I can remember when students in high school (those who could afford it) were sent to detention for using a calculator in math classes.
Monthly Archives: July 2017
Just saying:
The haploid human genome contains approximately 3 billion base pairs of DNA packaged into 23 chromosomes. Of course, most cells in the body (except for female ova and male sperm) are diploid, with 23 pairs of chromosomes. That makes a total of 6 billion base pairs of DNA per cell. Because each base pair is around 0.34 nanometers long (a nanometer is one-billionth of a meter), each diploid cell therefore contains about 2 meters of DNA [(0.34 × 10-9) × (6 × 109)]. Moreover, it is estimated that the human body contains about 50 trillion cells—which works out to 100 trillion meters of DNA per human. Now, consider the fact that the Sun is 150 billion meters from Earth. This means that each of us has enough DNA to go from here to the Sun and back m LINKED HERE.
More trivia: Chromosomes labeled with fluorescent probes for sequences on the p arm near a telomere, suggests that the chromosomes may have some areas of the p arm which are more prominently located at the periphery of each of their respective chromosome territories. This suggests some sort of coordinates for order of the all chromosome territories within the nucleus. Published as this article: https://www.researchgate.net/publication/8469152_Zimber_A_Nguyen_QD_Gespach_C_Nuclear_bodies_and_compartments_functional_roles_and_cellular_signaling_in_health_and_disease_Cell_Signal_16_1085-1104
Just thinking about what images i have seen, i have this suspicion that each pair of chromosomes is linked at some point to a pair of nuclear pores (maybe on the p arm near telomers) and that the distance between the pair is something on the order of about 75 degrees (as an arc) apart and that extensions to the various nucleoli for transcription are ordered as well. most of that sentence is found in articles, except the radial separation..at least I haven’t seen reference to that yet. Maybe not all chromosomes are separated by the same angle… looking at images visually, it is easy to be mislead because of the random flattening of nuclei during preparation for fluorescent dye labeling.
here is an image from an review article Meaburn and Misteli which shows three green line trackings. The central image from that would fit the TEM images of nuclear chromatin (at least condensed chromatin) best.
Iterations, reiterations, repeats, re-repeats, mirror and flip
ALL ART AND SCIENCE…. iterations, reiterations, repeats, mirror images, fitting things together.
Repeating designs, maybe with slight variations in size and color, is not new really, and here is an example on the brink of recorded history, the construction of the first temple, columns (jachin and boaz) with the famed two rows of pomegranates, repeating fruits, likely mirrored vertically and horizontally.
More ancient art has repeats than art created in the last few hundred years, the former comprising clustered natural objects, fruit, animals, or this and that, and patterns flowing in circular or rectangular borders, or radial distribution.
All these visual cues (and auditory, in the case of music) are samples of humans bringing “order” from what might be considered “chaos”. Even not so much order that the artwork becomes monotonous or painful, or annoying, but just enough repetition, with variation, to be soothing and stimulating at the same time, and to give us the feeling that “someone has intentionally ordered” the images or sounds. It seems that observing order has a positive influence on society at large. I don’t need to do much more than type in a google search for “effect of visual environment on social behavior” to drag up over 2,000,000 posts.
It would be fun to know how far back slightly ordered rhythm and visual stimuli can be sensed by animals (and plants). (I bet it is there from the beginning, a billion years ago — who would be surprised at that? not I).The light dark of day and night is sensed by plants and animals alike, that certainly is a reiteration. Temperature is sensed as well, that also reiterates, and has been amply programmed into our genome and epigenome. Going out on a limb here with an idea which has bounced around in my head for a long time, and that our bodies are also tied into the rhythm of food, that is, we benefit from eating only summer fruits and veggies during that season, and from winter harvested items in winter. Not just in terms of cost, or availability (because all foods are now available all year around) but because our evolution has been tied to these reiterations for millions of years. (haha… so here in the last 50 years we think it is OK to eat potatoes in summer!! watermelon in winter–we are at best–naive, at worst, obnoxiously arrogant).
Repetition, reiteration, symmetry from partial symmetry, radial symmetry from bilateral symmetry — all part of our creative spirit. And early on, i think the simple horizontal mirror, or radial spreading of an icon (coins are good example that three pomegranates, menorahs, and then there is this mosaic below which really presses radial iteration to the outer limits, ha ha). 
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I think of all the crafts, designs, and architecture which have the over-and-over-up-down-mirrored patterns… would it be cool to know what in the human mind (not even just my mind) loves the trick of horizontal and vertical mirroring, as well as repeats, splits and size variation? It is in music too! Think of how many stanzas of the same base drum rhythm can be found in a single tune. Bach was the real “reiteration, iteration” composer.
Think about Escher.. ha ha… that was pretty compulsive and highly obsessive (and I love it ha ha but would never do it)… classical block-quilting is a great example of reiteration (technically, repeating an iteration), mosaic another, so there is some hard wiring somewhere (at least in my brain) that relishes repeated visual and auditory sequences. It gives me “peace of mind”.
That said, it is clear that yoga, prayer beads, malas, rosaries, and orderly surroundings make the verbal and tactile iterations medically beneficial.
Chromatin, euchromatin, states of packing of heterochromatin: a way to measure?
Just wondering if there is a way to determine the density of the heterochromatin round-pattern “beads” found in electron micrographs. If there are different types of heterochromatin, then it makes sense that the packing of these distinct types (wikipedia, quoted below – seems to suggest more than the two mentioned in some literature more likely – “a continuum between the two extremes of constitutive and facultative heterochromatin”) will be visible with transmission electron microscopy. So how does one go about making the assessments – in terms of packing of the beads… i only call them beads because i haven’t found what anyone else has named them, and because nature likes to repeat it self when it finds a good solution for a problem (in this case winding up miles and miles of long stringie DNA in such a manner that i has enough order to be accessed for various purposes), and because wrapping around proteins works well… likely it is used more than in one variation.
With TEM, chromatin is found in two distinct configurations, traditionally named euchromatin and heterochromatin based on the density of heavy metal staining of ultrathin sections and this attributed loose and tighter packaging. Heterochromatin is usually localized to the periphery of the nucleus, but also includes centromeres and telomeres and inactivated X-chromosome in females.
If as reported by some, there are 4 or 5 different organizational states to condensed chromatin (probably a couple to euchromatin as well (particularly there are inter chromatin granule clusters right off the bat) there should be a way to measure the different areas — unless they wind with each other in close approximation, then that would be difficult to detect.
I have seen (maybe posted as well) differences in the densities along the inner nuclear membrane, and am wondering if these are related to nuclear pore occurrences, and certainly appear to be related to transcriptional and translational activity. Just thinking out loud. This could relate as well to the number of ribosomes that appear on the outer nuclear membrane in areas justaposed to heterochromatin on the inner nuclear membrane.
Ferret alveolar type II cell TEM: pseudo-colored
Just thought this was a nice type II cell, and was hoping that it might become part of a cover for a journal where an editorial on type II cells will be published. 10247_18356_ferret_62
Febreze syndrome: fake news: fake odor removal: fake politics – ill-advised fakes for the 21st century
What about policies for government, business, and personal morality in the 21st century? An alarming trend is that we FEBREZE (everything, our homes, our clothes, our bodies, our jobs, our policies, and our morals. I am going to use febreze in a broad sense, while actually saying something about the actual product Febreze (hydroxypropyl beta-cyclodextrin) as the motif. Why do i use febreze as an example? Because what P&G claims for febreze is a lie, it is also a perfect example of our national crisis in respect to fake news. This industry giant has claimed that febreze eliminates odors, which it certainly does NOT, it masks odors, the two don’t equate. If one dissects their statement, you have to agree that their claim is entirely untrue.
Odor molecules are volatile organics for the most part, in my limited understanding of olfaction and the olfactory epithelium. Whether we settle on the figure at the low end of the spectrum quoted in the literature for detectable odors (around 10,000) to the high end of the spectrum (1,000,000,000), olfaction is an important sense for us. I wont quibble on either side of those numbers. The chemicals in air enter primarily through the nose, but also the mouth, and bind to those cute little knobs with wonderful looking sensory cilia on the top (lumental side) of olfactory epithelial cells.
Not all epithelial cells in the nose are olfactory epithelial cells, mostly it is respiratory epithelium.
But the processes and brain connections from olfaction is tied to many other systems in the body. The olfactory neurons are THE ONLY neurons in the body to make a straight path to the cortex (the olfactory cortex) all other neurons have intermediate connectors. SO, for starters, neonatal bonding, absolutely necessary for survival and thriving, the infant being more apt so smell you than recognize your voice or face at birth. (THREAT: lots of febreze to make your nursery sweet smelling may not be that good for your baby, or their olfactory development (depressed senses) or bonding between you and your baby).
Memories from childhood about danger, about friends, about who your family and pets are is totally tied up in olfaction. In particular whether you grew up with no siblings, or in a family that was culturally related to neighbors, or more independent. Research shows that early childhood olfactory events can contribute to at least three different kinds of (expressed by questionnaire) self-relatedness information: some being private, others more collective and those that feel part of the greater public at large (THREAT: Is it possible that the odor depleted environment produces less awareness of society in general, a more selfish and indulgent view of humanity).
Are you thinking independently when you go shopping? Not likely. Volatile organics are pumped into many stores to increase the release of neurotransmitters, for alertness, for feeling peace and comfort which retailers deliberately want to control (the so called ambient scent and manicured right down to gender preferences. (THREAT: you many not even be aware that you are being manipulated by the marketing team of the retail store where you are…just a thought Joann fabrics always smells terrible to me… ha ha like formaldehyde, paint, plastic and preservatives offgassing, i wonder how the staff takes it and on the other extreme, the office worker down the hall sends out odors like Pier 1 imports… ha ha… totally out of context and really quite annoying.
Some odors stimulate neurotransmitter release – like that good smelling sweaty man or woman, in days gone by to ensure mating and the survival of the species (true in many species) and also to make some slippery-style guidance to have us choose “genetically similar/diverse” mates. As a young woman i can clearly remember the “differences” in odors of those men that I dated, and it made impact on my behavior. (THREAT: if you cant smell the mate that 100 million years of evolution has suggested for you, you may in fact make a mistake in your choice. The remedy.. well thats for you do choose)
The smell of rotten foods, dirty surroundings, foul water, smelly sofas, garbage putting obnoxious volatile organic chemicals in the air are detected for a reason — guess what. If it is rotten, bury it, throw it out, clean it up, don’t febreze it. (THREAT: febreze does not eliminate odors as P&G suggests, ha ha, i puts it instead in a small basket of dextrin to trick your olfactory knobs on your olfactory epithelium into thinking that there is NO odor. How is that eliminating odors to coat it with cyclodextrin to trick the nose… you are breathing not only the volatile chemical but the basket used to cover it up. Who has researched the long lasting effects of using febreze… ha ha…. go for it. NOT ME.
So the real issue here is that febreze does NOT do what it is claimed to do, it does not REMOVE odors, it masks odors, tricking the olfactory epithelium. GIVING THE OLFACTORY epithelium FAKE NEWS. Do you see where I am going with this.
Fake olfactory sensation is ok? no it isnt. Fake visual information (boob jobs, nose jobs, stomach bands, liposuction,etc etc etc) is ok? no it isn’t, one is fooling self, both psyche and morality. Fake news: well this is an entirely different blog, but the same principle. where is our morality.
Bottom line, we are all still idiots — so to speak, messing with natural functions (personal, family, child rearing, societal, dietary, pharmacologically induced)…the list is too long to waste time elaborating on…. it is everywhere and about all of it we are still clueless, and much of it is driven by profit and greed and power – what a sad commentary on humanity.
Chromatin exclusion zone and nuclear pore distances apart
The nuclear pores are really abundant around the bounding membrane of the nucleus, especially in fetal liver cells, and other metabolically active cells. This begs the question as to whether nuclear pores can be measured in order to predict their frequency, and the width of the chromatin exclusion zone around them. The diameter of nearby ribosomes, taken at 27nm, is used as a standard, as is the diameter of the chromatin beads just inside the inner nuclear membrane, just slightly larger than the ribosome. The inter-bead distance (aka the distance between-chromatin-beads at the margin of the chromatin exclusion zone) and distance from nuclear pore to this string of chromatin “beads” of the condensed chromatin beside it has been made, along between pore distances This being an alveolar type II cell instead of an hepatocyte, didn’t really define any great differences in these three measure compared with hepatocytes. 10291_18339_ferret_1_alveolar type II cell. Mean distance between nuclear pores in 6 samples so far is approximately 332nm+/-30nm (SEM)
What are these round structures? too big for coated vesicles?
Here are some nice round structures and were they always near the nuclear membrane i would count them as tangentially sectioned nuclear pores since they are sized so similarly (though i have not seen any central densities like i see in nuclear pores where actual proteins are being imported or exported. There are also some profiles of membrane (with contents) that are pretty linear for golgi seen as well, and don’t quite fit that golgi iconic morphology. This is a fetal hepatocyte. Arrows point to pore and to similarly sized rounded structures that are not likely to be tangentially section pores from the nucleus shown.
Might be a section of a clathrin coated vesicle…. when i google it, this wonderful model came up. Sure looks (at 100nm) like it could work. What a marvelous amount of research has provided the molecular structure (triskelion) shown by them (on wikipedia) in blue.
Nuclear pores from Gclc ko and wt mice
Apoptosis seems to cause a real reduction in the chromatin exclusion zone of hepatocytes. The area is very small on either side of the nuclear pores. This would have to be functional but whether it relates to something changing about the nuclear basket portion of the nuclear pore complex, or about the chromatin, or about some other proteins that are part of the exclusion zone is up for debate. These pores are from nuclei which appear to be undergoing apoptosis, showing lots of peripheral chromatin, a little different in texture than regular condensed chromatin and an euchromatin space which is a little denser and more populated with interchromatin granule clusters than a non-apoptotic cell would be. These cells would be from livers of animals either never rescued or removed from NAC. Pore complexes are about 120nm in their widest dimension and there is another (taken from a n of 5 random pore and their exclusion zone images) another 55nm of exclusion on either side. This is in agreement with a larger selection of chromatin exclusion zones measured in both Gclc ko and 14CoS ko mice… previous posts on this site, which was 48nm and 50.9nm.
Similar small chromatin exclusion zones are found in cells in liver in eminent apoptosis in the 14CoS null mice when they are NOT rescued with NTBC.
More nuclear pores, just randomly collected various cell types
More nuclear pores, just randomly collected various cell types. The criterion that I used was simply the presence of vertical filaments (either part of the nuclear pore basket on the nuclear side or the filaments in the cytoplasm on that side. These come from lung alveolar type II cells, from hepatocytes, and from CoS14 ko mice, rescued and non-rescued, and probably a couple from Gclc conditional KO mice. These are just to give the limit of what effects random sectioning through a block of tissue can do to a round or discoid object. These pores are cut perpendicular (side views), and chromatin is always on top, cytoplasm is always below.
