text:
Where happens MHCII coordination to a self-peptide, and what happens if the bond would be irreversible?
MHC-II proteins are presenting antigens on the surface of cells with lysosomal activities where they eventually might get transported off by some T-cell receptor-anti-gens, as far as I understand (pls apologise and correct me if I am wrong). I would be interested in two questions regarding this specific immuno-cascade reaction.

It appears that in cases self-pepties are bound to the MHC-II proteins (say HLA-DP2) when they are at the surface already. Where do such self-peptides come from? Do they come from inside the endosomal active cell or could they also come from "outside" from where the T-cell comes?
What would happen if (for some reason)
a) the self-peptide binds "irreversibly" to the MHC-II?
b) the self peptide binds irreversibly to the MHC-II and at the same time is structurally significantly distorted (e.g. if there is something, like a heavy metal bound in-between the MHC-II and the self-peptide)?

(I apologise for the case I got some terminology wrong or some basic concepts, I am no specialist in bio-chemistry.)

It appears that in cases self-pepties are bound to the MHC-II proteins (say HLA-DP2) when they are at the surface already. Where do such self-peptides come from?

Class II MHC molecules are capable of presenting any peptide of appropriate length, regardless of where it came from. Contents in a phagolysosome will contain both self and non-self peptides.

Do they come from inside the endosomal active cell

Some do, yes. While many proteins are degraded by the proteosome, some are actively imported into a lysosome and degraded there. This is termed chaperone-mediated autophagy. Full organelles may also be brought into the lysosome through "regular" autophagy.

or could they also come from "outside" from where the T-cell comes?

This is the case as well. Any ingested material from the outside could contain cellular debris, protein agglutinations, or foreign organisms. Peptides from all of these sources can be presented at the cell surface.

What would happen if (for some reason) a) the self-peptide binds "irreversibly" to the MHC-II?

According to this study, MHC II molecules are recycled, and their turnover is carefully regulated. There is no need for the bound peptide to dissociate during antigen presentation, so likely problems would occur when MHC II turnover is disrupted.

the self peptide binds irreversibly to the MHC-II and at the same time is structurally significantly distorted (e.g. if there is something, like a heavy metal bound in-between the MHC-II and the self-peptide)?

If the MHC itself is structurally distorted, it will not be recognized by any other cells. Remember that, during T cell selection, the cells must be able to recognize the MHC itself with a low affinity. T cells which bind strongly to the MHC itself undergo death by negative selection, whereas those which do not recognize the MHC at all undergo death by neglect. As a significant structural change would result in either an excessive affinity, or no affinity, no T cells capable of recognizing the complex would be present.

Thank you very much, that answers all but the last part. What I meant was what would happen if the self-peptide is distorted by the complexation. As far as I understand, there is (must be) some regulation against developing an immuno-response against self-peptides. But the question would be what would most likely happen if the self peptide is so strongly distorted, that it is no longer recognisable as a self-peptide. Does this make sense? In case what would happen?

"Class II MHC molecules are capable of presenting any peptide of appropriate length"  Just to clarify this, MHC molecules are not capable of presenting any peptide, but rather present a subset of peptides that have the required sequence determinants that allow binding in the MHC groove. Often there are key 'anchor' residues in the peptide that bind to hydrophobic pockets on the floor of the MHC binding groove. You are right in saying that it doesn't matter where the peptide came from though.


text:
ID please.Small insect from Brazil

Photographed in south east Brazil in the Atlantic rainforest during October 2017

source: Stack Exchange

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sort: votes


text:
Plant vs animal protein digestibility?
The protein scoring methodologies ( https://en.wikipedia.org/wiki/Protein_Digestibility_Corrected_Amino_Acid_Score) rate plant proteins of a lower quality than animal proteins. Now I can understand the reasoning that proteins have a lesser quantity of essential amino acids (allegedly) making them "lower quality" in terms of protein; but I don't see why there should be a difference in digestibility between plant and animal proteins (I can give links but it's common knowledge that plant proteins are less digestible). What is the basis for this difference in digestibility ? Whatever the amino acid composition, I don't see how that would affect digestion of proteins. So why are plant proteins considered less digestible ?

Anti-nutritional factors or antinutrients (wikipedia has a page about this) https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/anti-nutritional-factor

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text:
What do different fermentation products have in common?
I met with the following question in my masters course:

What do different fermentation products have in common?

Thinking about this, I have difficulty in identifying the similarities between lactic acid and alcohol fermentation.

Although there is  no net oxidation or reduction in glycolysis, a constant supply of  NAD+ is (paradoxically) required in order for glycolysis to continue. Otherwise, the glyceraldyde-3-phosphate dehydrogenase reaction (GAPdh) could not generate 1,3-diphosphoglycerate.
So how is the NADH generated in the GAPdh reaction converted back to NAD+? Both alcohol and lactic acid fermentation regenerate NAD+ by reduction of the carbon skeleton that was oxidized in the GAPdh reaction, albeit at different 'points' in the glycolytic reaction sequence.
In alcohol fermentation, alcohol dehydrogenase acts as aldehyde reductase, reducing acetaldehyde to ethanol and NAD+.  In lactic acid fermentation, lactate dehydrogenase acts as a pyruvate reductase, reducing pyruvate to lactate and NAD+.
In both alcohol and lactic acid fermentation, there is no net oxidation or redution: glycolyis is the splitting of glucose.
Finally, we may note that the electron acceptor in both cases is 'internal'  Neither process requires an external electron acceptor such as oxygen.  The electrons removed from the carbon skeleton in the GAPdh reaction (generating NADH) are added back to the same carbon skeleton (but with different molecular arrangement) in both the ADH and LDH reactions.

Q1. What do different fermentation products have in common?
A1. They are generated in a reaction in which NADH is reoxidized to NAD+, allowing anaerobic oxidation (e.g. of glucose) to continue.
Q2. What are the similarities between lactic acid and alcohol fermentation?
A2. They both generate ATP ‘at the substrate level’ (i.e. directly in reactions, without using oxidative phosphorylation) in a sequence of reactions which involve oxidation by NADH. The end-product of the oxidation (here pyruvate) is of no further use for anaerobic generation of ATP and so it is unimportant what it is reduced to by NADH.

This is illustrated below (see also this question):

(As mentioned in the answer from @xusr, pyruvate is converted to acetaldehyde before the NADH step.)
There are other types of fermentation with different end-products — see e.g. the Wikipedia article on fermentation — but the general principle is the same.

I posted this answer, despite the late stage because I think the diagram really makes things clear, and the other answer doesn't mention ATP.

Having taught this topic at university level for many years I maintain that this is the correct answer to the question. It would be useful to others reading this if those who have down voted it explained why they thought it incorrect. This should not be difficult given the sharp focus of my answers to the two questions. Without such a discussion, how is the reader to know?

Would "all fermentations are basically methods to recycle reducing equivalents for glycolysis to continue without invoking external electron acceptors" be a good tl;dr here?

@Dunois — Apart from one thing that sounds excellent to me. However I’m not sure that there aren’t processes other than glycolysis that can be supported in this way. I’d need to check and get back to you.

That would be awesome.

@Dunois — The qualification I would make to your summary is to add in parentheses after glycolysis: "(or its less common variant, the Entner–Douderoff pathway)". If you are not familiar with this, check it out in Wikipedia. You'll see it differs in the hexose steps of anaerobic glucose catabolism, but is similar in the triose steps which generate ATP at the substrate level. Like glycolysis it needs to reoxidize NADH (or NADPH) to continue, and can do this by reducing pyruvate, i.e. the whole process is a fermentation.

Thank you for taking the time to research this. I've only heard of the Entner-Douderoff pathway in passing, thanks for the link. I think your qualification in parentheses completes and complements my statement nicely.


text:
Best fundamental books?
I’m looking for internationally applauded  textbooks on fundamental biology. Books that are a must for a pre-medicine student/high school advanced. Currently, I study Biology by Neil Campbell, Jane Reece(and team) and I really like it. What I’m looking for is 21st century pedagogy and a modern writing style(as opposed to a stiff, unfriendly writing style that reads like a fact presentation pamphlet); books so good you don’t need an amazing teacher(which I definitely do not have.) Thanks.
P.S.- If you have come across amazing books in branches of biology like say biochemistry or neuroscience or immunology, even those suggestions are welcome.
P.P.S- My question is distinct from the “Books for beginners” question asked by user31782 because: 1.cost is no bar 2.I am not a beginner in biology, I’m studying pre medicine; and 3.All the resources suggested in the answers, I already know about them/have used them.

How can one study pre-medicine (note the hyphen)? Or is this an example of the modern writing style you yearn for? And as for 21st century Pedagogy, sounds like a film company or a rock band. I would suggest that you explain yourself more clearly.

@David, a number of universities require a year of basic biology, biochemistry, calculus, biostatistics and psychology after high school for admission to medicine. That preparatory year is called pre-medicine (hyphen duly noted). Pedagogy means the method of teaching; both an apathetic school teacher and an ivy league professor know that DNA is transcribed into RNA and RNA is translated to protein, but their methods of presenting that to a student is what creates the difference. That’s where pedagogy comes in.

My criticism of your use of words is because the lack of precision makes your request unclear, so that all that happens is people express opinions about books they like or use, which is both off-topic here and does not answer your question. Pre-clinical medical courses differ throughout the world and within countries (and in some ‘21st centurary pedagogy’ has replaced them completely by ‘problem-based learning’ — although this is clearly not what you mean by the term). The problem is that the adjective you use describe your emotions towards the books, rather than the books themselves.

To clarify further: What do you find ‘amazing”? (Do you really mean this or just good?) How is a book ‘unfriendly’? (Author frowning in photo?) What do you consider a ‘modern writing style’?  And when you have ceased to be a beginner, biology is not a single subject. Do you want to understand one branch at a less superficial (more chemical and mathematical) level, read something in which the science is related to medicine, or be inspired to do something about the apalling maternity mortality statistics in the US? Or do you, like most students, just want a book to pass an exam? Tell us.

For fundamental mammalian cell biology, and molecular biology, and fundamental biochemistry: "The Molecular Biology of the Cell" by Bruce Alberts and colleagues.
It is mostly written for first semester students at university and thus summarizes the basics in a very clear way. Moreover they state whenever findings have some ambiguity, and they use many nicely drawn pictures to convey abstract concepts.  Despite its approachability it covers most fundamental topics of many domains (also diseases).
While the ~2,000 pages of the complete edition might seem a bit intimidating they rarely provide unnecessary detail, and the individual chapters are written in a very concise way (even allowing you to skip some of them).

Best textbook is no textbook. Don't read textbooks. Textbooks are overpriced reviews.
Do a literature search like a scientist. Create a list of keywords from the books you already have. Search PubMed for review papers containing the keywords in the titles or abstracts and read:

titles;
sentences containing the keywords;
entire abstracts;
skim through the papers (look for pictures).

If you collect all papers for each keyword, thousands in some cases, you can learn a lot by reading just the titles. Some programming skills will be useful.

https://www.ncbi.nlm.nih.gov/pubmed

Biology by Brooker (and now additional authors Widmaier, Graham, and Stiling) 4th edition is one which I used, and I quite liked it. Great presentation of information, in my opinion.
Textbook of Medical Physiology by Guyton and Hall, though not friendly, is a decent book.
I mostly have recommendations in the field of biopsychology, etc.
Neuroscience: Exploring the Brain by Bear, Connors, Paradiso (2016 ver) is colourful, inviting and VERY friendly! Great for high school advanced or pre-med, though I suppose if you want more details in neuroscience, you'll need something like Kandel.

Have you ever had a chance to compare Neuroscience by Bear, Connors and Paradiso and Neuroscience by Purves, Augustine and Fritzpatrick? Are they the same level or one is more in-depth than the other?

Both seem to be on more or less on the same level. Presentation of the matter is better in B,C,P. Neuronal signalling is really good in P,A,Z, as in, it goes pretty in-depth. If you're a high-school student, I'd recommend B,C,P as your text book and P,A,Z as a reference book because B,C,P teaches better and that is what you want.

I really like The Molecules of Life: Physical and Chemical Principles from John Kuriyan. It does a good job of introducing basic to intermediate principles in biochemistry. In particular it is a great introduction to protein biochemistry and pharmacology.

I just got the book last month, I find it very helpful. Thank you.

My pleasure. Good luck!


text:
An introduction to nuclei in the pons?
I have a couple of questions regarding the nuclei in the pons, thus I figured it would be best to frame the main question in the way that I did.
My main question, however, is whether the basal pontine nuclei is part of the "cranial nerve nuclei" in the pons or is a separate pontine entity.
Quoting Kandel's Principles of Neural Science (2013),

The ventral portion of the pons contains the pontine nuclei, groups of neurons that relay information about movement and sensation from the cerebral cortex to the cerebellum.

Quoting Carlson's Physiology of Behavior (2013),

The pons contains, in its core, a portion of the reticular formation, including some nuclei that appear to be important in sleep and arousal. It also contains a large nucleus that relays information from the cerebral cortex to the cerebellum.

And while Wikipedia might not be the best source of information all the time, I must quote a few relevant portions which is causing me confusion,

A number of cranial nerve nuclei are present in the pons:
mid-pons: the 'chief' or 'pontine' nucleus of the trigeminal nerve sensory nucleus (V)
mid-pons: the motor nucleus for the trigeminal nerve (V)
lower down in the pons: abducens nucleus (VI)
lower down in the pons: facial nerve nucleus (VII)
lower down in the pons: vestibulocochlear nuclei (vestibular nuclei and cochlear nuclei) (VIII)

I now have broken information about these different kinds of nuclei but I do not know whether the basal pontine nuclei is a part of the cranial nerve nuclei or not.


text:
What determines sex in birds?
Is there production of TDF in birds? If so which gene produces it?

Sex Determination System
Birds have a ZW sex determination system meaning that males are the homogametic sex. Or yet, in other words, males have two Z chromosomes while females have one Z and one W chromosome. You might want to have a look at Do males of all sexual species have Y chromosomes? for a short review of the diversity of sex determination system.
Dosage compensation
In birds dosage compensation exist but appear quite different than in mammals (Mank and Ellegren, 2009; Mank et al., 2011; Uebening et al., 2015; Naurin et al. 2009)
Sex determining locus
The DMRT1 gene on the Z chromosome appears to be important for male sex determination by affecting the testicular marker, SOX9 however it might not be the whole story (Smith et al. 2009). It is possible that several loci are involved in determining sex in birds.


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What's the relation between Kinase, Phosphatase and ATPase, GTPase (GTP/ATP)?
I'm wondering what's the relationship between Kinase, Phosphatase, ATPase (ATP) and GTPase (GTP).
For example, when reading online the impression is created that ATPase is a type of Kinase (?). But I can't find any explicit information about it.

Related, with good answers: https://biology.stackexchange.com/questions/23589/what-is-the-difference-between-a-phosphotransferase-a-phosphatase-a-phosphoryl

Please do some homework before asking basic questions of this sort.

Enzyme names usually refer to the substrate of the enzyme, i.e. the molecule or chemical group that the enzyme targets and then removes or modifies.
Kinases are enzymes that add phosphate groups, usually to other proteins. One of the older enzyme classes that have a more "creative" name. Phosphatases remove phosphate groups.
In signalling pathways, kinases often transduce signals and phosphatases shut them down when their job is finished.
ATPases and GTPases target ATP and GTP respectively and catalyse the removal of one phosphate group by hydrolysis, the product being ADP or GDP. This makes them a type of phosphatase.
Many proteins are ATP/GTPases but have different names because there's a more significant function to name them after. Usually the ATP/GTPase function serves to deliver energy for the main function. Your impression might be caused by an enzyme which is both a kinase and an ATPase because it transfers phosphate groups from ATP to a target protein.
Enzymes that target ADP/GDP and add another phosphate group are called ATP/GTP synthases (rather than kinases).


text:
Viability of argon-oxygen atmosphere
Can humans breathe an Argon-Oxygen atmosphere, where Argon substitutes the inert Nitrogen gas which currently populates our atmosphere? I didn't quite know which forum to stick this one in; I put it here because I only want to know if such a mixture of gases can be feasibly inhaled, without the prospect of early death by some physiological component.

One may think that Argon, being an inert noble gas, causes no harm at all and can perfectly replace N2 in a mix with oxygen. After all, you've been breathing Argon your whole life, since approximately 1% of the air is Argon:

However, we are talking about a raise from 1% to 78%... and there are possible consequences here:

Argon is way denser than N2: Argon has a density of 1.784 g/L, while N2 has a density of 1.251 g/L (O2 has a density of 1.428 g/l). So, Argon is 40% denser than N2 (and also denser than O2 and denser than air). Without taking into account ventilation and other forces, there is a risk of argon not mixing properly with the incoming "air" in your lungs.
Argon is a narcotic: This may sound strange, but there are evidences that Argon has sedative properties. According to Nowrangi, Tang and Zhang (2014):

Argon gas is considered a small noble gas element that has been applied in a number of fields. It has been generally classified as a
  nonreactive or inert gas providing a view that it does not contain
  any biologically active characteristics. In fact, argon has
  demonstrated characteristics such as narcosis [...] The mechanism in which argon displays its anesthetic ability has been suggested to be from the stimulation of γ-aminobutyric acid type-A receptors. (emphases mine)

As an additional information, there is an Argon-Oxygen mix, called Argox, which is used for decompression research only, not as a scuba-diving breathing mix.
Also, this question from WorldBuilding has some interesting information (and some wrong information as well).
In conclusion: this Argon-Oxygen mix is not harmless.

Source: Nowrangi, D., Tang, J. and Zhang, J. (2014). Argon gas: a potential neuroprotectant and promising medical therapy. Medical Gas Research, 4(1), p.3.


text:
Do microorganisms contain water?
This may sound a bit strange question, but I am very new to biology. I would like to ask that do microorganisms like viruses, bacteria, amoebas, etc also contain water, as every living thing contains water?

The short answer, is yes, pretty much!
Do microorganisms contain water?*
Bacteria and eukaryotic microorganism
Bacteria and eukaryotic microorganisms (including amoebas) have a membrane that separates the interior from the exterior. And yes, they have water inside, in which all chemical reactions take place.
Viruses
Viruses, on the other hand, do not really have a membrane that separates the interior from the exterior. They are really just a bunch of proteins stuck together. As such, it is hard to tell whether you would consider the water in which those proteins float part of the organism or not.
Note however, that some viruses have a viral envelope (that can be derived from a host cell membrane). In such viruses, there is more clearly an interior and an exterior, and yes, there is water in the interior too! However, there is (except very few exceptions) no metabolism inside this envelope. This, by the way, is part of the reason viruses are not considered alive.
Dehydrated living things
Note that some organisms can survive with very little water. Some seeds can survive extremely strong dehydration. For example, some tardigrades can survive with less than 1% water in their body (see this New York Times article).

I think this answer is currently wrong Remi. Amoebas have endoplasm inside them. There is water in endoplasm and biochemical reactions require the presence of water but they take place in endoplasm. The same holds for other microorganisms. To me a strict interpretation of the question Are microorganisms made of water? is No, only water is made of water.

Yes, of course. I added the sentence "Of course, no living thing is made of 100% water. I will rather consider the question as meaning Do microorganisms contain water?" to clarify this point. Is it better?

@Michael_A you are technically correct... however, when you see that "also" at OP's question, you realize that they are simply talking about water as a constituent, as in the other organisms (presumably the visible, non-microscopic ones).

@Remi.b Just edit OP's question title, since it's clear that OP made a small mistake. +1. Oh, and remove that "mini-micro" stuff.

@GerardoFurtado Following your advice...

@Remi.b, Yes, that's good. I liked the original answer.

"Are viruses organisms?" and "Are viruses alive?"---André Michel Lwoff shared his opinions in "The Concept of Virus" (J Gen Microbiol, 1957):
:http://mic.microbiologyresearch.org/content/journal/micro/10.1099/00221287-17-2-239

I am the guy who asked this question. When I said "made of water", what I actually meant was "every living thing constitutes water". Since there is a general consensus among scientists that every living thing has water, so essentially it cannot survive without water or it would need water at some point in its life. As far as viruses are concerned, Remi pointed out that viruses have proteins. So are these proteins also constituted of water (or any liquid)? What about capsids of virus? Do these capsids also contain water (or any liquid)? What about viroids? Kindly answer.

No, a protein is not made of water. A protein is a large molecule. It is not a complex cell structure made of several different molecules. You might want to take an intro course to biology and biochemistry.

What about capsids of viruses? What about other microorganisms like viroids? Are these viroids even considered alive, as many argue they are not.

@Ren this is an entirely different question. Please open a new post for a new question. This question has already been asked though. Have a look at Why isn't a virus “alive”?

Thanks. But could please kindly clarify that does capsids of virus contain water? Please pardon my lack of knowledge. Thanks.

I am not a virologist but I don't think there is any difference between a capsid and an envelope. As I said, in the answer, yes, there is water in an envelope (and in a capsid).

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text:
E. Coli metabolization of paracetamol
For my science fair project, I did an experiment on how paracetamol and ibuprofen affected the growth of bacteria. By day 5, however, parts of the paracetamol blackened (image below). I am wondering if E. Coli can metabolize paracetamol and if so, what operon in the K-12 genome is responsible for this.

EDIT: I realized it may be metabolizing other ingredients in the medicine I used. I am including a list of the ingredients in the medicine I used.
Acetaminophen 160 mg in each 5 mL (duh)
Other ingredients (33.015873 mL):

Anhydrous citric acid
FD&C red no. 40
glycerin
high fructose corn syrup
microcrystalline cellulose and carboxymethylcellulose sodium
purified water
sodium benzoate
sorbitol solution
sucralose
xanthan gum

I thought it might be the fructose, but is the byproduct really black? Still confused...

I thin, you are using blood agar plates, isn't it? In this case, it could also be the heme which can cause the black colour.

No, the medicine I used colored the agar red. I used regular agar.

Is it possible the dye changes colour as the pH decreases?

Sorry that my answer is not a real answer, but this would be a good starting point for some more science.
Several of the questions you might ask and could answer (with some more experiments):

Does this happen in plates without E.coli?
You have a contamination on the right side, perhaps also on the black part. Could this be the culprit? Only half the plate is black, the rest is (still?) red.
You used a paracetamol tablet with red dye and a lot of sweeteners, does the same thing happen if you use one without the red dye? A dye would be a likely source, because it already contains an absorbing moiety. It only needs to be slightly modified to absorb different wavelengths.
What kind of agar are you using exactly? There are many kinds, often selecting for certain types of micro-organisms, with indicators for pH or other colored markers to detect and identify strains.

For your metabolic question you can take a look at https://ecocyc.org/ where you can find a database with all known metabolic pathways for E.coli K12. Unfortunately I couldn't find anything for paracetamol (or synonyms) but you could try to see if it produces a colored product for any of the additives.


text:
How to search NCBI in bulk for a list of accession numbers?
I have a large ( >100 ) list of accession numbers I want to look up and match to searches in NCBI (nucleotide); mainly for getting a tentative organism to match to the accession number.
ex:
KJ841938.1 would match to  Setoptus koraiensis
...
FJ911852.1 would match to  Uncultured eukaryote
...

I googled for tools, and I found this site. However, it is not what I really want since it doesn't list my queries in the same order as my list, which means I cannot match.
I also attempted to write a script in biopython using Entrez E-tools, but was unsuccessful due to a lack of coding skill.
Does anyone have any way I can go about this?
EDIT:
Via this tutorial,
I attempted to use this code sample:
from Bio import Entrez
Entrez.email = "Your.Name.Here@example.org"
handle = Entrez.efetch(db="nucleotide", id="AY851612", rettype="gb", retmode="text")
print(handle.readline().strip())
# expected output : LOCUS       AY851612                 892 bp    DNA     linear   PLN 10-APR-2007
handle.close()

But modified to take any list instead of the variable id, as below:
import Bio
print (Bio.__version__)
from Bio import Entrez
import time

Entrez.email = "Your.Name.Here@example.org"
id_list = ["KJ841938.1", "FJ911852.1"] # real list is about 500 elements

x = 0
while  x < len(id_list):
    handle = Entrez.efetch(db="nucleotide", id=id_list[x], rettype= "uilist", retmode="text")
    #print(handle.readline().strip())
    print(handle.readline())
    handle.close()
    x = x + 1

Output is:
1.69
673539906

283462561

However, I do not believe I am using the right "rettype" parameter in the .efetch function as I keep on getting GI numbers, where as I was hoping to get something like a species name directly. Unless I can then search with these GI numbers in batch with more code or a tool to produce a ordered list?

Can you post the BioPython code that you have tried and that didn't work? What specific error did you got? Have you modified the sample code from the tutorial?

Also, Accession number KJ841938.1 matches Setoptus koraiensis, not Gaeolaelaps aculeifer. So please update your question with correct sample input and expected results.

@BioGeek        I didnt know about that specific tutorial. I will try the example under "efetch" and see if it works. Thanks.

In your first attempt, when you use handle.readline(), you get only the first line from the genbank-formatted record. To get a list of all lines, you could use handle.readlines(). You might have gotten somewhere by this approach, but it appears that Biopython provides a way to parse the results more conveniently (see my answer).

After some trial and error in an interactive python shell and some documentation checking, I found that the relevant information is present in the genbank-formatted output (rettype="gb"), and this can be parsed using Entrez.read provided it is returned in "xml" mode (retmode="xml").
The following code that seems to work:
#!/usr/bin/env python3

from Bio import Entrez

Entrez.email = "Your.Name.Here@example.org"
id_list = ["KJ841938.1", "FJ911852.1"] # real list is about 500 elements

for accession in id_list:
    handle = Entrez.efetch(
        db="nucleotide", id=accession, rettype="gb", retmode="xml")
    gb_record = Entrez.read(handle)
    handle.close()
    organism = gb_record[0]['GBSeq_organism']
    print("{}\t{}".format(accession, organism))

(You don't need a while loop here, by the way: python has the more convenient forsyntax to loop over the elements of a list.)
Output:
KJ841938.1  Setoptus koraiensis
FJ911852.1  Gaeolaelaps aculeifer

If you don't want to bother with BioPython, you can use Entrez Direct for this as follows:
$ cat temp.txt
KJ841938.1
FJ911852.1
$ epost -db nuccore -input temp.txt \
    | esummary \
    | xtract -pattern DocumentSummary -element AccessionVersion,Organism
KJ841938.1  Setoptus koraiensis
FJ911852.1  Gaeolaelaps aculeifer


text:
What percent am I?
*If my Great Great Great Great Grandma was one hundred percent Hispanic what percent am I? I'm unsure of what percentage in this ethnicity I would be.

You need to include information about all 64 of them before one can answer. If for example the other 63 are each 0%, it needs to be included in your question.

That depends on which genes are passed on with each generation, all we can assess from the given information is most likely average estimated percentage of your ancestors DNA you carry assuming no other sources, which would be 0.5 raised to the 6th power. however these assumptions are rarely true.

Interpretation of the question
How do you define "being xth percent hispanic"? In a simple conversation, when people say that they are 25% hispanic (or any other etnic group of course), they just mean that they have one grand parent that was born in a clearly hispanic community/country and that all the others were born from completely unrelated etnical background.
Answer
You would be $\frac{1}{2^6} = \frac{1}{64}$ hispanic.

OP did not mention anything about the other 63, could be a trick question! :-)

@uhoh I think I made clear that I was making this assumption in my answer.

25% could be one grandparent... or two great-grandparents, or four great-great-grandparents...

@Remi.b what's that 0.01?

one percent as the OP indicated

one hundred percent.


text:
How to Calculate how many times an enzyme would cut a plasmid
I'm a little confused as to how to figure out the formula needed to figure this out.
I have a plasmid that is 7.3Kb and am told that it is cut with an enzyme of 4bp. For some reason I thought that the formula needed to figure this out is:
(1/4)^4 x 7300
But it gives me such a low number that I don't think it's right so I'm just a little confused.

Do not work from formulae people give you. Work from logic. You will find it here, among other places.

There are $4^4$ 4-cutters, which means that given a 4 cutter, you expect it to cut once every 256 bases on average. $7300/256 = 28.5$, so you expect 28 or 29 cut sites in the plasmid. This is identical to what you calculated.


text:
Has network theory been successfully applied to protein expression within a cell?
I saw the following passage in the NPR 13.7 Cosmos & Culture commentary post The Big Idea Behind Big Data.

Using the Internet's first generation of Big Data, researchers like physicist Albert-László Barabási of Northeastern discovered hubs controlling the behavior of all large networks from protein regulation to webpages.
"Nature evolved the metabolic network for cells over 4 billion years," says Barabasi, "but that same architecture emerged in the World Wide Web after just a decade."
Different networks, same laws.

In a complex multicellular organism there is plenty of signaling between cells types and organs, and this can be viewed as a network.
But does network theory also apply to protein regulation within a cell? I should really ask; Has network theory been successfully applied to protein expression within a cell?
I ask this because it seems according to this clickable timeline template that 4 billion years ago, life was single-celled.
edit: There is a single link in the Wikipedia article that points to this paper, but the abstract is over my head, and I'm not sure if this is a one-off attempt, or if network theory is an established method that has useful success in explaining/understanding/predicting protein expression within cells.

Yes, the tools of network theory can be used to analyze protein regulation, etc., within a cell. Lots of work on this, so this isn't an answer, just a pointer in one direction. One approach is to look at protein-protein interactions, etc, and see whether certain "motifs" in the network are more likely to occur in biology than randomly. An intro to some related ideas: Uri Alon, Nature Reviews Genetics 2007: http://www.weizmann.ac.il/mcb/UriAlon/sites/mcb.UriAlon/files/network_motifs_nature_genetics_review.pdf

@AJK OK that review is a great start! I'll give it a read, thanks.

https://biology.stackexchange.com/questions/92318/where-are-there-analyzable-signed-directed-network-datasets


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Why does excess dopamine activity in the pleasure centers results in less pleasure in schizophrenics?
According to the dopamine hypothesis of schizophrenia, there is an excess of dopamine in the mesolimbic pathway (nucleus accumbens), and this contributes to the positive symptoms of schizophrenia.
I am not sure what the cause of anhedonia (reduced interest), one of the negative symptom of schizophrenia. If nucleus accumbens plays a role in the reward system and there is an excess of dopamine, isn't it the case that there should be an increase in interest, that is, no anhedonia?

Welcome. Nice question! I edited the title to make a question out of it. Feel free to roll that edit back.

Hi @AliceD, thanks for the reply and great reference on Milan et al (2014). Sure, I am okay with the new title. Just to double check if I understand it correctly: it seems to be the case that we can not look at it only from nucleus accumbens point of view (as the author of the paper states, "amotivation and anticipatory anhedonia of NS ... in terms of defective cortico-striatal integrated processes indispensable for reward acquisition and anticipatory pleasure").

Yes, it's a lot more complex than DA + n.accumbens alone

Short answer
The dopamine hypothesis includes brain regions with reduced dopamine transmission as well. The prefrontal cortex in specific has reduced dopaminergic activity and is implicated in anhedonia. It affects pleasure seeking behavior through interactions with the nucleus accumbens.
Background
The negative symptoms of schizophrenia are less well understood as the positive counterparts. One thing is for sure, the dopamine hypothesis cannot explain everything. It is a very useful working hypothesis, but primarily based on the first generation antipsychotics such as haloperidol with mainly dopaminergic mechanisms of action. In turn, these drugs mainly and effectively target the positive symptomatology (excessive dopaminergic transmission).
Second-generation antipsychotics are more effective in treating the negative symptoms and are thought to actually increase cortical dopamine, as well as and acetylcholine release, as well as have a variety of effects on the glutamatergic system not shared by the typical agents first-generation antipsychotics (Meltzer, 2004).
In fact, the dopamine hypothesis has been improved and adjusted during decades of intensive research. One of the important things that has come out of this is that dopamine neurotransmission is regionally affected, with a prefrontal hypodopaminergia (prefrontal cortex, or PFC and a subcortical hyperdopaminergia (e.g. in the pleasure centers). An excellent review of the historic developments in the dopamine hypothesis was published by Howes & Kapur (2009)
Now on to anhedonia. Pleasure perception per se seems largely unaffected in schizophrenic people, it is the anticipation of pleasure that seems negatively affected. This is accompanied by reduced motivation and goal-directed actions to seek pleasure. Anhedonia is primarily attributed to disturbed interactions between the ventral (nucleus accumbens) and dorsal striatum (mainly the caudate) and the PFC and not so much in the experience of pleasure per se. In addition, insular cortex, amgydala and hippocampus may be involved. A dysfunctional coupling between the anterior cingulate and the insular cortex (the “salience network”) has also been linked to the failure to appropriately process reward in schizophrenia. Lastly, goal-directed actions needed to obtain the reward and dependent on the PFC is dependent on not only dopaminergic, but also adrenergic and other mechanisms. This is all nutshelled information and I would encourage you to read Milan et al. (2014), who have written an extensive and excellent review focusing on anhedonia in specific as a negative symptom. Fig. 1 is obtained from that paper and shows the complexity of anhedonia.

Fig. 1.  Cerebral circuits involved in negative symptoms, with a focus on deficits in anticipatory reward. source: Milan et al. (2014)
Reference
- Hows & Kapur, Schizophr Bull (2009); 35(3): 549–62
- Meltzer, Curr Opin Pharmacol (2004); 4(1): 53-7
- Milan et al., Eur Neuropsychopharmacol (2014)24(5): 645-92


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Terrestrial locomotion of bats and pterosaurs
Bats and pterosaurs have skin attached to their forelimbs that aid them in flying and when they are on land, they use all four of their limbs to walk in a quadrupedal posture. Can these organisms be considered as true quadrupeds? Is there a different term used for this type of locomotion?

Quadrupedal means walking on 4 limbs, so yes bats can be considered quadrupeds. The scientific name for how an animal walks is gait. However, keep in mind that the same animal can have different gaits, think of a horse that can walk, gallop, etc. It seems that not all bats walk the same way, this here might be of interest, where they tell about a paper published in Nature in which they find a very different gait in Vampire bats, compared to 'normal' bats. In this paper they say that normal bats: "...shuffle  awkwardly from  a  sprawled  position." So I don't think they have a real name for a 'normal' bat gait.
For flying pterosaurs, it is hard to tell, we've never seen one walk.


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Limits of phase-locking
In Rieke et al, Spikes, p. 31, I found this instructive picture showing and explaining phase-locking.

I take it for granted, that phase-locking is possible only upto a maximal stimulus frequency (well below the maximal firing rate of the neuron). Beyond this, phase-locking must break down: the neuron cannot follow the stimulus anymore.
My questions are:

Does this maximal frequency count as a characteristic of a neuron (type of neuron), and what is its name?
Are there typical values of this frequency, e.g. as a fraction of the maximal firing rate of the neuron?
Does the breakdown of phase-locking typically occur suddenly (as a phase transition) or gradually?
What happens beyond? Does the neuron follow a virtual stimulus of 1/n of the original frequency (which would be in phase with the original stimulus)? Or does chaotic firing take over?

see https://biology.stackexchange.com/a/67843/460

My question was about single neurons, not assemblies. Phase locking of assemblies is a different case. (Maybe the question about single neurons is not so interesting, because it's only assemblies that count - but nevertheless I dare to ask it.)

Phase-locking can occur at very high frequencies at the early stages of a sensory system. In addition to the answer provided in your previous question, let me offer an illustrative example from single neurons in the somatosensory system.
Deschênes, Timofeeva and Lavallée (2003), have stimulated the whiskers of an anesthetized rat with a sinusoidal stimulus while recording extracellularly in the main feed-forward brainstem nucleus of this system (Pr5). Practically all neurons responded with at least one action potential to all cycles of a stimulus up to a stimulation frequency of $300Hz$. Neurons always fired an action potential at first cycle up to the maximum frequency tested, $400Hz$, and ~$30\%$ fewer spikes upon subsequent stimulation (questions 2 and 3). The extend of coupling to the stimulation frequency depended on the amplitude, velocity, and direction of the stimulation.

 Encoding of high-frequency whisker deflections by primary afferent axons
(Figure 6 from Deschênes, Timofeeva and Lavallée (2003))
Given the physical limitations of the stimulation device (piezoelectric element) it was not possible to directly stimulate at higher frequencies. However, the authors took advantage of the harmonic oscillations of the stimulator to look at the phase-coupling of spiking to higher frequencies of stimulations. Remarkably, units that were sensitive to small displacements of the whisker were able to follow the harmonic oscillations of the stimulator up to at least $1kHz$ (see Figure above).

What happens beyond? Does the neuron follow a virtual stimulus of 1/n of the original frequency (which would be in phase with the original stimulus)? Or does chaotic firing take over?

It is important to note that $1kHz$ is very close to the refractory period of most neurons, thus I would predict that this could be the only limiting factor in these cells. Of course, different types of cells will show different responses to high-frequency stimulation based on their intrinsic properties, the degree of short-term synaptic plasticity of the activated synapses, and/or the filtering of the incoming inputs by upstream circuits.

Does this maximal frequency count as a characteristic of a neuron (type of neuron), and what is its name?

I am not aware of something like this. Stimulation at such high frequencies is not typically used to classify neurons as it is rather non-physiological for neurons beyond those receiving direct inputs from the sensory receptors. Most often researchers apply a DC pulse and observe the degree of spiking adaptation.

Reference
Deschênes, M., Timofeeva, E., & Lavallée, P. (2003). The relay of high-frequency sensory signals in the Whisker-to-barreloid pathway. The Journal of Neuroscience : The Official Journal of the Society for Neuroscience, 23(17), 6778–87. https://doi.org/23/17/6778


text:
Alternative to distilled water for pH test
I am looking to test soil pH in a remote location. The test results don't need to be perfectly precise, and a pH test strip should provide sufficient accuracy. However generally this kind of testing uses boiled distilled water - and in this location it will be very difficult to buy distilled water.
The location is off grid, and getting specialized equipment to the location is not an option. (This is for field experimentation with farmers in rural Africa)
The process I have seen used for this is:

Add 1 part boiled distilled water and 1part soil by volume, in a clean container
stir and leave to settle.
Test the water pH with a pH test strip

Would it be possible to use boiled rain water for this process, or would this be likely to contain impurities which would interfere with the test results?
If there are likely to be impurities but there are approaches that can mitigate for them, please explain.

Have you considered getting a portable distiller?  It would require access either to a socket or a car with a transformer, and they can cost a bit, but it would probably do the job.

That is a possibility; however the cost and logistical challenge of getting and running one is quite high (For example there is no grid electricity). If it comes to that it may be worth buying a full soil testing kit with it's required equipment, rather than just using pH strips. I am also considering the possibility of setting up a DIY distiller- suitable parts may be locally available.

I don't quite get your problem. If you have to take the probes by hand, you have to be there yourself. Guessing your weight somewhere between 50 to 100kg, whatever takes you to that location should be able to take 50l of distilled water along with you to that location, too.

@Ben What about commercially available solar distillers? Of course the cost may be more than pH strips but I doubt that is your only source of costs in the first place. I'm not too familiar with soil testing but what sort of size of sample and number of samples are you talking about here?

Have you considered making a single stage distillation unit by placing an inverted bowl above boiling water and capturing the condensate then maybe boil the water once more to kill off any air contaminants?

@GyroGearloose not that it really matters to the question, but I can post a pack of soil test strips to for my friend on location to pick up when he is next in town for about £4. Sending a still along with that is sure to cost >£40, even if you don't take account of the risk of loss and breakage in the post. Asking about an alternative costs nothing (but the 50 rep bounty), and I judged it to be an interesting enough question that it could benefit someone else sometime in the future.

Hi Ben, thanks! you can get global maps of acid rain and for the study zone. You can double check your rain medium by via it's reaction to a fraction of salt and compare it to 5.5 distilled water. if a few moles of salt raise the pH to 7 equally in both waters then the unknown water is similar. You can also take a 100g of citric acid with you, and check the reactivity of the soil (pHBC) very easily, i.e. in quartzy barren soil it would swing a lot. Unreactive sandy soil is poor and easy to amend, it's better than high pH chalk. I studied soil sciences in university, it's a good read.

The h2co3 content of unadulterated rain is 15 micromoles of H+/Kg at room temp. The pHBC of average field soil from a 3000km transect in asia varied from 10 to 188 - mmol-kg-ph unit... from 40 localities. This other research found soil values of 45-1000 pHBC. https://www.science.gov/topicpages/s/spiked+soil+samples.html
That means that H2CO3 would affect arid meadow soil by 0.08 to 1.0 pH points if 1kg of water reacted completely with 1kg soil in a sealed environment. And 0.33 to 0.015 pH points for the referenced research.
However, if you boil the water, the gases expand and leave the water even prior to boiling point, which can be seen as bubbles previous to 100'C, boiled water error becomes 0.2 to 0.003 pH points.
This is the only ref i can find:
https://www.engineeringtoolbox.com/docs/documents/1000/solubility_CO_water.png
ttps://www-engineeringtoolbox-com.cdn.ampproject.org/ii/w1200/s/www.engineeringtoolbox.com/docs/documents/1148/solubility-co2-water.png
That means that if you have unadulterated rainwater at pH 5.5, and you boil it and jar it, you will have water with a pH near 7 after sealing and cooling.
Pure water is not natural or biological and it is aggressive to get to equilibrium. Upon contact with the atmosphere, it will immediately begin absorbing CO2 and the pH will drop and settle in at about 5.5 after about two hours.
Carbonic acidification is a background effect of the athmosphere aerated soil and rain to similar degrees.
Strong acid - pKa < 2
Weak acid - 7 > pKa > 2
Weak base - 10 >pKa > 7
Strong base- pKa > 10
oxalic acid and citric acid have a pKa in the range of 1 to 3, they are fairly strong, whereas CO2 has a pKa of about 6.4.
If your rainwater has a pH below 5.3, something is wrong with it and if the rainwater is around 5.5, it's nearly the same as distilled water.
I micromole of HCl rects completely and gives distilled water a pH of 6, whereas 1 umol of CO2 causes [a pH of 6,997][6], because only 0.3% of it converts to H2CO3.
[6]: https://books.google.fr/books?id=yRMgYc-8mTIC&pg=PA124&lpg=PA124&dq=hcl%20micromole%20co2%20distilled%20water%20concentration&source=bl&ots=OFKb4CB3MI&sig=ACfU3U0a1XQ_GSIZ5E-nj7JgPsaeDv7SbA&hl=en&sa=X&ved=2ahUKEwib-vuMkc_hAhVEThoKHYIcDtQQ6AEwCXoECFAQAQ#v=onepage&q=hcl%20micromole%20co2%20distilled%20water%20concentrationhcl&f=false

I don't think the issue is the reactivity of CO2 with the soil, but rather that the rain water will have a pH below 6 and therefore would impact any pH tests that incorporate use of that water. This impact is significant if the distilled water being used for tests normally would have a pH significantly higher than the rain water. What the OP could do is test the pH of both water sources to see if they differ, and if so, what effect using the two water sources has on the soil analyses. I would think that water pH would have varying degrees of effect depending on the soil makeup.

However, your point about any water source absorbing CO2 to equilibrate with the atmosphere within 2 hours might very well be true and nullify this issue (though presence of N or S acids from air pollution would impact the rain and not the water source held by the OP). Regardless, please provide a source to back up this claim and the various others that you make in your post. I'll be happy to upvote with proper support :).

For agricultural purposes in rural Africa, rain is also part of the agricultural equation. High precipitation does change soil pH and leaches minerals, especially if it acid, and distilled water does too. distilled water is probably more important to test soil where for an arid region where it doesn't rain. For the purposes of the test, the dissolved elements will be present in the sample, and not leached. For agriculture, a good process is to use the tools that the farmers have, the local water and soil amendments and find the best soil mix. references would use pHBC.

https://www.researchgate.net/publication/236878026_Soil_pH_buffering_capacity_A_descriptive_function_and_its_application_to_some_acidic_tropical_soils the pHBC on the following page is measured as 1-2 mol/Kg of H+, versus the H2CO3 content of natural rain which is in micromoles/Kg of H+: https://www.google.com/search?q=soil+phbc&source=lnms&tbm=isch&sa=X&ved=0ahUKEwjWt8S2kcnhAhUGJBoKHUIsB_MQ_AUIDigB&biw=1271&bih=646#imgrc=wmfw9DvqBCAMWM:

So a soil's pHBC (more often, I believe, discussed in terms of CEC - cation exchange capacity) is all about determining just how much buffering capacity a soil has. So unless all soil types being sampled are of the same type (i.e., have the same CEC), then water pH would impact each differently. The impact of the difference could be directly related to the pH of the water solution used in the OP's pH test. Perhaps one soil sample has a pH that is more resistant to neutral but less resistant to acidic sampling methods...

IF the OP truly doesn't care about precision, then perhaps you're right that the pH difference in rainwater might not be significant. But to go into a study with that known potential source of error is not very good science. Again, I recommend that if rainwater is to be used, that the OP at least tests to confirm that it doesn't skew results.

Also, thanks @com.prehensible for including sources in your comment. However, please add the sources to the post directly. You also include graphs and make a number of very specific claims and assumptions without supporting them or citing their source. Your post would be made much stronger if you supported each claim directly and individually. Please provide context and source for your graphic, too. Thanks.

Hi, I have researched the query further, because carbonic acid is so very unreactive, that scientists don't bother with it very much, and so i had difficulty to find sources. I added some extra information, notably the notion that boiling drives of the CO2 in rain, that only 0.03% of CO2 becomes H2CO3 at pH 5.6, and some graphics. yours, apondecologist ;)

I want to accept this answer, and give it the bounty, but clearer references would be good.

A found a graph stating the co2 concentration of boiled water, which reduces the co2 by 5 at sea level, less at altitude, and perhaps 20 minutes of boiling brings the acid to zero, i don't know. Frankly it sounds like it would be worth making substrate analysis available to african farmers like it is here where we can post it to a lab to have CEC and pHBC minerals Calcium and organic content of it

Rainwater might not be the best option.
Rain water is naturally acidic due to the reaction of CO2 forming some weak carbonic acid [see here for explanation].

 Source: Wikipedia
As a result, pH of "pure" rainwater is usually between 5-6; usually around pH 5.6. See here.

Most rainwater has a pH of 5.6 to 5.8, simply due to the pressence of carbonic acid (H2CO3).

Presence of any sulfur or nitrogen oxides in the air (perhaps from burning coal plants or city traffic from 100s of km away) would lead to rain becoming even more acidic. From environment.co.za:

Sulphur dioxide reacts with water vapour and sunlight to form sulphuric acid. Likewise NOX form nitric acid in the air. These reactions takes hours, or even days, during which polluted air may move hundreds of kilometres. Thus acid rain can fall far from the source of pollution.

I had hoped that boiling the water would be sufficient to bring the levels of dissolved CO2 to a consistent low level. I am fairly convinced that this would not work reliably - after looking further into sulfuric and nitric acids as described in your answer, so I think this answer is correct. I think this answer would be even better if it addressed what if any effect boiling would have on the amounts of these impurities.

@Ben, a discussion about the impacts boiling has on water pH is really more appropriate for Chemistry.StackExchange, so I'd advise you to ask that question there.

@Ben: To hypothesize (because I don't know the answer): I would guess any solutes (if any) dissolved in the rain water would increase in relative concentration and as a result the water's pH would shift in relation to the acidity/alkalinity of the solutes. This is totally conjectural, and I'm not really sure there would be enough solutes to make a difference. You can read here for a discussion about the impact of boiling on water pH, though I don't think it quite answers your question.

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


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Biological significance of network parameters
I am currently working on networks and I have calculated various parameters for the network like diameter, average path length, average eccentricity, radiality etc. Could someone guide me to some articles I could read as to what biological significance these parameters hold with regard to a biological network (gene regulatory network). Example, what does a small diameter, radiality etc say with regard to the biological property of the network. On research I could only find one article which could be of some help. Thanks
Edit: I understand that this question has been identified as being too broad but all I require are links to articles that could perhaps guide me to an appropriate solution. Perhaps, the answer can be limited to how does a large network affect a radiality value affect a biological network?
Edit2: Its a cluster from a bigger network, is bipartite in nature, consisting of Transcription factors and genes with a size of 361 nodes. My aim is to check if the clusters are all different from each other and determine if there are significant differences between each cluster. The question was all about what biological inferences can be drawn from network parameters like diameter, radiality etc. For example, a network with low diameter means that network information is passed faster between even the furthermost nodes meaning pathways in that network could have genes with functions that require quick actions, say genes that govern sensory perceptions like reflex actions.

As it currently stands, I think your question is too broad. If you can focus on a single parameter though, perhaps you will have more success in obtaining a response.

You will have to limit this to what sort of question you are trying to answer with that network. You might want to use all of these features or none of them. You should also explain what size of network this is and whether it was built using one gene, many, the entire genome or what.


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Reaction centre in Photosystems of higher plants
In photosystems of higher plants, there are about 250-400 pigments (number wise) in a particular photosystem. Out of which,approx 170-180 pigments are of chlorophyll a molecules. And any one of them behaves as a Reaction centre in a photosystem.
My question is:

What are the factors and laws which decide which chlorophyll a molecule will work as a reaction centre?
What's the difference in chlorophyll a molecules present in reaction centres of PS I and PS II since they have different threshold energy. Is there any structural difference?

Your first question...

What are the factors and laws which decide which chlorophyll a molecule will work as a reaction centre?

... has no answer because it's based on a wrong premise: namely that, regarding the chlorophyll molecules, "any one of them behaves as a Reaction centre in a photosystem" (sic).
On the contrary, the special pair is bound to the reaction center's proteins (called D1 and D2). According to Berg (2002):

The photochemistry of photosystem II begins with excitation of a special pair of chlorophyll molecules that are bound by the D1 and D2 subunits. (emphasis mine).

Regarding your second question, it was already answered here.

Source: Berg JM, Tymoczko JL, Stryer L. Biochemistry. 5th edition. New York: W H Freeman; 2002. Available from: https://www.ncbi.nlm.nih.gov/books/NBK21154/

Thank you Gerardo! It helped a lot =) may you please answer a question I recently posted. -https://biology.stackexchange.com/q/68218/11647

Someone else too had asked your question no. 2. here Photosystem 1 and 2; P680/P700; Chlorophyll a/b
The answer basically quotes Molecular Biology 4 ed. by Lodish as follows.
"The chlorophylls in the two reaction centers differ in their light-absorption maxima because of differences in their protein environment."
[I could've just commented this but I can't locate add comment option on your post. Am new here.]

You couldn't find the comment option because you have less than 50 Reputation Points. Once you pass that threshold you'll be able to comment.

Thanks Gerardo. Could you please answer a question I have put up here https://biology.stackexchange.com/questions/68190/what-is-the-primary-electron-donor-in-the-photosystem-1-and-photosystem-2


text:
Mobile carriers of Light reaction in higher plants
The hydrogen carrier PQ and the electron carrier PC are the mobile carriers in light reaction facilitating electron transfer from PS II to PS I during non-cyclic process.
My question is -

How do they move in membrane, from PS II to cytochrome for PQ and cytochrome to PS I for PC?
I do know the membrane is quasi-fluid in nature so it'll be easy for carriers to move in it but my question is how do they reach their destination? What's the driving force?
Maybe they're just arranged that way on the membrane and some change like - because of change in density (when PQ accepts the H and converts to PQH2 ; I'm not sure about the density change part) which leads to change in side on which it's present or change in anything else, they reach their target?

Is my thinking correct?


text:
How is Coenzyme A Transported to the Matrix?
So, I've been researching cellular respiration on my own, and trying to keep track of most of the major processes. However, I do have one question left: I can't seem to find any sort of information about how Coenzyme A (I think it's made in the cytosol) is transferred to the matrix (the inside of the mitochondria, inside the inner membrane). Is it transported with a shuttle like for NAD+/NADH, a translocase like for ATP/ADP, or something else? Thank you for your time.

Good question, to which I cannot find the answer. I doubt whether it is a shuttle, because the nature of shuttles is that they don't transport the difficult bits. There is a carnitine shuttle for transporting acylCoA across the inner mitochondrial membrane, but it transports the acyl-carnitine, not the CoA. The mammalian enzymes for CoA synthesis were only identified this century, so I don't think it's text book stuff.

I noticed that PANK2 (a mitochondrial pantothenate kinase) seems to be essential for normal mitochondrial function.  1 2 Is the CoA being made in place?

Zhyvoloup et al. (2003) J Biol Chem 278: 50316-50321; emphasis mine:

CoA synthase is localized on the mitochondrial outer membrane.
  Moreover, we demonstrate for the first time that phosphatidylcholine
  and phosphatidylethanolamine, which are the main components of the
  mitochondrial outer membrane, are potent activators of both enzymatic
  activities of CoA synthase in vitro. Taken together, these data
  provide the evidence that the final stages of CoA biosynthesis take
  place on mitochondria and the activity of CoA synthase is regulated by
  phospholipids.

https://www.ncbi.nlm.nih.gov/pubmed/14514684

Thank you for the great information on CoA synthesis! However, the article doesn't seem to have any information on how that CoA is brought into the matrix. Do you have anything on the mechanism on which CoA is transported through the inner membrane of the mitochondria?

Since "the inner mitochondrial membrane is impermeable to low-molecular-weight solutes [such as CoA, acetyl-CoA, carnitine and acetyl-carnitine]," CoA must be first acylated by "a long-chain-length ATP-specific fatty acyl-CoA synthetase (EC 6.2.1.3) ... associated with the outer-membrane." --Haddock et al. (1970) Biochem J 119: 565-73.
https://www.ncbi.nlm.nih.gov/pubmed/5500317

I think this can clear your doubt...As it shows how the transport is done between the matrix and cytosol..
And it also explains the presence of coenzyme A ie CoA SH at both the sites.

It would be great to source this answer... as it stands, it doesn't have any authoritative references.  Thanks!


text:
What is the difference between the usages of bis-tris methane and bis-tris propane?
I came across "bis-tris" buffer in Rodney Boyer's Biochemistry Laboratory book and tried looking it up. Then I found that there's bis-tris methane and bis-tris propane that are both buffers. What exactly are they used for and are the usages different?

They have different acid dissociation equilibria and so buffer at different pH.
                    pKa1    pKa2
Bis-Tris methane    6.5     -
Bis-Tris propane    6.8     9

[source]
The two titratable secondary amines of Bis-Tris propane make it usable over a wider pH range.


text:
how to compare two different enzymes with same Km?
I have a test today I study at HUJI and I encountered this question which I can't figure out: if two different enzymes have the same kM and the same substrate what can I say about the two?

same Vmax
dosn't have the same Vmax
may or may not have the same Vmax
the proportion between kM to Vmax has to be 0.5

Km is the concentration of the substrate at which the rate of the enzymatic reaction is equal to 0.5 * Vmax. Km alone says nothing about the actual value of Vmax . . .


text:
Why eukaryotes have three different types of cytoskeleton filaments?
Ok: IF, microtubules and microfilaments serve different purposes. But whats the biological advantage of having these three types over other organisms? I don't know if I'm being clear.

Note that cytologically the most apparent property of eukaryotes is, in general, their higher internal compartmentalization (cpe: Gerhart et Kirschner's popular science book: "The Plausibility of Life"); Why eukaryotes have a seemingly higher compartmentalization is perhaps worth of another question :)

While eukaryotes contain tubulin-containing microtubles and actin filaments, prokaryotic homologues do exist.
For example FitZ protein, the most common bacterial Tubulin homologue[1], is involved in cell division. Genes for this protein are actually present in eukaryotic nuclear DNA and the protein facilitate the division of the mitrochrondria and chloroplast organelles which were created by endosymbiosis[2].
Similarly, MreB, functions as the most common prokaryotic analogue of actin.
Regarding IF filaments, certainly subsets such as nuclear lamins are uniquely found within Eukarya, however a paper published by Bafchi[4] has suggested that IF-like proteins are present within bacteria.

Bi, E., & Lutkenhaus, J. (1991). FtsZ ring structure associated with division in Escherichia coli. Nature, 354(6349), 161-164. doi:10.1038/354161a0
Margolin W. FTSZ AND THE DIVISION OF PROKARYOTIC CELLS AND ORGANELLES. Nature reviews Molecular cell biology. 2005;6(11):862-871. doi:10.1038/nrm1745.
Gunning, P. W., Ghoshdastider, U., Whitaker, S., Popp, D., & Robinson, R. C. (2015). The evolution of compositionally and functionally distinct actin filaments. Journal of Cell Science, 128(11), 2009-2019. doi:10.1242/jcs.165563
Bagchi S, Tomenius H, Belova LM, Ausmees N. Intermediate filament-like proteins in bacteria and a cytoskeletal function in Streptomyces. Molecular Microbiology. 2008;70(4):1037-1050. doi:10.1111/j.1365-2958.2008.06473.x.

So it actually depends on the biological advantages (functions) and how the organisms have evolved in time?


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What is this spider spinning a bright green web?
Here is the picture of it I took with my phone while I was out working:

Here is a close up:

Location: Texas (winter).

Welcome. Do you have a close up image of the critter?

Here are close ups on the so called critter (https://i.stack.imgur.com/9pUjL.jpg)(https://i.stack.imgur.com/0tWee.jpg)

As beautiful as they are one both dont spin weds at all and he is so hard to get a close up picture of because he is smaller then a fingernail + it's a phone camera so don't expect great quality as long as I lives never have I seen a spider spin a Wed other then the color white

Your image is not the best one, but this is probably the Magnolia green jumper, Lyssomanes viridis.
Here is a better image of it for comparison:

It also matches your location. According to the Wikipedia page linked above,

the species is native to the Southeastern United States plus Texas, and as far north as Maryland.

Check out the Green Lynx Spider (Peucetia viridans) here.  The spots on the body look similar.  If the legs are similar this is a good candidate.  It's hard to tell by the photos if this is it or not, but it may help.

Source: http://www.spiders.us/species/peucetia-viridans/

I'll go with the jumping spider, for two reasons - first, the Lynx Spiders make a normal brown egg sac, and second, there is a strikingly similar jumping spider in Australia, called Mopsus mormon, that also makes a green egg sac (although, to be fair, it's the eggs that look green rather than the silk..)
http://malcolmtattersall.com.au/wp/2015/10/mopsus-mormon-mummy/


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Feeding behavior of organisms that prey on microorganisms
Is there a specific term for organisms that feed on micro-organisms?

Use "-vore" and "-vorous" suffix [L. -vorus devouring, eating (cf. vorāre to devour].
For example: bacteriovores, algaevores, and planktivores.

Note: "Microorganism" is an unfortunate, albeit popular (viz. "microbiology") term. How small is "micro"? So small that one needs a microscope to see it? And what kind of microscope: "light" or "electron"? i would drop the term "microorganism" altogether. One can use "bacteria, "archaea," "chromists," "protists," . . .


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How are signalling pathways specific when secondary messengers are not?
I'm a biochemistry and physiology student and am aware that secondary messengers like cAMP and IP3 are used in specific signaling cascades.
However, they and other molecules can innervate a variety of effector molecules which makes me wonder how specificity is maintained.
For example, if GPCRa/Gsa activation leads to the activation of PkAa, why doesn't it lead to the activation of PkAb?


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Are freshwater jellyfishes really jellyfishes?
Articles from the aquaticcommunity.com and the Nature Conservancy suggest that freshwater jellyfish, Craspedacusta sowerbyi, are more closely related to the Genus Hydra. From the Nature Conservancy article:

It should be known that though Craspedacusta sowerbii is touted as a
  jellyfish, some argue it is more   related to the family Hydra than a
  "true" jellyfish. Many researchers still call it as such, but others
  may simply refer Craspedacusta as a jelly. The main difference between
  Craspedacusta swerbii and "true" jellyfish is the presence of a velum.
  Its velum is a thin, circular membrane around the cap that helps
  propel, or move, the jelly forward.

An articles from the US Geological Survey (USGS) states that Craspedacusta sowerbyi is a hydrozoan that can take the form of a jellyfish. From the USGS:

Craspedacusta sowerbyi is a hydrozoan (Phylum Cnidaria, Class
  Hydrozoa), which is most easily identified when it takes the form of a
  small, bell-shaped jellyfish, known as a hydromedusa.

The Merriam-Webster dictionary defines a jellyfish as follows:

a free-swimming marine coelenterate that is the sexually reproducing
  form of a hydrozoan or scyphozoan and has a nearly transparent
  saucer-shaped body and extensible marginal tentacles studded with
  stinging cells

This definition, to me, seems to suggest that Craspedacusta sowerbyi is a jellyfish, however there must be some other reasoning that I'm missing that makes others believe that they aren't. Any clarification would be greatly appreciated.

The issue here is simply the meaning of the term "jellyfish" and the term "medusa". The first has no taxonomic value and, as such, can be used the way the book/zoologist/layman/journalist wants, unfortunately. Let's see it:
Cnidarians (Phylum Cnidaria) have two basic morphological types: medusa, or medusoid form, which is free-swimming, and polyp, or polypoid form, which is sessile:

There are Cnidarian species that display only polypoid forms and there are species that display both medusoid and polypoid forms in their life cycles.
Regarding the taxonomy of the most common Classes of Cnidarians, Hydrozoa displays both the polypoid and medusoid forms; Scyphozoa displays both the polypoid and medusoid forms; and finally Anthozoa displays only polypoid forms.
So, we can clearly see that Craspedacusta (an hydrozoan) is a medusa, or, in other words, that it displays the medusoid form in some point of its life cycle. There is no doubt regarding this:

The problem comes when we try to use the term jellyfish.
Again, jellyfish has absolutely no taxonomic value. For instance, my teachers used to call an hydrozoan medusa as a "jellyfish". Some time later, when I started teaching zoology, I used to say to my students that an hydrozoan medusa is a jellyfish... that's not a big deal.
However, some zoologists apply the term jellyfish only to the scyphozoan medusae... in that case, jellyfish does have a taxonomic value. And, because of that, since Craspedacusta belongs to the Class Hydrozoa, its medusoid form cannot be called a jellyfish (again, if we accept the definition of those zoologists).
So, in conclusion, it depends on the book/zoologist: some say that that both Hydrozoan and Schyphozoan medusae can be called jellyfish, while some say that jellyfishes are only the medusoid forms from the Class Schyphozoa. That's the definition used by both the aquaticcommunity.com and the Nature Conservancy articles.
PS: Hydra is a Genus, not a Family. I edited your question just to realize that the mistake is from the original article, not yours.

I was starting to wonder if it depended on who is asked but could never have come to this conclusion on my own.  Excellent explanation.


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How do membrane proteins find their target locations?
The question might be asked for any kind of "bound" proteins, but I'd like to restrict it to membrane proteins.
Assuming membrane proteins (or their main parts) don't (or aren't) build in situ but at some distance of the membrane, I wonder by which mechanisms they travel from their generation site to their final destination inside the membrane (inner or outer).
Proteins that are distributed roughly evenly (or randomly) over the membrane don't pose a big conceptual problem: they could have gone their just by diffusion, possibly from many generation sites, distributed roughly evenly (or randomly) inside the cell.
But what about uneven distributions, where some proteins are more densely and non-randomly packed (significant and functional) at some sites of the membrane than at others, e.g.

receptors at postsynaptic densities
Na+ channels at action potential initiation sites like the axon hillock or the axon initial segment
Na+ channels at nodes of Ranvier?

By which mechanisms (forces, signals or structures) are these proteins led to
 their targets?
Maybe it depends, and there are different mechanisms. These I came up with (by contemplating first principles):

uneven distribution of generation sites inside the cell (due to what?)
uneven distribution of origins of attracting signals inside the membrane (due to what?)
some "self-attracting" forces or signals (leading to accumulation by positive feedback)
microtubules

Which mechanism is — possibly — predominant?

Related questions:

Life cycle of proteins
Pathways of ligand-gated ion channels
Distribution of synapses of CA1 neurons
Distribution of dendritic spike generating ion channels on the dendritic tree
Visual maps of the neuronal membrane
Distribution of sodium–potassium pumps

This is a great question. A comprehensive answer would be beyond the scope of an answer on a forum like this. I will summarize the best I can here, but if you are really interested in this you should look at some of the work by Randy Schekman and Tom Rapoport, who have done a lot of pioneering work in this field and have papers from more than two decades ago on their lab websites. I'll talk about membrane proteins generally, but I'm not sure what the state of the field is for Na+ channels specifically, so I can't comment too much on that particular case. Many of the details of the processes I will mention are still areas of active research, so I will try to stick mainly to what has been well-characterized (to the best of my knowledge).
To restate the problem, proteins are generally synthesized in the lumen of the endoplasmic reticulum, which is an aqueous environment similar to the cytosol in many (but not all) ways. However, membrane proteins, which are not stable in aqueous environments, must:
1) Find a way from the ER lumen into a membrane.
2) Get from the ER into the correct membrane so they may perform their cellular function.
We will start with step 1, but the key to both is a critical but often underappreciated aspect of protein biology called the signal peptide. The signal peptide is simply an N-terminal sequence of amino acids that precedes what we would normally think of as the beginning of a mature protein. It is relatively short, usually only ~30 amino acids in length. It is cleaved off the mature protein by a protease once the protein is folded and in the membrane. Until that time, the signal peptide serves as a molecular marker that indicates where the nascent protein should be heading and how it should be handled. Not surprisingly, there are many different signal peptides that serve multiple functions, and they are not only used for membrane proteins.
So let's say we are in the ER lumen, and have some mRNA coding for a membrane protein that is destined for the plasma membrane. The first amino acids that will emerge from the ribosome is the signal sequence, in this case a specific signal sequence indicating that this is to be a plasma membrane protein. Once the signal sequence emerges from the ribosome, it is recognized by a ribonucleoprotein complex (that is, a complex of RNA and protein) called the signal recognition particle. Once the SRP binds to the signal peptide, translation is halted, and the whole complex moves to the ER membrane, where it forms a complex with another large protein complex called the translocon. I can't go into the intricacies of these complexes and their functions in this answer alone, but the simple description is that the translocon contains an ATPase that can insert the membrane protein into the ER membrane as it is translated, with the correct orientation. The hydrolysis of ATP provides energy to move the emerging polypeptide chain into the hydrophobic membrane, where chaperones help it fold. This process is in part driven by the recognition of hydrophobic transmembrane regions of the proteins by the translocon. It can also move soluble, cytosolic proteins across the membrane through a similar mechanism.
Now that the protein has been translocated, a peptidase will cleave the signal sequence off the protein. From here, sorting signals will take over. Generally, these are simple sequence motifs in the first transmembrane domain that act similarly to a signal sequence, but they are not cleaved. However, sorting signals can be stretches of peptide throughout the protein too, in some cases.
These sequence motifs will be recognized by cell trafficking machinery. Without going into too much detail, the proteins will be gathered into vesicles, and transported to other organelles. Usually, the first stop for proteins is the golgi apparatus, which is typically where many post-translational modifications, such as glycosylation, take place. I am a biochemist and not a cell biologist, so I am not the most qualified to go into the details of subcellular trafficking. Suffice it to say, once the protein is finished being processed in the golgi, it will be trafficked into other organelles, such as the plasma membrane using vesicle transport as before. From my understanding, the protein will be sorted into the proper vesicles based on its sorting signals, as well as other markers (in some cases, certain post-translational modifications on certain proteins can influence its trafficking). The vesicles recognize the proper destination membrane in part by the lipid composition of that membrane. For example, phosphoinositides have extensive influence on membrane trafficking, and many membranes can be differentiated by their phosphoinositide signature.
Anyway, that is a very broad overview of the answer to your question. I'm sorry I can't comment too much on the intricacies of cellular trafficking, I don't quite have the expertise to go through that literature quickly enough to answer your question in a reasonable time frame. I hope this is helpful in pointing you in the right direction, and good luck!

Is active transport an answer?
With special signalling and interaction peptides inside of the protein, proteins can be targeted to different sublocations.If you are interested in how Na+ channels accumulate at the AIS, read for example Gasser et al. 2012, that is a very nice paper that shows the ankyrin binding motif is sufficient to cluster Na+ channels at the AIS.

Might be. But HOW are the proteins targeted to different sublocations (specifically)? I'm probably NOT interested in how Na+ ions do accumulate anywhere.

But I may be misled. Maybe Na+ accumulation is the answer.

Sorry, I meant channels, was missing the word.


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Cyanobacteria pools as carbon sinks
According to some scientists, at one point in time in this planet's history cyanobacteria almost drove life to extinction by reducing it to a snowball as they captured vast quantities of carbon and locked it up.
Today we face a different challenge where we have excess carbon dioxide (and other greenhouse gases) in the atmosphere leading to a warmer planet which threatens its current inhabitants.
As someone who studied applied physics I have very little understanding of how cellular and molecular biology work. But is it a viable solution to build artificial sinks of cyanobacteria in controlled environments at various places on the planet to capture this excess carbon dioxide? If not then what stops us?
I could think of some challenges:

As cyanobacteria need sunlight to capture carbon so the reaction will be limited to the surface where we will have most sunlight. But one can improve the efficiency by building columns which have embedded light sources (using solar/renewable energy only) at various points within.
Maintenance of these pools/columns.
An economic model to make this a profitable venture for companies. Can the end products produced by these bacteria be sold for money? Can they serve as an ingredient into some other (profitable) reaction?

Why do you think that "cyanobacteria almost drove life to extinction by reducing it to a snowball as they captured vast quantities of carbon and locked it up"?

The best cyanobacterial pool is the World Ocean.
No man, no amount of venture capital investment, no board of directors, no CEO, no CFO, no CSO, etc. can ever create, on the Earth, an equivalent to the World Ocean.

I agree that the world ocean is the best pool for cyanobacteria and other microscopic plants. But my question is what specifically stops us from engineering this process and turning the tables on greenhouse gas production? We don't have to beat the Earth --we just need to make up for the shortfall.

Is there a shortfall?

Yes. Please see https://www.sciencedirect.com/science/article/pii/S0079661114000135.


text:
Does the Histogen Theory apply to plant roots as well as stems?
My school textbook briefly mentions a certain "Histogen Theory" (von Hanstein) of plant growth/development. However, I can't find any authoritative source on this matter online.
According to my book, as well as this site, the Histogen Theory is only used to model the development of the shoot (stem) apex.
But according to the definition on Merriam-Webster, the Histogen Theory is applicable to both the shoot and root systems.

Question:
Is the Histogen Theory applicable to only shoot apices (as some sources suggest), or does it instead, apply to both shoot and root apices?


text:
identify this tree
location: trabzon(turkey) planted for recreational purpose

dont forget to accept good answer

It is Rhus typhina, also known as staghorn sumac. The plant is originally from north-east America, but is often seen all over the world in Parks or gardens.

It's basically a weed here in Canada.


text:
Suitable writings for self-study in general biology/chemistry
I have recently commenced a graduate education in mathematics. Since I am currently attending extra classes in programming, which are not included in my education, my institution will not let me attend further courses in biology. Hereby, my question is simple:
What are suitable writings for self-study in general biology/chemistry? By general, I mean somewhat of an university-level introduction of mentioned fields.
My level of knowledge is slightly above "advanced" high school chemistry/biology.
(I apologize for my bad english, I'm Norwegian.)

My personal favorite intro biology book is Campbell Biology. The new edition is a little pricy, but you can probably find one of the older editions for pretty cheap--my intro class used 9th edition, and I don't think much has changed other than some of the taxon names.
I'm not sure what branch of Bio you're interested in, but Campbell covers all of introductory cell biology, organismal/evolutionary and ecology. The "concept check" questions at the end of each chapter are fantastic open-ended responses, and I believe most (if not all) have answers in the back of the book
I'm not as solid in general chemistry, but some good ones I remember are Brown, Lemay, and Burston which got me through AP Chem, and Zumdhal which my university uses and I haven't heard any complaints. The Brown text is a pretty good intro though. It provides good information and I thought it was pretty enjoyable to read.

Thank you for your answer! I have decided to go for Campbell Biology, regarding self-study in biology. In chemistry I have decided General Chemistry: The Essential Concepts by R.Chang. Perhaps you have heard of this title?

That one is pretty decent--from what I remember it's a good bit shorter than most general chemistry texts. It has decent reviews though and is probably fine for self-studying. If you get stuck on any specific topics, the general chemistry Kahn Academy is outstanding.

Another suggestion for chemistry. If you ever feel the need to study organic chemistry go with 'Organic Chemistry by Clayden'. The solution manual + textbook should be ~200$ total and the book is a beast. Only two editions (1st and 2nd) have been published. For the general chemistry suggested if you get your hands on the Zhumdhal do not get anything above the 7th edition. The 7th edition is the last publication to have exercises on the book, the other editions give you a 1 year online access to them.

As a supplementary book to general chemistry I'd also recommend General Chemistry Linus Pauling but not as your main book. It's relatively cheap at ~30$. I think you might find it helpful as it takes a calculus based approach.

I recommend any Schaums Outline book on the matter. I've read several of them and, although there are books that are better and more specific in many instances, they follow a very easy to grasp format that is common to all other Schaums Outline books.
Therefore, they are a great start for self-studying any subject. The main good point is that, as they are not too dense, the chances you'll leave the book half-through, and stop studying in general, decrease a lot. They will increase your curiosity and understanding, so after reading them you should be ready to read more dense books later on.
I want to clarify that they are not equivalent to "for dummies" books at all. Although they are not dense, they are written assuming you are not dumb and under the principle of being able to make you pass your tests without attending classes. So they are serious books made for practical purposes; no pretence whatsoever.
Particularly on Biology, there are several books:
Schaum's Outline of Biochemistry
Schaum's Outline of Biology
Schaum's Outline of Microbiology
Schaums Outline Of Genetics
Etc. You can learn about any science with them, really.
I'll leave a link with more details on the one in Biology:
https://bookstore.lsue.edu/schaums-outline-biology
They have books on many other sciences. They are designed for self-study.

The post you are replying to is four years old. Furthermore this is a site about specific problems in biology that can be answered in an objective manner. Book recommendations are not that.

Welcome and thanks for your answer. Can you add links to the resources you mention, and in specific those that deal with Biology? Can you also expand a bit on what Schaums Outline exactly is? It seems a book series of some sort? Happy to upvote when you've added these details. Thanks.

@AliceD I think you are wrong to welcome a subjective answer to a book recommendation request which you yourself find lacking, and which is to a question that does not even explain the background knowledge of the poster. It seems to me that this sort of question — like many on Covid — would be better dealt with by a comprehensive answer on Meta, listing sources that are suitable for particular situations, their scope and required background. Allowing posts here encourages subjective material which isn’t of any use to anyone.

Please read the [Tour] carefully to find out who this site  is intended for and what sort of questions are suitable here. Also read the help on writing good answers. It is not our concern if people end up here for the wrong reasons. It is our concern if they then do not conform to the site’s guidelines. If they are not toId, they and others will continue to do so. I have voted to close this old question, but four more votes are needed. If you can answer one of the many scientific questions in your area of expertise, your contribution will be welcomed.


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Possible for bacteria to burst container?
This is kind of a thought experiment, but are there any conditions under which bacteria could multiply enough to burst the container they're in?
Thoughts so far: Bacteria often need oxygen to multiply, but I believe not always? They need a food source, but perhaps despite that mass already being present they might still have a larger overall volume afterwards?
For the sake of this question, I'd like to be fairly loose with the word "container", i.e. not necessarily something solid glass or even solid for that matter, but at least closed. Perhaps I could have bacteria in a bubble and they could burst that?
Thanks for indulging!

some bacteria can convert solids ot gasses so they can generate things that could burst a container.

thanks @John, do you know if there are bacteria that could still burst a container without producing gas? i.e. purely from the volume of the bacteria themselves? (I'd imagine they'd need to consume a fairly dense food supply)

Yes. Bacteria (and fungi) can digest sugar to produce CO2 gas. The latter occupies more space, and can burst contains such as closely sealed bottles (e.g.: for a bacteria / yeast co-culture: http://kombuchahome.com/how-to-prevent-your-kombucha-bottles-from-exploding/ )

thanks @tsttst! Do you know if there are bacteria that could still burst a container without producing gas? i.e. purely from the volume of the bacteria themselves? (I'd imagine they'd need to consume a fairly dense food supply)

@John: If the container is a closed system, the bacteria can only utilize the matter available within the container and thus cannot outgrow the container.

@MartinKlvana they couldn't acquire more mass, but could increase in volume/pressure to outgrow it, much like a shaken can of soft drink (but in this case I'd prefer to focus on a case not involving gas evolution)

@John: Yes, but only if the density of bacterial mass is much much lower than the density of the original content of the container. So, the question is then, what is the difference in density between the bacteria and the bacteria-free nutrients?

(Kombucha) Bottles exploding is related to unfermented sugar and active yeast remaining in the bottle at a temperature typically above 50F. Bacteria (acetobacter) are not busy without the presence of oxygen. Lactobacillus may be active but they produce low amounts of CO2 slowly.
Pressure - which may cause bottles to explode - is very temperature sensitive. At 42F the CO2 in the bottle will be contained within the liquid. The warmer it is the more the CO2 expands to the headspace. That same amount of CO2 at 42F just may explode the bottle at 100F
Temperature is crucial both for the activity of yeast (produces alcohol + CO2 in equal amounts) and for the Pressure.

Welcome ed kasper. Please take our [tour] and refer to the [help] for our guidelines. This represents a complete explanation. Answers are expected to show their references, to support why they are correct. You can improve this by [edit]ing to add these. Enjoy the site.


text:
Identify a bird by its feather
Gray feather with red tip, about 5 cm (2 in) total length. It was found in Lexington, Kentucky (central western USA).

Where did you find it (which type of ecosystem and what country / region)?

Good point. Sorry, I'm not used to posting here. But I think the answer is below. I'll try to give better information in the future.

@vknowles That's nice, thanks, but please tell us the location, so I can edit your question (making it complete for future reference).

It was in our back yard in Lexington, KY

It seems to be the secondary feather of a Waxwing, a bird from the Genus Bombycilla, like Bombycilla cedrorum:

Cedar waxwing. Source: https://rctfan2.deviantart.com/art/Cedar-Waxwing-285656802
Actually, that red tip gives the bird its name (from the Wikipedia link):

They have unique red tips to some of the wing feathers where the shafts extend beyond the barbs; in the Bohemian and Cedar waxwings, these tips look like sealing wax, and give the group its common name.

Therefore, the possible species are the Bohemian waxwing (B. garrulus)...

... and the Cedar waxwing (B. cedrorum):

However, since the secondaries of B. garrulus normally have a white area next to the tip...

... I'd guess that your feather belongs to B. cedrorum.
In conclusion
Besides the white patches in the feathers of Bohemian waxwings, OP just confirmed that the range of the Bohemian waxwing doesn't match. Therefore, this feather belongs indeed to a Cedar waxwing.

I think it is the Cedar waxwing because after reading about the range, it seems unlikely to be the Bohemian. Thanks!

Well, I’m impressed.


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Book recommendations: biological data analysis/error
I'm working as an undergrad in a tissue culture lab, and I have the most experience with statistics out of everyone in the lab. However, most of the knowledge I have in statistics is from my math courses which are mainly theoretical.
Does anyone have good recommendations for books on biological experimental design, data analysis, and statistical error? I'd prefer that they be specific to biology, but if there are some good general books with applications that works for me as well. I just want to get a feel for any specific knowledge I will need.

There are many books that teach statistics and R together. I would personally not recommend these books. Learn the fundamentals and just google what command already exist in R to perform the analysis you need to do.
I would recommend Experimental Design and Data Analysis for Biologists by Quinn and Keough. It is general, applied and pleasant to read.
As you already have good basis in statistics, you won't need an intro textbook but for other users (and because I personally work with one of the authors) I would like to mention The Analysis of Biological Data by Schluter and Whitlock.

The Quinn/Keough book looks perfect! Thank you. Ideally I'd also like a book that deals with more molecular-based exampels, but combining the book with our research and some of the papers we're drawing from will probably cover that.

I don't know this literature well enough to give you advice unfortunately. You might want, to ask it in a separate question. In the above question, you are asking for books on biological experimental design, data analysis, and statistical error?. In another post you could ask for a book on "statistical modelling in molecular biology". You might want to be specifiy exaclty what kind of analyses you are interested in (biophysics, detection of selection from genotypic data, epigenetic data, transcriptomic data, ....)