text:
Do all humans have an identical nucleotide sequence for certain proteins, e.g haemoglobin?
All humans have the same sort of proteins in our bodies. Take haemoglobin for example.
Is the gene coding for haemoglobin in my body identical to everyone else's gene or is there slight variations in the nucleotide sequence?
Are there examples of proteins that are always completely conserved at the population level?

Humans have many variants
There is variation. The project I use to help understand this natural variation is gnomAD.
Using VarMap and a slightly out of date gnomAD file, I counted
16007805 protein-coding variants across the human genome. This number will only go up over time.
Indeed, the 1000 Genome project found that on average each person has between 250-300 loss of function protein variants that are not found in their parents (The 1000 Genomes Project Consortium, 2010).
This is an important concept for human health.
ClinVar is one of many projects that aims to catalogue and study when these variations lead to disease in a clinical context.
Another is the 100,000 genome project by Genomics England which studies NHS patient data in cases of rare disease and cancer.
Haemoglobin has variants, including disease variants
At the time of writing, HBA1 (haemoglobin alpha subunit gene) has 183 gnomAD variants and 17 pathogenic variants in ClinVar (sourced from gnomAD).
Again, both of these numbers are likely to increase because the data will cover more people.
Constraints on highly important proteins
But the underlying question is, I think, "are there some proteins that are so important, that life keeps them highly constrained" i.e any variation will lead to an invalid cell or a disease phenotype.
gnomAD attempts to add "constrained" metrics to each protein record, and some are more constrained than others.
For example:

Haemoglobin scores a pLI of 0.01 (higher scores are more intolerant to variation, specifically loss of function variation).

p53 is a gatekeeper of the cell cycle, mutants of which are common in cancer cells. It has a pLI score of 0.53 which means it is very intolerant to variation compared to haemoglobin.

Ribosomal protein L5 has a pLI of 0.998 implying it can tolerate little if any variation.
The ribosome is critical in protein production, hence altering it may cause a complete breakdown of cellular life.

Variation and Evolution
There is an almost philosophical difference between human variation and human evolution. Variation is a static snapshot of our protein sequence from individual to individual. Evolution in the sense of a Dayhoff Matrix requires looking back millions or billions of years by comparing similar protein sequences across many species.

It is highly unlikely that there exist any protein that is made from completely identical nucleotide sequences across the entire human population. There will certainly be regions within a gene that are highly conserved, but there is little evolutionary pressure to conserve an entire gene's nucleotide sequence across the population.
This is in part due to the fact that different codons can translate into the same amino acid. So, even if a protein is (phenotypically) identical across the human population, the genes making that protein can use different sequences to code for the same amino acids. This alone can allow for an incredibly large number of possible gene variations that can code for an identical protein.

Related resources: Neutral mutation (wikipedia) and the neutral theory of molecular evolution (wikipedia)

Haemoglobin has two distinct chains. It would be better to give separate numbers for each.

Apologies, I'll change the note to be more generic, as "variants" is not a precise descriptor and depends on context, such as in the point @David mentioned.

The fact that different codons can code for the same amino acid doesn't give anywhere near "infinite possibility"! Most AAs are only coded for by 2 different codons, and only one is coded for by 6. Given a fixed length of gene, that is a far cry from infinite variability!

@terdon Hmmm... Even only considering two different codons for each amino acids for a small 100 amino-acids proteins, that gives 2^100 possibilities, a little in excess of 10^30... Not infinite, sure, but rather high !

Rather high indeed, absolutely :) Still a drop in the ocean when considering the full ~3billion bases in a human genome though. But yes, you're not wrong, even only the wobble positions give significant variability.

Anticodon are a funny example for conservation, because tRNA genes actually have a multitude of copies, and while itʼs true that thereʼs considerable negative selection on their anticodon loop, variability certainly exists — even here.

@GenTest This is a great answer, thanks. Just a heads up I edited the question to get rid of the term "mirroring". You might want to tweak your answer accordingly.

Variants are not limited to SNPs. There are rare instances (but a lot because of the size of the data!) of 2 nucleotide changes, and sometimes 3.

Edited answer to better suit edited question. Removed examples and language that may cause confusion. 1st time answering here, appreciate feedback. Please feel free to edit to improve answer, as original answer was provided in context as a reply to the OP's curiosity as a recent High School graduate and was structured as such.

@GenTest I'm glad you weren't put off by the comments and that you made the changes. I think the resulting answer is a great succinct answer to the question. Welcome to Bio.SE!

At the whole-gene level, there is likely no absolute conservation of any human protein-coding gene at the population level, though there might be complete conservation between individuals. Keep in mind that most human genes are on the order of tens of thousands of base pairs long, and only a portion of that length encodes functional motifs. There are, however, ultra-conserved elements on the order of hundreds of base pairs that are identical between humans, rats, and mice.  Most of these elements are non-coding, and some are transcribed as functional ncRNAs.

"At the whole-gene level, there is no absolute conservation of any human protein-coding gene at the population level," Are you sure about this? I wouldn't be surprised if there were a specific, very short gene with at least its coding sequence 100% conserved. Or even one with everything including UTRs conserved (perhaps a single-exon gene with no introns). I also wouldn't be surprised if no such thing existed, but you are explicitly ruling it out without a reference.

@terdon you're right -- I don't give a reference.  I should have qualified that first sentence with "As far as I know, ..." or, as Gen Test said, "It is highly unlikely ... "

@terdon I haven't come across a whole protein that is completely "constrained", but there are indeed heavily constrained regions in both coding and non-coding regions.

@James neither have I. If I had to bet I'd say that there is no case of a protein coding gene whose coding sequence is 100% identical across all (healthy) individuals, but this is the human genome, so nothing can be ruled out! :)

@terdon My delay in response was me awk|sort|uniq-ing my gnomAD file. I have 18922 uniq UniProt codes, so there are a lot less than the complete proteome! That is more likely down to bugs than biology though! I'll report back when I am more confident.

@James ooh, that's actually a bit of a fun project. I have to run now, but give me a ping either in The Biosphere or the Bioinformatics.SE chat room. I'd love to see the results and would be happy to help out if needed.

No gene and no base pair is immune to mutation. It is the natural selection pressure that keeps some gene relatively constant. Neutral mutations are not subject to pressure, so everything changes. And then, there are "almost neutral" mutations that also get passed by.


text:
Why was the Davson-Danielli model rejected?
According to my textbook, Davson-Danielli's model of a phospholipid bilayer sandwiched between two layers of globular protein was incorrect. The nonpolar protein portions would separate the polar portions of the phospholipids from water, causing the bilayer to dissolve. Meaning, the Davson-Danielli model is not only incorrect, but it is also impossible.
I understand why the model is incorrect, but not why it is impossible. In my view, the nonpolar proteins would remain together in a micelle shape due to hydrophobic exclusion. Because of this, the phospholipid bilayer sandwiched on the inside would remain isolated from the water.
Why would a bilayer dissolve if the proteins were in contact with water and the phospholipids were isolated from the water?
I think that my confusion stems from many misunderstandings about the chemistry and structure of the cell membrane. In depth illustration of the error that my book mentioned would be most helpful.

The original figure that Danielli and Davson proposed looks like this (from the original publication):

It shows the phospholipid bilayer of the membrane (which is correct) embedded between two layers of globular proteins. The hydrophobic tails of the lipids are orientated towards each other, while the hydrophilic heads are oriented to the outside.
Although the membrane composition is correct (this was already published 1925 by Gorter and Grendel), there are some problems with the proposed model:

Membranes are not identical. The differ in thickness and the ratio of
proteins:lipids.
Membranes have distinct inside and outside layers (defined by the
membrane proteins which are present on the surface of the membrane)
Other than predicted by the model, the membrane proteins do not have
a very good solubility in water - in fact they are amphiphatic,
meaning they have hydrophilic and hydrophobic regions. The
hydrophobic side is anchored inside the membrane.
When the membrane proteins would cover the lipid bilayer, their
hydrophobic regions would be in contact with water, which
destabilizes this construct. Even if they would be oriented towards
the membrane, they would face towards the hydrophilic heads of the
phospholipids causing the same effect. Additionally the proteins
would also seperate the hydrophilic phospholipid heads from the
water. So there is no real stable solution in embedding the membrane
with proteins.

Just remember that some proteins can stick to the membrane kind of that diagram propose, although they are not true membrane proteins. For example, Bee Venom Phospholipse A2 has a membrane binding surface where it binds to the membrane and hydrolyzes phospholipids. Of course it doesn't stick on the membrane forever, it binds to the membrane, breaks down a few lipids, then floats away to repeat the cycle.

But these proteins doesn't cover the whole membrane as the model suggested. Most proteins simply "float" in the membrane.

Problems with the davson danielli model :

freeze-etched micrographs:

This is a technique of rapidly freezing the cell and then fracturing them. The fracture occurs along lines of weakness and in these micrographs there were two prominent dark lines which indicate the phospholipid bilayer and but there were transmembrane proteins even in between the phospholipid bilayer unlike what the davson danielli model suggested (that the phospholipid bilayers contained two layers of proteins on top and on bottom.)

2)structure of membrane proteins :
improvements in biochemical tech allowed people to extract proteins from the membranes. They were different sizes and globular in structure.They were unlike the type that would form continuous layers on the periphery of the membrane. Proteins were hydrophilic in nature and hence should have been attracted to the tails and not the heads.
3)Fluorescent anti-body tagging :
red and green markers were attached to the antibodies that bind to membrane proteins. these two cells were fused together and 40 minutes later it was seen that the red and green markers were mixed throughout the membrane of the fused cells. therefore the proteins were free to move within the membrane rather than being fixed in a peripheral layer.

source: Stack Exchange

license: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/3.0/

sort: votes


text:
How to do a whole genome analysis of Multidrug-resistant Mycobacterium tuberculosis
I'm looking for tutorials and software that can help me study whole genome sequence data is and genome wide associations. I have Matlab and Bioconductor R so anything involving those packages would be preferable.

I have made some major edits to to your question to stop it being closed for HWK. Feel free to roll back :)

You've picked a fascinating and very important organism to study. Unfortunately there are many many steps with many software packages that you'll need and each next step will depend on what you find making any particular tutorial nigh on pointless. I'm sorry to say that I don't think anyone will dump an entire project proposal or workflow as an answer. I'll give you an answer to get you started on your research.
Example
An excellent example of such a study is Fellay et al., 2007 and you can find their materials and methods supplement here.
An introduction to this kind of research
First you need to find the sequences of proteins that you think are significant. There are a bunch of ways of doing this, but I suggest standing on the shoulders of giants and scouring the literature (regardless, find an example where this has been done elsewhere). If there isn't much out there or for an entirely new viewpoint on something, this answer might help for finding proteins in the DNA sequence.
Sequence alignments against other strains is your best bet of identifying mutations (and possibly an indicator of resistance, which is what I guess you're after). There are plenty to choose from, but BLAST is a good tool to start with. You should compare your resistant strain with non resistant strains. Be very careful when analysing the data, not every mutation will be significant.

Thanks for trying to help me. Nice photos you take, you are a talented photographer. I have 1000 books on bioinformatics and years of software engineering and computations experience. I need  a rational way and the best software for mutation analysis. I don`t like microbes at all.

biostars.org are a community with a focus on the software/programatic side of biology. Perhaps you could reframe your question there?

all_licenses: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/3.0/


text:
Why do we use an autoclave at 121°C (250F)? (Origin)
Let me start by saying I know why, but I am inquiring more about the origin.
My question is more related to literature that I cannot seem to find.
I’ve found some helpful papers and information on the origin of the using 121°C for sterilizing equipment, and killing bacteria but I wanted to ask the question anyways and see if anyone knew something more about it.
So to restate my question: Why do we autoclave at 121°C and not 120°C?
Originally I though it is because the experiments might've been conducted in °F and the inter-conversion from °F to °C yielded 121°C which is an odd number.
From what I could gather, it started in the food industry with a company that made canned products and their canned products were exploding. This company approached MIT and after some research they found that at 121°C (250°F) for 60 min in retort would kill the spores surviving the previous processing. (Further experiments reduced the time to 10 min, for canned clams.)
This is detailed in Contributions to Our Knowledge of Micro-Organisms and Sterilizing Processes in the Canning Industries, which was published in 1897.
The autoclave was invented in 1879 (18 years prior to the publication).
At the end of the publication it says:

Detailed descriptions of the organisms and of many more experiments will be given in our full paper on this subject to appear in a forthcoming number of the Technology Quarterly

I have not been able to find this specific issue of Technology Quarterly
The authors (S. C. Prescott and W. Lyman Underwood) also say:

As we have shown in our previous paper, in order to insure sterilization in practice, it is necessary to obtain and maintain a temperature in excess of 121° C. (212° F.) throughout the contents of the can. Intermittent sterilization may be employed, but is less efficient and is not practicable upon a large or commercial scale. We have found by experiment that sixty minutes at 121° C. (250° F.) is sufficient time for sterilizing corn, and it seems probable that this can be shortened somewhat or the temperature reduced.

They are using °C, but since it’s 1890s’ retorts (autoclaves) used in food industry might be °F and the authors probably converted retort equipment readings to °C for the scientific community.
Also, this was what pioneered the study of thermal death, and the temperatures they used seem kind of sporadic. Probably because they wanted to see what temperature and time would reach the center of the can. The length of heating, or processing, and the pressure that are given vary somewhat in different factories and that might’ve been what led them to the 121°C and not 120°C.
Further research was done in this field:
In 1956 and 1958, F.H. Deindoerfer and A.E. Humhrey found that 250°F (121°C) is the optimal temperature to avoid damaged nutrient media. They also discussed analytical methods for heat sterilization times here and here
What I've been specifically looking for is the first thermal death study with D&Z values that led to the widespread usage of 121°C – and the time and psi required for sterilizing biological samples.
I know and found papers on what is used to validate autoclaves, e.g., this one.
Geobacillus sterothermophilus (known as Bacillus sterothermophilus also) is used for validating autoclaves and that is due to it being highly resistant to heat, making it a good biological indicator of microbial life post sterilization. The one paper I found which had some graphical data about its thermal death rate uses °C instead of °F. I cannot seem find any information on the bacterial reduction at 120°C comparing it to 121°C. This answer might as well as be a mathematical equation leading to that temperature, but that is only venue I haven’t explored
If anyone can find that Technology Quarterly paper I mentioned at the start that'd be great.

I think your well-researched question is probably as close as you'll get to an answer here.  Still gets an upvote from me but I just doubt we have an expert in 19th century autoclaves. From a practical perspective, I doubt anyone has ever compared 120 to 121 - why would you? For one, the tolerance in the thermometer could very well include that degree of difference, especially decades ago, and the degree of sterilization is unlikely to be meaningfully different over any small difference in time or temperature.

At some point you might consider posting a different (i.e. not identical) but related question in History of Science and Mathematics SE. Have a look around and see if something can be written that fits the site.

Thank you, I'll look into that and rephrasing my question.

I have a strong suspicion that 250F was picked because humans like to round numbers to the nearest 5s, 10s, and consequently 50s. The conversion to centigrade leaves it at 121. If it ain't broke, don't fix it. Scientists can be lazy like that.

Quick answer:
For historical and engineering reasons, standards for sterilization with autoclaves were developed with steam pressure and time being the operational parameters.  Temperature wasn't even measured by autoclaves until decades after they were in widespread use. For human factor reasons, the most appealing combination of sufficient pressure and time was 15 pounds per square inch pressure (one rounded off Earth atmosphere) for 15 minutes.  The temperature that corresponds to 15 psi steam pressure is 121°C.
Long answer:
It's all about the history of steam technology and the numbers people find easy to use and remember.
Steam power was the basis of industrial process in the 19th century, and to use it safely required monitoring and controlling boiler pressure. Boiler explosions were not uncommon in the early days of steam power. The Bourdon pressure gauge was invented in 1849 and was a robust technology that yielded reliable and accurate measurement of steam pressure.
https://journals.sagepub.com/doi/pdf/10.1177/002029408702000803
When Chamberland invented the autoclave in 1879 from Papain's earlier pressure cooker, it relied exclusively on pressure measurement for control. Not until 1933 were autoclaves produced that monitored temperature at the drain line to confirm that air was exhausted and the steam was truly saturated.
https://www.steris.com/healthcare/knowledge-center/sterile-processing/everything-about-autoclaves
Study of steam engines was the basis for the development of thermodynamics and the kinetic molecular theory of gasses. Although steam is far from an ideal gas, there is a predictable relationship between temperature and pressure in saturated steam as well as well established properties of heat transfer. These can be found on standard engineering steam tables.
Examples: https://www.engineersedge.com/thermodynamics/steam_tables.htm
Saturated steam is very efficient in transferring heat. This is why scald injuries are so severe compared to simple burns at the same temperatures. It is also how saturated steam kills even heat resistant microorganisms in an autoclave. https://learnaboutgmp.com/good-manufacturing-practices-cgmp/saturated-steam-efficient-sterilization/
Many combinations of pressure and time will do the job, but some are more appealing to people than others.  One earth atmosphere of pressure at sea level is defined as 14.69 pounds per square inch (psi), though in reality it varies a little bit due to temperature and weather. Because of this variation and because humans using Arabic numerals, to do arithmetic and algebra like integer units in 5's, engineers often round off 1 atmosphere of pressure to 15 psi.
This amount of saturated steam pressure was well within the capacities of typical steam boilers of the late 19th century. And a nice round 15 psi of saturated steam will kill even highly resistant bacterial endospores in just 15 minutes.  This pressure/time combination yielding an obvious mnemonic for adequate sterilization: 15 psi for 15 minutes.
The temperature of that 15 psi of saturated steam? 121°C.
And that is why we use the very unusual 121°C for typical autoclaving. It's because we are really using a rounded one earth atmosphere of steam pressure for the same number of minutes as psi of pressure. And we did so without concern for direct temperature measurement for the first 50 years of autoclave use. Even today, the temperature of the autoclave is of secondary importance.

Nice answer. +1. Might I recommend taking a play out of one of our best answer writer's playbook: the summary/long answer style. See here, here, and here for examples. I write long posts like you, and I know my posts (e.g., here) began attracting more attention once I started emulating @AliceD. Not necessary, but it works well. cheers.

Thanks for the advice! I've used the short answer/long answer approach in other contexts, you're right it would be useful here.  I've also been trying to tighten up my answers more generally partly for readability, but also time writing, and less wear on my arthritic hands.

whenever you find a weird standard value in science the answer is usually we didn't use to use those units, but after standardization there was no reason the change the value when we changed units.

license: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/4.0/


text:
Is this a grass cell?
I found this picture online claiming it was a grass cell. Clearly it is a cross section image but I was hoping you could tell me if this is actually grass, or something else if anything.

I wonder how many people noticed a little something in this image.

@user1306322 Yes... Yes I did

@user1306322 Me too... :)

Matram Grass leaf Stained cross section

It's not a single grass cell, but this does indeed appear to be a micrograph of a leaf of grass—so it actually contains numerous cells. Here's another image I was able to find with a much more clear description of exactly what you're seeing:

Marram grass leaf. Light micrograph of a cross section through a closed (unravelled) leaf of Marram grass, Ammophila arenaria. The deeply grooved leaf is thrown into folds (seen here) and it uncurls when mature so that the folds do not face the centre. The folds conserve water and withstand salt, and prevent excessive evaporation. Round vascular bundles are visible inside each fold, serving to transport food and water through the leaf. Spines on the surface discourage animals from eating the leaf. Marram grass is important in coastal ecology, since it is one of the commonest grass species in Britain to stabilize sand dunes. Magnification: x22 at 35mm size. (Emphasis added)
Source: http://www.sciencephoto.com/media/30161/view

And here's another:

Transverse section of Marram Grass leaf , showing adaptations to prevent water loss; outer thick cuticle, curling by means of hinge cells to protect inner epidermis, stomata
  sunken into surface to maintain high humidity
Source: http://www.eplantscience.com/index/principles_of_horticulture/minerals.php

The coloration yielding the yellow 'happy faces' is artificial, either due to staining or direct post-processing of the image.

all_licenses: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/4.0/


text:
Why does an autoclave need to pressurize steam?
I've looked this up on other sites and they say that an autoclave needs high pressure in order to raise the boiling point of water so that you can achieve steam of a higher temperature.
If you look at this diagram though, it seems to me as if it would be much simpler to further heat the steam at the ambient pressure of the autoclave room. Does the pressure of the chamber play some role that I am unaware of?

An autoclave can sterilize both solids and liquids, whereas an oven with no pressure control is typically not suitable to sterilize liquids.
Not only do you need to heat the chamber to 121°C, but you also need to make sure that the things you are trying to sterilize are not degraded by the treatment.
For dry objects (e.g. glassware) you could heat the chamber up to 121°C at ambient pressure. In that case, the instrument you're using is called a "dry heat sterilizer" rather than an "autoclave" (REF)
So why use an autoclave at all, and not just a dry heat sterilizer? Quite often the things you would put in an autoclave are water-based solutions (for example, LB broth or buffers).
If you do not increase the pressure and try to heat to 121°C, the liquid in your bottles will first boil around 100°C until all the aqueous solvent is in the gas state (i.e. your solutions are going to evaporate) and then the temperature will increase to 121°C. However if the pressure is raised to stay at the liquid-gas phase transition, then the gas and the liquid are in equilibrium, therefore you neither lose or gain any volume in your solution.
So in theory, if you autoclave 1L of medium, then you get 1L back at the end. Note that in real life, the temperature and pressure of the autoclave are set based on the diagram for water, but for concentrated solutions these settings may be slightly off, meaning that the volume in the bottle at the end of the cycle is sometimes a little different from what you put in there at the beginning. See this illustrative diagram of how a solution behaves differently from the pure solvent:

(Copyright: Lumen Learning)

it would be much simpler to further heat the steam at the ambient pressure of the autoclave room

You cannot do that, physically. If you put water in a closed (water-vapor-tight) container, then heat it, the vapor "wants" to expand with growing temperature. But as it cannot expand your metal container (autoclave), the pressure goes up instead. It happens automatically, that's how molecules function in a gas (don't ask me to remember the name of that law please).
You could, I guess, try constructing an elastic autoclave where the pressure stays the same and the volume changes. But that would be mechanically challenging - what material are you going to use that is elastic, won't tire with time, won't deform on you during use, won't burn at the heat source, will conduct warmth well, etc.? Also, you will lose your convenient way of ensuring that you are at a target temperature. Since a certain pressure always equals a certain temperature (at constant volume), you can construct a weighted valve to keep a constant pressure in your autoclave - this is cheap, easily doable with 19th century tech, and more accurate and failsafe than creating a cybernetic control loop with a measuring device such as a thermometer or a manometer.
I don't know if there are also biological reasons to prefer it with with a higher pressure - the number of bacterial species which can withstand high temperature is higher or equal to the number of species which can withstand high temperature combined with high pressure - but I doubt that this was a driving factor in the design and adoption of autoclaves.
The standard autoclave is easy to invent, does its job, does it well, and is cheap and unfussy (when compared to a hypothetical room-pressure-wet-autoclave). The pressure is more of a side effect nobody sees the need to remove - on this site, I'm tempted to call it a spandrel.

https://en.wikipedia.org/wiki/Ideal_gas_law

Once the middle is dried, the steam can be overheated at constant pressure, the excess of steam is just released by a pressure relief valve.

As you say it is possible to increase the temperature of the steam over the saturation pressure. And with overheated steam, the instrument would reach the desired temperature as is the case in an autoclave.
But the difference is how many time it would take to heat the sterilized instruments. And the difference is actually huge, we are talking of order of magnitude. The reason is that the heat transfer inside an autoclave is evaporation-condensation. But if the autoclave were not pressurized, there would be a first efficient phase of evaporation-condensation followed by an extremely slow natural convection phase.
Let's try to explain it in few lines.
On the difference between the heat transfer by evaporation-condensation and heat transfer by condenstation
Evaporation - condensation is the most effective way to transfer heat. Just consider the fact that uranium is used in nuclear power plant to boil water.
Transfer of heat by natural convection of gas is very slow.
The difference is many order of magnitude, heat transfer by evaporation is typically of the order of 1'000'000 W/m² (1MW/m²). Heat transfer by natural convection it is of the order of 100 W/m².
What is happening when the autocalve steam is saturated.
Liquid water inside the autoclave boils. Its temperature is the saturation temperature that is a function of the autoclave pressure. The vapor moves and condenses on the surface of the instruments that are being sterilized. The temperature of the liquid film that is formed by condensation on the instrument surface is the boiling temperature. The heat transferred by this evaporation-condensation is huge, in few seconds the surface of the sterilized instruments get close to the saturation temperature and in few minute instruments are homogeneously heated.
What would happen if the steam was overheated without pressurization.
Liquid water boils at 100°C and then a heater in the gaz phase overheat this vapor. The steam reach the instrument and condense. But the temperature of the liquid film that is formed on the instrument is still the saturation temperature: 100°C, not more. So in few seconds the instrument surface reaches 100°C. After a few minutes, the instrument reach an homogeneous temperature of 100°C. Then start a second and slow phase: the condensed liquid films dries, then the instrument get heated by the overheated steam through natural convection, and this is very slow. It would take hours for the instrument to reach the steam temperature.


text:
Does the magnitude of gene-expression changes decrease the more downstream a gene is from the origin of change?
If I have a decrease or increase in expression in one gene, will the decrease/increase in expression in the downstream genes always be of a magnitude lower than the previous ones, or can they be higher?
I’m thinking in terms of signal propagation in a network. If I, for example, knockdown gene $X$ to 40% of its basal level, and it influences genes $Y$ and $Z$ in the following manner:
$$X → Y → Z,$$
Will I expect genes $Y$ and $Z$ to suffer lower decreases/increases than the previous gene, for example:
$$X: 40\% ~⇒~ Y: 60\% ~⇒~ Z: 80\%$$
Or could I have a scenario where a small change in one gene’s expression can lead to higher magnitude changes in downstream ones, for example:
$$X: 40\% ~⇒~ Y: 20\% ~⇒~ Z: 10\%$$
I suppose that in some networks the signal will always decrease in magnitude the farther it is from the source, but I’m wondering if, in a biological network, that will also happen and consistently in each step. I read papers with knockdowns all the time, but I never stopped to analyse if knockdowns always create lower magnitude changes in downstream genes or not. So I was wondering if this intuitive notion holds empirically or not.

It's going to vary depending on the gene. Some genes exhibit dose dependence, others don't.

@MattDMo I know some genes are dose dependent and some not, but I'm not sure that's the problem. Dose dependence would change downstream genes in acordance with the dose of the source of change, but that doesn't tell me if the magnitude will always be lower, or not. So if 40%X -> 60%Y and 20%X -> 40%Y, that's dose dependent, but will the magnitude always be lower like in this example?

@David well, I work with molecular biology and bioinformatics. And I don't see how that is making a simplistic mathematical assumption about biology. Biology is not simple, and cannot be reduced to simple assumptions sometimes. But other times it demonstrates very well conserved patterns. I'm making no assumption. I'm merely trying to discuss to see if there is a pattern here. It might not have. But if one cannot make very objective questions about whether some pattern exists or not in biological systems, then we should close all systems biology departments, because they would be pointless.

Gene expression can be very well described by Hill functions, i.e.:
$$c_Y(c_X) = \frac{c_X^n}{1+c_X^n}$$
when $X$ activates $Y$ and
$$c_Y(c_X) = \frac{1}{1+c_X^n}$$
when $X$ represses $Y$ (omitting units and all sorts of constants for simplicity). For the common case that $n>1$, these functions look like this:

As you can see, they are far from linear, but sigmoids. For $n→∞$, these become perfect step functions.
As a result, gene regulation mostly works like a switch:
As long as you are not close to the critical concentration ($1$ in the above example), changes in the regulator have a less than proportional effect.
For instance in the above example, it doesn’t matter whether the concentration of your activator is $2$ or $10$, the protein production is pretty much $1$.
Therefore, “signals” in gene-regulation networks get stabilised instead of diluted.
There are also some other self-regulation effects contributing to this such as genes that self-regulate, the availability of amino acids, and the limits of the translation apparatus.
Note that without these sigmoidal relationships, you would also have big influences of the inevitable fluctuations of the regulator.
As a result, it would be impossible to keep the metabolism in some stable state – the only stable state in a linear system is death.
Simply put, you would have to keep a very precise and regular diet, lest your body stops working.

Great answer, and exactly the kind of answer I was looking for. I remember reading about the Hill equations in Uri Alon's book many years ago in the begining of my masters in biochemistry. But I had other things in mind and ended up not finishing it, and forgot most, except the network patterns. Guess I should go back to it now. But just some questions: do we know the range and frequency of Hill coefficients in nature? Because it is going to be linear somewhere around n=1.5, right? But I guess the question is whether n=1.5 is a value that exists in practice.

Also, this switch behavior does make sense in terms of stabilizing the signal, but we can clearly observe some dose dependency when inhibiting genes in the lab. So, at the very least, it's not a binary switch, but one with many states (or steps), unless all the dose dependency we are observing is in the linear phase, in which case the functions are far from perfect steps. Is there some literature on that? And third, just stretching a bit, is there some general pattern of how much the expression changes after the "switch" is on?

@LizardMan: 1) I would have to search for a source on the distribution of Hill coefficients myself, but IIRC they are often considerably larger than 1. Of course there also are some cases, where you (or evolution) want the Hill coefficient to be small. 2) Sure, it’s not a binary switch, but for many practical purposes, it’s sufficiently close. Remember that in any cascade, it suffices if you are not in the intermediate region for one expression step. 3) I am not sure, what you wish to know here. The general pattern is that you have no expression if the switch is on and otherwise, it depends.

Ok, I'll try to look for this later. Thanks. 2) I meant binary in the sense of having only one step (two states), but I get it anyway. Just out of curiosity, are you aware of any gene for which all expression steps have been characterized? Something like, gene X goes through one step when it's TF is at concentration A, through another step at concentration B, and so on.

I meant something like this: gene X has a basal level (will not be zero for many); it's TF rises sufficiently to make it go through one step; after the step, X's expression is N fold in relation to it's basal level. Is N some kind of constant (either for each gene per step, or in general for all genes)?

2) I am not aware of any mechanism that would cause multiple steps. Beware that this is all a thermodynamic process which smoothens things like cooperative gene regulation (and are in fact responsible for $n>1$). 3) I don’t think so. The basal level depends on different things (how well does the transcription apparatus work despite lack of activation) than the activated level (how does the activation work).

Just to expand on @Wrzlprmft's great answer with a concrete example:
Sticking to your simple gene circuit with $X$, $Y$, and $Z$, now consider the possibility that $Y$ also activates its own expression via a positive feedback loop:
$X \to \underset{\circlearrowright}Y \to Z$
Here activation of $Y$ will be only minimally dependent on $X$. Once $Y$ is activated, the following self-activation makes $Y$ practically independent of further $X$ activity, causing $Y$ to drive its own activation until saturation.
If by decreasing $X$ to 50%, its levels are still above the minimum level required for activating $Y$, this would have practically no effect on the final (steady state) levels of $Y$. Conversely, if a 50% decrease brings $X$ below the $Y$ activation level, it would lead to a complete shutdown of $Y$.

Note that you need an additional ingredient for a positive feedback loop to act as a robust bistable switch which isn’t switched on by the slightest noise: Either $Y$’s self activation doesn’t suffice for a self-amplifying effect at low concentrations of $Y$ or you have something like “$Y$ suppresses $W$ suppresses $Y$”.

Indeed, good clarification! I was thinking of giving some examples of positive feedback in biology (cell cycle and lac operon, for example) where such "protective mechanisms" indeed exist, but didn't want to go too off-topic.


text:
How much of the weight of yoghurt is due to bacteria?
I recently started making all kinds of bacteria-processed foods by myself (such as yoghurt, but also Sauerteig and so on), and I found myself wondering how much of the weight of these products is actually due to the bacteria themselves in the end. But I couldn't find anything useful on the internet.
So, specifically for yoghurt, how much of its weight is due to the bacteria, i.e. dead and/or living bacterial cells, but not including the products of their metabolism outside the cells?
I would also be happy about numbers on other bacteria- or fungi-processed foods, but I wanted to keep the question simple.

I've asked myself a similar question for fermented stuff you don't want to eat: http://biology.stackexchange.com/questions/7251/is-1-g-l-living-biomass-for-a-biogas-fermenter-plausible

I'm voting to close this question as off-topic because it is about food analysis rather than biology in the terms of SE Biology.

Interesting question and it will only be possible to do some estimation. The problem is to know the exact bacterial composition as well as the mass of the bacteria. To start, it is necessary to know the number of bacteria in a defined amount of yoghurt. There are scientific publications on this topic, but the numbers in fresh produced yoghurt are in the area of 108 bacteria per gram yoghurt and declines over time. Based on the numbers in  reference 1 and 2 I use 2x108 bacteria per gram fresh yoghurt.
The other number we need is the mass of one bacterium. This is complicated, as bacteria are very light due to their size and cannot be easily weighted. There are some numbers available (we imply here that all bacteria weight the same, which is of course not the case), and according to them, one bacterium weighs about 1x10-12 grams.
Mutiplying both numbers gives the amount of bacteria in one gram of yoghurt, around 0.0002 gram or 0.2mg. One typical sized yoghurt of 150 gram therefore contains about 30mg of bacteria. The weight of the bacteria can thus be neglected against the total weight.
References:

Survival of Yogurt Bacteria in the Human Gut
Handbook of Food and Beverage Fermentation Technology
Mass of a Bacterium

Thanks for the analysis and for pulling out the references! As far as I understand the second reference, the number there seems to be for living bacteria. Do you know any estimates about dead bacteria? Do they just not die as long as they're producing the yoghurt, so that freshly produced yoghurt contains all the bacteria that ever lived in the yoghurt and they start dying afterwards?

I think the number is highest in the beginning (when the conditions are optimal) and then the bacteria die. Since they are not removed, the number should still fit.


text:
Is "A" inhibiting "B" and vice-versa, a positive feedback loop?
If product A inhibits the expression of product B, and product B inhibits the expression of product A, is this a positive feedback loop?
My thinking was to consider the scenario that A starts off high, and so B is naturally low. Then, a large amount of B is added to the system. This inhibits the production of A, so the level of A falls, and that in turn enables the production of more B, which further decreases the production of A and in turn further increases the production of B, in a never-ending cycle. This runaway amplification is characteristic of positive feedback loops, whereas negative feedback loops cause a return to equilibrium.
Yet the Wikipedia page says that, for it to be a positive feedback loop, it must be set up so an increase in A causes an increase in B.
So what is it?

This is probably not a biology question. The phenomenon you describe is a positive feedback IMHO.

In essence yes, because the more A, the less B, the more A.  In practice it would be a pretty unstable system so you'd end up with either all A, or all B.

The situation that you presented in which an entity A inhibits the production of another entity B which in turn inhibits A, is a positive feedback.
In a network path or a loop the overall sign of the loop/path is the product of the signs of individual edges (interactions). In this case it is negative times negative which gives a positive sign to the loop.
In simple words, a positive feedback should lead to an entity promoting its own production, directly or indirectly; it can auto-activate itself, activate an activator or inhibit an inhibitor. In this case A inhibits its inhibitor. Sometimes you can have large loops like this:

This is still a positive feedback.
Moreover, your case would exhibit (with the right parameters) the dynamic properties of positive feedbacks (such as bistability and hysteresis).
Sometimes people also refer to this type of positive feedback as double-negative feedback (which I personally do not like because it is misleading).

Positive and negative feedback loops may consist of a single component
  that activates and represses directly its own activity, respectively
  (Fig. 1B,C); or they may include several components and involve
  indirect interactions (Fig. 1D–G). The overall sign of a complex
  feedback loop (i.e. positive or negative) depends on the constituting
  elementary interactions (Fig. 1D–G).(1) For example, two mutually
  repressing components form a positive feedback loop (PFL, also termed
  “double-negative feedback loop”).

Mitrophanov & Groisman, 2008

However, not all positive feedbacks lead to runaway amplification. That is a property of an unstable system. The degradation of the molecules (or death) ensures a finite (and stable) steady state. Sometimes (with certain parameter combinations, as previously mentioned) positive feedbacks can have two stable steady states. Depending on the initial condition, the system can settle to either of the states. In your example the two states can be — High-A Low-B and Low-A High-B.

Further reading:
Mitrophanov, Alexander Y., and Eduardo A. Groisman. "Positive feedback in cellular control systems." Bioessays 30.6 (2008): 542-555.

Although the situation you describe involves amplification rather than homeostasis it is not a positive feedback loop under the standard definition of the latter:
In a a positive feedback loop:

An increase in A leads (directly or indirectly) to an increase in B.
The increase in B leads (directly or indirectly) to an increase in A.
This repeats step 1., leading to a further increase in B.

The second step is feedback, as it is affecting the initial propagator of the action, and positive, as it causes an increase in that propagator, A as well as target B.
Your model differs from this in two ways. First, only B is amplified — A is suppressed. Second, when A falls to zero B will reach a maximum, whereas in a positive feedback loop things theoretically keep on running out of control. (Yes they generally stop, but that is because of the intervention of something outside the simple A/B system.)
Some biological examples illustrate this difference (please, I am not concerned whether they are true or not).
An example of a positive feedback loop might be atmospheric warming (A) causing production of more water vapour (B) which has a greenhouse effect and increases atmospheric temperature (A), which...
An example of your model might be the territorial encroachment of smart and aggressive Homo sapiens (A) causes a decline in the population of H. neanderthalensis (B) which is then less able to resist Homo sapiens, leading to a further decline and eventual extinction of H. neanderthalensis.
At the end of the day, we are arguing about semantics. Your point of view would seem to be that the current definition of positive feedback should be extended to include your model. My point of view is that scientific terminology allows us to distinguish between similar but different things. So, (not meant as a serious proposal) one might include both effects under a broader description as ‘augmentative cycles’, including both the standard ‘positive feedback loop’ and your model, which could be called a ‘positive–negative feedback loop’ or a ‘terminal-positive feedback loop’ or whatever takes your fancy.
Postscript
There is a paper in Current Opinions in Cell Biology which discusses the type of motif you describe under the subheading ‘Positive Feedback Loops’, although also refering to them in the text and in the title of a table as ‘double-negative feedback loops’. As @WYSWYG mentions, the review he originaly quoted only uses the latter term, and has a diagram of two-component regulatory motifs, which I reproduce below, distinguishing this from positive feedback. This bears out what I wrote — not that your point of view is necessarily wrong — but that this is a question of semantics, and scientists find it useful to use different terms to distinguish different but related things. In any case, the authors of the review have done the reader a service in defining their terminology.

I disagree.  If you consider that increasing the presence of A increases the absence of B which increases the presence of A, then it fits your definition of a positive feedback loop.  In other words, the absence of B corresponds to an increase in the signal of its absence.  And what really matters is that more A leads to more A.  So it acts like a positive feedback loop because it is unstable.  Whereas a negative feedback loop would reach a stable equilibrium where more A leads to less A and vice versa.

@Kelvin -- I don't think there's much room to disagree. In the context of Biology a Positive Feedback Loop has a distinct definition; an increase in A leads to an increase in B, whose product or byproduct leads to an increase in A in an (IIRC) exponential fashion until a limiting factor is involved.

I concur with Kelvin. A inhibiting B and B inhibiting A is a positive feedback. @MCM there is a room to disagree because this answer is not correct. In a positive feedback, an increase in A should directly or indirectly lead to increase in its own levels. It can auto-activate itself, activate an activator or inhibit an inhibitor.

I think it's a matter of perspective: If you're more focused on the detail and technical definitions you see only the individual steps; but if you're more focused on the big picture, you look at the system as a whole.  And since biology itself focuses on big picture systems and outcomes (via evolution), it's probably more useful to think in the same way than get bogged down in largely irrelevant technical details and definitions.

@Kelvin Apologies to you and the questioner that my original answer did not address the question adequately. Late at night, but that's not an excuse. I have not changed my opinion over yes or no, but I have argued and discussed it in a manner that pays more respect to the questioner's arguments.

@David Even if you do not look at the big picture, a positive feedback does not mean that all the individual interactions should be positive in nature. Basic graph theoretical concepts (that are also valid for systems biology).

@David, no problem.  I think it's good that you keep your answer posted as is, because it does illustrate that the answer is not so clear cut.  In any case it's a very interesting question.

@WYSWYG — I'll look at the paper you cite, but it will take a wee while. Ultimately it may be a question of different usage among different communities. If dpdt is correct, someone should edit the Wiki entry. Easily done, whether or not you're signed up (although latter is preferable).

@David The paper actually calls the structure as a double-negative feedback (a terminology that I do not like because it is misleading). You can introduce another node in this network and a positive edge and this can no longer be called "double negative" but it is effectively the same. Double negative can also be thought of as two parallel paths of a negative feedback (imagine a situation in which A activates B and C and the latter two inhibit A). However, as per graph/network theory this structure would be called as positive feedback. I changed the reference actually. See that one.


text:
If your atlas is out of alignment, will the rest of your spine be out as well?
I just found out about this association called Nucca. Basically, they are a chiropractic association - their whole idea is that if your atlas is out of alignment, then the rest of your spine is also out of alignment, because your atlas controls it all. Also, the nerves will get pinched and therefore cause pain.

Is this legit?

https://www.sciencebasedmedicine.org/the-problem-with-chiropractic-nucca/

No, it is not. The "theoretic building" of chiropractic is nonsense - see the several articles from Edzard Ernst on it.


text:
Do transcripts always start and end with exons?
I realized that in all cases of "RefSeq Genes" annotations of hg19 I looked at spliced transcripts start (and end) with an exon. From the annotation there is no evidence of any sequence upstream or downstream of these exons that remain in the nascent RNA.
Does this reflect the biology or is it just a consequence of the spliced read mapping? In other words: Do transcribed regions upstream of the first exon and downstream of the last exon exist in nascent RNA?
These regions, if they exist, cannot be called introns when those are defines as 'spliced sequences between exons'. How would one call them?

Welcome to BiologySE... I agree with what you say at the end (i.e. "I guess if you have an answer for 1 and 2..." - I would narrow your question to get an answer (it's easier to answer a simple, straightforward question instead of a broad question with 5 subquestions). You can always ask more questions - the more specific the better

Very Good (and well-researched) question!! I am looking forward to answers here

@TalhaIrfan Thank you. I condensed the text to the basic questions.

Could you explain what you mean by "spliced read mapping" please.

@David, spliced read-mapping refers to the mapping of spliced sequences (e.g. RNA-derived sequence reads) to an un-spliced reference (DNA of reference genome). The algorithm that performs this kind of task has to be able to accept long insertions on the reference sequence without penalizing those as mismatches in the alignment. These read-to-reference insertions (or reference-to-read deletions) are introns.

@Herr Jemine - I see. Thanks for the explanation.

Most (almost all, AFAIK) mRNAs and lncRNAs start with exons for the reasons already mentioned by David. In a typical splicing event, the nucleotide that is 5' to the splice donor site (lets call it pre-donor) and the one that is 3' to the acceptor site (lets call it post acceptor) are joined together and the intronic sequence between them is removed.
If you look carefully at the mechanism, you'll notice that the pre-donor (i.e. the 3' end of the first exon) renders a nucleophilic attack on the phosphorous of the post acceptor (i.e. the 5' end of the second exon) which leads to the release of the intron.

 Image courtesy: http://mips.helmholtz-muenchen.de/proj/yeast/reviews/intron/spliceo_splicing.html

Therefore there is always an exon preceding an intron, in the transcript.
However, RNA processing can occur via a different mechanism in which the ends are just chopped off. This happens in tRNA processing, where RNAseP chops off a portion 5' to the mature tRNA region, called the leader sequence (see the figure below). I am not aware of such a mechanism happening in the case of mRNAs but a possibility certainly exists. One possible reason for mRNAs not having this kind of mechanism is because their 5' end is capped (co-transcriptionally) and cleavage of the 5' would lead to loss of cap and destabilization of the mRNA (all guesses, though). Similarly, the 3' of mRNAs is polyadenylated which also renders stability to them. Many lncRNAs are also capped and polyadenylated but there are exceptions (mRNAs too).
Since this mechanism is not very common, there is no systematic name for the excised ends. For the case of tRNA, it is simply called the "leader" sequence.

 Image courtesy: Leigh & Lang, 2004

Thanks for your detailed explanation. As David and you point out it is very unlikely that the splicing mechanism would be able to remove sequences upstream and downstream of the first and last exon respectively. Another important hint is that 5' CAP processing occurs co-transcriptionally. This, and the fact that a method called 'CAGE' is used to identify promoter regions by CAP-specific sequencing of mRNA 5' ends gives some confidence that 5' removal of a 'pre-exon sequence' is likely not happening in 5' capped mRNA. Yet we have not discussed the 3' end.

@HerrJemine I don't really know a reason for why that is not common. Even for the 5' part this was just a wild guess. Do not take it as a fact. BTW, the 3' end has poly-A which is also critical for RNA stability. However an RNA can be stable in the absence of cap and poly-A tail too. Since such cases are also very few, we can guess that this could be a factor for low occurrence of end chopping in RNAs.

I found some hint on post-transcriptional 3' end truncation in alternative polyadenylation on wikipedia (second paragraph of intro and section 'Alternative polyadenylation'). I'd suggest that you add this aspect to your answer and I'll accept it.

https://en.wikipedia.org/wiki/Polyadenylation

As far as I am aware, transcripts always start and end with exons. The reasons I wouldn’t expect otherwise (apart from my observations when examining Drosophila transcripts) are given below.
As you will be aware, the spliceosome (at least for mRNA) is a highly sophisticated multi-component ribonuclear protein complex, and has functions to both splice out the intron and ligate the ends of the exon. The diagram below, from a recent review, suggests that recognition of the splice sites also involves the exon.

And the authors write (my italics):

“Base pairing between the 50 end of U1 snRNA and the first six
  nucleotides of the intron, and up to three nucleotides of the exon,
  provides the main driving force for specific sequence recognition.”

So I think that the contemporary machinery for removing mRNA introns requires exon mRNA to ‘get hold of’.
If such removal of introns could serve a functional purpose you would imagine the machinery would have evolved to accomodate such situations, but if the main function of introns is to allow differential splicing of exons that specify regions of the protein, introns at the end of a mRNA would have no purpose.
Another point to consider is the RNA-polymerase binding site on the DNA (the extended and complex promotor). If introns arose originally as mobile elements (something suggested by the authors of the review) then an insertion at the 5' end would likely have inactivated the promotor, so no transcript would have been produced.
Of course, Nature is full of exceptions, and it would be foolish to exclude that introns of the type you postulate do exist (in some galaxy far away...).

So why the mark-down? If you vote someone down have the guts and the decency to explain why. What is so reprehensible about the idea that splicing evolved because it allowed variants of proteins by differential splicing and the machinery evolved to deal with that? That although there are introns in the UTRs of a mRNA, which perhaps affect ribosome binding etc, these are likely to have been secondary. If you have a complex that needs to bind two parts of a rope before it can snip and join it, it makes perfect sense for it not to work at the end. Or don't you like my last para?

Didn't downvote, but I would guess that the theoretical and unsourced nature of this answer would play a significant role. Also, I find it strange why you would ask for someone to explain their downvote in such a defensive manner.

@MarchHo I won't shoot the messenger, but when you down-vote you are prompted to make a comment. It is most annoying to provide a structure-based answer to a theoretical  (more hypothetical) question and end up with -1 so a casual visitor would assume something basically wrong with your answer. My guess now is that the self-deprecatory and whimsical Star Wars reference was misunderstood as an attack on the question. Perhaps I'll change it to Shakespear when I add a pic of the spliceosome later to clarify my argument.

Your answer is touching the point but a little explanation and some diagrams would make it better.

@David Thanks for the answer to my question. I like that you pointed out the structural difference between a splicing between exons and a potential sequence removal upstream and downstream without a 'splicig partner'. By the way I didn't down-vote either, but my upvote did not count yet (missing exp.).

@WYSIWYG - I've added an appropriate diagram, and hardened up the argument. I didn't switch to Shakespeare, but the quotation I had in mind was "There are more things in heaven and earth...". For example this week's Nature reports that N6-methyladenine has been found in eukaryotes where it was thought not to exist. Never say never.

@David thanks. I have already given you a +1. I understand that there are many unknown mechanisms (and yeah I had seen that article too) but I think we can possibly justify why they are rare.

@David just as a point of clarification, users are under no obligation whatsoever to explain or "justify" their votes, up or down. The message you are referring to appears to low-rep or casual users of a site, but not to more experienced users, who theoretically understand the voting guidelines. I would also point out, as March Ho did, that lashing out in such a defensive and insulting manner, is neither useful to the overall tone of the site, nor likely to prompt anyone to explain or change their vote. Be nice.

@MattDMo OK, OK. However I did get such a message recently and I have been posting quite frequently. The message does imply that that is the correct etiquette, which longstanding users should have learned.  And btw, I do not consider my manner was insulting. It was forceful and direct, but no more. However when I explained a downvote re. another posting recently I got my head bitten off, so I guess one should just accept the guidelines are more honoured in their breaking.

Thank you for a great question.
I would like to start by clarifying some terminology.
First, nascent RNA refers to an RNA molecule that is currently being transcribed and has not been processed. Processing can include the splicing out of introns or polyadenylation at the 3' end, for example. Mature RNA is (typically) spliced and polyadenylated.
Second, the current consensus definition of an exon is a transcribed region of the genome whose sequence can be found in mature RNA species. Importantly, there are two classes of exons: non-coding exons, and protein-coding exons. I think you may have these confused and I have included an image to help clarify the distinction between introns, coding exons, and non-coding exons, using the human GAPDH gene as an example.

In the figure, the solid blue boxes represent exons, which are present in the mature mRNA. These exons can contain both protein-coding and non-coding sequences, as I mentioned. For example, exon 1 of GAPDH contains only non-coding information that belongs to the 5' untranslated region (UTR) while exon 2 contains both coding and non-coding sequence information.
When you view the RefSeq annotation, you are viewing all exons (coding-and non-coding). For some of the genes, such as GAPDH, the first exon will be non-coding. Other genes may begin with a coding exon (I have yet to find one and since the 5'UTR is involved in ribosome binding, I am doubtful that many examples exist).
The regions of an mRNA molecule beyond its coding sequence are referred to as the 5' and 3' untranslated regions (UTRs).
I hope this helps answer your question.

This does not actually answer the question. I think the OP knows about exons and UTRs. Their question is about why a transcript always has to start with an exon. Perhaps you can add some explanation for this point.

I have not heard of a classification such as coding and non-coding exons. You can have exons that have a part of the CDS and a part of the UTR.

Thanks for your reply. But my question did not concern whether exons contain coding or non-coding sequences. I am aware of the fact that exons can be part of the 5' or 3' UTR in the mature mRNA and also that there are non-coding RNAs in general. As @WYSIWYG pointed out I would like to know if the unprocessed, nascent RNA always starts and ends with an exon or if their might me a removal of 'head' and 'tail' RNA sequences that were transcribed from the DNA.

@WYSIWYG Thank you for your comment. Perhaps coding vs. non-coding is restricted to certain bioinformatics circles, which is where I came across the term. I think the 5'/3' UTR convention is more intuitive.

@HerrJemine Thank you for clarifying your specific needs. As someone pointed out above, only a very limited subset of RNAs are cleaved at the 5' end post-transcriptionally (I wasn't able to find any examples of mammalian RNAs that are cleaved at the 3' end). You may be interested in exploring a technique called NET-seq link. It demonstrates pervasive transcription outside of the transcriptional unit in yeasts, flies, and humans.


text:
Why do mutations not take place in mRNA of higher eukaryotes?
Is it because it is too short-lived to be mutated? Both DNA and RNA are nucleic acids so how is mRNA protected? RNA viruses undergo mutations to evolve so I guess it is not immune to mutations

Do you have a reason to believe mutations do not occur in mRNA?

If mRNA gets mutated then it would make malformed proteins which in best case might get degraded or in worst case hamper with cellular metabolism or even lead to cancer if cell cycle regulatory protein coding mRNA were to be mutated.

The premise of the questions suggests that mutations cannot take place in the mRNAs of higher eukaryotes.
To answer your question I think it is important to consider two viewpoints:
First, from a theoretical point of view, since DNA and RNA are as you pointed out composed of nucleic acids, they both can be mutated if enough energy is provided (UV light, chemicals, etc) which invalidates the premise of the questions.
Now, from a practical point of view, as you mentioned most mRNAs molecules have a short half life typically in the minute to day range whereas DNA molecules exist during the whole existence of the organism.
While it can occurs that mRNAs are mutated people are not interested to study this aspect for the following reasons:
You pointed out in the comment section, a mutation in a mRNA molecule might lead to translated malformed protein which can easily be degraded. It will be only one mRNA transcript from thousands transcripts. With a short half life, the mRNA an proteins will be degraded which will not have a long standing impact of the cell/organism. As such it will be very difficult to observe a phenotype which will affect the whole host.
Thus RNAs mutations have only transient effects which will not affect the host in the long term. RNAs molecules are not more protected than DNA molecules just that they are short lived so the host is protected from the effects of RNA mutations.
Hope this helps!

Your supposition is incorrect. RNA does accumulate "mutations" because the RNA polymerase also makes errors. The misincorporation rate of bacterial RNA polymerase is ~10–5 per nucleotide (Traverse & Ochman, 2016). Compared to that, DNA polymerase has much higher fidelity and has misincorporation of ~10–10 per nucleotide per generation (Zhu et al., 2014).
As pointed out in the other answer, RNA mutational effects are short-lived as RNAs are short-lived. However, RNA mutations can contribute to phenotypic heterogeneity which can, in some cases, be beneficial to the organism (Ackermann, 2015).

There is nothing special about higher eukaryotes as replication and transcription process is quite similar across different domains of life. Viruses are special, however. They rely on higher mutation rate for faster adaptation.

Additionally DNA is inherently more stable due to the removal of the hydroxyl group from the C2 carbon on the ribose making it less reactive. This could be pointed to as an example of the limiting factor in the inherent complexity of any organism that uses RNA instead of DNA for long term data storage. That would be a discussion for another thread though.

Your answer is more of a comment as it does not really address the main issue of the question.

Mutations do occur in mRNA. This can occur during transcription, when RNA polymerase incorporates a non-cognate nucleotide into the nascent RNA strand (this may be because the DNA forms a short lived tautomer from quantum tunnelling, or because ). Alternatively, just like DNA bases, RNA bases are inherently unstable due to things like deamination events, but RNA is also capable of base catalyzed hydrolysis. To say that mutations are not interesting in RNA is also wrong as RNA editing is something that may be used to treat numerous diseases. RNA editing is transient, which is useful for treating diseases caused by temporary changes in cell state and modifying disease-related signal transduction through editing serine, threonine and tyrosine residues to affect phosphorylation sites. mRNA mutations are also important in understanding the affects of splicing on phenotypes and I'm sure there are more reasons, but these are just off the top of my head.
For more information about RNA editing see: DOI: 10.1126/science.aaq0180, a really cool potential of CRISPR


text:
Enzootic vs Epizootic?
I'm studying microbiology and I see these words - epizootic and enzootic, often but there are no clear explanations for them online. Can someone help please?

Analogous to endemic and epidemic.

I can't believe I didn't see that before! Could you please put that as an answer so I can credit you?

Enzootic and epizootic are analogous to endemic and epidemic, respectively.
Enzootic means something that affects a population of non-human animals  in a limited spatio-temporal region whereas epizootic is relatively more widespread.
Endemic and epidemic are more general terms and do not, technically, apply to only humans.


text:
Is this in vivo or ex vivo?
This question has probably been asked a few times but I get the concept I just dont know how to apply it for this paticular experiment
I aim to use cherry tomatoes and determine its glutamate content after drying for varying amounts of time.
This would involve putting the tomatoes into the centrifuge to extract its juice.
Due to this, I am 'preparing' the tomatoes in vivo (I think need clarification) but I am observing the Glutamate content outside of the organism (ex vivo)
I dont know how I should be classifying this experiment (between in vivo and ex vivo)
Help will be greatly appreciated !!!
Thank you!!

This would all be in vitro work. See my comment below the (incorrect) answer. This may also be helpful.

Personal opinion: nevermind. Provided it is clear from the your experimental description what you actually did, who cares what to call it in latin ... As the below answers and discussion shows, there is no real consensus on exactly what these old latin terms mean nowadays, and I really think most people just include them in journal articles to appear sophisticated ;-)  Just describe your experiments as clearly as possible when writing your paper, so the reader to can judge for him/herself how relevant the data is to the organism you study.

The classification usually applies to the experimental conditions. Are the experimental conditions applied to an organism, or to a less than whole organism (cells culture --> all the way to test tube chemistry reactions)?
This is somewhat subjective, but in your case, since the experimental conditions are drying time of the pretty much whole organism (the tomato), I would call it an in-vivo experiment.
Think of it this way, if you treat animals with X and examine Y, this is an in-vivo experiment regardless of whether you are isolating proteins, DNA, RNA etc... to examine afterward to characterize the change in Y.
Now if you isolated cells first from mice and plated them to grow in cell-culture, and then treated with X to examine the same endpoint, this has become more ex-vivo.
In-vitro would be to isolate a single enzyme from mouse cells, put into a test tube, and examine its ability to reduce some substrate after X treatment.
In your case, if you isolated enzymes from tomatoes and then used them in a test-tube to reduce some agent and measure activity before and after a given treatment, this would be more ex-vivo and have gone all the way to in-vitro.
EDITED: Matt pointed out I had confused in-vitro and ex-vivo on my continuum and he was correct.

This is completely incorrect. You're mistaking ex vivo ("out of life") with in vitro ("in glass", referring to old-fashioned Petri dishes). An in vivo experiment is performed in an experimental organism, such as giving a mouse cancer. Ex vivo refers to taking samples from that organism and processing them separately - surgical or post-mortem removal of the tumor for analysis of the cells and structure. Creating a cell line from the cells and culturing them would be in vitro.

@MattDMo In vitro studies are performed with microorganisms, cells or biological molecules outside their normal biological context.    In science, ex vivo refers to experimentation or measurements done in or on tissue from an organism in an external environment with minimal alteration of natural conditions. Ex vivo conditions allow experimentation on an organisms cells or tissue under more controlled conditions than is possible in in vivo experiments (in the intact organism), at the expense of altering the "natural" environment.  I'll change my test tube example but rest is correct.

@MattDMo In response to : Ex vivo refers to taking samples from that organism and processing them separately.  This is not correct. Ex vivo also means that experimental conditions are applied after taking samples from the animals. No room above, but links to ex vivo and in vivo definitions here: https://en.wikipedia.org/wiki/Ex_vivo and https://en.wikipedia.org/wiki/In_vivo  The distinction is where the experimental conditions are applied, to the whole organism or to parts isolated from it, not the processing as you stated.

@MattDMo To add, I routinely process mouse tissue taken from experimental mice in order to determine their protein/RNA expression levels. I would definitely consider these in vivo experiments.

It depends upon your field, and its proximity to native specimen. In practice, in-vivo and ex-vivo are used to stress a relative difference.

If you are biochemist in a field / research area that usually uses purified components and reconstitution: in-vivo
If you are biochemist in a field / research area that usually measures glutamate within undried tomatoes: ex-vivo
If you are a cell biologist: ex-vivo
If you are a developmental biologist: ex-vivo

(Similarly cell culture is usually considered in-vivo by a cell biologist, but ex-vivo by a developmental biologist).


text:
What does fluorogenic mean for fluorescent probes?
Many fluorescent probes are described as being fluorogeninc as an advantage for fluorescence microscopy but what does fluorogenic mean? Dictionary definitions state that it means generating fluorescence, but i've read somewhere that it involves switching the fluorescence on or off for super resolution microscopy. I just want to understand the exact meaning in this context. Thanks in advance for the help.

@BryanKrause Sorry bout that, check edits for clarification. thanks

@BryanKrause here's one example, albeit a poor one, "fluorogenicity provides a high signal-to-noise ratio"

@BryanKrause Thank you so much Bryan for the help. It's now clear to me what it means thanks to your explanation.

I summarized my comments into an answer and added some references for anyone else that stumbles across this.

The usage of "fluorogenic" is typically applied to probes that are not currently fluorescent but can be, typically by some enzyme action or other reaction. For example, see here, here, or here. Essentially they are precursors to the fluorescent molecules of interest.
As one example, you could get a higher signal to noise ratio if you only "activated" the fluorogenic compound in one area, perhaps inside cells vs in the extracellular space, for example, so you aren't dealing with stray light from that "unwanted" signal.
References:
Shieh, P., Hangauer, M. J., & Bertozzi, C. R. (2012). Fluorogenic azidofluoresceins for biological imaging. Journal of the American Chemical Society, 134(42), 17428-17431.
Lukinavičius, G., Reymond, L., D'Este, E., Masharina, A., Göttfert, F., Ta, H., ... & Blaukopf, C. (2014). Fluorogenic probes for live-cell imaging of the cytoskeleton. Nature methods, 11(7), 731-733.
Friscourt, F., Fahrni, C. J., & Boons, G. J. (2012). A fluorogenic probe for the catalyst-free detection of azide-tagged molecules. Journal of the American Chemical Society, 134(45), 18809-18815.


text:
Recognise this thing found in beach?

Kindly help me identify this thing found in beach
Chennai, India . Size would be just 1.5 cm in diameter..across maximum size. It's shelled and has something inside it. It make a small noise when it is shaked completely closed on all sides. It's hard surface ( but " fine" texture ) to touch.

Thanks for the edits. Could you explain what you mean by "fine"? It's not quite clear to me what you mean in this case. Thanks.

Did you ever find out was this was? We just found one in Florida.

give us a cross section. describe the material, is it mineral or organic? is it an egg? google lens app will recognize a HD photo if there are other images of the same thing on google images. I just put that specific image through google lens and it returned "chennai, india"...

I believe it’s the seed of a Guilandina bonduc shrub. The seeds are known as nickernuts or sea pearls, and can be found washed up on beaches throughout the tropics. The seeds are often used as counters in the traditional board game manuals.

Welcome to the site. Please take a [tour] and visit the [help] for more information on the Biology Stack Exchange and what we do here. Please note there is a section in the help on what makes a good answer. We particularly value answers here that contain references that support the answer. To improve your answer you could provide links to the shrub and images of the plant and seeds (try wikimedia/wikipedia and iNaturalist) for these in your answer.


text:
Hollow stalks in celery
When cutting a section of a celery plant stalk it appeared hollow inside, i.e. the cortex was hollow and encircled by the cambium, the vascular bundles, some cortex and the epidermis layer, thus the structure appeared similar to the celery stem's one and to the one of many other vascular plants, but the cortex. I have struggled to find answers on this topic: the cortex has a pivotal structural role, since it becomes turgid and keeps the plant straight, not to mention its water storing properties. Then why would it be so thin in such an important part of the plant, (stalks develop into leaves)?

Can you post a picture of what you observed? ———
I've never seen a celery plant that had been allowed to develop branches, so I suspect you are talking about the petioles ("stalks") of the leaves. If so, it would be clearer if you edited your question to use the correct terminolgy ...

Celery is a wetland plant, and likes to have a constant supply of water. Other vegetables can "bounce back" after experiencing a short drought, but celery  usually has more difficulties. If the plant is young during reduced water, it typically will become dwarfed, and fail to grow to full size. If the plant is older, it will develop defects, and suffer long term damage such as what you have described.
Defects are also possible if the celery does not have sufficient micro nutrients, or if the weather is very warm during growth.
In short, this is caused by non-ideal growing conditions of the celery. The celery was stressed to a point where it sustained damage that it could not repair. Celery is one of the more difficult crops to grow because of how finicky it is to drought.
Sources:
-https://www.gardeningknowhow.com/edible/vegetables/celery/why-celery-is-hollow.htm
-https://harvesttotable.com/celery_growing_problems_troubl/
-Personal experience trying to grow celery

Welcome to Biology.SE! This sounds very reasonable, but your answer is much more likely to receive a favorable response if you [edit] it to include supporting references (primary literature is best, but a textbook or other authoritative source are acceptable). Without this your answer is indistinguishable from opinion and make it impossible for non-experts to verify your assertions. ——— You may also wish to take the [tour] and then consult the help pages for additional advice on [Answer] effectively on this site. Thank you!


text:
How does Cro protein expressed by lambda phage kill its host?
I read that the DNA segment of lambda phage integrated in host DNA could switch between lysogenic state where cI represses the expression of Cro and lytic state where Cro expression takes over and self produces more.

But how exactly does the high production of Cro kill its host?
The virus has a DNA segment shielded with a protein coat. While entering host it gets attached to host membrane and releases DNA inside without damaging host. Then how does host get killed when virus goes outside it which happens during lytic phase and doesn't happen when it got inside?
And if the virus has to go outside host, it needs protein coating. How is that produced? Is it produced only during lytic phase or also during lysogenic phase?

Have a look at the wikipedia page on lambda-phage (it is nicely illustrated and referenced).
See this map of the lambda-phage genome (Source).

Cro (Controller of Repressor's Operator) does not kill the host. It is a transcription factor that represses cI. cI, in turn, represses Cro and other pro-lytic genes (expressed from the PL promoter), thereby forming a positive feedback loop with Cro (some people also use the term "double-negative" feedback loop which in my opinion is incorrect).
During infection the virus just injects its linear DNA into the host via a porin protein (a sort of membrane channel). But at the peak of the lytic cycle many virus particles are formed inside the host cell (not just DNA but fully packed viruses). The viral proteins R and S cause breakdown of the cell membrane and the cell wall, which facilitates cell lysis.
As mentioned in the previous point, the virus is fully packaged while inside the host. This happens only during the lytic phase. During lysogeny, the viral DNA gets integrated with the host genome and remains dormant until triggered by some kind of stress such as UV (which actually leads to activation of SOS response protein RecA which by degrading cI tilts the balance towards the lytic cycle).

I thought that a positive feedback loop is when a gene product either directly, or indirectly, stimulates its own activity, essentially an amplification mechanism.  I don't understand how cI and cro together form a positive feedback loop; doesn't each one shut down the other one?

@mdperry the sign of the loop is the product of all the individual interactions (or edges). So negative times negative is positive. By repressing its repressor Cro is indirectly activating its own synthesis (same for cI ).

The viral replication happens only due to the host reproduction, so one cell divides into two, each of the cells have only one viral dna segment integrated in their dna. At any time one host has only viral dna. Then even in the lytic phase only one virus will get out of host which should not burst it. Am I right or does virus replicate in a single host into many copies of itself? If so, how does it perform?

@Pavan No viral replication is not dependent on the host. See this section of the wikipedia article.

@AlwaysConfused Yes. The link doesn't seem to work. I don't know the original source of this image. Unfortunately, I am not able to find a better (easy to understand but yet descriptive) replacement for this image.

After infection of the bacterial host, but before initiation of DNA replication of the viral genome, the phage has to decide between two mutually exclusive fates:

A lytic infection that will lead to the death of the host by lysis, and a simultaneous burst of phage growth.

OR,

A lysogenic infection where the viral genome integrates into the host's chromosome, and remains dormant, like a parasitic passenger.

Upon entering the host cell both the lambda repressor cI protein AND the cro protein are synthesized from viral transcripts. Essentially, whichever one "wins" will throw that switch. If cro levels are high enough they will shut off transcription of the cI repressor, leading (eventually) to cell lysis. If cI levels are high enough they will shut off transcription of the cro gene leading to integration and lysogeny.
This explanation is a bit simplified; there are other players that influence how the switch gets "thrown."
In a lysogen, just about the only phage protein being made is the cI repressor, and it keeps all the early genes shut off.
In the general viral life-cycle, early genes are transcribed before DNA replication of the viral genome, and late genes are transcribed after DNA replication of the viral genome.  So typical early gene products are regulators, and DNA replication and recombination proteins.  Once there are many, many copies of the viral DNA typical late gene products are the structural proteins that make up the viruses protein capsids, and enzymes required for packaging the DNA into the phage pro-heads.


text:
How to determine if two mutations in a gene are on the same or different alleles?
I would like to know, except a familial study, is there another way to determine if a mutation/variation is cis or trans (i.e. on the same or different alleles)? For example by sequencing technique or other molecular biology procedure.
CIS               TRANS

+  +              +  +
|  |              |  |
A  |              A  |
|  |              |  |
B  |              |  B
|  |              |  |
+  +              +  +

Thanks

Yes, it can be determined by sequencing but the sequencing read has to be long enough to span both the mutations. PacBio sequencing allows long reads but it also has higher error rate than the short read sequencing platforms like Illumina. If you know the gene locus then you can amplify the region using PCR and use Sanger sequencing too (for this the amplicon has to be cloned in a plasmid, transformed into bacteria and then single colonies must be sequenced; see Why does one combine PCR and cloning as ways for amplification of sequences?).
Another possibility is to look at the RNAs from this gene. If the two alleles have different expression then comparing the number of reads for each mutation might tell if they occur together. However, as I said it already depends on the two conditions: expression and dissimilar expression.

Thanks for your reply. So, the family study seems to be the easiest and the cheaper method if both mutation are far away.

@dridk There are some problems with family study: the two mutations may not have linkage and can segregate during crossover. Also, if you want to know about the current generation you might have to wait for them to have offspring. You need data for all of the family members. Moreover, if you don't have a very distinct trait associated with the different mutations then you would again have to rely on sequencing; so back to square one.


text:
How many proteins are synthesized in human body throughout life?
My idea to calculate this is:

Define up to what age will do the calculation. (for instance 60)
Determine how many cells born and died up to that point in life. (by type of cell)
Determine how many proteins are synthesized in the cells life. (by type of cell)

Points 2 and 3 are not constant throughout the life of the human body. To calculate this data I need a function.
After obtaining all the data: complete calculations of addition and multiplication.
The question is not about mathematics, but about useful data to make these calculations. Another approach would be welcome too.

Related question.

Also related, protein turnover.

you will probably want to take a mean lifetime of human cells - some of them are very slow growing and life practically forever, others relatively short - just a few days.  (blood cells and male gametes for instance).  the amount of protein synthesis would also similarly vary.  a single cell type with good measurements would be good to see..

Just to add another factor, there are many proteins that are often recycled and persist for quite some time.  I would be impressed to see some solid arguments on this.  I think you might have some luck by trying to break down to average masses of the various tissues, but I believe this will be quite a challenge.

Hmm. Maybe measuring mRNA content can help to estimate the speed of protein construction. It is a hard question btw...


text:
Why are the results of local BLAST and miRbase BLAST different?
I am trying to reproduce locally on my computer what I get running mirbase on their website using BLAST. The search sequences is: mature miRNAs which I had downloaded on my computer and make it as a BLAST database with command:
./makeblastdb -in /home/marianoavino/Downloads/mature.fa -dbtype 'nucl' -out /home/marianoavino/Downloads/mature

then on mirbase I see they use an e-value of 10, which I leave locally.
On mirbase at the end of the analysis they give you these parameter setting:
Search parameters
Search algorithm:
    BLASTN
Sequence database:
    mature
Evalue cutoff:
    10
Max alignments:
    100
Word size:
    4
Match score:
    +5
Mismatch penalty:
    -4

and this is the command line I use on my computer for BLAST
./blastn -db /home/marianoavino/Downloads/mature -evalue 10 -word_size 4 -query /home/marianoavino/Downloads/testinputblast.fasta -task "blastn" -out /home/marianoavino/Downloads/testBLast.out

The results of the two analysis are different, with mirbase finding much more stuff than local BLAST.
Do you have any idea on which parameters I should use on local blast command line to match those listed mirbase parameters in order to get the same answer?

The main problem I could identify is that your scoring matrix is not the same; as you said miRbase uses match score of +5 and mismatch penalty of -4.
The BLASTN defaults can be found here. However, I ran the local BLAST using the exact command that you mentioned and the default values that it used were:
reward = +1
penalty = -2
Matrix: blastn matrix 1 -2
Gap Penalties: Existence: 0, Extension: 2.5

The other reasons could be the difference in the database itself (the sequences used) or the version of BLAST used in the two cases.


text:
How well can proteins discriminate between ATP and GTP? Can ATP act as a GTP mimetic?
GTP and ATP are similar structures with the adenosine and guanosine groups differing. Both are involved in a vast array of biological functions.
However it has been shown that in certain cases, GTP and water can mimic ATP (Niefind et al., 1999).

Are there examples where ATP has acted as a mimetic of GTP? Or in other words, are there any proteins that can't discriminate between GTP and ATP very well?

There are certainly some enzymes that don't discriminate (well) between the two purines. Is that what you mean by mimic?


text:
What are all of the currently known variations of the G zipper motif?
The G zipper motif is found in transmembrane proteins at an above random frequency and there are models explaining how it might help with multiple transmembrane intra-membrane helix bundle assembly.
However there are a bunch of different "flavours" of these G zipper motifs. Here are the ones I have come across so far:

GXXXG
GVXXGV
GXXXGXXXG
AXXXGXXXG
SXXXGXXXG
GXXXGXXXS
GXXXGXXXT

I don't think I am completely up to date so that is a non-exhaustive list. Have I missed any? Broadly speaking what accounts for their variation?
note: X refers to a non specific amino acid in FASTA protein sequences.

It seems to be a small family as per pfam. And frankly I had never heard of glycine zippers till now (so thanks for that). Perhaps this may be useful.


text:
Is chloroplasts per cell indicative of the photosynthetic power of a plant?
Plant-A has on average N chloroplasts per cell. Plant-B has on average M chloroplasts per cell. If N > M, is plant-A more efficient in turning carbon dioxide into oxygen? Also, is it possible to see chloroplasts with a standard bright-field microscope?

You can say that but chloroplasts do not have uniform morphology across different species. Moreover some organisms such as red algae have chloroplasts of different origin.
Real indicator would be lets say number of chloroplast ATP synthases and/or light harvesting photosystems; these can be perhaps indirectly approximated by the total surface area of the thylakoids.
But for all practical purposes and comparison between not so distant species density of chloroplasts is a decent enough approximate for photosynthetic power.
About turning carbon dioxide to oxygen:
You should note that the source of oxygen is not CO2. Oxygen comes from photolysis of water; this is the initial step in the electron transport chain (ETC) in chloroplasts. The ETC results in production of ATP and NADPH; the latter is used in the Calvin-Benson cycle to fix CO2 to sugar.
So photosynthesis and carbon fixation, though associated in chloroplasts are basically different biochemical processes. Theoretically as long as NADPH is provided a plant should be able to fix CO2 [this is just my guess].
It is difficult to observe internal structure of chloroplasts with normal bright-field microscope but you can count them easily at 40x magnification. See here.

As @wysiwig already pointed out the different morphology of chloroplasts is something that is hard to come by. This influences the amount of chlorophyll in these organelles which is the key for photosynthesis. So it is very difficult (to impossible) to compare chloroplasts of different plants as they differ pretty much. There is one paper from 1929 which goes into detail here:

The relation between maximum rate of photosynthesis and concentration
of chlorophyll.

However, there is a paper which studies the photosynthesis rate in connection to the number of chloroplasts when manganese ions are a limiting factor. Manganese is part of the active center of the Photosystem II in the photosynthesis. So without maganese, photosynthesis is not possible.
The article finds the number of chloroplasts in cells approximately reduced to the half compared with leafs without maganese-deficiency. Testing the photosynthesis capacity of these leafs, they find that the photosynthetic activity in the manganese-deficient leaves is reduced by about 40%, which fits nicely to the reduction in chloroplast number. They do not find other significant changes in the biochemistry of the photosynthesis in these plants, so is the ratio between chlorophyll a and b not affected, and also the ability to transfer electrons is not affected. The findings are presented in this paper:

Reduction in chloroplast number accounts for the decrease in the
photosynthetic capacity of Mn-deficient pecan leaves


text:
Do bald people not grow hair, or does their hair simply fall out immediately?

This image is not directly related but it made me wonder if there was a relationship between the nature of the hair follicle and baldness, namely that the follicle cannot 'hold' the continuously growing hair, and it constantly falls out in. I wonder if this is the case or if the hair literally just does not grow out from the follicle at all.

There are different causes of baldness. Perhaps you can check out the wikipedia page on hair loss and make your question more precise.

I'm no expert on the whole matter, but I know that at least when it comes to male pattern baldness, it is caused by a hormone called dihydrotestosterone. As those men with the right (or wrong genes, however you choose to look at it) age, this hormone causes the hairs to progressively lighten and thin up until the hair stops growing altogether. The hair follicle dies out basically.

Welcome. Answers need to be backed up by reputable sources, preferably journal paper citations. As of now this is more of a comment and not an answer.


text:
Why clotting does not occur during Menstruation
As we know when we get injured our body's clotting systems stop the bleeding. So why does it take days for menstruation to stop ?

http://medcell.med.yale.edu/histology/female_genital_tract_uterine_cycle.php


text:
How is the eye damaged by computer screens?
Eyes are damaged by persistent use of computer screens. On giving it some thought, it felt quite magical that your eyes are damaged simply by looking at something. I googled where there were articles about blue light and stuff and having felt dissatisfied come to the wiser community here for help.
The question is pretty plain, how does the simple action of looking at a computer screen cause damage to the eye? Is it due to focussing the eye continuously at something close-by?
Is the damage caused to the retina, or the cornea or some other part and in what form? Does the light reshape the lens or something?
Edit: I got glasses of power +1 for both eyes about 3 years ago and 4 years ago, my exposure to computer screens increased to about 6 hours a day. Before that, it was hardly an hour or two a week. The ophthalmologist I consulted also credited it to increased exposure to computer screen.
Hope the questions are clear.

You really need to support the claim that eyes are damaged by computer screens in particular - that is, aside from the problems caused by spending extended periods focussing on any close work.

@jamesqf Sorry but, I'm not getting what you are trying to express.

You need to show some credible source that looking at computer screens damage the eyes. Without it, your question is a wild guess.

How old are you? Becoming long-sighted is nothing unusual with age.

I am barely 18 years:)

Re your edit, being rather older than common access to computer screens, I remember that the same thing would be said about people who'd spend a lot of time reading, or doing other close work like sewing.  IOW, it's not something unique to computer screens, but to the muscular effort involved in keeping the eyes focussed on something close.  Eventually they adapt to it.

The light from computers is safe, it can only be the distance and the reading habit which are a problem, so the same applies to books. avoiding excercising your eyes in their near and far ranges is known to be a problem, that's why reading is not recommended to those with growing eyes.

This would be better placed at skeptics.