text:
Nature of transmarginal inhibition
I've recently become aware about existence of such phenomena. From my naive point of view, I understood it as existence of two general types of neural cells, one type serve inhibitory purpose and the other one provide excitation, all of this happens through variation of concentration of different mediators in synaptic connections, right? So in this process (transmarginal inhibition), in a nutshell, provoked by overwhelming stimuli, layer of cells which inhibit inhibitory cell start to show increase of activity and hence inhibitory cells can no longer control activity of currently "excited" cells which result in "paradoxal", reversed behavior. Sorry for this clumsy explanation of how I understood this, please correct my view. If i can abstractly think about evolution of some particular part of biological system as a function which tries to arrive at "local maximum", what type of arrangement of environmental variables could introduce this kind of structure which suffer from such horrible drawback. I mean, there was some input and desired output (adaptation), in result we got construction which could be shut down be intensive external influence and permanently corrupted.

I'm having trouble following the logic of your explanation, can you rewrite, or cite a source? It doesn't look like transmarginal inhibition specifically is a common area of study in neuroscience today, it's an old term from Pavlov. And I'm wondering why you think this is adaptive - most of the references to it are talking about conditions like schizophrenia or post-traumatic stress. Just because a phenomenon is observed in nature doesn't mean it helps survival.

Hello Bryan,  thank you for response, i have a pleasure to attend a lecture related to brain structure in local university, and professor accidentally mention Pavlov and this subject in particular, i reproduce as i remember his explanation. I probably poorly state final part of question, will edit it right now.

I'm not completely convinced that this is a bad trait, because sometimes lack of response can be adaptive (e.g. "playing dead" can be an adaptive response). However, see this question and the answers.


text:
What is cognate miRNA?
I understand what miRNA are, but I'm unsure of what cognate means. Looking at this post, it seems that a cognate miRNA is a known miRNA vs. a recently discovered/possible miRNA. Is this thinking on the right track?

The use of the word cognate in molecular biology reflects adjectival definition 2 from Lexico:
2 formal Related; connected.
‘cognate subjects such as physics and chemistry’
The example given shows that this can be used in the most general sense of related, so that there is no requirement for some common antecedent as a surrogate for a human mother or ancestor.
Specifically there is no implication of the involvement of a common DNA sequence, as in the answer from @Dirigible, nor that of a common origin as invoked in an earlier answer on this topic.
This is quite clear if one considers the much earlier usage of cognate in molecular biology in relation to an mRNA codon and the tRNA anticodons that can recognize it, or a tRNA and an aminoacyl tRNA synthetase that can aminoacylate it.
As far as the usage with microRNAs is concerned, a cognate mRNA is one with which the miRNA can interact by base-pairing — no more, no less.

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text:
How to stop a mosquito from flying?
Researchers have found mosquitoes cannot fly in dense fog because fog particles adhere to its halteres and stop them working. Is it possible to disrupt mosquitoes flight by mimicking fog particles?

Most of mosquitoes species don't fly if the wind speed is over a certain (normally low) limit. That's the logic of using fans to get (some) relief, and it's the most widespread form of artificially (just joking, I don't know what you mean by artificially) preventing mosquitoes from flying.

Welcome to Biology.SE. Remove its wings by pulling on them is one way to stop a mosquito to fly "artificially". Does it answer your question? If not, then you should probably clarify your question.

It would be good if you shared the link of the paper with this discovery.

@Tytoalba link has been added - it's pretty cool! :-) Anything that gives mosquitos a hard time around me is a good thing. I'm going out to buy some custom Krypton/Oxygen mix now.

@VictorChung this is a really interesting paper, thanks for bringing it to people's attention! Can you consider focusing your question on something specific that could be answered? Something that's not necessarily answered in the paper itself?

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text:
What is the name of this green berry tree?
Location: South India
Month: May
Location: Outside, Metropolitan.
Tree with berry fruits (poisonous or not, I don't know):

Its leaves:

@JM97 "Before I die, I will definitely find one or more new unknown species." from the profile - maybe hoping that one day they can post a plant no one can identify?

Leaves and branches apparently looking like Carissa carandas; but no comments about edibility of OP's specimen.

@AlwaysConfused I am afraid, It is not Carissa carandas, leaf design not matching with my plant.

Don't taste unknown fruits. However no idea about leaf size from the post.


text:
why should someone study mRNAs instead of miRNAs as a biomarker
why should someone study mRNAs instead of miRNAs as a biomarker from liquid cell-free biopsy like from exosomes? Is it wrong to do it? Does it offer you something different? Thank you in advance

What do you think? Have you looked anywhere for pros and cons? Can you add that information to your question/rationale?


text:
What sort of biofiltration is best for a small, portable, biofiltration unit?
I've been exploring the idea of a system to allow re-use (drinking) of RV greywater, or at least the freedom to dump in storm drains (I think the requirements are looser about this, but it still has to be somewhat purified)
Greywater is wastewater that does not contain feces. The primary contaminants would be food waste, various soaps (probably only biodegradable or non-antibacterial), and used shower water. I would also probably add urine, after sterilization to remove pathogens.
I was thinking of pre-filtration to remove larger fragments and detritus. Probably with the highest grade of this
-Processing rate would have to be 10 liters per day absolute minimum. 2x to 3x that would be best.
-Weight and volume are both at premium

How are you testing the purity or cleanliness of your filtrate (the water thats been filtered)?

why portable considering shower? any aquarium filter generates a heap of bacteria that process all useable impurities in the water to grow a mat. the bigger aquarium filter the better. it's ultra simple question to me having worked with many dank water ecologies and aquaria. it's only a function of bacterial medium substrate (sponges) temps and wather throughput in a given surface are of sponge. aquarium filters are designed fo rthat, soaps are mostly phosphate.

Any kind of sponge and pump filters will breed nitro bacteria to remove organic content. Added to a drip filter made from pure mineral sands and clays, you'd have a bacterial sponge and plant aquarium plus a sand filter.
You can make you own activated carbon too.
Urine requires at heavy plant growth to purify. You already have a tank, volume not given so I'll say it's 125 L. Here's a two stage bio filter: one with an incoming and circular bacterial filter to filter incoming water in graded sponges up to about .05 - 1 mm finest incoming particles for foods and stuff.  Use 2 divisions in the tank, one of 100 L, one of 25 L that you can prepare 10 L from every day.
Use 2 fish filters AC of 7 - 20 watts (?) or 12 V (DC) pumps similar to fish ones. Use 500 ml - 1L volume of filter sponges with fast access so you can squeeze out the bacterisl mats periodically because they will fill with nitrogen and phosphate and oxygen based pond organisms.
If you can fill the 100 liter tank with algea, it's ideal.
Put a valve to keep 2nd 25 L tank separate. Filter final 10 L drawn daily through mountain mineral sand from places with great spring water, i.e. dolomites / chalky to add trace elements. It's recommended you use sunlight and lots of plants in the first tank.


text:
How could cyanobacteria survive the anaerobic conditions of ancient earth?
I was reading about cyanobacteria and came to know that they are the first organisms that filled the atmosphere with oxygen around 2.3 billion years ago but then I realized that they themselves are aerobic and I couldn't understand how an aerobic organism would be able to survive the oxygen poor atmosphere in the first place to make enough oxygen that filled the whole atmosphere and caused almost all anaerobic organisms go extinct

Kindly shorten the title :/

Suggest something please

Where did you read that they were obligately aerobic?

I am pretty sure they are as nowhere it is mentioned that they are facultative aerobes

The first cyanobacteria were probably anaerobic, and this matter seems to be a hot topic of contemporary research. A recently published studya that performed a phylogenetic analysis of various Cyanobacteria genomes states:

The most parsimonious inference from these data is that the last
  common ancestor of the Cyanobacteria did not use oxygen and that the
  three classes [of Cyanobacteria] acquired aerobic respiration independently after their
  divergence. The absence of aerobic respiration in ancestral
  Cyanobacteria suggests that abiotic oxygen sources on early Earth were
  insufficient to allow for its evolution until after the appearance of
  oxygen produced by photosynthesis.

Reference
a Soo, Rochelle M., et al. "On the origins of oxygenic photosynthesis and aerobic respiration in Cyanobacteria." Science 355.6332 (2017): 1436-1440 (http://web.gps.caltech.edu/~wfischer/pubs/Sooetal2017.pdf)

So, were the common ancestors photosynthetic themselves?


text:
Why is an initiator tRNA required, distinct from the methionine tRNA used in elongation?
I'm confused by why there is a need for different tRNA-methionine complexes for translational initiation and elongation.
This paper mentions that

It is important that each type of methionyl tRNA be restricted to its separate function, as competition for tRNA by the initiation and elongation machinery could lead to serious problems for the cell

I don't understand what these problems may be.

Interaction with tRNA-binding factors is why separate tRNAMet species are employed

A specific tRNAMet is required for initiation as the initiating
  met-tRNA must interact with a specific tRNA-binding initiation factor
  (IF2) in order for it to bind to the P-site on the small ribosomal subunit.
  The elongator tRNAs share common structural features that enable them to
  interact with an elongation factor (EF1), which is needed for binding
  to the A-site of the whole ribosome. If the elongator met-tRNAMet were
  able to interact with the initiation factor, so would all the other
  aminoacyl-tRNAs. It is this competition for the initiation factor (and
  the small ribosomal subunit) that a separate initiator tRNAMet avoids.

This answer applies to all modes of prokaryotic and eukaryotic initiation, regardless of the manner in which the ‘correct’ initiation codon is recognized, as the interactions mentioned (shown in the cartoon below for those unfamiliar with this) are universal and ancient.

[E-TBF and I-TBF are my own non-standard abbreviations for Elongation tRNA-binding factor and Initiation tRNA-binding factor, respectively. The several arrows following the formation of the ternary complex are to indicate that several steps (which for initiation may differ between kingdoms — and between mRNAs in a single genome) occur before the final specific interaction of the tRNA anticodon with the appropriate mRNA codon on the appropriate ribosomal species.]
The cartoon representation of the factors and complex are taken from a diagram by Awchen and illustrates the interaction of the bacterial elongation factor (the original name, EF-Tu is used) and aminoacyl-tRNA. The structure of the initiation factor and its interaction with the tRNA is different (as is the conformation of the tRNA). Although not important for this answer, they are shown below in a comparison diagram from Schmitt et al., which unfortunately does not show the same orientation for the tRNA.

Why separate tRNAs, rather than a single multifunctional tRNAMet?
The answer given above describes how — in contemporary biological systems — the existence of two tRNAs for methionine prevents competition from elongator tRNAs for the initiation factor, IF-2, and hence competition for the small ribosomal subunit in its ‘initiation state’. However it is reasonable to ask why a separate initiator tRNAMet was necessary for such discrimination — surely IF-2 could have been specific for a single tRNAMet by recognising the same features that a single met-tRNA synthetase does. (The argument that then there would have been competition for EF-1 seems weak.) This is a distinct question, about which one can only speculate. My observations regarding it follow.
This argument presupposes that in the development of a single AUG initiation codon from what one assumes was a non-specific initiation system, all that was required in the tRNA was an appropriate anticodon — the sequence context and accessory proteins (initiation factors) being responsible for selecting the initiating AUG and triggering the initiation process. However this is evidently not the case in contemporary biological systems.
The initiator tRNAMet is structurally distinct from the elongator tRNAs. There is a striking reflection of this in the fact that although eukaryotic initiator tRNAMet is not formylated and no transformylase exists in eukaryotic cells, this species — but not the elongator species — can be formylated in vitro by the E. coli transformylase (see, for example, review by Kolitz and Lorsch). Clearly, specific structural features of initiator tRNAMet have been conserved over a long period of time, despite the evolution of different methods of selecting the ‘correct’ initiation codon (Shine and Dalgarno, Kozak scanning, ribosome landing pad).
Because of these latter differences in contemporary initiation it is impossible to know what the ‘original’ system was and why there was a need for structural differences in the initiator tRNA. However one answer is suggested by the fact that in contemporary eukaryotic initiation by the predominant Kozak scanning method the initiator tRNA binds to the small ribosomal subunit in the absence of the AUG codon. One suspects recognition of the P-site on a single subunit was as important as  codon–anticodon recognition.
Given the requirement for major structural changes in tRNAMet for initiation, the development of multi-functionality in single species would seem considerably more difficult than the creation of new species by gene duplication and subsequent mutation. Creation of new tRNAs by gene duplication is a relatively common process, and in this case would have left the original elongator tRNAMet untouched while the duplicate (still containing the recognition features for the met-tRNA synthetase) was free to evolve features which changed its ribosome- and factor-recognition properties.

I have added this answer because although one answer has been accepted, it does not address what I regard as the key point — the interaction of tRNAs and proteins synthesis factors. I will add more references to some of the protein synthesis background later, if requested.

(This comment is in two parts to get around the character limit.) Does this answer address the key point? Clearly there ARE different tRNAs for initiation and elongation so it would be surprising if the translation system had not evolved to exploit these differences. But why does it have to be this way at all?

Part 2. If there were only a single species of met-tRNA it doesn't seem to me to be much of a tall order to imagine that initiation factors would be able to discriminate between met-tRNA and other tRNAs.  After all, this level of discrimination between uncharged tRNAs is what aminoacyl tRNA synthetases do. Meanwhile the elongation pathway wouldn't need to discriminate. So what was the driving force behind the partitioning of met-tRNA into two separate pools?

@AlanBoyd — The answer addresses the question in a factual manner. It makes it clear that the key point is to prevent elongator tRNAs competing for the P site on the small subunit during initiation and that that is done at the stage of interaction with the initiation factor responsible for binding the initiation tRNA. You raise a different question — why did this mechanism for preventing competition arise, rather than a single met-tRNA binding both EF-1 and IF-2. That is argument and speculation, which I decided not to include unless there was interest. I'll extend my answer over the week end.

@AlanBoyd — It's not the weekend yet, but I have now extended my answer to deal with the points you raise. I was going to discuss the evolution of the initiation codon and protein synthesis factors, but that would make the answer far too long — perhaps a separate question. However I would like to make the answer to this question as useful as possible, so if you have any other points that you would like me to clarify do say so.

I didn't mean to imply that the use of a single tRNA "would be more advantageous to the cell", and I can't see that in my comment. My purpose was to ask, like the OP, "why there is a need for different tRNA-methionine complexes for translational initiation and elongation". You say: because that makes it easier to separate those processes. Yes, but I still don't see the driving force behind that separation. If you think it likely that initiator tRNA arose before the protein factors then all sorts of possibilities arise for an initiator tRNA having 'special powers' in relation to the P site.

@AlanBoyd — OK. Are we agreed on: 1. At some stage a single initiation codon (strictly aa) arose, 2. There would be an advantage in not having all the other aatRNAs competing for initiation, 3. Two possible ways this might have evolved were (i) a change in the structure and function of tRNA-met (ii) gene duplication and change of function of a second tRNA. ? If we are agreed, then you seem to be suggesting that alternative (ii) required some special "driving force" which (i) did not. I say the driving force was 2, and that alternative (ii) was at least as likely as (i) and argue in its favour.

@AlanBoyd — On reflection, perhaps your concern is something on the  lines of "Why wasn't it enough to have IF-2 recognise the same features that met-tRNA synthetase does on the single met-tRNA when initiation plumped for AUG (in a particular context)? One could argue that there would be competition for EF-1, but I don't find that very convincing. What is clear is that the initiating tRNA developed structural changes that one presumes must have reflected other requirements for interaction on the ribosome than codon–anticodon interaction. I can revise my additional section to deal with this.

Yes, agreed, the more functional requirements you posit for the initiator tRNA then the stronger the case for having to evolve a separate tRNA species. I was groping towards a case based upon the kinetic limitations of two different processes feeding from a single pool of met-tRNA, but I haven't even convinced myself.

@AlanBoyd — Done that now. Cut down the previous arguments to a single para and focussed on what would appear to be the main concern. Also depersonalized it.

+1 from me. According to Fig 2 in https://doi.org/10.1017/S0033583505004026 initiator tRNA binds the 30S subunit before mRNA in all three kingdoms.

@AlanBoyd — Thanks. Makes sense. When I was following the protein synthesis literature seriously (20 years or more ago) I used to feel that that would be a unifying feature, but the data then didn't seem clear. This has made me think about the evolution of proteins synthesis. For example, were there ribosomes without subunits originally, and subunits emerged when the RNA transcript got cleaved and this allowed specific initiation? I'm sure there must be literature discussing this sort of thing, but I tend to be rooted more in the present.

I think the key to understanding this is to appreciate how different the initiation process is from the rest of translation.
The 30S ribosomal subunit recognises start codons via an interaction with the Shine-Dalgarno sequence that lies upstream in the mRNA. The remaining steps of initiation involve recruiting fMet-tRNA and, critically, placing it into the P site of the ribosome. In contrast, during elongation, aminoacyl tRNAs enter at the A site before their amino acid cargo is joined to the growing polypeptide which is held in the P site as a peptidyl tRNA. So you can see that the initiation process is special because of the need to prime the whole translation process by placing the first 'peptidyl' tRNA (actually N-formylmethionyl tRNA) into the P site.
There are two tRNAs for methionine, tRNAfMet and tRNAMet, and only the former is a substrate for the enzyme methionyl-tRNA formyltransferase. This effectively partitions the supply of methionine into two separate pools, one for use in initiation and one for use in elongation. In fact you could argue that initiation involves a different amino acid (N-formylmethionine) which is also coded by AUG.
Since an N-formylmethionine is essential for initiation, the simplest alternative would be to have a situation where a single species of methionyl-tRNA was a substrate for the transformylase. This would mean that N-formylmethionine would have to be allowed into the A site, and all those formyl groups would have to be subsequently removed from the internal methionines.
Update in response to comment from the OP
Having re-read the original question, I can see that I jumped the gun and actually answered a different question. The real question is much deeper.
Firstly, although the details differ, both bacteria and eukaryotes feed methionine through separate pathways for initiation and elongation.  Bacteria are discussed above; eukaryotes channel methionine through two different pools of tRNA, tRNAiMet and tRNAMet. Clearly this channelling is a universal feature of translation systems.
Next, let's look at tRNAMet abundances in E. coli. Since all protein-coding genes have a single start codon and, on average, a few internal methionine codons, we might anticipate that there would be more tRNAMet than tRNAfMet. But this isn't the case: according to Dong et al 1996 tRNAfMet is present at around 3x the level of the elongation species.
This suggests to me that there is something inherent to initiation that requires a higher level of the corresponding methionyl tRNA. Now you might say that this discrepancy is rather small but bear in mind that one of the properties of Met-tRNAfMet is that is easily rejected by elongation factors (reference). This is important because any charged tRNA can enter the A site before being compared to the current codon. By being easily recognised as 'wrong' for elongation, Met-tRNAfMet is, to some extent, excluded from the elongation process.
So far I have presented facts -  what follows are my own ideas.
If a single Met-tRNA species was used both for elongation and for initiation it would have to optimised for entry into the elongation process, spending time interacting with ribosomal  A sites. In order to maintain the level of free Met-tRNA required to drive initiation I conclude that much higher levels of this single Met-tRNA would therefore be needed. This in turn would increase the transient entry of this species into all A sites, and it would essentially act as an inhibitor of elongation.

thank you, but I still don't understand. The recruitment of the initiator tRNA into the P site is dependent on IF2. In fact the formyl group is not necessary – in eukaryotes, Met is not formylated, and the process is driven by the closely homologous eIF2. So what problems would there be if IF2 recognized "standard" Met-tRNA?

@AlexMayorov I've extended my answer.

Thank you! Your idea is very interesting and makes a lot of sense!

@AlexMayorov and thanks to you for a great question!

The same paper states the following just before the part you have quoted:

The cell acquires an additional degree of control by having a separate tRNA for initiation, and thus regulates the levels of
  initiator and elongator methionyl tRNAs separately.

It is just another factor that controls translation. If there is no initiator tRNA, the ribosome cannot start synthesizing a certain protein. Imagine the cell needs to synthesize e.g. 100 copies of a protein. If initiation and elongation tRNA were the same, it would be much harder to determine how many methionyl tRNAs would be required to synthesize 100 copies, especially since the cell cannot tell how many methionins are required for a certain protein. Instead, if initiator tRNA is separate, 100 initator tRNAs will lead to 100 synthesized proteins (provided the other initiation factors are present, obviously).

Thanks! But isn't the cell face the same problem with other elongation tRNA, e.g. with glutamoyl tRNAs the cell doesn't know how many to synthesize and the synthesis is just based on the average demand? So how is this different? Couldn't the cell just synthesize a bit more Met tRNAs?


text:
Phase Shift in Grid Cells
I would like to fully understand the phase shift in the grid cell in MEC. From my understanding, since there is a hexagonal (i.e. equilateral triangle) lattice, and hence there are 3 $\phi$'s, I have the following questions in regards to that:
1). If there are 3 $\phi$'s, how does the phase shift happen in (I guess) 3 phases, i.e. why are there 3 shifts? I am just very confused at a fundamental level: why does the phase shift happen, is it because of the phase resettling in neurons?
2). As Wikipedia defines it: "Phase shift is any change that occurs in the phase of one quantity, or in the phase difference between two or more quantities", so my question is, what is the "quantity" in the example with grid cells or what is "the phase difference between two or more quantities" here?
In other words, why there is the 1st shift, the 2nd and the 3rd? Why do the second and the third happen? Is it because the pattern of grid cells is an equilateral triangle and the 1st type of signal produces the 1st grid field (the blob) and the 2nd type of signal produces the 2nd blob, here I edited this picture to illustrate my thought:

and we can see, if we model it with cosine, since

Can you include a reference you are basing some of your confusion on? My initial read through your question suggests that you might be mixing together a couple concepts but I'm not certain (and it's been awhile since I thought in depth about grid cells, but I don't know of a resident grid cell expert here on biology.se).

Or to be a little less vague...when people are talking about phases in grid cells I am most familiar with phases with respect to theta, an oscillation in time, not spatial phase. So there is no reason for those phases to be in particular unit steps, like pi/3. Maybe this is where you are getting your "3 ϕ"s idea from so that's what I am wondering about a reference for.

I think this is about soft matter physics + hexacon + phase shift. Can you please describe your wished area.

There are two phases I can think of: The time phase in relation to the theta rhythm, as mentioned by Bryan Krause and the spatial phase. If you change the spatial phase, it means you are shifting the whole grid in relation to the environment it encodes without rotating the grid. Apart from these two, I don't know what the third phase could be.

This might help:
http://www.scholarpedia.org/article/Grid_cell  (written by the Mosers themselves)
"The grid of each cell can be described by three parameters:
o) spacing (the distance between fields),
o) orientation (the tilt of the grid relative to a reference axis), and
o) spatial phase (displacement in the x and y directions relative to an external reference point)."

I do not completely understand your question. Are you talking abotu three spatial phases? Or about the three angles of the triangle? Or about three shifts of the same phase parameter? I'm no expert on grid cells, but I've learned my share about them and have seen talks by the Mosers on conferences. Once I understand the question, I'll try to formulate an answer (if still required at that point)

@atiger "o) spatial phase (displacement in the x and y directions relative to an external reference point)."-so the "external reference point" is the true location of the rat in a box (or whatever the environment of the experiment is)?

@jen the grid is fixed to the animal's environment (for our purposes right now). It does not move around with the animal, so the animal's position is irrelevant if we are talking about the grid encoding of the environment. the external reference point is in the environment. E.g, a corner of the rat's box, an item in the room or something like that. something that you can look at to determine where in the room6environment you are.


text:
What is the body density of insects on average?
What is the body density (in $\text{g}/\text{cm}^3$) of insects and is there a list of animals and their value of body density?

A recent studya measured the volumes (using a 3D scanner) and dry masses of 113 different insect species. They found the following relationship between the dry mass of the insects and their volumes ($V[mm^3]$ and $m[mg]$):
$\ln (V) = 1.019 \ln (m) + 1.46$
$\Leftrightarrow V = 4.30596 m^{1.019}$
Thus, since $\rho = \frac m V$
$\rho(m) = \frac m {4.30596 m^{1.019}} = \frac {0.232236} {m^{0.019}}
 $
Figure: Scatter plot of the measured dry masses and volumes

Reference:
a Kühsel, S., Brückner, A., Schmelzle, S., Heethoff, M. and Blüthgen, N. (2016), Surface area–volume ratios in insects. Insect Science. doi:10.1111/1744-7917.12362

On the graph the Volume is in $mm^2$ $\ddot \smile$ So the density is a decreasing function of the mass. Below, 0.2 grams, the density becomes very important. To make the graph in R: f=function(m) {0.0346737 / (m^1.34633)}; x = seq(0.01,20,0.01); plot(x=x,y=f(x), log='x', ylab="density (mg / ml)", xlab="Body mass (mg)")

@Remi.b I did not make this graph, it's from the study. Yes, the density function graph is a hyperbola.

Of course. I just wanted to comment on this 'weirdosity' and to offer a code to display the relationship you describe.

@adjan
Thank you. I am new to this site. this was a very cool answer! Do I give gold to the best reply how does this work? (:
I am not very good with math, how do I, if possible, convert the value to a   g/mm3 or a cublic number?

@AndreasJørgensen If you find an answer helpful, upvote using the arrow up button. Additionally, you can mark an answer as accepted by clicking on the checkmark icon. The function gives density in $\frac {mg}{mm^3}$, so just multiply with $10^3$ to get $\frac g {mm^3}$.

*Divide by $10^3$.

$$\log_{10} V= 1.019\log_{10} m+1.46 \rightarrow \log v-\log 28.8403= \log m^{1.019}\rightarrow \log V/28.8403 = \log m^{1.019} \rightarrow V = 28.8403 m^{1.019}.$$ Where does 2.34633 come from?

@daniel from mistakenly assuming my calculator's $\log$ was $\log_{10}$, not $\ln$.

Can anyone clarify why it says: "volume (mm^2)" on the y-axis and not "volume (mm^3)" ?

@AndreasJørgensen i guess it's a typo. there are four charts on that page of this paper, two of them are about area ($mm^2$)

@AlexDeLarge If you had read the edit comment you'd have known that this is a current SE bug and it makes no sense to change all HTML sup's on SE because it just got broken today. I used it in many of my previous answers and the bug only occured today. Wait till the SE team has fixed it!

Uups, must have overlooked that, my bad. I was not aware of that! Sorry. :) I'll delete my comment.

It seems that the maths does not match the plot: The $\log$ should be the $\ln$ (natural log, basis e), then the derived formulas indeed describe the data from the plot. Otherwise the formula yields a volume which is approximately a factor 6.7 too high.

@DominikS I think now it should be correct

I did the following estimate, based on the honey bee, to get an idea of the order of magnitude of the density of insects: According to Wikipedia (sorry for the german), we have:

The average mass of a honeybee is about 80 mg.
The length is 12 mm in average.

In order to estimate the volume, I model the body in three parts (see Wikipedia again):

The head as a sphere with a diameter of roughly 2.5 mm
The torso as a sphere with a diameter of roughy 4 mm
The abdomen as a cylinder of length 6 mm, and a diameter of 4 mm.

This will yield a very rough estimate of the volume, but we can expect it to have the correct order of magnitude. It is:
$$ V \approx \pi \cdot\Big (\frac 43\cdot \Big(\frac {2.5}2\Big)^3 +\frac 43\cdot \Big(\frac {4}2\Big)^3  +\Big(\frac 42\Big)^2\cdot 6\Big)\approx 117\text{ mm}^3 $$.
We have not accounted for antennae, legs, ..., so given the uncertainties of my estimates, the volume of a honeybee should be in the range of 100-200 mm^3. This is also in accordance with the graph in @adjan's answer.
With this the density of a honeybee should be between 80/200 and 80/100 mg/mm^3, so $$0.4\,\frac{\text{mg}}{\text{mm}^3} < \rho <0.8\,\frac{\text{mg}}{\text{mm}^3}$$,
which is interestingly slightly less than the density of water.


text:
How does a tiny spider interpret/cope with gravity?
The Question:
Does a tiny spider know that it is walking on a wall or a ceiling as opposed to the (horizontal) ground? Does gravity play a role in this knowledge?
Further thoughts:
I am interested in how other organisms sense gravity, and how they are affected by it. I have read how gravity played an important role in the physical evolution of all animals, but am interested in how the animals perceive gravity, and to what extent they are aware of/affected by it.
Can you point me to any research in this area?
The following is an excerpt from work of the German Aerospace Center, showing how the orientation of a fish is guided via a mixture of gravity and light:

Your question's title ("Sense of gravity felt by other organisms" - edited since it was originally posted) is quite broad, since "other animals" is all Animalia except Homo sapiens, which gives us at least 1 million species...
Therefore, I'm going to answer only your "The Question", regarding spiders:

How does a tiny spider senses gravity?

First, it's worth noticing that while the gravitational acceleration is a constant (at sea level), the weight of the organism depends on its mass. Thus, for tiny animals, the effects of the gravitational force can be extremely small, and because of that those animals require very precise sensitive structures in order to measure the gravity.
Aquatic invertebrates have statocysts and statoliths, which are well known. However, spiders use another method to perceive gravity: they use their sensorial "hairs". According to Bender and Frye (2009):

In the absence of wind, an animal standing at rest is acted upon only by the force of gravity. An animal might not explicitly calculate the global gravitational vector per se, but rather may actively modulate local joint angles and torques to implicitly compensate for gravity's pull. In many instances, insects and crustaceans measure the angles of their appendages' joints using clusters of mechanosensitive hairs, called hair plates.

According to Seyfarth, Gnatzy and Hammer (1990), one of these organs is the coxal hair plate:

Natural stimulus situation and the spike response to maintained deflection suggest that these hairs are used in proprioception and graviception.

Here is an image:
However, the same authors say:

Yet behavioral changes following selective hair-plate ablations are not very pronounced. Unilateral removal of hair-plates produced significant increases in average body height in 7 of 10 animals, while the angular orientation of the long body axis with respect to gravity remained unchanged after hair-plate removal.

That means that another sensors may play a role in graviception, such as proprioceptors. Still according to Bender and Frye (2009):

In addition to measuring joint position, invertebrates also have specializations for measuring joint load. Whereas our bones have no active sensory capacity and instead our sensors are imbedded in surrounding, soft tissues, many invertebrates are equipped with sensory arrays embedded in the exoskeleton at strategic points and with specific orientations. Called campaniform sensilla in insects, lyriform organs in arachnids and centipedes. (emphasis mine)

Sources:

Bender, J. and Frye, M. (2009). Invertebrate solutions for sensing gravity. Current Biology, 19(5), pp.R186-R190.
Seyfarth, E., Gnatzy, W. and Hammer, K. (1990). Coxal hair plates in spiders: physiology, fine structure, and specific central projections. Journal of Comparative Physiology A, 166(5).


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Are human disease-causing organisms living in other creatures helpful to them?
There are many examples of this.
How is rabies helpful to a dog?
How are Zika virus & Malaria helpful to a Mosquito?

"Disease causing organisms" do not necessarily benefit the host; more commonly they do nothing or actively harm the host somehow. A good example is malaria; it can only be carried by a specific mosquito because it causes death in some and in others can't fulfill its mosquito-required part of the cycle. Dogs die of rabies.


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Why should we preceed neostigmine by atropine in tubocurarine toxicity?
Why should we precede neostigmine by atropine in tubocurarine toxicity ?
I know that neostigmine act as anticholinesterase thus increasing the number of Ach molecules rendering them able to displace the tubocurarine, but I don't get the idea of atropine I know it's muscarinic inhibitor but we are speaking about nicotinergic receptors?

Please present your thoughts on the topic or at least an attempt at finding out the answer you seek. What are the actions and target sites of neostigmine and atropine?

I know that neostigmine act as anticholinesterase thus increasing the number of Ach molecules rendering them able to displace the tubocurarine , but I don't get the idea of atropine I know it's muscarinic inhibitor but we are speaking about N receptors

Tubocurarine is a non-depolarising neuromuscular blocking aqgent, that is, it acts as a competetive antagonist of Acetyl Choline at the Nicotinic receptors.(Toxicity/Effect: $-N$)
Atropine is a competitive antagonist of the muscarinic acetylcholine receptor, classified as an anticholinergic. (Effect: $-M$)
Neostigmine blocks acetylcholinesterase, increasing the concentration of ACh at, and stimulating both muscarinic and nicotinic receptors. (Effect: $+M+N$)
Hence, to counter the only nicotinic deficiency of ACh, we give Neostigmine, which will also stimulate the muscarinic receptors, leading to muscarinic side effects. To counter the latter, atropine is given. A similar formulation is used in a disease like Myasthenia Gravis, with a functionally similar lesion.
$$(+M+N)+(-M)+(-N)=0$$


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In the NCBI Taxonomy tree what does "no rank" mean?
NCBI publish their taxonomy browser at https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi
While many taxa have a well defined rank (Order, Family, Genus etc..), some of them have "no rank".
For example, Amniota:

Taxonomy ID: 32524
Genbank common name: amniotes
Inherited blast name: vertebrates
Rank: no rank
Genetic code: Translation table 1 (Standard)
Mitochondrial genetic code: Translation table 2 (Vertebrate Mitochondrial)

What does "no rank" mean?

Can you quote them? The information in the link can be accessed only when the software is installed. It's not fair to make people do this when you are asking for help.

@Tytoalba point taken.

@Eden I changed the link for a web working interface and also added an example, "Amniotes", to clarify your question.

Well, welcome to Phylogenetic Systematics.
The Linnaean Taxonomy is a rank-based classification system. When Linnaeus first proposed it in 1735, in his famous Systema Naturae, he created 5 ranks: Regnum, Classis, Ordo, Genus and Species (in Latin).
Today (more on that below) Linnean Taxonomy uses 8 main ranks:

Domain
Kingdom
Phylum
Class
Order
Family
Genus
Species

If you add the prefixes super-, sub- and infra- to that, you get more ranks.
However, in the 60's, a new systematics was proposed by Hennig, called Phylogenetic Systematics. I'll not explain in details what Phylogenetic Systematics is in this answer, there are plenty of good sources for you to read about. My point here is only one: showing you that there is no rank in Phylogenetic Systematics.
Have a look at this cladogram:

The group made by A + B is a monophyletic group. The group made by A + B + C + D is also a monophyletic group. The same way, the group made by A + B + C + D + E + F + G + H is a monophyletic group (by the way, there are 7 monophyletic groups in that cladogram). And all those groups have names.
Now comes the important part: in Phylogenetic Systematics, the number of monophyletic groups between the more exclusive set (you) and the more inclusive set (your very first ancestor, more than 3 billion years ago) is enormous! It is, of course, way bigger than 8 (or than 32, if you add all those prefixes). Even if you add uncommon ranks, as Tribe  or Section, you don't get even close to the number of monophyletic groups between you and your oldest ancestor.
As I read some time ago in a phylogenetic systematics paper: "We need names. Lots of names!".
That's why modern taxonomy has a problem with the traditional notion of ranks, some biologists defending that we should drop the ranks altogether (except, of course, the Species). And that's why I was uncomfortable in writing today some paragraphs above: there is an increasingly number of biologists that use phylogenetic nomenclature, which is incompatible with Linnaean taxonomy.
So, to give you an example: Mammalia is a Class. However, Mammalia lies inside a higher group, that we call Synapsida. Synapsida is neither a Class nor an Order nor a Phylum... it does not have a rank. Synapsida, by its turn, lies inside Amniota (animals with amnion), which also doesn't have a rank...
The examples abound: Sauropsida, Eudycots, Opisthokonta, Reptiliomorpha, Viridiplantae etc are all groups without a rank.
Thus, when a biologist says "that organism is an Amniota", she/he is just saying that the given organism belongs to the monophyletic group called Amniota. If you ask him/her "what is Amniota? A Class, an Order, a Superfamily, a Subphylum?", the answer will be: "none of them". Monophyletic groups don't need to have a rank in Phylogenetic Systematics.
Finally, quoting the Taxonomy Help from NCBI:

The ‘preferred scientific name’ for a taxon may be either formal (e.g. Homo sapiens) or informal (e.g. Homo sp. Altai, or uncultured fungus). Taxa above the species level may also be either formal (e.g. the order Mammalia) or informal (e.g. the unranked node eudicotyledons). (Emphasis mine)

Source: https://www.ncbi.nlm.nih.gov/books/NBK53758/#taxonomyqs.Overview

Thank you very much! I come from computer science background and I'm still learning all this.

you also have the issue that some ranked groups fall inside other groups of  equal ranks, like class mammalia* and class Aves are both inside class Reptilia,  all three of which fall inside class Sarcopterygii. So many biologists argue that the rank system is more than just not helpful, but downright counterproductive by making it more confusing.


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Carbohydrates in acidic stomach
How does the acidic environment in the stomach affect carbohydrate and fast digestion? Does it aid, impede or remain neutral in their digestive process?
Or do the carbohydrates, fats and proteins leave the stomach straight to small intestine once the churning is over?

As Will below mentioned stomach acid mostly exists to kill ingested bacteria not break down the food.

As for the digestion of fats there are two digestive enzymes active in the stomach:

Lingual lipase (produced with saliva)
Gastric lipase (produced in the stomach chief cells)

Both have activity optima in the acidic pH range.
On the other hand, the salivary amylase that breaks down starch seems to be inactivated by the acidic environment.
Sources:

https://www.ncbi.nlm.nih.gov/pubmed/2134569
https://en.wikipedia.org/wiki/Gastric_lipase
https://en.wikipedia.org/wiki/Lingual_lipase
https://en.wikipedia.org/wiki/Alpha-amylase

People who have no stomach acid because of medicine or surgery still digest their foods.  Otherwise you would predict incomplete digestion / weight loss / diarrhea would be a consequent of stomach acid suppression.
Acid is there to kill germs.  That probably used to be a lot more important than it is now but it is still important.  Acid suppression is associated with an slight increased pneumonia risk and possibly increased risk of enteric infection.  These studies are all done in the first world.

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


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Quantifying DNA in a band on gel electrophoresis
I am a first year science undergraduate and I am just asking this as a more theoretical question rather than for carrying out a protocol, so I would appreciate if answers do not involve lots of complicated chemical names.
I was wondering how one would go about quantifying the amount of DNA in a given band on a gel electrophoresis. Some ideas I have had so far are:

Cut out the DNA band and extract the DNA. Quantify using some known method such as measuring the absorbance at 260nm of the DNA in solution to find the concentration.
When the DNA is stained with ethidium bromide, clearly there will generally be more stain uptaken in a band region if it has more DNA so it will fluoresce with greater intensity when illuminated with UV light. However I would have reservations to using this method because I would think that the amount of stain uptaken would depend also on the state of the DNA (i.e. if it is supercoiled or not), but then again I do not know how much of an impact this could have on how much stain is uptaken. Of course, if you know that all of your DNA is in the same state then there shouldn't be a problem with this method I think. Although here you would have to be aware that the concentration of ethidium bromide in a certain band depends on the concentration of nucleotides there, which depends both on the number of the DNA fragments and their size (which is known from the position of the band). Compare this with the final method...
Finally, if one is making the DNA for example using dideoxy chain termination/Sanger sequencing in PCR, then you can use a radioactively labelled primer. The intensity of the image on the radioautograph would then directly tell you the number of molceules of that DNA fragment present in the band.

I was wondering which of these are viable options to use in the lab, and why/why not.

All three methods could be used to measure the amount of DNA. However in practice, method 2 (estimation by dye brightness) typically works best in a normal workflow. It really depends on what you plan to do as your downstream application.
Problems with method 1:

Yield from gel purification methods is sometimes finicky and prone to loss.
Absorbance of remaining agarose can influence the results. DNA cleanup is a must.

Problems with method 2:

Quantification is difficult as you must estimate the band brightness against a known standard (add a known quantity of your ladder and use that for estimation).
Supercoiling of plasmids causes multiple bands to appear, so the estimation must be performed multiple times and then added (now it's less of an estimation and more a guess)

Problems with method 3:

Working with radioactivity adds a significant amount of safety protocols into a simple procedure
All products from radiolabeling must also be handled as radioactive material
Using an image has the same issue as method 2 where you're estimating instead of actually quantifying.
You could get more quantitative results from a scintillation counter, but then the products become more difficult to use because of purification from the scintillation fluid (maybe this is possible but I never tried it).
You're limited to procedures which would incorporate the radiolabeled nucleotides
If you do something like dA-tailing, then you're not quantifying the amount of DNA, but the amount of copies of a transcript.


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College Genetics: Xist vs. transposon
I'm taking introduction to genetics and I'm trying to understand the following question: Lets say there is a male cat with blue ears, a single gene mutation called BLU.
We try to obtain pure bred blue-eared cats, mating the above cat we recieve:
*Males with a different colored ears
*Females with blue mosaic ears.
Now I'm trying to understand which is more likely. BLU being silenced by Xist or having non autonomous transposon on the BLU gene while only females have autonomous genes.
Thank you in advance!

Why do you think a transposon would cause this?


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Is this a bacterial colony?
On the physics StackExchange site people are trying to figure how and why these branching structures formed. The two questions can be found here and here. The latter had no cooling fans and was situated in an unventilated cupboard. There are many processes that could explain such structures without them being a bacterial colony, for example by Diffusion-limited-aggregation as explained in my answer here. To me it looks like this could be a bacterial colony. Is there any way to rule this out or say with precision that this is a bacterial colony?
I think some organic material and humidity could latch on to the irregular edges upon which bacteria could then grow in a warm environment.

What ways are there to tell from just a picture if this is a bacterial colony or  not?
What ways are there to tell if this is a bacterial colony or not if you have the structure at hand?
What ways are there to rule out or say that this is some kind of fungus or living thing if you have the structure at hand?

The second pic was taken by Wossname:

"the equipment is in a temperate climate in a non-aircon area of an
  office building near the external door. In high summer it would get to
  probably 40 Celcius and 85% or more relative humidity in my
  estimation. It's an area of the building that people most definitely
  don't loiter in during July/August. :)"

Unlikely to be living bacteria or other microorganisms as the environment is dusty plastic with moving air, so moisture would be at very low levels, probably too low to support bacteria.

Wow so similar to dendritic -pseudofossils

@mgkrebbs In the image below there was no cooling fan or real airflow. It could have been humid and warm. Some organic material and humidity could have accumulated along the irregularities upon which bacteria could grow.

If it is a microbial colony indeed, I'd say it looks like a fungus rather than a bacterial colony. Not sure it's really a living thing though

@macco, the second pic was taken by me, the equipment is in a temperate climate in a non-aircon area of an office building near the external door.  In high summer it would get to probably 40 Celcius and 85% or more relative humidity in my estimation.  It's an area of the building that people most definitely don't loiter in during July/August. :)

looks crystalline to me

Microbiologist here, I agree with @Flo's comment. These do not look like bacterial colonies to me, the morphology is way too unusual. If anything they more resemble fungal colonies. However, I have my doubts  as to whether these structures are caused by living organisms. Have you got some microbiology guys at your institution? You could inoculate some agar plates with a small sample and see if something grows?

Just scrape some material off and get it sequenced.

These look like crystallization structures when liquids dry up. But if it were to be a living thing, I'd go with fungal colonies. In my opinion, the best methods to tell is to scrape off a small piece, flood with KOH, and observe under a microscope, if you see filaments then it is definitely a fungus, and alternatively you can inoculate an agar (Sabouraud agar could work, or LB agar) to see if something grows. If its a fungus, it can take from 4 days up to 3 weeks to grow depending on the species and the growth conditions provided.
Good luck.
Here's a ref that might help you.
Microscopic potassium hydroxide preparation:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3994805/


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What type of bird is this?

Can someone identify this white colour bird?
Location: unknown (image taken from someone's profile pic).

Please comment about the location where you found the bird / where this picture was taken. Thanks.

From the picture, it looks like Cacatua sulphurea

[Source: Wikipedia]

The yellow-crested cockatoo (Cacatua sulphurea) also known as the lesser sulphur-crested cockatoo, is a medium-sized (approximately 34 cm long) cockatoo with white plumage, bluish-white bare orbital skin, grey feet, a black bill, and a retractile yellow or orange crest. The sexes are similar.[Source]

Habitat and ecology:

It mostly inhabits evergreen, deciduous, monsoon and semi-evergreen forests.
It nests in tree cavities or a pre-existing hole made by any another species.(Nandika et al.)
Observations made on Masakabing Island suggests that it's favourite diet include male fruits of Artocarpus communis, flowers and fruits of Cocos nucifera, Young leaves and flowers of Ceiba petandra, mangroves and male fruits of Brassus sudaica.(Metz et al.)
It mostly nests on C. nucifera, A. communis, C. petandra, Tamarindus indica and Avicennia sp. (Nandika et al.)
[Source]

Why it is not Cacatua galerita?

The plumage is different and the skin around the eyes are more white. [Source: In description part]
In the picture of the OP there is a blue ring over the eyes and it is also known as blue-eyed cockatoo. [Source: In the description part]

I don't know where the OP's photo was taken, but I assume it is a pet bird. The yellow-crested cockatoo is classified as a critically endangered species, so it's rather unlikely someone would own it as a pet.

@adjan But from the plumage it still looks like Cacatua sulphurea

I would say it's a sulphur-crested cockatoo (Cacatua galerita). It is a quite common pet bird.

Image source: https://commons.wikimedia.org/wiki/File:Cacatua_galerita_Tas_2.jpg


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What kind of predators do the snail's shell protect against?
Growing a shell is a significant material and energy investment for a snail. They have lots of predators which can easily eat them, having beaks which can pick them out or teeth strong enough to break the shell. Those which are not big enough to have a strong enough jaw, are small enough to be able to reach inside the shell.
Why do snails still have shells? Is there a large group of animals which cannot eat snails because of their shells, and would be able to if the snails had no shells?
I'm thinking of commonly known land snails.

What research have you done before asking it here?

Just think about what animals eat animals the size of snails but do not eat snails. lots of small predators do not eat snails. Its like turtles, are there things that eat turtles yes, but there are far fewer turtle predators than predators of other reptiles of the same size.

@John : my argument would be that if a predator is small enough, it can reach or crawl inside the shell though the opening where the snail retracted itself. Could you please provide an example of a predator which is incapable of eating a snail, but would eat one if it had no shell?

You may want to familiarize yourself with snail anatomy, the opening is not left open.


text:
A hypothetical nerve damage question
If a 100 pound bucket is dropped on someone's hand, what will this do to the nerves, will they get crushed, will they die? And how will this affect that person's ability to feel or move their hand?

From what height?

About 3 feet off the ground


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Identify this beetle from Bangladesh
Location: Bandarban, Bangladesh

It is from Coleoptera (beetle), right?

Where did you find this insect? Inside your home? If so, where? What "habitat" was this insect in?

This appears to be some species of beetle (order Coleoptera) in the Bostrichidae family.

Commonly called auger beetles, false powderpost beetles, or horned powderpost beetles.

 Xylopsocus capucinus
Identification to species can be difficult, but fortunately for you Sittichaya et al (2009) created an illustrated key for IDing species associated with South Asia.
Based on their key and visual characteristics of your specimen, my guess is that your specimen is Xylopsocus capucinus

 Source: Sittichaya et al 2009 . a. lateral view; b. elytral declivity; c. intercoxal process of the 1st abdominal ventrite; d. dorsal view.

Description: 3-5.5 mm long; 1.4-1.7 mm wide. Shape is cylindrical and similar in general appearance to other common species of the family Bostrichidae.
Distribution: throughout South and Southeast Asia from India to the Indonesian archipelago.
Hosts: apparently polyphagous attacking almost any woody plant in suitable condition.
Phenology: adults emerge mainly
between May and November.

Like most false powderpost beetles, the head cannot be seen from above as it is downwardly directed and hidden by the thorax:

 Source: UFL IAFS

Sources:

Sittichaya, W., Beaver, R., & Ngampongsai, A. (2009). An illustrated key to powder post beetles (Coleoptera, Bostrichidae) associated with rubberwood in Thailand, with new records and a checklist of species found in Southern Thailand. ZooKeys, 26, 33.
Woodruff RE, Gerberg EJ, Spilman TJ (2005). A False Powder-post Beetle, Xylopsocus capucinus (Fabricius)
(Insecta: Coleoptera: Bostrichidae). University of Florida, IFAS Extension Publication No. EENY-179.
Institute of Food and Agricultural Sciences, University of Florida, 4 pp

This appears to be a Powder-Post Beetle (order Coleoptera, family Bostrichidae); a local reference is needed for further identification.

Please provide a reference for your identification if possible.

The post by @theforestecologist gives you a good example of how a well-researched answer to a species ID question looks like, even though your ID is also correct - as far as I can tell, and that is the problem: it needs some effort for me to check even though answers should be self-explanatory. Please try to give more comprehensive answers.


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What is this wasp?
We live in central New York and these large (1.25") wasps are invading our house pretty regularly. I want to say it's a great black wasp, but the pale yellow striping makes me wonder.
A sample specimen
Edit
Confirmed the answer: these have all been female Northern Paper Wasps:

Apparently they can be almost solid black in some communities.

Do you have a better picture? It would be nice to see more details. I'm pretty sure the great black wasp is all black, but there are several other big wasps that are striped.

I'll take one next time they move into my house

If by "great black wasp" you mean Sphex pensylvanicus (the common name per the Wikipedia page here: https://en.wikipedia.org/wiki/Sphex_pensylvanicus); no.  The folded forewings visible in the picture are characteristic of the family Vespidae; I'm thinking Polistes, but bugguide.net has seven pages worth of possibilities (starting here: http://bugguide.net/node/view/572/bgpage?from=0).

This specimen is most likely a Polistes sp. from the Vespidae-family. Some Polistes species are sometimes referred to as paper wasps.
Coloring is not the primary criterion for identification here. The folded wings leave no doubt that it is a wasp from the Vespidae family (which excludes the Great Black Wasp, as suggested in the comments). Since there is only one picture, with not many details, further identification gets more difficult here. Based on my experience, I would guess that it is a Polistes sp. (no way of saying which particular species it is, based on the photo) - this would also be consistent with your observation that they invade your house frequently: Polistes, besides Vespinae (e.g. Yellowjackets), are the only 2 social Vespidae subfamilies, i.e. they live in colonies. Also, Vespinae can be excluded, they have a visible edge at the beginning of their abdomen, which the wasp in your photo doesn't have. This would leave Polistes as the most plausible option.
A detailed view of the head, the legs and the unfolded wings would be necessary for a more specific identification - there are several 100 different Polistes species alone!

We've got paper wasps around here. They seem to have stopped poking around...I just hope they're not living in my house somewhere I can't see.


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What are the distinct neurochemical components of sexual pleasure?
Sexual activity is usually described as pleasurable.
What neurochemical systems does sex activate? Does the presence or absence of a partner make a difference -- say, in the activation of the oxytocin system?
Undoubtedly, sexual activity is salient, and so it surely involves dopamine. (Salient activities, whether painful or pleasurable, activate the dopaminergic system.)
What about these systems:

adrenergic
gabaergic
cannabinoid
nicotinic
opioid
serotonergic
cholinergic
glycinergic
histaminergic
glutaminergic

The post contains multiple questions, you will obtain better answers if you split the post.

Sexual response is primarily related to nitric oxide and its products. All of the systems you mentioned play a role, however the core pathway is from touch stimuli, to oxytocin release, to nitric oxide and dopamine accumulation, to motor response (orgasm) followed by prolactin to counteract said neurochemicals and temporarily suppress sexual response.

Supporting references please.

Sex gives you dopamine, oxytocin, adrenaline, and endorphins.

Please add some references


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Breathing faster to lose (more) weight?
I understand that when the human body loses weight, the vast majority of that weight is lost as $CO_2$ (and a small bit is lost as water). I expect the predominant way $CO_2$ exits the body is through exhaling.
So, let's take a human with no influx of carbon (they are not eating); I expect such a person is slowly losing weight, a near infinitesimal amount with each breath (correct me if I'm wrong).
If the person breathes faster (more breaths per minute), that causes an increase in the rate at which $CO_2$ is expelled, correct (more mass per minute)? Is this rate expected to decrease, i.e., as one breathes faster, less $CO_2$ is contained in each subsequent breath? Or, does perhaps the body mobilize and oxidize carbon fuels (carbohydrates first and eventually lipids) to generate $CO_2$ in an attempt to restore homeostatic equilibrium?
Could breathing quickly and heavily possibly cause an increase in the $CO_2$ content of exhaled breaths? That is, would voluntary hyperventilation cause an increase in heart rate (and thus increase in carbon catabolism)? How much $CO_2$ is in a typical exhalation during exercise?
I realize that without exercise, the amount of $CO_2$ being lost during normal breathing is nearly negligible. But perhaps laying down and breathing quickly could cause a measurable increase in the net rate at which mass leaves the body. What do you think?
Thank you for your time.

Well, if you lay down and do situps & pushups, you will breathe faster and probably lose weight.  (Unless you eat more to compensate for the calories burned.)  Likewise if you stand up and walk faster, or run.  But just breathing faster without some sort of exercise will most likely just cause you to hyperventilate and pass out.

I remember reading somewhere that if you breathe faster that your body will adjust. Now I'm talking about breathing a little faster bit by bit... not going straight to a panic attack.

Are there any other ways to remove Co2? https://biology.stackexchange.com/questions/111133/does-all-co2-from-the-blood-leave-the-body-through-the-respiratory-system

The rate of CO2 production is normally set by the rate of metabolism and breathing rate is determined by the level of CO2 in the blood.  What you are suggesting is known as hyperventilation. Because blood CO2 plays an important role in maintaining the pH of the blood, hyperventilation can lead to a dangerous increase in blood pH, referred to as respiratory alkalosis.
Apparently one response to respiratory alkalosis is an increase in metabolic rate as the body tries to compensate for the increased rate of loss of CO2. However, respiratory alkalosis is dangerous so I don't think hyperventilation is a viable strategy for losing weight.

There are two organs which govern pH: the lung and the kidney.  If one is having some problem the other steps in to correct it.  The body does not like pH to drift far from 7.4.
CO2 gas is blown off or retained by the lungs.  More CO2 = more acidic.  CO2 is in equilibrium with bicarbonate HCO3-.  The kidney handles that.  More HCO3- = more alkalinity.
Chronic respiratory acidosis is pretty common - people have bad lungs and they cannot get rid of CO2.  If you have acute respiratory acidosis (like a heroin overdose, and you are not breathing enough) it is hard for the kidney to move quick enough to help.  But for the chronic form you see the kidney holding on to a lot of HCO3- and not letting it go in the urine, to keep the pH up.
Chronic respiratory alkalosis is unusual but the kidney would do the same thing in reverse: dump bicarbonate to let the pH come down.
So in the short term you can screw up your pH and get rid of a trivial amount of calories but in the long term net CO2 loss will be the same.
A better way to exhale calories as CO2 is to produce more CO2.  Your respiratory rate will automatically increase to get rid of it and keep pH normal.  A good way to produce more CO2 is to oxidize fat and glucose molecules to produce ATP for your muscles.

Disclaimer: Not a doctor, a biologist, or a scientist.
This TEDx talk by Ruben Meerman explains the process of the mass loss via CO2 via exhaling.
The mathematics of weight loss | Ruben Meerman | TEDxQUT (edited version)
His explanation to increasing CO2 by-product of oxidizing fat was to increase O2 intake by raising your heart rate. This raises your respiration rate.
So increasing your O2 intake is one way. What about increasing your body's oxygen level as measured by an oximeter? And during exercise, does the oxygen level go down? How about during sleep? Would using an oxygen mask during exercise, or during sleep, increase your oxygen levels?


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Can you identify this fossil?

I found this fossil near a beach in Victoria, Australia. Can anyone identify it?
It is roughly the size of an Australian 20 cent piece (~30 mm). I think it might have been washed down from an eroding cliff.
I found another similar sized but less detailed fossil near by, which might be the same thing.

That's an Echinoid, or Sea Urchin (Phylum Echinodermata). We can clearly see the five rows of ambulacral groves and the base of the spines.
Here is an image of a fossil Echinoid, from the Melbourne Museum, for comparison:

Fossil echinoid (sea urchin), Lovenia bagheerae; late Miocene (c. 8 my old), Portland, Victoria
Photographer: Frank Holmes / Source: Museum Victoria
According to the museum:

Victoria contain fossils of many different kinds of echinoderms, including sea stars, brittle stars, crinoids, cystoids, blastoids, edrioasteroids and carpoids. They occur in the Heathcote, Kilmore, Kinglake, Melbourne and Lilydale districts. In much younger rocks of the Cainozoic Era (less than 65 my old), the most abundant echinoderms found in Victoria are the echinoids or sea urchins. They occur mainly in limestones exposed in coastal areas including the Portland, Port Campbell, Torquay, Geelong and Lakes Entrance districts. (emphasis mine)

Your second image, from below, really seems like this image of Lovenia bagheerae:

Source: Museums Victoria

PS: I live in Melbourne. Whereabouts did you find that one?

It's a sea urchin (Echinoidea). It looks like a specimen of Lovenia or another genus from the heart urchin (Spatangoida) family.
What you see is just the shell without the spines.
Lovenia woodsii

Fossil sea urchin spines

Image sources:

http://www.thefossilforum.com/index.php?/collections/echinoderms/echinoids/lovenia-woodsii-r488/
http://www.fossilguy.com/species/invert/echino/aurora/lc_urchin_spine.jpg


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Are primary lysosomes same as vesicles budded off from golgi bodies containing hydrolyzing enzymes tagged with mannose-6-phosphate?
SO, as far as I understand, lysosomal hydrolyzing enzymes are first synthesized as proteins in rough ER and then they are budded off from the ER. The vesicles containing those proteins reach cis golgi and then they are properly folded to proper hydrolyzing enzyme but they are tagged with mannose-6-phosphate at this point, so they font have the ability to hydrolyze molecules just yet. In the mean time, some molecules can be engulfed by the cell and and these enter the cell as a membrane bound vesicle (endosome) containing proton pumps in its membrane which maintains an acidic environment inside the vesicle (which matures to late endosome). Vesicles containing hydrolyzing enzymes now move to those late endosomes and fuse with them. The low pH cleaves the mannose-6-phosphate tag from the enzymes and they become functional thus late endozome matures to lysosome.
The definition of primary lysosome says it is that lysosome that directly buds off from the golgi bodies and secondary lysosome is that lysosome which gets formed when primary lysosome binds with a vesicle and hydrolyse its content.
So are primary lysosme and those vesicles same?

What is the question here? If you want a fact check,  try wikipedia or if you are more academically inclined try searching on pubmed.gov for articles about lysosomes.

Flagged question, as this is more of a fact check, which the asker should perform personally.

The question is clearly visible at the top of the page. Then I mentioned what I know about them so far. Had wikipedia been an authentic source of information, I wouldn't have asked here. And I could not manage to find anything that answers my query in pubmed as well. Stop flagging my question for no reason, questions get flagged if there is no attempt of research has been shown. When it is shown, it becomes fact check. What do you want me to do?

Sorry for my french, but essentially you are asking a yes/no question, which you should be able to check yourself. I see that you have edited your question slightly, but the remain the same.


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Where can I find a list of transcription factors that are used in somatic embryogenesis?
Where can I find a list of TFs that are used in somatic embryogenesis or zygotic embryogenesis?


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How do aminoacyl-tRNA synthases distinguish between similar amino acids?
How do aminoacyl tRNA synthases recognize the right amino acid for their tRNA? What is the structural reason behind the selective recognition? I have difficulty in seeing how, for example, leucine and isoleucine can be selectively recognized by different binding pockets when they exhibit similar hydrophobicity, molecular volume etc.

"it seems a little bit absurd"... why? enzymes can even distinguish stereoisomers of the same molecule, let alone different molecules.

I have rewritten the title so it reflects the question and tightened the wording .

Aminoacyl-tRNA sythetases are highly specific to their corresponding amino acid. First, the activation site, where the amino acid binds, constitutes a complex network of intermolecular interactions. For example, threonine, catalyzed by  threonyl-tRNA synthetase, is very similar to valine and serine. Valine has a methyl group instead of the hydroxy group of threonine, and serine, on the other side, has no additional methyl side group. Uniquely to threonyl-tRNA synthetase, it contains a Zn2+ ion that exhibits an interaction structure specific to threonine. Nonetheless, the threonyl-tRNA synthetase could still be mischarged with serine because the zinc ion site is not specific enough, leading to 1% mischarged tRNAs. For this purpose, aminoacyl-tRNA synthetases have a second, editing site that proofreads the charged tRNA.  The editing site can recognize serine and cleave it from the tRNA.
Figure: Interaction network of the activation site of the threonyl-tRNA synthetase in A. pernix. The  threonine-AMP  is shown in green.

Sources:
a Berg JM, Tymoczko JL, Stryer L. Biochemistry. 5th edition. New York: W H Freeman; 2002. Section 29.2, Aminoacyl-Transfer RNA Synthetases Read the Genetic Code. Available from: https://www.ncbi.nlm.nih.gov/books/NBK22356/
b Nagaoka, Yoshiyuki, et al. "EVOLUTION AND tRNA RECOGNITION OF THREONYL-tRNA SYNTHETASE FROM AN EXTREME THERMOPHILIC ARCHAEON, Aeropyrum pernix K1." Viva Origino 1.31 (2003), http://www.origin-life.gr.jp/3101/3101062/3101062.html


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Frequency of dominant phenotype (Hardy-Weinberg)
The question is:
The frequency of a recessive allele a is 0.6. If a population is in Hardy-Weinberg equilibrium, what is the frequency of the dominant phenotype?
This question is a bit confusing to me. I'm not sure how to use my knowledge about Hardy-Weinberg in this problem. I know that when q = 0.6, p = 1 - 0.6 = 0.4. But when they are asking for the dominant phenotype, should it be p^2 or the squareroot of p? I have watched several YT-videos about this, but I still can't get the hang of it. There's not much help in my teacher or books. I would be really grateful if someone could clear up my confusions!

I was about to recommend the post Solving Hardy Weinberg problems but then realized that you are the OP and that you have accepted the question suggesting that the answer did not help much. The difficulty of this problem is to remember what genotype have the dominant phenotype and then sum their frequencies, just like Alan Boyd did (+1).

Hi! If you are referring to your answer in my previous post - it did help a lot, but these problems still get me confused. You suggested opening a new post with my question, so I did after a while. If you are referring to the answer I got here - also helped, but I'm afraid that when I'm coming across another problem phrased slightly different than this I won't know how to break it down. Anyways I'll check back later

Yep. I did not ask for justification. It is all good :) Glad the other post helped.  Good luck @Thomas

Ok! Aha - I read the last bit of your comment just now, thanks for the tip. Are you some kind of moderator? Can you think of any good sources to clear up on my confusions about this? My examdate is getting closer and closer

p = p(a) = 0.6
q = p(A) = 0.4
Frequency of homozygous recessive, aa = p2 = 0.36
All other genotypes have dominant phenotype therefore the frequency of the dominant phenotype is 1-0.36 = 0.64
(Frequency of homozygous AA = q2 = 0.16
Frequency of heterozygous Aa = 2pq = 0.48)
And if you want a deeper explanation you really should study this answer by Remi.b

Since the frequency of the dominant allele is 0.4, or 40%, the chance of each allele being the dominant allele is 0.4. Since you are asking what is the probability of BOTH alleles being dominant we use the multiplication rule of probability, 0.4*0.4 = .16.
This is similar to the probability of flipping two coins and having them both be heads. Each coin has a 50% chance, therefore the probability of both being heads is 0.5*0.5 = 0.25.
That is the logic behind the Hardy Weinberg formula, p^2 + 2pq + q^2 = 1.

“Since you are asking what is the probability of BOTH alleles being dominant” — No. The question is asking after the frequency of the dominant phenotype. That is, any one dominant allele is sufficient. See the other reply for the correct answer.


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Lengthening muscles not good from evolutional perspective? Why do we do it with explicit stretching?
Stretching has many advantages, among other things it helps us to be flexible in our movement (which is an advantage?!).
But why do we need to actively stretch, it seems that the body wants to shorten the muscles by evolution (e.g. when training often in fitness studio). This is the opposite of what we do when stretching.
It seems to be that there are advantages of being not stretched. So what are these advantages / what is the evolutional rationale?
Edit: Why this question is different from this question:
That question asks, why we automatically stretch sometimes after e.g. sleep. The answer is that we stretch the soft tissues because of transitions of high and low activities (especially after sleep, in which we ease the tension in our muscles [muscular antonia]).
This question asks something different. It asks about explicit stretching in sports and not about automatically stretching behavior. The aim is different. In sports we stretch because, we want to lengthen our muscular. The question is why lengthening doesn't seem to be a good thing from an evolutional perspective.
Edit 2: I'm not sure, if it is clear for everybody, what I mean, so I add a succinct example: Why would it be bad (evolutional rationale), if everybody could do a split (gymnastics) by nature (disadvantages?)? In our reality, the ability to do this is almost always an result of stretching. This is only one extreme example, mostly people don't strech to such extremes. Maybe this now  helps to understand, for what this question heads.

Now I understand your question, thanks for editing it. I just retracted my close vote.

@GerardoFurtado Thanks, shall I edit the title to "Lengthening the muscles not good from evolutional perspective? Why do we do it with explicit stretching?"?

Yes, I think it's a little better. But certainly a top user will edit it again to make the title even more clear.

I don't know enough about this to make an answer but I wonder if you might find some answers in looking up "hypermobility" or "hyperflexibility", and why it can be bad. There may be a tradeoff between mobility and strength; sometimes you want to bend, but sometimes you want to have a limb "locked in place", and if the muscles/ligaments can stretch too far then you need to spend energy keeping them contracted where you might otherwise not need to.

Muscles only ever work by shortening, as you say, but muscles in the human body tend to be found in antagonistic pairs.  These pairs of muscles act in opposite directions, one example being the biceps and triceps muscles - the biceps bends the arm (a flexor muscle) while the triceps straightens the arm (an extensor muscle), another example is the quadriceps-hamstring muscle pair in the upper leg.
If our muscles remained shortened, our mobility would be impaired.  If the biceps muscle remained too short, it would be impossible to extend our arms, for example.  Muscles do work by shortening, yes, but it's important for them to be able to stretch as well, and remain long enough for antagonistic muscles to have their full movement be possible as well.

Welcome to Biology.SE. Your answer seems good enough to me but please add references (peer-reviewed articles are best, Wikipedia articles or blogs are also okay for common knowledge) to back up your claims and give people starting points for further reading. Thanks!

This doesn't answer my question, or at least what I meant. I edited the question. This question heads for streching in the meaning of lengthening the muscle at its maximum resting length (and maybe to shorten the completely contracted length of the antagonistic muscle partner).

Thanks for your comments, both.  Apologies that I don't have any references, it was purely reasoning that lead me to my answer so please take it with a pinch of salt, obviously!

Sorry I haven't been able to answer your question entirely. Perhaps it's just the case that stretching to such extremes aren't that frequently used in a natural setting.  It may not be detrimental, but it may not be advantageous enough for it to have been selected for over the course of evolution.  This article has some suggestions too: http://www.ideafit.com/fitness-library/does-stretching-reduce-injury-risk-0


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is this true to select 100 volume higher concentration of a drug test?
I am interested in knowing how to find/optimise the concentration needed for a drug effect in cell. and different organism
For example, if I use 1 micro molar for treating a cell. Should I use 10 nM when I use C.elegant ? how do you define or tune such a concentration ? Please give me reference too if there is any

Typically when working with compounds I come from two directions:
Does the drug appear in the literature and what concentration do they use?
I think a quick literature search is a wonderful thing because like many problems, often times someone else has asked your question (what's the right concentration?), and done the necessary legwork to find you a starting point. I don't think we can avoid this next part though, especially if your drug has never been used in your system/organism/etc.
Titrate your compound
For almost anything out there, even if the manufacturer has a number in mind you should always titrate for your own application. Things aren't simply going to work for you as they did for another investigator, in part, because you're never asking the same question as another investigator. A good literature search can help strengthen your finding, however.
In finding the working concentration for your compound you aren't going to be doing the optimizing. It doesn't make sense to find the best concentration when you don't know what concentration works to begin with. As a rule of thumb I try to make the range of titers broad enough that I can see where undesirable or no-effect is, so for example with a drug I'd try 100µM, 10µM, 1µM, 100nm, 10nM, 1nM, 0.1nM.
If you can pick out a good working concentration there, you can optimize by using a tighter criteria. For example, I find that 10nM works the best; now I know 100nM and 1nM are my respective maximum and minimum. May I'd try 40nM, 20nM, 10nM, 5nM, 2.5nM.
It's important to reduce technical variability by using the same starting materials such as cell number for each condition to get the best titer.

thank you so much for your message. This is definitely good. however, my main question is that is it normal that a drug with nano mollar works in a cell while with a 100 fold more work in e.g. C.elegant? or any other animal model? how can I justify that? do you have such an example?  for example when i use more than nano molar the drug will kill the cell imagine what will happen if I use micro molar . is this ajustable ? do you know of any paper with different concentration in cell and animal model?

I have no way of knowing without the identity of the drug.

for instance Rapamycin

So rapamycin as an example: I'd probably find my usage close to 10-20nm in cell culture, which I think is standard. However, I can find two references, immediately, that use rapamycin at 200µM and 100µM, respectively (ref1, ref2). Reference 1 makes an important point: higher concentrations are needed for C. elegans due to bioavailability.

Important to note is that different species have different kinetics to their usage of the same drug.


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Facultative anaerobic organism
While I was studying Cellular Respiration: Harvesting Chemical Energy, I found this question:

An organism is discovered that consumes a considerable amount of sugar, yet does not gain much weight when denied air. Curiously, the consumption of sugar increases as air is removed from the organism's environment, but the organism seems to thrive even in the absence of air. When returned to normal air, the organism does fine. Which of the following best describes the organism?
A) It must use a molecule other than oxygen to accept electrons from the electron transport chain.
B) It is a normal eukaryotic organism.
C) The organism obviously lacks the citric acid cycle and electron transport chain.
D) It is an anaerobic organism.
E) It is a facultative anaerobe.
Answer: E

I wonder why the answer is E not D. How can I know that it is a facultative anaerobe? Do anaerobic organisms die in air?

Strict anaerobic organisms cannot proliferate when air is present. Facultative on the other hand can.

But he didn't say anything about proliferate

I think "does fine" implies proliferation, but I agree the wording could have been clearer.

There are organisms with anaerobic metabolism that tolerate oxygen: aerotolerant anaerobes.  "Anaerobic" refers to the metabolic system.  You cannot be sure of oxygen tolerance based solely on metabolic system.
Factors influencing the tolerance of anaerobic bacteria to oxygen
Here is why this is a facultative anaerobe.
This organism does not gain weight when denied air.  One concludes its metabolism is less efficient.

Curiously, the consumption of sugar increases as air is removed from
  the organismʹs enviroment

Anaerobic metabolism uses sugar less efficiently than aerobic metabolism in organisms that can use both methods. This means oxidative metabolism is the preferred method.
So:  this is a facultative anaerobe because it can get by using anaerobic metabolism, but two pieces of information show that for the organism, anaerobic mode is less efficient than aerobic metabolism.  Brewers yeast is such an organism.

My answer is correct, since i only talk about obligate anaerobes. Just as described in the book in the link.

I edited your answer for the reasons specified in the edit history. If you disagree with this change, please feel free to rollback.

Yes, (obligate) anaerobes die in the presence of  oxygen (at atmospheric levels). They do not have the detoxifying enzymes that convert toxic metabolic products such as hydroxyl racials or superoxide anions into nontoxic H2O or O2. These enzymes present in aerobic and faculative anaerobic organisms are superoxide dismutase, peroxidase, among others.
Reference:
a Hentges DJ. Anaerobes: General Characteristics. In: Baron S, editor. Medical Microbiology. 4th edition. Galveston (TX): University of Texas Medical Branch at Galveston; 1996. Chapter 17. Available from: https://www.ncbi.nlm.nih.gov/books/NBK7638/


text:
Do all RNA polymerase in Eukaryotes share the same transcription factors?
I know that TFII proteins bind to cis elements in DNA and help initiate transcription for RNA polymerase II. But do RNA polymerase I and III also use these proteins when transcribing genes? Also, do all genes require promoters/cis elements? Do all genes put in a vector require promoter regions/cis elements?

TBP is common to all three polymerases, even though RNAP I and III promoters don't contain the TATA box. I believe all other core transcription factors are unique to their respective polymerase, though some may be paralogous to TFs for other RNAPs. If I have time, I'll find some references and post an answer later.

Except for the TATA-binding protein (TBP), there are no common transcription factors for each RNA polymerase. However, there are homologies between many of the factors used by the different enzymes.
The paper Conservation between the RNA Polymerase I, II, and III Transcription Initiation Machineriesa gives a good overview over the different initiation factors of each RNA polymerase enzyme. It contains a comparison of various transcription factors in yeast.
Here is an excerpt form the paper showing the homologies between some of the initiation factors of the TFII group and their homologous counterparts. (The first schematic is RNA poly II, the second RNA poly I, and the third RNA poly III):

Source:
a Alessandro Vannini, Patrick Cramer, Conservation between the RNA Polymerase I, II, and III Transcription Initiation Machineries, Molecular Cell, Volume 45, Issue 4, 24 February 2012, Pages 439-446, ISSN 1097-2765, https://doi.org/10.1016/j.molcel.2012.01.023.

Probably.
https://en.m.wikipedia.org/wiki/Conserved_sequence
Here you can find a variety of conserved sequences, not just in eukarayotes but across all organisms. RNA polymerase has only been extensively studied in e coli, where about 100 RNAP related genes have been found. All bacteria seem to share a set of genes such as rpob, terminal domains, and omega subunit. In eukarayotes you furthermore have the 5 polymerase proteins, which closely correspond to archea RNAP. Poxvriuses have their own similar RNAP.
As for retroviruses, the entire science behind them is rather vague so we cannot say exactly what RNAP genes they employ. It is claimed (without much evidence) that they employ a few genes labeled "pol" to achieve a similar functionality.
The promoter regions are not thought to be strictly necessary although they do greatly speed transcription if most genes. They are usually conserved as well.


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Queen ant identification
I'm planning to start an artificial ant nest and I'd like to learn something about this specific species of ant that I captured in central Colorado.
Could you tell what kind of queen is that? Is there any image reference that would help me find out? Ideally with some location search possibility.

Where was the ant collected? There are some online resources for different countries that may be useful but unless there is some information to help narrow it down, you must start with the 12,500-22,000 species found across the globe.

It was captured in Colorado. Hopefully someone with more experience than me has a pretty good guess because all the sites I have found have not been to helpful.

The picture is unclear but this ant looks like a Solenopsis queen. Maybe a Solenopsis invicta! Sorry if I'm wrong, I've only ever kept Camponotus and Lasius queens. I hope this is helpful though

This is clearly wrong, there is a post-petiole and a petiole in Solenopsis whereas you can clearly see that there is only one on his picture.

There is clearly only one segment between the thorax and the abdomen, which rules out the possibility that this ant is a Myrmicinae.
It looks like a queen of Formicinae, probably in the genus Camponotus.

@lucas Adam: I think so you have captured the wrong ant (worker), because the queen's head will always be shorter than its thorax. It's probably a carpenter worker ant. Further , capturing a queen is a big task because queen ants rarely come outside. And if you capture it , the entire colony it have already created will die within 2 days or maximum by a month.


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Rationale behind washing off unbound protein antigen in indirect ELISA
My question is with regards to the usability of the indirect ELISA in measuring protein concentration. Suppose we want to quantify the concentration of a protein. The indirect ELISA method would require one to coat the bottom of the well with protein antigen and wash off unbound antigens.
My question is that wouldn't washing off unbound proteins mean you are 'diluting' the actual protein concentration? Your resulting colour intensity will not reflect the actu protein concentration. Thanks!

The method is based on the principle that the amount of antigen bound to the plastic will be proportional to the concentration in the sample being tested. And of course an ELISA will usually be run with a calibration in parallel so that the signal from your sample is compared to that from standards.
The wells will be rinsed anyway in subsequent steps to remove unbound antibody molecules: if you didn't wash off unbound antigen it would simply compete for binding the antibody then disappear later in the procedure.


text:
Why do cells not store glucose?
I understand that glucose is soluble and hence it is not stored by cells. However, my teacher said that I also have to say that "it would have an osmotic effect on the cell." I don't understand what that means.

The issue here can be explained by colligative properties:
In short, colligative properties are properties that depend upon the concentration of the molecules, but not upon the type of those molecules. And osmotic pressure is a colligative property.
That being said, have in mind that 10 molecules of a huge polysaccharide in a given volume or 10 molecules of a small monosaccharide in the same given volume will have the same osmotic pressure.
So, let's imagine that the cell needs a given amount of glucose. Let's say 1000 molecules, just for an oversimplified example. The osmotic pressure can be calculated by (assuming Van't Hoff factor is 1):

π = MRT

Where M is the molar concentration, R is the ideal gas constant and T is the absolute temperature.
Thus, the osmotic pressure created by those 1000 molecules can be calculated taking into account their molar concentration.
However, If we simply polymerize those 1000 glucose molecules into a huge polysaccharide (be it starch, glycogen or cellulose, it doesn't matter)...

1000 molecules of glucose → 1 molecule of starch

... the molar concentration will be 1000 times smaller, and the osmotic pressure will drop 1000 times.
As the actual numbers are way higher than this simplified example, we can clearly understand that cells avoid storing glucose to prevent a deadly osmotic pressure, in which the cell bursts due to the amount of water that moves in (specially animal cells, which have no walls that could prevent the membrane from rupturing).

Could you elaborate the 'deadly osmotic pressure (specially animal cells, which have no walls)'?

@Tytoalba https://en.wikipedia.org/wiki/Cytolysis

I wonder what torture what look like where every cell of the victim is ruptured at once?

@Chloe a bad SF movie special effect where a deathray causes its target to melt into a puddle of goo?

Sorry but I am a GCSE Biology student but is the osmotic effect the same as osmotic pressure and when you say the osmotic pressure do you mean pressure by glucose/starch molecules outwards from the cell?

@RishiMalhotra Well, osmotic pressure (like any other pressure) wants to get equalized in an environment. So if you have no cell wall, the natural thing to happen (pure physics) is to equalize the pressure by either moving the substance outside (which may be impossible depending on how the membrane behaves) or moving water inside.

You most have misunderstood something... Cells do store glucose, however they do so by combining glucose molecules into longer storage molecules such as starch or glycogen.
 https://en.m.wikipedia.org/wiki/Glycogen

...and they do this precisely to avoid osmotic effects.

@Jeppe and you seem to have missed the point of the question...

Then the question was poorly defined... as it did not specify storage method.

They do. Some cells can store glucose.
In human beings, liver cells and muscular cells do store glucose in the shape of glycogen which is a polymer of glucose (= a chain of glucose).
Muscular cells can use it during their contraction. The liver use it to put it in the blood to keep the blood sugar steady.
However it is not the preferred form of energy storage : the energy is stored in triglycerides (=fats).
A theory that explains this is that :
Glycogen is hydrophilic : it is very hydrated so it takes a lot of room
Triglycerides are lipophilic : it takes less room for equivalent energy
Therefore, glycogen storage are limited. In muscular cells, the glycogen storage is used after about 40 minutes (unless you are trained for endurance) and in the liver, the glycogen lasts about 24h.

Storing glycogen isn't storing glucose: it's storing something that can be made into glucose.

You maybe asked the question Why cells do not store glucose?
Answer: Cells actually store glucose in the form of glycogen.
Glucose is soluble or dissolved and it has a higher osmotic effect so cells can swell up which means it can become larger due to storing glucose directly.
i hope it is super clear to you and you might find helpful

You might be struggling with the question, 'Why cells do not store glucose?'
Cells already have glucose in the form of glycogen- they convert the glucose into glycogen. This is because glucose is soluble and may be dissolved, as a result, the cell will become turgid. The cell will finally burst out at the extreme point!
I hope you hit the bull's eye.

Welcome to Biology.SE! It isn't clear that this adds anything to the existing answers — unless you have new information to add it would be best to focus on unanswered questions. In addition, answers are much more likely to receive a favorable response if you include supporting references (primary literature is best). Without that support, your answer is indistinguishable from opinion. ——— Thank you for taking the [tour], but please also consult the help pages for additional advice on [Answer] effectively on this site and then delete or [edit] your answer accordingly. Thanks!


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Possible to cause the cells to produce less/no chemicals?
I have a question regarding cells producing chemicals, e.g. some metabolite, inside the body. Is it possible to inject something (at least theoretically possible, and maybe practically possible in the future) into the body to inactivate these chemicals (e.g. enzymatically), or inject something which makes the cells produce less/none of the chemicals?

Please define killing a chemical.

I just mean that I would like the chemicals to decay very fast so that it does not affect the traction force exerted by the cells any more.

Now I'm more confused than before...

Okay, but do you believe we can do something to increase the decay rate of the chemicals without killing the cells?

Welcome to Biology.SE! I tried to clarify your terminology in an edit - does that capture what you mean? Please feel free to further edit. And does that make things clearer for you, @GerardoFurtado?

It will depend on the metabolite, metabolic pathway and the cell of interest.

Okay. I am thinking about cancer cells distributed inside of a spherical collagen gel.

Basically all of pharmacology consists of something that can be injected, consumed, applied topically, etc to cause cells to produce more of something or less of something.


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Bioenergetics and equilibrium
"The living state is a non-equilibrium steady state to be able to perform work."
I know that a "steady state" is the one in which the rate of energy gain is equal to rate of energy loss. Then how can living beings do work?  Can you simplify it?

Posting text as image isn't a best practice on SE. The same pdf should allow copying and pasting the text into your question ( [edit] ). Images are not searchable, and can not be interpreted by screen readers for those with visual impairments. See this for more information.

Think about why body needs energy to maintain this steady state?

@Tyto alba I understand now. I have removed the image.

The clue is in the non-equilibrium part. The energy is spent to prevent collapsing to the equilibrium, that is indeed death.