Evolution Turned Upside Down

Midbody and exosome research are hot topics right now! There is even an entire journal devoted to them and other subcellular particles: Journal of Extracellular Vesicles. Lots and lots of papers on this! Check out my models that demonstrate a connection between midbodies, exosomes, and cellular differentiation!

How TADs can communicate with each other and alter gene expression via enhancer connections based upon my models for DNA replicons.

Ring chromosomes in humans, animals, and plants are well known to the scientific community. They are the result of chromosomal translocations and are usually deleterious and unstable. The current thinking is based on a linear chromosome model of replication. My models are circular by nature. As a result, they can better explain how these circular chromosomes come to be during aberrant chromosomal separations.

TADS AND ENHANCERS PRESENTATIONDownload

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If eukaryotes have linear chromosomes, what the heck are these doing in mouse cells?

Circular DNA’s  can be found in the nuclei of human cells. They are so small that roughly 24,000 of them could fit inside the smallest human chromosome. Since they are not part of the chromosome, they are easily separated out from the main DNA without damaging them. However, much larger DNA circles are subject to breakage under the hydrodynamic shear used to separate DNA from non-DNA materials. This would almost certainly occur if they were part of the chromosome.

“BACTERIA” MADE US WHO WE ARE TODAY?

Did you know Archaea have circular chromosomes?

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If you work with tissue culture cells, try out my protocol and see what you get!

In 1988, I graduated with my PhD at Ohio State University. The title of my thesis is “Eukaryotic DNA Superstructure”.  I continued my research at OSU and discovered something so amazing that it blew our collective minds.  I had stained cells from mice to illuminate their DNA content. Most researchers would have expected to see brightly stained strands of chromatin, the stuff that makes up chromosomes. I saw the same exact thing too, until I chemically teased the chromatin apart. That’s when I discovered brightly illuminated, beaded circles in a wide variety of sizes. This was a novel and controversial finding that I thought would spark further research. But the scientific review process was as painful as it was illuminating. Nobody contacted me for further inquiry, not even today!

So I am reaching out to my fellow scientists, hoping to stimulate discussion, share information and, ideally, encourage additional scientific research. Is this discovery a biological sea change in understanding?  Can the discovery process be reproduced? Could cancer cures be just around the corner, if we understood chromosome structure better than we do now?  Do these questions warrant further investigation? Without additional research, we will never know. Contact me at fabernathy@sbcglobal.net.

The classic linear DNA model for human chromosomes violates the second law of thermodynamics

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HOW CAN ANIMAL CHROMOSOMES BE PUT TOGETHER VIA ENDOSYMBIOSIS?

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How Acid Hydrolysis Revealed the Circular Nature of Eukaryotic DNA

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When it Comes to Chromosomes, You Have Been Misled

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This is actually two blogs in one

Blog #1 can be found under the page tab: General Posts. This is the one you may want to check out first. I update the blog here whenever I discover new exciting information.

Blog #2 is about the fallacies associated with the study of science and how they interfere with the general pursuit of knowledge and discovery. These are under the page tab Rantings of a Mad Scientist.

The biological models tab contains a list of reference links relating to the models that is periodically updated.

Throughout Blog #1, you will find a variety of microphotographs, some of them repeated for emphasis. Here is an example of one of them:

   (click image to enlarge)

It’s pretty, mysterious, and full of little beaded circles that appear to be emanating from a larger “mother ship”.  At least, that’s how my Ph.D. advisor described them at Ohio State University almost 25 years ago. These were actually discovered after I had already completed my Ph.D., so you won’t find them in my dissertation or any subsequent manuscripts. They came out of mouse cells that were in the process of dying under the microscope. The green color is due to fluorescence from a dye the cells were exposed to that allows nucleic acids to light up under this kind of microscope.  I managed to “coax” them out of dying cells using dilute acid that partially degrades the DNA.

If you are a DNA biologist, you may want to skip down to the part where I “boil” the blog down regarding origins of replication, promoters, enhancers, and splice sites.

Since I have no idea of your level of mastery of biology over the years, I am going to assume that you at least know something about human chromosomes and perhaps other mammals. If you don’t, you may need to do a quick google review before you go any further. If you find this intimidating or overwhelming, I will give you the “skinny” on it. You can always review it later.

Here is how a typical textbook depicts a mammalian chromosome:

Looks like four weiners stuck together. If you check more closely, the textbook will indicate that each “weiner” is composed of a single, tightly wound, continuous thread of DNA covered with other materials like proteins. Such a complex is called chromatin. This thread travels from one short weiner to the adjacent long weiner. The weiners on the bottom are considered as “copies” of the ones on top as long as sex isn’t involved. The two weiners (long and short), together with their copies are connected together in the middle by a structure called a centromere.

There is a particular kind of chromosome called a lampbrush chromosome discovered  back in the 1880’s. You can get a good idea of what they look like using the Wiki link above. These chromosomes have loops of DNA sticking out from them, making them look like old-fashioned lampbrushes. It is generally assumed that these loops are merely part of a continuous structure of DNA making up the entire chromosome. However, they are not randomly produced and have defined fixed locations within the chromosome. Studies in the late 1970’s show such loops appear to be universal among all kinds of chromosomes. A good source for understanding the relation of DNA loops to global chromosome structure can be found in the following 2002 NIH reference link. These loops behave like individual DNA domains, as if they were separate chromosomes themselves. Such an arrangement indicates complex temporal coordination of gene expression. In other words, these DNA domains cooperate with one another for the greater good of the cell. How these structures may have come to be part of our chromosomes is the main subject of this entire blog: smaller chromosomes building bigger chromosomes.

Bacterial chromosomes are generally circular in shape and have a wide range of sizes. A circle with a circumference of 340 microns (millionth of a meter) would be in the lower size range. Breaking this circle and laying it out end to end gives you a linear length of 340 microns which is 34 times the diameter of an average human nucleus. There is more than a million microns of DNA within this nucleus. To give you some idea of this magnitude, check out the graphic below:

We need more than 29 of these “blocks”, each containing 100 threads                                                                          of DNA to fill in the human nucleus with all 46 chromosomes.

That’s a lot of DNA to fit inside that tiny little nucleus, don’t you think? However, according to textbooks, all of that DNA is fused together into just 46 pieces of “rope”called chromosomes. Now imagine a piece of DNA like the one shown above breaking off or replicating from the main strand of a relatively small human chromosome, say one that is only 1700 times the length of the diameter of the nucleus. Now imagine this piece of DNA somehow coming back on itself and ligating the ends to form a  340 micron circle. Not much wiggle room is there? Even if there was, the chances of this  meandering 340 micron thread of DNA spontaneously doing this is pretty remote at best. Yet, somehow it happens. Textbooks indicate that pieces of DNA the size of bacterial chromosomes can form into small circles within the human nucleus. You can learn more about this under general postings.

Wouldn’t it make more sense if that piece of DNA was circular to begin with? Imagine again, circles of DNA attached to other circles like grapes on a vine, easily plucked off from the main body. The photomicrograph shown above shows exactly this, only the grapes are beaded circles. Could these circles be a plucked version of lamp brush loops?

You would think scientists would be jumping all over this, wouldn’t you? You would be wrong. Indeed, the greatest mystery of all may be why they are NOT jumping all over this. After all, it has been 28 years since they were first discovered, and still nothing crops up in the literature. Now why is that?

You will find more about this under Blog #2.  Suffice it to say, when a well-respected scientist tells you privately that “they will kill you for this!”, something is definitely rotten in Denmark, don’t you think?

Well, the stakes are high here. Many people are completely invested in a linear DNA human chromosome model, even to the point of sweeping aside discoveries such as these. Just check the literature and you’ll see what I mean. So in the great scheme of things, should it really matter to you how a human chromosome is put together? Well, only if you want to expand our knowledge of  genetic diseases, aging, human development, and cancer, among other things.

You realize this doesn’t have to be the end of this. I know there are some very wealthy philanthropists out there looking for a worthy cause. All they have to do is contact me to learn more and how to move it forward. If you know anyone like that, please ask them to contact me.

Questions and comments are welcome.

Best regards,

Dr. Frank Abernathy

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If you are a DNA biologist, please continue reading…

Let me boil things down about this blog as best as I can in as little space as possible. I believe the following things about chromosomes:

They are comprised of interconnected circles of chromatin joined together at their origins of replication. These circles are capable of fusing together during differentiation or completely separating, resulting in the loss of DNA circles.

Paired origins of replication from adjacent replicon circles of DNA give rise to promoters of transcription by fusing together and losing DNA vital to replication.

Paired origins of replication give rise to enhancers of transcription and/or replication when they separate from one another and one of them is discarded.

Paired origins of replication from adjacent replicon circles of DNA give rise to splice sites by fusing together and losing DNA vital to both replication and transcription.

These processes occur through phylogeny and ontogeny. In other words, these events occurred eons ago (ancestral) or they occur only when the embryo begins to differentiate into tissues (species specific).

You will understand what I am saying more clearly if you click on this video link. It is a roughly 40 minute presentation.

Here is some preliminary evidence to support my hypotheses. There are many additional references within this blog, my website, dissertation, and manuscripts. I would appreciate any additional information you can provide to help me fill out the table below:

1a) http://www.cell.com/ajhg/abstract/S0002-9297(07)62467-7 (2001)AT rich palindromes are associated with translocations

1b) http://hmg.oxfordjournals.org/content/10/23/2605.full (2001)Long AT-rich palindromes and the constitutional t(11;22) breakpoint

2) http://www.pnas.org/content/79/2/381.full.pdf (1982)SV 40 origins of replication missing AT rich regions within the palindrome could not replicate

3) http://genesdev.cshlp.org/content/2/9/1115 (1988)Enhancers required for replication once an embryonic nucleus is formed in mice.

4) http://nar.oxfordjournals.org/content/16/23/11207 (1988)Do transcriptional enhancers also augment DNA replication?

5) http://www.ncbi.nlm.nih.gov/pmc/articles/PMC400889/ (1989)Replication origins can act as enhancers for amplification of other origins in Drosophila.

6) http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4403523/ (2015)multiple origins of replication in bacteria. Double origins of replication.

7) http://www.ncbi.nlm.nih.gov/pubmed/9453148 (1997)TATA box in origin of papillomavirus 18 and requires and enhancer of replication

8) http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1000454 (2009)CpG Islands: Starting Blocks for Replication and Transcription

9) http://www.ncbi.nlm.nih.gov/pmc/articles/PMC401248/  (1989) An enhancer located in a CpG-island 3′ to the TCR/CD3-epsilon gene confers T lymphocyte-specificity to its promoter.

10)http://www.sciencedirect.com/science/article/pii/S0014579303010925 (2003) Methylation at CpG islands in intron 1 of EGR2 confers enhancer-like activity

11) http://www.ncbi.nlm.nih.gov/pubmed/12704365 (2003)Characterization of a palindromic enhancer element in the promoters of IL4, IL5, and IL13 cytokine genes.

12) http://www.genomebiology.com/2004/5/12/251 (2004) The origin of recent introns: transposons?

13) Mapping of a replication origin within the promoter region of two unlinked, abundantly transcribed actin genes of Physarum polycephalum. (1996)

14) Origin pairing (‘handcuffing’) as a mode of negative control of P1 plasmid copy number.  (2001)

15) Bacteria may have multiple replication origins (2015)