What is the surface area of the vitreous humour in contact with aqueous humour? This is a question regarding the anatomy of the human eye, however for my purposes medium sized mammals should do. I am interested in estimating the surface area of the hyaloid membrane of the vitreous humour which has contact with the aqueous humour circulating in the posterior and anterior chamber of a typical human eye.

The surface area in question is highlighted in red in this schematic of the cross section of the human eye.

Area=πr², d≈2cm (less than maximal d) -> r≈1cm,  thus the area in question is roughly

3.14*1cm*1cm≈3.14cm²

UPD by request (ref):

The vitreous body base middle is at ora serrata (+-2mm), so we should calculate the area at this level. Here is the reference of the diameter:

from: Basic and Clinical Science Course, Section 02


Why is binding energy the difference between ∆G catalyzed and ∆G uncatalyzed? I think the title explains it pretty well -- I'm confused on what 1) exactly binding energy is 2) and why it's the difference. Like in this diagram:

my teacher sort of said it was the energy the enzyme uses to make interactions to the substrate, but that doesn't really click for me.

There's two binding energies in your diagram, and it's the difference between them that's the critical point in understanding enzyme catalysis and the difference between $\Delta G$ catalyzed and $\Delta G$ uncatalyzed?

$\Delta G^R_{bind}$ is the binding energy of the enzyme-substrate complex. That is, it's the difference between the energy of the apo-enzyme and substrate in the non-bound form ("$E+S$") and the enzyme and substrate in the bound form ("$ES$").

The other binding energy is $\Delta G^T_{bind}$. This is the (theoretical) binding energy of the transition state. That is, it's the energy difference between the enzyme-transition state complex (here labeled "$T_{uncat}$", for some reason; it probably should be "$ET_{cat}$") and the apo-enzyme and the unbound transition state ("$E+T_{uncat}$").

Now remember that free energy is a state function. A free energy change ($\Delta G$) is simply the difference between the free energies of the starting state and the ending state - it doesn't depend on the path you take to get there. (The absolute free energies of any given state are unmeasurable, but you can infer information about relative free energies by measuring the $\Delta G$ of transitions between them.)

The two equations at the bottom are derivable from this definition of free energies as a state function. You know that the free energy difference between the $ES$ and the $E+T_{uncat}$ state is the same regardless of the path you take. So if you go first through $ES$ the free energy change ( $- \Delta G_{bind}^R  + \Delta G_{uncat}^\ddagger$) will be equal to that if you go through "$T_{uncat}$" ($\Delta G_{cat}^\ddagger - \Delta G_{bind}^T$) - you don't necessarily need to have physically realizable reactions for the state function property to hold. The second equation is then simply a rearrangement of the first.

In looking at the rate of catalysis, you're primarily interested in how big a free energy change it is to the relevant transition state from the previous state. (This is a basic principle of Transition State Theory.) To speed things up, the enzyme needs to make that energy change smaller - that is, to make $\Delta G_{cat}^\ddagger$ smaller than $\Delta G_{uncat}^\ddagger$. If the enzyme binds the substrate and the transition state equally well, $\Delta G_{bind}^R$ and $\Delta G_{bind}^T$ are the same, and $ES$ and "$T_{uncat}$" are lowered by the same amount, such that $\Delta G_{cat}^\ddagger$ and $\Delta G_{uncat}^\ddagger$ are equal: no catalysis.

But if instead $\Delta G_{bind}^T$ is greater than $\Delta G_{bind}^R$, then the "$T_{uncat}$" state is lowered more than the $ES$ state, making the gap between them ($\Delta G_{cat}^\ddagger$) smaller than the gap between $E+S$ and $E+T_{uncat}$ ($\Delta G_{uncat}^\ddagger$): the enzyme thus speeds up the reaction. This is what that second equation is saying.

This sort of thermodynamic analysis is what leads to the "transition state stabilization" hypothesis of how enzymes work: enzymes speed up reactions because they bind to the transition state more tightly than the substrates or the products.

(P.S. You may be wondering why we have the enzyme hanging around in the uncatalyzed reactions. This is simply a bookkeeping measure to make sure we're using the same reference state for the very start of the reaction ($E+S$). In the uncatalyzed reaction the enzyme doesn't change, and so doesn't really contribute to any free energy change.)


Can you Transfer Cancer Between People via Saliva or other Bodily Fluids? This may sound like a strange question. But could a Cancerous cell be transferred from one person to another from Oral contact e.g. Through Saliva, or other exchange of bodily fluids?
I know that other diseases from Bacteria / Viral can be transferred in this way, but does the same apply to Cancerous cells? - or would the recipient's body just breakdown and destroy the cancerous cells?

Although transmissible cancer has been found in some species, such as Tasmanian Devils and clams, it is quite rare in most species. Certain viral and bacterial agents that cause cancer, however, can be transmitted. One example is HPV, which can cause cervical cancer


Does the brain and the body use the same energy source (glucose/ATP)? I've heard that the brain consumes quite a lot of oxygen and energy, compared to the rest of the body. What I'm interested in is if this is the kind of energy and oxygen that the rest of the body competes for?

For example, does running divert resources from the brain to the
muscles, leading to decreased cognitive performance?
Does digesting food divert resources from the brain to the gut?

Does the heart rate or blood pressure have anything to do with how much resources, like oxygen and energy are available to neurons?

Thank you for your input!

You can grab any university level text on human physiology and you will find that the brain is a unique organ for cellular respiration. The brain is only capable of using two metabolic subtrates: glucose for oxidative phosphorylation (producing ATP) and ketone bodies.

Exercise does indeed divert blood flow toward the muscles. After all, they are undergoing higher levels of respiration and need nourishment. Your body will always balance muscular needs and the needs of the brain and the rest of the body. Similarly, digesting food has a similar response, although this is more involved. Eating food has a autonomic reflex to increase blood flow to the stomach and digestive tract to facilitate the processing and distribution of nutrients.


Why is the hexose monophosphate shunt called a direct oxidative pathway? Why is the hexose monophosphate shunt (pentose phosphate pathway) called a direct oxidative pathway( Ref. Biochemistry by Satyanarayana , 4th edition, pg.no: 244) , even though oxygen molecule is not used for oxidation? It uses NADP for its oxidation. So if utilisation of NADP is direct oxidation then what will be indirect oxidation?
How can I differentiate direct and indirect oxidation? Is the use of Electron transport chain considered as secondary oxidation?

This answer is based on a 2002 autobiographical account of the work of Bernard L. Horecker entitled The Pentose Phosphate Pathway. Here he refers to “direct oxidative pathway” but does not unambiguously explain this, so I shall summarize my interpretation and then provide evidence in terms of quotations.

Summary of my interpretion of Horecker’s account

When what I shall initially refer to as the hexose monophosphate shunt (HMS) was being elucidated in the late 1930s and the 1940s it was thought that its main purpose was the same as that was envisaged for aerobic glycolysis — to oxidize glucose to provide energy — and was merely an alternative way of doing this. The term ‘direct oxidative pathway’ was used to distinguish it from the glycolytic pathway (then refered to as the Embden–Meyerhof–Parnas pathway), presumably because six cycles of the oxidative phase e could completely oxidize one molecule of glucose 6-phosphate to carbon dioxide, whereas glycolysis only oxidized it to pyruvate. Presumably this was regarded as ‘indirect oxidation’ because complete oxidation required the further metabolism of pyruvate using the tricarboxylic acid cycle.

The term ‘direct oxidative pathway’ fell out of use as it was realized that the main functions of the pathway were to provide pentoses for nucleic acid synthesis and NADPH for synthesis of fatty acids, steroids, and reduction of oxidized glutathione. It was for this reason also that the name most commonly used for the pathway changed to the pentose phosphate pathway, transfering the emphasis to one of the products.

Quotations from Horecker

  …Haas arrived from Warburg’s laboratory in 1939. Haas asked me to join
  him in the search for an enzyme that would catalyze the reduction of
  cytochrome c by reduced TPN (now NADP). This reaction was thought to
  be the missing link in the electron transport chain from substrate to
  oxygen and marked the beginning of my interest in what was then
  thought to function as a direct oxidative pathway for the metabolism
  of carbohydrate but is now known as the pentose phosphate pathway…

  …These observations gave rise to the hypothesis that the oxidative
  pathway was really a cyclic mechanism for the direct oxidation of
  carbohydrate. With each turn of the cycle one molecule of carbon
  dioxide would be produced, and the pentose phosphates formed would be
  metabolized back to hexose phosphates to start another cycle. Six
  turns of the cycle would result in the complete oxidation of one
  molecule of glucose…

  …The function(s) of the new
  pathway, however, turned out to be quite different from the pathway
  for the direct oxidation of carbohydrate that we had expected. It
  provides two mechanisms for the production of ribose 5-phosphate. One
  is the “oxidative branch” of the pathway, which also generates 2 eq of
  TPNH (NADPH). Ribose 5-phosphate can also be formed directly from
  hexose and triose phosphates by the non-oxidative rearrangements
  catalyzed by transketolase and transaldolase. Where large quantities
  of NADPH are required, as in the synthesis of fatty acids or sterols,
  the excess pentose phosphates produced would be recycled back to
  hexose monophosphates.

[My emphasis]

Google Books ngrams of term usage


What kind of spider is this?(Rajasthan, India) Hi there, I found this insect in India/Rajasthan. Is this a spider or scorpion? It was nearly 50 mm in length.

That's neither a spider nor a scorpion (and, of course, not an insect). That's a solifuge, a different group of Arachnida.

The most common Genus of solifugae in India is Galeodes, which resembles the specimen in your photo:

Genus Galeodes

However, narrowing it down to the Genus may be a little bit more complicated.

It's worth mentioning that, despite their frightening appearance, they are not dangerous to humans.


What biological processes cause leaves to change colours in Autumn? I am curious to learn what are the biological mechanisms that cause leaves of deciduous plants to change colour? What happens to the chlorophyll?

What environmental phenomena (temperature/air pressure/length of sunlight) are they responding to?

Here is a quite nice Chemistry of Autumn Leaf Color. And here is a less chemical, but more detailed explanation regarding the triggering of colour change, which is quite similar to the one from the University of Illinois that @Oreotrephes already gave.

As I understand it, during sunny days a lot of chlorophyll is broken down, but also built up. When after the summer the days get cold and dark, chlorophyll is built up slower (or not any more at some point) and you start to see the colour from the carotenoids and anthocyanins. A harsh change from sunny to cold and dark is supposedly bringing up the brightest colours. At some point, also the carotenoids break down and leaves get brown. The faster the change to cold and dark the larger is the frame between having all chlorophyll broken down and having the other colouring molecules broken down (-> bright colours).

But that's the amateurs explanation.


What are the blood groups for human beings? Human blood groups are of 4 types with negative and positive of each types (Wikipedia). But according to this forum thread there are some other types too:

  A+,A-,B+,B-,O+,O-,AB+,AB-,A1+,A1-,A2+,A2-,A1B+,A1B-,A2B+,A2B-

I'm going to make software for blood donation, where I need to put a dropdown list of actual blood types. I had intended to use:

[ Select Blood Group V ]
[ O Negative           ]
[ O Positive           ]
[ A Negative           ]
[ A Positive           ]
[ B Negative           ]
[ B Positive           ]
[ AB Negative          ]
[ AB Positive          ]

But now I am uncertain whether this is appropriate. What is the most suitable list of blood types for donors?

As far as I am aware it is the RhD and ABO blood groups that matter with blood donation - though you may wish to contact a blood donation organisation for more specific information on how they handle & categorise the blood.

But using just RhD and ABO gives 8 combinations, positive and negative of A, B, AB, and O. You can find out more about the blood groups, blood donation, and the characteristics of blood groups here.

The subgroups you allude to are due to differences in the number of the antigens on the surface of the blood cell, for example the A1 group have ~1,000,000 A antigens per cell whereas A2 variants have ~250,000. The A group has ~20 subgroups, the vast majority of people are A1 (~80%) or A2 (~20%), and the other groups make up less than 1% of the population.

  These two subgroups are interchangeable as far as transfusion is concerned, but complications can sometimes arise in rare cases when typing the blood.


Viral Mutation Mechanism I think I have a wrong concept about viral mutation process. First of all what is mutation actually? I mean, I know it's a sudden change in DNA, happening when subjected to mutagenic agents.

But can it occur due to internal urge of an organism, say virus? If not then how can virus like Ebola undergo rapid mutations so that no vaccination can be given as specificity for antigen is lost?
What accounts for such a viral behaviour?

In evolution, internal urge for survival causes development of  some beneficial characters. What is meant by this at molecular level. like gradual mutation!!

A mutation is a change in the genomic sequence - this can either be in the DNA or for viruses also in the RNA which carries their genetic information. This can either happen due to external influences (chemicals, radiation) or internal (mistakes while copying the information) reasons. See the figure below which shows the principle:

DNA based lifeforms usually have pretty good proof reading functions which eliminate most mutations, as they are often causing problems. RNA based viruses (as the flu virus or the ebola virus) do not have a proof reading function which raises their mutation rate drastically. See the figure below, which shows the mutation rates of several organism groups (image from this paper):

These higher mutation rates indeed produce high number of mutated viruses which are different from the original form. This leads to a high number of viruses which are non-functional due to this mutations, but also to a few which are better adapted or look different due to this mutation. This can help in evading the immune system (when surface proteins of the virus change) or to adapt better to a host.
Since the number of viruses in an infected individual is very high (billions of viruses) it doesn't matter and the the mutations which are beneficial for the virus are positively selected for.

This can lead to difficulties in the production of vaccines when the proteins used in the vaccine mutate. Usually this is accounted for by using proteins for immunization which only mutate slowly or not (because their function is important and mutations disrupt it). For more information have a look at the following review:

RNA virus mutations and fitness for survival.


How could be the concentration of airborne pathogens in a specific indoor space be measured? I wonder if it is possible to measure the concentration of airborne pathogens in a specific indoor space in order to extract a percentage value. This value would be helpful to determine specific infection control strategies that would decrease this percentage and improve the indoor air quality.

I have no idea how practical it would be for your intended application, but people do estimate airborne concentrations of fungi and bacteria by sampling aerosols (i.e., filtering a volume of area to extract dust etc. that can carry the target organisms) and then using quantitative PCR with primers targeted at generic fungal or bacterial DNA sequences to estimate concentrations of particular classes of organisms.

Luhung, Irvan, Yan Wu, Chun Kiat Ng, Dana Miller, Bin Cao, and Victor Wei-Chung Chang. “Protocol Improvements for Low Concentration DNA-Based Bioaerosol Sampling and Analysis.” PLoS ONE 10, no. 11 (November 30, 2015). https://doi.org/10.1371/journal.pone.0141158.


What's up with this leaf? This cool design was "tattooed" on this leaf.

I found it on the windshield of my car.

What's up with it?

That is the work of a leaf miner. A leaf miner is the larval stage of an insect that feeds on the inside layer of leaves. Notice how the galleries (tunnels) start small and then get larger as the larva matures? Most leaf miners are moth larvae (Lepidoptera)
https://en.wikipedia.org/wiki/Leaf_miner


Can the "Cas9"(involved on the Crispr-cas9 mechanism) be considered as a restriction enzyme? I have many questions about the Cas9 enzyme. When the Cas9-guideRNA (crRNA and transcrRNA) complex is attached to the DNA sequence, what is the type of bond that cuts the Cas9? Does the Cas9 degrade all the sequence of DNA complementary to the guide RNA?

If the question before is "Not", then how is the sequence that is going to be cut on the DNA complementary to the guide DNA, determined? What type of enzyme the Cas9 is?

Cas9 is an endo-deoxyribonuclease (UniProt-Q99ZW2). It also has a 3'-5' exonuclease activity by which it trims the DNA a little bit, from the cut site (but not too much).

Although, Cas9 is an endonuclease and is evolved as a mechanism of immunity against viruses (like restriction enzymes), they are not considered restriction enzymes. One of the most important differences is that the restriction enzymes do not need an RNA or a DNA as a tether to identify the target sites in the DNA; their DNA binding domains can recognize the restriction sites by themselves.

Cas9 cannot just cleave any DNA complementary to the guide RNA. It needs PAM (protospacer adjacent motifs) sequences adjacent to the target site to cleave that latter.

For details check out the wikipedia page on CRISPR or read a review.


Chunks of cells after trypsinization Recently I've came across a problem after trypsinization of my stably transfected CHO-cells. When I add medium to rinse off the cells from the bottom of the flask, there are usually big chunks of cells, which I almost cannot resuspend properly... I also tried to increase the incubation time with trypsin, but it did not help much.

Does anyone have a solution for this? The trypsin I use is the same batch as usual and in the meantime I also thawed 2 different freezing stocks, but I still have the same problem.

I also tried different pipettes, from 25 to 5mL. But I can pipette like a maniac up and down and up and down... still there are big chunks of cells floating around...

Gibco has an anti-clumping agent verified for CHO cells, as does Lonza, but I like Gibco reagents more. Cells tend to clump for a number of reasons, including extracellular DNA from lysed cells and the presence of Ca and Mg ions (important ions for cell adhesion and aggregation).

You could try these:

1) Wash and resuspend in balanced salt solution without magnesium or calcium. Like Hank's balanced salt solution.

or

2) Treat with DNase I. I think you could go as low as 1 IU/mL for 30min-1hr to bust up a fair amount of DNA clumping. You can do this in a basal medium (like RPMI, DMEM, etc.), or the balanced salt solution. Your medium can contain serum only if the serum has been heat-inactivated as proteases in the serum with inactivate your DNase. Incubate with DNase under gentle agitation at 37°C (I always had a tube rotator in an incubator for this purpose, just put your cells in a 50mL conical and set them to agitate for 1hr. You could also use a heated shaker unit). If you don't have this setup, you can agitate at room temp, but for a little longer perhaps.

and maybe

3) Once of the other obvious choices is to avoid passaging your clumping cells and collect the rest. You can do this by putting all your cells into a flask incl. the clumps, agitate for a moment, and let it sit so that the chunks quickly fall to the bottom, and collect everything but the stuff that fell to the bottom.


What is the scientific opinion on plus lens therapy? Plus lens therapy is the theory that most myopia is environmentally triggered and that conventional corrective minus lenses increase nearsightedness over time. Thus the hypothesis that applying plus lenses for nearsightedness will invert the environmental pressures and halt or reverse existing myopia.

What is the scientific majority and minority opinion on plus lens therapy?

Plus lens therapy can indeed reverse myopia, but it does take time. Your eyes did not develop myopia in a few days.

The eye represents its environment. Fitting chicks, monkeys etc. with minus lenses always INCREASED the amount of myopia, while plus lenses always reduced myopia and resulted in hyperopia (lens compensation).

Putting monkeys in a confined environment showed a myopic shift. Monkeys in an open
environment showed a refractive state about +1.00 diopters.

IMPORTANT: As I have said: Unfortunately, it does take time! Do not expect results after 1 week of plus lens therapy. That is why so many people give up and think that myopia is irreversible. You also do not build muscles after 1 week.

Kind regards.

EDIT:

Optical defocus and effects in HUMANS: http://www.ncbi.nlm.nih.gov/pubmed/20592235
Defocus on chicks: http://www.iovs.org/content/44/7/2818.full
Monkeys in a confined environment: http://www.iovs.org/content/2/6/571.short


How would I explain different properties of the same protein in different species? I recently finished an experiment where I analyzed the rate of ATP hydrolysis of Heat shock protein 104 in three species of fungi. They have shown to all have different rates of ATPase activity. How would I explain these findings based on structure/ATP affinity?  The experiment was done in vitro.

The species under consideration:
Candida albicans,
Saccharomyces cerevisiae,
Schizosaccharomyces pombe

As nobody has answered this good question, I'll have a go.

Firstly, let me state that I have little-or-no knowledge of heat-shock
proteins. What follows are some general observations and thoughts.

It would not be unusual for the same enzyme from different
species to have different kinetic properties. For example, yeast and
horse liver alcohol dehydrogenase (EC 1.1.1.1) vary quite dramatically in this regard
(see below).
It is  to be expected that the same
protein from different species will have different amino acid sequences.

Even the sequence of cytochrome C (~104 amino acids), one of the most
conserved proteins, differs between species. There are 44 amino-acid differences
between human and yeast cyctochrome C, for example (although there is no
difference in amino acid sequence between the human and chimpanzee
proteins) [see Creighton, 1993, p116, quoted below].
This fact alone could explain the kinetic variation, but it might be
very difficult (and require a lot of work) to pinpoint what differences
in amino acid sequence (if any) account for the observed differences in
kinetic constants.
In the case of hsp104, a quick alignment (out of curiosity)
of the amino acid sequence of the  Saccharomyces
cerevisiae and Candida albicans enzymes showed quite a number of amino acid differences between these obviously homologous proteins.

I used the
TCoffee
sequence alignment algorithm (a new version of ClustalW) at the
xPASy server. (I received an alignment score of 98).

For the record, the accession numbers used are the following:

hsp140 from  Saccharomyces cerevisiae, 908 amino
acids, Accession Number AAA50477

hsp140 from Candida albicans, 899 amino acids, Accession
Number AAK60625
Of course, the observed kinetic differences may not be due to
amino acid sequence differences at all, or may not be
only due to such differences.  Post-translational
modification (such as phosphorylation) and differences in quaternary
structure are other possibilities.

I notice from this
reference (Parsell
et al., 1994)  that hsp104 from
Saccharomyces cerevisiae forms oligomers in the
presence of ATP, and this might be very important in any explanation of
kinetic differences. (My whole knowledge of hsp140 does not extend
beyond this excellent paper).
Yeast and horse liver alcohol dehydrogenase (ADH) are
homologues and catalyze an identical reaction.  Both also contain zinc.

However, the yeast enzyme is a
tetramer, whereas horse liver ADH is dimeric.

Another difference worth
pointing out is that in vivo yeast ADH functions as
an aldehyde reductase (making ethanol), whereas liver ADH functions as
an ethanol dehydrogenase (in alcohol elimination). [I am aware there are
other isozymes of yeast ADH, which may have different functions].

As an ethanol dehydrogenase, the yeast enzyme has a
kcat value of 455
s-1 (pH 7.05, 25oC;
Dickinson & Monger, 1973) whereas the horse liver enzyme has a
kcat value (for ethanol
dehydrogenation) of only 1.67 s-1 (pH 6.0,
25oC; Dalziel, 1962, 1963).

In the reverse direction, the
kcat for acetaldehyde reduction is
3850
s-1 for the yeast enzyme (pH 7.05,
25oC, Dickinson & Monger, 1973), whereas it
is only 125 s-1 for the liver oxidoreductase (pH
6.0, 25oC; Dalziel, 1962, 1963).

How can we explain these kinetic differences from an analysis of
structure? In my view this is a very tough question.  It may be due to some or all or none of the differences I have highlighted.
Perhaps the question needs to be rephrased as follows: Is there any fundamental
difference, at any level, in the catalytic mechanism, or in the form of the enzyme in
solution, or in the amino acid sequence, or in the tertiary or quaternary structure, that can reasonably account for the observed kinetic variation?
Are the differences worth explaining?  Perhaps one needs to go no further than to record the individual variation under rigorously-defined reproducible conditions?

Before such questions may be answered, it is important to establish the nature of the observed kinetic differences.  What follows are merely some guidelines, most of which you are probably aware of.

Is the velocity versus enzyme plot linear in all cases at both high and low substrate concentrations? That is, in kinetic jargon, is the   ν vs [Eo] linear?  As the enzyme is known to form oligomers in the presence of nucleotides (see above), this might be an important control.  Does doubling the enzyme concentration exactly double the rate, and does halving the enzyme concentration exactly half the rate (at both high and low substrate concentrations)?

An example of an enzyme where the ν vs [Eo] is often not linear is phosphofructokinase.
I notice you are using a coupled assay with two coupling enzymes.  What effect does doubling the amount of one and/or both of these enzymes have on the observed rate?  It should have none, otherwise the assay is not valid.
The substate is ATP.  Almost certainly, the 'true' substrate for the enzyme is MgATP2- (correct me if I am wrong about heat-shock proteins). How much Mg++ do you have there?

In determining kinetic parameters for ATP-utilizing enzymes one needs to be aware of ionic equilibria during experimental design. Failure to do so may give rise to spurious kinetic effects.

A solution containing ATP and Mg++ will contain many ions, probably only one of which is the substrate for the enzyme, and whose proportion will vary with concentration.  It is essential that this is taken into account. The problem and posssible solutions are explained very well by Cornish-Bowden (2003, pp 86 - 89) and by Storer & Cornish-Bowden (1976).

One experimental design is to keep the concentration of MgCl2 in constant excess over total ATP concentration (CB recommends 5mM).  This is an important one.
Are Michaelis-Menten kinetics obeyed in
all cases? Is there any evidence for substrate inhibition, or substrate
activation?

Are the double-reciprocal plots (Hanes plot,
Lineweaver-Burk plot, Eadie-Hofstee plot) linear in all cases?.  Non-linearity may be an indicator of kinetic complexity, or of poor experimental design.

If you plot the kinetic data for all three enzymes on a single double-reciprocal plot what sort of a pattern do you get?  Competitive? (no
differences in kcat, but
differences in Michaelis constants).
In comparing enzyme kinetic parameters the Michaelis constant has the big advantage that it is independent of enzyme concentration.  Thus any differences are likely to be 'real' and not due to errors in, say, protein concentration.

But what about Vmax? If, say, you determine that the maximum velocites differ by a factor of 1.4, can you be certain that you are not inadvertently adding slighly more enzyme in the higher case, and that the catalytic constants are in fact identical?
As I said above, these are just personal thoughts.  Most you probably already aware of.

References

Creighton, T.E. (1993) Proteins. Strutures and Molecular Properties. 2nd Edn. W.H. Freeman & Company.
Cornish-Bowden (2004) Fundamentals of Enzyme Kinetics 3rd Edn. Portland Press, London.
Dalziel, K. (1962) Kinetic Studies of Liver Alcohol Dehydrogenase. Biochemical Journal, 84, 244-254.[pdf]
Dalziel, K (1963) Kinetic Studies of Liver Alcohol Dehydrogenase and pH
with Coenzyme Preparations of High Purity.  J. Biol. Chem., 238,2850-2858. [pdf]
Dickinson, F.M. & Monger, G.P. (1973)  A study of the kinetics and mechanism of yeast alcohol dehydrogenase with a variety of substrates. Biochemical Journal,  131, 261-270.  [pdf]
Parsell, D.A., Kowal, A.S & Lindquist, S. (1994) Saccharomyces cerevisiae Hsp104 Protein. Purification and Characterization of ATP-Induced Structural Changes. J. Biol. Chem.,  269, 4480-4467. [pdf]
Storer, A.C. & Cornish-Bowden, A. (1976) Concentration of MgATP2- and Other Ions in Solution. Calculation Of the True Concentrations of Species Present in
Mixtures of Associating Ions. Biochemical Journal 159, 1-5 [pdf]


Cleavage of RNA by restriction enzymes? Six restriction enzymes discussed in Sequence-specific cleavage of RNA by Type II restriction enzymes (Murray et al.) have the ability to detect and cut RNA strands with that enzyme's recognition sequence.

As you know, restriction enzymes come from a system carried by some bacteria referred to as a restriction-modification system.

With this fact in mind while reading the paper above, I wondered how the bacteria carrying one of these six systems protects it's own RNA from restriction. Do the corresponding methyltranferase in each system methylate DNA as well as RNA? Would this not greatly sacrifice gene expression rates seeing as the methyltranferase surely cannot methylate all the RNA sequences being produced?

Perhaps I misunderstood the paper somehow. Could it be only in some circumstances outside the cell that these restriction enzymes have this unique ability?

This paper found that these enzymes recognize RNA:DNA heteroduplexes. Such duplexes are unlikely to be encountered in vivo. They are present when DNA is primed for replication, but these duplexes are relatively short and thus are less likely to randomly contain a recognition sequence. Furthermore, if the recognition sequence is found in the primer, the gDNA will be methylated specifically to protect it from degradation. RNA:DNA duplexes are also found during transcription, but they are also short and the gDNA would be methylated. Additionally, the transcription bubble where the heteroduplex forms is protected by RNA polymerase, which subsequently displaces the transcript from the gDNA as it leaves the elongating complex.

It's also important to note that this paper found that these enzymes don't cleave RNA:DNA as well as they do DNA:DNA duplexes and these results occurred under experimental conditions with relatively high concentrations of enzyme and substrate. The lower catalytic efficiency is likely due to lower binding affinity, which could be caused by:

presence of uracil in RNA (this was explicitly mentioned in the paper)
2'-OH presenting a steric barrier
helix shape (RNA tends to adopt an A-form helix)


Current Trend in Evolution of Human Intelligence Up front, I am specifically not interested in philosophical or ethical considerations re Eugenics and related concepts. In an effort to receive a concise answer I'll post a narrowly defined question following this preamble to set the stage.

Preamble:
In the movie Idiocracy there is a montage at the beginning "explaining" how the human population degrades, vis-à-vis intelligence, to an alarming (and absurd?) extent due to unplanned differential breeding resulting from several generations of the intellectually "more capable" people limiting their number of progeny, through active and passive family planning, while the bulk of humanity leaves caution to the wind. This exponential social differentiation eventually makes for a global imbalance that degrades our species' overall intellectual fitness to a debilitation level.

Question:
Is the premise of this movie merely a gag or is our species already doing something very much like this?
If yes or no, how might one measure the impact of differential procreation of this sort? Since testing results are always relative to the population as a whole and computers along with the Internet of Things would tend to obfuscate the initial degradation of mental capacity.

EDIT:
Based on the brief discussion in the comments - a summary of fecundity and IQ would potentially answer my question but only if it accounted for the current selection process we see going on in modern technophile societies. That is, it must account for the effect of our most educated couples generally choosing not to procreate and here I'm assuming there is in fact an effect (cf. Idiocracy for the (absurd?) degree to which the present-day trend may work itself out).

There appears to be some - note that this, of course, is highly controversial - evidence pointing at the direction that intelligence declined in the US and UK during the last century. There is a relatively new review by Michael Lynch (2016) in which he suggests that modern humans are accumulating slightly deleterious mutations with increasing rate due to relaxed purifying selection (a consequence of technology, medicine, ...), resulting in a 'future genetic load'. Let me just sum up some of the major points he makes that are relevant to assess current evolution of human intelligence:

Heritable mutations that lead to a reduction in fitness of 1% take about 100 generations to be eliminated by selection. Many of these mutations have a direct or indirect effect on the mutation rate (mostly increasing) and relaxed purifying selection on them might cause a positive feedback loop that causes even more mutations. Additionally, parental age increases the number of mutations passed on to the offspring. Most mutations will be slightly deleterious (keep in mind that the majority of new mutations is neutral, the majority of the remainder is deleterious and only very few mutations are beneficial. Therefore the really deleterious ones will still be selected against, but the slightly deleterious ones will not be removed by purifying selection). Accordingly, relaxed purifying selection increases the amount of slightly deleterious selection and decreases the efficiency of getting rid of them.
Lynch argues that the brain might be particularly sensitive to mutations as brain function depends on the finely tuned expression of thousands of genes which for him leads to the proposition that the effect of germline mutation rate on psychological disorders could be higher than expected by chance. In support, he cites Iossifov et al. (2015) who have suggested that autism spectrum disorders might be caused by de novo mutations in at least 30% of the cases and also looked at mutations interfering with IQ measurements.
Finally, he cites two papers that are of interest here as they deal with the change of intellectual abilities of humans over time (Crabtree (2013) and Woodley (2015)). The latter is a meta-analytic study based in the US and UK and Lynch already points out that there there are the usual issues with entangling genetic and environmental factors. However, in that study a slow decline of general intelligence of about 0.39 points per decade due to selection and about 0.84 points per decade due to mutational load is suggested. Interestingly, Woodley points out that there are two major hypothesis for this decline: (i) Since the industrial revolution people with lower general intelligence have higher average number of offspring (that might be the 'differential procreation' you have been hinting at). (ii) Mutation accumulation due to relaxed purifying selection against deleterious variants. Woodley concludes that the decline is a combination of both.

Of course, these points are strongly debatable. One of the major conceptual criticisms on Lynch's view is that slightly deleterious mutations (that Lynch claim to be accumulated as a consequence of relaxed purifying selection) are not slightly deleterious but totally neutral if they do not have a fitness effect. In terms of evolution it does not make a difference if an allele is neutral or negative selection is not acting on it because of technological interference. Another objection - more relevant to your question - is that measuring intelligence in general, or the IQ in particular, is a controversial thing to do and not at all easy to standardize which causes great difficulty in obtaining comparable data. Moreover, tracking down underlying genetics, estimating heritability of intelligence (a trait we even have difficulties to properly define and that is known to be strongly influenced by the environment), and consequently putting together a comprehensive assessment of the evolution of intelligence in humans is really tricky, set aside the ethical problems that may arise which we have not even touched yet.

A last note: In your edit you write:

  [...] a summary of fecundity and IQ would potentially answer my question but only if it accounted for the current selection process we see going on in modern technophile societies.

This is problematic as to date it is really difficult, if not impossible, to detect recent selection. This is mainly due to the fact that most methods depend on detecting changes in allele frequencies over time and this needs a considerable number of generations to integrate over.

There have been some efforts to develop more accurate methods, but looking at selection in the last 100 years (which you would need to be able to when looking at the technologically modern populations) is not possible so far. The best attempt I am aware of so far is Field et al. (2016, preprint) who looked, based on genome-wide association study data, at recent selection in the last 2000 years. However, they do not mention intelligence.

Update: This paper was a pre-print. It is now published in Science: Field et al. (2016).


How is sebum secretion regulated? The principle of homeostasis in biology says that living organisms try to maintain some sort of equilibrium. Doing that requires the use of feedback mechanisms to regulate things like temperature, salinity, etc. Are there any feedback mechanisms the body uses to regulate the output of the skin's sebaceous glands? If so, what are they, and on what timescale do they operate?

Nice question! Unfortunately, the complete list of pathways involved in regulation of sebum production and secretion rate by sebaceous glands are not understood yet (Picardo et al, 2009). However, we know that sebum production is continuous and is not regulated by neural mechanisms (Thiboutot et al, 2004). Retinoids, hormones, and growth factors are known to influence sebaceous gland growth and differentiation (Zouboulis et al, 1998). Also, androgens and growth hormones are known to promote sebaceous gland differentiation (Deplewski et al, 1999, Rosenfield et al, 1998) whereas estrogens and retinoids, like 13-cis retinoic acid, inhibit their differentiation (Strauss et al, 1962).

In retinoids, isoretinoin is shown to have greater sebosuppressive action as compared to all-trans or 9-cis retinoic acid (Hommel et al, 1996). In androgens, androgen receptors have been localized to the basal layer of the sebaceous gland and the outer root sheath keratinocytes of the hair follicle, and testosterone and dihydrotestosterone are the major androgens that interact with these receptors (Liang et al, 1993). However, the molecular mechanisms through which androgens interact with these receptors and sebaceous glands are not understood yet (Thiboutot et al, 2004). Apart from this, insulin and Insulin-like Growth Factor 1 (IGF-1) also play a critical role here. Acne is considered as IGF-1 mediated disease, and high levels of sugar (caused due to diet) induce high levels of insulin and IGF-1. Both these hormones amplify the stimulatory effect of GH on sebocytes and augment mitogenic downstream signalling pathways of insulin receptors, IGF-1 receptor and fibroblast growth factor receptor-2b (Melnik et al, 2009).

Other (known) substances which are found to regulate sebum secretion include histamine (due to presence of H-1 receptor on sebocytes, Pelle et al, 2008), LXR ligands (due to presence of Liver X Receptor, Zouboulis et al, 2009), PPAR ligands (due to presence of Peroxisome Proliferator-Activated Receptor, Trivedi et al, 2006), vitamin D deficiency (Yildizgören et al, 2014), neuropeptides (Ganceviciene et al, 2009), etc. See the image below (from Makrantonaki et al, 2011) for visual representation:

In spite of this, elucidating the mechanism of regulation of sebum secretion by sebaceous glands is a difficult task since, although evidence suggests that nonendocrine factors may also be an important part for regulation along with endocrine factors, the nature of this secretion and the regulation of the secretory process seem to differ among the various types of glands which, in spite of being similar in structure, might be different in function and regulation (Thody et al, 1989).

References:

 1. Picardo, Mauro et al. “Sebaceous Gland Lipids.” Dermato-endocrinology 1.2 (2009): 68–71. Print.

 2. Diane Thiboutot, Regulation of Human Sebaceous Glands, Journal of Investigative Dermatology, Volume 123, Issue 1, July 2004, Pages 1-12, ISSN 0022-202X, http://doi.org/10.1111/j.1523-1747.2004.t01-2-.x.

 3. C.C. Zouboulis, L. Xia, H. Akamatsu, H. Seltmann, M. Fritsch, S. Hornemann, R. Ruhl, W. Chen, H. Nau, C.E. Orfanos
The human sebocyte culture model provides new insights into development and management of seborrhoea and acne
Dermatology., Volume 196, Issue 1, 1998, pp. 21–31

 4. D. Deplewski, R.L. Rosenfield
Growth hormone and insulin-like growth factors have different effects on sebaceous cell growth and differentiation
Endocrinology., Volume 140, Issue 9, 1999, pp. 4089–4094

 5. R.L. Rosenfield, D. Deplewski, A. Kentsis, N. Ciletti
Mechanisms of androgen induction of sebocyte differentiation
Dermatology., Volume 196, Issue 1, 1998, pp. 43–46

 6. J.S. Strauss, A.M. Kligman, P.E. Pochi
The Effect of Androgens and Estrogens on Human Sebaceous Glands
J Invest Dermatol., Volume 39, 1962, pp. 139–155

 7. L. Hommel, J.M. Geiger, M. Harms, J.H. Saurat
Sebum excretion rate in subjects treated with oral all-trans-retinoic acid
Dermatology., Volume 193, Issue 2, 1996, pp. 127–130

 8. T. Liang, S. Hoyer, R. Yu
Immunocytochemical localization of androgen receptors in human skin using monoclonal antibodies against the androgen receptor
J Invest Dermatol., Volume 100, 1993, pp. 663–666

 9. Melnik BC, Schmitz G. Role of insulin, insulin-like growth factor-1, hyperglycaemic food and milk consumption in the pathogenesis of acne vulgaris. Exp Dermatol. 2009;18:833–841

 10. Edward Pelle, James McCarthy, Holger Seltmann, Xi Huang, Thomas Mammone, Christos C. Zouboulis, Daniel Maes, Identification of Histamine Receptors and Reduction of Squalene Levels by an Antihistamine in Sebocytes, Journal of Investigative Dermatology, Volume 128, Issue 5, May 2008, Pages 1280-1285, ISSN 0022-202X, http://doi.org/10.1038/sj.jid.5701160

 11. Zouboulis, Christos C. “Sebaceous Gland Receptors.” Dermato-endocrinology 1.2 (2009): 77–80. Print.

 12. Nishit R. Trivedi, Zhaoyuan Cong, Amanda M. Nelson, Adam J. Albert, Lorraine L. Rosamilia, Surendra Sivarajah, Kathryn L. Gilliland, Wenlei Liu, David T. Mauger, Robert A. Gabbay, Diane M. Thiboutot, Peroxisome Proliferator-Activated Receptors Increase Human Sebum Production, Journal of Investigative Dermatology, Volume 126, Issue 9, September 2006, Pages 2002-2009, ISSN 0022-202X, http://doi.org/10.1038/sj.jid.5700336

 13. Yildizgören, Mustafa Turgut, and Arzu Karatas Togral. “Preliminary Evidence for Vitamin D Deficiency in Nodulocystic Acne.” Dermato-endocrinology 6.1 (2014): e983687. PMC. Web. 23 Apr. 2017.

 14. Ganceviciene, Ruta et al. “The Role of Neuropeptides in the Multifactorial Pathogenesis of Acne Vulgaris.” Dermato-endocrinology 1.3 (2009): 170–176. Print.

 15. Makrantonaki, Evgenia, Ruta Ganceviciene, and Christos Zouboulis. “An Update on the Role of the Sebaceous Gland in the Pathogenesis of Acne.” Dermato-endocrinology 3.1 (2011): 41–49. PMC. Web. 23 Apr. 2017.

 16. Thody, A. J. & Shuster, S. Control and function of sebaceous glands. Physiol Rev 69, 383–416 (1989)


Mutations in organisms I was researching mutations and came across an interesting question:
Do mutations occur in the DNA or mRNA of an organism? Is this more opinion that science?

Thanks in advance!


Please name this plant What is the name of this plant? It was found in a village in Bangladesh, in the month of February.

I believe this plant may be Rotala rotundifolia

Quoting from Wikipedia,

  It is a common weed in rice paddies and wet places in India, China, Taiwan, Thailand, Laos, and Vietnam, and has been introduced to the United States.

This makes sense, as Bangladesh is located near both India and China.

  The emerse form has rounded leaves, the submerse leaves are narrow lanceolate. It is very variable dependent on light and environmental conditions. Under strong light, the leaves can become almost wine red. It has pale pink flowers.


Can only fully matured sperm fertilize an egg? Are only mature sperm able to fertilize an egg? If so, is there typically a reserve of mature sperm that are saved after an ejaculation or does a male need to wait for new sperm to mature before trying to fertilize an egg again? In humans it seems that the the shortest maturity period for sperm is around 42 days (New Findings on Sperm Life Cycle Could Impact Fertility Treatments). Do the new immature sperm serve any purpose after ejaculation?

As far as I know, sperm cells undergo maturation in the epididymis, where they become motile. As Eliane pointed out, this is a continuous process, so the male does not have to "wait", because there is continuously a batch of sperm cells that will shortly become mature. Furthermore, maternal factors are required for the process of capacitation in which the sperm cell becomes capable of fertilization and undergoes motility increase.

An immature sperm cell is simply non-motile and even if present in the ejaculate, it will not be able to travel towards the fallopian tube to fertilize the oocyte. A sperm cell which did not go capacitation will also have no ability to fertilize an egg (that's why prior to IVF it's important to capacitate sperm).

My sources:

https://kjcscientific.wordpress.com/project-excalibur/
Gilbert's Developmental Biology (2009)


Species I.D. hardwood tree There are two of these trees, growing in old fence rows, along my yard, in central VA, Augusta County, Shenandoah Valley.  They have smooth, leathery leaves, pale wood, quite hard to cut, and tough to break.  The close ups are of some limbs I trimmed, yesterday. The biggest is about 10 inches in diameter, and perhaps 40 feet tall.  Branches tend to grow strangely hooked elbows that send branches off into strange directions, which makes trimmed limbs tangle and hook together.  This is what the foliage looks like in mid September.

I'm thinking this is a Quercus imbricaria, which has the nickname of "shingle oak"; they're native to the eastern regions of the United States, which includes your state and county, exhibited immediately below.

Distribution
 Brown = absent; Dark green = present in state/Native; Light green = present in county/Native.
(source)
The leaves
The leaves are mostly linear in shape, with entire margins & a combination of pinnate and dichotomous venation. The overall color, size and sheen also seem to match quite well.

Overall tree
Surprisingly, I had a difficult time finding a decent image that showed a close up of the branching for this tree, so I decided to use an image of a Quercus laurifolia instead, which is of the same genus as the proposed species, and is also found in the eastern [but more southern parts of the] United States.


Why can't cell division happen the other way around? Mitosis in eukaryotes happen in this order: DNA replicates and then the cell divides. Why doesn't it happen in reverse order (i.e., cell divides and then replicates the DNA)?
I am talking about diploid cells.
Why has evolution favoured the first way?

If you are thinking of a process like meiosis but followed by DNA duplication, the problem is that this would create daughter cells that do not have the same genome as the parent cell.

The diploid genome of a sexually reproducing species' cell has different alleles of the same locus. If the cell replicates itself by passing one chromatid to each daughter cell which then duplicate that to make a diploid genome, the resulting cells will not have the same DNA as the original one since each of the daughter cells will have inherited only one of the available alleles. They will then make an exact copy of the DNA they have inherited and become diploid but with a new genome, one that did not exist in their parent. This is not good since the cells of an organism need to have the same genome in order to function in the same way.


Difference between the spinal cord and vertebrae column What is the difference between the spinal cord and the vertebrae column, they both run through from the head to the abdomen. Does any one have any idea.

The vertebral column is a bony, segmented structure that supports the torso/head and thorax. The spinal cord is a bundle of nerves that runs inside the structure of the vertebral column. So - they run together, but are completely separate.


How to visualize the ECM? Specifically, I'd like to look at changes in HA (hyaluronic acid) production. Most often you only see people staining the cell surface or removing cells from culture for fixation and then imaging. Does anyone know how to analyze the ECM (extracellular matrix) and proteoglycans that surround a cell if you're looking to see if a condition may be changing the way a cell remodels it's ECM? Is it even possible with some fluorescent tags?

Different components of the ECM can be stained differently but since you asked about hyaluronic acid (HA) I'll limit my answer to its staining.

See this paper. They use Hyaluran Binding Protein (HABP) as a specific probe for HA.

  Because HA has a very simple, conserved composition and is
  ubiquitously expressed in all animals that have a developed immune
  response, HA is not immunogenic. Therefore, there are no antibodies
  that specifically recognize HA, and traditional immunohistochemical
  methods of detection of HA are not possible. Fortunately, a very
  specific and tightly binding protein, the hyaluronan binding protein
  (HABP), which is composed of the HA binding domain with the link
  module from aggrecan, was isolated (Hascall and Heinegård 1974;
  Tengblad 1979) and adapted as an HA probe (Ripellino et al. 1985).
  HABP is now widely employed for specific detection of HA.

Biotin tagged HABP can be used for IHC based visualization procedures.


Why don't amino acids get linked in the functional groups of acidic and basic amino acids? There are 'acidic' and 'basic' amino acids like aspartate and histidine.

When protein is synthesized with those amino acids, what ensures that the to-be-assembled amino acids will not bond to the amine groups or acidic groups in the functional groups of the amino acids in the polypeptide?

When the amino acid comes to the ribosome it is in the form of an aminoacyl tRNA in which the carboxyl group of the amino acid is esterified with the 3' OH group of the ribose moiety at the 3' end of the tRNA.

There is already a growing peptide bound in the P site of the ribosome with a free -COOH group which will react with the -NH2 group of the incoming amino acid in the A site to form the next peptide bond. This reaction takes place in the context of what is essentially an enzymic active site. The reactants will be held in the correct positions for catalysis to take place (in this case the catalysis is carried out by the ribozyme activity of the small ribosomal RNA).

So the answer is that the selectivity of this reaction is just another example of the way in which enzymes are able to carry out highly-specific reactions. So, for example, the enzyme hexokinase, which phosphorylates glucose at the 6 position has, potentially, four other -OH groups that, chemically speaking, could be phosphorylated.


How is it possible to even hope for an ebola epidemic of this current size to remain contained to a relatively small part of Africa? As of 2014-09-14 at least 5347 cases of ebola have been identitied. Some estimates are much higher. While experts are sounding the alarm to try to get sufficient resources to contain the outbreak, some people are also speaking very hopefully about containment to roughly the current affected area. This article puts the risk of the outbreak reaching the United States as low as 3%. I'm not an expert in the field, but it seems like there are almost countless ways in which an increased number of cases increases the risk of further exponential growth. It's encouraging to hear that in countries with better healthcare, death rates would likely be much lower, but at this point, isn't it inevitable that the outbreak will run its course as a global pandemic?

For example, which of these possibilities is just my imagination, or likely so improbable that we don't need to worry about it?

Scared carriers not yet showing symptoms sneak or force their way across boarders to unaffected regions.
Objects, food, or water touched by the infected go unnoticed until they end up leaving the containment zone.
If it can jump from bats or monkeys, thousands of infected humans increase points of contact to create vectors into other species, perhaps one that will travel unnoticed far beyond the containment zone.
After months of the same security precautions day in and day out, airport checkpoints, and other points of entry become lazy, and let infected through.

With numbers as high as they are, and possibly higher than we even know, is this really containable at all?

This is too long for a comment, so my thoughts about this here. The CDC Director said a few days ago after a visit in Africa "The window of opportunity is closing".

This can happen. However, you are not getting contagious unless you show symptoms. This is different in other diseases like chicken pox or measles where you spread the virus before showing symptoms. So there has to be a lot of awareness. Also doctors need to be very careful with patients showing these symptoms. This is most likely one of the main reasons for the wide spreading of the disease.
Same problem as in 1. Theoretically this is easy to prevent, but in a situation of chaos this can cause problems. But since infected people which show symptoms will not handle large amounts of food, this is most likely less of a problem.
Every crossing of a species-barrier is a rare event. Double-crossings are even less likely. So I don't think this is a problem. Besides this, we already have to independent Ebola outbreaks which has never happened before. One is the one in West-Africa, the other one is happening in the Democratic Republic of Congo. Both are independent cross-overs.
This can cause problems. The advantage of the first world is that we have functional health care systems. They allow better care for the persons and also better isolation of contact persons. I think it is unlikely that it would spread widely. The perspective will be different, if the virus makes the jump into the densely populated regions in South-East Asia. There a lot of people live closely together, this can cause real problems. Fortunately for us the virus is not highly contagious. To infect yourself you need unprotected contact to the body fluids (blood, stool, feces, sweat etc.) of infected persons.


Do mycorrhiza only form with angiosperm? if not than with which Phylum it forms

Mycorrhiza refers to any fungi that forms a symbiotic relationship with a plant. There are many different species, and they are necessary for healthy plant growth in ~70%-80% of vascular plant species with representatives from more than ~90% of plant families. Needless to say, mycorrhiza associations with plants are very common.

What you may be thinking of is rhizobia, which are not as ubiquitous.  Rhyzobia are soil bacteria associated with legumes (peas, soybeans, clover, lentils, etc.). Rhizobia fix nitrogen for the legume, and the legume forms root nodules where the rhizobia live. The nodules provide an ideal location for the rhizobia to live and thrive. This relationship has only been observed in legumes (scientific name: Fabaceae).

In summary:
Both mycorrhiza and rhizobia form Symbiotic relationships with plants. Mycorrhiza are fungus that form relationships with most species of plants. Rhizobia are bacteria that form relationships only with plants in the legume family.


How to generate protein graphics for illustrating articles? The structure of insulin shown below appears in a Wikipedia entry.

What software was (or can be) used to create pictures of this type?

All comments are great, there are numerous software programs that allow you to make such images.

Gathering information about the insulin structure

By simply clicking on the image in wikipedia it will provide you with  valuable information:

  Created by Isaac Yonemoto created with en:pymol, en:inkscape, and
  en:gimp from NMR structure 1ai0 in the en:pdb. Ref: Chang, X.,
  Jorgensen, A.M., Bardrum, P., Led, J.J.

So the creators used pymol, inkscape and gimp, but let's dig a bit deeper. Unfortunately Isaac Yonemoto, the editor of this wiki, did not provide a direct link to the original publication (see wiki file history). However by searching the author names in combination with insulin we quickly find the article: Solution structures of the R6 human insulin hexamer. In the first paragraph we see:

  The atomic coordinates of the 20 refined hexamer structures and the
  NMR-derived restraints have been deposited in the Brookhaven Data Bank
  (PDB ID codes 1AIY and 1AI0 for the symmetric and the nonsymmetric
  hexamer, respectively)

You can find the structure that was depicted in this wiki article by searching the PDB id.

Creation vs visualization
You can interpret 'create' in your question in two ways here:

Creating this whole structure from nothing
Visualizing a structure someone else determined

If you refer to the former you should look at the article corresponding to this structure. Note that this is quite detailed and requires  knowledge of several concepts, such as molecular dynamics and NMR spectroscopy. If you refer to the latter than you should take a look at the programs mentioned earlier such as pymol, inkscape and gimp

Not generalizable
This boils down to what @David already said in his comment:

  You are surely aware that Wikipedia's contributors (not users) are
  completely independent and thus use whatever software they choose to
  create molecular images.


Technical reason that specialized embryonic cells form During the embryonic stage of human development, rapid cell division occurs and specialized cells form to build the various parts of the developing fetus.

I'm curious:

Why technically do specialized cells (such as brain cells) form?  I suspect this is due to a DNA sequence, but why chemically / mechanically should a genetic combination cause a certain specialized cell-type to form?
Have we (the international scientific community) reproduced the fundamental chemistry that causes any specialized cell-types to form?

There is indeed chemical signaling that triggers the differenciation. There are gradients of chemical species during the development. Look at https://en.wikipedia.org/wiki/Morphogen ! There are also other references there.

PS: there is a stack exchange question from today about something related Can gap genes delay their expression?


What are some of the known fungi with heat resistant spores Are there any fungi whose spores can survive 100+ degrees for 15 minutes and grow in a sugar-deprived medium?

According to Sterflinger, some black yeasts may qualify: http://www.ncbi.nlm.nih.gov/pubmed/10081587

  Rock inhabiting meristematic fungi are extremely tolerant against high
  temperatures, desiccation and osmotic stress. Their temperature
  tolerance increases with increasing dehydration of the fungal thallus.
  Air dried mycelia of black yeasts stand temperatures up to 120 degrees
  C for at least 0.5 hours

More recently, Suryanarayanan et al. (http://www.ncbi.nlm.nih.gov/pubmed/21872180) have published the discovery of several fungal environmental isolates able to survive dry heat sterilization for 2h at 100+ degrees C. Growth testing was done on Potatao Dextrose Agar (PDA).

  Among 25 species of Ascomycota isolated from leaf litter, nine were
  able to grow after incubation in a drying oven for 2 h at 100 °C; the
  spores of two of these species survived 2 h incubation at 110 °C, and
  one survived exposure to 115 °C for 2 h." (...) Craphigera and Phoma sp.
  survived 2 h incubation at 110 °C; the conidia of Bartalinia sp. were
  the most resistant and survived exposure to 115 °C for 2 h

The isolates which survived at least 2h at 100 C were:

Bartalinia sp. (NFCCI 2307)
Chaetomella raphigera (NFCCI 2308)
Curvularia sp. isolate 2 (NFCCI 2311)
Drechslera halodes (NFCCI 2312)
Leptosphaerulina sp.
Pestalotiopsis sp. isolate 1 (NFCCI 2309)
Pestalotiopsis sp. isolate 2 (NFCCI 2313)
Phoma sp. (NFCCI 2310)
Pithomyces sp. (IMTECH 9398)


Hypothetically, what is the smallest functional form of human? Since the my first encounter with doraemon manga, I've been wondering many things, one of them is the small light.

Assuming we had an instrument, such as small light, which enabled people to grow and shrink as they wanted to, what would be the smallest and the most compact functional form of a person?

First, I can rule out that we couldn't be as small as an atom because we couldn't be function as human being if we were compressed into 1 atom. So did 1 molecule. and so did 1 cell.

Second, you need more than 1 cell to construct organs, i.e. I couldn't imagine an eye which consists only several atoms or molecules.

Therefore, there should be a limit to the the size of human organs in order to fully retain their functions and thence, there should also be a limit to the minimum size of human organs.

What are the limits of size of each of human organs?

What are the limits of size of human then?

This question is for Doctor Frankenstein!

The answer would depend on what you would accept to consider being a human.

Does it still need to be able to make simple calculation in order to be a human?
Yes, because otherwise we would have lost some functions. But then you may ask…
Does it need to have big enough hands in order to fulfill the social function of hand shaking.
Does it has to be attractive to the other sex?
Does it need a heart or is it fine if oxygen diffusion through tissue only is enough for this creature to live?

I guess that if you change the number of cells you will necessarily change the functionality. I am not saying that small guys are not as functional as big guys. For example, big guys are better runner, while small guys are better climber.

Are we allowed to shrink the cells to have minimal sized cells?
Are we allowed to shorten the DNA in order to shrink the cells?

Notes:

There are approximatively 200 different cell types in a human

My reference is not a peer-reviewed article (ref). Wikipedia lists cell types and it doesn't seem to go over 200. However, it is important to realize that it probably very much depend on how you define cell types.

Terminologica Anatomica lists over 7,500 names parts of the human body
There are 13 or 14 (depending on the gender) gland types
This article provides an estimation of the number of cells in the human body
Here (wikipedia) is a discussion on the concept of the minimal cell
Here and here (biology.SE) are discussions on the minimum number of genes/amino acid to sustain life
Here (biology.SE) is a discussion on which species has been found to have the smallest genome


Methanol and brain damage -- special affinity for optic nerve or just really toxic? Methanol is known for causing blindness. One explanation I have read is that the optic nerve is especially active and so methanol will be preferentially taken up by the cells there which then die.
But I assume methanol is also bad for neurons concerned with, for example, memory and cognition. But is this wrong? Could it be that methanol for some reason tends to cause temporary or permanent blindness but is no more toxic to other neurons than ethanol is?

Methanol toxicity is relatively rare and comparatively little is known about its etiology. I found a correspondence published in the journal Nature in 2004, it seems to a good review of the literature, given that I could not find a recent review on the topic. Please take a look, especially at the sources that the following paragraph cites:

Methanol is particularly toxic to the optic nerve, leading to acute
blindness. Based on a histopathological study, the retrolaminar optic
nerve myelin sheath seems to be selectively vulnerable to methanol
poisoning due to its anatomical structure. In the acute phase, the
hyperaemia and swelling of the optic disc has a papilloedema-like
appearance. The axoplasmic flow stasis at the nerve head and
alteration of the myelin sheath in the retrolaminar nerve segment were
demonstrated in experiments using rhesus monkeys. The pathogenesis is
presumed to be histotoxic anoxia in a vascular watershed area, which
is the result of direct inhibition of cytochrome oxidase by formic
acid. Additionally, the increasing pressure following oedema in the
visual pathway might further aggravate the deterioration due to
ischaemic changes. Therefore, effective methods to treat the oedema
might be important, such as the use of intravenous steroids and
diuretics. The mechanism of subsequent optic atrophy in patients with
methanol poisoning is still unknown, it was suggested to be due to
progressive demyelination. The distinct glaucomatous-like cupping of
the optic disc suggests extensive loss of retina ganglion cells, which
has been thought to result from retrograde degeneration of optic nerve
axons.

It seems that in our best understanding, the optic-specificity of the action of methanol seems to be due to the nature of the myelin sheath that insulates the optic nerve.


Detecting a Fasting State in the Body via Lasers I was just wondering wether it would be possible to detect if the body is in a "fasting" state, via lasers attached to the body. If it is possible, what sort of laser would be needed?

If by a fasting state, you mean blood glucose levels, researchers seem to think it is feasible. See for example Pleitez et al. (1) and Guo et al. (2). Their designs both utilize infrared IR laser light to measure glucose levels in the skin.


What's this spring-like structure in the plant parenchyma cell? I observed a transverse section of an amaranth stem in biology lesson today. When I boost the magnification to 600X, I found this spring-like structure in one of the parenchyma cells near a vascular bundle. I could only find one of these in the section. Can anyone tell what structure is it?

It looks like a part of a xylem cell (particularly vessel). Take a look at pics in wiki article. Another good example is here on pic. 36. Possibly you have dragged a part of it during cutting. So it is presumably not a part of parenchyma cell.


Is there a standard format for plant community composition data? FIA has a nice database of forest Inventory data, this would be great except that it does not seem capable of handling data from non-tree species (e.g., grasslands, wetlands).

Is there a standard database or flat-file format for collecting plant community data (e.g., biomass, cover, dbh as appropriate)?

There does not appear to be a current standard, but Veg-X is a standard that has been developed to facilitate exchange of plot-based vegetation data, and may provide the closest to what you are looking for.

Veg-X is described in Wiser et al 2011 and the project home page is http://wiki.tdwg.org/Vegetation/

From the abstract:

  The exchange standard for plot-based vegetation data (Veg-X) allows
  for observations of vegetation at both individual plant and aggregated
  observation levels. It ensures that observations are ﬁxed to physical
  sample plots at speciﬁc points in space and time, and makes a
  distinction between the entity of interest (e.g. an individual tree)
  and the observational act (i.e. a measurement). The standard supports
  repeated measurements of both individual organisms and plots, allows
  observations of entities to be grouped following predeﬁned or
  user-deﬁned criteria, and ensures that the connection between the
  entity observed and taxonomic concept associated with that observation
  are maintained.

Wiser, S.K., N. Spencer, M. De Caceres, M. Kleikamp, B. Boyle, & R.K. Peet. 2011. Veg-X -- An international exchange standard for plot-based vegetation data. Journal of Vegetation Science 22:598-609.


Could be an union/synergy between Math, Computer Science and Marine Biology? I'm studing for my bachelor's degree in Natural Science and I have to chose the path for my future life. I have to chose the right kind of graduate studies. Since I love computer science, maths and marine biology more in details I love the tropical ecology especially that of the coral reefs and atols in the pacific ocean, the whales (e.g. the humpback whales and their migrations), the computer simulations and mathematical models. Thus, I want to ask you if is there a branch of marine biology that allow me to study and specialize myself in tropical ecology and in math & computer science too, because in my current course we don't have any exams of computer science and only one of maths, and I'm feeling sad for this. The right path coul be the computational biology? Exist in biology, some field called "Computational Marine Biology" or "Computational Marine Tropical Ecology"? One last thing, what about Ecoinformatics?

This advice is America-centric; graduate programs in other countries may be different, especially in regards to assigned course work, etc. But this should more-or-less be solid. Also, I'm assuming you're interested in a PhD.

I don't know if what you're looking for is a proper field, but that doesn't matter.  Ideally, grad school is where you do research on your own terms, and what lab you join is the single most important consideration. What you want is a competent program that:

gives you the flexibility to create your own subfield
has supportive and knowledgeable faculty that you can work under
has excellent computer science AND marine biology programs (or analogs)

First, find faculty who are doing research you are interested in, and look at the programs available at their schools. Since they're the most important consideration, everything else will fall into place after that.

Next, email 5 of those professors with an introduction of what you're interested in, particularly about their research.  Ask them what programs are most appropriate at their university, and how flexible you can be in taking appropriate coursework.

At some point, you'll probably want to decide if you want to be more of a marine biologist or a computer scientist. Your diploma at the end of the decade is only going to say one of those things.  That shouldn't make a huge difference as to your job outlook, but is worth thinking about.  Practically, the question is whether you want to get your hands dirty, go out on a boat, and collect your own data.  Alternatively, if you join a CS program, you are more likely to be analyzing large datasets collected by other scientists.

At most universities, you'll likely only have the option to join a biology program. But there are certainly excellent CS programs with biology oriented faculty.  Even then, the CS faculty is more likely to be doing genomics and such.

For practical recommendations, the University of Washington in Seattle would probably have something appropriate to your interests. While I was there, my lab was adjacent to an Oceanography lab that had a video wall for visualizing ocean currents and such. Not precisely marine biology, but UW has a very collaborative faculty and I'm sure the two departments work together.

UW also has a strong computational biology program that you can go into either through CS or through one of the many biology programs. You should also check out the Institute for Systems Biology at UW. I saw a presentation there specifically about DNA exchange between marine microorganisms.  I'm not saying UW is your best option, I just know that school because I did my PhD there.

A final word of advice. Once you're in a program, it's very likely your interests will change as you learn about other research going on. And also, it's quite possible you won't get into the lab you want simply because of money or logistics. With both of these in mind, be flexible about where you're willing to go. What you do during your PhD isn't really that important anyway.  If you're going to be research scientist, it's what you do during your Postdoc that will establish your career. Just take the opportunity to learn everything you can and see what's out there.

Hope this helps.  Good luck!


How to define drug-resistant or -sensitive cell line when knowing the IC50 values? I have got the IC50 data for a drug on different cell lines. How to define if the cell line is sensitive or resistant towards this drug?

Could anyone tell me how to define this?

From this post.

The IC50 is the concentration of inhibitor required to reduce the activity of a molecule/protein by one-half. It is the inverse of EC50. Usually inhibition curves looks sigmoidal so the IC50 is the middle point of the S curve. Here an example. (Note that the Y-axis can be pretty much anything, like enzyme activity and the X-axis is the concentration in a logarithmic scale).

Now for your actual question. The IC50 you got is by plotting a measure of the cell death rate vs the concentration of the drug. IC50 is expressed as a concentration so the higher the concentration of drug needed to kill the cell line the more resistant that cell line is. If the IC50 is very low then the concentration (or amount) of drug needed to kill the cell line is also very low which means the cell line is more sensitive.


Why is angiotensin converting enzyme localized in the lungs I understand that it's also found elsewhere, such as in renal capillaries, but I can't see logic behind it being located in the lungs. Isn't ACE's function, through making more angiotensin II, causing increased fluid and sodium retention and increasing peripheral resistance? What benefit does that purpose get from ACE being mainly in the lungs?

ACE is present on the luminal surface of vascular endothelia throughout the body and is abundantly present in the endothelium-rich lungs.

ACE in the kidney—particularly in the endothelial cells of the afferent and efferent arterioles—
can produce enough ANG II to exert local vascular effects.

Thus, the kidney receives ANG II from two sources:

✓ Systemic ANG II comes from the general circulation and originates largely from the pulmonary region, and

✓ Local ANG II forms from the renal conversion of systemic ANG I.

• In addition, the proximal tubule secretes ANG II into its lumen and thus achieves intraluminal concentrations in excess of
those in the general circulation. ANG II in the circulation has a short half-life (~2 min).


Why does our eyes got wet when we feel emotional or whenever we are hurt? I was thinking like whenever when we feel emotional or whenever we got hurt we got tears from our eyes but why is that happen ? Why our eyes got wet ?

The lacrimal gland, the major source for tear production, is situated just above the eye. It sends it's secretions to the eye via the lacrimal duct. Tears secreted collect in the conjunctiva of the upper lid. There is also a nasolacrimal duct which drains the tears from the eye into the nasal cavity. Hence the sniffles when we cry.

How is it controlled? The lacrimal nucleus in the brain is the major source for innervating the lacrimal gland, is a subnucleus of the superior salivary nucleus in the tegmentum of the pons (part of the brain stem). The lacrimal nucleus is connected to the lacrimal gland by the facial nerve (more specifically the greater petrosal nerve). This is parasympathetic (meaning it is part of the autonomic nervous sytem) and the neurotransmitter transmitting the signal from nerve to gland is acetylcholine (the receptor is muscarinic subtype of the cholinergic... though strangely wikipedia says nicotinic subtype is involved as well, but maybe this is simply poorly worded and is just refering to the ganglia stopover between pre/post ganglionic parasympathetic neurons), this information helps explain how some drugs affect lacrimation (tearing up).

Taken from source (1) [I do not know how reliable this website is]: How is the lacrimal nucleus told to start lacrimation? The lacrimal nucleus receives projections from the autonomic nervous system as well as from various brain structures, including the frontal lobe, globus pallidus, thalamus, and hypothalamus. The projections from the frontal lobe are thought to be important in human psychic lacrimation (crying because of emotions).

What I know: Another brain area called the limbic system is involved in production of basic emotional drives, such as anger, fear, etc. The limbic system [in the case of sympathetic nervous system it would be the hypothalamus specifically, but this is irrelevant here since parasympathetic nerves cause lacrimation] also has a degree of control over the autonomic system. As I under stand it, the frontal lobe usually inhibits the limbic system.

Again from source (1): While humans across the world produce psychic tears in response to both positive and negative emotions, and while similar emotions have been identified in other animal species, no reports exist of other animals showing psychic lacrimation.

according to wiki (3): Compared to tearing for physical reasons,  tears for emotional reasons have s different chemical composition. They are composed of more protein-based hormones, such as prolactin, adrenocorticotropic, and leucine enkephalin (a natural pain killer), which is suggested to be the mechanism behind the experience of crying from emotion making an individual feel better.

sources:

(1) http://carta.anthropogeny.org/moca/topics/lacrimation-tearing

(2) http://en.wikipedia.org/wiki/Lacrimal_gland#Innervation

(3) http://en.wikipedia.org/wiki/Tears


What kind of memory is "keyboard/keypad memory"? I work in IT and I have observed many people who cannot remember their iPhone passwords or computer passwords off the top of their head. However, if presented with a keyboard or a phone with a functioning keypad, they can instantly remember exactly what their password or passcode is.

I'm curious to know what this kind of memory is called. Since it's somewhat related to visuals, but not necessarily (you don't need to look at your keyboard to type out your password.)

Short answer
Motor memory

Background
A striking personal example of your account pictured in the question was my experience where I had to type in my PIN at the bank counter on a keypad. It turned out I entered it incorrectly several times in a row, despite the fact that I had used that PIN a zillion times on ATM machines. Luckily, the bank employee had seen this phenomenon many times before, and she explained to me that the standard computer keypads have a different numerical layout than ATM machines. So to type in my PIN correctly I had to do it under visual guidance - an awkward experience. It showed quite strikingly that I had been entering my bank PIN using motor memory.

Much of our motor behavior is learned - think of learning to walk, cycle or ice skate. To achieve motor learning, the central nervous system is believed to use internal models that predict the mechanical dynamics necessary to execute a task. In theory, the internal model is an association from a desired trajectory for the hand to a pattern of muscle movements. This map is basically unique for the objects that we have learned to interact with. Because we routinely use our hands to interact with a remarkably diverse variety of mechanical systems, the ability to learn and recall internal memories is thought to be a fundamental property of the motor system (Shadmehr & Brashers-Krug, 1997).

Reference
Shadmehr & Brashers-Krug, J Neurosci (1997); 17(1): 409-19


Difference between flexion and contraction? i asked this to my anatomy teacher and he said there is no difference but when it comes to specialy in body building when you say to flex their bicep they freeze their upper limb in order to do that but when you say contract your bicep they only isolate it an shortens it.
am I right with my reason?

Flexion: the movement that decreases the angle between two parts [1]. Examples: clenching the hand into fist, sitting down.

Contraction: the property of muscle to generate tension when actin and myosin filaments are crossing. There are a few types of contractions. The isometric contraction is when the muscle generates tension but its length doesn't change (for example when you try to lift something that you can't). The isotonic contraction is when the muscle changes its length [2]. This kind of contraction leads to movements and can lead to flexion too.

References:

Wikipedia contributors, "Anatomical terms of motion," Wikipedia, The Free Encyclopedia, http://en.wikipedia.org/w/index.php?title=Anatomical_terms_of_motion&oldid=612679254 (accessed June 26, 2014).
Wikipedia contributors, "Muscle contraction," Wikipedia, The Free Encyclopedia, http://en.wikipedia.org/w/index.php?title=Muscle_contraction&oldid=609265714 (accessed June 26, 2014).


Identify this dragonfly with orange body and orange wings? The photo shows a red dragonfly on top (in front of some hot pink snail eggs) but an orange dragonfly with orange and perhaps translucent(?) wings near the bottom. This is the best resolution I could get. While the red one is easy to photograph (see Identify these two big, beautiful dragonflies in Taiwan?) this orange species is really jittery and difficult to approach.
I believe I have seen dozens of them in an isolated grassy patch in a parking lot, but they never landed and I could not capture a photo or see them clearly, but today this one was "available" for a photoshoot.
The orange dragonfly's body is about 4 to 5 cm long, the location is Hsinchu county Taiwan. That's all I've got, except that the last centimeter or so of the wings appear to be almost transparent.

These seem to both be Neurothemis taiwanensis.
On iNaturalist, if you search for dragonflies in Taiwan, it finds 104 species observed and submitted, and this Neurothemis taiwanensis is the most popularly-submitted species.
Browsing the gallery of photos in their database shows both red and orange varieties. If we filter the sex on just males, we see mainly deep-red ones:

...and filtering on just females yields mainly orange ones but also some red ones:
https://inaturalist.ca/taxa/503081-Neurothemis-taiwanensis/browse_photos?term_id=9&term_value_id=10&place_id=7887


Color vision across species Is it true that color vision is sex-linked for all species with binary sexes? Is there an evolutionary significance to the fact that color vision is X-linked in humans? E.g., only female humans can be tetrachromats.

Short answer
Human females do not benefit much from an extra cone class, as color discrimination is hardly affected in most tetrachromats. In fact, tetrachromats often show increased error rates in their color discrimination. In dichromatic New World monkeys the heterozygous females do functionally benefit from their extra cone as they gain trichromatic vision.

Background
Anomalous trichromats have all of their three cone types to perceive colors, but one type of cone perceives light slightly out of alignment. There are three different types of effect produced depending upon which cone type is affected.

The different anomalous conditions are protanomaly (reduced sensitivity to red light), deuteranomaly (reduced green sensitivity - the most common type) and tritanomaly (reduced blue sensitivity - extremely rare). People with deuteranomaly and protanomaly are collectively known as red-green colour blind and they generally have difficulty distinguishing between reds, greens, browns and oranges. They also commonly confuse different types of blue and purple hues. Red and green cones are indeed coded on the X-chromosome.

One source of variation is the very common Ser180Ala polymorphism that accounts for two spectrally different red pigments and that plays an important role in variation in normal color vision as well as defective color vision. The most common source of variation is the existence of several types of red/green pigment chimeras. The red and green-pigment genes are arranged in an array on the X-chromosome with one red-pigment gene followed by one or more green-pigment genes. Recombination events have given rise to red/green hybrid genes and deletion of the green-pigment genes. Only the first two genes in the tandem are expressed. The severity of red-green color vision defects is inversely proportional to the difference between the wavelengths of maximal absorption of the photopigments encoded by these two genes.

Females who are heterozygous for red and green pigment genes that encode three
spectrally distinct photopigments have the potential for enhanced color vision, as they are effectively tetrachromats (Deeb, 2005, Neitz et al., 1991). However, sensitive color-contrast testing on 43 tetrachromats has revealed that most of these females have no deviating color-discrimination whatsoever. 8 subjects showed relatively small effects, while only one showed a clear increased sensitivity in a narrow range of frequencies. It is believed that the human visual system is not plastic enough to cope with the extra spectral input. In fact, in the group there was an overall increase in error rates on some color tests (pseudoisochromatic plates, and Nagel anomaloscope color matching) (Jordan & Mollon, 1993).

In New World Monkeys, however, the situation is different. Squirrel monkeys are basically a dichromatic species, but two-thirds of the females are heterozygous, and gain trichromatic vision by expressing two of three possible alleles coding for pigments in the middle- to long-wave range of the spectrum. X-chromosome inactivation serves to segregate the alternative allelic products in different subsets of cones. The visual system of the heterozygous female is apparently plastic enough to take advantage of the presence of three classes of cone, because heterozygous monkeys have enhanced color selectivity in the red-green range that are impossible for all males and for homozygous females. This advantage perhaps enables the heterozygote to judge better the ripeness of fruit, or to find fruit or conspecifics (Jordan & Mollon, 1993).

Note that the emergence of trichromacy in humans and some other primates was the result of the red/green gene duplication. Trichromacy in primates was evolutionary selected for likely because of the enhanced capability to discern (ripe) fruits (Lucas et al., 2003). It has nothing to do with sex-differences, because not many human females benefit from tetrachromacy in terms of enhanced color vision.

References
- Deeb, Clin Genet (2005); 67: 369–377
- Jordan & Mollon, Vis Res (1993); 33(11): 1495-1508
- Lucas et al., Evolution (2003); 57(11): 2636–43
- Neitz et al., Science (1991); 252(5008): 971-4

Further reading
- Is our color vision calibrated to sky, vegetation, and blood?


How RNA primer on leading strand is removed during DNA replication and how the gap is filled? Please can you explain me how the gap created by the removal of primer on 5'-3' leading strand is filled.

The group of cellular enzymes that remove RNA primers include the proteins FEN1 (flap endonuclease 1) and RNase H. The enzymes FEN1 and RNase H remove RNA primers at the start of each leading strand and at the start of each Okazaki fragment, leaving gaps of unreplicated template DNA. Once the primers are removed, a free-floating DNA polymerase lands at the 3' end of the preceding DNA fragment and extends the DNA over the gap. However, this creates new nicks (unconnected sugar-phosphate backbone).
In the final stage of DNA replication, the enyzme ligase joins the sugar-phosphate backbones at each nick site. After ligase has connected all nicks, the new strand is one long continuous DNA strand, and the daughter DNA molecule is complete.

Source: Boundless. “DNA Replication in Eukaryotes.” Boundless Biology. Boundless, 08 Jan. 2016. Retrieved 14 Mar. 2016 from https://www.boundless.com/biology/textbooks/boundless-biology-textbook/dna-structure-and-function-14/dna-replication-101/dna-replication-in-eukaryotes-437-12941/


Molecular animations of, say, protein synthesis, are simplified, but how exactly? In several animations of biological processes (eg protein synthesis (go to frame 1.20mins), DNA replication, etc), molecules such as amino acids are shown heading straight to the replicating protein as if drawn by a magnet. As far as I know they move randomly. But still, translation occurs at a rate of about 15 amino acids/second and 75 ATP/second, so the rate of gobbling shown in the video clip is not off the mark.

I can think of two explanations:

1) The microscopic world is counter-intuitive. It is so frenetic that normal diffusion is enough to supply the hungry protein. The video simply doesn't show all the input molecules in order not to clutter the picture but essentially it is correct. However, amino acids are not small, and they are attached to the much larger tRNA, so they must be moving relatively slowly by Brownian motion.

2) There are additional helper proteins that concentrate or channel amino acids and ATPs in the vicinity of the ribosome or replicator. Never heard of these.

What is the real explanation?

Edit: To clarify, the question is not about the simulation side of things as such, such as how hard it is to actually make a true simulation. Most simulations, including weather prediction, involve a certain degree of approximations and simplifications. But in this case, there is something definitely untrue in the video clip, namely the molecules being attracted to the ribosome. As explained by a moderator, this means that it is not a true simulation but a "cartoon". So the question is: what would an ideal "non-cartoon" true simulation look like? Would the tRNA be diffusing in at a very fast rate, or are there helper proteins that, for example, tether tRNA in the vicinity of the ribosome? The moderators seem to indicate that diffusion is enough, but I would like to see a reasoned out answer with numbers that show this is the case.

tldr:

Making these things accurate representations is really hard
Accurate representations can be hard to look at anyway, so aren't always good to convey understanding

Molecular dynamics simulations that span long periods can be really expensive because of how computationally demanding they are, and they rely on accurate structural information about all of the molecules involved which isn't always available. The animation you linked might not be an actual simulation for that reason, but you'd have to check for yourself. Really fine grained accuracy probably isn't a priority for making a cool teaching tool like this one, you just want people to understand the just of it and the Brownian motion there might be a stylistic choice. Again, you'd have to chase it up for this specific example, I just want to give you something generalizable to other animations.

To make macromolecules like this actually interpretable by humans it's important to simplify them. One of these simplifications is normally called a 'cartoon', I don't think they guy in your comments was taking a dig at credibility of the video. It's also important to hide all the water molecules because they get in the way of you and seeing what's going on, so that's another way in which it's been simplified.

If you haven't already, have a look at some proteins in the PDB on the structure viewers and switch the mode from the cartoon/ribbons to other models like ball and stick. Ribbons are a useful way to simplify the structure representation so that you can see what the backbone is doing.

Here's one that I like:
https://www.rcsb.org/3d-view/4KEY/1

And you're right, at the systems level of something like protein synthesis, lots of stuff is involved and it's not practical to show all of it. For something like that it's easier to show these processes a a graph (term for connected nodes), check out the KEGG database for examples:

https://www.genome.jp/kegg/pathway.html#cellular

Hope this helps


Why are transcripts translated from 5' to 3' direction? What is the mechanism?
In other words, how does the tRNA know whether the codon is in 5' to 3' direction? I also heard that anything that is translated from 3' to 5' direction is degraded. Is it true?

The tRNA is not acting alone, it has the help of the Ribosome.

The Ribosome assembles at the beginning of the transcript and starts the translation at the first AUG codon. It then binds the first tRNA which fits to the mRNA. The tRNA is then moved from the A-position to the P-position and the next tRNA is binding (the move around and bind by chance. A nice animation is found in the Wikipedia article on translation (which is also the source for the image above).

Translation can't go into the other direction, it is always in 5' -> 3'.

To recognize the right direction (and the right starting point) the Ribisome is not simply starting at the 5`end of the mRNA. Before the start codon AUG the mRNA contains a regulatory, untranslated region, the so-called 5'UTR. The end of the 5'UTR of eukaryotes contains the so called methylguanosine cap (and is only present in mature mRNA), in proaryotes this is done by the Shine-Delgano sequence. Both are recognized by the ribosome. After binding to the mRNA, the ribosome slides along the nucleotide chain until it reaches the first AUG to initiate translation. The image is from this description (which contains a lot more details, if you are interested in it).


Why are veins not blocked by plaques? In my textbook, it is written that atheromatous plaques block the artery. This leads to heart attack and and heart failure. But my question is why do the plaques only block arteries and not the veins? Do the plaques also block the veins?

Atherosclerosis can develop in high pressure systems, such as arteries, and not in low pressure systems, such as veins. It is high blood pressure that can damage the lining of the blood vessel and initiate the process of atherosclerosis.

BUT, atherosclerosis can develop in veins that have been used as grafts instead of arteries, for example, in a coronary artery bypass surgery.

Springer: Atherosclerosis:

  In this regard, we may note that atherosclerotic lesions do not
  develop in the veins in their normal environment of low pressure and
  high flow, but that the lesions do develop when the veins are used as
  arterial bypass grafts where they are subjected to high pressure.
  Similarly, atherosclerotic lesions develop in the pulmonary arteries
  only in pulmonary hypertension.