text:
Why are my calculations for O2 requirements of daily metabolism so far off?
When I attempt to calculate the O2 necessary for a day of metabolism at rest (for an imaginary average human) and compare it with the expected O2 consumed per day my results differ by a factor of 3. I don't expect it to be 1 to 1, but a factor of 3 makes me think that I am missing a fundamental concept.
For our fictional human, I'm starting with the values for 1 MET. Specifically:

RMR (kcal / kg / hr) = 1
VO2 (mL / kg / min) = 3.5

I then define the weight of my human:

weight (kg) = 70
RMR (kcal / hr) = 70
VO2 (mL / min) = 245

And convert to more useful units:

RMR (kcal / day) = 70 * 24 = 1680
VO2 (L / day) = 245 * 60 * 24 / 1000 = 352.8

At this point, my understanding is that consuming 352.8 L of oxygen should produce somewhere in the ballpark of 1680 kcal at rest. My next assumption is going to be that aerobic respiration of glucose is accounting for all of the energy throughout this day of rest. I'm aware this isn't reality, but I wouldn't expect it to be 3x off. I'd guess that either this assumption is wrong or I'm misunderstanding something in the following math.
Let's start with some more constants regarding cellular respiration.

ATP creates 7.3 kcal / mol
An average of 30 ATP are generated per glucose (glycolysis, krebs, etc)
6 O2 are required to aerobically metabolize 1 glucose

Given the energy to ATP ratio, we can compute the ATP necessary per day. I should note that the result here is about twice as high as reference numbers I've seen so I am suspicious.

ATP (mol / day) = 1680 / 7.3 = 230.1369863
Glucose (mol / day ) = 230.1369863 / 30 = 7.671232877
O2 (mol / day) = 7.671232877 * 6 = 46.02739726

To convert the O2 requirements for our ATP from moles to liters, we use Avogadro's law at standard pressure (100 kPa) to conclude there are 22.712 liters per mole in a gas.

O2 (L / day) = 46.02739726 * 22.712 = 1045.374247

And finally, we can see that my calculation says that you need 1045.37 liters of oxygen to produce 1680 kcal of energy through aerobic respiration, but earlier I computed that you should only need 352.8 liters using 1 MET as my basis. There were assumptions made in there, but these results make me think that I am still misunderstanding a fundamental concept.

The math was correct, but there was a misunderstanding in what some of the numbers represent. The energy expenditures listed for RMR include resting dietary thermogenesis in addition to the actual ATP energy used for work. You can see that the same is done for reporting Calories in food (e.g. 4 per carb) at http://www.fao.org/docrep/006/Y5022E/y5022e04.htm
When this is taken into account, we use 686 kcal/mole of glucose to get similar oxygen numbers. This includes the energy for the ATP and the energy from heat.

In other words, RMR accounts for energy actually burned while ATP from metabolism accounts only for energy that can be made use of. The reference values arrive at 4 kcal/g glucose RMR and about 1.2 kcal/g glucose useful energy. This is an extremely interesting result tbh, surely somebody must have published about this inefficiency of metabolism..?

Yeah, there’s stuff out there about that efficiency and how it changes under certain conditions and for different pathways. I found it interesting that rmr and estimations for exercise and the like basically get made for the efficiency of a specific mix of fuels (e.g. carbs/fats). Thus they should be less accurate for calorie balancing if you have a keto diet or some other extreme. With all the other variables, it’s probably lost in the noise, but definately news to me.

Your 1680kcal/day estimate for a resting human of 70kg sounds about right.
Pages around the web agree to about 11000 L of air inhaled and 550 L of oxygen consumed from it per day. I'd guess that includes resting + activity, so the 350 L estimate for resting metabolism sounds roughly accurate.
At 7.3 kcal / mol ATP and 30 ATP / glucose, you arrive at 219 kcal / mol glucose.
Wikipedia lists -2880kJ/mol of glucose (https://en.wikipedia.org/wiki/Cellular_respiration). That's 688.3 kcal/mol glucose. Unfortunately, the page doesn't cite a source, but continuing your calculation from there: For 1680 kcal you then only need 2.44 mol of glucose per day, 14.64 mol of O2 and therefore 332.6 L of O2. So 688.3 kcal/mol glucose fits the expected O2 consumption roughly.
The molecular weight of glucose is 180.16 g/mol. For 219 kcal/mol, you would arrive at 1.22 kcal/g. Conversely, 688.3 kcal/mol gives you 3.82 kcal/g. Again, the latter value is definitely closer to nutritional information found for glucose from different generally accepted references (3.75-4kcal/g).
The only explanation I can offer for this is that the ATP generated from glucose metabolism accounts only for about 35% of the energy contained in the glucose - which implies that the remaining energy is wasted.

Both of those reference values appear to be completely correct: https://en.wikipedia.org/wiki/Adenosine_triphosphate#Chemical_properties

As Aidley mentions, those values seem widely accepted. The 36 ATP number you found is more of a theoretical upper limit that isn’t going to happen in practice. However, I do agree that if they were wrong, it might help :)

I updated my answer with some additional thinking )

Most sites list that the efficiency of ATP production is 38% with the rest of the energy lost as heat due to the total energy in the glucose against the usable ATP produced. This site also says it can be up to 50% in a cell, but I haven't seen that elsewhere: http://www.tiem.utk.edu/~gross/bioed/webmodules/ATPEfficiency.htm  All that said, I don't think any of that heat energy is usable by the body - you need to ATP to actually do the listed daily work of RMR.

I found another site listing intracellular conditions creating more energy per ATP (13 kcal/mole which is one higher than the prior site I listed). Running the math with 13, I get that 129 mol/day of ATP which is much closer to the reference numbers I have seen. For O2, I get 587 L/day which is much closer. I'm not sure if it's within range of error, though.  https://eng.umd.edu/~nsw/chbe482/energy.htm

It is also very suspicious that your math using all the glucose energy (100% atp efficiency) get so close to the expected result. It makes me wonder if there is actually just a misunderstanding on what initial RMR represents. My expectation is that it would be the actual atp energy actually used by the muscles and organs and not the lossy energy burned from the glucose, but maybe that is wrong? Yes I think so! So the missing piece here (regardless of ATP kcal) is that the RMR is including dietary thermogenesis (the extra heat energy).

This is also included in the nutritional values reported on food: http://www.fao.org/docrep/006/Y5022E/y5022e04.htm Thus, I think the numbers we see for Calories for RMR/BMR/exercise aren't the actual energy of the work performed but the energy that was there to start metabolizing. I'll post an answer with my misunderstanding. Thanks for the help!

So the conclusion is that our glucose metabolism is actually just that inefficient...

Yep. That said, Ive found a lot more info saying that in a living cell, you get far more atp out of the system due to the amount of other stuff (adp, etc) and ph and so on. Efficiency can go up to above 50% or somethin around there.


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Loss of antibiotic resistance due to long term storage
How possible is it for antibiotic resistant bacteria stored for a long time to lose such resistance?

What do you mean by "stored for a long time"? For example, do you mean "frozen in a laboratory"?

It is possible due to the fact that some antimicrobial resistance genes are induced by the presence of antibiotics themselves and are not promoted in the absence of a specific antibiotic, so the production of certain antimicrobial structures (enzymes, pumps, etc.) will be reduced once the bacterial medium is antibiotic free for enough time. This is sometimes refered to as "antibiotic pressure" referencing to some extent the genomic concept of selection pressure.
Take for example the phenomena reported in this paper's summary; they studied a patient hospitalized because of an infection by 2 K. pneumoniae strains. They knew beforehand that one of the strains was suceptible to carbapenems while the other one had a certain degree of resistance to this antibiotic. As the infection unfolded and a treatment with meropenem was administered, they took several samples and studied them via whole genome sequencing (WGS). They found out that the strain previously characterized as suceptible to carbapenems had acquired a plasmid (possibly by vertical transmission from the other strain) and hence now exhibited resistance to carbapenems, however when this strain was left in observation (and without being exposed to meropenem) it lost its previously acquired resistance.
In conclusion the sole presence of antibiotics induces resistance by different mechanisms in bacteria, but in some cases the lack of antibiotics in the medium can also revert resistance if this condition lasts for enough time. It is important to mention though that some resistance profiles will never be reverted no matter for how long the bacteria remains away from an antibiotic due to their nature. For example a gram-negative bacteria will always have instrinsic resistance to regular penicillin no matter what due to its cell structure itself (lack of a thick peptidoglican cell wall and presence of an outer cell membrane).

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why nucleosome spacing is longer in heterochromatin than euchromatin
Heterochromatin is defined as tightly packed form of DNA. But some experiments show that the average spacing of nucleosomes associated with H3K9me3 and H3K27me3, both heterochromatin marks, are longer than those with euchromatin marks. why packed DNA has longer spacing?
e.g in article :Genome-Wide Nucleosome Positioning Is Orchestrated by Genomic Regions Associated with DNase I Hypersensitivity in Rice. it says:"The average spacing of nucleosomes associated with H3K4me1 and H3K27ac, both euchromatin marks, are 178 bp and 179 bp, respectively. In contrast, the average spacing of nucleosomes associated with H3K9me3 and H3K27me3, both heterochromatin marks, are 205 bp"

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text:
Do antibodies binding to the same epitope have similar electrophoretic mobility?
Serum protein electrophoresis is a commonly used blood test in medicine. It is often used for detection of paraproteins in the gamma-globulin region. If there is a narrow band with sharp borders present, this is interpreted as presence of a monoclonal antibody.
However, this is a large jump into conclusion. The presence of a narrow band with sharp borders simply tells us that there is an accumulation of antibodies with similar electrophoretic mobility. Of course, one possible cause of this accumulation is presence of large numbers of antibodies created by one clone as they will all have the same electrophoretic mobility. One of the possible causes for this is an accumulation of a single clone of abnormal B-cells which produce this single type of antibodies.
This is usually the only cause that is taken into regard when assessing for the cause of a narrow band in the gamma-globulin region, so the differential diagnosis consists of malignant and premalignant hematological disorders. However, there are also other possible causes for this electrophoretic pattern. In this article which evaluated the causes of presence of this narrow band in children, it was noticed that it can appear in a variety of diseases - immunodeficiencies, hematological malignancies, aplastic anemia, autoimmune diseases, infectious diseases and also some others. As this study was done in the pediatric population in which monoclonal gammopathy of undetermined significance is extremely rare, it is highly likely that these conditions were in fact the causes of the narrow band in the gamma-globulin region and that the patients did not have concomitant MGUS.
The authors explain the pathogenesis of the electrophoretic pattern in these conditions by refering to an article which attempted to to categorize the causes of monoclonal gammopathy. However, the author of this categorization also assumed that the narrow band is caused by a single B-cell clone proliferation and admitted that the pathogenesis of the presence of a narrow band in the gamma-globulin region in autoimmune diseases wasn't understood well enough.
Different autoimmune diseases have different pathways of mechanisms. The most common mechanism is the presence of a humoral response towards self-antigens. As different antibodies can bind to the same epitope, an autoimmune disease can cause massive overproduction of multiple different antibodies targeting the same self-antigen.
This is where my question is coming from. Do antibodies binding to the same epitope have similar electrophoretic mobility? If this is true, then the premise that a narrow band in the gamma-globulin region of serum electrophoresis is always caused by a single B-cell clone proliferation is wrong. Because that would mean that an overproduction of multiple different antibodies binding to the same epitope could also cause the narrow band. This could be an explanation of how some autoimmune diseases cause the narrow band.


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Is there a database of pollen-seed distances across plant species?
I was enjoying Richard Smith's excellent answer to this question, and wondered:
If you consider the pollen/seed distribution range to be plant locomotion, is there a database that compares these distances across plant taxa, or perhaps a paper that treats these distances as a trait (in a phylogenetic context, for example)? One might assume that in the transition from wind-pollination to animal pollination (or from wind seed dispersal to animal seed dispersal) there is a sacrifice of decreased distance for increased "accuracy", but maybe this isn't the case.
It seems like this information should be around somewhere – it has relevance to evolution, speciation, climate change adaptation, etc.

In my searching I didn't find a comprehensive database of this information. There are biologists interested in analyzing seed dispersal distance as a trait however.
Vittoz and Enger (2007) used plants with known seed dispersal along with characteristics about these species to predict dispersal distances for other species.
There is another study here that examines the relationship of plant height and seed dispersal. They provide interesting background information as well on the trade-offs associated with a particular dispersal mode. For example,
"It is often assumed that there is a trade-off between maternal provisioning and dispersal capacity, leading small-seeded species to disperse further than large-seeded species."
It is certainly an area of research actively being pursued but there doesn't seem to be a list or database of these dispersal traits by species. There is information on dispersal distance by mode in the appendix of the second link I've provided.

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text:
Values of Miu_max and Ks from parameter estimation?
Background
I have this simple biomass growth model:
$$
\mu = \mu_{max}\cdot \left(\frac{S}{K_S+S}\right) \cdot \left(\frac{1}{1+S/K_{iS}}\right) \cdot \left(\frac{K_{iP}}{K_{iP}+P}\right) \\
\frac{dX}{dt} = \mu \cdot X \\
\frac{dS}{dt} = -1 \cdot ( \frac{\mu}{Y_{XS}} \cdot X + mS \cdot X) \\
\frac{dP}{dt} = a \cdot \frac{dX}{dt} + b \cdot X$$
Problem
I can fit the model on experimental data (see the Figure), but the values of $\mu_{max}$ or $K_S$ are often quite unrealistic. In this plot the $\mu_{max}$ is 3.9 and $K_S$ is 10.

Question
Since $\mu_{max}$ and $K_S$ are bounded in Monod-based $\mu$ expressions, is it possible to get real values of both of these particular parameters through parameter estimation techniques? Or one of these parameters should be obtained by other methods?

If you are getting unrealistic values in your model fitting then something is missing or wrong in your model or assumptions. That's the beauty of mathematical models, when they fail, they tell you something is missing :) Plus I don't know why do you think those are unrealistic ?

Can you give some more details on how you fit the model?  A nls fit tends to create strong correlation between the fit parameters. A fit using heuristic rules of thumb can be sensitive to a few points.

@Dexter : the biology professor I'm working for tells that $\mu_{max}$ can be no higher than 0.7 or 0.8. According to that, Ks=10 might be ok, but $\mu_{max}$ so high can never be ok.

@Hans : I use summed RMSE from multiple experiments with different initial substrate concentration. The values are estimated for 8 parameters (miu_max, Yxs, mS, Ks, Kis, Kip, a, b), so they fit fairly well with all experiments. The parameter estimation is done by a global optimization algorithm Differential Evolution from SciPy. I have also set bounds for the parameter values according to the literature. The problem is only with values of $\mu_{max}$ and Ks. When I increase boundaries for them, they both tend to increase until one of them has reached the defined ceiling.

@MartinsM My experience fitting time series tends to yield highly correlated parameters.  You might look at the joint distribution of the $K_S$ and $\mu_{max}$ fits (that is a plot of the objective function for z, and the two parameters for x and y).  It is possible they fit for a realistic pair, but the best fit is when both are way off.

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text:
Mitosis versus Meiosis I: What's the difference?
At the end of mitosis, one cell has divided into two diploid cells. But at the end of meiosis I, there are two haploid cells. How are the two processes different to produce these two types of cells?

At the start, all the cells are 2n, diploid cells. By far the largest difference between meiosis I and mitosis is that mitosis results in genetically identical, diploid somatic cells. Meiosis, in it's entirety, results in gametes of haploid genetic information, but the genetic information is not identical due to crossing-over events that happened during meiosis I.
What you should also note from the figure: Each chromatid represents 1 DNA molecule. In mitosis, the cell will begin with 4 chromosomes and 8 chromatids. After cytokinesis, the somatic cell will have 4 chromatids and 4 chromosomes. This propagates during the next round of mitosis. In meiosis: The cell starts with 8 chromatids and 4 chromosomes. After meiosis I each cell has 4 chromatids and 2 chromosomes. After meiosis II, each cell has 2 chromatids and 2 chromosomes. You're halving the amount of genetic material each round of meiosis, and this can't be propagated indefinitely.

Source: Tortora, GJ (2008). Principles of Anatomy and Physiology. 12th ED.

Where have you found this figure?

@Ana Wiley library system, source link. It's Tortora "Principles of Anatomy and Physiology," 12th ed.

the difference with easy way that the arrangement of chromosome on equatorial plate in metaphase
1- in mitosis all chromosome arrange on equatorial line randomly and single  so when it separate in anaphase separate to chromatide ( all chromatides), and each cell have 2n
however
2- in meiosis 1 chromosome arrange in duple or couples so when it separate as one chromosome , and each cell have n only
i hope it is useful for u

This doesn't make any sense


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What are two butterflies doing when they fly together, 'hitting' each other?
I've Googled this subject extensively but couldn't get an answer:
My country is full of butterflies and moths, I've seen a lot of butterflies performing what looks like some kind of fight or mating ritual: Two butterflies of the same species flying together and 'hitting' each other, and when they do that a noise can be heard, I don't know if it's from the actual 'impact' or a noise they produce, but sometimes it's very loud and resembles an electrical arc.
I'm extremely curious on what that is all about. I thought they were actually mating but I've seen so many species doing that, including some that I know don't mate like that.
I live in Brazil - in the humid southeast region.
Any help or clue is really appreciated. I'm putting a link to a YouTube video below which shows more or less what I'm talking about, but strangely the butterflies in the video aren't of the same species:
https://www.youtube.com/watch?v=FpRQLtyIRog
Thank you for your time.

They both appear to be eastern swallowtails (the females can be black or yellow); the yellow one definitely is an ES. I can't speak to your Brazillian butterflies, but butterflies can be aggressively territorial with mid-air fighting. Like birds.


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How do opportunistic infections affect an immunocompromised or AIDS patient?
I mean, everyone knows that AIDS patients don't die of the HIV infection, rather the opportunistic infections. But if HIV only affects T lymphocytes, and destroys them, then that means only cell mediated immunity and humoral immunities are affected (since B cells need helper T cells to be activated).
The body should still be producing other types of leukocytes like neutrophils and macrophages, which should eliminate most bacteria. So does HIV infection render the mononucleaf phagocytic system useless as well? If yes, how so?

Clinical diagnosis of AIDS in a person infected with HIV is based on the following criteria:

A CD4+ T-cell count below 200 cells/µl (or a CD4+ T-cell percentage of total lymphocytes of less than 14%)

OR

The patients has one of the few "indicatory" diseases that strongly suggest severe immunodeficiency. See the list of this diseases here. Usually they have fatal consequences.

As we can observe, there are mostly fungal and viral infections that live inside the host cells or (in case of tuberculosis) diseases caused by intracellular bacteria. They can be overcame only with working mechanisms of cellular immunity. Other mechanisms are simply too slow, not specific or not precise enough.
Another issue is an impairment of the immunological surveillance and much higher risk of cancer in individuals diagnosed with AIDS. Precise elimination of malignant cells is fully dependent on cellular immunity.
[EDITED]
For further reading, recent paper analysing the most common causes of death in patients with AIDS in the era of anti-retroviral therapy.

First, without support and amplification from the adaptive immune system, the innate response is less efficient.
Second, virtually every pathogen, whether obligate or opportunistic, has mechanisms that allow it to evade or subvert the innate immune response. That's why AIDS patients are susceptible to pathogens (including opportunistic pathogens) but are still not infected with non-pathogens, such as environmental agents or pathogens of, say, plants or insects even though we're constantly soaking in those non-pathogen microorganisms. Those agents don't have the needed ability to avoid innate responses.
So even in AIDS patients, innate immune responses are helpful, it's just that they're not enough, on their own, to prevent infections by pathogens with ways of evading innate immunity.


text:
Why are semi log graphs used in drug Dose response curves?
Why are Dose response curves, as well as most biological graphs shown in semi log graphs and not normal graphs? What is the advantage of semi log graphs over regular graphs? I still haven't gotten an intuitive sense of the answer, can someone explain, maybe with a diagram?

The reason is to make it easier to determine a suitable dose from the graph.
Normally, using a arithmetic scale, the response curve is a hyperbolic, with most of the information squished together in a small section of the graph. By using the log the function usually becomes somewhat sigmoid, with a relatively linear section in the transition from low-high response. This means that this dynamics in this section can be studied more carefully.
See e.g. this example (with data from https://www.idbs.com/media/396649/dose-response-comparison-example-hr.jpg), where I have reversed the x and y-axes, and used a secondary y-scale to show the log dose (so the graph is flipped compared to a normal dose-response curve). Here, the orange line shows a semi-log dose-response curve, and the blue line shows the same data using a normal arithmetic scale. Note that the orange line (log dose) should be read against the right scale and the "normal" dose against the left scale):

Here it is obvious that the normal scale doesn't give any possibility to interpret the region where the dose is effective, while this is obvious in the log graph.
The statistical modelling of these data is to some extent a separate issue though, where probit model or logit models along with data transformations are often used to analyse the data. Note also that the "usefulness" of the semilog-plot only lies in the visual presentation, and whether it will add anything depends on the dose series used in an experiment. If the doses used are not exponential (as in this example), the semilog-plot will not add much. In the statistical test of an effect the log dose is also usually not important, and I suspect (as someone not working in pharmacology) that the semilog plot is to some extent a historical artifact from the time before computer analysis of results, when the appropriate dose was determined in  a more manual way (e.g. linear analysis of the middle portion of the semilog graph).
Example data:
dose (conc.)    response
0.00001         0.993
0.0001          1.02
0.001           3.12
0.01            6.36
0.1             31.97
1               51.2
10              75.96
100             89
1000            97.932
10000           98.8

Regarding your point about the historical background of the semi-log graphs, there's a few more factors. Namely, adding a competitive antagonist causes a parallel shift to the right in a semi-log graph - this is much simpler than the change in a graph that isn't semi-log. It also allows you to make a Schild plot comparing the amount of the parallel shift with the concentration of the antagonist, which can tell you the strength of the antagonist.

It also allows similar advantages for the analysis of noncompetitive antagonists and partial agonists.

@Jam Thanks for the additional background, and feel free to add to and edit my answer. Good to hear from somebody with more specific knowledge on dose-response curves than me.


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use of antibiotics in selection of good plasmids
I have not understood the role of antibiotic medium in filtering the bacteria containing the recombinant plasmids with the ones having normal plasmids. Since all the plasmids of a certain bacterial species have a antibiotic resistance gene regardless if its recombinant or not , shouldnt there be no effect of the antibiotic on the colony?

Please tell us what you have read about this topic with reference to your text or web pages and more detail about what you understand. Also search for other questions on recombinant selection on this list. We expect you to show a little more evidence of having tried to solve the problem yourself.

Short answer: selection protocols are designed to work
When choosing a selectable marker for a plasmid, one chooses a gene that is known to be absent in the host organism of interest. For example, standard lab strains of E. coli are free from extragenomic plasmids and are susceptible to the antibiotic ampicillin. As such, plasmids that confer resistance to ampicillin are commonly used to maintain plasmids in E. coli lab strains.
Other things worth noting:
1. Antibiotic resistance genes are not universal.
That is, a bacterial strain that has a gene imparting resistance to one antibiotic may still be susceptible to many other antibiotics.
2. Not all plasmids carry antibiotic resistance genes.
Many naturally occurring plasmids are selected for in the wild because they carry genes that enable the bacteria to perform new metabolic functions, or impart virulence genes that enable bacteria infect a host organism: (https://en.wikipedia.org/wiki/Plasmid#Properties_and_characteristics).
This is also true of recombinant plasmids. Many commonly used yeast plasmids are selected for by enabling the host strain to produce a necessary nutrient that is absent in the growth medium.


text:
Why green light is good for our health?
I have a knowledge that when you woke up and see green light it increases your sight power. How it does so?

Any more specifics or evidence for that claim?

http://applications.nam.lighting.philips.com/blog/index.php/2015/08/06/the-subconscious-effect-of-colored-lighting/

There's nothing in there about green light increasing sight power, or about green light and waking. It reduces glare and provides good contrast for red objects, but it doesn't make your eyes any more powerful.


text:
Why do we have an immune system?
My daughter asked a question that I could not answer.
If you have a cold, you have symptoms such as fever, cold and sore throat. These symptoms, however, are the reactions of the immune system to bacteria, viruses and other germs.
So my question is: What would happen if the immune system did NOT respond? I know that bacteria can produce certain poisons. And viruses can capture human cells and make them produce more viruses.
Now to the naive part: But what's wrong with that?

Are Viruses dangerous because these cells would then no longer perform their function?
Without any immune system: Would a virus simply take over all human body cells?
Is it not the organism in the first place, who puts itself in mortal danger (such as high fever or inflammations) because of the defense reaction?

Thanx!

I hate to say it but, it depends. There may well be some pathogen which would otherwise be harmless, if not for the body's defense mechanisms. However, we are talking about a system which has evolved over thousands of years. In turn, the pathogens have also been evolving for thousands of years. There have been countless variations over the years. One thing is for sure, people who have an issue with their immune systems tend to die from pathogens which people who have healthy immune systems do not die from.

Basically you would rot from the inside out, as bacteria and viruses destroy your cells.
Fever is your body using heat to denature the viral proteins (viruses don't have chaperone proteins like us so they are more vulnerable to heat) Sore throat is you body killing infected cells before the virus can reproduce inside them, normally the virus will reproduce inside the cell until the cell bursts or simply runs out of resources and dies both release huge numbers of the virus.
Check out the virus life cycle. https://en.wikipedia.org/wiki/Viral_life_cycle


text:
Virus plaque assay, pfu/ml calculation on plates with too little plaques formed
I am a student, so I hope it is okay to put this question here. I've done the virus plaque assay in a practical recently and have a few questions regarding the plaque count for pfu calculation.
In the plates corresponding to times 0 and 10 mins, a few plaques formed (less than 5 plaques in every plate where plaques could be seen) Should I still calculate pfu with those results, or should I leave it as 0 pfu, and use only plaque counts that are at least more than 10?

Wouldn't the actual number of plaque forming units be more precise? Would it make any if your following steps more difficult or why do you want to simplify it?

http://www.microbiol.org/resources/monographswhite-papers/counting-colonies/

Sorry, I don't understand what you mean by simplyging? We were told to count the plaques we could see in the petri dishes and calculate pfu from there. What I don't understand if I should calculate pfu even when there's only one plaque in the plate. The protocol says we should choose the plate that has 20 to 300 plaques for the calculation, but I cannot do that with the plates for time 0 and time 10, because all plates have less than 10 plaques in them. In plates of time 0 the maximum I have is 2 plaques. So I don't know whether it's okay to calculate pfu of 2 plaques or it is usually left out

What is the virus?  If, for example, it is a bacteriophage, then you would not expect any virus particles to be produced at those early time points, right?


text:
Stem cell research and female egg synthesis
In terms of years, how far is stem cell research from being able to produce a female human egg from other female body cells?

I suppose that there is no connection between producing egg from somatic cells and stem cell research. The thing that you have mentioned: "produce a female human egg from other female body cells" was already done in 1996 (!) in sheep. Technically, there is no reason that this procedure will not work in Human as well. So in term of years: this was possible 20 years ago ... :-)

Thank you for your answer, but when will it be possible to do this for reproductive reasons and get perfect results, unlike with the sheep where lots of defects emerged from the clones/newborn sheep? Thanks.

This does not answer the question which is about whether egg cells can be produced from somatic cells. What you are describing is SCNT and it is quite a different case.

I see, so what you are actually asking is about reprogramming cells to become eggs?


text:
Are there any known rules that neurons always follow while transmitting/receiving signals?
I'm new to neurobiology so I don't know much about it. However, I have worked on artificial neural networks. Man-made AI networks all follow a handful of simple rules.
I was wondering if biological neurons also have a set of predictable rules?
E.g
What does a neuron do if it does not get stimulated/receives no signal for a long time. Will it die ... or try to find new connections that might send signals?
What does a neuron do if it is over-stimulated?
What does a neuron do if it receives a signal -> does it broadcast it to all of its connections, or only 1. Does it have a preferred output path for any incoming signals.
Can a neuron send out a new signal without having received a signal from anywhere else.
How does a neuron know if it has done his job "well". How does it get positive feedback.

Short Answer:
"Always" is always a dangerous term in biology.

Longer Answer:

What does a neuron do if it does not get stimulated/receives no signal for a long time. Will it die ... or try to find new connections that might send signals?

What neurons do when they aren't stimulated depends on the neuron and phase of development. Typically, thresholds for spiking will decrease, but it's also normal for cells to atrophy and die: neuronal death is a critical part of development, and loss of synaptic connections and some neurons is the most obvious feature of human brain development during adolescence, rather than birthing new neurons or growing new synapses.

What does a neuron do if it is over-stimulated?

Overstimulated neurons may die, they may also reduce the efficacy of their inputs either by increasing their thresholds or reducing synaptic weights by removing postsynaptic receptors. Calcium is an important mediator of these signals - you could read about its role in long term depression for example (this has nothing to do with 'depression' in mental health, just reduction in synaptic weight). There are also short-term effects that limit overstimulation of particular pathways, with many acts on the pre-synaptic rather than post-synaptic cell. Neurotransmitter is held in vesicles, and after release, there are fewer vesicles available for the next release event. Presynaptic terminals also often have autoreceptors that cause negative feedback and limit subsequent transmission.

What does a neuron do if it receives a signal -> does it broadcast it to all of its connections, or only 1

Of all your questions, "does it broadcast it to all of its connections" has the simplest answer: biological neurons almost always broadcast to all of its forward connections in response to any sufficient input (just like most artificial neural networks). However, the release probability at any one synapse is typically <1. Therefore, a given cell can make much higher-fidelity (and also higher-amplitude) connections with another cell by the number of contacts. If a typical cortical neuron makes only one synaptic contact with another cell, there will be a high rate of failures of transmission between the two cells. It's common for stronger connections to involve up to hundreds of individual contacts, just between two cells.

Can a neuron send out a new signal without having received a signal from anywhere else

Some neurons are spontaneously active. There are various types, but the most familiar are the ones thought of as intrinsically oscillating. An example are the sinoatrial node cells of the heart (although these are not really neurons, they act a lot like neurons; there are similar cells that are neurons that control respiration). There are also some CNS cells.

How does a neuron know if it has done his job "well". How does it get positive feedback.

This question is the most complex of all the questions you asked, entire textbooks and journals are needed to answer it, and it isn't at all possible to answer here. I'll just say that many of the learning rules used in artificial networks are not biologically plausible, they are simply computationally efficient. Biological neural networks use a lot more recurrent activity than artificial ones do, and a lot of the feedback like this occurs within that recurrent network. Biological networks are also built to do a variety of computations, and learning rules that apply in one may not apply in another. For example, pattern separation versus pattern completion require completely different learning rules.
However, the very general principle of updating synaptic weights in response to errors or outcomes does hold between artificial and biological networks.


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How do plastic containers and other thrash end up in the ocean
There are many photos of the ocean, which in some parts is littered with all sorts of waste, often plastic bags, containers etc. But I just wonder - how do such large amounts land in the ocean/sea? Isn't waste disposed at secure sites - so such a bug would either be recycled or in the worst case end up on some landfill? Of course rogue companies or entities could occasionally dump some thrash into the ocean, but the massive amounts of it seem surprising to me.
Beside, often the argument is to not use plastic bags, containers etc. but simply USING them doesn't put them in the sea. So what does, and can it be stopped?

Welcome to Biology.SE. I'm voting to close this question as off-topic because it has little to do with biology! SustainableLiving.SE might accept this kind of question.

Thank you for pointing me to another Stack Exchange, I was looking for one but this one seemed most fitting. Certainly I don't intend to spam, so if there is one more suitable I am more than happy to move the question here.

I am sure you did not mean to spam. As your post has been now posted on sustainableLiving.SE (and has a good reception), you might want to delete your post here on Biology.SE.


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How do ants get oxygen in deep colonies?
With ant colonies getting to be +7 feet deep, how does oxygen renew that deep for their respiration demand?

A basic Google search returns several relevant papers, which could be a start:   nest aeration ant colony oxygen

Thank you. Obviously I tried searching google first. The connotation of your use of "basic" is belittling.

Sorry, that wasn't my intention. My point was that it was a quick search without much effort or thought on my part, that still looked useful. I didn't have time for anything else right now (or an answer), but thought that it could still be useful to get an overview, or to rephrase the question based on a bit more background. Also, if you tried searching google before asking, it is useful if you add some of what you found, and what information you are missing/found lacking.

We do expect questions to show some effort to research answer prior to posting (homework rule). so if you include some prior research you will be fine. google provides a few useful sources but not a lot. Ant have multiple strategies and it is a hotbed of research right now. keep in mind the true extent of some ant colonies was only recently discovered.


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Is there a distinction between the fisherian runaway theory and Fisher's sexy son theory?
In many websites/books they are referred to as part of the same process whereby:

"runaway" describing that the process continues even after traits become maladaptive
the "sexy son theory" explains the mechanism that underlies this.

However many sites (like wikipedia) describe them as two alternative processes.
What am I missing?

The Fisherian runaway is the observed phenomenon of an "arms race" of features and traits in sexual dimorphism, the Sexy sons hypothesis is the theory of why it happens. One is factual/known data and the other is a hypothetical explanation as to why we see that data.

It is necessary to emphasise the role of female directional selection observed in the Fisherian runaway. Koinophilic peahens will select the most ornamental peacocks - it is an arms race of sexual characteristics, even if maladapted to the environment. The Sexy Sons hypothesis is not purely a descriptor of why it arises - it demonstrates that females select males with the probability of ornamental sons capable of widely spreading the mother's genes. The Fisherian runaway could be effected by a non-(Sexy Son) origin.

@epistemonaut- thanks for your response. Please could you give me an example of how runaway selection could arise in the absence of the sexy son mechansim. As I am still unable to understand how this is possible.


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I am trying to identify this plant
I am trying to identify this medium arching shrub growing to about 1.5m high x 2m wide in the subtropical climate of the Mt Coot-tha Botanic Gardens in Brisbane, Australia. Unfortunately there was no label with it. The inflorescence is about 3cm across, a greenish yellow, and made up of many tentacle-like florets.  I don't think it is an Australian native plant.

Opposite, pubescent leaves with acuminate tip and truncate base. White stipule in background. Inflorescence appears to  be a compound cyme? Not sure if those are strange pubescent petals
(unlikely?) or sepals or bracts in 7s. Initially made me think of Hamamelis flowers, but the yellow "tentacles" are not ribbon-like enough to be any Hamamelis I know or could find. Hmmmm

@theforestecologist could it be Listea glutinosa? It is native to Australia.

@trinitrotoluene doesn't look the same to me. E.g., leaf base and flowers look different. http://www.geocities.ws/wessaaliens/species/laurel.htm

@theforestecologist yeah you're right. I hadn't properly seen the leaf bases. Maybe op could post some more pictures from different angles.

See if you can find any pieces of fruit under the tree. some photos of the bark and the tree/shrub total shape would be help too.

This is a bit of a wild guess, but it might be Arabian jasmine, Jasminum sambac.
This page has a really similar picture (though they admit that the identity of the pictures in question is not fully certain):

https://www.calyx.com.au/jasmine.html
https://www.calyx.com.au/gal/jasmine/jasminum_sambac_maid_of_orleans_8.jpg
But searching for Jasmine sambac (and in particular, 'maid of Orleans', shows similar appearances of the flowers after bloom. And note that there seems to be a possible flower bud deeper in the branch. The appearance of and the arrangement of the leaves also seems plausible...

(from wiki, https://en.wikipedia.org/wiki/Jasminum_sambac)

Finally, I found the info about this plant:
Common name: Buttontree
Botanical name: Terminalia pendula
Family: Combretaceae (Rangoon creeper family)
Flowering: June - September
Buttontree is a moderate sized tree with small leaves, which fall early in the dry season. Before falling the foliage of these trees turns a beautiful yellowish red. The leafy branches are pendulous and hang down gracefully. Leaves upto 3 cm appear in nearly opposite pairs. Tiny yellowish green flowers occur in spherical heads about 1 cm wide. Protruding stamens are prominently visible like a fuzz on the round heads. Fruits are sort of circular, clustered in round heads.
Source: Terminalia pendula - Buttontree

This appears to be incorrect. You could try to update with explicit evidence, but I'm not convinced your species is correct

You can try google searching the species, you will get the same result. Also, I reconfirmed my answer with my Botany Professors and its correct.

I agree that Terminalia is incorrect. At a minimum, Terminalia lacks the long sepals(?) of this plant. Terminalia flowers also have a long style, while this plant has essentially no style.

It's hard to find a match. Based on the shape, margin and venation of the leaves it could really be Terminalia but I think we need more information.


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What does 'kinetically accessible' mean in protein folding?
The hydrophobic collapse model discusses this term in the energetics section. What does this actually mean?

At some point during protein folding, there may exist lower energy states from a thermodynamic perspective (lower ΔG free enegy) which are actually unreachable in a given environment, because the required activation energy is too high. These are kinetically inaccessible states, conversely accessible state are those that can be reached.
For example, that could mean a protein could reach a lower energy state by unfolding a bit, but exposing hydrophobic amino acid even temporarily would require too much energy. So the lower energy state is not kinetically accessible.
This is somewhat similar to the concept of kinetic and thermodynamic reaction products in chemistry.


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Bird identification by sound; midwestern US
This one's been bugging me for a couple of years. Location is southwest Michigan.
Here are a couple of song samples (I couldn't separate it from the Titmouse... they're pretty chatty these days):

Unidentified Bird 1
Unidentified Bird 2

Closest I can come up with is an Eastern Towhee, but the trill doesn't seem quite right. All the samples I've been able to find have it pretty constant in pitch and tempo, but this one gets a little higher and slower as it goes on.
This is a rural area. Our property is about half grass/prairie, half wooded. The sounds seem to come from a line of tall evergreens at the front of our property (an otherwise more open area), but I have yet to actually find the bird, so I can't be sure. A creek runs behind our house in a wooded area, about 400 feet from where the sounds appear to be emanating. These clips were taken about an hour after sunrise.
Can anyone identify this bird?

Can't really help, but if you aren't already aware of it, xeno-canto provides a good database of bird calls.

Xeno-Canto (fm ning's comment) seems to be a good site with well-versed users, and has a "mysteries" page where you can submit.


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Bacteria without plasmid
I am currently working on antibiotic resistance and I would be very interested to know which bacteria has no plasmid, in a similar way than M. tuberculosis.
This would help me a lot for my work and I did not succeed to get that much information online.
Thank you very much for your answer !

You might want to take a look at Bacillus subtilis. Most of the lab strains don't contain plasmids, though they have been found in some environmental isolates.
https://academic.oup.com/femsre/article/21/4/337/490925
All this depends on exactly what you're looking for: a species with no known plasmids in any isolates, or some commonly used lab strains with no plasmids?
M. tb is a pretty unique case. Most of the other species in the Mycobacterium genus do contain plasmids.

Thank you very much for the information, this will be very usefull !
I am looking for bacteria which, as MTB does not share (or sharing few) plasmids so the antibiotic resistance cannot be detected by mapping their genomes with common antibiotic resistance genes. Some just as MTB, which have developped SNP which induce resistance.

Another way to approach this is to do it by genes rather than organism. For instance, gyrase and topoisomerase proteins are targeted by some antibiotics. Because these are produced by essential genes, resistance has to arise from point mutations (more or less). So you could look at these genes across a wide range of organisms. Just depends on what your objective is.


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Pressure on the heart
Is there more pressure on the heart when lying down flat as opposed to lying down with head and knees slightly elevated?
Also is there more pressure on the heart standing up as opposed to lying down in either a flat or with head and knees slightly elevated


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What bird is this seen trekking in Nepal during descent on Manaslu circuit?

What bird is this seen trekking in Nepal during descent on Manaslu circuit?

You found an Alpine accentor (Prunella collaris). It's a bird of mountain areas in the Paleartic.
Here is a picture for comparison:

The only similar bird in the area is the Altai accentor (Prunella himalayana), but you can tell it apart because your bird does not have streaked flanks and the more uniform grey head (in your picture it is clearly visible the supercilium)


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Agarose gel electrophoresis - wrong running conditions?
Please have a look at the electrophoregram.
The DNA ladder used is GeneRuler 50bp (loaded according to the instructions), size of the gel is 6*7cm, lane width is 4mm, agarose percentage is 1%, TBE buffer. The power supply is Consort EV243. Running conditions were: 120V, 200mA, 45W, 40'.
What went wrong? The ladder is very far from the lane, and the sample bands look fuzzy. During run voltage remained constant (120 W), while current and power were  slightly changing (56mA and 7W ~in the middle of the run). Should I change running conditions? And/or make a fresh TBE running buffer?

How long did you let it run? I think time is a factor here. I would cut the time down by 15 mins.

@GabrielFair 40’ = 40 minutes.


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Is this experiment to check enzyme reaction rate according to substrate concentration correct?
We just had an experiment to check enzyme reaction rate according to it's substrate concentration.
In the experiment, we used a varying amount of substrate and the same amount of enzyme:
(1.5mm enz, 4.0mm water, 0.5mm subs)
(1.5mm enz, 3.5mm water, 1.0mm subs)
(1.5mm enz, 2.5mm water, 2.0mm subs)
(1.5mm enz, 1.5mm water, 3.0mm subs)
(1.5mm enz, 0mm water, 4.5mm subs)
We check the rate by looking at the optical density after 3 minutes.
Upon staring at this, I couldn't help but wonder: We don't only change the substrate concentration! We also change it's amount!
While 3.0/4.5 is a higher concentration than 0.5/4.5, it's also a higher amount resulting in longer reaction time for sure. If we check after 3 minutes, there's a chance that the 0.5mm subs would already be gone.
If we really wished to look at the rate according to concentration, shouldn't we have only changed the amount of water? It also changes the concentration of the enzyme but there is there any way to isolate either of them?

I think there are a few important answers in your question

The concentration of enzyme is the same in each reaction chamber.  The volume of each chamber is 6ml, and you are using 1.5 ml of enzyme in a final volume of 6 ml, so the dilution factor (the same in all chambers) is 1 in 4. So if stock enzyme concentration is 4 micromolar (as an example), the concentration of enzyme is 1 micromolar in each reaction chamber.
The concentration of substrate varies in each reaction chamber.  You MUST take the dilution factor into account when calculating the final substrate concentration.  You do no tell me what the stock substrate concentration is, but if it is 1mM as an example, then in reaction chamber 1 you are taking 0.5 ml of a 1mM solution in a final volume of 6 ml, which is a 1 in 12 dilution.  The substrate concentration in the reaction chamber is therefore 1/12 mM (about 83.33 micromolar).  In a similar way, the concentration in the final reaction chamber (4.5 ml in a final volume of 6 ml, dilution factor of 1.33) is about 750 micromolar.
You are right, measuring the reaction velocity by taking a single time point after 3 minutes is dangerous!  You must of course measure the initial rate if you want to analyze results according to the Michalis-Menten equation. The assumption you are making is that the rate is linear over a period of 3.   minutes for all substrate concentrations.  If this is not so, you will need to redesign your experiment to take a number of time points and take the tangent to the curve. I think you must be interested in determining the Michaelis constant.
In the language of enzyme kinetics you are doing a discontinuous assay with a single time point after 3 minutes as a measure of the initial rate at a series of substrate concentrations.  A better approach if available is to use a continuous assay, for example by continuously monitoring the change of absorbance of NADH with time at 340nm.  But of course continuous assay not always available.
I am surprised that you use water to dilute. Where is the buffer? And how control pH in your chamber?  Maybe the enzyme and substrate stock solutions are made in buffer, is this the explanation?
You should also check that the velocity versus enzyme concentration is linear at all substrate concentrations.


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Are similar smells usually based on similar chemicals?
Building off of this question: Why does freshly cut grass smell like a watermelon?, is it usually the case that things that we perceive as having similar smells are, in fact, the same or a similar chemical hitting our noses (as in the case of cis-3-hexanal in watermelon/cut grass), or is it often a cognitive thing (we're bad at parsing smells, so when confronted with a new smell, we fish around in our experience to find something that seems familiar, even if there's not much chemical similarity)?

With regards to the similar chemicals having similar smells, it does seem that there are trends with smell association and functional group.  This wiki article has a good list of compounds and their smells, and some classes definitely give similar types of smells, amines are rotting/fecal smells (hence the names putrescine and cadaverine), while esters are often fruity.  As you can see its not perfect, but there are definitely patterns.
There are some weird dose-dependent effects like in the case of indole which is labeled as flowery/fecal, which are two pretty distinct smells.  Apparently its fecal at high doses, and smells like jasmine at low doses.  My guess is that this has to do with different binding affinities of the different olfactory receptors (ORs) that are expressed in the olfactory receptor neurons (ORNs).  Many odorants will bind to multiple ORs, which means they will stimulate a characteristic sub-population of ORNs.  The binding to the different ORs will of course have different affinities.  This probably means that at low concentrations of indoles, you stimulate a certain population of ORNs that your brain recognizes as nice flowers, but as you increase the concentration you get the activation of ORNs with ORs that have a weaker binding to indole, changing the population of activated ORNs to one that your brain recognizes as feces.  Its definitely a strange pairing though..
I'm not familiar enough with the literature to know if the similar smelling things have similar ORN activation patterns, but my guess would be that they do.  If you have a population of different ORs that your odorant is binding to, a slightly different odorant will probably bind to a similar subset of ORs, just off by a few if its missing or has gained a functional group that is in the binding pocket of some of the ORs.  This probably means that if you are presented with a chemical that you have never smelled before, it will probably activate a similar ORN population as other similar chemicals, and your brain will probably say it smells like one of those similar chemicals.


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Why is venom more common in fish and snakes than other vertebrates?
Reading this question, I wondered why is it that we associate vertebrate venoms so often with snakes and fish, and more rarely with lizards, amphibians, mammals, and birds (apparently never, in birds?).
Are venoms more advantageous for snakes and fish, or more expensive or dangerous to produce for the other taxa? Or is it connected to evolutionary history – is venom somehow more 'evolvable' for snake and fish lineages?
Or, perhaps, is it just chance?

This write up by Carl Zimmer basically covers anything I could have said.  He links to a number of resources, in particular Casewell et. al. 2013, which at a cursory glance looks utterly fascinating and very well done.  Zimmer recapitulates figure 1, which sums it all up, or to quote Carl:

"Each lineage of venomous animals became deadly on its own, independent of all the others. And yet, in the end, their venoms echo each other... These results show that there are a limited number of ways to kill your victim quickly. No matter what genes you borrow for the evolution of venom, they will end up very similar to other venoms."

Another Zimmer piece specifically points out research purporting to show that snake venom genes are much older than snakes, maybe 200 million years old.  That gets around but doesn't quite answer your question.  An older review tried to coalesce things (as best as he could in '92), spending time focusing on insectivora and dealing with mammals.  The theory is that while venom is an excellent advantage, it requires a significant investment and is often slow-working.  In a world with sharp teeth capable of tearing, venom may not be necessary.  Mammals, for example, might evolve to not use venom, as it may not be suitable for their high daily energy demands.  The pdf linked above briefly touches on the concept of "reverse recruitment," where venom genes may be usefully re-purposed for other biological processes.
Reference:
Nicholas R. Casewell, Wolfgang Wüster, Freek J. Vonk, Robert A. Harrison, Bryan G. Fry. Complex cocktails: the evolutionary novelty of venoms. Trends in Ecology & Evolution
Volume 28, Issue 4, April 2013, Pages 219-229

+1. Your "this pdf" link is broke. Would you mind providing the titles and authors of the articles you cite in case the links break? Thank you.

From the Zimmer source, it's this 2013 paper by Caswell, et al: https://www.sciencedirect.com/science/article/abs/pii/S0169534712002935 (https://doi.org/10.1016/j.tree.2012.10.020)

Old answer:
Venom production is a "hard" adaptation to achieve**. So it is conceivable that simpler organisms had enough evolutionary time to get the adequate mutations for this to happen, which would explain why venom is almost absent (I know only of a platypus as being poisonous) in mammals and birds, and seemingly abundant in fishes, amphibians (such dart frogs) or reptilians.
Also, as I understand there should be great selective pressure and mutation in simpler organisms is more likely to produce viable offspring than in more complex ones, which can be a contributing factor.

**UPDATE:
It has come to my attention that the answer I gave is not exactly correct. Upon investigating venomous mammals many more came up (not only platypus - male platypus to be more precise),  such as vampire bats, solenodons, many types of shrews (thanks @releseabe), moles and even primates (the slow loris , being the possible single candidate)
There are no birds know to be venomous, but some (such as the pitohui, the ifrita and the roufous) can be toxic to eat.
My initial belief that toxicity is hard to achieve (this is hardly my area of expertise, and perhaps I should have refrained from answering something incomplete), does not seem to be really substantiated by literature, where lots of different organisms seem to have developed toxic/venomous adaptations.
Maybe it should be noted that many of these animals have evolved poisonous glands from salivary glands/sudoriferous glands and that they are described as presenting convergent evolution. Another caveat is also that most(all?) poisonous birds have Batrachotoxins that comes from their diet (which they concentrate on their skin and feathers), not something they produce themselves and are not as potent as the ones produced by dart-frogs. In this sense they are maybe less toxic than other animals, and the intensity of this effect may be related to co-evolution of those organisms and their prey/predators.
It's also worth mentioning that the slow loris, while considered venomous, has the poison from its gland that resembles a cat salivary allergen, and maybe would be better described as allergy inducing, rather than a poison, or perhaps cats could be considered venomous (my opinion, hardly worth anything). Another possibility is that the substances used in marking territory are the same and eliciting allergy is an unintended consequence (from the paper: "Rather than possessing a brachial gland like the loris, small cats directly add salivary allergen proteins to inanimate objects (... ) The idea that species recognition systems share a close relationship with immune recognition").
My opinions about toxic and venomous animals changed as I was reviewing this subject and, as I view it now, it is a property that is ubiquitous on many different branches of the tree of life .
Wikipedia link about venomous mammals. it is not very good to reference because people may change it at some point and the information to which I am refering would no longer be there, but it is strongly peer reviewed see here
shamelessly stolen from wikipedia about slow loris venom characterisation Talking Defensively: A Dual Usefor the Brachial Gland Exudate of Slowand Pygmy LorisesLee R. Hagey, Bryan G. Fry, and Helena Fitch-Snyder
pitohui:     JP Dumbacher, BM Beehler, TF Spande, HM Garraffo, JW Daly. Homobatrachotoxin in the genus Pitohui: chemical defense in birds?
slow loris paper:  Nekaris, K. Anne-Isola, Richard S. Moore, E. Johanna Rode, and Bryan G. Fry. 2013. “Mad, Bad and Dangerous to Know: The Biochemistry, Ecology and Evolution of Slow Loris Venom.” Journal of Venomous Animals and Toxins Including Tropical Diseases 19 (1): 21. https://doi.org/10.1186/1678-9199-19-21.

also shrew is a mammal with venom.

I note that both fish and snakes lack limbs and in fact many venomous and poisonous creatures would be almost helpless without venom/being poisonous to eat or touch. There are cases of poisonous creatures whose sole defense is their coloration advertising their poisonous nature and the poison itself (and of course their are false advertisers); these creatures rely on predators choosing not to eat them, not any kind of active defense at all.
So I suggest lacking limbs and/or being slow and/or being small/fragile favors evolving toxins as a means of self-defense or for killing.


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Do large animals experience a meaningful delay when moving their most distant appendages?
According to the Physics Factbook, nerve impulses travel at speeds anywhere from 1 meter per second up to around 100 meters per second. Blue whales reach up to around 30 meters long.
For a full-size blue whale, this means that a nerve impulse to move the tail muscles could take from 0.3 seconds to 30 seconds to reach the tail. While I'd imagine factors such as myelination and other adaptations function to keep this closer to the 0.3 second measure above, this is still a best case scenario, and would certainly be a noticeable delay were it a human being.
Do large organisms experience meaningful delays when moving their most distant appendages?

Humans have a delay of around 0.3 seconds for moving arms (training helps for many situations). Part of that is the transmission speed, but there's also the serial problem - neurons arranged in a sequence gain considerable delay. That's why we have so many "automatic" systems that don't rely on inputs going from e.g. leg to the brain, get processed and transmitted back. You usually don't notice because your brain lies to you all the time - there's some real fun experiments that cheat your brain to thinking reactions happen before their stimulus (e.g. pressing a button to light a bulb).

Yes, larger animals do experience larger delays in movement.
There have been studies of size difference vs sensorimotor delays in terrestrial mammals, https://www.ncbi.nlm.nih.gov/pubmed/30158304

That graph is for innate reflexes of a needle to the hind versus a kick-time. Perhaps no one dared to prick a blue whale.
Elephant vs shrew, heartbeat of 30 vs 1500 BPM, elephant 50 times slower than the shrew. Larger animals compensate with a better ability to predict physics and kinematics using their larger brain.
There are other kinds of movements which have more complex neural pathways that the graphs of pin-prick reflexes, that are even slower compared to size, you can study the physiology of eye to hand response in humans which varies from 120ms to 270ms for different humans.
It does have an effect on survival for example with a mongoose versus a snake, the mongoose has more versatile and faster reactions.

There are also weasel attack videos on the web.
some graphs here

Good presentation. Would benefit from a
#Yes, larger animals do experience larger delays in movement.
Introduction

"heartbeat of 30 vs 1500 BMP" I think you meant "BPM (beats per minute)"?

It may be valuable to point out that (most) invertebrates have a far slower conduction velocity than vertebrates due to the former not employing saltatory conduction.

It's a shame humans are not on the pain reflex graph, and that there's no non-human data for eye-hand reflex.


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Fluorescence assays to identify protein concentration without adding a large peptide sequence?
I'm trying to find a way of tagging a protein with something visually quantifiable to track protein concentration through potential purification steps and screen for the most efficient such steps. However, GFP and its cousins are very large proteins that would change the properties I'm targeting for purification, making them non-starters.
Is there a tag that through fluorescence, colorimetrics, etc. can be used to quantify concentration of a single protein while minimally altering chemical/physical properties of the protein for purification?

It is difficult. There are "click chemistry" tools but you would need to find a way to make some modifications on the desired protein in vivo.

Are small tags an option (FLAG-tag, HA-tag, Myc-tag)?

@Dr.H.Lecter the tags by themselves are insufficient. You would need an antibody to mark the protein.

Indeed, but you can generate a fusion protein much faster than creating an specific antibody from scratch. Besides antibodies against the tags I mentionned are commercially available and easy to get.


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Biological Nitrogen Fixation
I just studied Biological Nitrogen Fixation and saw it's reaction but i do not understand why there is 8 electrons and 8 protons are involved and Hydrogen molecule is formed side by side along with 2xAmmonia... According to me there should be 6electrons and protons because it needs 2electons in each step from Nitrogen to Di-imide and 2electrons from Di-imide to Hydrazine to give out 2xAmmonia

The reason why two additional electrons are required is to reduce two additional hydrogen ions to one molecule of hydrogen gas, as any text book account makes cleaer e.g. Berg et. al.  Are you asking why this latter occurs, when it seems unnecessary? The absence of an explanation in such texts tells its own story.


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Projects in DNA Computing
I am physicist and have recently heard about DNA computing. I want to work in this area.
I want your ideas on a "feasible but new project" (maximum time I can put on the project: 6 Months ), I can work on.
(I have already heard about songs, image storage on DNA and don't want to repeat the same process for some other song or image).

DNA computing is a branch of computing, not biology. I am voting to close as off-topic.

Note that asking for research ideas is likely to be close as off-topic even when asked on the right SE site. If someone has a good novel idea for a research project she/he would probably not give it away to a random stranger.

Hi @ParasKoundal and Welcome to Stack Exchange. SE is a bit different than some other sites, questions need to be fairly specific and have factual answers. "What do you think..." questions will usually be closed quickly. Specific questions about the chemistry of DNA computing might theoretically be on-topic in Chemistry SE but I don't see any there yet. There are several SE sites related to computing and math and physics as well. In fact there are almost 200 Stack Exchange sites to choose from. Have fun!

You mostly need to learn which machines and what budget permits a certain type of program in DNA form. you can try biostars forum. https://singularityhub.com/2018/07/24/dna-computing-gets-a-boost-with-this-machine-learning-hack/#sm.001305vt3155je0yvct1toklipjuy


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Has an ape ever drawn/painted something?
I know there are plenty of examples of apes making paintings and drawings, but has there ever been a recorded case of one representing something in their art?

Welcome to Biology S.E. if you have any questions, please visit the help center! Just out of curiosity, have you done any research on this topic? And if you have, could you share some of the results of that research in your question?

You meant a non-human ape of course.

Yes. The objective clarity of what constitutes representation is not certain, but here: https://www.youtube.com/watch?v=nSHQyLsPm4Q you can see something relatively convincing. The elephant really slays this, but your question is about apes; I don't know how species-specific you intend to be. I find that non-biologist laypersons assume that finding humanoid traits necessitates searching in human-like animals. Often not so! In fact, I wouldn't be surprised if someone came up with an octopus capable of a transformative masterpiece.

The elephants in those attractions paing the same thing every time: https://en.wikipedia.org/wiki/Animal-made_art#Painting_elephants So it's not clear that the animal is representing something (from its own mind), as opposed to the trainer doing that through the animal.

Part of the problem is ascertaining whether something is representative, outside humans primate lack the fine motor control needed to make realistic art. And normally you cannot ask them what something is. individual chimps and gorilla have painted or drawn and clearly take pleasure in the activity without any reward.
However there is one way in which the ape could tell us what their art is, some chimps and gorilla know sign language.. Both Koko and Micheal the gorilla sometimes named their paintings, this is by no means conclusive but the combination of colors and titles is suggestive of a the art being representational. however no exhaustive study of their art has been done to determine if this is cherry picking the data.
Likewise chimps who both know sign language and paint like Washoe, will title their art and when later asked identify them as the same title. More notably some claim their art patterns to their art, when asked to paint a dog for instance Washoe produces similar shapes each time. However again these are interpretations by keepers not independent studies, which it should be noted would be very difficult given the language skill of the animals. But like all behavior science, conclusiveness is nigh impossible to achieve but they are certainly suggestive even if they must be taken with a huge grain of salt.
It is also worth noting apes there is a notable difference between self motivated and reward motivated "artists" those prompted to paint for a reward show significantly less care, planning, or evaluation but just make something quickly then demand a reward.
Sauce
Source 1
Source 2
One of the first studies on the subject, which I desperately wish was available online.


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Can you extract specific data from EEG
First of all, sorry if this is the wrong place to ask this question, please redirect me if it is so.
I have a project in mind involving and EEG, which is the following :
Using a "consumer-grade" EEG (see this one, for example) I would like to be able to control a binary system with my mind (for example, turning a led on and off). From what I've seen until now, this seems to be possible since the headset is able to detect eye blinks, for example. It also gives access to two variables "focus" and "relaxation", which you can learn to control somewhat accurately (accurately enough for a binary system, at least).
Now here's my problem. While the methods that I described above do work, they would also continuously activate even when I don't want them to. Everytime I blink, my led would turn on, even though my intention wasn't to turn the led on. Everytime the "focus" level goes over 50/100, the led would turn on, even though I'm just focusing on my physics problem.
Having said that, I was wondering if it is possible to pick up more subtle and "controlled" information on the EEG. One thing I was thinking about is, if I think and visualise the color red, maybe that could cause a signal that can be picked up ?(Of course the led would activate when I look at something red, but that's still an improvement) Or even looking at the led I want to turn on, would that have any discernable effect on the EEG ? My guess is that those "thoughts" are way to subtle to be picked up by an EEG, which is just an average of the brain activity, but I'm not an expert on the subject !
So I guess my question is : what are the "kind" of thoughts that I can somewhat reliably see on the EEG data ? For example, I know I can reliably pick up a eye-blink. Are there any thoughts that are not related to muscle movement that can also be reliably read on a EEG ?

I'm sorry, although this is an interesting question there is way more to this than you are probably realizing. Like, this is the sort of thing people write entire theses on. You really just need to read scientific papers about this sort of thing, there's no quick fix for EEG processing from the perspective of biology. It's an interesting question but I am voting to close as too broad.

If there are papers discussing this, that would be great if you could suggest some ! If you want I could change my question to be less broad : what I really am interested in is if I can control a binary system with my mind, so I really need to know if it is possible to detect a binary signature of something in my mind, that isn't related to any muscle movement.
I do understand your point of view though, and if it gets closed, so be it !

https://scholar.google.com/scholar?hl=en&q=brain+machine+interface

You can add "EEG" or "binary" to limit to EEG studies of binary detection.

It is certainly feasible if your device is decent enough (not sure about the model you linked to). You either need to select a frequency range or a component of the event related potential. According to the first paper I linked to, you could imagine making a movement towards the target. Just don't expect 100% accuracy.

Short answer
The key word in EEG-driven mind control is brain-computer interface (BCI). In contrast, eye blinks can simply be detected with an eye tracker.
Background
As far as I know, EEG-driven computer control (The force is strong in you) is based on recording the EEG while thinking of certain actions, or simply doing them. As you likely understand by now, thinking of moving your arm activates much of the same brain circuitry as actually making the move, up until the pre-motor cortex. The motor cortex itself stays silent (otherwise you would actually make the move (Griggs, 2013).
So EEG correlates of motor activity can be translated into digitized electrical brain activity. In turn, these brain waves can be put to use from playing pong by mind force, to state-of-the-art applications like driving artificial (bionic) limbs for the lame. By using artificial neural networks / deep learning techniques / and multiple EEG electrodes, the combined activity can be registered of many brain regions and certain signatures may pop out and be trained for a computer to learn them. In tun, that can be used to, say, play a computer game.
For a commercial alternative, delivered with an SDK, check out (Pogue, 2012):

Emotiv's EPOC

References
- Griggs, New Scientist, January 2013
- Pogue, Sci Am, December 2012)


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largest and smallest gram positive, gram negative and fungal pathogens
As I stumbled through this question:

A 16-year-old female patient presented to her family physician
  with a complaint of an abnormal vaginal discharge and pruritus
  (itching). The patient denied having sexual activity and recently
  completed a course of doxycycline for the treatment of her acne.
  An examination of a Gram-stained vaginal smear revealed the
  presence of gram-positive oval cells about 4–8 μm in diameter.
  Her vaginitis is caused by which of the following agents?
  (A) Bacterium
  (B) Virus
  (C) Protozoa
  (D) Fungus
  (E) Prion

I noticed that in order to answer such question, one possible way is to know the diameter range of each pathological group because gram stain can be positive in both fungi and bacteria and so is gram negative.
I have googled and searched but found no such information; all i found was about largest bacteria in general (not pathogenic bacteria) and same for fungi.
It would be extremely useful to know the following diameter range of:

pathogenic gram-positive bacteria
pathogenic gram-negative bacteria
pathogenic fungi
pathogenic viruses

P.S. by pathogenic i mean pathogenic to Humans

I think you should search for side effects of doxycycline treatment to ànswer this question. It causes vaginal yeast infection.

Yes @Mesentery, I figured that out later. But still, knowing the diameters of pathogen groups will give extra hints and help in excluding other options even if one doesn’t know/recall side effects of drugs or whatsoever. I really hope that someone will answer this question :)


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What happens to Bacteria at a low pH?
I am conducting an experiment on how different pH levels effect the growth of E.coli. After researching, it is predicted that the most acidic pH level (pH 2) will be most effective at killing (or at least slowing down the growth) of bacteria. But my question is what does pH actually do to the bacteria cell and the biology behind it. How does the pH actually affect the E. coli cell itself? Thanks for your time.

pH affects the structure of all macromolecules that compose bacteria, and indeed all cells.
Here's a shortlist of examples:
Lipids
Lipids are hydrolyzed by extreme pH levels. They undergo chemical reactions and fall apart into constituent molecules, which may be toxic. The membrane is made of lipids; if it is disrupted, the cell ceases to exist.
Nucleic acids
At low pH, RNA and DNA hydrolyze - bonds are broken between individual bases (phosphodiester bonds) and nitrogen bases break off from the (deoxy)ribose groups. Structures and hydrogen bonding (necessary for DNA replication or transcription of genes) are impaired.
In alkaline conditions, DNA typically denatures but remains intact. Structures and hybrogen bonding are still strongly impaired though.
Protein
Low or high pH environments affect ionization of amino-acid functional group ionization. This affects hydrogen bonding in such a way as to denature the molecule, because it adopts very different conformations. This of course renders the protein or enzyme non-functional, and may cause it to aggregate or become cytotoxic. If any one of the hundreds of essential enzymes fails to function correctly, a bacterium will die.
Potentials across membranes
Changes in pH have drastic effects on proton concentrations both in and outside the bacterium. Respiration depends on a concentration gradient of protons. Low or high pH will make it difficult for cells to establish a potential (different in concentration across a membrane). This gradient must be upkept for a bacterium like E.coli to generate energy, and it's difficult if protons are being neutralized or are in sheer excess!
Any one of these is enough to have a bactericidal or bacteriostatic effect! This is also why cells that do live in slightly alkaline or acidic environments have to specialize, and they have narrow windows of pH that they can survive under, because they have to compensate so much to counteract the protonation or lack-thereof in their environments.

Thank you so much! I really appreciate your help!


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What is this bird - sound attached - (Atlanta Georgia)?
We live in Atlanta Georgia (northern suburb) & this bird starts singing in the middle of the night !!
And goes on for almost 2 hours without stopping.
Here is the link to it :
https://drive.google.com/open?id=0B3WzrpCj4uKeQ3l5MnJPY1RfcUpiVzkxRHBsWEN4RnYtTlNB
Any way to politely ask him/her to stop singing at night ? :)
Would highly appreciate any help in this regard !

It sounds like a Chuck-will's-widow; click the "sound" icon in that link for the song. They're native to Georgia and sing interminably at night, so the story checks out.

Thanks ! You are correct ! Now I just need to find out how to put it to sleep at night. Since it sleeps on ground, maybe I can do something..


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Rubisco and Nitrogen Shortage Condition
Suppose a plant sprouted when $t=0$ and died when $t=T$. Let $t_*$ be the time when the plant shifts the resources usage to maximize its reproductive organ. In the case of nitrogen shortage during plant growth, it is known that $t_*$ becomes earlier. Would someone please explain this phenomenon by relating to Rubisco?
Here are some of my findings:

It was shown that the decrease in the amount of Rubisco during leaf
senescence is higher compared to plants grown under suboptimal
N‐feeding conditions (Tercé‐Laforgue et al., 2004).
Rubisco is also considered as one of the most important Nitrogen
source that can potentially be remobilized and translocated to growing
or storage organs.

Currently, I understand how the nitrogen shortage is related to Rubisco, but I still do not how to relate this to the prioritization of reproductive organ. This might be a mere uneducated guess, but does this have something to do with survival of the plant? Say, it senses that Rubisco itself cannot replace the needed amount of nitrogen, then it is wiser for the plant to reproduce rather than growing.


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mRNA and Protein relation
A and B are two different proteins:
1- can they have same mrna
2- is it possible that the gene types which encoding the synthase are same ?
my answer is yes to both .
because after protein synthased cell can remove aminoacids with  post-transcriptional modification etc.

It also depends on what you mean by the same mRNA? Same mature mRNA? The same transcript can be differently alternatively spliced, leading to different proteins.

What on earth is meant by "the synthase"? No synthase has been mentioned. And what is meant by "gene types". Please clarify the question, i.e. give it in full. And provide a better explanation of your reasoning for each part.

1) Can two different proteins have the same mRNA?
This isn't clear enough to give you an answer:

Can two different proteins be made from the same mRNA molecule?

Yes, polycistronic mRNAs can encode several proteins which are translated separately (we can engineer this using internal ribosome entry sites, IRES).
Yes, different proteins can be translated from one open reading frame by failure of peptide bonding between two amino acids (we can engineer this using 2A peptide sites).
Yes, identical proteins can be translated from one mRNA and then modified differently after translation to yield different "final" proteins.
Yes, identical polypeptides can be translated from one mRNA and then incorporated in different protein complexes.

Can two different proteins be made from the same mRNA code?

No, not made in the sense of translated.
Yes, as above, identical proteins/polypeptides can be made and treated differently after translation.

2) Is it possible that the gene types which encode the synthase are the same?
Gene types? Do you mean genotype, i.e. allele? What synthase? Sounds like a homework question to me.

I don't understand what you mean by failure of peptide bonding between two amino acids. Do you mean post-translational cleavage into two chains like insulin? And if you want to ask a new question of whether two proteins can be translated from the same eukaryotic mRNA without any post translational modification of any sort, I can give you some examples that might surprise you. (This question has already got 4 close votes, so I imagine it will be closed soon.)

2A peptides don't cleave in the sense of proteolysis, rather, the ribosome "skips" peptide bonding and releases the current polypeptide while continuing translation of the ORF into a second polypeptide. So it's not strictly a post-translational modification. E.g. https://www.ncbi.nlm.nih.gov/pubmed/11297676 and more recently https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5438344/. (Note this doesn't always work, the ribosome will sometimes cancel and not translate the second polypeptide, and sometimes it won't skip and make one long fusion polypeptide)

My guess is there are also miRNAs that can modify what polypeptides an mRNA molecule produces; but sure, shoot :)

Answer is yes, by a logical approach, in superior organism where alternative splicing and post-transcriptional modification alter the protein structure.
In bacteria, this thing is not allowed. This scenario isn't common in functional protein, and start occurring by some alteration in the splicing process.
In real life, this is nearly impossible. A protein domain could be conserved, and so different protein can share parts of the amminoacidic sequence and, by that, the mRNA. But, as far as I know, there's no study confirming the evidence of same transcript and different proteins.

Alternative splicing produces different mRNAs, so the first part of your answer is incorrect. You echo the poster's incorrect "post-transcriptional modification". It should be "post-translational modification", and it hardly counts as a separate protein anyway.

He's not arguing about "after" or "before" splicing.
So, starting from the same template, you could get different mRNA. For the 2nd sentence, you're right.

And, just for completeness, you're saying that post-translational modification doesn't change protein structure at all. Here, you're wrong.

Don't put words into my mouth. I know perfectly well what effects post-translational modification can have on proteins. I don't answer unclear homework questions because questions of that type should be unambiguous, and the answers often depend on the teaching context. In this case, unless it was specifically mentioned in class I would assume the reference was to a different amino acid sequence.


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What does the final (Illumina) RNA-seq library contain? ss cdNA or ds cDNA?
I guess the oligos on Illumina's flow cell only hybridize to to single-stranded cDNAs (sscDNA).
However, when I read the TruSeq protocol (googled: TruSeq® RNASample Preparation v2 Guide) at the PCR step (AmpPCR, page 41) it looks like that the last cycle (d) is just elongation.
Therefore, since no denaturation (separation of dscDNA strands) happens, the final library input to Illumina should contain only dscDNAs which do not hybridize to flow cell's oligos!
My question is that then: when does denaturation happen? Inside Illumina? Or am I missing something?


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What is meant by pro-acinar cell?
What is meant by "pro-acinar cell" in the following sentence? progenitors/precursors?

A transient decline in Neurog3 expression from E11 to E12 coincides with peak segregation of MPCs into proximal, Ptf1aNkx6-1+ bipotent progenitors (BPs) and distal, Ptf1a+Nkx6-1 pro-acinar cells (PACs).

Thanks

Could you include a link to the original source from the quote? Thanks.

With the help of Google Scholar, this is from https://www.sciencedirect.com/science/article/abs/pii/S1534580720300162

'Pro-' is a general Latin preposition and English prefix with many meanings, but often in biology, as in this case, it means "before".  A proacinar cell is not yet an acinar cell (a cell of the acinus) but will be.  A related usage occurs with peptides such as proinsulin.
In Latin, "acinus" means a cluster of grapes.  You can find 'acini' in many places, notably exocrine glands, but in this case the pancreas is discussed.  With the help of Ms. Elbakyan, they tell quite a beautiful story, but the answer to this question is mostly in the first sentence of the abstract:  the stem cells (multipotent pancreatic progenitor cells) can become pro-acinar cells (which become secretory tissue of the acini, producing the pancreatic digestive enzymes), or else are reserved as bipotent progenitors that create the ducts and the islets of Langerhans.

what is meant by "pro-"? like pro- in English or pro from progenitor?

Thanks for pointing out this omission!  I've updated the answer.


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snRNAseq vs scRNAseq in cancer
my question is about phagocytosis as response to cancer. It is known that cytotoxic T cell may kill a cancer cell and sends cytokines to phagocytes like macrophage or dendritic cell to engulf and digest the killed cancer cell. From this, my questions:

can one assume that mRNAs of the cancer cells can be captured and sequenced along with those of the phagocyte by scRNAseq? In this case, the phagocyte should show a hybrid expression profile
if 1 holds (that I have observed in practice), can snRNAseq show a similar result? I ask this because in snRNAseq we deal with nuclei not the entire cell. However, I have observed hybrid expression profiles in phagocytes analyzed by snRNASeq.

It might help if you added links or an explanation of the techniques involved, and what you have found out - particularly about transport of foreign nucleic acids to the nucleus...

This is a very interesting question and I will give you an outline of the scenario I think is most likely.
I'm using the same hypothesis to explain another common observation in single nuclei RNA-Seq: In all snRNA-Seq data I have analyzed so far I have found reads for mitochondrial genes although they are not transcribed in the nucleus. How did they get there?
When doing single nuclei RNA-Seq the cells necessarily need to be broken to isolate the nuclei. The nuclear envelope is quite stable but most other cellular membranes will be permeabilized. As a consequence, mRNA from all over the cell is liberated and can stick to the nucleus. When the nuclei are isolated, the mRNAs sticking to them will be isolated too and then will be sequenced as part of that nucleus.
In the end it does not matter if the contaminating mRNA is from mitochondria or from cells taken up via phagocytosis.
I have seen mRNA from hemoglobin sticking to cell membranes in single cell RNA-Seq after > 5 washing steps, so I think it is not unlikely to assume mRNA can stick to the nuclear envelope as well.
You could try and see if the non-phagocyte genes have a higher percentage of splicing than the phagocyte genes. Since most mRNA in the nucleus will not be spliced this would be a hint that these genes come from outside the nucleus. How well this works will depend on the technology you are using. 10X only sequences the very 3' end of the mRNAs and you are not guaranteed to have a splice site in there.

Thank you for your interesting answer. I use 10x which outputs UMI counts for each gene so I don't have transcript/splicing information. When you say most nuclear mRNAs don't undergo splicing, do you mean splicing happen in the cytoplasm? Otherwise why is it that? It is worth mentioning that in the phagocytes showing such hybrid expression profiles, genes coding MHC II we're highly expressed, meaning they were most probably APCs as well

Splicing happens in the nucleus but the spliced mRNA is quickly exported to the cytoplasm. This is why is is recommended by 10X to include introns when mapping single nuclei data (page 9 top of right column).  Unfortunately, I'm not an expert in immunology and cannot comment on the expression of marker genes in your cells of interest.


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Spoiled 1% milk
A friend of mine gave me a jug of 1% milk and when I got home to put it in my fridge I noticed that it was already out of date so I set it on the counter next to our trash can and at the time we didn't have a vehicle to holler trash off so it's not on my counter for about 3 days and all of a sudden one night me and my boyfriend are sitting there in a room and the milk just starts projectile shooting out of a hole that it made in the side of the jugs not out of the lid just spraying everywhere all over the kitchen and I want to know why it for 1 started spraying spoiled milk as if it was pressurized and for 2 how did it make its own hole in the plastic jug???

Interesting story, well told. It was pressurized. When the microorganisms fermented the milk, they give off carbon dioxide, which builds up and creates pressure. This is why beer is carbonated. They did not however make the hole in the milk container directly. It was likely a weak spot that burst from the pressure.


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If evolution is true, how do all organisms have varying amount of chromosomes?
I thought genetic mutation changes genes and therefore evolution happens, but it doesn't explain how  chromosomes are created/removed if the first organism had a set amount and now all the organisms have different numbers of chromosomes. How does this happen?

Your understanding of evolution is over-simplified.  There are chemicals (colchicine is a common one) which can cause the number of chromosomes in a cell to double.  This is regularly used in e.g. plant breeding, as multiploidy often makes larger & stronger plants.  Do a search on "inducing tetraploidy in plants" if you're interested.  Other copying errors can affect single chromosomes &c.

Number of chromosomes. Amount of DNA.

Are you asking about hte origin of chromosomes or how they change?Bacterial chromosomes are very different than eukaryotic chromosomes so which are you talking about?

A mutation is a general term referring to any alteration of a nucleotidic sequence. It includes small mutations like indels (insertion or deletion of a single nucleotide) and substitutions, or bigger mutations such as e.g. chromosome fusions, whole chromosome duplications, whole genome duplications and gene deletions. So yes, some mutations do change the number of chromosomes (and ploidy number).
If you are interested in a very short and very introductory course to evolutionary biology, consider having a look at Understanding Evolution by UC Berkeley


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What is this 2-3cm insect found in Slovakia?
Noted in the West Slovakia at the garden

You have with you a Carpenter bee, which are species of the genus Xylocopa  of the subfamily Xylocopinae
Xylocopa violacea, the violet carpenter bee, is the common European species of carpenter bee, and one of the largest bees in Europe. It is also native to Asia.

Here is a link to a youtube video documentary about the bees.


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Which blood craving bug is this?
While sleeping in a Tajik homestay these guys have been feasting on my blood and left (they didn't bother to hang around in my skin). The bite marks are pretty nasty, this one is 5 days old. Locals say they come out of the ceiling, that it is normal and we shouldn't worry. Are they right? (https://i.sstatic.net/slA9L.jpg)
Bite mark (https://i.sstatic.net/Mx33E.jpg)

Those are ticks. You should check the internet for tick-bourne diseases in Tajik.

Hi Arjan! Those do look like ticks, as @KarlKjer said. I'm in America, so I can't say for sure if you should worry, but there are vector-borne diseases in Tajik, some of which are from ticks.  I strongly recommend having a doctor look at that bite, just in case. If possible, bring a bug or two with you. The doctor can identify it and test it for disease if they feel it's necessary. Hopefully the locals are right and it's just uncomfortable.

Thanks! We have contacted a doctor and were recommended to wait and contact again when we develop fever. After 6 days we are still allright. We only took pictures and threw them away but we should have collected them in a jar or so...  good idea for next time (but hopefully there will be none).

Some sort of soft tick, as you've already heard.  Here's a paper on tick-transmitted diseases in the are, for your amusement..  https://www.acq.osd.mil/eie/afpmb/docs/dveps/tajikistan.pdf


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What causes Nepenthes gracilis leaves and pitchers to turn red?
In Borneo, I normally see Nepenthes gracilis with green leaves and pitchers that are mostly green. However, I found one plant with red leaves and red pitchers:

Context (red plant is at bottom right of photograph):

What could be the causes of the red coloration? Could it be due to environmental factors such as soil nutrients? All plants in the picture above are exposed to full sunlight.