text:
Similarities Between Cells?
Which of the following are usually identical between a lung cell and a brain cell, from the same person, assuming that they are normal (non-cancerous) cells?  Circle your choice(s).
a.  Size
b.  Shape
c.  Specific proteins found in the cell
d.  Specific genes in the cell’s genome
e.  Which genes are expressed
f.  Which parts of the DNA are methylated
g.  The specific DNA sequence of chromosome 12
h.  All of the above
i.  None of the above

I said only D and G because all cells have the full genome.  The difference between cells is how the these genes are expressed.  All of the other options are results of different amound of gene expression.  Is this the correct thinking?

Seems right. I would choose those answers as well.

I would also go for d and g. All the others may vary. Strictly speaking, you may even have random, point mutations that have changed the genomic sequence between two given cells so even d and g might not be true in some cases.
I would also like to point out that recent evidence implies that differential expression of non coding, regulatory RNA molecules may play as, or even more, important a role as differential expression of proteins. See the ENCODE papers or here for a recent review.


text:
Auxotrophic complementation test with yeast
If auxotrophic strains grow on minimal media do they complement each other or not?  Also, is complementation the same thing as complementing each other?

If the yeast strain A is auxotrophic for AA 1 and the yeast strain B is auxotrophic for AA 2, neither would be able to grow in minimal medium by itself. But combined they complement the lack of AA1 in strain A by strain B and vice versa. That is metabolic complementation.

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sort: votes


text:
Molecular simulations without capping n- and c-terminus of polypeptide
When running molecular simulations, what is the consequence of not capping the n- and c-terminus?
I have been following gromacs tutorials and haven't come across any that deal with capping the termini, so is it important?

Capping the termini neutralizes their amine or carboxylic acid moieties. If this was recapitulated in the biological context, it could be important for an accurate MD simulation to neutralize those charges. Termini are mobile enough without extra charges in the mix!

Interesting question. I have to admit, that I haven't really come across it, but for the moment it seems to me that this mechanism is used mainly to protect short alpha helices and stabilize them.
See this articles: "Helix stop signals in proteins and peptides: the capping box." and this one: "Helix capping."
A lot of research is done in combination with actin filaments, where the capping plays an important role in stabilizing the filament strands - either prohibiting the addition of new monomers and on the other hand preventing the removal of elements from the polymer strand.
This review gives an overview:"F-actin capping proteins."
This research article might also be interesting when doing simulations:"N- and C-capping preferences for all 20 amino acids in alpha-helical peptides." As always, if you have some problems with access to the articles, let me know.

As I explain in my answer, I don't think 'capping' in this context is the same concept as 'helix capping.'

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Are there statistics on Sickle Cell Traits based on country of origin?
And where was it originally from and how does it spread?
Thanks.

How have you tried to answer this question? A simple google search answers the first for me.

@kmm - By country and by province, I have not found any statistics. If you stumble over an article, please kindly post it here.

Can I say all the Chinese with SCT have recent African or South Asian ancestry?

For "where does it come from and how does it spread?", why not read Wikipedia?  Short answers: (1) malarial regions of sub-Saharan Africa; (2) movement of people and genetic introgression.
Googling 'sickle cell "country of origin" turns up, for example:
"Sickle cell disease in areas of immigration of high-risk populations: a low cost and reproducible method of screening in northern Italy" Blood Transfus. 2014 Jul; 12(3): 346–351. doi:  10.2450/2013.0188-13 PMCID: PMC4111816
Country    Selected     Enrolled/   Enrolled/
                        negative    Hb variant
-----------------------------------------------
Ghana      241 (51.4%)  112 (47.1%) 53 (57.6%)
Nigeria    152 (32.4%)  77 (32.4%)  29 (31.5%)
Guinea      15 (3.2%)   8 (3.4%)    4 (4.3%)
Cameroon    13 (2.8%)   10 (4.2%)   1 (1.1%)
Senegal     12 (2.6%)   8 (3.4%)    1 (1.1%)
Ivory Coast 10 (2.1%)   9 (3.8%)    1 (1.1%)
Other       26 (5.5%)   14 (5.7%)   3 (3.3%)
Total      469 (100%)   238 (100%)  92 (100%)

"The burden of sickle cell disease in Cape Town", South African Medical Journal 102(9), 2012 Wonham et al. http://www.samj.org.za/index.php/samj/article/view/5886/4421

Distribution of sickle cell disease patients by country of origin. Up to 93.1% (n=54) of the patients were originally from other countries in Africa, mainly from the Democratic Republic of Congo (62.1%, n=36).

Thanks. Since SCT is spread by inheritance, not by malaria or mosquito, I wonder if the spread of this trait is correlated with the improvement of transportation technology and the human migration that came after it.


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Why were wisdom teeth not eliminated by evolution?
Supposedly evolution was very efficient and evolved many human proteins over a few thousand generations. Yet obvious detrimental traits like wisdom teeth remained. Why?

You're asking about one specific case, but I think the more general question here has good answers for you.

Not everyone has problems with impacted wisdom teeth, and removing them is a profitable enterprise, so please use caution before you say we should evolve to 'x'. We have always had wisdom teeth, but removing them is a relatively recent affair.

Please explain why wisdom teeth are "obviously" detrimental, because it's certainly not obvious to me :-)

I dunno who would describe evolution as "very efficient", it can result in amazing solutions that would be incredibly hard to arrive at by design but making random changes and throwing away the bad ones is not exactly quick or waste-free.

I would also point out that evolution does not have a will! It just happens. The fact that some traits change faster or slower over time is a matter of chance.

I am changing the title by removing "yet it evolved several proteins". "Evolution evolved" is like saying "change changed" — redundant. And the idea that only several proteins evolved is quite wrong. All proteins evolved.

@Liu Considering the answer to the question this is supposed to be a duplicate of gives a long lost many possible factors, you could make this a valid question just by asking which point or points on the list are responsible in this case. including the list or a link to it would a good idea if you do this.

In addition to other points, Google says that wisdom teeth usually come in in the late teens or early 20s.  In prior ages, many people would have had at least one offspring by then, perhaps more, reducing the space for evolution to act against any detrimental effect.

Reductions in the size of our lower jaw that result in wisdom teeth sometimes becoming impacted result from changes in our diet, and are not the direct result of the evolution of a smaller jaw. This means that natural selection has had at most 8000 years to act on the phenomenon, which occurs in people in their mid to late 20s (who, historically, probably would have already reproduced if they were going to), and so the selective advantage of lacking wisdom teeth has not had enough time or been strong enough to cause the no-wisdom-teeth phenotype to spread throughout the human population.
Global human mandibular variation reflects differences in agricultural and hunter-gatherer subsistence strategies - Cramon-Taubadel, PNAS (2011)
Before Agriculture, Human Jaws Were a Perfect Fit for Human Teeth - Smithsonian.com (2015)
Incongruity between Affinity Patterns Based on Mandibular and Lower Dental Dimensions following the Transition to Agriculture in the Near East, Anatolia and Europe - PLOS One (2015)

the real risk with wisdom teeth is splitting the jaw, but as you said that only became a problem after the invention of soft processed food.

I would wager that removal of impacted wisdom teeth has resulted in more deaths than infection from said teeth. There is not a single randomized trial proving - or even attempting to prove - that removal of wisdom teeth has a beneficial effect on quality/duration of life. The UK's NHS stopped paying for the standard procedure, and the Cochrane Report advises against it. I have my wisdom teeth; my dentist was peeved because one of them had a small cavity. When I asked why he was upset, he answered that they were hard to fill way back there. He advised me to have it removed. Um, nope.

Furthermore, neither of your your citations (one depends on the other) does not deal with wisdom teeth, but with malocclusion. You need better sources. -1 for misinterpretation/misinterpretation of support sources.

@John - Whaaaaaat???

@anongoodnurse It's possible that wisdom teeth cause problems and also removing wisdom teeth causes problems. I wasn't arguing in favour of surgery, or against it, modern surgery is irrelevant to the discussion.
The PLOS One paper discusses jaw size changes as a result of change in lifestyle, I've found another paper that discusses it more explicitly. I've made the assumption that this would be the cause dental crowding and impaction of wisdom teeth problems, I suppose this assumption could be wrong.

Your assumption ignores the much more common malocclusions which create "problems". Modern surgery is not irrelevant to the discussion. The death rate from impacted wisdom teeth is not known (contrary to your statement that infections from impaction kill), nor has it ever been known. In other words, the "problem" of wisdom teeth is largely a recently manufactured problem. Malocclusion is not. Yet we have lived with it for 10 millenia or more.

It seems a fairly safe bet that before antibiotics all infections carried a risk of serious repercussions, but I don't actually know that, so fair enough.

@anongoodnurse, problem=/= death. The fact that our change in diet is responsible for smaller jaws in industrial societies and this is responsible for the majority the problems associated with wisdom teeth is what matters for question. The cost/benefit of surgery was not mentioned becasue it is irrelevant.

@John - I'm not sure what you're talking about. My comment to you was about wisdom teeth splitting jaws. In almost 40 years of treating patients, I have never heard that one! If you could cite a source, I need to read it, please. Otherwise I will continue to believe it's a whopper, that one; it is indeed! We're scientists here.

@anongoodnurse http://www.sciencedirect.com/science/article/pii/S1079210405802999 You should not rely on anacdotal evidence, esspecially when refering to something that became a problem prior to the development of modern medical technology. And I was referring to several of your above post, I would not normally rely to "Whaaat?" or anything like it.

@John - Thanks for the link. Please note that there is no control group; everyone in that study had a fractured mandible. What percent of people with M3s have mandibular fractures? Is it significant? And, please note: people make a great deal of money by pushing for the removal of M3s. Whenever someone who does this for a living publishes a study which supposes to support it, you should always ask, is there a conflict of interest? In other words, quis bono? Too many third parties have found differently. Again, quis bono?

control groups for injury causes tend to be prohibitively expensive to create becasue you must have a much much larger sample size usually combined with an extremely long study length, it doesn't bother me in the slightest they don't have one.  We already know wisdom teeth are more likely to develop impaction, the cost/benefit of surgery is largely individualistic and irrelevant to the discussion. If you have links to any of these third party studies showing no connection that would be helpful to your case.

It is not irrelevant that the researchers have a vested interest in promoting the agenda that impacted wisdom teeth should be removed.

@John: http://onlinelibrary.wiley.com/doi/10.1002/14651858.CD003879.pub2/full "There is some reliable evidence that suggests that the prophylactic removal of asymptomatic impacted wisdom teeth in adolescents neither reduces nor prevents late incisor crowding."

@anongoodnurse you do realize that does not show no connection,  just no connection between a very narrow subset of wisdom teeth and another narrow set of complications. If you want to continue this I suggest creating a chat.

Wisdom teeth do have a function. If you are missing a molar before the age of 20, a wisdom tooth can easily move in to fill in the gap, by filling in the space or by pushing the molar ahead of it.
This trick has been used by dentist to "fix" the teeth of teenagers who have  molars with large cavities but still have wisdom teeth that have not erupted. So rather than go to extremes to save a bad molar, it is just yanked out and the wisdom tooth slips in. Problem solve. ( of course it depend on the actual wisdom tooth as some wisdom teeth are improperly positioned or appears unlikely to erupt to enable this  trick to be used) example
Modern dental hygiene is good (but not good enough). So people tend to have all their molars in their early 20s (but not in their mid 30s). The the wisdom comes in too early to be useful to modern people. But i am guessing it had more use in earlier times.
That said... the trait for (third molars) wisdom teeth does not appear to be under positive selection in the human population as not everyone has it. Numbers vary depending on population.  10 to 25 percent of Americans of European ancestry are missing at least one third molar. For African Americans it is 11% and Asian Americans, the figure is 40 percent. The Inuit, a group of people who live in the Arctic regions of Canada, Greenland and Alaska, have the fewest wisdom teeth; about 45 percent of them lack one or more third molar.
percentage

You need a source for your statement that wisdom teeth are being selected against. That is not a credible claim.


text:
Medium preparation, using calcium hydroxide instead of potassium hydroxide
As the question states, I am interested in growing alkaliphile bacteria. I have seen many media use KOH, mainly to neutralize, and was wondering if it is possible to change this to Ca(OH)2?
Is there a reason KOH is used instead of any other alkali solution to neutralize media?

Calcium is a bad choice as it will form precipitates with either phosphate ions as well as with carbonate or CO2.

As @Chris said, $\ce{K+}$ salts are soluble in water whereas plenty of $\ce{Ca^{+2}}$ salts such as $\ce{CaSO4}$ and $\ce{Ca3(PO4)2}$ are insoluble in the aqueous medium. Therefore it leads to the precipitation of phosphate-containing proteins and sulfate-containing metabolites. In addition, $\ce{Ca^{+2}}$ forms coordination complexes with calcium-binding proteins which participate in discrete signaling pathways. Interfering with this system could lead to subtle and irreproducible results. $\ce{K+}$ ion mostly participates in creating a voltage gradient across the membrane, nothing more.
Moreover, ionic strengths should be considered. $\ce{Ca^{+2}}$ is a divalent cation. A solution of $\ce{KOH}$ and a solution of $\ce{Ca(OH)2}$ with the same pH would definitely have different ionic strengths. Therefore despite achieving the same pH of the medium, ionic strengths vary depending on the salt used. Abnormal ionic strengths affect the structure of proteins in many ways. In general, it has been proven that changes in $\ce{K+}$ concentration lead to less severe outcomes compared to $\ce{Ca^{+2}}$.
EDIT: $\ce{Ca(OH)2}$ forms precipitates in an aqueous solution because it is barely soluble in water ($K_{sp}$ $\pu{=5.5 \times 10^{-6}}$). The pH of a saturated solution of $\ce{Ca(OH)2}$ is 12.347. To achieve other pHs one must add strong acid or base (a standard $\ce{KOH}$ solution perhaps) or use dilution; so as you can see, introducing $\ce{Ca(OH)2}$ just leads to unnecessary complexity, best to be avoided. Also, $\ce{Ca(OH)2}$ leads to the formation of $\ce{CaCO3}$ in the presence of atmospheric $\ce{CO2}$, making it even a less appropriate material for the preparation of the medium. Calculations using $K_{sp}$ shows a saturated $\ce{Ca(OH)2}$ solution has pH = 12.347 and [$\ce{Ca^{+2}}$] =  0.01111

For my research I am interested in using bacteria to precipitate CaCO3 and at the same time prevent the formations of soluble salts like potassium and sodium sulphates/chlorides. As such, my approach was to try replace them with Ca-containing buffers and salts. Would there be any other Ca-containing salt/buffers that would be better suited? I am new to media preparations so still trying to understand how everything plays a role in bacterial growth. Ideally, I will find alkaliphiles that are low-sodium/potassium demanding.

@Franco Grosso
If you need to create an environment with a determined Ca+2 ion concentration and little Na+ and K+, you’ve got to consider some items. First Many famous culture mediums contain NaCl and using it is most likely inevitable even in your research. See [1] [2] [3] [4]. As you know a 15mM NaCl, 150mM KCl solution renders the cytosolic environment perfectly while a 150mM NaCl, 15mM KCl represents extracellular medium nicely [5].
Therefore K+, Na+, Cl- ions should exist in your system at least in trace amounts for successful cell culture.

@Franco Grosso, Still, you can use R-NH2/ (R-NH3+ Cl-) buffers if you insist on lowering Na+ and/or K+ ions demand. Examples of such organic compounds are CAPS, PIPES, TRIS, TAPS, glycylglycine [6]. Subsequently, adjust pH by adding HCl. Here arises another problem.  Chemicals mentioned above as well as Phosphoric acid, carbonic acid buffers have the potential to chelate your Ca+2. Therefore, it is best to avoid them. Look in some papers for the exact protocols and the best buffer systems. CAPS can be appropriate. Its pKa is 10.4 and can be used to grow alkali bacteria.

@Franco Grosso, But still search for better results. Avoid making mixtures of buffers.
Inject Calcium ion by simply adding CaCl2(aq) to the system. Remove the excess amounts by EDTA (forming stable EDTA-Ca complexes). In this way, you can adjust your calcium ion properly. A somewhat related paper about similar calculations on Mg+2 ion.[7]
The precise ingredients of your culture depend on your research topic but you get the general idea. [8]
I hope that I’ve understood your question correctly :)  good luck!
[1] : https://microbenotes.com/chocolate-agar/

[2] : https://microbenotes.com/new-york-city-agar/
[3] : https://microbenotes.com/sorbitol-macconkey-agar/
[4] : https://microbenotes.com/category/culture-media/
[5] : Molecular Cell Biology of Lodish 8th edition page 496 Figure 11-18
[6] : Wilson and Walker’s Principles and Techniques of Biochemistry and Molecular Biology 8th edition Chapter 0
[7] https://pubmed.ncbi.nlm.nih.gov/11772/
[8] : https://www.sciencedirect.com/science/article/pii/S0091679X08611152

thank you very much for the detailed explanation! I think you have understood the question better than I did haha. Now I understand better what parameters and considerations I need to include on my medium. Also, great references.

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text:
Questions about RNA Polymerase
I'm confused about the terminology and directions described in processing DNA to proteins in this paragraph.

RNA polymerase reads a DNA template in the 3’ to 5’ direction to
  synthesize RNA in the 5’ to 3’ direction. Transcription can occur in
  either direction, but not in either direction from a single promoter.
  RNA polymerase can only transcribe in one direction (5’ to 3’) with
  respect to reading one strand of the template DNA in the opposite
  direction (3’ to 5’). In general, each promoter recruits RNA
  polymerase to a particular site and indicates in which the direction
  RNA polymerase will move along the DNA. As RNA polymerase is moving,
  there will be only a single strand that can be used as a template to
  allow 5' to 3' synthesis of a transcript.

Sentence 1:
What's the difference between reading and synthesizing RNA?
Sentence 2:
What's the difference between synthesizing and transcribing?
Sentence 3:
Didn't this just contradict sentence 2?
Sentence 4:
If RNA polymerase is recruited at a site to and directed to "move along" the DNA, what is it doing when it "moves along" (reading? synthesizing? transcribing? wtf?).
Sentence 5:
My understanding is this is the "transcribed strand", not the "coding strand" of DNA, correct?
Question:
I don't understand this paragraph and the more I read it, the more confused I get. Could someone please clarify (preferable with visuals)?

I think if you search youtube for "rna transcription animation" you will find plenty of visual demonstrations.

What's the difference between reading and synthesizing RNA?

What's the difference between reading and writing a book? Synthesizing RNA means producing an RNA based on a sequence in DNA. Reading it means processing RNA that is already produced. Reading also implies that protein will be produced based on the sequence in RNA.

What's the difference between synthesizing and transcribing?

"Synthesize" means to produce any chemical molecule. "Transcribe" is specifically the synthesis of RNA form DNA via a polymerase (as opposed to for instance inorganic synthesis of RNA de novo, as might be done in a chemistry lab).

Didn't this just contradict sentence 2?

It's just saying that genes can be oriented forward or in reverse. Reverse genes are on the opposite strand, so they are still 5' to 3' (the 5' ends of the two strands are on opposite ends of the DNA). But every gene must still have a promoter on its 5' side.
And actually, that bit is not quite true: There are bidirectional promoters that will cause transcription in both directions.

If RNA polymerase is recruited at a site to and directed to "move along" the DNA, what is it doing when it "moves along" (reading? synthesizing? transcribing? wtf?).

Usually, it will transcribe (so it will also synthesize, or "read"). But technically, RNA pols belong to a family of proteins which are "molecular motors", meaning that their fundamental activity is to move along DNA step by step like a little monkey climbing a ladder. With RNA pols, RNA synthesis is coupled to this movement, so each step on DNA also causes a letter to be added to the RNA they are making.
Also, technically the RNA pol is not only moving and making DNA, but also unwinding the two strands of DNA and separating them. But this may be outside the scope of your material.

My understanding is this is the "transcribed strand", not the "coding strand" of DNA, correct?

RNA comes out matching the sequence of the gene (except for T->U), and it is assembled through basepairing to DNA. If it paired with the strand the gene is on, the RNA would come out as the reverse complement of the gene. Instead it is assembled on the opposite strand, which is already the RC of the gene. RC of RC of a sequence is the same sequence. Thus we say RNA is transcribed from the "non-coding" strand, but keep in mind that these coding/non-coding assignments are arbitrary and only used by us humans, the cell does not have a special marking for it (beyond the 5'/3').

I don't understand this paragraph and the more I read it, the more confused I get. Could someone please clarify (preferable with visuals)?

It's very simple: DNA is a directed (because of 5'/3') string of ACTG. It is coupled to another, complementary string that runs opposite to it. The sequence on either strand may be meaningless, or parts of it may encode genes. Genes consist of a promoter, some sequence, and terminator. RNA pols can slide along either strand, but only in 5' to 3' direction, so they will slide in opposite directions on opposite strands, like cars on a two way street. When RNA pol encounters a promoter, it starts synthesizing an RNA: It separates the two strands, and lets single RNTPs basepair with the opposite-direction strand, when they do so it glues their phosphate backbones together. It keeps sliding and making RNA like this until it reaches another sequence, the terminator, at which point it stops assembling RNA and releases it. The RNA snaps off DNA and goes off on its merry way, the two strands of the DNA that were separated by RNA pol come together again.
Thus for every promoter-terminator pair, whatever sequence is in between them will be transcribed into an RNA. These are basically genes. These genes may be on either strand of DNA, and they must always be oriented along the 5' to 3' of the strand they are on. Thus genes on opposite strands will appear "reversed" with respect to each other.

"Sentence 1:
What's the difference between reading and synthesizing RNA?"
Sentence 1  relates to what is the most trivial if most important to not mis-understand: RNA polymerase is said to "work" ( Wikipedia, RNA polymerase) in 5' to 3' direction.
In order to paraphrase your question accordingly: What would "to work" mean in that sentence? It would mean "synthesizing" RNA, it would not mean "reading" DNA (the reading I circumscribe as "unraveling/traveling" from '3 to '5, while, at the same time,  "elongating" in '5 to '3 direction). As it now occurs: The text says "... RNA polymerase reads a DNA template..."! Thus,   changing  your question to "...difference between reading DNA (do not omit "DNA") and synthesizing RNA apparently answers the question. However, that is not the whole story. I think it doesn't come easy to see that, see above, the "work" is like  old fashioned homework (in German: "Stricken"): What you have just seen is what you got to add - to the end (to paraphrase some common acronym).
If polymerase had some bench or large table it'd go "a-head" and work from 5 to 3, not the other way round. Polymerase must put the letter that it had just read as  been ordered to the end of the list that "goes out",  that polymerase thus "table-waited"  from 5 to 3,  which makes "sense". So - "reading" might very well be "synthesizing" in terms of direction - however, defined by mechanism, it is not (it is first in, DNA, first out, RNA, "nothing in store"). Again, in some surprising way - to be specific: in terms of direction -   reading could be, but is not synthesizing.
"Sentence 2:
What's the difference between synthesizing and transcribing?"
Sentence 2 does not use the word transcribing. In the context of sentence 2 synthesing and transcribing are synonymous.
"Sentence 3:
Didn't this just contradict sentence 2?"
Sentence 3 does not preliminarily explain what sentence 4, the following, explains:  "...each promoter  ... indicates in which the direction RNA polymerase will move along the DNA." Thus sentence 3 does not seem to "clear up"  the ambiguity of sentence 2 which lies in the issue of "direction". The word "direction" in sentence two does not make clear how "direction" relates to the concept of direction as the author makes use of in  sentence 1.  One specific gene defines "any" direction (which you wrote about in some answer of yours).*
"Sentence 4:
If RNA polymerase is recruited at a site to and directed to "move along" the DNA, what is it doing when it "moves along" (reading? synthesizing? transcribing? wtf?)."
It transcribes (most general term) by reading (the  template/anti-sense)  DNA and synthesizing RNA (cp. answer on sentence 1 above) accordingly, first in first out, elongating first becomes last (there is no memory).
"Sentence 5:
My understanding is this is the "transcribed strand", not the "coding strand" of DNA, correct?"
Correct.

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text:
When does histone synthesis occur in relation to DNA replication?
Do histones have to be synthesized before DNA is replicated to allow the DNA to coil around histones?

Only nucleic acids are replicated — proteins are synthesized from mRNA. If you didn't know this you shouldn't have posted but done some preliminary work instead. However your basic question on the coordination of DNA and histone synthesis is worth asking, so I have edited your question appropriately.

I love this question the way it is.

Yes, they have to. But that is just half of the story.
The (canonical) histones which are used in DNA replication are synthesized at the beginning of the S phase, and subsequently transported into the nucleus. Studies have shown that newly synthesized DNA is immediately packed into nucleosomes. Thus, it is necessary that these structures are available prior to (or at least just in time with) the replication.
However, there are different models on how the histones are inserted into new DNA. One model assumes that old and new nucleosomes are both incorporated into newly synthesized DNA after the replication fork. Others assume a semi-conservative approach where the old histones are disassembled into their subunits and then mixed together with the newly synthesized ones. For example, there is a model that proposes that the parental H2A/H2B and the H3/H4 dimers disassociate, while another assumes a disassociation of the H3/H4 dimers as well.
Figure: Nucleosome synthesis models for DNA replication

References
a Angélique Galvani and Christophe Thiriet (2013). Replicating – DNA in the Refractory Chromatin Environment, The Mechanisms of DNA Replication, Dr. David Stuart (Ed.), InTech, DOI: 10.5772/52656. Available from: https://www.intechopen.com/books/the-mechanisms-of-dna-replication/replicating-dna-in-the-refractory-chromatin-environment

In Molecular Biology of the Cell (Chapter 4), it is written that

The major histones are synthesized primarily during the S phase of the cell cycle and assembled into nucleosomes on the daughter DNA helices just behind the replication fork (see Figure 5–32). In contrast, most histone variants are synthesized throughout interphase. They are often inserted into already-formed chromatin, which requires a histone-exchange process catalyzed by the ATP-dependent chromatin remodeling complexes discussed previously

This is too much simplified. Old histones are reused, and probably mixed together with new ones.

@adjan You are right. If necessary I will put my answer as a community wiki in order to improve it with your explanation. Otherwise, we can leave them side by side.


text:
Cells in tissues
Tissue (biology): In biology, tissue is a cellular organizational level intermediate between cells and a complete organ. A tissue is an ensemble of similar cells from the same origin that together carry out a specific function.(Wikipedia)
Are all the cells of a tissue of a kind?
In the definition Tissue  what is from the same origin?

Welcome to SE Biology. Please read the instructions on constructing good questions. A title should be a one line phrase indicating what the question is about, not an extract from WIkipedia. Also, you are expected to write in standard English and a single question mark after a question is sufficient. I have corrected your question. Please try to do better next time.

What you say is true that most of the cells in a tissue are of the same kind. However, as with most rules in biology, there is almost always an exception to these rules. There are only four types of tissues (can be split up into further subdivisions): muscle, epithelial, connective and nervous. Also, a muscle tissue is made up of an ensemble of myocytes (muscle cells). Therefore, the answer to your question would be yes, the cells in a tissue are (if not all, then) almost all of the same kind.

Many different types/kinds of cells comprise a single tissue.  For instance, the epithelial tissue of mammalian skin can contain cells that produce hair, excrete sweat, or do neither of these things but simply serve as a barrier.  These cells are all epithelial tissue.   Here is another example of the diversity of cell types in a single tissue: the cells of the brain are part of 'nervous tissue', but there are thousands of different kinds of neuronal cells (the precise number is growing actually; see this website, where this image was grabbed).

Blood is technically a tissue, and yet there are many, many different kinds of blood cells.

In reference to your second question, the cells share a common origin in a tissue because they come from a small number of precursor cells, like the depiction in the image above for blood cells.


text:
What kind of fish is this, caught in Cape Coral, Florida?
What kind of fish is this?
It was caught in the canal in Cape Coral, Florida. The canals are clean brackish water — a mix of saltwater from the Gulf of Mexico and freshwater from the Caloosahatchee River — but the canal where the fish was caught has gulf access so it should be saltwater. The fish was about a foot long, a little less maybe.

Please provide approximate size if possible. Also, please comment whether this fish is fresh water or saltwater, since the canal is fed by the Caloosahatchee River. Thanks

The canals are clean brackish water (a mix of saltwater from the Gulf of Mexico and freshwater from the Caloosahatchee River bu the canal has gulf access so it should be saltwater, the fish was about a foot long.

It looks like the spotfin jawfish, Opistognathus robinsi. The larger ocellated spot on the foredorsal fin is a key identifier for this species. They are not so common in Florida, but do inhabit sandy bottoms, such as canals. Are you sure about the length? It looks about 5 inches from the photo provided, when compared with the the size of the hole on the dock. This species grows to about 5 to 6 inches.
See here for more info.

Thanks a lot, that should be it, you are right about the size.

Hi @johan, thank you for your reply. Jawfish are pretty amazing fish and many species keep their fertilized eggs stored in their large mouths until they hatch! If this or any other future answer has solved your question please consider accepting it by clicking the check-mark. This indicates to the wider community that you've found a solution and gives some reputation to both the answerer and yourself. There is no obligation to do this.


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Why is the separation of biochemical synthesis pathways safer and more economical?
During our first lecture of plant physiology, our teacher told us that the separation of biochemical synthesis pathways was advantageous because it was safer and more economical. The problem I got, while studying this back at home, was that he didn't explain why it is so.
I can understand why it is safer (for example, a lysosome could break down a lot of major components of the cell if that lysosome was not restricted to its area), but it's quite difficult for me to understand why it's more economical, in terms of energy. Any clear/simple explanation about this would be greatly appreciated.

False Economies?
Goodness knows what the poster’s teacher meant by saying that the separation of biochemical pathway is “more economical”! This is not a term usually applied to metabolism and, anyway, in life people who are economical do not always get value for the money they do spend, never mind obtain a better quality of life.
Most treatments of the separation of biochemical pathways justifiably emphasize the advantages of being able to regulate forward and reverse reaction sequences independently. However let us have a look at the separation of pathways in terms of energy, as the poster requested.
Some basic thermodynamics
The poster also requested the explanation be clear and simple. The following is simple, as long as you are familiar with the some basic ideas of chemical thermodynamics. If you are not, I suggest you read the three pages in  Section 8.2 of Berg et al. online. (Whether it is clear or not I leave others to judge.)

What determines whether a chemical reaction proceeds is the overall
(Gibbs) free energy change (ΔG). If it is negative, the reaction is
thermodynamically favourable.
The actual free energy change depends on ΔG0, the standard
free energy change (reflecting the chemistry of the reaction(s)),
together with the actual concentrations of reactants and products.
Enzymes are necessary to catalyse reactions in living organisms,
but do not affect the position of their equilibrium.

Argument
For simplicity, let us consider a series of reactions interconverting compounds M and P:

M ⇄ N ⇄ O ⇄ P

No separation between pathways
Consider a situation in which the forward (M➞P) and reverse biochemical transformations (P➞M) involve the exact same chemical changes catalysed by the exact same enzymes, i.e. no separation between pathways. In order for this to work the overall ΔG0 must be near zero, otherwise reaction in one direction will be very difficult to achieve (require a very high concentration of starting reactant). For a ΔG0 near zero there will be equilibrium (no net reaction) at equal concentrations of M and P. In order to cause a flow of metabolites, say in the forward direction, there must be an increase the concentration of M relative to P.
There are two problems with this.
First, quite a large ratio of M to P, say, would be required to achieve net flow through the pathway, and this would involve having a large pool of unreacted M. (Section 8.2 of Berg et al., cited above, has some calculations that illustrate this.) This may or may be regarded as economical use of thermodynamic energy, but is not particularly economical in the  use of resources. However, a ‘pathway’ in which it is employed is glucose transport in the liver (actually a single transport process).
Second, the direction of overall reaction is controlled solely by the ratio of M to P, a situation that lacks flexibility.
Separation between pathways
If separate pathways are involved, the first problem of a single pathway mentioned above is overcome in the following way. Each overall reaction can have a high negative ΔG0, so that it does not require such a large pool of reactant and is essentially unidirectional. One might ask how this can be, as the value of ΔG0 for the chemical reaction, M ⇄ P is fixed. The answer is that separate pathways will involve  other reactants, so that the overall forward reaction might be
M + X ➞ P + Y
whereas the reverse reaction might be
P + A ➞ M + B
This is considered for glycolysis and gluconeogenesis in Section 16.3.6 of Berg et al. — with actual equations. The ΔG0, for glycolysis is quoted as – 84 kJ/mol, and that for gluconeogenesis as –38 kJ/mol.
Of course, if both reactions have a thermodynamically favourable values of ΔG0, it is necessary for the cell to prevent the uneconomic cycling of P back to M after it has been formed. However the fact that the pathways are different means that different enzymes will be involved, which are the targets of regulatory molecules that can switch them off and on. These regulatory molecules usual reflect supply and demand, but need not be intermediates in the reaction sequences, and they can act as far more sophisticated ‘switches’ for the enzymes. The particular details of this for glycolysis and gluconeogenesis can be found on the first page of Section 16.4 of Berg et al.
…the price of everything, the value of nothing
So are separated biochemical pathways energetically more economical? The large free energy change that drives these reactions is ‘lost’ as heat, so one could argue that the reverse is actually true. Or, then again, one might say that “you get what you pay for”.


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Terminology of the sequences of promoters in relation to DNA strands
I'm studying molecular biology and I'm trying to understand an experiment which shows the importance of promoters in the relative transcription level (RT). The image below comes from Rolf Knippers' book "Molekulare Genetik" (8th edition).

The legend says (among other things):

Die erste Zeile gibt die normale "Wildtyp"-Sequenz der 5'-flankierenden Region wieder.

Which, in english, means something like:

The first line repeats the normal wild-type sequence of the 5' flanking region.

The column on the right gives the relative transcription (RT) level, 1.0 being the highest possible level of transcription. As we can see, the lines where some parts of the "5' region" have been deleted give quite low RT levels, since some regions of the promoter are missing.
My questions are the following:
1) According to this and this, I understand that RNA polymerase reads and uses both coding and non-coding strands in order to synthesize RNA. Therefore, how did they manage to use the sequences strands regions had been deleted to make a polymerase "read them" and perform transcription?
2) If the polymerase reads the template strand in the 3' -> 5' sense, shouldn't we talk of "ATAT box" or "TAAC box" instead of "TATA" or "CAAT" boxes? Does it mean that the "promoter" regions they are using on the graphic above are actually on the coding strand?
Thanks a lot for your help.

Could you clarify your problem. As far as I can see the results are (1) deletion of them globin-specific element reduces transcription to 10% (2) further deletion of the CAAT-box reduces it to 2% (3) further deletion of the TATA box reduces it to 0.5%. Are you asking why the values for (1) and (2) are not zero instead of small but non-zero? (I would say (3) is zero.) Also, the papers you cite say nothing about coding sequences (i.e. those with triplets that contain amino acid info.). Do you mean coding strands?

PS I have used your term "coding strand", but it is one that is best avoided as it causes immense confusion. If you clarify your first question I will deal with your second question, which illustrates the knots you can tie yourself when you use these terms.

@David Yes, I meant coding strand, sorry about that. The main problem that I have (for my 2nd question) is that, since RNA polymerase is supposed to read a template strand (i.e. non-coding strand) in a 3'->5' sense, I don't understand why the promoter's regions (TATA box & co.) are on the 5' side of the transcription's initiation site.
My first question actually concerns the methods of the experiment: how could a polymerase read or use a strand that is in a 5'->3' sense (since she's supposed to read in a 3'->5' sense), and, moreover, how could she use it since the coding strand is not there?

Gene sequences are given as the coding strand by convention. This does not say anything about which strand transcription factors bind to. The protein that binds the TATA box, for example, actually interacts with both strands.

OK. It would seem your problems are those of a beginner unfamiliar with the conventions, which stem from a combination of history, logical consistency and scientific neutrality as regards interpretation. I'll post a comprehensive answer, if nobody else does. But now its Mahlzeit here in Europe and I'm tied up tomorrow morning.

I've edited your question, altering the title to focus on the nomenclature question and making a few other minor changes. You can always revert them if you don't like them.

It appears that this question is one of terminology, so I am answering it as such.
Convention for representing features in DNA sequences
The convention is that in indicating any sequence feature† in a protein-coding gene on double-stranded DNA, a single strand‡ is represented — the one from which the amino sequence could be read using the genetic code (conceptually, with T substituted for U). Like any other nucleic acid sequence§, it is always written in the 5ʹ to 3ʹ direction in the same manner as the mRNA transcribed from it, without this being explicitly stated.
† An exception might be hemi-methylation, in which case both strands would be shown.
‡ I call this the sense strand. I discuss the nomenclature further below.
§ An exception is that tRNA anticodons are sometimes written in the 3ʹ to 5ʹ direction for ease of comparison with the codon, but in this case the directionality is indicated.
Origin and justification for this convention

Historical. The amino acid sequence of the protein (the product of the gene) is central to this convention because knowledge of the genetic code, and hence representation of the region of the mRNA that encodes protein — and by extension the DNA — was the first sequence information to be known.
Logical consistency.  Later other sequences features were identified (some of which initially may have just been genetic features), e.g. ribosome binding sites, polyadenylation addition signals, transcription start sites, promoters, transcription factor recognition sites. It was logically consistent to represent them on the same strand as the coding sequence.
Functional agnosticism. In many cases the function of a sequence followed its description, so there was no reason initially to place it on any particular strand. However, even if it were thought that the function of some sequence were to be recognized on the opposite strand (what I would call the anti-sense strand), it would be unwise scientifically to  change the representation to indicate this. Science progresses and interpretation changes. Better to separate concrete descriptive features from conclusions about their function.

It couldn’t ever be an ATAT box
Even if you represented the TATA box on the anti-sense strand, it could never be called an ‘ATAT box’ (as suggested by the poster) because, according to the basic convention, ATAT is 5ʹ-ATAT-3ʹ, and on the antisense strand the sequence is 3ʹ-ATAT-5ʹ, i.e. TATA!
Terminology for referring to the two strands of dsDNA
Whereas the above is the convention followed universally, the following is just my opinion. In science terminology is important to communicates ideas unambiguously, so I think it worthwhile explaining the ambiguity in some of the terms, the use of which I discourage.
Sense and anti-sense
This is my preferred term because, although not perfect, it avoids the pitfalls of the others. The idea seems to me clear that when you read the string of codons that encode the amino acid sequence from this strand they ‘make sense’. (Anti-sense is used in preference to non-sense, as ‘nonsense’ was the term used historically for mutations that converted amino acid codons into stop codons.) It can also be extended to non-protein coding genes (e.g. for tRNA), where ‘sense’ correlates with the sequence of the gene product.
I shall use ‘sense’ and ‘anti-sense’ as reference terminology in discussing other terms.
Coding and non-coding
This has the disadvantage that it cannot be extended to non-protein coding genes. However my primary objection is that it can cause confusion, as coding only unambiguously refers to mRNA. As the anti-sense strand is the template for RNA polymerase, one might make the mental association between this and ‘coding’, whereas it is the sense strand that is meant in this (admittedly common) usage.
Template and non-template
Template might be a more logical term for the anti-sense strand as this is the template for transcription by the RNA polymerase (although mRNA is also a template — for translation). However it is used only infrequently.
Plus and minus
This terminology is used for single-stranded (especially RNA) viruses to represent the whole genome, where in plus-strand viruses the genome is also the mRNA, i.e. the sense strand. One problem here is that it can be confusing for the beginner, who by extrapolation may assume that in double-stranded DNA genomes one strand is the sense strand for all genes. It is not.  Which brings me to my final point…
…whatever terminology you use, it is better to make sure it is clear that you are referring to the sense or anti-sense strand of a gene, not of the whole genome. You need to employ some other terminology to distinguish between the two strands of e.g. bacterial or plasmid DNA if it is necessary to distinguish them.

Thanks a lot for your complete answer! It was very informative and I will probably come back to it if I get confused about all this again. :)

@AlwaysConfused — I did check the IUBMB, but all I could find dated from the 1960s or thereabouts. I think the question of IUBMB approved terminology has diverged from the empirical practices adopted by the databanks. I studied the GenBank format carefully to write a computer program that parsed it, so what I have written is, in effect, my own description of that. The only document I have is "The DDBJ/EMBL/GenBank Feature Table" (2000), which describes the annotation rather than the sequence convention". You might find something at https://www.ncbi.nlm.nih.gov/WebSub/?tool=genbank.

@AlwaysConfused — I gave a link to the BankIt because if you are submitting sequences it presumably tells you explicitly what the convention is at some stage. You'd have to take the time to check it thoroughly to find out.


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Weed Identification
These are are weeds which grow on the silt of a lake, in India , climate is semi-tropical monsoonal

They dont look native probably exotic species. What are they?
Height is probably 1.5 feet.
Lake is this

Is there any reason you don't believe they're native plants?

@Jude they are not found elsewhere except on lake bed everyear, moreover lake was constructed 50 yrs back ,

Please edit your question with the location (e.g. 1) what the lake name is, 2) what's the name of the river that drains into the lake, 3) the rough height of the plants). This would help a lot along with any other relevant details you can add.

@AlwaysConfused make this as answer

The first one looks similar to artemesia vulgaris, which grows in many places opportunistically in the south of europe. If you rub the seeds, do you get a very strange smell? if so it could be an artemesia. The second plant originated in America, the first plant from america to arive in the old world is Datura, for which the importation date is perhaps millenia old as similar to Datura in indian and chinese documents. It is an american solenacea related to tomatoes and datura.

As Always confused already suggested, the second picture is Xanthium strumarium.
This is a very variable species, and there is a lot of debate around splitting this species into (sub)species. There is a possibility this is plant belongs to one of the few accepted species that wikipedia lists, some even native to Eastern Asia. However, I can't verify this because pictures of these are scarce.
But from my personal field expierence, this plant looks exactly like the X. strumarium and the habitat also matches, so I am comfortable to call this X. strumarium.
As to your first plant:
- It will be hard to say without a close-up of the flowers/seeds.
- It would be better to ask only one plant per question, so please remove it here and ask a new question.


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Why do some tissues have insulin-dependent glucose transporters and others not?
Insulin upregulates GLUT-4 glucose transporter insertion in skeletal muscle and adipose tissue. But there are many tissues in the body that use insulin-independent glucose transporters (like GLUT-3 in the brain). Would there be any disadvantage to have the entire body use insulin-independent transporters like GLUT-3? Why involve insulin in this? Wouldn't the concentration of glucose in the blood regulate the influx of glucose via concentration gradients anyway?

I don’t understand why there has been a call to close this question as too broad. It may be naive, but it is quite specific and answerable quite simply and relatively briefly.

I have edited the title of your question to make it clearer, and removed the superfluous and generally ill-advised assertion that something is well-known. If you think I have changed your meaning do say so. Also, calling your question 'naive' was not meant in a depreciatory manner. "Basic" would have been a better term. I think my summary makes it clear why this is basic, but I still think it is a valid question, and that my answer will be useful to others.

Summary
The whole point of hormones is that they allow the organism to control the metabolism of tissues in an integrated manner, rather than each tissue acting independently. Insulin, glucagon and epinephrine are classic examples of this in relation to carbohydrate metabolism. In the fed state, the fasted state and in stress situations it is appropriate for different tissues to respond in different ways. The presence or absence of a hormone receptor — together with the enzyme complement of the tissue — achieves this. Allowing all tissues to have only GLUT-3 (or all GLUT-4) would mean they would all respond to changes in glucose availability in the same way — a totally inappropriate situation for the organism, with potentially disastrous consequences.
More Detailed Answer
Insulin is an indicator of the fed state. In such circumstances there will be a surplus of glucose and it is of benefit to the organism for it to be taken up by muscle and adipose tissue for storage as glycogen and fat, respectively. Conversely it is important that in starvation blood glucose is not so utilized, but spared for those tissues for which it is vital in any conditions. (Muscle can utilize other metabolites such as fatty acids.) Hence, for these tissue allowing glucose transport to be controlled only by blood glucose concentration would not produce a sharp cut-off and result in deny this resource to those vital tissues which cannot replace glucose by other energy sources.
The tissues you mention such as brain (and erythrocytes) depend absolutely on glucose, irrespective of whether the organism is in the fed or fasted state. If they had only an insulin-dependent transporter they would be starved of glucose during the fasted state, with lethal consequences. The insulin-independent transporter allows continued transport down the glucose concentration gradient, even as the blood glucose concentration falls.
Note that blood glucose concentration in the fasted state is maintained by the liver, so that this tissue has an insulin-dependent transporter, not to allow glucose uptake, but to allow the glucose produced by gluconeogenesis to be transported out into the blood.
Further Reading
I would hope that the logic of my answer will be sufficient convincing, but it is good practice in Biology-SE to provide references to support one’s arguments. Section 30.22 of the online edition of Berg et al. discusses the metabolic profile of different tissues and includes some discussion of glucose metabolism and glucose transporters. (The liver glucose transporter is actually different from that in nervous tissues, as is that in erythrocytes — see Wikipedia article.)


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What would life expectancy be in the western world in the absence of Ischemic heart disease?
In 2012, the leading cause of death was Ischemic Heart Disease.  In 1st world countries, what is the life expectancy for people who do not die of Ischemic Heart Disease?  I'm interested in the USA, but I'm happy for you to provide information on other 1st world countries if USA data is unavailable.
My motivation for asking the question is a curiosity of how much our life expectancy would increase if IHD was abolished.

This will be a tough question to answer, but people tend to die from one of only a handful of age-related diseases (other deaths are either infection related, accidental, or "rare" diseases).

You may want to play a little bit with this: http://www.theguardian.com/news/datablog/interactive/2012/dec/13/how-people-die-global-mortality-visualised

This paper from 1991 is intervention-based, so it reports the effects of behavior modification on lifespan in people who turned 35 in 1990.  The authors report the gains for each individual behavior and then say:

Eliminating coronary heart disease mortality is estimated to extend the average life expectancy of a 35-year-old man by 3.1 years and a 35-year-old woman by 3.3 years

Which they feel is a modest increase but I rather disagree.  This report estimates the that reduction in death due to heart disease of over 50% between 1950 and 1995 gained around 3.5 years, although most of that is probably due to better medical treatments.  This 2004 study used 1998 data from the UK and estimated that:

The average gain in life expectancy from the elimination of cardiovascular disease risk as a cause of death was 4.0 years for all the 35 year-old men in the sample (n = 24), and 1.8 years for all the 35 year-old women in the sample (n = 32).

Although I would note the low sample size.  I didn't expect to find much, so I was surprised to find these... and with similar results!  One big issue is that a lot of the more recent research has focused on smoking, weight/BMI, and blood pressure reduction, rather than all IHD/CHD/CAD; I found tons of those.  As a side note, simply reducing TV watching to less than two hours a day can lead to a gain of almost 1.5 years.

Kind of surprising only 3.5 years, what's the point, I'd rather my KFC.  Do you think the small increase is because of other forms of atherosclerosis though, such as stroke?

Perhaps - stroke is #2 in the 75+ crowd - but don't forget about cancer.  Cancer as a whole kills more than strokes at that age, and a few forms of cancer usually come out ahead in other age groups as well.  That the number is so low is more of a testament to how successful our medical system is despite the deadliness of IHD.


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Why does hypertension occur in obstructive sleep apnea?
What is the physiological mechanism behind systemic hypertension resulting from obstructive sleep apnea?


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Basic definitions for biology terminology
I am currently writing a mathematical biology paper, however it is very hard for me to follow the existing literature due to specialized terms. I have tried googling but most explanations are very technical and filled with more biology jargon. I have absolutely zero biology experience, so if anyone could please give a very very basic, non technical/rigorous, and intuitive explanation of the following terms, that would be great.

Nucleotide
Protein
DNA
Adenine, Thyine, Cytosine, Guanine
RNA
Single Nucleotide Polymorphisms (SNP)
Base: e.g. "1% of the human genome (about 30 million base pairs) will
be treated."
Eukaryotic
Genome
Genome sequence
Whole-genome
Partial-genome
GC content
conservation: e.g. "degree of evolutionary conservation"
conserved region: e.g. "functional elements are more likely to be
found in DNA regions that are the best conserved across species"
conserved sequence
chromosome
binary sequence
non-coding DNA/RNA
non-protein-coding genes/sequence/portion/elements
protein-coding genes/sequence/portion/elements
gene sequencing
gene promoters
purifying selection
positive selection
functional element: e.g. “…classes of functional non-coding elements
remain to be discovered”
non-functional element: e.g. "identify all non-functional elements in
the human genome."

Wow, these are quite a lot of questions. How do you want to write a paper on mathematical biology without at least a basic understanding of biology? My advice would be that you go into the stuff and then ask more specific questions.

There are too many questions that ask for too many explanations, I don't think anybody wants to answer to all that. It is not really possible to give a "very basic without technical term" definitions to most of these words. If you want to write an article in mathematical biology, I am afraid you will have to take some time to learn a bit about biology. Go through some books that will guide in the basic understanding of biology. I know we all would like things to be easy when starting a new field but unfortunately there is no easy answer to your questions. This book for example might help you. It is a classic in first year Bachelor in biology.
If you have some specific questions, you are very welcome to ask them. But this post asks for a whole book!
Here is a small quickly written text that will maybe help you a bit. Note: it might be oversimplified sometimes!
DNA is a big molecule made of (among other things) nucleotides. There are 4 nucleotides (adénine, cytosine, tyrosine (or Uracile on RNA) and guanine often just called ACTG and they can be categorized in two types of molecule depending on their number of cycles) which sequence form the genetic information. DNA, in eukaryotes (which are cells that contains DNA in a nucleus (which is the case of all non-virus, non-bacteria and non-archaebacteria)) is grouped into chromosomes (which are usually represented by a "X" as they more or less appears at the metaphase (a phase during the life cycle of a cell)).
DNA is transcribed into mRNA (a kind of RNA) which is then translated into protein (by rRNA and tRNA). While RNA and DNA are made of nucleotides, the protein is made of amino acids. Three nucleotides (one codon) codes for 1 amino acid.
In the genome there are sequences that code for proteins, sequences that code for RNA, sequences that allows other proteins to bind into in order to influence gene expression, promotors, enhancers… You will have to accept taking some time learning a bit about that stuff I guess.
Sequencing is the (artificial) process of reading a DNA sequence. This can be achieved on a whole genome or on small chosen sequences.
As the nucleotides G binds only with C and A binds only with T (two nucleotides together form a base pair)(there are two strands of DNA linked by the nucelotides), the amount of G equals the amount of C and same for A and T. The GC content gives the proportion of G and C of the total number of nucleotides of a sequence (or a whole genome). Oh by the way, a genome is the totality of the DNA of a given individual.
Positive/purifying selection are cases of natural selection. Natural selection is a process by which the frequencies of alleles (variant of a gene) does not vary randomly. They vary according to the reproductive success (= fitness) they confer to the individuals that bear the allele. Positive selection on an allele means that this allele is selected for. Purifying selection refers to the wildtype allele (most frequent allele) is selected for and all mutations (DNA modifications) that appear are deleterious and therefore counterselected,
A SNP is a genetic variation between individuals in a population (or along populations or species) that involves only one nucleotide.


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Why are there N's after Sanger sequencing?
After sending a DNA sample for sequencing, the resulting sequence had N's in the beginning and end of the sequence.  I know the N's mean that the computer can't tell what the base pair is, but why is this?

Typically Sanger sequencing will run into a few errors. Sometimes the traces will overlap as below in red and the computer will call N. If you truly wanted to figure out the correct basepair, you can look at the trace.

This is not really an answer. In effect it just says “it happens” but not why. The wisdom of crowds seems an oxymoron in this context.

As you accurately stated, N bases in sequence data generally means the software is unable to identify the base. N bases may appear at the beginning of the sequence result for a number of reasons. One reason would be purification of the amplified product before electrophoresis. Salts in the sample or a poor purification could leave excess dyes in the sample and appear as "dye blobs." Another reason is the software may have started analysis too soon before accurate sequence begins. Typically, quality sequence data begins 30 bases from the primer. N bases at end of the sequence simply could be the end of sequence data as stated earlier. Other reasons include hairpin loops and poly base regions that cause early termination. The best way to determine the cause is to look at the trace data.


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What range of dose should be used?
This is a dose-response experiment testing a new cancer drug.  the darker line represents cancer cells.  what range of dose should be used? I think it's 2-4 because this affects cancer cells only.  is this correct?

Assuming that that's % cells rather than # then the ideal dose would be the minimum dose that killed 100% of cancer cells - minimum because you want to stay far away from the healthy cells line.  This would be a pretty amazing drug however, in real life those lines are likely to overlap long before 100% cancerous cell death, hence the problems of dosing chemotherapy.

In the most basic sense you want to kill the most cancerous cells whilst minimizing the regular somatic cell death. Almost all cancer medications affect regular cells, too - though the better ones do so at a minimum whilst being effective. In reality, it's also nearly impossible to kill all of the cancerous cells. The goal is to bring them below detectable levels, which can allow the body to finish the job. Leaving significant amounts of cancerous cells alive won't do the patient any good - they'll just continue to proliferate and the patient will be back for more operations or treatments soon.
So, with the goal of minimizing benign cell cost and completely eradicating the cancerous line, on your crude chart that falls at about "4".

so what would the range be? 0-4 or 2-4?

Probably 3-4. A dose of "2" isn't killing significant amounts of cancerous cells. Though everything is a bit vague about the question you're asking. Normally doses are determined by mg/kg depending on the utilization and persistence of the drug in the body.


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Translate DNA to Protein
Assuming the sequence shown is read left to right, what is the sequence of the protein produced?
sequence: 5’-ATGTACTTCCATCTGGAATAG-3’
MY ATTEMPT: I know RNA is synthesized 5 to 3.  This is throwing me off because if we read the above sequence from left to right then we are going to synthesize 3 to 5.  If I ignore this for now, I get an mRNA of 3'-UACAUGAAGGUAGACCUUAUC-5'  from this i could easily get the protein looking at a mRNA to protein chart.  Is this correct?

Since the sequence starts with an initiation codon and ends with a stop codon I think it's safe to conclude that this is the coding strand.  The coding strand has the same sequence as the transcribed RNA (except T>U). This is because it is the other strand of the DNA that is the template for the synthesis of an RNA. The RNA is indeed made 5'>3', but the template it uses has to run in the opposite direction.
5’-ATGTACTTCCATCTGGAATAG-3’
3'-TACATGAAGGTAGACCTTATC-5' template strand

5'-AUGUACUUCCAUCUGGAAUAG-3’ mRNA transcript
3'-TACATGAAGGTAGACCTTATC-5' template strand (read from left to right by the polymerase)

and the sequence of the protein is MetTyr...etc

but this way the sequence i gave is not being read from left to right.  you read the complement from left to right

Depends what you mean by "read". The polymerase moves from left to right reading the bottom strand as template and making the RNA from left to right. You read the top strand from left to right as you look up codons in a genetic code table. You use the top strand for this because it is this DNA strand that has the same sequence as the mRNA.

EMBOSS has a tool for doing this:
http://www.ebi.ac.uk/Tools/st/emboss_transeq/


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Which process is needed to complete male reproductive development?
In order to properly complete male reproductive development:
A. primordial germ cells must begin Meiosis I in utero.
B. Sertoli cells must produce testosterone.
C. Dihydrotestosterone must masculinize Wolffian duct derivatives
D. the paramesonephric ducts must degenerate
E. the metanephros must form the genital epithelium

My attempt:  I think the answer is C because testosterone turns into DHT which then masculinzing the wolffian duct.  Other people I am studying with claim the answer is D (which is true) except that I dont think the loss of the paramesonephric duct is needed to complete male repro development.

Regarding option C:
Although it is correct that testosterone is converted into DHT, it is the former, not the latter, which is responsible for differentiation of the mesonephric (a.k.a. Wolffian) ducts:

Between 8 and 12 weeks, the initial secretion of testosterone stimulates mesonephric ducts to transform into a system of organs—the epididymis, vas deferens, and seminal vesicle—that connect the testes with the urethra.*

DHT (dihydrotestosterone) is produced in the Leydig cells by the 5α-Reductase enzyme. It is required for induction of the external male genitalia (urethra, penis, and scrotum) and prostate from the embryonic ureteral groove, and for testicular descent into scrotum.
Regarding option D:
Sertoli cells secrete Anti Müllerian Hormone (AMH), which causes degeneration of the müllerian (a.k.a. paramesonephric) ducts between weeks 8 and 10.  It is normal to speak about degeneration of the müllerian ducts as a defining aspect of male embryology, and thus I believe answer D is correct. Your point is taken, however:

Nevertheless, small müllerian duct remnants can be detected in the adult male, including a small cap of tissue associated with the testis, called the appendix testis, and an expansion of the prostatic urethra, called the prostatic utricle.*

*Larsen's Human Embryology , Fourth Edition. Chapter 15: Development of the Urogenital System. pp 479-541.
Copyright © 2009 by Churchill Livingstone, an imprint of Elsevier Inc.


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White/Gold vs Blue/Black dress
So I'm sure you've all seen the dress photo where people see the dress as either White and Gold or Blue and Black.
It has essentially 'split' the internet because some people see the dress and they think that it is coloured blue and black, whereas the other half think that it is white and gold. It is trending on most social media sites as people fight about what the colour difference is.
So my question is why do different peoples eyes perceive different colours in this picture specifically?
For reference the photo with a color breakdown can be found here

possible duplicate of How can you test what color different people perceive?

Sorry, I meant this as a specific question for this photo, not just in general. As far as I can tell, perceptive difference is totally random.

Whether you see it as blue/black or white/gold depends on how you interpret the spectrum of lighting in the room. I would guess that different interpret that differently based on the subtle cues available in the rest of the picture. But I don't have a solid explanation of what those differences might be or why people might cue on different aspects of the image.

U did put up the pic later so you can hardly blame me for closing it as a duplicate

True. Not blaming in the slightest, simply clarifying what I meant.

Please add more information about the background of the question otherwise it is likely to be closed as unclear

It's a possible duplicate of http://cogsci.stackexchange.com/questions/9405/what-color-is-this-dress-and-why on Cog Sci.SE and it has been quite neatly addressed there in an answer.

Two popular articles on this: http://www.dogonews.com/2015/3/6/white-and-gold-or-blue-and-black-the-great-dress-debate and http://www.wired.com/2015/02/science-one-agrees-color-dress/


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Kinesiology Tape Benefits
Recently, kinesiology tape has become popular, especially in CrossFit. I have also noted its' use in the NFL, and I want to say Tennis as well.
What beneficial effects does this tape offer our bodies (muscles, joints)?  Is there any definitive proof of its' benefits? Can there be negative effects? I don't foresee any, but if it does something to your body, I could see a possibility of prolonged use causing some kind of alternate effects.

This is in the discussion for quite a while. I have found no scientific studies which back the claims of kinesio tape. A review article (from which the quote below is taken) found no clinically important results which support the claims of the tape. The results about range-of-motion were inconsistant and it is not clear if the changes found were beneficial or not. They state:

KT had some substantial effects on muscle activity, but it was unclear
  whether these changes were beneficial or harmful. In conclusion, there
  was little quality evidence to support the use of KT over other types
  of elastic taping in the management or prevention of sports injuries.
  KT may have a small beneficial role in improving strength, range of
  motion in certain injured cohorts and force sense error compared with
  other tapes, but further studies are needed to confirm these findings.

The study can be found here (links to the PDF):

Kinesio Taping in Treatment and Prevention of Sports Injuries

Other (also critical) studies are these:

A systematic review of the effectiveness of kinesio taping for
musculoskeletal injury.
The clinical effects of Kinesio® Tex taping: A systematic review.

The problem with these studies is that they are obviously not rigorous enough to make clear statements if KT is beneficial or not. Or (and this is also very possible) that the effect which is claimed to be there does not exist. Besides this, a placebo effect exists very well, since there is an intervention and also something present on the athlete.
There is now a new study avalaible which is blinded and placebo-controlled. This study finds no benefits for Kinesio Tape above a placebo. The study can be found here, there is also a summary available here.

In response to your answer, I have added one more piece to my question. Please see my edit. Your citation confuses me a little bit, and perhaps my confusion isn't directed towards you, but towards authors of that piece. How is it unclear if changes were beneficial or harmful?

@OverMind I have expanded my answer.

This may be opinionated - but do you think more quality tests will come in the near future? I am wondering if its' placebo effect has instilled itself into athletes because it's "new" and some big-named athletes have worn it in public. I would love to see some truly definitive evidence of its' effects and not same half-ass claim that "it can provide benefits and has been related to alleviating swelling.." blah blah.

I am not sure. Personally I am sceptical, since effects should clearly show up in a properly done study. I haven't looked up all the studies in the reviews but a few and these looked ok.

I'm a skeptic as well, and agree 100% with your gut feeling. Thanks for answering.


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Modifications of free nucleotides
We know that RNA can get modified post transcriptionally (RNA modification). So when the RNA is degraded, is it possible for such modifications to still be present on the individual nucleotides -- such that when the nucleotides are recycled for constructing another RNA, those modifications persist?

It's unlikely that a chemically modified nucleotide would be recycled into a new RNA.

Why is that? As in which chemical reactions during the course of degradation -> recycling are likely to remove the modification(s)?


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Slow-oxidative fibres vs fast-glycotic fibres
Why do slow oxidative muscle fibres contain more mitochondria compared to fast-glycolytic muscle fibres?

If I remember correctly, the slow oxidative fibers compose mostly structural muscles (thing multifidus, longissimus, capitus muscles) which are "on" a lot of the time but don't retract quickly like fast glycolitic fibres. Because the SO muscles need to be active most of the day, they probably have higher energy requirements - whereas FG muscles can get by with less because you can store enough energy for occasional activation (you're not doing pushups all day). It's been a while, though.

This is well-explained at the Wikipedia page on skeletal striated muscle.

There are two principal ways to categorize muscle fibers: the type of
  myosin (fast or slow) present, and the degree of oxidative
  phosphorylation that the fiber undergoes. Skeletal muscle can thus be
  broken down into two broad categories: Type I and Type II. Type I
  fibers appear red due to the presence of the oxygen binding protein
  myoglobin. These fibers are suited for endurance and are slow to
  fatigue because they use oxidative metabolism to generate ATP. Type II
  fibers are white due to the absence of myoglobin and a reliance on
  glycolytic enzymes. These fibers are efficient for short bursts of
  speed and power and use both oxidative metabolism and anaerobic
  metabolism depending on the particular sub-type. These fibers are
  quicker to fatigue.

In the terms used in the article, the Type II fibers rely on anaerobic, glycolytic metabolism, whereas the Type I fibers use oxidative metabolism which, of course, requires mitochondria for the TCA cycle and oxidative phosphorylation.The Type I fibers also contain myoglobin which promotes rapid movement of O2 through the cytosol to the mitochondrial ATP synthase.


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Which sex is homogametic in side-blotched lizards?
I'm just trying to find out whether the male side-blotched lizard is the hetero- or homogametic sex in side-blotched lizards (Uta stansburiana) - some reptiles are ZW system (female heterogamete) and some are XY (male heterogamete).

Lizards of the genus Uta are apparently male heterogametic (XY) (Pennock et al. 1969). The XY system seems to be the most common mode of sex determination in iguanid lizards (Kasahara et al. 1983).

Kasahara, Y et al. 1983. Chromosome mechanisms of sex determination, G- and C-band patterns and nucleolus organizer regions in Tropidurus torquatus (Sauria, Iguanidae).  Genetica 60: 151-156.
Pennock, L.A. et al. 1969. Minute Y chromosome in the lizard genus Uta (Family Iguanidae). Cytogenetics and Genome Research 8: 9-19.


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Identification of species found in fly lab
I just found this in my Drosophila lab (within a closed vial) - unfortunately it was dead having been frozen for two weeks. Can anyone help id what it is, and whether it poses a risk to my flies (like mites do)? My inclination is that it is some kind of (moth?) larvae. Note the awesome corkscrew tail...
Found in Uppsala, Sweden, May 2014 in a vial of Drosophila with food (a yeast, sugar, and agar mix). Length is about 3-4mm excl. tail.

I'd guess it's a larva of one of the carpet beetles (Dermestidae), some of which are synanthropic. They probably would be interested not in live flies, but in their food and cadavers.
Its appearance seems to be very characteristic - someone would be able to identify it to generic or even specific level.

Attagenus gebus is known for having longer tails than other dermestid beetles. See Orkin, for example.


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Is perceived time compressed or expanded while dreaming? (or does it match reality)
I often dream long extended dreams.  Sometimes I wonder if the timeline of the story of my dream occurs compressed, in a moment, or other times extended slowly over a long duration.

Is there any way to scientifically detect this, and how would it be accomplished?
Are there any prior examples of this study being performed?

Cognitive Science SE might be a better community to ask.

I agree, this isn't really a Biology question, although it's an interesting question.

OK asked it here: http://cogsci.stackexchange.com/q/10521/8716

I'm closing this question as off-topic because it is already cross-posted in cogsci.se which is probably a better site for this question.

@WYSIWYG agreed, definitely.


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Any examples of animal behavior in response to meteor showers?
I just spent two nights observing the Perseids and was wondering whether any animals have been recorded to exhibit unusual behaviour in response to meteor showers.
It is known that some animals change their behavior at night in response to moonlight and artificial illumination (e.g. eagle owls call more frequently at full moon), but I am not aware of any materials indicating behavioral changes in response to short-term lights like those produced by meteor showers or far away lightnings.
Any pointers would be appreciated.

There are a significant number of major meteor showers in the earth's orbit, especially in the Northern Hemisphere. Nocturnal animals have good night vision (obviously) and their acclimation to the dark plus time spent awake at night (if they look up at all) means they see many, many more meteors on average than humans do.
The year's parade starts with the Quadrantid shower.

January overall has good meteor rates restricted to the last third of the night. Rates to 20/hour can be obtained.

Meteor "showers" (if they can be called that) continue until mid-march, when they drop off to a "very poor" rate of 10/hour or less, continuing this pattern into early June, except for the Lyrids (max: April 22/23) and the Eta Aquariids (max: May 7/8).

February, March, and April evenings have another notable feature. An unusual number of sporadic fireballs come in this interval, possibly one every few nights.

In the last half of July, we get the Delta Aquariids (July 29/30) and Alpha Capricornids (July 27-28).  Then the Perseids (maximum: August 12/13), rich to our eyes at about 100/hr at their peak, moon and weather permitting.
From September to the first half of December is pretty rich.

Mid-October to mid-December is a nearly continuous period of heavy meteor activity. The Orionids (max: October 21/22) during the second half of October have a prolonged, plateau maximum for several nights, usually rich. The Taurids (max: October 11 for S. Taurids, November 13/14 for N. Taurids), active for two months, are most numerous in November’s first half, and can be rather variable in strength. This period is the best for a couple of Taurid fireballs each night, if the shower is not too weak. The Leonids of mid-November (max: November 17-19) are quite unpredictable, with rich displays occuring roughly every 33 years.

Finally there's the Geminids of mid-December (max: December 13/14) with "the strongest dependable and observable display" (usually passing 60-70/hour at maximum.)

Finally, the oft-overlooked Ursids complete the year’s activity, reaching maximum on December 22/23. Nearly half the year’s visual meteor activity is crammed into the two-month interval just described.

What does all this have to do with biology and your question? I'm guessing here that the Perseids, though rich for humans, are probably nothing exciting for animals. The diurnals and crepusculars don't see them at all (they're soundless and certainly not bright enough to wake anyone up). The nocturnals see the (or not, depending on where they're looking) all the time. So a study wouldn't likely detect much, would be challenging to design well, would cost some big bucks, and wouldn't really help humans like studying animal behavior before earthquakes and such.
As a child, I once saw some very funny chicken behavior on my grandmother's farm during a total eclipse of the sun. It was so funny that I remembered it all the years since.
I searched, as I'm sure you did, and the first hit on regular Google was this question. A scholar search brought up possible animal behavioral changes before fireballs.
Major Meteor Showers

The entire middle part of this answer seems to be an almanac and has nothing to do whatsoever with the question.

@MarchHo - How to say "Nah, it happens all the time" without proof? That's not like me.


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What is the difference between "physical interaction" and "genetic interaction"?
I searched sac1 in uniprot to know more about this gene. in interaction I selected this link and there I see that this gene has some "physical interactions" and "genetic interactions". I am wondering that what is the difference between "physical interaction" and "genetic interaction"?

Physical and genetic interactions are described in the help wiki, accessed via the top menu bar on the page you linked to.
Physical interactions refer to experiments where the gene product (protein) has been shown to physically interact with another protein, such as by co-immunoprecipitation, fluorescent staining, yeast two-hybrid system, etc.
Genetic interactions refer to experiments where changes in a certain gene reflect in changes to your gene of interest (or vice-versa) - dosage lethality, dosage rescue, synthetic haploinsufficiency, etc.


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Why we do not use RNAi to control ebola?
As you know using RNAi we are able to prevent gene expression. so why we do not use it to stop viral genes expression?

Because siRNA is very hard to deliver to tissues in an animal. That said, Tekmira is working on an siRNA based ebola therapy called TKM-Ebola. I've seen the preclinical data on monkeys at a conference last May, and it looked pretty good. Will take some time before we know if it works in humans.

Question: How do you deliver ths siRNA into the body without having it degraded? Free nucleic acids outside of cells are an alarm signal for the body.

siRNA can be chemically synthesized, allowing for modifications with 2'F or phosphorothioate backbones that resist RNase activity. I've been trying to deliver mRNA, which is too large to chemically synthesize so we're still trying to figure out how to avoid degradation.

Delivering siRNA in vivo is a difficult prospect, but has been overcome in research environments and several commercial in vivo solutions are on the market see examples from Life Technologies here.
The bigger problems come from potential off-target effects. siRNA tend to be double stranded and both the 'guide' and 'passenger' strand can occasionally target multiple sequences that you did not intend. Additionally, siRNA tend to activate the body's immune system in ways that would inhibit therapy or cause excess inflammation and cell death. See the detailed review here.
In short, it is a good idea, and the current research in the field is working to overcome technical challenges, but we are not there yet.

The siRNAs offered by life technologies look like the siRNA itself. How are the RNAs targeted to specific tissues and passed through cellular membranes?

RNAi therapies can be targeted by nanoparticle encapsulatin. Generally, a nanoparticle containing the siRNA can be conjugated to an antibody for the (cell surface) disease marker. Antibody brings nanoparticle to the diseased cell, cell endocytoses nanoparticle, siRNA is delivered. Alternately, I have delivered RNAi therapy by local injection in in vivo models. However, the Ebola case is much simpler. Ebola infects the endothelial cells and liver. siRNA packaged in lipid nanoparticles will accumulate in the endothelium and liver cells when intravenously injected.


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How long does an enzyme work?
I googled this, and I found only that shelf lives are around 2-3 years, but the enzymes use to work even after 5 years if you store them properly. I'd like to know how long I can use an enzyme in solution? Is it hours, days, months? If it is a lot shorter than the shelf life, then why is that?

Which enzyme and how are you storing it?

@WYSIWYG I'd like to decide whether an inorganic catalyst or an organic one would be better for a task. It should catalyze a reaction for at least 2 years without any maintenance in the 10-30°C range. I think enzymes are not that durable, but I am not entirely sure.

@inf3rno I don't know of any enzymes that are stable in those conditions for that long.

@inf3rno Most enzymes will have significantly degraded in days catalyzing a reaction at 10-30°C

Okay, thanks! Actually I was thinking about using enzymes in fuel cells. Something similar to this: https://pubs.acs.org/doi/abs/10.1021/jp102616m

The product manufacturer can define a suitable shelf life at a stated storage condition because they've performed stability studies that confirm the product in question remains suitably potent in that timeframe. Often times an expiration date ends abruptly at 1-3 years because the manufacturer chooses not to test out any longer. So that's to say, if you receive a protein with a shelf-life of 3 years, if stored properly the protein may be suitable long after.
It's a fairly different question, however, if you took and reconstituted the reagent, because chances are that stability wasn't tested in that form. In order to make a claim about the stability of a processed/reconstituted protein you need either a statement from the manufacturer, data from someone who has tested stability on it themselves, or you need to test stability for yourself. The fairly short answer is you can't know, and the answer depends on a lot of variables such as the structure, concentration, diluent and storage temperature. All such variables can cause structural changes to the enzyme, i.e. protein degradation, that will result in a different activity for that product.

Can it be even years with the right enzyme in the right conditions? Actually nowadays enzymes can be even designed so my guess would be that this can be maxed out for any enzyme.

@inf3rno Certainly. People have stored antibodies for IHC for years at -80°C. The problem is you can't make that claim with any professional certainty without data to back it up. It's problematic in GMP-compliant processing and FDA-regulated development because you can't use expired reagents for clinical administration, for example, and the only way you can claim to use something past expiration is to test it yourself.


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Which complexes physically pump protons in photosynthesis?
The cytochrome b6f complex is often drawn as pumping protons, but then someone told me that actually there is no pumping, rather the Q cycle.
According to this view, what actually moves the protons is that a PQ takes up 2 H+ from the stroma as it is reduced and another two PQ release 2H+ into the lumen as they reduce PC and partially reduce the first PQ. The complex, therefore, does not physically pump the protons.
I now wonder if any of the photosynthetic complexes pump protons. For example, the PSII complex has PQ reduction with 2H+ removed from the stroma and its oxygen evolving complex releases O2 and 4H+ into the thylakoid lumen, so this could be its ‘pumping’ contribution.

General Approach
Although I am not an expert in this area, as an ex-chemist I find this topic one of the most fascinating and fundamental in chemical biology. I have constructed an answer starting from my copies of the 5th (available on line) and 6th editions of Berg et al. Biochemistry (2003 and 2007, respectively), and then searched the Protein Data Bank for structures of the cytochrome b6f complex, and worked from the papers associated with more recent entries.
Definitions
First, it is important to be clear on the following:

What is meant by a proton pump (physical or otherwise)?

I think that the question — and the scientific community in general — probably assumes a pump to have some sort of channel or revolving door through which the protons are driven from one side of a membrane to the other. If one were able to tag an individual proton to follow it, one would find that it was physically translocated across the membrane. (A model for this might be the Na+/K+-ATPase. See also Berg et al. Biochemistry in Chapter 13 “Membrane Channels and Pumps” although this does not actually mention pumps in relation to either photosynthesis or oxidative respiration.)
This would be in contrast to the net translocation of protons across a membrane by chemical sleight of hand. A reaction at one side of the membrane would consume protons, and a reaction at the other side would emit protons. However no individual proton would pass through the membrane.
Both these processes would be working against a concentration gradient and require energy, in this case in the form of reducing power — not, of course, ATP.
This difference is illustrated in Berg et al. with respect to cytochrome c oxidase (Fig.18.21) in which both processes occur, where the authors refer to ‘pumped protons’ and ‘chemical protons’:

And the answer is…
That the situation in photosynthesis is similar to that for the oxidative electron transport chain:

Net translocation of protons across the membrane is achieved both
  chemically (in photosystem II) and by ‘pumping’ (in cytochrome b6f).

So the ‘someone’ in the question was correct in saying that the chemical type of net translocation occurs in photosynthesis, but was incorrect in saying that this was at the cytochrome b6f stage.
Structural Evidence
The cartoons shown above (taken from Berg et al.) are based on a wealth of indirect experimental data. However some of us are never convinced until we have seen the stigmata. The structure of the cytochrome b6f complex was reported in Science in 2003 by William Cramer’s group, and in the diagram below (my modifications) there is a channel through which the passage of protons is indicated.

A more recent (2013) paper from the same group considers the proton transfer pathway in cytochrome b6f in more depth, and I reproduce below Fig. 1B from that paper to indicate the type of molecular detail.

Heavy reading, but wonderful stuff!

in my undergrad lectures I thought we were told that Mitochondrial complexes I, III and IV do physically, via internal channels, 'pump' protons across the membrane, mainly in contrast to complex II not doing so. Is this wrong then?

@Mirte — As I commented previously, my initial answer was wrong and has been revised. Apologies. I have only addressed the question of proton pumps in the mitochondrial complexes indirectly, as the final answer was long enough restricted to photosynthesis. But, yes, proton pumping (and some 'chemical' net translocation) is thought to occur in mitochondria. There is a 2011 Annual Review of Biochemistry article on the topic.

Thank you, your revised answer is great and I've accepted it!


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Could higher carbon dioxide levels be beneficial to plants?
C4 plants take ATP-expensive routes to ensure photorespiration does not occur.
They minimise oxygen concentration in cells where the Krebs cycle occurs and cart carbon dioxide into these same cells. To over-simplify, they increase the carbon dioxide concentration and decrease the oxygen concentration in these cells.
Despite the ATP this costs them they are enormously successful (in hot areas at least).
Considering this, would human-caused carbon dioxide emissions, i.e. increased concentration in environmental carbon dioxide, be beneficial to plants?
Considering @Cell's comment: I mean beneficial from the 'plant's point of view', i.e. the plant can grow faster-reproduce sooner or less photorespiration occurs; due to the higher level of carbon dioxide. I think we can disregard ocean acidification for now, climate change is relavent but perhaps it could be disregarded initially? Especially as climate change effects different areas differently.
Please note: I am not encouraging or supporting human caused carbon emissions; this is a genuine question asked out of curiosity.

Don't worry this is a standard question asked in most intro to biology classes. So you will find it welcomed here

Except that it seems to show a lack of prior research.  Google Scholar shows about 1.8 million hits on "CO2 concentration plant growth".

I think it might be helpful if you describe in more detail what you mean by beneficial. Anthropogenic climate change entails more than just increase in CO2 levels, for example drought and ocean acidification. It would be like me eating nothing but cheesecake everyday. Sure it makes me happy and it's an energy source, but there are other factors that can make it an overall unhealthy habit.

I have made some minor corrections. Note especially 'Krebs', named after Nobel lauriate, Hans A. Krebs, is not a possessive. Krebs is a German singular noun meaning 'crab' (and also 'cancer').


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Identification of an insect (?)
This one was found in the woods of northern Poland. It was about 5 cm long and crawling pretty dynamically. For me it seemed a little too big for a butterfly larva.

What is it called?

Related: What kind of creature is this?

It's an  elephant hawk-moth, Deilephila elpenor. Here is an image from Wikipedia to compare with:

Agreed; that's definitely it. Since OP saw it in Poland I don't know if a (British) 20p will be helpful for scale; for non-UK readers, the coin is 21.4mm in diameter so size is spot-on.

I think it is the larva of the sphinx purple butterfly.

Size of the larva is arround 70 mm

I haven't heard it called that before but from the photo it sounds like this is an alternative common name for Deilephila elpenor. Nice photos!


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Interpretation of agarose gel electrophoresis of a plasmid
I am performing agarose gel electrophoresis of plasmid which is 2.5-3 kb in size. I am getting more than 3 bands, after restriction I got single band at 3.5kb in size.
Electrophoresis conditions- 0.5X TBE, constant voltage 150V.
why am I getting more than 3 bands after agarose gel electrophoresis of plasmid?

Please convey the question in the title

It is probably due to the presence of supercoiled plasmid. You can try to heat up your plasmid in a thermocycler , 90 C for 20 min, this will denature the proteins responsible for the supercoiled structure and you will eventually see only one band representing the circular plasmid. The fact that you see only one band after digestion it's a good sign that you indeed have only one plasmid in your prep.

Thank you for reply. I am using sure spin column for extraction of plasmid. how does protein present in sample?

@alec_djinn Is it known which bacterial proteins are responsible for maintaining the supercoils in purified plasmid DNA?

@RosieF specific DNA gyrases are responsible for inducing the coiling, then histone-like bacterial proteins keep the structure in place. Have a look here https://en.wikipedia.org/wiki/Bacterial_DNA_binding_protein and here https://www.ncbi.nlm.nih.gov/pubmed/26928284

@SonamPatil the silica columns used for minipreps retain the DNA and the  histone-like proteins attached to it. Sometimes more, sometimes less, you always have some protein (and RNA) contamination, you can check it by spectrophotometric analysis (260:280 / 260:230 Ratios), it's not uncommon to co-purify some proteins together with your plasmid.

The closed plasmid comes in three different forms: nicked-relaxed, supercoiled and circular single-stranded. All three forms have a different tertiary structure and thus they run differently on the gel. This should look like this (image from here, there you also find a more detailed explanation):

When you digest the vector you linearize all the forms and they all have the same tertiary form.