Pour 1 milliliter of alcohol into the second test tube.
12) Use the glass rod to remove the DNA from the first test tube by 
    twirling the rod in a circular motion.
13) Place the DNA into the second test tube containing the alcohol. 



Tips:

If more DNA is desired, repeat the procedure making sure to wash 
your mouth more vigorously in step 5.
 - - - - - - - - -  - - - - -

DNA AND GENOMES

Introduction:

DNA is a relatively simple molecule consisting of three chemical 
components: a phosphate group; deoxyribose a five-carbon sugar; 
and one of four nitrogenous bases. These bases belong to one of 
two categories of chemicals: purines or pyrimidines. Adenine and 
guanine have a double-ring structure; these are purines. Cytosine 
and thymine are pyrimidines; they have single-ring structures. 

The three chemical components of DNA are assembled into monomers 
termed nucleotides (commonly referred to by letter designations 
A, T, G and C denoting the type of nitrogenous base attached).

DNA is a polymer of two chains of nucleotides that form the shape 
of a double helix. The sugar-phosphate components are oriented to 
the outside of the molecule and are linked via phosphodiester 
bonds. The two chains of nucleotides are oriented in an antiparallel
configuration; one chain is oriented 5’ to 3’ while the other is 
oriented 3’ to 5’ where these numbers refer to the orientation of 
the numbered carbons in the deoxyribose (see Figure 2-5 in 
Griffiths et. al., 2002). ). The two strands are held together 
by hydrogen bonds between the nitrogenous bases. There are only 
two types of base pairings that occur: A with T and G with C.

A is associated with T via two hydrogen bonds while G is associated 
with C via three hydrogen bonds. Typically, we use the base pair 
(bp) as the unit of measurement of length of DNA. A thousand base 
pairs is termed one kilobase (Kb).

Genetic information is stored within the nucleotide sequence of the 
DNA and organised into discrete units called genes. The complete 
set of genes in an organism is termed a genome.

Genomics is the study of the structure and function of entire genomes. Although genomes
from all organisms are composed of DNA and contain genes, there are 
huge differences in terms of size, complexity, and organization of 
genomes. Typically, genomes of prokaryotes are smaller and less 
complex than eukaryotic genomes.

It is possible to extract DNA from any living organism. If large 
enough quantities of starting material are used, DNA may be 
precipitated out of solution and observed with the naked eye,
appearing as a cloudy white mass. We can also use a technique 
called agarose gel electrophoresis to visualise DNA. 

This technique in conjunction with a technique called restriction 
endonuclease digestion allows us to compare in a more quantitative 
fashion DNA from a variety of sources.

Electrophoresis literally means "to carry with electricity". 
Negatively charged phosphate groups in the backbone of the DNA 
helix result in a net negative charge for all DNA molecules. 
Hence, when placed into an electrical field, DNA migrates towards 
the positive pole. The smaller the fragment of DNA, the faster 
it migrates. If DNA fragments migrate through a solid gel matrix, 
the differences in migration speed are more obvious and a small
change in size can be readily detected. To determine the actual 
sizes of the fragments, a marker consisting of DNA fragments of 
known size is run along with the samples.





Now the strange marriage of a film about DNA and 
Strange Culture, A new film by Lynn Hershman LeesonThe
surreal nightmare of internationally-acclaimed artist
and professor Steve Kurtz began when his wife Hope
died in her sleep of heart failure.

lda Swinton, Peter Coyote, Thomas Jay Ryan, Josh
Kornbluth and Steve Kurtz



Just throwing in a few random comments as a college biology
student:

E. Coli is nothing to be afraid of--the variety which
I used in more than half of the labs in my intro bio
class at the University of Minnesota is completely
harmless, and is used in a wide variety of classroom
exercises and basic experiments. I'm perfectly willing
to believe that there are many scientists and other
interested individuals out there who have private
labs that they work on it at.


The same goes for the "DNA extraction kit," which could
be a wide variety of things: again, in my intro bio
class, we extracted DNA using a microfuge and some
standard lab equipment (beakers, reagents, etc.).
Throw in an incubator, which can easily be rigged
out of household equipment, and you basically have
everything you need for gene injection. Yes, it
would be necessary for a bioterrorist to use this
equipment. But it also is ubiquitous in even the
most elementary of bio labs, and none of this is
stuff whose sale or possession (as far as I know--
other than some of the chemicals involved) is
regulated in any fashion.


strangeculture.net
aspace....?


nodalresearch


From Kurtz recent book, you decide if you are being played.

Steven Kurtz and CAE's work has been shown in major
museums around the USA and the world without incident
in the past, and in fact is being shown right now at
the Massachusetts Museum of Contemporary Art.

There's a story about Kurtz in the L.A. Weekly today.
The reporter talked to the FBI.
phttp://www.laweekly.com/ink/04/28/news-lewis.php" target="_blank">
As to why the FBI is pursing this, perhaps it has
to do with the artwork itself, which would allow
everyday consumers to test food for genetic
modifications.

For more info, see

caedefensefund



bioluminescent rabbit


"Alba", the green fluorescent bunny, is an albino rabbit.


At Ars Electronica, we did a whole festival
on Life Science as art. Artists, including Steve,
publish their works, talk about the impact, and
often teach.


She only glows when illuminated with the correct light.
When (and only when) illuminated with blue light
(maximum excitation at 488 nm), she glows with a
bright green light (maximum emission at 509 nm).
She was created with EGFP, an enhanced version
(i.e., a synthetic mutation) of the original
wild-type green fluorescent gene found in the
jellyfish Aequorea Victoria. EGFP gives about
two orders of magnitude greater fluorescence in
mammalian cells (including human cells) than the
original jellyfish gene [2].



Among the most common domesticated of mammals,
the dog is a quintessentially dialogical animal;
it is not self-centered, it is empathic, and it
is often prone to extroverted social interaction
[3]. Hence, my current work: GFP K-9. GFP stands
for Green Fluorescent Protein, which is isolated
from Pacific Northwest jellyfish (Aequorea Victoria)
and which emits bright green light when exposed to
UV or blue light [4]. Wild type Aequorea GFP
absorbs light maximally at 395 nm and the
fluorescence emission spectrum peaks at 510 nm
[5]. The protein itself is 238 amino acids in
length. The use of the Green Fluorescent Protein
in a dog is absolutely harmless, since GFP is
species independent and requires no additional
proteins or substrates for green light emission.
GFP has been successfully expressed in several
host organisms and cells such as E. coli, yeast,
and mammalian, insect, fish and plant cells [6].
A GFP variant, GFPuv, is 18 times brighter than
regular GFP and can be easily detected by the
naked eye when excited with standard, long-wave
UV light. GFP K-9 (or "G," as I affectionately
call it) will literally have a colorful
personality and will be a welcome member
of my family. Its creation may be years or
decades away, because it faces several
obstacles, among them the mapping of the
dog genome. The number of genes in the
entire dog genome is estimated at about
100,000 [7]. However, collaborative research
is under way to map the canine genome, the
results of which will eventually enable
precision work at the level of canine
morphology and behavior. Independently
of the subtle phenotypic alteration, i.e.,
the delicate coat color change, GFP K-9 will
eat, sleep, mate, play and interact with other
dogs and humans normally. It will also be the
founder of a new transgenic lineage.

The Ultimate Gamble!
 genome, genetic sequencing, Bio-Technology, Bio-Engineering, Proteins, 

nbsp;       gambling on genetic drugs, HGP, Bio-Ethics, Viagra, etc.

     Studied extensively about PERL and it's heavy use in the HGP
Prior to writing "The Ultimate Gamble" site. Research includes list below.


    CN's bioinformatics & other WWW training links ie. DBMS,  bio-sequence search sites, protein pattern searching, gene finding, general bio-info

   Below is a list of some of the topics covered on the site:

     Protein structure/homology modeling 

     Sequence comparison 

     Barton tutorial pages 

     3D molecular  structure viewers 

     Lists of bioinformatics sites 

     Tool-center pages (list of biotech tools) 

     DNA micro arrays 

     Genome-scale analysis 

     Gene regulation 

     Perl in bioinformatics 

     International nucleotide sequence 

      database collaboration 



    
Perl 5 by Example: Introduction

    
How Perl Saved the Human Genome Project.

    
Problems encountered with perl (bio dot perl dot org)

    
Sequences of related Proteins Using 3 sequencing techniques. (SAM-T98, PSI-BLAST, and Intermediate Sequence Search (ISS) procedures.
   (SCOP) structural classification of proteins database. 

    
In Silico Biology - Articles and databases (predictions and databases of protein folding, behavior, and characteristics)


DNA and new cellular superconductivity theory: (On training)

Alternate Medical Site

      ie. MCT OIL and cancer fighting 

       Fucoidan  With JavaScript slide show! 


Cancer fighting Fucoidan info site

NEW! Great links! Jan-22-2004

Another addfreestats returns example below: