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How does mutualism arise?
How can a mutualism between two species arise? I have thinking about this for a while and I have come up with the following points
1.If mutualism gives one specie a competitive edge over its competitors then it could arise. Suppose you are being really pounded by your competitors and there is now way you can survive except if you give in to mutualism, even if it means "selling your soul".
2.The benefits received from the partner species outweighs the costs involved in helping it out.
I cannot think of any more examples. Please suggest a few; also point out if there are flaws in my reasoning.

What does "selling your soul" imply?

I am afraid this question is too broad and I am voting to close. Evolution of inter-specific mutualism is a large subject. Here is not a complete answer but just a few comments on your two conditions

1.If mutualism gives one specie a competitive edge over its competitors then it could arise.

This is mainly wrong. Mutualism is likely to increase if mutualistic behaviour offer increases the fitness of the individual performing it, you would expect mutualistic behaviour to increase. You would not really expect the same by comparing species ability to survive in relation to their level of mutualism.

2.The benefits received from the partner species outweighs the costs involved in helping it out.

Again, you are talking about the benefit for a species. You should boil down your arguments to the individuals. It is true that mutualism can evolve only if the individual performing the mutualistic behaviour enjoy a higher fitness benefit than fitness cost (if any).


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What are tail currents?

This is a voltage clamp on an ion channel. When the voltage is stopped there is a still a current at the end (the tail current). I understand that the gates aren't completely closed because of which there is still some current flowing.
What I don't understand is that why does the current suddenly jump to a small value? Shouldn't it gradually go down?

I'm voting to close this question as off-topic because  it appears to be a physics question

@rg255 it's Biophysics and on protein ion channel gating. Bio, most definitely

This trace looks a bit funny - I am guessing the OP has abandoned the site, but if OP happens to return and can give a source for this image that will really help with providing an explanation specific to this example.

@BryanKrause Fwiw, an image search yields no other copies of that image, however, figure 4 of this paper shows the same effect.

As for an answer I have no idea but in general electrical systems you would expect a sudden jump like that if a switch/gate was opened or the voltage was cut. Without knowing anything about this topic, from an electrical perspective that signal still seems to be reasonable to me (not that that means anything of course). As a wild guess I'd assume the slight curve after the jump is due to capacitance somewhere downstream of the gate? Or some complicated thing with the kinetics of the gate that I don't understand.

@JasonC I also attempted an image search with no success; I agree that Figure 4 of the link you share does show nice tail currents, but it doesn't show the rapid jumps in current that the OP's picture shows, and the "tail currents" there also look funny: they increase then decrease, rather than the smooth decay of normal tail currents like the article you link. My suspicion is that there is some artifact contributing in the OP's post.

@JasonC The artifact would be from a failure to normalize the pipette capacitance. So it wouldn't have anything to do with the biology but rather an incorrect setup of the patch clamp amplifier. In a good electrophysiology experiment you should not see that artifact, the traces should look like Figure 4 of the paper you linked.

@JasonC And to explain the biology a bit, there are two things going on here: 1) The experimenter is applying a constant voltage using a patch clamp amplifier. On each trial, that constant voltage starts at one value, briefly steps to another value, and then back to baseline. 2) The step in voltage is activating voltage-gated ion channels. The opening of these biological channels changes the amount of current that needs to be applied to maintain the voltage specified - that current reading is what is plotted in the OP's figure. Those channels do not close instantly, which produces tail current

OK, I know this is old, but here goes. The tail current is the current at -55mV after the voltage step, here:

The current shrinks as the voltage changes, this causes a massive shift in the driving force for the ions either side of the cell membrane. Going from -125 to -55 mV for the largest step. As commented, the dense vertical bands either side of the step are due to fast capacitance readings, basically ignore unless you want to go down a whole other avenue.
The reason for the tail currents is some channels remain open and close gradually after the step ends "tailing" off. We can't really say what channels these are as we know nothing about the recording conditions/cells involved. However these currents are large, so most likely to be sodium/potassium.

I think I understand the question a little better now. When voltage increased, OP expected an exponential decay but instead saw a peaking to positive value and then going back down to negative value at which exponential decay happens.
Pretty much think of this as two current sources superimposing on each other. One is the current caused by difference in voltage (Ih). Ih is a mix of potassium and sodium current. While it is voltage dependent, it doesn't follow simple Ohm's law as this has to do with activation of channels rather than membrane. source The other is current caused by capacitive property of the membrane. Since capacitive current is proportional to rate of change in voltage, increase in voltage results in positive capacitive current.
So when voltage increased from -125 to -55 mV, there is a positive capacitive current as well as exponentially decaying Ih. These two superimposing each other almost leads to the picture we see in OP's question. I cannot explain why there is the huge negative spike in current after the small positive peak though.
Source: I learned this in class one year ago.
and nice animation of what happens during voltage clamp experiment

This answer doesn't answer the actual question about tail currents and contains several errors. Actually the OP is a better source for what tail currents are from: the channels that are still open and haven't yet returned to the equilibrium at the new voltage.

@BryanKrause do you mind checking to see if there's still errors? More on those errors would be appreciated.

Tail currents are observed because current $I = g(V-E)$ suddenly changes with $V$, whereas $g$ changes gradually following some kinetics. Thus, at sudden transition of voltage $V$, $I$ changes by a factor, which is observed as tail current with a jump.

This is correct and might answer the title question, but it doesn't actually answer the OP. Unfortunately this question has sat for quite some time without feedback from OP and we probably need to get rid of it now.

OP stands for "original poster"/"original post", in this case the question/question asker. Oliver Houston's answer and my comments address the question the OP was actually wondering about, which was the presence of the sharp transients in addition to the tail currents.

How is jump not explained by this ?

If you plug some numbers into the equation in your answer, it would be obvious why you don't get what the OP shows. The paper linked up in the comments by JasonC has an example of what tail currents look like when not impacted by artifacts: http://jn.physiology.org/content/79/5/2345

when you close a switch, an arc of lightning jumps in the air because the voltage rises at that particular point in space momentarily towards a theoretical infinity as the current behind the closing switch places pressure on the edge electrons and force them to jump. that change in voltage is similar to a tail current.

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Could someone identify these microorganisms on microscope?
I'm new in this StackExchange forum, so I don't know if this is an appropriate question.
Can someone please help me recognize these micro-organisms on these photo taken with my phone during my biology lesson using microscope.
Location: Kyjovka river (Czech Republic)
Magnification: 200x

What's the source of the sample? The resolution isn't good enough for me, but the source would be very important.

Unfortunately this is my own photo taken on my smartphone, so there is now way I can give you a better photo. Anyways thank you for your reply. I do not really need the exact name of specific species, anything would help me I think.

Are you asking about the wormy things? These are most likely some type of nematode (identification of nematode species is usually only achievable biochemically). If you mean something smaller in this sample, I doubt we can help you out (microorganisms are not easily or confidently identifiable by eye)

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Dna based question
We know that dna is an acid which is elaborated by deoxyribo nucleic acid.It has 4 nucleo bases.Now,the question arises, why dna has no uracil base?

this question has been already answered on SE. The link is given below:- https://biology.stackexchange.com/questions/171/why-is-thymine-rather-than-uracil-used-in-dna

First of all, uracil can be in DNA.
Cytosine can spontaneously convert to uracil by a process called hydrolytic desamination. This causes guanine, which was originally bound to this cytosine, to be bound to uracil instead (remember: uracil normally binds to adenine). The next time the cell replicates its DNA, the place opposite this uracil would be occupied by adenine instead of guanine, correctly changing the information on this DNA section. This process of cytosine deamination is one of the most common DNA damage, but it is usually effectively corrected.
In DNA, thymine replaces uracil. Uracil can be produced relatively easily from cytosine by deamination and hydrolysis, which then alters (mutates) the base sequence and possibly alters the information genetically encoded in the nucleotide sequence.
Desamination of cytosine to uracil
Thymine, on the other hand, differs from uracil in that it has an additional methyl group and thus cannot easily be formed from cytosine. Uracil present in the DNA can thus be recognized as a mutation and exchanged for cytosine by base excision repair.

This question is a duplicate (as well as badly written); so your answer here would not be very useful. You can post an answer to the linked question if you think it addresses an issue not covered by other answers.

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How many kingdoms are there actually?
I am wanting to learn (memorise) some of the tree of life; the classification of organisms. So I have come across a lot of kingdoms in my research. Basically, I don’t want to waste my time learning the wrong thing, so my question is this. Is there an official or most recent system of classification, some authority in organism classification that we look to? After kingdoms it seems pretty clear, the phyla in (say Animalia) seem pretty defined and uncontraversial.
These are all of the ‘kingdoms’ I have found while researching. Some are called kingdoms in one source and not another. I know that some overlap others. This is just to throw every possible example out there.
Animalia, Apusozoa, Archae, Archaebacteria, Archezoa, Bacteria, Biliphyta, Chromista, Chromophyta, Ciliofungi, Cryptophyta, Eufungi, Euglenozoa, Excavata, Filastera, Fungi, Monera, Nucleariida, Plantae, Proteoarchaeota, Protista, Protozoa, Rhizaria, True bacteria, Viridiplantae
I don’t ask that you go through them and explain them. Only what the actual system of classificating organisms is. On that note. As far as I’m aware, there’s two types of domain systems. Two are Eukaryota, Archae/-bacteria, Bacteria. Another is Eukaryota, prokaryota. A clarification on this too would be appreciated.

All of the hierarchical classification schemes are somewhat arbitrary. There is a real tree (with some complicated attachments due to horizontal gene transfer), but the labels placed on different levels of the tree are made up and subject to opinion and argument. The kingdoms are probably the most poorly defined within that classification because as a group they are not monophyletic at all.

Welcome to Biology.SE! As @BryanKrause says, there is no "correct" answer since these are classifications made assuming a simple branching topology that can not completely encompass the complexity associated with living organisms. The wikipedia article on this and the many linked articles are a good place to start learning about this subject. ——— As for domains, "prokaryota" is invalid since it is not monophyletic.

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

Why do you wish to memorize this? Science involves understanding, not recall of “facts”.

@David as you can see I am not a biologist. I lurk more in the realm of mathematics, and so naturally, systems of organisation interest me, so why not that system which organises all living organisms. It's mostly for trivia because I think it's interesting; I don't intend to use these 'facts' in my occupation when I'm older.


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What are the exact characteristics for something to be considered a novel virus?
I've heard viruses being referred to as "novel" - is there an exact definition for what this means?

"Novel" means new, as in never been seen/identified before, that's all.


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Relation of root length to plant size
I am thinking of making an aeroponics system.
But after i finished my primary design I though to myself how deep should I make the container for the roots of my plants? Since I want to make my system applicable to a range of plants image from microgreens to lettuce. I was thinking how can I determine the size of the roots of the desired plants? I there a way to determine this from the size of the plant or not?
This would be important since if the container is too small the spriklers my get covered my the roots of some plants. And if the container is too big some roots my not get enough water. Next to this a more space efficient container would be better (So it also looks a bit nice)
I am a complete newbie to this so please let me know if any clarification is needed :) And if this is even the right place to ask.

Root length is something that plants change in response to their environment.

Ok, so let's say the environment for the roots is very optimal would that result in longer or shorter roots?

Compare, for example, root system depth for trees such as oaks vs the Welwitschia plant of southern Africa...


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Open Reading Frames vs Coding Sequences (CDS), are they different?
The two terms confuse me for a long time. What is the difference between ORF and CDS. Some people say ORF could contain intron and CDS does not. The wikipedia definition of ORF does not contains intron. Could someone define the two terms and point out their differences? Thanks!

I (mostly) like the definitions given on this page.

An ORF is a sequence of DNA that starts with start codon “ATG” (not always) and ends with any of the three termination codons (TAA, TAG, TGA). Depending on the starting point, there are six possible ways (three on forward strand and three on complementary strand) of translating any nucleotide sequence into amino acid sequence according to the genetic code. These are called reading frames.
The Coding Sequence (CDS) is the actual region of DNA that is translated to form proteins. While the ORF may contain introns as well, the CDS refers to those nucleotides (concatenated exons) that can be divided into codons which are actually translated into amino acids by the ribosomal translation machinery.

However, I do not entirely agree with this statement:

In Prokaryotes the ORF and the CDS are the same.

While it’s true that all CDSs are within ORFs, not all ORFs are CDSs. You can have ORFs that are transcribed as noncoding RNA elements, and ORFs that are not transcribed at all. CDS refers specifically to the ORFs whose post-transcriptional fate is to be translated.

I just found a post on biostar with the same question and lots of discussions: https://www.biostars.org/p/47022/


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How does DNA shape a living organism?
I'm haven't studied biology so excuse me if I'm getting something wrong.
I'm trying to understand how the DNA from a sperm and egg cause the egg too multiply and form a perticular shape (shape of a fetus). Or in case of plants how does dna in a seed cause the sapling to grow into a plant of perticular shape and size?
I mean how does DNA cause the cell to multiply and grow into hands and legs and heads of a certain shape and size in animals. Or to stems, branches and leaves in plants? How does DNA shape a living organism?

Answer to this question can fill (and has filled) multiple textbooks. Entire branch of biology - developmental genetics - studies exactly this. If you are interested I recomend starting with some introductory book about genetics. If you don't significantly narrow your question I doubt someone will be able to answer you here.


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Why pick just a single bacterial transformed colony
So after bacteria have been transformed to perhaps grow up a plasmid of interest, why pick only a single bacterial colony from a selective plate for further expansion?
I understand that this is to ensure that you are only working with a single genetic makeup because each separate colony is derived from only a single bacterium. What I can't rationalize is that if I am trying to expand and isolate a plasmid of interest, all colony expansions on a selective antibiotic plate should contain my plasmid. So is it really necessary to take only a single colony, because all colonies I pick should  be useful to me.

If you want to do multiple preps, then by all means pick multiple colonies, but keep them separate. The point of picking a single colony is that it's (theoretically) a single clone, so you're sure that your starting material isn't contaminated with another sequence.

Right, when I make a plasmid, I typically grab 24 colonies because my centrifuge can hold 24 tubes. Keep them all separate and labeled. There have been times when only 1 of the 24 had what I wanted.

Why risk a heterogeneous culture? Pragmatic workflow is always best.

This is a matter of pragmatism in the culture process.
Taking 100 colonies instead of 1 increases the inoculation volume by a factor of 100, which then saves you perhaps 2 hours of bacterial growth time before your culture reaches the OD you want.
However, mutations and loss of plasmid in culture, while unlikely, are possible, especially if the bacteria were not cloning strains with their recombinases knocked out. In such a case, you would risk the downstream experiments being contaminated with mutants, be that protein expression, retroviral plasmid production, or something else.
Worse still, the mixture of bacteria containing mutants is less likely to be detected, since had you picked a single mutant colony, there would be absolutely no result, but a contaminated culture would produce a low but still positive result. Therefore, you may end up wasting many days or weeks troubleshooting your downstream experiments.
Therefore, picking single colonies is simply a matter of "better safe than sorry".

While all colonies on a selective media SHOULD contain a resistance gene, that's a long way from them containing the plasmid you want. A typical cloning experiment will insert a gene of interest into a empty vector backbone to make an intact plasmid. The backbone usually contains some antibiotic resistance gene. If your gene of interest is not correctly inserted, but the empty vector religates on itself, it will make a viable colony without your gene.
Additionally, I have seen mutations happen even when an insert is correctly inserted, and if you're doing blunt end ligation, there is always a risk of getting your insert in backwards or ligating two vectors together.

And that all make sense but let's say for instance that we are growing up a plasmid from a stock solution which has already been sequenced and the resistance gene and the gene of interest are both on a single plasmid. Now is it relatively safe to just pick any number of colonies and assume that they would all have the gene of interest?

You can easily test this. Resuspend a few scrapings of your frozen stock in a small volume of media and plate serial dilutions on both plates with drug and plates without drug. Let the same culture grow in a shaker for 90 min (with drug) and do the same two sets of serial dilutions. If the frozen stock is pure the counts will be the same plus/minus drug. Likewise after growing in liquid. If you grow the liquid long enough the drug will get used up and you may start to see cells that lack a plasmid start to accumulate.

@TheNightman You will get your plasmid but it is not relatively safe. If the downstream analysis/experiments are complex then you want to make sure you start with the best material you can. You might extract plasmids with mutations if pooling colonies together and this could be very problematic for subsequent experiments. Sometimes very little details make an experiment succeed or fail.

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Reason for the source of fetal bovine serum
What is the reason that perhaps the most commonly used serum in labs is fetal bovine derived? Is there something about fetal serum that is particularly useful over say serum just harvested periodically from adult cows, or cows going to slaughter?

As a cattle farmer, I can contribute a little to why FBS is so expensive at least. Slaughterhouses HATE receiving pregnant cattle, so they go out of their way to not buy them. Therefore stockyards avoid buying them as well, and will send a cow back to the rancher if they determine it's pregnant. This means that the number of bovine fetuses that evade detection and make it to the slaughterhouse for processing is small, which keeps the supply of FBS low and prices high.

The reason fetal bovine serum (FBS) is used is because it supports a wide variety of cells and really supports their growth.  It has a high concentration of growth factors, but also a low concentration of antibodies.  So it promotes growth in almost any cell or tissue type without also having antibody reactions with it.
Adult cows blood will have the opposite concentrations, higher levels of antibodies and lower levels of growth factors as they have already grown.
There are currently several research projects looking for a alternative or synthetic FBS, but nothing has worked as a total replacement.  There are a few substitutes for specific purposes, but nothing with the diversity of uses that FBS has.


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Purpose of antibody wash
It is common practice after surface staining cells for flow cytometry analysis to wash the antibody out of solution before analyzing a sample. I have tried analysis with and without washing the antibody out and notice no significant difference by flow. So is there a reason people do this step that maybe I'm just not noticing?

I'm not 100% sure but I was thinking it's to avoid getting weird background from cross-reactivity with the unbound antibodies, as in when they bind to any labelled secondary antibodies.

@Kendall So in this case there are no secondary antibodies. But if there were, I could understand, as extra primary in solution would just soak up the added secondary.

Two reasons for antibody wash:

To limit non-specific epitope binding. All ABs have specificity.  Washing is usually trying to remove weaker binding to non-intended targets.
For flow, excess AB that is not bound, if also pre-conjugated to a fluorophore, may allow for excitation of the fluorophore while going through flow even though the antibody isn't bound to the cell type of interest.

If you had a very specific AB, and very little excess, you may not notice a thing. I'm sure there are additional reasons; these are the two that immediately come to mind based on my own flow cytometry experiments.


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How can a virus be determined to cause a disease?
How can a virus be determined to cause a disease?  From other posts I have read here, humans carry hundreds of different strains of viruses.  How is a study structured and carried out to determine that one virus is the cause of a disease, and not any of the other viruses present?  Any examples of studies are greatly appreciated as well.

A modified form of Koch's postulates is used to guide experiments that establish that a particular virus causes disease.
As a specific example of such a study, the SARS-CoV virus was determined to cause the SARS disease by fulfilling these criteria:

SARS virus is found in people suffering from SARS, and not found in those who are healthy.
The virus can be isolated from infected people and grown in cell cultures (here, Vero cells).
Viruses grown in culture can be reisolated and compared with (and found identical to) the suspected pathogenic virus.
This isolated virus can re-infect people (or infect model organisms; in this case, a species of macaques).
Virus in reinfected organisms can be isolated, grown in culture, and found identical to the original pathogen.
The immune system is observed to respond in similar ways to the infection (pneumonia and lung tissue lesions).

That's right, Koch's postulates have undergone adaptations over the years. Still, for some pathogens, the original postulates still succeed in proving causality. Above, I cited some more modern models, such as the Falkow criteria (which you cite as Koch's molecular postulates) and the Bradford Hill criteria; but they are all based on Koch's originals.

I'm going to submit an article, from 1996, written by Fredericks and Relman, which presented the most important updates to the original postulates:
Sequence-based identification of microbial pathogens: a reconsideration of Koch's postulates.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC172879/


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L strain of SARS-CoV-2?
Early in the epidemic, Chinese researchers (Jian Lu, et al,) reported in the National Science Review earlier this month that there was an aggressive more virulent L strain compared to the older S strain of the virus. Of the 103 viral genomes they scoured, 70% were of the L-type variant using phylodynamic analysis of samples taken during the earliest phase of the outbreak that began in Wuhan late last year.
But subsequent later samples taken later in the course of the epidemic were mostly of the S strain.
Peer review by researchers at other institutions have recently called this study into question.
Does anyone know where this stands currently? Has an aggressive L strain been confirmed? Do current rRT-PCR tests make any distinctions between L and S strains?

Are you referring to X Tang et al, On the origin and continuing evolution of SARS-CoV-2?

Related if not duplicate (given the comments there)  https://biology.stackexchange.com/questions/90892/where-can-i-find-the-genome-of-the-l-strain-coronavirus-and-the-s-strain-coronav?rq=1

As you may already be aware, there are some interesting comments on this paper on PubPeer.  The authors' response may be found here

One and a half year later we see that the L strain (corresponding to Pango lineage B and all of its descendants, and to all Nextstrain clades except 19B) was winning the evolutionary race, mostly because of the emergence of Pango lineage B.1/Nextstrain clade 20A with mutations ORF1b:P314L and S:D614G that had a decisive advantage over the other virus variants. The S strain is still extant in form of Pango lineage A/Nextstrain clade 19B and its descendants, but marginalised numerically.

S/L refers to the amino-acid at ORF8:84. Also this split is more interesting than it seems because this mutation ORF8:S84L plus the other one C8782T it comes with are found in bat viruses, so it is believed that the ORF8:S84L lineage (or A or 19B) is ancestral. The problem is that all the market samples were from the S84 lineage (or B or 19A).

@reuns Indeed the split is interesting, as there are no published sequences with just one of the two differentiating mutations, which suggests a double introduction to Wuhan city from a yet unknown source.

@reuns You probably got the news that now also the A or 19B clade can be traced to the seafood market, and even to the same area inside that market.

Yes, thank you, I'm following it closely


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What is the name of this insect? Is it venomous or possess any threat to human life if someone gets stung?
I found it in Northern part of India, on a mango tree. When I intended to move it away from home, it seems to bite like a snake with front part lifting like a king cobra.
This insect is 6-7 inches long, 1-2 inches wide, and appeared during summers.

That looks like some kind of lappet moth caterpillar. Although I am no expert in them, especially not species that would appear in India. But hopefully my answer gives you the right direction of research.
You can see some visually similar observations on iNaturalist:

https://www.inaturalist.org/observations/42382365
https://www.inaturalist.org/observations/40958993
https://www.inaturalist.org/observations/40137289


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What kind of sieve does one use to extract meiofauna?
Suppose I have a core of sediment, and I want to extract the meiofauna from it, in order to study these organisms. According to the sources I could find, this involves using a very fine (e.g. 45 μm) mesh that will filter out and retain the meiofauna (as they are larger than this e.g. 45 μm that I mentioned earlier, and so, will remain on the mesh).
I have found lots of information on the mesh size, how many μm it should be, etc., but barely anything else about what kind of sieve should be used.
So now, if I want to buy a sieve to use for extracting meiofauna, I don't know anything about what it should look like, except the mesh size. What should I care for besides that, if I want to buy one? Can I just buy any laboratory sieve provided the mesh is of correct size? Or do I need some special kind of sieve to conduct such study?


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Is studying chemical and physical properties of chemical substances that make up organisms really a task of molecular biology?
I have read in a high school textbook that (translated into English by myself): "Branch of science that concerns itself with studying chemical and physical properties of substances that make up organisms is molecular biology".
Is this statement accurate? From what I understand, molecular biology deals more with "biological processes at the molecular level", and so it would be biochemistry, or maybe even "standard" organic chemistry, that would study chemical and physical properties of such substances, not molecular biology.

If you look at the Google ngram for the term ‘Molecular Biology’ you will see that it first appears just before 1960, and it is relevant that the Journal of Molecular Biology was founded in 1959. It is not biochemistry — indeed the name was meant to indicate its difference from biochemistry, and I heard second-hand (so I cannot vouch for its truth) that Hans Krebs (Professor of Biochemistry at Oxford University at the time) referred to it as “biochemistry without a license”. What I can vouch for is that the contempt was mutual.
At the outset the term ‘molecular biology’ was used to combine two rather disparate areas of biological science that today we might refer to as Structural Biology and Molecular Genetics. The link between these was the work on the structure of DNA and proteins at this time,  and the molecular analysis of the genes that controlled the synthesis of proteins.
If you look at the definition in the short Wikipedia article, only Astbury — who worked on protein structure in Leeds — is quoted, but The Journal of Molecular Biology was initially almost the house journal of MRC Cambridge, the love-child of Crick and Perutz, as it were, with an emphasis on nucleic acid as well as protein structure, leading to the other side of the coin which was the genetic code, the lac operon and the study of bacteriophage.
Of course, terms change their meaning as science changes and what was once new and trendy becomes “yesterday’s girl”. It really doesn’t matter that much. Systems Biology anyone?

I seem to recall having written some of this previously, but I can't find where.


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Can anyone identify this spider? Found in Italy
My cousin found this spider at his place. He lives near Milan, Italy, in a small town. It's a humid region, around there the are a lot of fields but it is a 15 km from the city. It's still hot in these days. He told me that in the picture it seems a little bit too yellow. In reality it is more of an orange shade. He has never seen anything like that around there. Any clues?

Is there a spider somewhere on the second picture? I can't see it!

No, it's just to give a rough idea of the dimensions

Oh ok! You might want to just state something like about 6cm in diameter (legs included) or something.

@Gitana Yes please give a number, we don't know the size of your hand.

Judging by the photo and the web it may be an orb-weaver spider of the family Araneidae.  Orb-weaver spiders get their name from the circular webs they spin.  It's possibly an Araniella cucurbitina, also known as a Cucumber spider, which are commonly observed hanging head down in it's web.  Several photos can be found at eurospiders.com.

If I understand well, the Araniella cucurbitina seems smaller than my cousin's spider. I read that it measures at most 1 cm, whereas the spider he found is several centimetres long

@Gitana Is your cousin maybe exaggerating a bit for dramatic effect? The perspective of the picture might be a bit confusing but "several cm" might be closer to 2 cm, with the body about 1 cm.

It looks like marbled spider. Araneus marmoreus, commonly called the marbled orb-weaver, is a species of spider belonging to the family Araneidae. It is sometimes also called the pumpkin spider from the resemblance of the female's inflated abdomen to an orange pumpkin.[2] It has a Holarctic distribution.


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Tissue fluid water potential
just a quick question. Is the tissue fluid the same water potential as the cells it surrounds? I am a bit confused because if it was lower it would cause water to leave the cell and if it was higher water would enter the cell and both aren't really good for the cell. I believe tissue fluid is isotonic, am I correct?

Yes, cell membranes are highly permeable for water. While diffusion through the membrane is possible (description, and some science), it is most effective through water channel proteins (aquaporins). The different expression levels of aquaporins in different cell types result in differences in the permeability.
And yes, the tissue fluid has to be isotonic to the cell interior. The water balance in the body is therefore highly regulated. If not enough water is available, the blood osmolarity (ratio between solubles and water) increases. This is sensed in the hypothalamus (an area in the brain which is a major player in hormone regulation) and results in production of the hormone vasopressin. This will not only increase your thirst (and therefore add more water to the system) but also regulate aquaporin expression, improving reabsorbtion of water in the kidney (nicely shown here, actual science here). Urine production is of course also important in the response to drinking too much, which can be harmful as well..
If tonicity is deregulated, this has serious consequences for the body (some more science). For example, mutations in vasopressin or kindney aquaporins can result in very similar phenotypes, characterized by dehydration because water levels cannot be properly regulated (even more science).
edited for more explanation, because people complain when I give short answers to short questions ;)

Can you elaborate? It's (again) a 2-liner - such posts are often recognized by the bot as low-quality and face deletion. Please explain why membranes are permeable to water (they are hydrophobic! - aquaporines) and what the dangers are of tonicity dereg. Note that the first answer is not great, so it's great you are trying to add a better answer.

Hi, thank you Alice for saying exactly what I was about to. Why are the cell membranes permeable to water? Aren't they hydrophobic? Unless the water can only move in and out through aquaporins?

I have already added more explanations and resources after Alice' comment. Membranes are highly permeable because of aquaporins. Water can nevertheless also cross the lipid bilayer by itself. I am not a physicist and won't be able to explain the atomic forces, but there is a lot of water compared to lipids and the cell has a very large surface. That's why the chance of this interaction is high. https://youtu.be/ePGqRaQiBfc

Not necessarily-
cells are surrounded by a plasma membrane that creates a waterproof seal from their surroundings. This membrane contains embedded proteins, called transporters and channels, that enable the selective passage of water, ions, and solutes to maintain a membrane potential, or concentration difference between inside and outside. This enables cells to maintain homeostasis, despite changing external conditions.
You can learn more about these processes here:
https://en.wikipedia.org/wiki/Membrane_potential

But the membrane doesn't prevent water from moving through it right? So if the water potential was higher or lower water would still leave the cells right?

Yes that's true, most animal cells passively conduct water. Notable exceptions would be some epithelia- for instance cells in the kidney are able to concentrate urine. This means they must be able to establish osmotic gradients.

Sorry, this is wrong. The cell membrane is highly permeable for water. The membrane potential you are talking about is the electrical potential from the distribution of charged ions.


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Red Blood Cell Size Vs White Blood Cell Size
I have just found out that white blood cells are larger than red blood cells and now I'm confused due to something I learnt in class. Basically, I was taught that there were spaces between the endothelial cells lining the capillary and these spaces allow white blood cells to escape and enter infected tissues to help clear out the infection. Why don't the red blood cells escape then if they are smaller than white blood cells they should fit through the spaces as well right?

there are several types of white blood cells (at least 4) and they vary greatly in size from type to type.
white blood cells are not rigid, they can squeeze through very small openings. it always buts me in mind of watching a octopus squeeze into a bottle.

So are red blood cells rigid and thats why they can't go through the small spaces between the cells? Also what happens to the white blood cells once they get to the infection? Are they broken down or do they manage to enter the capillary again?

they are more rigid, but more specifically lack the mechanism that actually squeezes the cell through, it is not a passive process, the white blood cells is physically pushing itself through the gap similar to how an amoeba moves. The last question would be a great seperate question.

I should point out that RBC precursors do need to extravasate through bone marrow endothelium to end up in the blood to begin with, but if you look at reticulocyte morphology, for example, there's a big difference compared to a terminally differentiated RBC.

Thank you for your comment CKM but I have no clue what your talking about lol. Your too clever for me :) Can you explain what you said in an easier way please? If not it is okay but I'm only in my first year of biology yet and so I don't know much other than the basics.


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Why do we use different micropipette tips for different volumes?
Isn’t it easier to use a 1000 µl micropipette tip for all volumes? I don’t understand why there are different tips for smaller volumes. Does it affect the accuracy of the pipette for very small (<5µl) samples?

This question is about fluidics and principles of physics rather than that of biology.

The short answer is yes, the accuracy is affected.
Automatic pipettes are most accurate in the middle of their range. The average error on a pipettes is already about 2%, but this is worse at the top end or bottom end of the pipettes minimal and maximal volume.
More subtly, have you ever tried to pipette 1 uL with a 1 mL pipette? Or even 5 uL. The bore of the pipette is too wide for starters, and the expulsion force/pressure to eject the fluid wouldn’t work very well.
On top of that, the surface tension would seriously hamper any ability to actually manipulate the fluid.


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Genetics, sickle cell anemia
Sickle cell anemia is autosomal recessive. Then Why is it an example of codominant alleles? I thought a person with sickle cell trait is heterozygous because one of his/her alleles is recessive and the other one is dominant which is not codominant.

Whether alleles are "codominant" or "recessive" or "dominant" depends on the level at which you look at it.
If you look at it from the organismal "healthy vs sick" point of view, then sickle cell anaemia is "recessive" because the individual is only sick when they have both sickle cell alleles.
If you look at it from again the organismal point of view, but this time looking at the trait as well, then you find that (if we say "A" is the anaemic allele and "N" is the normal allele) AN has a different trait (called sickle cell trait) than NN, so you could say the alleles are codominant because both the A and the N "do something" in the heterozygote.
If you look at the molecular level, again you will find that sickle cell anaemia is codominant. The gene codes for the haemoglobin beta gene. So if you have AN, then one of your alleles will be coding for the defective haemoglobin, and the other will be coding for the normal one. So you would have 2 types of haemoglobin in your blood, which means that it is "codominant."


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Could deutrium oxide be used to make organic compounds with Deutrium instead of hydrogen?
I am wondering for prokaryotes if Deutrium Oxide could be made into Deutrium Glucose or other biological compounds with Deutrium.

Homework questions are off-topic on Biology unless you have shown your attempt at an answer. For more information see our homework policy. Moreover, this question is not really about biology.

I am sorry that this is not for biology but this is not homework. I am a Freshman in High School. I am currently learning about Meiosis and Genetics. If this is not biology then what would it be? It relates to living organisms, and it ain't physics.

We don't mean homework just in the literal sense. For any query that you have out of interest or as a result of your academic courses, you should make an attempt at finding out the answer yourself with whatever resources that you have and can understand. Did you try simply googling this query? Your query relates to isotope exchange which I would consider a chemistry question. If your query was more about whether organisms can survive and function properly with deuteriated biomolecules, then it may be considered a biological question.

Yes, this is possible and inter alia used to clarify biosynthetic pathways.
For example in this study. Rats were given deuterated water and the average number of D atoms incorporated in cholesterol and fatty acids was determined. Also deuterium was found in plasma glucose and liver lactate and pyruvate.


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Reasoning behind CO2 mouse euthanasia precharge prohibition
I have been at two universities now and the first permitted the precharging of a cage with co2 before a mouse is put in, but the second does not. I was wondering what the reasoning is behind the ban on precharging a cage with Co2.
When I think about this, it seems that it would be less stressful for the mice to fall unconscious very quickly rather than a slow and gradual suffocation. Is there some shock associated with the precharged cage that makes this more stressful in some way?

Upon some research, I have found more guidelines from universities attributing to NOT PRECHARGING the chamber with CO2. Precharging actually results in more distress for the rodents.

Quoting from guidelines to CARBON DIOXIDE EUTHANASIA OF RODENTS from University of Pennsylvania >>

Do not “pre‐fill” the euthanasia chamber with CO2.  Start with room air then slowly fill the chamber with CO2 over several minutes
  (OLAW).  CO2 is heavier than room air, thus the chamber may need to be
  “purged” between groups of cages.
“Because inspiration of high
  concentrations of CO2 is both aversive and painful, a recommended
  procedure is to place animals into a chamber that contains room air
  and then to gradually introduce CO2.” (ACLAM)
CO2 first renders the animal anesthetized and then, with adequate exposure time, will result in death by CO2 narcosis.  Animals should
  be left for additional time within the euthanasia chamber, after
  spontaneous movements have ceased, with CO2 continuing to flow.
“Animals should be left in the container until clinical death has been
  ensured.” (NIH)

Also, according to an article in The Scientist by Kerry Grens >>
It's been realized that at high concentrations, CO2 causes creatures torment. After reaching mucosal surfaces, it transforms into carbonic acid, which stings. Also, in people, even low fixations can be upsetting, bringing about shortness of breath.Therefore, explaining why high levels of CO2 is actually more painful for the rodents.

I know I'm not supposed to use comments for this, but +1 for a very well presented answer.

I have always understood that in all methods of "humanely" euthanising animals, the idea is not to kill them fast, but to first softly get them unconscious and then kill them in their "sleep", as whatever is killing them will usually cause distress in a lethal dose. But this is just from having to watch pets be put down as a child.

@anongoodnurse Thank you. It is nice to get into this community.

@skymningen True, on research, I found that sometimes when the rodents are unconscious, they are killed by a two part neck dislocation. I cant quite remember the steps correctly  now. There is actually research going on to minimize the distress with CO2 as much as possible and there are articles that talk about using anaesthesia instead.

@skymningen in my experience, cervical dislocation (CD) is the most rapid, humane, and cost-efficient method of euthanasia, of course when performed by well-trained researchers or staff. The way I learned it, you keep the mouse in its cage up to the very end, so it doesn't become stressed. You then remove the animal, and (very important) out of sight of any other animals, you place the mouse perpendicular to the wires on the top of an old-fashioned regular cage and grip its tail near the base until it reflexively grabs onto a wire. [...]

[...]  You then quickly place the blades of a closed pair of scissors behind its neck, press down firmly and very slightly forward to immobilize the head, and quickly and smoothly pull on the base of the tail until you feel the pop of the spine disconnecting from the base of the skull. From placing the animal on top of the wire to death should take no longer than 1-3 seconds at the very most. The mice pretty much have no idea what's happening, and they're gone in an instant. There's no worrying about measuring the flow of $CO_2$ or of the killing cage smelling like death or anything.

@MattDMo Cervical dislocation is what I meant. On what I was reading, there were also practices where they would make the mice unconscious with the CO2 and then perform the cervical dislocation. They say it is more easier when the mice are unconscious as they dont fiddle around. Isnt this more easier than having the mice alive while performing this technique?

@ImtiazRaqib knocking out the mice with $CO_2$ kind of defeats part of the purpose of CD, although in times when I've had to euthanize via $CO_2$ I've also done CD on the bodies just to make sure they're dead. Even if you do asphyxiation slowly (in my experience, at least), the mice still get panicked as they realize there's not enough air, but before they're knocked out. Maybe I was just adding the gas too quickly, I'm not sure. The reason I used CD in grad school was because I was in an immunology lab, and stress can activate the immune system, altering your data. Proper CD doesn't do that.

@MattDMo Cervical dislocation is actually prohibited at our institution as a primary means of euthanasia. In many cases a secondary method is required, and CD is permitted as a secondary method where I am. It does seem silly for CD to be used after CO2, but still can be required.

@TheNightman just curious, do you know why it is prohibited as a primary means?

@MattDMo I don't know why this is the case, maybe just to avoid instances where people perform it improperly?


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Prokaryotes Genome

What function of repetitive sequences of Prokaryote?
I see a gap (intergenic region) between 2 coding strand. But just only a single origin region in Prokaryotes. How it can transcription coding strands after the intergenic region?
I read documents say the genome of Prokaryote is small. So it needs to overlapping transcription in a chromosome. How its works with a single origin region?

A google search resulted in finding this site, which I believe explains a lot about the prokaryotic genome: https://courses.lumenlearning.com/boundless-microbiology/chapter/prokaryotic-genomes/

An additional resource for making sure you understand the basics of biology is Khan Academy. The reason I'm suggesting that site is because your questions reveal that you are confused about some the difference between transcription and replication. ——— Please also take the time to take the [tour] and then go through the help pages starting with [Ask] questions effectively on this site. Thanks!


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Swing bucket for PCR
I see a swing bucket rotor for PCR trips and don't know what step is using? What difference if I use fixed - angle? In addition, Which step I can use swing bucket instead fix - angle in molecular biology (Example: extraction, purification,..) to improve centrifugation efficiency?

For a PCR preparation, swing bucket or fixed angle does not make any differences. The only thing you want is that everything is soluble, in the same volume, and homogeneously mixed.
The main difference between swing bucket and fixed angle is how the pellet will be formed in the tube. Depending on the type of extraction or purification you are doing it would be advantageous to have a large pellet on the side (fixed angle) or at the bottom (swing bucket).
This article explains it in much more details if you are interested: https://handling-solutions.eppendorf.com/sample-handling/centrifugation/this-and-that/detailview/news/when-to-use-a-fixed-angle-rotor-or-a-swing-bucket-rotor/


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How many times did photosynthesis evolve?
Was it a 1 and done thing? Plants seem to have developed photosynthesis by the endosymbiosis of cyanobacteria. Is the latter the one time in Earth's history that the process independently came about?
Any answers would be greatly appreciated

see also some related questions: https://biology.stackexchange.com/questions/53336/evolution-of-plants-and-chloroplasts?r=SearchResults&s=3|25.0882 , https://biology.stackexchange.com/questions/36311/why-is-there-a-seeming-dichotomy-between-mobility-and-photosynthesis

Welcome to Biology.SE! Please take the [tour] and then go through the help pages starting with [Ask] questions effectively on this site and [edit] your question accordingly. In particular, we expect prior research and questions informed by what you have learned (with references to reliable sources). This wikipedia article seems like a good place to start. See also this sites criteria for "homework", which can apply to questions even if they are not assigned as homework. Thanks!

The emergence of photosynthesis has occurred rather independently in multiple organisms. One way of looking at this is to look at the taxonomic distribution of photosynthesis reaction centers, which points to 5-10 origins according to current data (mostly in bacteria). That number has some big error bars as we are talking about very deep, old branches of the tree of life.
There are other criteria that we could use- for example the evolution of carbon fixation. However, that includes also chemoautotrophy, and is thus a bit more expansive.
Note that by some definitions the acquisition of cyanobacteria in plants may not even represent an independent emergence of photosynthesis, as the cyanobacteria already did photosynthesis!
If your question is more narrowly "how many times did photosynthesis evolve in eukaryotes" (not bacteria or archaea), then you would also need to include animals that do photosynthesis in a way similar to (though I believe less efficiently than) plants. They seem to similarly use endocytosis to acquire photosynthetic machinery from photosynthetic cells that they eat.
Update
In response to comment from @shigeta, I'll add that the review that I link focuses on the reaction centers (RC) genes. They note that the RC genes probably had a single emergence, but that horizontal gene transfer is probably responsible for the current distribution of the organismal trait of photosynthesis:

Significant evidence indicates that the current distribution of photosynthesis in bacteria is the result of substantial amounts of horizontal gene transfer, which has shuffled the genetic information that codes for various parts of the photosynthetic apparatus, so that no one simple branching diagram can accurately represent the evolution of photosynthesis (Raymond et al., 2002).

Hey @maximilianPress a good citation but the conclusion at the bottom of the review is: "Current evidence suggests that the earliest photosynthetic organisms were anoxygenic, that all photosynthetic RCs have been derived from a single source, and that antenna systems and carbon fixation pathways have been invented multiple times."  you can see on their phylogenetic tree that the RC1 and RC2 appear on all these branches, which implies they came from the same ancestor, lost in time.

@shigeta a good point, which highlights the importance of whether you mean the emergence of photosynthesis (the organismal trait) or genes for the reaction centers. Indeed the RC genes are probably a single emergence, which were simply passed around by horizontal gene transfer. (Note that there is no ambiguity about eukaryotes independently evolving photosynthesis several times, through endosymbiosis!) The exact count of events comes down to a matter of how you like to parameterize your models. This exact issue is why I give a range of values. I'll edit answer.

... well in this case the structures of RC1 and RC2 and their ubiquity in photosynthesis suggest a single source, lost in time.  usually parallel evolution creates completely different protein structures for same function.  a classic example are 'crystallins' - several genes have filled in for crystallins - the protein families are quite divergent.

@shigeta the genes or proteins have a single origin. This is in the same way that e.g. Type III secretion system genes all have a single origin. However, this does not mean that Type III secretion-mediated pathogenicity has a single origin. Type III secretion systems get passed around on plasmids constantly, such that the parallel origins of this pathogenicity are certainly due to HGT. See e.g. the parallel evolution of Shigella from E. coli- Shigellas are polyphyletic in origin! Photosynthesis is like pathogenicity, only it evolves much less frequently. This is what the authors mean.

that is an excellent point @Max!  i'm going to make a supllementary answer to yours with some details.  i upvoted you tho!

Agree - you can't expect any more than this when you are looking at a ~ billion year old gene!

Im going to expand my comment into an answer because the discussion was just too interesting.
the conclusion at the bottom of the review cited is: "Current evidence suggests that the earliest photosynthetic organisms were anoxygenic, that all photosynthetic RCs have been derived from a single source, and that antenna systems and carbon fixation pathways have been invented multiple times." you can see on their phylogenetic tree that the RC1 and RC2 appear on all these branches, which implies they came from the same ancestor, lost in time.
@maximillianPress points out in his comment that lateral gene transfer is very common and this creates the exact pattern  Many gene functions can arise more than once, but when you look at the gene, if a protein is achieves a function, like RC1 and RC2 their shape and detailed sequence will not resemble each other.
A classic example is the evolution of the eye. Eyespots and photosensors with lenses have evolved many times in microbial evolution and in may have evolved separately in molluscs vs vertebrates depending on how you define it. Light detection is a microbial innovation and the opsin light sensors in animals bear a strong resemblance to those in archaebacteria.
Enzymes form a clearer example.  Studies of some of the carbohydrate metabolizing enzymes show that some specific roles are filled by multiple very divergent protein families.  The role of a protein may change over time but its very unusual for the way the protein folds to change.
An third example is the crystallins whose function is to form the lens of the eye which has to remain stable for a lifetime. In different animals these genes are radically different - distinctly different proteins can fulfill this role.  that is a gene role which may have evolved twice, but the role is fairly broad so its been filled by different proteins in different parts of the evolutionary tree more than once.
My thought is that the lateral transfer of microbial genes may confuse the evolutionary tree but the difficulty of creating a photoreaction center is much higher. There is only one bacterial reaction center protein family, so the predominance of evidence is that this phenomenon only evolved once and may have been transmitted by lateral gene transfer many times since.

I think that I agree with all this, happy that we've had a good discussion on this. With regard to the reconstruction of trees of life and the influence of HGT, a big distinction is the tree of genes vs. the tree of genomes vs. the tree of cells. Gene trees are noisy, genome trees have a central tendency but fuzzy, and the tree of cells has to exist but our only way of knowing it is the tree of genomes. For some of the (now older) work on this see https://science.sciencemag.org/content/311/5765/1283 and https://genomebiology.biomedcentral.com/articles/10.1186/gb-2006-7-10-118

i agree @MaximilianPress the good discussions are what we can all hope for in the best case!


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If plants "alternate generations" between sporophytes and gametophytes, why don't we say the same of humans?
I've been reading on Wikipedia about how plants alternate generations between a diploid sporophyte (usually the dominant part) and haploid gametophyte (in flowering plants, the pollen and ovule sacs).
Mammals also produce haploid gametes. But in mammals we don't describe the gametes as a separate generation that alternates with the dominant "sporoid." The gametes are just the organism's means of reproduction.
What is it about plant reproduction that warrants describing their gametes as a separate "generation" or "phase"?

Well, I do. But my biologist friends don't find it funny.

There's an old joke that a zygote is just a gamete's way of producing more gametes.

The big difference is that in humans, there is no mitosis in the haploid phase.
There are three terms that are important here:

Haplontic: Most of the life is spent in the haploid phase
Diplontic: Most of the life is spent in the diploid phase
Haplodiplontic (aka. diplohaplontic): About as much time is spent in the haploid phase than in the diploid phase

At the extreme, when there is absolutely no mitosis in one of the phase, then the organism is clearly not haplodiplontic. Haplodiplontic organisms have an alternation of generations.
Note that the term alternation of generations is also used for systems that are much more complex than haplodiplontie. Examples of such complex alternation of generation include many parasites such as the giant liver fluke

Hmm, I guess the follow-up question would be why plants benefit from haploid mitosis, while mammals do not? Is it merely divergent evolution, or is there some conditions that make it more useful for plants or v.v.?

This is a good question but one that is difficult to answer. I don't think a clear consensus has been reached on this question but there certainly are some research (there certainly are some theoretical models at least). I opened a new post (here) to ask this question and we will see if someone can come up with a nice answer

@JAD In addition to the hypothesis in Remi.b's linked question, you can check out one of our canonical answers here: https://biology.stackexchange.com/questions/35532/why-do-some-bad-traits-evolve-and-good-ones-dont which might also apply to some extent.


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White blood cells after dealing with an infection
I just have a quick question. If there was an infection of a tissue within the body, white blood cells would leave the capillaries around the tissue and enter the tissues to help cure the infection. How would these cells leave the tissue after that? Would the white blood cells be broken down or would they manage to find their way back into the capillary that they came from?

White blood cells, especially neutrophils, rapidly leave the blood and migrate in tissues toward infections (or other forms of stimulations). Many of them do die at the location of an infection, but they can also migrate back. The simplest route for this is to follow lymph flow. Lymphatic fluid is picked up by lymphatic vessels, which work in parallel to blood vessels, and from there can move back into blood. Just as an example of migration through lymphatics

Thus, we provide in vivo evidence that neutrophils, like DCs or inflammatory monocytes, migrate via afferent lymphatics to lymphoid tissue and can shuttle live microorganisms.

--Neutrophils rapidly migrate via lymphatics after Mycobacterium bovis BCG intradermal vaccination and shuttle live bacilli to the draining lymph nodes


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Blood pressure in the blood vessels
Why do the capillaries have a lower blood pressure than the arteries even though the capillaries lumen is much narrower. Wouldn't the narrowness of the blood vessel increase the pressure? Also the arterioles have an even larger lumen than the arteries so shouldn't the capillaries have a larger blood pressure than them as well?

Answer: You are right that if you had one big pipe that was getting progressively narrower, the pressure in that pipe would increase. In the vascular system, you have one big pipe emptying into exponentially more small pipes. The total lumenal diameter of the small pipes is actually greater than the single big pipe.
Even though each individual capillary has a smaller lumenal diameter than each artery, the sum lumenal diameter of all of the capillaries is much greater. This is because there are way more capillaries than there are arteries.
More detail: The following image plots total cross-sectional area and pressure in the pipe against the level of the circulatory system. The sum cross-sectional area of the vessels is highest in the capillaries, simply because there are so many capillaries. You can see the pressure decreases accordingly.


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Ciliated Epithelium & Goblet Cells Lining The Trachea
My book states this - The cells produce mucus that traps particles of dirt and bacteria in the air breathed in. The cilia on these cells move this debris up the trachea and into the stomach. Isn't the stomach below the trachea? Wouldn't it move the dirt and debris up the throat so it can be removed via the mouth? My book does also state that the debris is pushed up the throat as well so does it do both?

There are two pipes from your throat, downwards. A foodpipe and a windpipe. One, called the trachea, feeds air into the lungs, i.e. connects your head with your lungs. Another pipe, called the esophagus, leads to the stomach.
Both pipes meet and share the same passageway in your throat and oral/nasal cavities. Let's call this the common pipe.
The lining of the trachea, made up of ciliated cells and mucus-producing cells, does indeed move debris UP and OUT of the trachea, away from the lungs. Once this debris is at the common pipe, it can go to the stomach or into the mouth or into your nose for clearance.

Thank you for your answer and response. I understand what you mean :)


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Micelles Sticking Together
I have a quick question regarding micelles. I have tried googling the answer but can't seem to find the answer. The question is, during digestion lipids are emulsified into micelles in order to increase their surface area for digestion but my question is, why don't the micelles stick together and form a clump which would decrease it's surface area?
Thank you.

Micelles have a hydrophobic core and a polar, hydrophilic surface. This surface will preferentially associate with water molecules and become solvated, rather than sticking to lipids.
Negative charge on phospholipids at the micelle surface mediate electrostatic repulsion to other micelles, keeping them from sticking together.


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Can anyone help me identify what type of horns these are?
I picked these up at an estate sale a few years ago and now need to identify them for shipping purposes.
They are 29x18x10.5 inches in size.
A friend who works in antiques believes the are over 100 years old based on the wood they are attached to and thinks they belong to some kind of ram. That's all the information I have on them.
Any help would be appreciated.
Thank you.

almost certainly that of a goat (see here, here, and especially here)

Those look very much like "Catalina" goat horns. They're a popular trophy game to hunt, specifically for these sorts of displays. The goats themselves originate in Spain but are commonly found in the United States, now.


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Beta Sheets vs Alpha Helix - Strength
Is there a hard and fast rule of which one is stronger than the other, or does it depend on their context in a protein?

The mechanical stability of a protein (I am assuming by strength you mean mechanical stability) depends greatly on the general context and there is no clear connection between alpha helix or beta-sheet content and stability. For example fibroin, one of the main components of spider silk and one of the strongest proteins known, consists mainly of beta sheets while keratin another very stable structural protein (the stuff hair and fingernails are made of) consists of four alpha helices alternating with three beta turns is believed to get most of its strength from hydrophobic interactions within its alpha helices. Also, actin and myosin muscle fibers consist mainly of alpha helices. The list goes on and on with no clear pattern which secondary structure forms more stable proteins.


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Transfer of electrophoresis bands to MS
I have a lab question that is confusing me. Just to be clear this is a homework question but I've done some extensive research and can't find what seems to be a "good" answer.
The question is this:
List the steps in order that need to be taken between gel electrophoresis band excision and MS?
The only things I can think of are cleaning the salts out of the sample if salting out was used and removing any detergents that were used like SDS. The question seems to imply that there is a specific order or steps required leading me to think there is something I am missing. Any thoughts appreciated.

There are plenty of protocols available on line for Protein identification  by LC-MS from gel bands. Just google for it, also try searching for in-gel digestion.

You have to remove the salts, remove the dye, digest the protein, extract the digested peptides from the gel etc.
For details, see this protocol.


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Hydrophobic elution times in ionic exchange columns
What would the order of elution be of say Gly, Val, Leu?
My argument is that hydrophobic residues will try and get away from the resin and the more hydrophobic the residue is the faster it will elute. This seems to run contrary to the steric argument however, where larger residues would take longer to elute. Which argument is right?

What kind of column are you using?

Does it matter? Since all the pI's are the same?


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Does CoA always bind to organic molecules through a thiol bond?
Does CoA always bind to organic molecules through a thiol bond? Sometimes I see it written as SCoA in textbooks but sometimes it's just written as CoA, are those actually chemically different, or just laziness on the part of the author?

This is coenzyme A (CoA). As you can see, it has an -SH group at its end. So when it interacts with other reagents, it forms thiolesters. CoA is just shorter.

Your answer is correct. However, I would mention a third alternative that the questioner may encounter — the one I prefer myself. This is not to use SCoA, but HSCoA in equations. That way e.g. acetylCoA can be written as CH3CO-SCoA and the chemistry of the reaction is apparent.

@David CoA-S-Ac is a term  for acetyl CoA, that I have commonly encountered.

@WYSIWYG Fashions change. I distinctly remember writing CoASH, in fact, but that was many years ago. There may well be a rationale for the change/variation. Anyway readers may encounter different abbreviations for the same thing.

Okay, thanks for these hints. This may will diminish understanding issues.


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Are there any primary structure sequences that strongly suggest b-sheet or alpha helix?
Is there a particular sequence of amino acids that we know will take on a beta-sheet or an alpha helix or is it essentially random?

Yes, there are certain amino acid sequences that tend to form alpha-helices, and others that prefer to form beta-sheets. There is no perfect correspondence between sequence and structure, but there is a statistical relation where presence of certain amino acids in particular sequences makes one conformation or the other more likely. For example, alanine, glutamate, leucine and methionine tends to be present in alpha helices.
This topic has been studied for 50 years or so, and there are many methods available for predicting structural features from an amino acid sequence. See this list of available software, and this article about protein structure prediction in general.
See this table from another answer on this site which shows which individual amino acid prefers which secondary structure (higher value shows higher preference):


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Use of western blotting
I ran across this paper recently.
http://www.ncbi.nlm.nih.gov/pubmed/21151122
I am confused on their use of Western blotting. Their unmodified protein (no PTM group) has a band and their modified protein (succinylation of Lys) has no band, yet they use this as evidence of successful identification of the PTM. Can anyone see what they are doing here?

They are doing a peptide competition assay (see abcam protocol).
The antibody is incubated with a purified sample of the antigen and used in a normal Western-Blot of cell lysates. Any cross-reactivities of the antibody would still be visible as only the interaction with the epitope of interest is blocked. So all bands that disappear after such treatment are indicators for the substance that was used for blocking. A Western-Blot with non-blocked antibody is normally used for comparison.
In the experiment you mentioned, they vary the principle a bit, as they are comparing two blots - one blocked with a succinylated library, one with a non-succinylated one. As the band disappears after treatment with the succinylated library, they confirm that their antibody is specific against succinylated proteins - at least in these three cases.

So the the succinylated library blocks the binding of the antibody?

Right! And only the succinylated one, as the antibody does not recognise the Lys as such as you can see in the blocking with the non-succinylated library

Why do it in the negative this way? Why not have an antibody that recognizes SucLys and then show that it's positive for the PTM and negative for the unmodified?

Or do such antibodies not readily exist?

I think its just an experimental problem: They have three proteins that contain SucLys and they have those libraries as they are commercially available. For a comparison as you propose, they would need a SucLys and a Lys version of their protein that would have to be (reliably) created beforehand.

I see, that makes sense, but wouldn't you also need to test against all other PTMs here...or was that the point of the final part of your post...you can only prove that it isn't the other PTM if the band doesn't disappear? (So many negatives I get confused : ) )

You are right, they only show that the AB does not recognize unmodified peptides, but succinylated ones. There is no information on the reactivity towards other PTMs in this experiments. But it may be hard to show this, as you would need whole cell lysate without any SucLys.


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PDB id to protein environment ph
How can one find the information of a protein environment ph from its PDB id?
Can one assume the ph to be the same as its cellular location?

I know that ENSEMBL, PDB and the Human Atlas give known locations for many proteins at different levels of certainty, but such data is far from complete. Also experimental indication of a proteins localization does not prove the absence at other locations. Dependent on your scientific questions it might still be valid to theoretically look into specific scenarios of a proteins localization and to assume a certain pH of that sub-cellular context. SO to answer your question: Higher pH-resolution than the hypothesized cellular sub-localization is unrealistic, and the justification of the assumption of localization depends on your specific plan.

So can one assume that a protein https://www.uniprot.org/uniprot/O96693 located in the apicoplast will function at that ph (the one of the apicoplast)?

I am not saying that it is correct to make that assumption, but that high-resolution pH estimates seem unrealistic to me, as you clearly don't have enough information, as you wouldn't ask the question if you did. For me your assumption of taking the pH of the known compartment seems to be the least problematic one, out of all options. Only you can make that call in the end.


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Is there a database of plants chemical contents?
A database where given the name of plants, one can know the molecules it contains.

Let me know if this helps you. http://bidd.group/CMAUP/

The Biology.SE community has agreed that questions that show little or no prior research effort are off-topic on this site as are request for resources (these end up being opinion based). Please [edit] your question to ask as specific focused biological question and tell us where you've looked for answers, what you do know about the topic, and where exactly you still have questions. Under researched questions may be subject to down-voting and closure. Please see the [tour] and consult the [help] starting with [ask] for details.


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Photosynthetic Absorption Spectrum - Pigment vs. Absorption Spectrum
This is a very confusing question to me that came up while I was studying photosynthesis.
Halobacterium has a photosynthetic membrane that is colored purple. Its photosynthetic action spectrum is exactly complementary (opposite to) the action spectrum for green plants. What wavelengths of light do the Halobacterium photosynthetic pigments absorb?
A) red and yellow
B) blue, green, and red
C) green and yellow
D) red and green
E) blue and red
I don't understand how the answer to this is possibly "blue and red," since the pigment is purple (eliminates violet end of spectrum since purple is transmitted) and the question says the action spectrum (synonymous with the absorption spectrum) is complementary to that of green plants. Green plants absorb best in the blue and red ranges, so naturally I would think the answer is C, green and yellow. What am I missing? Am I confusing the color of the photosynthetic pigment with the absorption spectrum?
Thanks!

Halobacteria use bacteriorhodopsin in a photophosphorylation to synthesize ATP. Their bacteriorhodopsin pigment absorbs and uses the yellow green middle of the visible spectrum and reflects both ends, which would then be visible as purple, so you are correct, the answer to your question is C)


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Do all Viruses have the same RNA
Let's take the Influenzavirus as an example, and I have 5 of it. Would all 5 viruses have the same RNA with the same base order? Or would the RNA base order differ from eachother?

Different viruses have different viral genomes.  This is the case for different strains of flu, too.

A person infected with a strain of a pathogenic virus will have copies of that virus in their body.
Virus particle genomes could contain a number of substitution, insertion, and deletion mutations. The surface proteins on enveloped and non-enveloped virus copies could contain mutations. Most mutations are deleterious and those particles will not be infectious.
But the genome sequence of that virus will be largely identical, these mutations aside, and copies will be packaged so as to attempt to reinfect and reproduce.
Actual mutation rates depend on the virus type (RNA, DNA, single- or double-stranded, sense; see Figure 12.1 about the Baltimore classification of viruses), and how it uses reverse transcriptase, RNA, or DNA polymerase to make copies of its genome for use in expression (to make viral proteins) and reproduction (to make viral genomes).
For instance, RNA-dependent RNA polymerase has a lower fidelity rate — makes more copying mistakes — than DNA polymerase. Reverse transcriptase can also introduce mutations when turning the viral RNA genome into DNA, and vice versa. These processes can also introduce errors in expression of membranous or capsid proteins in enveloped and non-enveloped viruses.
The RNA virus family Orthomyxoviridae contains the strains of influenza that infect humans. These are enveloped, negative-sense, single-stranded RNA viruses. They use RNA polymerase to turn their genome into forward-stranded RNA molecules that can act as both mRNA (messenger RNA that is translated into viral proteins) and as a template (again, using RNA polymerase) for making copies of the influenza genome, itself.
Errors introduced at these two steps will result in copies that are different from the parent.

That's another way of querying the virus mutation rate. HIV has a 100,000 faster mutation rate than Herpes(HSV).

Then, the mutation rate is measured as the number of substitutions per nucleotide per generation, defined as a cell infection in viruses (μs/n/c)...
I think that means that every virus varies by about one base pair, which means that they are all different. most viruses that explode out of a cell are indentical except for 1/10,000th of their genome.

RNA viruses mutate 100 times more than DNA viruses.
Viruses with high mutation rates could be combated by the administration of mutagens. HIV develops drug resistance very fast (one day), that's why they have to use multiple drugs. Mutation rate evades the immune system and helps jump the species barrier.
ref: https://jvi.asm.org/content/84/19/9733
For lots of graphical illustrations of virus mutation, search images for "virus mutation rate".

AIDS is not a virus, but the disease caused by the HIV virus.

Ok, speaking a bit simply. corrected.


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Osmosis and hydrostatic pressure
I'm confused about the role of hydrostatic pressure compared to osmotic pressure.
Q1:If I have a U-tube with a membrane permeable only to water molecules and equal volumes of water on either side but only 1 side (side B) has NaCl, the osmotic pressure would cause water to move from side A to side B,correct ?
Q2.But then hydrostatic pressure would cause water to move back to side A.
So, the water would move from side A to side B until the effect caused by the hydrostatic pressure = effect caused by osmotic pressure ?
Q3. The last statement wouldn't be correct If I said that "water moves until the hydrostatic pressure=osmotic pressure" would it ?
and lastly, My friend said the water would move until the hydrostatic pressure on both sides was equal
Q4. If water is moving from side A to side B then the we have more water molecules at side B, how would side A ever reach the hydrostatic pressure at side B ?
Do I have a misunderstanding in the concept of hydrostatic pressure ? In this context, I understand that it is the pressure exerted by the water molecules on the selectively permeable membrane.
The more I google hydrostatic pressure the more lost I get because all sources seem to explain in terms of equations and physics and I'm only taking this for an introductory course in physiology.

Do the answers at https://biology.stackexchange.com/questions/89609/osmotic-pressure help you?

I understand everything thats written in that page, I think of osmotic pressure  as a vacuum too but I might have a misunderstanding in hydrostatic pressure and what equals what at equilibrium


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Identify this gray spider with distinctive white mark
I was out back in the garden tonight and found an extremely long strand of web running about 10 ft. At the end was a kind of spider I’ve never seen before. It’s about a .75-1 inch, fat body, with a distinctive white mark on its back. It was very docile while I took the pic. I’m in Austin, TX and this was night time. Any clues?

An Orb Weaver - I dont know what sort. Giant lichen?


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Is brachydactyly due to mutation?
I have this so called "clubbed thumbs"also known as brachydactyly.
It is of D-type.
I searched for it on internet and found that it is a dominant inherited disease.
But to my surprise,none of my family members have such thumbs.Not even  my great grandfather/mother had this type of thumbs.
If it is a dominant trait then why didn't it show in any other family person. Is it that I have had any mutation in my genes?

You are correct that brachydactyly is a dominantly inherited disorder and is usually caused by mutations in the BMPR1B gene.
However, not everyone who has the mutation, will have clubbed thumbs (the phenotype). This is due to a phenomenon known as penetrance and expressivity.
Penetrance essentially is an all-or-none phenomenon whereby certain individuals who have a mutation express the phenotype (in this case, clubbed thumbs) and some do not express it at all.
Expressivity is when individuals who have the mutation, will express the phenotype to varying extents. For example, only one thumb may be clubbed.
I hope this helped.


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What happens when the parietal cells of gut epithelium becomes partially non-functional?
The options are
a) The pancreatic enzymes will not work properly
b) The pH of the stomach will fall abruptly
c) Steapsin will be more effective
d) Proteins will not be adequately hydrolysed by pepsin into proteoses and peptones.
The answer is D because pro enzyme pepsinogen gets converted to active pepsin in presence of HCl.
But, Why can't the answer be B ? Because if HCl is not secreted by perital cells then obviously pH of the stomach is going to fall down ?

If you think you got the answer that you wanted then please accept it by clicking on the "tick" mark near the top left corner of the answer (below the vote buttons). If you think the answer was helpful then you can upvote it as well.

Parietal cells are responsible for acid secretion (HCl) in the stomach.
pH is inversely correlated to H+ concentration; the higher the H+ concentration, the lower the pH.
If the stomach's parietal cells become partially non-functional, there will be less acid secreted into the stomach (a lower H+), and the pH will rise.
Answer (b)

(b) The pH of the stomach will fall abruptly

is the opposite of what would be expected to occur.
The correct answer is d), for the reason you listed.

Proteins will not be adequately hydrolysed by pepsin into proteoses and peptones.

Regulation of Acid Secretion


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Is the number of nucleoli in a nucleus fixed?
A nucleus can have multiple nucleoli. But are there any constraints on the number of nucleoli in a nucleus?

Can cells of individuals of different species have a different number of nucleoli?
Can cells of different individuals of the same species have a different number of nucleoli?
Can cells of different types have a different number of nucleoli?
Can different cells of the same type have a different number of nucleoli?

I've found snippets of information implying the number of nucleoli is fixed per species, but none authoritative enough to stoke my doubts.

I'll directly go to your fourth question, as all of them can be answered with a yes. This rather old mouse paper already got to the point. Sadly, only the abstract is freely available. Briefly, the number can be variable in the smallest unit you are interested in, the cell type. From the abstract:

The distribution of the number of nucleoli in many diploid cells
exhibited a mode of two or three nucleoli per nucleus, and a range
from 1 to 6 nucleoli.

In the paper, there are histogram of different cell types of mouse and all of them seem to be variable in their number of nucleoli.

Exactly what I was looking for, thanks!


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What is the structure of heterochromatin?
A short article about euchromatin and heterochromatin mentions that the structure of heterochromatin usually depicted in images "has never been visualized in vivo, and its existence is questionable". Obviously, heterochromatin exists, since you can see it on photomicrographs, but what about its structure?
Is it true that the structure is not confirmed? Are there any other candidate structures?

It has never been visualized in vivo because the sample preparation steps involved in imaging at that level of magnification will kill the cells. Electron microscopy is very harsh; it must take place in a vacuum, and SEM involves coating the sample with ultra-thin layers of metals such as uranium.

@MattDMo - your comment sounds as an excellent answer - could you turn it into one? It's best not to answer in the comments, because it may deter others who are willing to write up a full answer from doing so.

@AliceD sure, I'll see what I can put together.


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How is the glycemic index computed from a blood sugar curve?
The definition of the glycemic index is often given as the area under curve (AUC) of their two-hour blood sugar response. However, it's essentially meant to be a measure of whether food causes a fast or slow rise in blood sugar level. Why is the two-hour AUC a good measure of the speed of the rise?
When ingesting the "same" amount of sugar, no matter the form, the AUC should be the same, right? The only explanation I can find is that the two-hour cutoff means some carbohydrates are metabolized beyond that cutoff, so their AUC and hence their GI is lower, is that what's happening?
The reason I'm a bit confused is that all of the images of blood sugar curves illustrating low & high GI seem to show two curves with the same AUC, both going to 0 before the two-hour cutoff.

First of all, yes, the cut-off at 2 hours will make most of the difference. But I think your question asks about what would happen without that 2h cut-off, e.g. measuring 10 hours instead.
In theory, the AUC of identical dosages of sugar can vary, dependent on the kinetics of how sugar is removed from the blood stream.
Mathematically, if sugar exponentially decayed in a first order rate, which seems true during the initial insulin spike, then the long-time AUC would be identical, independent of the digestion speed.
If we assumed that some aspects don't fully scale-up (less than first-order), e.g. alcohol is mostly metabolized in a 0 order reaction rate  [2], then even the long-term the AUC would be lower if digestion was slower.
However, reality is complicated. Looking at an example insulin and glucose day-curve [3], you can see, that lower insulin levels drastically reduce the glucose elimination (via uptake by cells). From this, it's not clear how long-term AUC would look like and one could actually speculate, that actually slowly digested food could have a higher long term AUC, given its glucose acts during smaller concentrations of insulin.


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What software do I need to read-write cas9? and .dna files?
I am still a complete beginner to crispr and I am still trying to learn what it is and how to actually use it. I now realise that you have to order the crispr components after you have actually designed them yourself in software that lets you design and alter the components.
Am I correct so far?
I am wondering if anyone could help me find which software I should use to design and or alter .dna files . Preferably free and open-source software. Are there any good tutorials for someone who wants to get more into crispr?

You have a long journey ahead. This guy spent about 4 years to learn what he is doing here.
He is using Snapgene software

Thank you! :) The site doesn´t allow me to upvote because I have a to low reputation but know that I am really thankful! :)

I use Snapgene for my work the interface is nice, but with the free version you can't edit files to insert/delete bases.


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What is these mushrooms in my indoor pot?
I am living in Japan and in summer, it's very hot and humid even inside my room.
Today, I've found two mushrooms in the pot of a plant.
What is this species? It's very surprising than within one day they grew like this.

Looks like Lepiota sp.

@RHA Please don't answer in comments.

@kmm It's not an answer but a suggestion.

Suggestion: If you leave them and the cap turns to black slime .they are comatus coprinis, shaggy mane.  Good to eat ( the next crop).

Note: regardless of the expertise of anyone here, do NOT try to eat anything you have identified by someone on the internet.

Thanks! Yes, I'm not gonna eat anything. It's maybe edible in the wood but inside in a pot I've put some unknown fertilizers.. don't wanna try haha

They do look a lot like a common mushroom called "shaggy mane" mushroom (Coprinus comatus). This may not be a correct identification though, so do not eat them.  They are widespread around the world, but usually grow outside.
Yes it is amazing how rapidly the fruiting body of many fungi can grow. I am providing an interesting Wikipedia link with more information. You can also search to find other images using Google images online.
https://en.wikipedia.org/wiki/Coprinus_comatus