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Identifying whether amino acids are hydrophobic or hydrophillic
How do you figure out whether an amino acid is hydrophobic or hydrophilic? (other than memorization) I know that it has something to do with the R groups of the amino acids, and that polar molecules are hydrophilic, while nonpolar molecules are hydrophobic, but that's about it. Please give a simple answer, I don't need too much information other than an easy way to tell.

This question isn't about biology but about learning it, so no doubt it will be closed very soon. However the general answer is that you need to learn chemistry in order to know other than by memorisation. Like it or not, biochemistry/structural biology/molecular biology involves basic chemical knowledge. Without that you are going to have to memorize things without understanding them. I would start learning chemistry  as soon as possible.

Checkout: "What is the difference between polar and charged amino acids?" on Biology StackExchange

@mdperry if you're going to reference a different question, please include a link.

Does the side chain contain any Nitrogen (N), Oxygen (O), or Sulfur (S) atoms?  If it does, then chances are high that this particular R-group is polar (although it may not be charged).
The converse is also true, if the R-group lacks any of those three atoms then chances are high that the side chain is polar.  There are exceptions; Methionine has a Sulfur, but is quite hydrophobic (non-polar).  Tryptophan has a nitrogen but is non-polar.

...and lysine and arginine can be considered both hydrophobic and hydrophilic, as can tyrosine (the latter being particularly important in certain enzyme mechanisms). Encouraging this sort of rote learning of dangerous half-truths is anti-science. The only decent advice is to learn some very basic chemistry, for which there must be dozens of reasonable on-line sources.

I know this isn't how you are "supposed" to do it, but it isn't easy to memorize all 20 amino acids, and this helps a lot with identifying whether they are hydrophobic or hydrophilic. I'll just have to remember that methionine and tryptophan are hydrophobic.

@Anonymous you need to learn basic chemistry first. Going along with what david said, it's not just a matter of memorizing the 20 AAs and saying "W is hydrophobic, S is hydrophilic". You need to be able to understand why, and how some can be classified as both, depending on context.

@MattDMo I'm studying campbell biology right now, didn't see anything that would help with learning that

@Anonymous Thank you for selecting my anti-scientific "dangerous half-truths" as the answer to your question; I am very glad that you found it helpful.  I realized I did not provide you with a reference of any sort, so here is a biochemistry textbook of mine: https://www.pearsonhighered.com/program/Moran-Principles-of-Biochemistry-5th-Edition/PGM264296.html.  I fear I am growing old and may not be up-to-date on the newest methods for learning these chemical principles.  We did indeed memorize all 20 a.a. structures as biochemistry undergraduates in the 1970s (in our Organic chemistry course).

@mdperry Your answer helped a lot with my question, and that's what an answer is supposed to do. Btw, studying biology really hasn't really changed much besides extra information to know


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Where did the nondisjunction occur?

A father with gene AC has a child with gene ACC. Where did the nondisjunction occur? (Meiosis I, Meiosis II, none of the above)

I do not know because both Meiosis I and II have the possibility of producing gametes with n+1. Is there something I'm missing here?

It can happen during any of the two Anaphases.

There are three forms of nondisjunction: failure of a pair of homologous chromosomes to separate in meiosis I, failure of sister chromatids to separate during meiosis II, and failure of sister chromatids to separate during mitosis. Nondisjunction results in daughter cells with abnormal chromosome numbers (aneuploidy).

@zainabrija That's nice and all, but it doesn't really help me answer the question

Think about what gametes the father could have given the child. If the mother contributed an "A", then the father gave two "C"s, if the mother contributed a "C" then the father contributed an "A" and a "C".
In meiosis I, the father's chromosomes duplicate, so he has AA and CC - normally, at the end of meiosis I, these would be pulled into separate cells, so one of the resulting cells would be AA (and then in meiosis II, split into two further cells both with one "A") and CC (which in meiosis II splits into two further cells both with one "C"). The final result would be four gametes (sperm cells), two with "A"s and two with "C"s.
Since this is tagged "homework" I'm not going to give the final answer - but think about what phase of meiosis would have to go wrong to create an "AC" sperm, and what phase of meiosis would have to go wrong to create a "CC" sperm.

AC - Meiosis 1 and CC - Meiosis 2?

You got it! (Or I suppose to go with your username, I could also say "!ti tog uoY")

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Memory capacity of the human brain in bytes?
Is there an estimate out there for how much memory (in bytes) an average human brain can have? Is there a physical limit?

This is heavily subjective. For example, one way of thinking about this whats the longest series of numbers (limited to 0 or 1) that you can actually remember? It's probably not that long. Does that mean one has the brain capacity of a dozen or so bits? Or do you say that it takes petabytes of memory to simulate the synaptic connections in a rat brain and extrapolate from there? Have you already hit the physical limit (odds are you can't remember what you had for breakfast 5 Tuesdays ago)?

Memory is much more than "remembrance". The cells store countless information. Technically every single molecule of certain proteins can store at least a bit of memory. You cannot really measure cognitive memory in terms of bits and bytes.

Here's one fun way of thinking about it: Say that the brain stores information as a connection between two neurons, so a bit is simply whether there is a connection between two neurons. There are estimated to be about 100 billion (1e11) neurons in the brain, so that's  2^(1e11 choose 2) bits, which is some absurdly large number (way way more than the number of atoms in the universe).

Not sure what I was thinking in the last comment -- it would of course just be (1e11 choose 2) bits, which I guess is about half a zettabyte, which apparently is approximately the content of the entire www in 2009 (wikipedia).

This not a bad question I think. I agree that brain information storage is not easy to define, and probably it's not feasible to give a good estimate, but the brain does store information, and information can be measured in bits. Yes, you need to be a more specific on what you consider "information" in this context, and probably you need some type of "fuzzy" or probabilistic measure, like how much information a normal adult would be capable of recalling on average. But I wouldn't be surprised if there are some estimates of this, or at least attempts to estimate it.

There are quite a number of very similar questions over at [cogsci.se]. You can start here and use the Related list of questions on the right.

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How does the blood of the veins in the legs get to the heart?
Does it have something to do with the valves? Thanks in advance!

You are expected to do some research on your own before posting here. That is the kind of question you ask google not here.

It has to do something with "muscle pump" and pressure in the right atrium. You can find out this from any decent explanation of the circulatory system...

The veins in your legs have one way valves. These prevent blood from flowing down, but do not actively push it up. However, normal muscle movement from walking etc will squeeze the veins to push blood through these valves, and so it will work its way up to where negative pressure in your heart atrium can begin having an effect. This does however mean that blood accumulates from long periods of standing without movement, and so exercises are needed to prevent fainting, for example, for soldiers on parade (see Pathophysiology, Homeostasis and Nursing
By Roger Watson, Tonks N. Fawcett, Josephine N. Fawcett)

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ECG detection using minimal number of electrodes
Disclaimer: Hello, I'm someone from an electrical engineering background, so this question may sound dumb.
I wish to make a wearable ECG monitoring device for arrhythmia detection. Since the device is to be wearable, it has to be small and should not obstruct normal behavior (kind of like those ECG patch monitors).
My question is, which lead should I monitor for arrhythmia detection. I read that I do not need all 12 leads for this purpose. The leads should preferably involve electrodes close as possible to reduce area of contact with the body.

hi and welcome. Question is not dumb, but could you share what you've found on your own? That will help us to understand gaps, and answer better

First, let's talk about electrodes.
Background
What do the electrodes measure?
When we talk about ECG signals, we generally talk about leads - that is, difference of electrical potential between two electrodes. This voltage change comes from change in polarisation in the heart as the rise in electrical potential is created in SA node and travels to AV node before coming down and finally spreading to the ends of Purkinje fibers.

Conduction system of the heart (source)
Signal
The plotted signal you get from each lead will give you your PQRST curve, but note that even though the events are there, the plots look rather different.

Raw signals from a multi-lead setup (source)
You can see that if all you are interested in are the times and durations of the PQRST events, all you need is one lead. But which one is the best? In order to find that out, we need to talk about heart vector.
Heart vector
Heart vector is the sum of all the small depolarisations happening in the heart, and points roughly in the direction of where the most depolarisation is happening. During the heart cycle this vector changes in time.

Heart vector changing during the heart cycle (source)
You can see that the highest heart vector variation is on the subfigure B, which roughly lies on the line crossing an electrode on the right shoulder and the left leg.
But wait! Before you start working on your single-lead ECG patch, consider, that this will only give you the magnitude of a projection of the heart vector on the diagonal axis described in the previous paragraph. If you add one more electrode, you can build an Einthoven's triangle and actually find the heart vector (or rather it's close enough approximation).
Electrode placement
In Einthoven's triangle method, 3 electrodes are used - 2 are placed on the shoulders and 1 on pubis, or you can place them more distally - on arms and left leg.

Einthoven's triangle (source)
This gives you 3 leads, from which you can use any two to find the heart vector (guide here).
Number of electrodes
OK, but why is it so important, that we have found the heart vector? We had to add a whole electrode to our setup!
Averaging all heart vectors occurring during a heart cycle will give us (an approximation of) mean electrical axis, which can aid in diagnosing pathological hearts.
Setups with higher electrode and lead count can give you even more insight into the heart function, but I will omit them in this answer for the sake of brevity.
Similiar projects
3-lead ECG patch
Probably the closest to what you want to achieve is a 3-lead ECG patch described in the Quality of ECG Monitoring with a Miniature ECG Recorder (Janata, 2008). They compare the performance of a small ECG patch placed in 4 different locations to a Holter monitor for rhythm analysis. They find that the patch is useful, but there is some information lost compared to the Holter monitor. Not that the channels in the patch look really similiar compared to the ones from the Holter monitor, so placing the electrodes close together does limit the amount of information you will be able to gather.

ECG patch used in the study
Single-lead ECG arrhythmia detection
If you really are limited to to electrodes, there has been some luck in detection of arrhythmia from a single lead signal using machine learning. An example would be Detection of Atrial Fibrillation from RR Intervals and PQRST Morphology using a Neural Network Ensemble (Khamis, 2018). However, keep in mind they used a proper lead I (LA-RA) setup, not a single ECG patch.

You could try to dig into the specs of the new/upcoming Withings ECG smartwatch for some insights https://www.withings.com/uk/en/move-ecg

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Do four-leaf clovers have some disadvantage in reproduction?
As far as I understand, four-leaf clovers are caused by genetics, so when reproducing, they should produce four-leaved children. I haven't found any disadvantages of four-lead clovers (e.g., infertility or worse survival capabilities), so I wonder why four-leaf clovers are so rare. Do they have any competitive disadvantage that makes them less likely to reproduce?

Neutral selection could mean that the probability of fixation is simply very, very low... A complement to the question: based on a (non-quantitative) examination of photographs of four-leaf clovers among wild type clovers, it seems to me that the area of individual leaves is the same, meaning that four-leaf clovers could potentially be better at harvesting light (?) so I'd be curious to have an answer too

I don't think that Neutral selection is a concept! Do you mean absence of selection (hence a probability of fixation of $\frac{1}{2N}$, where $N$ is the population size).

@v6ak As far as I understand, four-leaf clovers are caused by genetics After a quick look, it seems that the question of whether there is a genetic based to this phenotypic variation is not resolved. It might just be a rare phenotype caused by some developmental instability or specific micro-environmental conditions. Do you have any reason to think the opposite? Note that some clover can have five leaves.

An allele does not need to be at a selective disadvantage in order to be rare. Using that logic, one could say that anything that does not exist would be at a selective disadvantage (as something cannot be more rare than if it does not exist).

I haven't said that there must be some competitive disadvantage, just there might be some. And I am curious if there is some.


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"Imperviate" is it a word what can be substituted?
Sentence:
The aquaporins allow water to pass through the membrane and imperviate any solute molecules from diffusing across.
I'm looking for a word that pretty much is the opposite of perviate or to occlude.
http://www.etymonline.com/index.php?term=impervious

Since this question is not about biology but language, it is off-topic here. I will move it to english language and learning.


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Why is the inside of a cell negatively charged
So my teacher asked: "$[K^+]_i$ (k+ on the inside) is about forty times higher than $[K^+]_o$ (k- on the outside). With so many more positively charged potassium ions inside versus outside, why isn’t the interior of the cell positively charged compared to the exterior?"
My Thoughts: I am assuming that there must be enough negative charges inside the cell from other things like chlorine or ATP and proteins that the net coulombs on the inside is lower than the net coulombs on the outside. Does this seem like the correct answer? I am hesitant to use this because so far my teacher has only talked about potentials and not charges. I completely understand that the potential is negative, but potential and charge are two different things.
Edit: posted exact question from teacher as opposed to original summary of question

Since we're just talking about a potential differences, it doesn't have to be additional negative charges inside; it can also be additional positive charges outside. The Na/K ATPase also pumps out a lot of Na+ ions.  See this page:  https://en.wikipedia.org/wiki/Na%2B/K%2B-ATPase

this is a fair point. So Na+ is pumped out and K+ in at a ratio of 3:2 respectively. Therefore is it safe to assume that there are a greater number of Na+ outside than there are K+ inside, hence the greater positive charge on the outside?

That's right.  Now you could answer your own question! :-)

Net Potential on a cell surface is always measured in comparison to the extracellular media...so it is a relative parameter. So inside of the cell membrane is negative implies that there is more negative charges inside or more positive changes outside compared to the respective opposite side of the membrane. As we do not deal with the "absolute potential" we need not calculate the values of them.
K+ concentration is more inside the cell compared to outside...but there are other ions in and outside cells...e.g. Na+, Ca+,  proteins, Cl- etc...all of them together determine the potential difference across cell membrane.


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Does parasitism, one of Bacteria's lifestyle?
The parasite is an organism that lives in or on a host. It depends on its host for survival.
Bacteria lives in decaying organic matter, within human organism (colon, oral cavity). It can be a saprophyte or commensal.
Does the parasitism, one of bacteria's lifestyle ?

Welcome to Biology.SE! We encourage you to do some research on your own and then, informed by what you have learned, ask any questions you still have (ideally with references to reliable sources). For this question, you should be able to find answers quite easily from reliable sources and as such this question seems to fit this sites criteria for "homework". ——— Please take the [tour] and then go through the help pages starting with [Ask] questions effectively on this site. Thanks!

In particular, your definition of parasite better fits "symbiont", which suggests you might benefit from doing some reading of introductory material. I have found that when learning about a new area starting with a relatively accessible and reliable source like Khan Academy is very helpful. Wikipedia is also generally a good starting point and you can then check their references. Finally, textbooks with a good level of detail are also freely available online e.g. from NCBI.

If you are asking whether some bacteria are parasites, then absolutely yes. I think this is absolutely clear and evident to any and all biologists and would require no discussion. I could expand with some examples, but they would not be very representative of the incredible diversity of parasitic bacteria.
Parasitism
Many bacteria parasitize and live selfishly on hosts. Among them are obligate and facultative parasites. Many become parasitic if there are changes on their host (e.g. think pH in your oral cavity). These are endless. And to expand on this ecological discussion, I think another related and interesting relationship in nature exists which is not technically parasitic but falls into a similar category...
Commensalism
Yet many other bacteria are symbiotic commensals, i.e. do not benefit nor harm the host. As commensals, they have various commensal relationships with the host:

chemical commensals

(exploit the available chemistry of the host),

inquilinism

where the bacteria will live in the host's prepared environment (think ant hills or termite mounds or bird nests; or sewers, air vents, the list is endless especially for human environments)

metabiosis

(when the aprasite depends on the environment previously prepared by another organism; think how bacteria may parasitize fungi on the ground, which digest dead plant matter; the fungi deploy antibiotics to prevent this kind of parasitism, and we've used these defences for our own medicine... penicillin is from fungi!), and

phoresy.


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Can heterotrophs use anabolism to obtain energy?
With that question I mean: directly.
Please bear with me, as I don't know much about Biology or Chemistry (those are my main difficulties while studying).
I know that energy that biological beings use can be stocked in molecular bindings so that they can have it available later, when needed.
But in that process, if anabolic, it is not obtaining energy, but 'spending', stocking some energy in chemical bindings, so that it, through catabolism, can be liberated and used.
Wouldn't heterotrophs, then, obtain energy exclusively through catabolism?

@John — Please follow the instructions in the comment box and do not use comments to answer questions.  Your answer is incorrect imho, but I cannot vote it down or comment on it.

Welcome to Biology.SE! Please take the [tour] and then go through the help pages starting with [Ask] questions effectively on this site and [edit] your question accordingly. We encourage you to do some research on your own and then, informed by what you have learned, ask any questions you still have (ideally with references to reliable sources). For this question, you should make sure you understand the terms you are using such as anabolism, which I think should make the answer self-evident. (See study suggestions in next comment.) Thanks!

I have found that learning about a subject is easier if you start with a relatively accessible and reliable source like Khan Academy. Wikipedia is also generally a good starting point and you can then check their references. Online platforms called MOOCs offer free (or very low cost) courses on a wide variety of subjects — two I am familiar with are Coursera and edX. Finally, textbooks with a good level of detail are also freely available online e.g. from NCBI.

@tyersme Thank you so much for your replies and your help. I'm afraid I did some research on the topic. I started studying metabolism for a test and there it was given the definitions on both anabolism and catabolism. Anabolism would be the constructive part of the metabolism, in which we have the storage of energy and the catabolism we'd have the release of energy.
But later I came across a question in which the correct answer was : 'heterotrophs use both catabolism and anabolism to obtain energy". And I wondered why. (Continues in next comment) -->

I wondered why because if the energy is stored in anabolism, if anything, I would think the organism wouldn't be able to 'obtain' energy if it was spending it so it could be stored and used when needed. Later I came to think that if an organism synthetizes, for exemple, enzymes so that it can be more efficient in obtaining energy. Maybe the positive balance of energy would allow us to state that a heterotroph would use both anabolism and catabolism to obtain energy. Please let me know if that reasoning make sense.


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Will a less favorable allele's frequency go to 0?
For example, a pond is dark in color. There are two alleles. The dark color allele is dominant over the light color one. Let's assume that the relative fitness of both the homozygous dominant and heterozygous is 1, and the relative fitness of the homozygous recessive is 0.5. When I ran the simulation, I changed no other values.  My data after 251 generations is this:  My question is that being homozygous recessive is clearly less favorable, and even though being homozygous dominant and heterozygous carry the same advantage instead of heterozygote advantage, why wouldn't the recessive allele disappear?

You only run your simulation for ~250 generations - what makes you think that this is enough to generalize the results. I honestly don't myself how many generations are 'enough' to be sure that the results won't change anymore (you'd probably have to check if your model converges to a stable state with your given parameters).

If you have a way to run a deterministic model that calculates the expected allele frequency over time, that would probably clarify things (e.g., I agree with @Nicolai that you probably just haven't run the simulation long enough)

Welcome to Biology.SE! Have you thought about what happens as the frequency of of the "r" allele drops? Take the extreme example of a population with only a single heterozygous individual being present in the population — how much selection would there be at that point against the "r" allele? ——— You may also want to take the [tour] and then go through the help pages starting with [Ask] questions effectively on this site. Thanks!


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sperm reaction of virus infected
we know when a human body cell infected by a virus , create interferon 1 to call other cells that surrounded it  , but red blood cells couldn't do this because they loose their nuclear and other organelles . I have a question about sperms , can sperms produce interferon 1 when they infected with viruses?

Could you please be a little more precise and specify the virus that you have in mind that infects sperm?

Welcome to Biology.SE! Please take the [tour] and then go through the help pages starting with [Ask] questions effectively on this site and [edit] your question accordingly. ——— We also encourage you to do some research on your own and then, informed by what you have learned, ask any questions you still have (ideally with references to reliable sources). Thanks!

well David I don't have any special virus just I ask this in general


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Why is bacterial meningitis worse than viral meningitis?
My field is not biology related, but it is commonly said that bacterial meningitis is far more dangerous to the individual than the viral kind. It seems to be true even with antibiotic treatment. What is the biological reason for this?
If this question has already been addressed or this is the wrong stack exchange, feel free to redirect this question to the more appropriate place.

One needs to be careful making broad generalizations about meningitis. The term simply refers to inflammation of the meninges (the outer layer surrounding the brain and spinal cord). Meningitis can occur due to a number of causes, most notably viral and bacterial infections, but can also also be due to fungi, parasites, toxins, cancer, etc. There is a vast range in severity of meningitis depending on the aetiology.
For example, rabies infection can progress to a fatal meningitis. Rabies is a virus. You therefore cannot say that bacterial meningitis is worse than viral meningitis.
That being said, what you have likely heard is that viral meningitis tends to be less severe than bacterial meningitis. This is true not necessarily because viruses are worse at causing meningitis than bacteria, but because the common causes of viral meningitis are often more easily cleared by the immune system.
Non-polio enteroviruses and herpesviruses are the most common causes of viral meningitis. These are the same groups of viruses that commonly cause mild cold or flu-like signs. Usually, when we have these signs, we don't go to the doctor to be treated with antivirals, because in healthy individuals our bodies are usually good at clearing the virus. The same is true when the virus is affecting the meninges. However, this does not mean that these viral infections cannot be severe in some cases.
The most common bacterial causes of meningitis in people are Neisseria meningitidis, Streptococcus pneumoniae, and Haemophilus influenzae type b. The pathogenesis of disease is broadly speaking similar to that caused by viruses, but the inflammatory response of the immune system tends to be more severe with these bacterial organisms compared to the common viral causes of meningitis. Bacterial meningitis is also typically accompanied by sepsis affecting other organ systems. While antibiotics exist that are effective at treating these bacteria, many antibiotics do not cross the blood-brain barrier, which makes treatment of bacterial meningitis challenging.
Finally, it is worth mentioning that widespread vaccination may have had an effect on our perception of meningitis severity. For example, at one time polio was a major cause of viral meningitis, but vaccination has vastly reduced rates of this disease in many parts of the world. Similarly, mumps and measles used to be more common causes of viral meningitis, however due to widespread use of the MMR vaccine these are now less common causes of viral meningitis. On the bacterial causes, there are now several common vaccines such as meningitis B/C/Hib/pneumococcal vaccines which are effective at reducing rates of infection with these bacterial organisms.

I think the question is fine, though some might find it too broad and it is hard to give a precise answer.
It's really just because they are two different diseases, the only thing that is the same is the tissues that are targeted. Bacterial meningitis is associated with bacteria that destroy tissues, release toxins, and cause a strong immune response - that immune response can sometimes be as dangerous as the infection itself. The blood-brain barrier can limit the effectiveness of some antibiotics because the drugs don't get to the affected tissues, though infection also damages the blood-brain barrier (this reference talks about both of these issues).
Viral meningitis can also damage tissues but typically more slowly, and in most individuals without immune problems the immune system is able to limit the virus before the infection gets out of control.


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Calculating the human carrying capacity for turtle tours?
I am looking to calculate the human carrying capacity of a leatherback nesting beach in the Caribbean to inform conservation policy on the maximum number of people allowed on turtle tours; yet after an exhaustive search, I have found very little. Could anyone point me towards a research article that could be of assistance?

The carrying capacity of a species at a given location is the number of individuals of that species that can live at this location. I suppose what you are looking for is rather something like the maximum number of humans that can live at a given location while keeping a carrying capacity for leatherback above a certain level. You might want to rephrase the question


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Pigmentation in Jaundice
My textbook says that the yellow appearance of a jaundiced person is due to the accumulation of bile pigments in the skin. I am unable to understand why these pigments are not deposited in a healthy person? Please help.

Because our liver breaks them down and makes sure they are excreted.

@Chris, my question was why couldn't the breakdown(that you are referring to) happen in a healthy person?

The breakdown does happen in a healthy person which is the reason they are not getting yellow.

The yellow color comes from the accumulation of Bilirubin in the body. Bilirubin is a breakdown product of hemoglobin (contained in erythrocytes, also known as red blood cells, and responsible for the oxygen transport in the body). (This is also the reason why bruises get colored, as the blood which was released into the skin gets removed.) As erythrocytes live only for around 120 days, the hemoglobin needs to be recycled at the end of the life cycle, as free hemoglobin is a pretty problematic substance.
The recycling of the erythrocytes happens in the liver, the iron is recycled, and the hemoglobin is split in the globin (which is further broken down into the amino acids) and the heme which is oxidized by the heme oxidase to biliverdin and further by the biliverdin reductase to bilirubin.
As bilirubin is not water soluble it is bound to albumin and released into the bloodstream for the transport to the liver. In the liver this process goes on further until the bilirubin is water soluble and can be released with the bile into the intestine where it is finally excreted. See the image (from here) for an illustration:

If your liver is not working properly (for example due to an infection) the break-down process of the albumin-bound bilirubin is reduced or doesn't work and the yellow bilirubin accumulates in the body until the skin gets yellow. So this indicates a liver malfunction and is usually nothing to take easy.


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Is my cell-culture contaminated with mold?
I am growing cell cultures at the moment, and I sometimes find 1-2 of these elongated, black structures in one of my 8 wells. Should I be concerned?
I have been growing these for about 5 days at this point, replacing the media every the other day. I figure that the life-cycle of mold is pretty fast, and that if it were truly mold that it would overpopulate the well pretty quickly. Perhaps it's just debris?

They could be pieces of tissue paper. Do these "things" grow after a while? Cell debris is generally smaller than the cells. Is there a picture with the cells in focus?

4-15-2021:
Same thing happened to me. Same look from picture above but way more. Even if the cells were growing well and all,I was about to throw away the flask. I wiped down with ethanol the bottom exterior and looked again under microscope and I would say 90% of them were gone. A simple thing to try.

Most of the time you can find shards of plastic, defects in the plate and other non-cellular debris in brightfield that look suspicious. Even some cellular debris can look suspicious, like when your viability is really poor. That doesn't look like anything to me. You'd know if you had contamination because it would be in more than 1 field, you'd have more than 1-2 of them, and your culture would either change in color, turbidity or smell. If it's a plate defect, you probably wont see it move if you re-suspend the well, either.

I know this thread is over a year old, but I found myself referring to this thread just this week (6.24.20) for help so I thought I'd post my experience in case anyone else is looking at this these days! I'm growing rabbit corneal epithelial cells and the original passage looked great the whole way through, I passaged about a week after plating, and 3 days into passage 1 contaminants EXACTLY like the ones in OP's photos began popping up. At first it was just a couple in one plate, but after a couple more days all 3 of my plates were covered. I knew it wasn't a live contaminant because the cells remained healthy and it didn't move, grow, or change; but still more and more showed up. After 5 days of this, I finally noticed that the contamination was worst around the ledge/rim on the bottom of the plate; which didn't make sense because why would a rim on the outside of the plate affect debris on the inside... and that's when I finally wiped down the entire outside/bottom of the plates with ethanol and sure enough all contamination was instantly gone.
So, if you've come here because you're seeing weird things in your plate, do yourself a favor and start by wiping down the outside/bottoms of your plate first. Might save you a lot of grief!

It would be best if you could show us some pictures of your own observations. As of now, there is nothing in your post that the community can use to validate your answer. Ideally, every answer should contain scientific references, or at least some sources or links to credible web pages. In this case, I understand personal experience can be valuable to share, but then the minimal thing to add are some images. Cheers.


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Why are birds have balls in the form a cork screw i dont have the scientific name
Why do birds have penises in the form of a cork  screw?

Please use a proper vocabulary. "balls" is a slang. Also, balls refer to the testicles, not to the penis.


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Naming the Rings of Flagellar Structure
I will apologise ahead of my very basic question.
I just read about Flagella Structure and learned that there are 4 rings, namely "L Ring", "P Ring", "MS Ring", "C Ring".
I tried looking online for why the rings are named as such, but i could not find anything related to their naming.
I am guessing
L Ring = lipid ring?
P Ring = Periplasm ring?
MS Ring?
C Ring = Cytoplasm ring?
Thank you in advance for enlightening me.

Your guesses are correct. More detailed, assuming you are referring to Gram-negative bacterial flagella and flagellar motor structure:

L ring associates with the Lipopolysaccharides (more general S-layer for archaea and Gram-positive bacteria)
P ring associates with the Peptidoglycan layer
MS ring is embedded in the plasma Membrane (not sure why S maybe tranSmembrane?)
C ring is a Cytoplasmic protein attached to the MS ring acting together as the rotor of the flagellar motor

As a structural biologist here is some recommended literature on high-resolution (cryo-EM) structures of flagellar proteins:

3D cryo-EM imaging of bacterial flagella: Novel structural and mechanistic insights into cell motility
Structure of the molecular bushing of the bacterial flagellar motor


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What cell types comprise the median eminence and the tuber cinereum?
I have tried pretty hard to get a detailed description of what exactly the median eminence and the tuber cinereum are but to no avail. I am very familiar with their anatomical relationships (spatially) with the hypothalamus, 3rd ventricle, mammillary bodies, etc; however, I still do not quite understand what they are or what cell types comprise them.
Are they areas of grey matter? Are they some sort of modified ependymal cell layer of the 3rd ventricle floor?
Or are they areas of connective tissue that merely "house" white matter projections from the hypothalamus to the pituitary? So, to repeat the inquiry from above:
What cell types comprise the median eminence and the tuber cinereum?
And, moreover, what's the actual function of the cell types that comprise them?

Have you read the Wikipedia articles on both structures?

I do not see anything in the articles that even remotely talks about cell type...and seeing as that is the topic of this inquiry.

The tuber cinereum is the "swelling" at the ventral surface of the hypothalamus (Subarachnoid space surface) at the base of the infundibular stalk. The median eminence (a circumventricular organ) is an elevation on the ventricular surface of the infundibular recess of the 3rd ventricle.

Welcome and thanks for your answer. Unfortunately it doesn't answer the question as OP specifically says they are familiar with anatomy of said structures.

Since the question title asks specifically about the cell types, could you maybe edit your answer and add this information?


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Assumptions for Nernst Equation
While I am familiar with some of the conditions for the Nernst Equation, for example:
1) "The membrane is only permeable to one ion even if there are several other ions in the system"
there is an assumption/condition that I have yet to see mentioned (and I am pretty sure that it is an essential one that must be included). That assumption is as follows:
The two solutions separated by the selectively permeable membrane must initially have the same total charge...i.e. there is no initial potential difference between the 2 sides of the membrane
I believe this must be true because of the following 3 cases:
for all 3 cases, only potassium is permeable, and there is a "Left Side" and a "Right Side" on either side of the selectively permeable membrane.
A) Left Side: 25 mM K+, 125 mM Na+ |&| Right Side: 125 mM K+, 25 mM Na+
B) Left Side: 25 mM K+, 10000000000 mM Na+ |&| Right Side: 125 mM K+, 25 mM Na+
C) Left Side: 25 mM K+, 0.00000000001 mM Na+ |&| Right Side: 125 mM K+, 25 mM Na+
Without using my proposed assumption, in all 3 cases, the Nernst equation for potassium would be the same:
(RT)/(ZF) * ln (25/125)
However, I fail to see how case B & C could have the same Nernst potential for potassium as case A when the electrical forces on the left side of the membrane are completely different! Let's use case B as an example. Clearly, the potassium concentration differences exist between the two sides (25 mM vs 125 mM), BUT there is an enormous electrical repulsive force imposed by the sodium (1000000000 mM Na+) so there is no way that the same amount of potassium will pass over to the left side as it would in Case A, right?
Could someone please clarify?

Assumption (1) is not really even true. The Nernst equation is always valid to find the reversal potential for a single ion: that is its purpose. To determine the equilibrium potential for a number of ions, you use the Goldman/GHK equation. It happens to be that the Goldman equation reduces to the Nernst in case of single-ion permeability, which of course never happens for real but is a reasonable approximation in some cases.
As far as your additional assumption, no, that assumption is not required. The Nernst equation doesn't tell you which directions ions flow, it tells you what the reversal potential is for an ion. If you add a voltage from some other source (like your example of adding a bunch of mysterious unaccounted for positive charges outside the membrane) that doesn't change the reversal potential, it changes the voltage. If you put a large positive charge on the left side somewhat like your situation (B), potassium would flow up its concentration gradient towards the Nernst potential for potassium.
Note also that your example is utterly ridiculous: if you want to know what happens when you have 10000000 M Na+ ions together on one side of a membrane you need to consult a physicist, not a biologist. I don't know where you put all the other negative charges, but you're probably about to have a) A very expensive electric bill, and b) a very big hole in your lab.
In real biology, the number of charges on each side of the membrane is similar enough that you can call it equal (see for example Why is it possible to calculate the equilibrium potential of an ion using the Nernst equation from empirical measurements in the cell at rest?). In any case where someone describes "adding sodium" to one side of the membrane, they don't mean just sodium, they mean sodium as a salt with some negative ion, it's just that the identity of that negative ion doesn't matter if it isn't membrane permeable (relative to the other ions involved).

Just so other people know, I put this question over in the physics stacks, and the only person that answered stated that each side must be electrically neutral. So, I don't know if your answer is necessarily correct. Further, I don't agree with your logic. The Nernst Equation can also be reinterpreted as the voltage at which the electrical force and diffusive forces are balanced. So if one compartment has a fundamentally different electric potential, then the electrical force experienced by the permeable ion should be fundamentally different.

Yes, that interpretation still holds. My answer fully agrees with the answer posted at physics, you are misunderstanding both answers.


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Are large cell bodies of neurons harder to depolarize than small cell bodies of neurons?
In order for the axon to initiate an action potential, we know that the axon initial segment must be brought to threshold. So my question is as follows:
Say we have the minimum charge input, "X", necessary to depolarize the axon initial segment of Neuron 1.
Now, we have Neuron 2, which has a larger soma. Will this same input X be sufficient to depolarize the axon initial segment of Neuron 2?
I am trying to explore how physical concepts like capacitance manifest in biological systems. Neuron 1's soma (approximated as a sphere) presumably has a lower capacitance than Neuron 2's soma (approximated as a sphere), due to the difference in cross sectional area of the somas. Therefore, I would assume that Neuron 2's axon initial segment requires greater input to depolarize than Neuron 1's axon initial segment.
Is this simplistic idealization of somas actually observed in experiments?

Your intuition is correct, in order to attain the depolarization necessary to trigger an action potential you need more charge in the bigger neuron. This is simply because you have a larger capacitor.

Great! Knowing this, could you please explain then, WHY larger diameter axons convey action potentials more quickly than smaller diameter axons? (assume they are both equally myelinated) Shouldn't the larger diameter axons "require more charge to depolarize" and therefore actually take longer to convey an action potential?

Larger axons also have more sodium channels, so they move more charge. The reason why larger axons have faster conduction is because the have less internal resistance.

Can't I apply that exact same logic to the soma of the neuron? It has a larger diameter...therefore it has less internal resistance...it has a larger diameter, therefore it has more surface area available for ion channels to be present...etc
AND YET the conclusions are different between the two: big axon depolarizes more quickly but big soma depolarizes more slowly.

The soma doesn`t contain voltage dependent sodium channels, the voltage is propagated in a passive way. In the axons, conduction is active even though if you have an external input, larger axons need more charge. You can play with axon simulation in this web page http://nerve.bsd.uchicago.edu/nervejs/MAP.html you can change parameters of the axon such as the radius or stimulus amplitude and see how that affects the propagation of the action potential.

I will say that the main source of your confusion is between propagation velocity and charge needed for depolarization. They are related, but they don`t mean the same.

within the myelinated segments of an axon, however, the voltage IS propagated in a passive way. So I still fail to see how for the same conditions, different results are observed between axons and somas.

I really recommend that you run neuron simulations to see how the different parameters you`re interested affect conduction velocity. This program will allow you to play with myelination and axon diameter https://neuron.yale.edu/neuron/

Again, larger axons need more "stimulus" or charge to reach the threshold for the propagated axon. Nevertheless larger axons have more sodium channels in the node of ranvier, so the only difference will be the length constant. Somas don`t have sodium channels so you need more external stimulus to charge the membrane.


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What is the name of the wrinkles occurring in people's lips?
I was wondering if there is a name for the wrinkles occurring in people's lips.
Just curious.

What research of your own have you tried performing to answer this question? We ask that all question askers perform their own research before posting . Thanks.


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Identifying statistically significant gene rich and gene poor regions
I am just wondering If there any adapted way of Identifying significant gene rich and gene poor regions in each chromosome for a given genome say mm10?

What research effort of your own have you put into answering this question? We ask that all posters here do some of their own research, report what they've performed and what they found out, and then specify a question that  focuses on something specific about a topic that they still don't understand. Please update with some of your own research effort findings and sharpen your question some. Thanks!

Interesting question. I don't myself know how to do this but a literature search returns some older papers on how this was achieved for pig and chicken genomes over a decade ago. The best way to do this today is to look through annotated genomes (like the mouse mm10) and use a gene density metric. You can achieve this with R code, writing your own code, trying to use some of the rich features provided in-browser at the UCSC genome browser (for mice, otherwise start here), or perhaps try to search literature for gene density stuff. I defer to others for more specialized answers.
PS. Since you're also interested in determining statistical significance, you probably will need to apply this over a sliding window across chromosome lengths, and this kind of question has been answered often elsewhere on SE (example). Sorry I can't be of more help; good luck!

Thank you for your comment. I found that coverageBed from bedtools  has some useful output for identifying gene densities.


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Histone Deacetylase Inhibition
So I am trying to brush up on my knowledge of HATs and HDACs.
I am reading the just the 1st paragraph of the background of this study
I remember learning that HATs turn things on on, and HDACs turn things off.
It says that sodium phenylbutyrate (PB), can epigenetically regulate gene expression by inhibiting histone deacetylase.
Does this mean that one of the effects this drug can have is turning the thing that turns things off to produce the effect of turning it back on? Similar to that of a double negative?
Thanks.

Yes, Sodium phenylbutyrate can upregulate the transcription of silenced genes by inhibiting the activity of Histone deacetylases (HDACs).
Histone acetylation performed by Histone acetyltransferases (HATs) helps in activation of genes, while deacetylation performed by HDACs is responsible for gene silencing. This makes HDACs a potent drug target to treat malignancies.
The inhibitors of HDAC regulate the chromatin structure which loosens the chromatin and hence effect the binding of transcription factors to DNA.  This binding modulates the expression of genes playing role in cell cycle and apoptosis, thus effecting cell growth and differentiation. (Reference)
But this is not similar to double negative. Double negative is term used in embryogenesis, where a particular repressor gene is activated in specific regulatory state. (Reference)

Just for clarification - you are agreeing that PB acts as a negative feedback mechanism? (Not sure if that a better terminology than double negative?) Because when I used double negative I meant it in the sense that two negative processes could create a positive "constitutive on" for binding of TFs and hence turning gene expression?

yes.. you are right, but I think that term can't be used in this case.

Sort of. Histone deacetylases act on a particular region on the chromatin fiber to decrease or even silence the expression of the genes in such region. According to the study, PB has the capacity to inhibit the activity of histone deacetylases, which implies that the effect of PB, is to the make the cell less able to decrease the expression of certain genes, so one could crudely say that PB is turning off the thing that turns off the expression of certain genes, but this does not imply that it will turn the genes back on.


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Where do the lysines come from during ubiquitination?
I know that Ub forms an isopeptide bond with lysine, but where do the lysine come from?
Are they just always available for the Ub to find to during the ubiquitination process? Is there a free lysine available on each of the additional Ub added to the chain? After the first Ub is added onto the target protein, does the E2/E3 complex still have to bind each time a Ub is added to the chain?

The Wikipedia article on Ubiquitin gives a pretty good answer to your questions. Look at the referenced articles if you want to get more detailed answers.

Are they just always available for the Ub to find to during the ubiquitination process?

Yes, This [Ubiquitination] process most commonly binds the last amino acid of ubiquitin (glycine 76) to a lysine residue on the substrate.

Is there a free lysine available on each of the additional Ub added to the chain?

Ubiquitin has seven lysines and each one of them can be bound to the N-terminal glycine of the next ubiquitin.

After the first Ub is added onto the target protein, does the E2/E3 complex still have to bind each time a Ub is added to the chain?

Yes, but this is more complicated than the general mechanism. A poly-ubiquitin chain can be attached just like a single ubiquitin or one more ubiquitins can be conjuated to an exisiting ubiquitin-protein complex. See for example Brown et al and David et al.


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Approximate Cell Doubling Time?
If I know it takes 12 min to occur in mitotic fibroblast cells and I count there are 32 dividing cells in the microscope slide out of a total population of 32034 cells, how do I calculate the approximate doubling time in hours?
My colleague says it should be around 200 hours. But I don't understand how they reached to this conclusion, can anyone explain this to me please?
Thanks

I figured it out, 32034/32 = ~1000
1000 / 5 = 200 hours
Because 12*5=60 min = 1 hour


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Small mammal identification
Small skull found in Alberta, Canada. Do not know the region. Skull is about 17 mm in length. Trying to identify the species, narrowed it down to most like a species of vole but can't figure out which one. Below are pictures of the teeth under a dissecting microscope that we were using to ID, upper jaw and then lower jaw respectively.


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Vitamin B12 deficiency Megaloblastic anemic
I have two doubts regarding Megaloblastic anemia which shakes my mind
(1) first is- I know that vitamin B12 is required for thymidine synthesis which is further required for DNA synthesis and so if there is vitamin B12 deficiency than the DNA synthesis will get impaired which will affect the progression of cell cycle in the proliferating cells. This is what I know ,, now my question is that if the deficiency interferes with cell cycle progression then how bone marrow hyperplasia can be seen in vit. B12 deficiency??
(2) my second question is that how B12 deficiency interferes with nuclear maturation or rather what actually nuclear maturation is?
What  nuclear maturation signifies ?


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What are all the elements affecting human reaction time?
I'm helpless at biology/science-y stuff in general. But, as a writer, for the sake of story research, I often have to delve into it. I make use of the Worldbuilding Stack Exchange, but this question didn't seem like it would be a good fit for that site, because it's more about clarifying my understanding of certain scientific concepts than about anything specifically worldbuilding related.
I am looking to create a character with high-speed reflexes and reaction time. However, my question is not about how to accomplish this (scientifically dubious) feat, as this would belong on the worldbuilding forum, but rather whether I have properly identified the elements necessary to do so.
From the research I've done, it seems that the most basic steps regulating how quickly someone reacts to something are a) sensory neurons recognize a stimulus b) they send a signal to the brain/spinal cord and c) this signal is processed and another signal is sent to the muscles, resulting in whatever physical reaction observably occurs.
Hypothetically, then, no matter how fast any single element in this chain (if given a brain that could process signals 10x faster than normal or nerve signals that traveled 10x faster (bear with me)), the speed with which the final action was triggered and completed would still be limited by, say, the eyes' tracking speed and the speed with which the eye converted light into electrical signals on one end, or the speed the muscles were capable of contracting at the other end of the chain.
How am I doing so far?
So, by my estimation potential limiters of reaction speed are as follows:

the speed the eye moves (or would speeding up other things, such as muscles and nerve signals, also increase this?)
the speed the eye converts light into signals
the speed that signals can travel from sensory neurons to the brain/spinal column
the speed with which the brain can process these signals (and potentially its ability to handle multiple tasks/stimulus simultaneously)
similar to (3), the speed that signals from the brain (or spinal cord) can travel to the muscles
the speed with which muscles can contract

Am I confused about or missing anything? Thank you!


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Would it be correct to say that viruses are genotoxic?
I know it is an unconventional way to describe viruses, but would it still be technically correct?

From wiki

In genetics, genotoxicity describes the property of chemical agents that damages the genetic information within a cell causing mutations

While some viruses tend to cause mutations, most don't have such a strong mutagenesis effect. As such, they are not really genotoxic. Also, even if a virus is genotoxic, one should definitely not reduce the activity of a virus to its genotoxicity. A virus has a life-cycle and is able to reproduce. It is clearly more than a simple genotoxic chemical agent such as metal chromium.
So, in short

Reducing viruses to their genotoxic effect would be a misrepretentation of what virsues are
Most viruses don't have a strong genotoxic effect and therefore you can not make the claim in the general sense.


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Where does reverse transcriptase come from?
I can't figure out whether the viruses provide reverse transcriptase, or their RNA has the code for it, or the host cell normally contains it.
Multiple sources just introduce the enzyme without explaining who provides it / where it comes from. Apparently, both the host cell and viruses have processes that are dependent on reverse transcriptase, so I guess the answer is all of above / case-dependent?

Interpretation: "Where does reverse transcriptase come from" ... which is a. found in cells b. found in virus?

I was about to write an answer saying that all reverse transcriptases are viral genes/proteins, but then wikipedia reminded that the telomerase is technically also a reverse transcriptase.
To answer your (main?) question:

I can't figure out whether the viruses provide reverse transcriptase or their RNA has the code for it

Retroviruses have (almost by definition) the code for a reverse transcriptase in their genome. However, they also have the enzyme (or rather an inactive pro-enzyme) packaged into the viral capsid. The reverse transcriptase is a part of the Pol gene.
There are some other viruses that also use reverse transcription, but aren't retroviruses - in these cases I'm not sure, but I would guess that they also have an RT in their genome.
Now going back to the telomerase and retro-transposon elemnts:
These are ancient genes/elements in the eukaryotic genome, that basically do the same thing as viral reverse transcriptases: they make DNA from RNA.
Retro-transposons are generally believed to be viral additions to the genome, collected over the course of evolution. However, also the Telomerase enzyme probably has one common origin with viral reverse transcriptases (Nakamura 1998, take a loot at figure 2 at the end), (Witzany 2008). The thing about these evolutionary events is that they go way back, up the point were eukaroytes just started evolving from ... something. The sources I cited argue that many "eukaroytic" features (e.g. nucleus, RNA processing, vesicular transport) were originally taken from viruses.

As the question is not restricted to retro virus the answer might also elaborate on  any non retro virus using reverse transcriptase "being found" in cells.

It is important to note that not all viruses have a reverse transcriptase gene. These kind of genes are a defining feature of retroviruses.
Retrovirus are single stranded RNA-viruses. Once a retrovirus infects a cell it uses reverse transcriptase to convert its single stranded RNA into double stranded DNA. The genes on this DNA are then transcribed and translated into new reverse transcriptase and other protein by the host cell. When new viruses are assembled within the host cell, both RNA containing a reverse transcriptase gene and reverse transcriptase enzymes are packaged into a new virus.
So to answer your question: Host cells do not normally contain reverse transcriptase. Viruses contain both the gene and the enzyme.
Alberts

There are no double stranded retro viruses?


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Cardiac pacemaker: how can different nodes have different frequencies?
Primary SA node creates 70 beats per minute and secondary AV node 40-60 beats per minute. Is the AV node inactive (and other subsequent nodes) while the SA node is functional? If the primary, secondary and tertiary nodes are working simultaneously, wouldn't the difference in the beats per minute cause a mess?

The AV node and any other nodes are suppressed by the SA node because it is the fastest.  If the SA node is sick or slow or there is a conduction problem one of these other nodes can take over calling the beat.
http://www.cvphysiology.com/Arrhythmias/A018. bold emphasis mine.

The higher frequency of SA nodal firing suppresses other pacemaker
  sites by a mechanism called overdrive suppression. If a latent
  pacemaker is being depolarized at a higher frequency than its
  intrinsic rate of automaticity by an adjacent cell that is driven by
  the primary pacemaker, then the increased frequency of depolarizations
  leads to an increase in intracellular sodium ions because more sodium
  ions enter the cell per unit time. This increased sodium stimulates the Na+-K+-ATPase (increases its activity) to expel more sodium from the cell in exchange for potassium (see figure). Because this pump is electrogenic, increased pump activity increases the amount of hyperpolarizing currents generated by the pump. This drives the membrane potential more negative, thereby offsetting the depolarizing pacemaker currents (If) being carried into the cell. This effectively prevents the pacemaker currents from depolarizing the cell to its threshold potential, and thereby prevents the spontaneous generation of action potentials. If the cell ceases to be driven by the SA node (e.g., because of AV block), then the additional hyperpolarizing currents will be lost and spontaneous depolarization and action potential generation can occur.


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Are synaptic boutons always located on axons?
I am learning about the protein Synaptophysin and I have read that it is an integral membrane protein localised to synaptic vesicles. I have also read that it is a specific and sensitive marker for synaptic terminals. On this site, I have read that synaptic terminals are the presynaptic endings and on Wikipedia that the presynaptic axon terminal is also known as the synaptic bouton. From what I have read online it seems to me that synaptic boutons are located only on axons.
However, I have found out about dendrodendritic synapses which are connections between the dendrites of two different neurons. Can the presynaptic ending of a dendrodendritic synapse be referred to as a synaptic bouton or are synaptic boutons only located on axons? Any insights are appreciated.

Axonal boutons are named as such due to their shape. Dendro-dendritic synapses do not resemble this shape and are never referred to as boutons. It does not appear that synaptophysin is expressed on dendrites (Fletcher et al. 1991), but I am unaware of a study that targeted dendro-dendritic synapses specifically.

References
Fletcher, TL, P Cameron, P De Camilli, and G Banker. ‘The Distribution of Synapsin I and Synaptophysin in Hippocampal Neurons Developing in Culture’. The Journal of Neuroscience 11, no. 6 (1 June 1991): 1617. https://doi.org/10.1523/JNEUROSCI.11-06-01617.1991.


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What are the units of the band intensities in a western blot image?
I have done a Western blot and I am measuring the band intensities in Image J. Using the rectangle tool, I have outlined the band and then calculated the area and the mean intensity of the band. I have then calculated the total intensity of the band by multiplying the area of the band with the mean intensity. I was wondering, what are the units of the band intensities? Are they in arbitrary units? Any insights are appreciated.

The units in your case are arbitrary units.
For instance, you may have taken a photo of the bands with a camera that saved a gray-scale file with an 8-bit depth. That means that the brightness values of each pixel have 256 gradations (or 2^8 values of brightness possible between minimum/blank and maximum/saturated). The program only takes the pixel brightness value anywhere between black (0) and fully white (256) and simply performs the calculations so. There is no real connection between actual band intensity and the output from ImageJ or any software.
Alternatively, you can also have relative units. Say you have a reference: a positive or a negative control. If your reference has a brightness of 10, and your band has a brightness of 7, you could express the band intensity as "0.7 relative units"; here you have to specify your reference, i.e. what you are calibrating your relative units to, hence the term relative.


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Can proteins be located on the surface of the mitochondria?
I am learning about the mitochondria and I know there are proteins present in the mitochondrial matrix such as SOD2, but I was wondering for a protein to be located on the surface of the mitochondria does it always have to be a membrane protein (e.g. inserted within or associated with the mitochondrial outer membrane) or can other proteins which are not membrane proteins be present on the mitochondrial surface?
Any insights are appreciated.

What kind of protein? Do antimitocondrial antibodies count? What function might it have, to be near but not integral to the mitochondrial surface? I'm not sure what you're asking.

I believe that one needs to think chemically about this. If a protein is present on the surface of a membrane, there has to be an interaction causing it to be there. By definition such a protein will be a membrane protein — either integral or peripheral. So are you asking whether there are peripheral outer membrane proteins?


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Does the term 'protein expression' refer to the production of proteins only or also their regulation?
I am learning about molecular biology and I have come across the term 'protein expression' in a research paper. I have searched the definition of this term online and on the Thermo Fisher Scientific website it states that "Protein expression refers to the way in which proteins are synthesized, modified and regulated in living organisms". However, on the National Cancer Institute website it states that protein expression "Refers to the production of proteins by cells".
I was wondering, between these two definitions, which one is more correct? Can protein expression also be used to refer to how proteins are regulated (e.g. can you use the term protein expression when discussing how one protein regulates the activity of another)? Any insights are appreciated.

I like MattDMo's answer, but I would add that the two definitions you cite are likely meant for two different audiences. The Thermo Fisher site is primarily a source for scientists and students of science (i.e. those that may buy TF products), and the definition is therefore more technical.  The cancer.gov site is likely meant to be a resource for cancer patients and laymen interested in better understanding cancer biology, and thus makes no reference to protein regulation or modification.

There are no formal definitions accepted in science for ambiguous
phrases such “protein expression”.

If you wish to know what a particular author who uses such a shorthand phrase means you need to examine the context. If you wish to write scientific reports that are comprehensible to others you must express yourself precisely, defining any shorthand phrases that are necessary to avoid clumsiness.
In the context of the question, all that “protein expression” means to me is “expression of protein” — the synthesis of the protein from some entity that has the potential to do so. It a fundamental level that would be a gene or mRNA that encodes a protein (or proteins — that too is unclear), in which case this might be less ambiguously expressed as, for example:
“…expression of protein from gene X inthe plasmid construct Y…”
“…expression of proteins from mRNA in vitro…”
(I would generally retain the preposition. Be kind to it, poor little thing!)
To indicate that one was interested in the potential of tissues to synthesize proteins, then (with all due respect NCI, who are probably simplifying for the layman) one would need to write something like:
“…expression of protein in liver cells (after prolonged starvation etc.)…”
Under no circumstances would I imagine the term “expression” to imply or include “regulation” or “post-translational modification”. To illustrate why, consider the following example of a perfectly valid use in this sentence:
“A problem with expression of mammalian proteins in bacteria is that the required post-translational modification does not occur.”
If I wished to indicate I was also writing about regulation I would say so specifically:
“The expression of haemoglobin in reticulocytes and its regulation”
(and expect others to do so too.)
The fact that, as a professional molecular biologist, I disagree with @MattDMo, who is likewise a professional scientist, only demonstrates that the term is ambiguous. We would both like the context.

You made some good points about context - I was assuming one when we really don't know what it is without more info.

The Thermo Fisher definition is more explicitly accurate, although one could argue that the term "production" in the NCI definition implies regulation and post-translational modification (PTMs) as well. Either way, protein expression definitely includes regulation. Typically, when you measure protein expression, such as via Western blot, you are looking at the total amount of your target (regardless of whether you're using an antibody for total protein or PTM-specific) at a single timepoint. That amount has been influenced by regulation of various kinds.
EDIT
As David talks about in his answer, context is key. Given your recent questions about Western blotting using mammalian extracts, I implicitly assumed that context in my answer above, when in fact there could be other, very different contexts (such as bacterial or cell-free protein production where there is no regulation other than the promoter(s) present).

Adding a third viewpoint, I'm primarily an electrophysiologist in neuroscience. In my corner of the world, I have to say we can be a bit sloppy about terminology from molecular biology.
There might be more precise meanings intended in other areas, but when someone writes "protein expression" I typically translate this roughly to "we measured protein". It's sometimes presented as a contrast to "gene expression" which roughly translates to "we measured mRNA", or as "activation/activity" of some protein which means "we measured phosphorylation/we measured enzymatic activity by looking at products/reactants".
In this way, like in MattDMo's answer, "protein expression" includes everything leading up to translation of proteins and everything after in terms of modification and regulation, because what's actually being measured is protein level at some moment in time. That also might be all we care about, if the goal is to infer something about that protein's role in some cellular process. The details of how exactly you got to those protein levels might be important to someone else, but are left out when using a vague term "expression".
If this is what is meant, why not just say "protein", instead of "protein expression"? I think this is because it shifts the "agency" of what's going on from protein molecules to a more wholistic view of cell biology. When we talk of changes in protein expression, it is meant to imply that there is a regulatory change, not just some stochastic variation in protein levels: it's an active process that the cellular machinery is involved in, even if the specific steps involved are not mentioned. Additionally, this terminology leaves open the possibility that an observation involves other downstream effectors.


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How do geneticists determine if a gene mutation is pathogenic?
I am analysing information about patients with neurodevelopmental disorders using the DECIPHER genomics database. I am looking for patients who have only a specific gene deleted and no other mutations and have intellectual disability.
One thing that I have noticed is that some these patients have deletions of just one gene and have intellectual disability. However the pathogenicity of the gene deletion is reported as benign.
Why is this the case? Since the patient has deletion of only one gene and no other mutations, it's most likely that the gene deletion is responsible for the patient's intellectual disability.
In general, I was wondering how do geneticists who study patients determine whether a given gene mutation is pathogenic or benign? Are there any established standards/conventions for determining this?
Any insights are appreciated.

The presence of a single variant relative to reference in a single patient is usually not considered adequate evidence to say that the variant causes a patient phenotype. It might be considered an interesting anecdotal observation, but there is plenty of room for error in genotyping, phenotyping, or the possibility that the disorder is not genetic.
Another important note is that you are looking at a specific database (DECIPHER) which has their own bespoke workflow for inferring pathogenicity. Their practice relies upon and integrates information from other data sources, but it may not be identical to any other process for determining variant pathogenicity or disease causality.
For this variant specifically in DECIPHER, it is marked as "Benign" not because of this patient, but because of prior evidence that variants in the gene don't have strong phenotypes. You can click the "?" symbol and it gives you some info:

So you can see that the benign classification is the result of a statistical model looking across patients. (Though as you can also see in the blue box, it does incorporate information from this patient; for more information about this data's lifecycle, you can see the doc here). I should be clear that I don't see documentation of what models exactly DECIPHER is using, or how they are applied, though I haven't searched exhaustively.
You can further click through the OMIM link for the gene in question, which gives more info about what is known about the gene- in this case, that it doesn't seem to have strong effects.
Also, this variant is heterozygous, which is to say that the patient has a functional copy of the gene. There is not evidence for haploinsufficiency of this gene (e.g. that one copy knocked out is bad enough to cause a phenotype). You can see this under the "ClinGen DS" entry for the gene.
If many more patients with this deletion and also similar phenotypes were observed, and there were no control individuals with this deletion, then that might change the weight of evidence towards it being pathogenic. But at present there simply isn't enough evidence to indicate that this variant is pathogenic.
Alternately, if there were evidence that the disorder were genetic from a pedigree of a family, and that this variant were co-inherited with the disorder, that would also be strong evidence.
Yet another form of evidence would be if someone made the gene deletion in e.g. a mouse or a human cell line, and showed that there were a related phenotype.
CAVEAT
Having written all that, I have to say that there are probably situations in which most people would probably accept a one-patient anecdote variant as causal. Examples might be large previously unobserved chromosomal abnormalities coupled with strong phenotypes. But that would be a gut-feeling kind of decision, not really based on rigorous scientific reasoning.

This is a bit of an off-the cuff/high-level answer, but I will leave you with a few things to think about.

The human genome, while one of the highest-quality and most thoroughly analyzed ones we have, is still "poorly" understood and "under construction".

There are large stretches of genomic material called scaffolds that we know exist but don't know where to place in the rest of the genome. Regions around chromosome centromeres are also poorly understood as centromeres are notoriously difficult to sequence though.  There are also alternate loci and other genomic phenomenon that are less understood and often overlooked when people analyze genetic data.
Why does this matter?  Just because you have sequenced someone's genome doesn't mean we have a complete set of information about it.  Maybe they have a SNP on a scaffold, maybe they have a SNP or indel in an unannotated cis- or trans-regulatory element, ect.  You are only looking at variation in "known" things but there are also a lot of known "unknowns" that you are not going to have the means to quantify.

The quality and depth of the sequencing will greatly impact your ability to call SNPs and indels (read: genetic variation).

Often in clinical settings and wide-scale studies people go for quantity over quality since the goal is often to gain statistical power through aggregating at the population level.  If your sample falls into this category you likely don't have either the depth or read length (ie sequencing quality) to call some of the more subtle genetic variation that might be present.

Everyone has genetic polymorphisms (SNPs, indels, ect.)

Estimates vary on exactly how many the average person has, but no one is ever truly genetically "normal".   The real question is, "are any of that person's variants detrimental?" and that is often a very hard question to answer. Even if polymorphisms in a gene are usually benign, you can never completely rule out the possibility that the particular polymorphism you are seeing just happened to hit a sweet spot that perturbs the gene's function enough to manifest in disease.
So it is almost certain your given patient has genetic variation in locations other than just the one gene you mentioned.  It is possible they are in unknown/unannotated regions (1) or not detectable given your sequence quality (2), but they almost certainly exist.

Phenotype = Genetics + Environment

With any phenotype there is always the possibility that some combination of genetics and environment play a role in its manifestation. Maybe its purely genetic, maybe its purely environmental, often its a mix of the two. You always need to keep these two factors in mind when studying any disease.
Putting it all together
If after sequencing you only detect a significant polymorphism in one gene, why can't you conclude that must be the root cause? The answer is a combination of 1-3 as well as a litany of other reasons.  Essentially genetic sequencing (in terms of genome-wide or other forms of high-throughput sequencing) has a lot more slop and squishyness to it than most people make it out to have.
You should never believe you have seen all there is to see, and often should be fairly critical of even what you do see.
Another point I want to make relates to point 4. The intellectual disability you see in your patient may be entirely due to environmental causes. For example, in Autism Spectrum Disorder there is a theory that severe viral infection of the mother during pregnancy may cause the maternal immune system to attack the developing fetal brain, leading to developmental deficits and eventually ASD.  It doesn't matter if this theory is actually accurate (although there is a good amount of data that seems to suggest this), but it does suggest one of many ways that a recurring phenotype in the population may be caused entirely by environmental rather than genetic factors. This possibility is always important to keep in mind.
So how do we actually figure out if genetic variation is causing disease?  The very short answer is through many complimentary methods and that it's still quite complicated.
The slightly longer answer is that we usually start with correlational data over a large population.  We gather a bunch of subjects, measure some trait (in this case presence or absence of disease), sequence their genomes, and see if we can find any recurring associations between genetic polymorphisms and the trait in question. One form of these types of studies is called a Genome Wide Association Study (GWAS) which you might want to read up on.
Another method is by looking at conserved sequences. By looking at similar genes across species, or identical genes across many samples of the same species, we can identify areas of genes that have identical or near-identical sequence (ie that are well conserved).  The theory goes that these sequences tend to get conserved because they are vital for a given gene's proper functioning, whereas less conserved sequences may be able to tolerate some change without causing significant issues.  So, if a given patient has a significant polymorphism in a highly conserved region, that's usually good evidence something might be going on and often warrants further investigation.
These types of approaches are just the start, and often lead to a list of "candidate genes" for a given disease/phenotype. At this point biochemical or other forms of experimental methods take over to physically investigate the functions of these genes. Often this involves manipulating the gene in some sort of model system (cell lines, model organisms, ect.) with the end goal usually being to a) determine the gene's functional role in disease and b)the mechanism by which the gene carries out said function.
Often the overall path looks something like this: association with gene -> deleterious variants within gene identified -> experimental modeling of variants-> biochemical investigation of models -> mechanism.  The standard can vary by field, but almost no one will say a given mutation/gene is "pathogenic" without at least some experimental evidence to back that claim up.
So, as a final thought, why is this still so complicated/why doesn't this approach work for all diseases? Rather than answer directly, I'll leave you with a (hopefully) thought-provoking example.
Let's go back to my ASD example and point 4 (P=G+E). Let's say that the theory is true and severe viral infection during pregnancy causes a significant proportion of ASD cases. If you were to do a GWAS study on ASD, you would likely turn up polymorphisms in immune system related genes (if we assume that genetic variation in certain genes could make you more susceptible to viral infection).  Now those genes aren't really the "cause" of the disease, they might just make you more likely to get infected (or more likely to become severely infected, ect.), but the viral infection itself is probably what most people would think of as the "cause".  Even more subtle still, while it is these genes in the mother that confer vulnerability to disease, they may still show up as a signal in the affected children since a decent proportion of them will inherit these genes from their mother.  So while what might show up from your study is variation in immune-related genes in the affected individuals, this actually tells you very little about what actually causes the disease. This is just one of many ways that trying to nail down a disease using genetic sequencing alone can be significantly challenging.

I think that this is overall a good answer, but it might benefit from 1) linked sources, 2) a round of revision to make it a bit shorter, 3) a tl;dr upfront, or 4) taking advantage of illustrative figures or SE formatting to make it easier to follow the argument.


text:
Are androgenic-anabolic steroids a form of gene editing?
Is taking AAS a form of gene-editing? Steroids alter genes in some way since they allow people to build more muscle than what's naturally possible -- so they sort of "break" natural genetics somehow.
Given this, would this be considered a form of genetic-engineering on living humans/etc.? What about relative things like myostatin-inhibiting to prevent muscle growth cell limitation or HGH use?
In summary: does the use of AAS/performance enhancing drugs/etc. constitute gene editing? If not, why -- and if so, why and how is it comparable to things like CRISPR and stem-cell/etc. methods?

Steroids are not a form of gene editing
A gene is a sequence of DNA. Gene editing means changing this DNA sequence, kind of like changing the letters in a book.
Essentially all drugs, steroids included, affect the body without changing DNA sequence. Often they bind to a protein, which is the product of a gene, and alter its function. Steroids bind and alter the activity of transcriptiton factors, which are kind of like switches that turn certain genes on and off.
If gene editing is like rewriting a book, taking a drug would be like changing how, when, or where someone reads from the book, without altering the text itself.
If you are interested in how all of this works, you can check out some great free online courses like this:
https://www.khanacademy.org/science/biology#intro-to-biology


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Are modern gene-editing techniques capable of creating genetically-superior versions of humans?
Can we alter the DNA in, say, a small-framed, low muscle mass male to those of elite bodybuilders?
Can we alter the DNA sequence that stops balding and hair loss? How about the genes responsible for bone metabolism, hormonal profiles, and the entire endocrine/hard tissue foundation of humans?
Can we alter the genes responsible for looks and alter them so they make an ugly personal hotter?
Basically, summarize this to: "Can gene editing create genetically-advanced versions of ourselves?"
Uglier prettier? Shorter taller? Weaker to stronger? Slower to faster? Dumber to smarter?

Please don't flag this as "vague." I make it clear by labeling "genetically-superior" as basically "any advancement of one's current genetics and gene expression to a superior level" as previously explained.

For example, genes limit muscle growth and can make what is known in gym culture as a "hard gainer" or "non-responded" AKA someone who works out and does not make much progress due to genes. Superior version of this would be one extending this possibility or altering it to a more fashionable and fulfilling extent where muscle building genes are then more comparable to elite-genetic bodybuilders or at least closer to this goal. Same with genes and hormones, soft/hard tissue, looks, and all the way to intrinsic, internal abilities like learning ability, intelligence and etc.

When you say alter the DNA, do you mean at adult age or at the stage of the zygote?

@Remi.b Adult age I mean.

Short answer is clearly "No", then. You might want to read about 'gene therapy' to see what we can do and what are the classical difficulties of such therapies.

So I guess the only way people can be stronger and prettier would be surgery and drugs....

How about eating healthy, and having a healthy level of physical activities?!

@Remi.b Eating healthy and going to the gym doesn't make an ugly face sexy.

You said "stronger and prettier", not pretty face. You can definitely get stronger through the appropriate physical activity 2) healthy lifestyle improves skin and eyes appearance.

@Remi.b Yeah, I don't doubt it's possible to improve somewhat, but often it's not enough if you don't have the genetics in the first place. What I mean is that all the health/exercise in the world won't make an average, plain person to be more beautiful -- only cosmetic surgery and etc. has a better shot at that.

No, this is still science fiction. There have some of experimental efforts to correct very simple, monogenic, diseases. Some of experiments seem to have helped the patient, many were ineffective, and some killed the patient or gave them cancer. Gene therapy in humans in still in the very early experimental stage. On top of that, the traits you are talking about are almost certainly governed by multiple genes, and the genetic networks are "incompletely understood", to put it mildly.

Is there a such thing as "beauty genes?" Are people born to be potentially attractive determined by genes -- or is physical attraction a combination of genes and environment? Some people not born goodlooking cosmetically achieved some level of "beautification" so it's a complicated issue I get, yeah.

@FullofPowers Clearly children tend to look like their parents, so much of our appearance is determined by genetics, However, the details involve the interaction of hundreds of genes and gene regulatory regions. Even the genetics of something as straightforward as height is still poorly understood. Something as nebulous as beauty is going to be even more difficult to analyze.

So it's possible that one can predict a threshold or range of attractiveness potential genetically?

@FullofPowers , no, that's not what I wrote. It's even more complicated then height, because unlike height which is an objective measurement, beauty or attractiveness have strong cultural components.

I don't know about that. It's pretty clear that beauty is very objective, even if also somewhat subjective too.

Look for example at people popularized in the media (celebrities, models, etc.); those non-famous who are regarded as attractive more so than others; those who live better lives due to their appearance; etc. It's hard to argue that beauty is "very subjective" when we can measure down all of the so-called factors that influence facial beauty in males and females, even if slight subjectivity always exists.

For example, AI can already look over pictures of people and make smart "guesses" as to which are more attractive based on symmetry, face shape, facial balance/proportions, EME angle, FWHR, feature shape, etc.


text:
Could a mammal convert ingested dissolved CO2 to usable energy?
I'm trying to find out if it's possible that a mammal could orally ingest dissolved CO2 and convert it to energy for body heat, organ function, etc.
Unfortunately, most of the scientific sources I've been able to find talk instead of CO2 gas inhaled by mammals. All the sources speaking to orally ingested dissolved CO2 begin their argument with the assumption that all of it is converted to (and expelled as) gas in the digestive tract, but they never bother to prove that or cite anything.
It seems like this would rarely be observed in nature, and therefor not really be studied or documented, so I'm curious what degree of chemical or biological certainty there is about this, and what research has been done.

As a new contrbutor you are welcome to SE Biology. However I would suggest that you be polite in your criticism of the sources you have read. It is fine to say "they do not prove…", but "they do not bother to prove…" is derogatory. Admitedly you do not name them so they won‘t be offended, but the principle of polite and objective scientific argument is the same. And people in glass houses shouldn‘t throw stones — you haven‘t cited your sources, which we might have expected and would have strengthened your question.

No.
What is lacking from the question is a logical framework for the possibility suggested — that carbon dioxide can be a source of energy — and I suspect that this is because it lacks a clear chemical conception of what energy is and how it is formed in living organisms.
The generation of energy in a biological context can be considered as the consequence of a chemical reaction or physico-chemical process which involves  a negative (Gibbs) free energy change. For use by the cell (except in exceptional circumstances like heat generateion) the energy released in this process must be used to drive the thermodynamically unfavourable formation of a molecule (e.g. ATP) in which this can be ‘stored’. The stored energy is used when the hydrolysis of ATP is coupled to a thermodynamically unfavourable biological reaction or change, hence providing the ‘energy’ for it. This topic is covered in most biochemical texts, e.g. Berg et al..
So if carbon dioxide were to be a source of energy, it would have to undergo some reaction with a negative (Gibbs)free energy change. Other carbon compounds that are sources of energy are so by virtue of their ability to be oxidized (again see Berg et al.). However, as has already been mentioned in a comment, carbon dioxide is the most oxidized form of carbon and so cannot generate energy this way:

So unless the question could proposes another chemical or physico-chemical in which carbon dioxide could participate that has negative (Gibbs)free energy change, there is no reason to consider the postulate.

Finally, some sense.  The question as worded is just not going to be answered directly.  Just a no suffices.

Thanks for your answer. One quick follow-up: Is it possible that the microbiome of a mammal's digestive tract could produce glucose if it comes into contact with dissolved CO2? Meaning the ingested CO2 contains no usable energy, but the act of ingesting it results in the production and consumption of usable energy inside the mammal? And is there anything other than the microbiome that might be able to do this (like something else being consumed together with the CO2)?

@Adelmar — No. As has been mentioned, photosynthetic organisms use carbon dioxide to make glucose, and carbon dioxide is fixed in gluconeogenesis, but these processes require energy in the form of ATP derived from other processes to do this (and I don't think there are any photosynthetic organisms in the human microbiome).  You don't say why you have this idea. The only related thing I can think of is the way the ATP synthase of Ureaplasma urealyticum utilizes a pH gradient it generates from hydrolysing urea to ammonia in the bladder. But dissolved carbon dioxide is acidic.

There isn't any biologically useful energy in CO2. In fact, humans and all other animals produce CO2 as a waste product at the end of metabolism specifically because it is low-energy. You don't need to ingest it or breath it in as a gas, and if you didn't breathe it out you would die.

You're kind of just saying "no" here, and the statements about CO2 in waste and the necessity of ingestion/exhalation aren't really relevant to the question. I'm hoping for more specifics than this.

@Adelmar What sort of specifics? I included those other facts because it didn't seem from your question that you realized CO2 was a low-energy metabolic waste product, and because you were talking about the possibility of differences depending on ingestion versus inhalation of CO2. Those don't matter, because there is already dissolved CO2 being produced all over.

@stormy That isn't relevant here; also, even photosynthetic organisms do not use CO2 as energy.

Bryan, without CO2 those plants will not have ANY energy to use to MAKE their food, carbohydrates that plants have to have to survive.  Period. What are you saying??

@stormy Yes, petroleum is high energy. When you burn petroleum, you release energy by turning the hydrocarbons back to low-energy carbon dioxide. The reaction is "Hydrocarbons + O2 -> CO2 + Water + Energy". Plants do not use CO2 for energy, they use the sun for energy. They store that energy by taking low-energy CO2 and making it into high-energy molecules like carbohydrates.

Bryan oh my.  YES the plants use sunlight, turning that sunlight into carbohydrates that the plant can use for growth, reproduction and repairs.  If you think for one moment photosynthesizing chlorophyll can make carbohydrates WITHOUT CO2?  You are absolutely wrong.  Without CO2 that photosynthesis will not happen at all!  To include chemistry such as nitrogen , phosphorous, potassium minute amounts of boron, calcium, iron, sulfur, magnesium, manganese...at least 13 different micro chemicals.  Otherwise, photosynthesis does not work does not make energy usable to plants.

@stormy Did I say plants didn't need CO2? I said CO2 is not the source of energy.

About this unit
There's a lot of carbon in your body - in DNA, proteins, carbohydrates, fats, and other key biological molecules. How did that carbon get there? Drumroll... photosynthesis! Learn how plants and other photosynthetic organisms use light energy to make sugars from carbon dioxide and water, bringing both chemical energy and readily usable carbon into Earth’s global ecosystem. excerpt from https://www.khanacademy.org/science/biology/photosynthesis-in-plants

Without CO2 and macro/micro chemicals there is no making of an energy source to support life.

Plants without CO2 as well as O2 for the roots, the rest of the chemistry will not be able to use sunlight for energy.  Animals certainly are unable to harness the energy of the sun directly either.  What is more important?  Sunlight or chemistry?  BOTH are critical to convert the energy of sunlight to something usable by plants and animals.  Critical, just as much as sunlight.  Why are we arguing? Sunlight alone will not be usable to any life form, that is why we have so many processes to take the energy of the sun to convert it usable.  Petroleum, is sunlight captured because of CO2 +

CO2 does not yield any biological energy.
Living things can oxidise compounds like glucose and drive ATP synthesis from it.
This energy keeps us alive by not letting us fall into a state of equiibrium(death).
If mammals had any speacial complexes that converted light into chemical energy in their digestive systems they would have been able to derive energy from ingested CO2.
We don't even have any reactions in our metabolism that oxidise inorganic minerals(like chemosynthetic bacteria) to drive carbohydrate synthesis.
So I don't think mammals can convert ingested CO2 into useable energy.