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If cells regularly renew, why do we have scars?
Question may sound bit poetic but I have a pretty basic question here: Often we get a minor wound and cells renew and quickly "cover" it. But when we have deeper wounds, often they leave behind scars. Why does it happen?
I was researching around and saw this comment on a related question:

That's not true - some cells turn over quite quickly, others take months or years, others never replicate.

But how come we get some wounds "completely filled", while others leave scars on almost the same skin/body part? And ok, if a deeper cut has resulted in inner (different type of cells) being damaged, why do we find the scar on epidermis?
Thanks a lot for your guidance.

Scar is mostly collagen( a fibre, not cell)

I think you will get all your answers here. I can add this as an answer if others in the community don't tend to close it as off-topic...

Scar tissue formation is part of the normal healing process in which fibrous material braces and pulls the wound together, in other organisms (and young mammals) this process is mild and just serves to temporarily reinforce the damaged tissue as new cells migrate in to begin replacing the missing tissue, sometimes to the point of replacing missing limbs in lizards and amphibians. However in adult mammals and birds the process of fibrous tissue is far more exaggerated, creating longer lasting or even permanent scars, Here the wound keeps filling in with more and more fibrous tissue instead of moving on to regenerating what was there originally. This dense fibrous tissue often prevents new cells from easily migrate into the tissue, essentially stalling the healing process. It seals the wound much faster than the more mild deposition of other animals but can often prevents replacement of the fibrous tissue which would otherwise happen as the missing tissues is regenerated. This mass of fibrous tissue is what we call a Hypertrophic scar. this is why scars can also fade, as cells often can migrate in and slowly replace the the matrix but this is severely limited by the dense packing.
Note there is a second rarer form of scar tissue that can form, called keloid scarring. This form of scar spreads beyond the original wound area and seems to be caused by some form of runaway extracellular matrix deposition. It should also be noted adult mammals sometimes do regenerate decent portions of tissue, albeit not well, possibly because some of the controlling cellular signalling machinery has be lost or reappropriated. All the factors that affect this are not understood and are a main focus researched. We do know it varies quite a bit from tissue to tissue and is not terribly consistent.
It is believed that mammals and birds develop this stronger matrix deposition which leads to permanent scar tissue becasue healing fast is more important for them than healing completely since their metabolism runs so much higher. They can't wait around for it to heal they need to get moving as soon as possible or risk starvation,additionally a stable body temp makes for a more inviting environment for bacteria so sealing the wound is paramount. Thus sealing and mechanically reinforcing the wound is more important than regeneration. As you can imagine the worse the injury the more important it is to plug it fast which is why minor injuries are less likely to scar. This is also why lizards and amphibians end up with less permanent scars they can take the time to better regenerate the tissue. Of course this is difficult hypothesis to test, however there has been some success in getting mammalian tissue to regenerate more by removing scar tissue as it forms or just preventing collagen production.
Evolution is one lang story of "good enough" and scar tissue is good enough functionally that the speed at which it can seal a wound favors it over slower regeneration.

@another'Homosapien' It isn't the same meaning as in chemistry. Endotherms are warm-blooded animals. But I don't see any reason to connect endo versus ectothermy to scar tissue formation...

This is a teleological proposal of (perhaps) why scar tissue forms, not an actual answer. Scar tissue formation is not a fast process.

@anongoodnurse it is compared to regeneration. Scarring is just the inflammatory and fibrous tissue formation of the healing process run rampant, it interrupts further complete regenerative healing other organisms experience.

Then write that as your answer, not a teleological proposal. I don't think it's quite "run rampant". Aggressive cancers are "run rampant". Healing is physiological.

@anongoodnurse I did write it up as well as why it evolved in the first place.  The OP asked "why?" which is ultimately a question of what would cause such a seemingly counterproductive mechanism to evolve in the first place.


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Definition of "Niche Complementarity"
What does "Niche Complementarity" mean?

On this website they define "Niche Complementarity" as:

The tendency for coexisting species which occupy a similar position along one niche dimension

I don't quite understand this definition. The tendency to do what?

Notes:

I know what is an ecological niche and therefore what is a niche dimension. There is no need to define this.
I am particularly interested in the use of this concept in speciation and adaptive radiation.

There's more to the definition, it's less clear because of the inserted e.g.'s. The definition is: "The tendency for coexisting species which occupy a similar position along one niche dimension to differ along another;" I took out the examples of altitude and diet.

@A.Kennard I still donn't get how you manage to read the whole definition but anyway, the important thing is that I now understand the concept of "niche complementarity"! Thank you. You can make an answer out of your comment if you wish.

As it has been said by @A.kennard in the comments, the definition the OP found is not complete. The full definition on the link he gave (here) is:
Niche Complementarity:

The tendency for coexisting species which occupy a similar position along one niche dimension to differ along another.

The concept that two competing species will tend to evolve different evological niche is called character displacement. The definition from wikipedia is

Character displacement is the phenomenon where differences among similar species whose distributions overlap geographically are accentuated in regions where the species co-occur, but are minimized or lost where the species’ distributions do not overlap.

There is a really good discussion of this in Chesson & Kuang Nature 2008, they propose a way to measure niche complementarity accounting for competition and predation.

Niche complementarity: If the competitor species overlap for one resource dimension then they will differ for another resource dimension. E.g; All the plant species pollinated by humming birds flower at different time of the year.

Welcome to Biology.SE! Please add some references to your answer.

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Will tagging a protease with HlyA for secretion inactivate the protease?
We are looking to secrete the protease proline iminopeptidase by attaching the secretion signal HlyA to the protease in a gene circuit. Since the natural HlyA secretion sequence in Escherichia coli isn't cleaved from the protein, it will remain attached to the protease in the extracellular matrix.
Will the protease still function and cleave the peptide chain at the n-terminal proline residue with the HlyA signal still attached?

Unless someone has actually done this specific fusion and reported on the activity, this question won't have an answer. I can't find anything about proline aminopeptidase fusions, but enzyme-HlyA fusions have been done that retained activity similar to the wild-type protein (examples: cutinase, β-lactamase). Your fusion might work fine or folding might be disrupted after secretion (either by the tag itself or by the absence of chaperones, if required). In other words, you need to try it yourself.
Bacillus subtilis is commonly used for secretory protein production and may present another/better option.

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Following DNA replication during S-phase of the cell-cycle, are all genomic regions subjected to the same stringent level of DNA-Repair?
To my (limited) understanding, there are 2 main ways that mutations can occur in DNA: Environmental (UV, etc) and mistakes during cell division.
I was wondering if there is a mechanism that can give priority to certain genes to be accurately duplicated. Some sort of trigger that says "double-check this specific gene before continuing with the duplication".
And if there is such a mechanism, then I wonder if there is some sort of dependency system for genes that control groups of other genes. So that if a certain gene "activates" the double-check trigger, it would automatically add that trigger to the group of genes which are affected by it.
Thanks.

All DNA is proofread during replication. It is also constantly monitored for damage.

are all regions have same mutation rate? bonus points: independent of sequence (only location). E.i., are there markers of super-stable sequences

Can you add some details. Your exact question remains unclear to me. Gene duplication is not essentially a regulated process.

No such mechanisms as far as I know. Some DNA regions are harder to repair, notably repeated sequences but I am not aware of any mechanism giving a specific higher priority for repair to any genes. Also I think you want to use the term "replicated" and not "duplicated". @aandreev while interesting, mutation rates seem irrelevant for this question.

So far, the known mechanism of DNA repair is to recognize mismatches or damaged nucleotides by enzymes surrounding DNA rather than by scanning along DNA. Therefore double check could not happen under such conditions.

I was wondering if there is a mechanism that can give priority to
  certain genes to be accurately duplicated. Some sort of trigger that
  says "double-check this specific gene before continuing with the
  duplication".

A mechanism that would say: "double check this part, it's important" isn't known to me neither, but if I understood your question correctly I think the answer to your question lies somewhere else.
Let's start with the mutation rate you mentioned, some sequences are harder to replicate by DNA polymerase (it makes more mistakes there, such as in highly repetitive sequences, methylated cytosines etc.), so the mutation rate is higher in these segments (they are called mutation hot spots), but otherwise the DNA polymerase makes errors randomly, throughout the whole genome. These are in better case repaired. No special care given, repair polymerase tries to repair everything.
Now, to my point. What if the repair fails? In genes, that are critical to cell survival, development of organisms etc. (for it's life) you really see less mutations (if any) present. (and I believe this was the reason for the question, correct me if I am wrong.)
Moreover, these places in genome can be highly conserved between different organisms. More here. What this says is that nature doesn't allow cells/evolution/whoever to experiment (or make errors) on these positions. If mutation occurs here and isn't repaired, the cell simply dies and therefore you cannot see the mutation. The reason for death may be accumulation of toxic protein, which cell is not able to get rid of with disrupted enzyme, or lack of energy, because it cannot oxidize fuel... there are plenty possible lethal outcomes. For some genes, the cell can substitute their product by another protein, but some are essential.
(In multicellular organism can substitute for it, unicellular won't care because it's dead already)
I believe this is the mechanism, by which cell can distinguish between important and "less important" genes you were asking for.

DNA mutations arise from either replication errors or the effect of mutagens. Cell division can go into what is known as the G0 phase where division is put on hold. This state is also referred to as a quiescent state (see the related genes here), which is distinct from senescent states where damaged cells are prevented from replicating by, for example, the p53 gene family. The proteins of these last mentioned genes are up-regulated to suppress uncontrolled division in cancerous cells, while genes controlling the G0 phase act under normal physiological conditions, unless these related genes are deficient themselves. Carcinogens are a subset of mutagens that typically affect genes involved in the cell cycle.


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Are all dipeptides synthesizable?
Probably a basic question, but are all possible dipeptides synthesizable?
For 20 amino acids, there should be in principle 190 dipeptides; do they
all exist or is there chemistry that makes some combinations unstable?
A straight forward generalization would be to ask what percentage of
peptides (or proteins) are synthesizable (in the lab or in cells).

Yes, all dipeptides can be synthesized - it's simply connecting the carboxyl group of the first amino acid to the primary amine of the second amino acid. No big deal. The second part of your question does not make sense - what do you mean? Given a supply of amino acids, a cell can synthesize any protein in its genome. There are limitations of polypeptide synthesis in the lab which increase as the peptide chain grows. There is a large body of literature on this.

I'm pretty sure any peptide can be synthesized in a lab. Length is probably limited by yield, but I imagine that can be overcome by, say, ligating or elongating previously synthesized peptides.

@MattDMo, I'm asking the question without necessarily  referening to genomes or what happens in the cell. As an abstract alphabet of 20 letters you can create a huge number of combinations of words of length N; translating the letters to amino acids and the words to peptides, how many of these words are synthesizable? It seems your answer for N=2 is 100%. For larger N I can't imagine this to be true,  or maybe I'm wrong.

@secretlyfamous You mention cells in your question, which is why I brought them up. In cells, N can be quite large, well over 34,000 in the case of the muscle protein titin. As I mentioned in my previous comment, there is a large body of literature on the capabilities and limitations of chemical polypeptide synthesis, with yield inversely proportional to length. A quick Google search yielded this page, which describes the synthesis of 169 AA by the ligation of several shorter precursors.

@canadianer I highly doubt titin could be synthesized in the lab, though with a good deal of work a lot of (much) smaller proteins probably could. N is not infinite, though. I know antibodies can't be chemically synthesized (two 50 kDa chains and two 25 kDa ones for IgG). Plus, post-translational modifications like disulfide bonds could present a lot of problems.

@secretlyfamous If your interests are entirely in the realm of chemical peptide synthesis, you may find a lot more experience at [chemistry.se] than here. While biochemistry is on-topic here, this question seems to have a lot more chemistry than bio.

@MattDMo, thanks for the clarification. My interest is mainly in the statistics. The actual mechanism is far too complex for me to pursue. I wasn't sure about which tags to use; plus it looks like some of my tags were editted out.

@MattDMo I really don't know anything about it, though I did say peptide and not protein. Is it impossible to synthesize antibodies or just not practical?

Yes. There is nothing magical or mysterious about a peptide bond.

@canadianer Yields drop off very quickly above 20 - 30 amino acids, with bad products making up more of the mix. Disulfides are a pain, but there are ways to control them using protecting groups. The nice thing about peptide synthesis is being able to use a huge variety of amino acids, which has allowed some neat stuff.

I see no reason why not. Just to make sure, I decided to test. I ran a search on all human proteins (using the UniProt flat file) for all possible dipeptide combinations of the 20 standard amino acids (selenocysteine is also present in humans but only in 22--or so, depending on how you count them--proteins, so I wouldn't expect all possible sec-containing dipeptides to be present) .
As expected, each of the 400 possible dipeptides were indeed present in at least one human protein. In case anyone wants to repeat this, the "protocol" is as follows:

Download the human flat file from Expassy.
Extract the peptide sequences
perl -ne 'if(s/^\s+//){s/\s+//g;print}' human.flat > human.pep

Generate the list of possible dipeptides:
AA
AC
AD
AE
AF
AG
AH
AI
AK
AL
AM
AN
AP
AQ
AR
AS
AT
AV
AW
AY
CA
CC
CD
CE
CF
CG
CH
CI
CK
CL
CM
CN
CP
CQ
CR
CS
CT
CV
CW
CY
DA
DC
DD
DE
DF
DG
DH
DI
DK
DL
DM
DN
DP
DQ
DR
DS
DT
DV
DW
DY
EA
EC
ED
EE
EF
EG
EH
EI
EK
EL
EM
EN
EP
EQ
ER
ES
ET
EV
EW
EY
FA
FC
FD
FE
FF
FG
FH
FI
FK
FL
FM
FN
FP
FQ
FR
FS
FT
FV
FW
FY
GA
GC
GD
GE
GF
GG
GH
GI
GK
GL
GM
GN
GP
GQ
GR
GS
GT
GV
GW
GY
HA
HC
HD
HE
HF
HG
HH
HI
HK
HL
HM
HN
HP
HQ
HR
HS
HT
HV
HW
HY
IA
IC
ID
IE
IF
IG
IH
II
IK
IL
IM
IN
IP
IQ
IR
IS
IT
IV
IW
IY
KA
KC
KD
KE
KF
KG
KH
KI
KK
KL
KM
KN
KP
KQ
KR
KS
KT
KV
KW
KY
LA
LC
LD
LE
LF
LG
LH
LI
LK
LL
LM
LN
LP
LQ
LR
LS
LT
LV
LW
LY
MA
MC
MD
ME
MF
MG
MH
MI
MK
ML
MM
MN
MP
MQ
MR
MS
MT
MV
MW
MY
NA
NC
ND
NE
NF
NG
NH
NI
NK
NL
NM
NN
NP
NQ
NR
NS
NT
NV
NW
NY
PA
PC
PD
PE
PF
PG
PH
PI
PK
PL
PM
PN
PP
PQ
PR
PS
PT
PV
PW
PY
QA
QC
QD
QE
QF
QG
QH
QI
QK
QL
QM
QN
QP
QQ
QR
QS
QT
QV
QW
QY
RA
RC
RD
RE
RF
RG
RH
RI
RK
RL
RM
RN
RP
RQ
RR
RS
RT
RV
RW
RY
SA
SC
SD
SE
SF
SG
SH
SI
SK
SL
SM
SN
SP
SQ
SR
SS
ST
SV
SW
SY
TA
TC
TD
TE
TF
TG
TH
TI
TK
TL
TM
TN
TP
TQ
TR
TS
TT
TV
TW
TY
VA
VC
VD
VE
VF
VG
VH
VI
VK
VL
VM
VN
VP
VQ
VR
VS
VT
VV
VW
VY
WA
WC
WD
WE
WF
WG
WH
WI
WK
WL
WM
WN
WP
WQ
WR
WS
WT
WV
WW
WY
YA
YC
YD
YE
YF
YG
YH
YI
YK
YL
YM
YN
YP
YQ
YR
YS
YT
YV
YW
YY

Save that list as dip.txt.
Use that file to search the protein sequences:
perl -ne 'BEGIN{open(A,"human.pep"); while(<A>){chomp; $k.=$_}}; chomp; print "$_\n" if $k=~/$_/  ' dip.txt

The script above will print each dipeptide that was found in at least one protein. Since all were printed, all dipeptides exist in the human proteome.

thanks for the detailed answer. Your answer looks at things from a slightly
different angle (dipeptide occurrence in proteins) which is actually a more interesting
angle. I asked a simplified question about dipeptide occurrence on their own first;
the answer to that seems to be yes. I am also in fact interested in the case for larger
N and the statistics of their occurrence in proteins. I'll take a shot at modifying your
script to do some more searches. BTW, you caught a mistake in the number of possible
combinations of dipeptides, it is in fact 400 and not 190 as I put in the question.

Yeah, a negative result wouldn't have been conclusive but a positive one is. My assumption was that if a dipeptide occurs in a protein, it can be synthesized. You seem to be suggesting that the dipeptide alone might not be stable and could need the rest of the peptide in order to be so. That's quite interesting and may well be the case but my structural chemistry knowledge is pitiful so I won't venture an opinion on it. As for larger Ns, my script won't help you much. It's a very simplistic approach.


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How does the emerson effect produce a higher rate of photosynthesis?
Can anyone explain how the emerson effect works to increase the rate of photosynthesis, and as the original studies were done over 50 years ago, how much research is still done into this area? Or is it well understood now as to not need further work?
I am obviously not a biologist but from what I have been reading, photosystem 2 absorbs light at 680nm due to the primary electron donor p680 and photosystem 1 at 700nm due to p700. The rate of photosynthesis when exposed to light at these 2 wavelengths simultaneously is greater than the sum of the rate of photosynthesis if exposed to these wavelengths separately. Sorry for any mistakes, I am just starting to try to learn about it. I'm interested to find out how this higher rate of photosynthesis occurs when using light in the red and far red end of the spectrum at the same time.

You are expected to show some attempt to answer this on your own, even a brief description of what you know about the emerson effect would be beneficial. You may also want to look up photosystem 1 and photosystem 2.

I have added some more info into the question to show what I think I know so far.

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Is coral photosynthesis dependant on the wavelength or frequency of light?
When buying a light fixture for a marine fish tank, it is often sold with some technical data reguarding the spectral output of the light, with a peak in the blue region of visible light, somewhere around 430 to 460nm in air.
As light enters the water with a refractive index of approximately 1.33, the peak wavelength will reduce, but the frequency of light will remain constant. So, for example, a monochromatic light with wavelength 460nm in air would have a wavelength in water of about 345nm, but the frequency is the same. Physics so far, so here comes the biology question....chlorophyll a and b have peak responses between 400-500nm light, so is it the wavelength of light in water that is important to photosynthesis, or is it actually the frequency(therefore the photon energy) that is what counts?
If we were to discover a purely theoretical new plant that grew equally well in air or water, and discovered that photosynthesis only occurred at 650nm wavelength light in air, and not at all to any other wavelength. Then we place this plant in water indoors in the dark and shine a monochromatic 650nm light source at if from air, into the water,  would photosynthesis still take place because the photon energy is the same in water or air (e = hf). Or would we need to shine a monochromatic light source of approx 865nm in air, which would reduce to 650nm in water (865/1.33)? I suspect the answer is that photsynthesis is dependent on the photon energy not wavelength, but I am far from sure about this!

Its is my hunch that it is the photon energy/frequency that counts not wavelength in much the same way our eyesight works with colours, but i would like to see it confirmed either way. I often wonder if artificial lighting for plant growth should be aimed more towards replicating natural sunlight (there is a Japanese company doing just this), especially regarding corals from shallow waters or propagated frags from tanks where some red light still makes it through the first few metres of water. Still I am interested to know what drives photosynthesis specifically underwater.

Short answer: Coral doesn't need the light, it's the zooxanthellae that is symbiotic with some corals that relies on light to grow; it adapts to the frequency spectrum available at the depth the particular coral grows, full spectrum at shallow depths and at over ~30m the zooxanthellae relies on blue light because other frequencies are absorbed by water.
Some species of coral, such as Lophelia pertusa, grow in water so deep that there is too little light for them to rely on zooxanthellae, instead their polyps gather food directly with their tentacles, feeding heterotrophically.
There are even instances of coral feeding on jellyfish, see: "Opportunistic feeding by the fungiid coral Fungia scruposa on the moon jellyfish Aurelia aurita" (May 21 2009), by A. Alamaru, O. Bronstein, G. Dishon and Y. Loya
Longer answer:
The physics portion of your question is best answered on our Physics.SE site's question: "Why doesn't the frequency of light change during refraction?"
Light's wavelength and frequency are related to each other based on a mathematical formula, it's the intensity that is affected by passing through a medium; different materials will attenuate some frequencies more than others. Water doesn't transpose light's frequency or wavelength as much as it absorbs (filters) the frequencies of light affecting which color can penetrate deeper.

"What is a light wave?
Light is a disturbance of electric and magnetic fields that travels in the form of a wave. Imagine throwing a pebble into a still pond and watching the circular ripples moving outward. Like those ripples, each light wave has a series of high points known as crests, where the electric field is highest, and a series of low points known as troughs, where the electric field is lowest. The wavelength is the distance between two wave crests, which is the same as the distance between two troughs. The number of wave crests that pass through a given point in one second is called the frequency, measured in units of cycles per second called Hertz. The speed of the light wave equals the frequency times the wavelength.".

See this other Physics.SE question: "Does light color change when refracting?":

"The color will not change. What you're not taking into account is the speed of light in the medium. It's not the same $c$ en vacuo. The frequency stays the same. What changes is that speed of light in the refracting medium and as a result wavelength.".

Here is what sunlight (natural light) looks like underwater:

Despite that fact in shallow water enough full spectrum light penetrates sufficiently, and the zooxanthellae adapts to the spectrum available, no longer requiring blue light for growth.
See: "The spectral quality of light is a key driver of photosynthesis and photoadaptation in Stylophora pistillata colonies from different depths in the Red Sea" by T. Mass, D. I. Kline, M. Roopin, C. J. Veal, S. Cohen, D. Iluz, O. Levy in the Journal of Experimental Biology 2010 213: 4084-4091; doi: 10.1242/jeb.039891

"Depth zonation on coral reefs is largely driven by the amount of downwelling, photosynthetically active radiation (PAR) that is absorbed by the symbiotic algae (zooxanthellae) of corals. The minimum light requirements of zooxanthellae are related to both the total intensity of downwelling PAR and the spectral quality of the light. Here we used Stylophora pistillata colonies collected from shallow (3 m) and deep (40 m) water; colonies were placed in a respirometer under both ambient PAR irradiance and a filter that only transmits blue light. We found that the colonies exhibited a clear difference in their photosynthetic rates when illuminated under PAR and filtered blue light, with higher photosynthetic performance when deep colonies were exposed to blue light compared with full-spectrum PAR for the same light intensity and duration. By contrast, colonies from shallow water showed the opposite trend, with higher photosynthetic performances under full-spectrum PAR than under filtered blue light. These findings are supported by the absorption spectra of corals, with deeper colonies absorbing higher energy wavelengths than the shallow colonies, with different spectral signatures.".

"Fig. 4. Percent surface irradiance received of different wavelengths at 3 m (grey) and 40 m (black) depth in the waters adjacent to the Interuniversity Institute for Marine Sciences, Eilat, Israel, on 3 April 2008.".

So if you deep dive for your own coral you should be aware that it will thrive under blue light. If you obtain shallow water coral, or buy from the local aquarium supply store, white light is suitable.
Also from: "The spectral quality of light is a key driver of photosynthesis and photoadaptation in Stylophora pistillata colonies from different depths in the Red Sea", (full info above):

"Studies in the Caribbean have found that other corals that are found along a broad depth gradient switch from hosting clade A or B zooxanthellae in shallow water to clade C in deeper water, possibly owing to the ability of the different clades to adapt to different light levels (Rowan and Knowlton, 1995; Baker et al., 1997).".

Hi Rob. Thanks for the detailed answer. I'm not sure it answers my actual question though. I have a physics degree, I understand electromagnetic radiation, so my question was not about physics. I understand that light will be scattered, reflected, absorbed in different ways in water. I also understand that it is the zooxanthellae that photosynthesize. I am not a biologist though, so,  very specifically my question is this - is photosynthesis dependant on wavelength or frequency, baring in mind the wavelength changes in water, and the frequency doesn't (and therefore photon energy)?

@Justanengineer Is this answer more helpful, that is the frequency or wavelength in a vacuum, depending if you want to measure in THz or nm. Moving from space to air, glass or water affects the wavelength because the medium is changed, it affects the diffraction and filters which frequencies can pass more freely than others but it doesn't alter the frequency, the color, of the light by transposition. Changing the speed of light by passing through water only affects the wavelength.

Hi Rob, all the information you have provided is great, although I feel i already have a good grasp on the physics of this question. Its the biology i need to learn about! I understand refractive index, downwelling irradiance from the sun, the filtering of different wavelengths of light dependent on water depth. Its the biology of photosynthesis i do not understand. It seems to me that it would be more helpful to measure solar irradiance in THz or electron volts, as this does not change in different media. I need to rephrase my question I think somehow....

Maybe a better way to phrase this question is: "Is it accurate to say that photosynthesis occurs under light irrandiance of frequency 430-770THz, regardless of the refractive index of the medium it takes place in, and therefore regardless of the measured wavelength in that medium"?

Am I on the right track here...1.82ev is needed to activate the chlorophyll complex p680, which drives photosystem 2 at the start of the light dependent reactions and is needed to oxidize h20. So when we think of light for photosynthesis, we should think in terms of electron volts required for redox reactions? Can anyone point out my beginner mistakes or point me towards some further reading?

Ok I apologise for upsetting you but it IS still the same question it always was. Is coral photosynthesis dependent on the wavelength or frequency of light? That is all. That is the title question and the only question I am asking and it hasn't actually been answered. The scope has not expanded in any way the question still stands. All the rest is background because I was finding it hard to clearly ask the right question, so I tried to give it context. Its my first post here, so in future I will just ask a very straight question and see what comes back.

If you deep dive for your own coral it will want bluer light, as will some non-aclimatized coral (which a reputable aquarium supply store won't sell a beginner. --- I do appreciate that it is difficult to 'ask the right question' or figure out what it is you want to ask. I have to assume that you've done some initial research and that upon reading your question that either I can answer it or I can not. --- You don't want to worry about electron volts, just don't buy to big a light for your tank. You don't want your coral and plants to grow like crazy unless you are trying to sell them.

Hi Rob. Thanks for all your input it's really useful. The fault is mine, in that I did not know enough biology to ask the right question. I know a little more now and realise the question I needed to ask should have been very specifically about energy needed for photosynthesis to occur. I am going to put it that you have answered this question because you have given so much relevant information to a question that wasn't worded clearly enough to answer.

@Justanengineer I'll clean out my superfluous comments. If you have enough information for a different question ask and see if someone can help you here or elsewhere.

For the non-biologists,
@Rob isn't wrong about the existence of heterotrophic coral—they exist alright. But the absolute vast majority of productivity (creation of biomass), ecosystem function (e.g., facilitation of diversity, nutrient cycling, energy flow, trophic complexity), and density of corals are features of symbiotic corals. The mentioning of heterotrophic corals here doesn't seem to be relevant to the question.

@ChrisMoore There used to be another half dozen back and forths that you are missing. Currently, I'm working on something else. If you can offer a better answer we all welcome that.

@Rob I imagine more context would help. I nevertheless think it's a really good post, I would just cut the "shorter answer" section. (It's more of a digression than a short answer.) Everything after that is apt and relevant. I'll edit it.

Yes, coral photosynthesis and growth (actually, Symbiodinium symbiont photosynthesis) is dependent upon the spectra of light provided.
Each photosynthetic organism has a characteristic 'action spectrum' which is the photosynthetic rate (Y axis) plotted vs. the wavelength of light (X axis).
Or, we could plot an action spectrum for growth, which is a step removed from photosynthesis.
Either way the action spectrum is a product of:
-absorbance of light at a given wavelength
-yield of conversion of absorbed light to achieved photosynthesis (or growth), at a given wavelength.
-second order effects related to the complex propagation and scattering of light through tissue or coral matrix
For any oxygenic photosynthesis the action spectrum is going to include absorbance by chlorophyll a (peaks at ~440 nm and at ~680 nm), but will be modified by other secondary pigments.
http://jeb.biologists.org/content/206/22/4041
Fig. 6, rough action spectra.
Some methodologies.
https://www.advancedaquarist.com/2014/5/aafeature
The situation is complicated because:
-some wavelengths (short blue, ~420 nm) can drive photosynthesis but also drive photoinactivation of photosynthesis more so than longer wavelengths. This can lead to cumulative light stress, depending upon the absolute level of light, the duration of illumination and the wavelength.
-corals 'use' light for many things other than photosynthesis and these regulatory and signalling functions can be disrupted if the spectrum or duration of light is not appropriate.
-different corals will have different requirements.
Long answer, tough question, still a research topic.

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


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Species specific White Blood Cells (WBC) composition
In our ongoing immunology undergrad course I learnt that neutrophil primarily fights off bacterial infection and lymphocyte is produced in response to viral infection. I also learnt that neutrophil count in humans is about 70 % in human WBCs while in horse lymphocytes account for 68% of WBC. It is supposed to make humans more immune to bacterial infection and similarly horses better adapted to fight off viral infections. However I cannot find out any relevant material as to what could be the reason that such biased WBC cell component composition has evolved in different species. Please help me find out relevant material on this.

World Boxing Council? Please do not use abbreviations in titles and define them the first time you use them.

Sorry about that.


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Unusual terminology of vector used
What is the significance of a+ in the name pET-28 a(+)? Is there any a- strain and differences between a,a+,a-?

This is not a bacterial strain. pET is a plasmid system generally used for protein overexpression. If your stocks are labelled like this then you should ask the person who created them.

There are 3 versions (a,b, and c) of this plasmid with different multiple cloning sites.
You can safely ignore the "(+)" part unless you are packing your plasmids into viruses.
You can learn about the details and see sequences from the resources available on the Millipore website.  I found this by searching for "pET-28 a(+)" ...


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Genetic Drift: Models, assumptions and empirical observations
There two main mathematical models to describe the process of genetic drift are Moran model and Wright-Fisher model.
My questions concern the assumptions of these models, the existence of other models of genetic drift, explanation of the advantage/disadvantage of these models and the empirical results supporting one or another model.

What are the assumptions of each of these models?

stable population size?
iteroparous/semelparous
what about the probability density function of the fitness?
…?

What advantage/disadvantage do these models have? Or I should say, to which population do these various model applies?
What kind of biological population has been empirically shown to fit better one model rather than another one? What are the key experiments to test the validity of these models?

Please do not hesitate to post even if you answer only partially to the questions! Thank you!

This question has been around for a while, so I'll try to start with a partial answer.
The basic assumptions of the standard Wright-Fisher-Model are:

Constant population size $N$.
Discrete, non-overlapping generations.
Neutrality (e.g. all individuals are equally likely to reproduce)

I prefer looking at the model for haploid/chromosomes. If you bundle up chromosomes to polyploids, then you get the additional assumption of random mating, e.g. all pairs of individuals are equally likely to reproduce.
I might have missed something, but these assumptions should be sufficient to generate the Wright-Fisher-Dynamics: When we build a new generation, we have to fill $N$ spots again (follows from the first two assumptions). As each old individual is equally likely to reproduce (third assumption), e.g. to become parent of a new individual, we get the multinomial offspring distribution.
The main difference in the Moran model is that it assumes overlapping generations. Main assumptions here are:

Again constant population size.
Individuals reproduce at a constant rate.
Neutrality (however the Moran model can relatively easily be adapted to incorporate positive selection).

Every time an individual reproduces, another one instantly dies to maintain the constant population size.
Interestingly, the models have the same diffusion limit, e.g. they behave similarly for large populations (and identically for an 'infinitely large population'). If you trace the ancestry of a sample back in a large population, you will get close to Kingman's Coalescent under both models.
I think the two models exist more because of their distinct mathematical properties, than because one fits better to certain natural populations than the other. I'm not aware of any experiments that have shown how well they fit, maybe someone else can jump in here.


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How does RNA polymerase II CTD bind to the RNA modification proteins if the tail is flexible?
The tail of RNA polymerase II is flexible, not folded into a fixed structure , but does each repeat have more "rigid" structure (i.e. fold into a structure that has less rotation freedom inside a repeat)? If not, then how can the proteins bind some repeat with high specificity? (you can't make lock and key with soft material)

Please clarify. First provide a source for your statement, even if it is a textbook. Is “flexible” really the right  word, or do you mean it has no fixed structure in a crystal of that protein alone. Second, what do you mean by secondary structure? The repeat is only seven amino acids — why would you think it would be alpha-helix or beta-sheet, and why do you think this is a requirement for protein–protein interaction. Your question seems to me to make a series of assumptions, the dubiety of which you don’t appear to realize.


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Speed of protein conformational change?
Although the speed may vary a lot based on factors like protein size/scale of conformational change/type of changes (small block change/arm movement,etc), are there examples of experimental results of time scale of such processes? (Only a single conformational change is considered i.e. the time delay between the begain and the end of a single conformational change event of a single protein (or subunit to be more precise?) )

This paper uses "ultrafast 2D-IR vibrational echo chemical-exchange spectroscopy" to track switching between different protein conformations and finds that they take place on the order of 50 pico-seconds ($ 1 \times 10^{-12} $ seconds). Another paper finds something similar but notes that full equilibriation can take on the order or nanoseconds:

Although the main conformational change of the backbone is completed after only 20 ps, the subsequent equilibration in the new region of conformational space continues for times >16 ns.


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Recombination due to crossover, outcome?
Garden peas normally have 7 pairs of chromosomes (n=7, 2n=14). Please calculate how many different types of gametes can be produced through the meiotic process if no crossover happens. If cross-over happens regularly, how many different types of gametes can be produced and why?
I have tried the question, I would suppose the answer to be 2 ^ 7 = 128 for the types of gametes that are produced( that is without crossing over).
However, I am not sure what is the solution what is the answer if cross over does happen. appreciate any solution to the problem.

The question asked for the number of gametes, not the recombination frequency (which cannot be 128 by the way, a frequency is by definition bounded between 0 and 1). For crossovers, the question is unclear as it depends on the crossover frequency and if recombination hotspots are present.


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How to define ammonites?
I miss the definition of ammonite. In my opinion, many authors confuse the term "Ammonite" and "Ammonoid". Ammonoids (Ammonoidea) are large group of cephalopods including for example goniatites (Goniatitida), ceratites (Ceratitida) and ammonites (Ammonitida?).
But what do we call "true ammonite"? Is it an ammonoid with ammonitic suture? This way, many triassic, jurassic, creataceous and possibly paleogenic (danian) ammonoids could be called true ammonites, because they have complex (ammonitic) sutures.
Can you show me where ammonites are on phylogenetic tree? Can we call phylloceratina, psiloceratina, lytoceratina, ammonitina, haploceratina, perisphinctina and ancyloceratina ammonites? Can we call phylloceratina, psiloceratina, lytoceratina ammonoids, but not ammonites?

Ammonites are not strictly defined. One can reffer to ammonites as to the whole group of ammonoids (Ammonoidea, ammonites sensu latto). This is common, but not supported by most researchers. Researchers use the term "ammonoid" for paleozoic ammonoidea and "ammonite" for Jurassic and Cretaceous Ammonoidea (ammonites sensu stricto). Ammonites sensu stricto reffer to ammonoids with complex (ammonitic) sutures, which are typical for Jurassic and Cretaceous ages. However, complex ammonitic sutures are not exclusive for Jurassic and Cretaceous ammonoids. Ceratitic sutures are not exclusive for Triassic either and occur in Jurassic ammonoids, too.

So caution must be exercised when using suture lines as a means of
  classification. To obviate some of the problems posed by this
  simplistic classification, Wedekind, in 1918, introduced the terms
  palaeo-, meso- and neoammo-noids to classify ammonoids better.

(PDF) Goniatites. Available from: https://www.researchgate.net/publication/262048294_Goniatites [accessed May 12 2019].


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Do mitochondria contain the genes to specify themselves?
My book says :
"Mitochondria contain their own genetic material so when a cell divides, the mitochondria replicate themselves under the control of the nucleus."
The book means that the mitochondria contain the genes which produce the mitochondria right  ?

The answer is a bit more complicated than that. Mitochondria contain their own genome called mitochondrial DNA (mtDNA), encoding 13 proteins that are part of respiratory complexes I, III, IV, and V, 22 transfer RNAs (tRNAs), and two ribosomal RNAs (rRNAs). The separate tRNAs and rRNAs are necessary because the mitochondrial genome uses a slightly different genetic code than the nuclear genome.
So, the mitochondria contain nearly all of the genes necessary to construct the respiratory chain, as well as the machinery to translate the mRNA into protein. However, it does not contain any of the genes necessary to actually replicate the mtDNA (DNA polymerases, etc.) or construct the mitochondrion itself - synthesize the components of the different membranes, arrange the membranes in their required conformation, chaperones to assemble the complexes of the respiratory chain, etc. - these are all encoded in the nuclear DNA.


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What does “energy transfer in cells” mean?
"ADP and ATP are involved in energy transfer in cells."
I know what is ATP and I know how ADP is formed, but I don’t understand what “energy transfer in cells” means.

Lets imagine the energy budget of a cell as the economy.
Using this analogy a glucose molecule is like a 5kg bar of silver. It is very valuable, but it is hardly convenient if you want to pay for chocolate milk or buy a cup of coffee. What you need is an exchange that will break that silver bar into smaller units of currency like a stack of $1 dollar bills. The smallest and most common currency of energy in a cell is ATP.
Most (but not all) chemical reaction in a cells that requires an input of energy uses ATP. This is why ATP is said to be used in energy transfer within the cell.
Glucose is a 5kg bar of silver.
The mitochondria and the TCA cycle is the exchange.
ATP is a $1 dollar note.

Cells require a constant supply of energy to generate and maintain the biological order that keeps them alive. This energy is derived from the chemical bond energy in food molecules, which thereby serve as fuel for cells.
Cellular nutrients (components in foods that an organism uses to survive and grow) come in many forms, including sugars and fats, so food molecules are rich sources of energy for cells because much of the energy used to form these molecules is literally stored within the chemical bonds that hold them together.
Cells release the energy stored in their food molecules through a series of oxidation reactions. Oxidation describes a type of chemical reaction in which electrons are transferred from one molecule to another, changing the composition and energy content of both the donor and acceptor molecules. Food molecules act as electron donors. During each oxidation reaction involved in food breakdown, the product of the reaction has a lower energy content than the donor molecule that preceded it in the pathway. At the same time, electron acceptor molecules capture some of the energy lost from the food molecule during each oxidation reaction and store it for later use. Eventually, when the carbon atoms from a complex organic food molecule are fully oxidized at the end of the reaction chain, they are released as waste in the form of carbon dioxide.
They (Cells) do not use the energy from oxidation reactions as soon as it is released. Instead, they convert it into small, energy-rich molecules such as ATP and nicotinamide adenine dinucleotide (NADH), which can be used throughout the cell to power metabolism and construct new cellular components.
Sources :

How Cells Obtain Energy from Food ?
Cell Energy and Cell Functions

For more informations :

What Are Nutrients ? - Definition & Examples
Cellular energy production


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Can a phosphodiester bond form between RNA and DNA?
In the initiation of DNA synthesis:

the RNA segments are first synthesized by primase and then elongated
  by DNA polymerase (Wikipedia).

What does 'elongated' mean in this context? Is it possible for RNA and DNA to form a phosphodiester bond to make a single strand which is part RNA and then part DNA?

A biochemistry book, such as Berg et al. online, is far better than Wikipedia. Your question is answered in section 27.4.1 — see Figure 27.26. Try other books on the NCBI Bookshelf searching for Okazaki fragments.

@David thank you very much David , I've read the section 27.4.1 and the figure 27.26 but a bit unsure about it. It mean that a RNA and DNA can forms a sugar backbone bond between them to make a single strand RNA-DNA ?. I used to think that the RNA cannot forming bond with DNA like that and I was wrong. Thank you again!

The problem is not forming a phosphodiester bond between ribose and deoxyribose (chemically the same) but that one would expect a DNA polymerase to discriminate against the 3'OH of the ribose. You are in good company being surprised that it happens — it was an unexpected discovery at the time. I suspect that some component of the DNA polymerization process confers this changed specificity, but it is not my field and I haven't time to check this. If anyone knows the details I suggest they formulate them into a more comprehensive answer.


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Are junk DNA's mb also counted when it is stated that human DNA contains 3mb?
The human DNA molecule (chromosome) is about 2 meters in length. See here. We have 46 of them so in total 92 meters (imagine we would place all our DNA in a row...)
In this article it is said that the Protopterus Aethiopicus (a.k.a The marbled lungfish) has the most base pairs (about 133mb vs about 3mb of the human genome) of all living beings (flora and fauna) residing in the DNA of its cells.
That's a huge difference! That's why I ask if junk mbs are accounted for too in the 3mb in human DNA.

Some notes and suggestions: 1) A diploid human genome is ~6.4 megabases in length — bases are not bits. 2) The relationship between DNA bases and genes is similar to that between letters and sentences — you will get a better response if your questions don't conflate these concepts. 3) Please don't refer to "junk DNA" — this is a misleading and inaccurate term. 4) You won't find a (reliable) source for your claim that human DNA contains the most "junk" because it isn't true! ——— I encourage you to make the time to understand the basics of genetics and molecular biology. ...

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

@tyersome Information is measured in bits (or bytes). Not in bases. Well, you can assign one bit to one base, but basically this is the same. Do you have a source that my claim is not true? I referred to junk DNA as non-coding DNA. Just read! Thank you very much.

DNA is a molecule — the size you quoted is a length (in base pairs) not a measure of information content. The information content of a sequence that contains highly repetitive regions (like a human chromosome) is not equal to the sequences length and since DNA contains four bases it certainly is no way "basically the same"!

Well, anyway, this is not a question of what the unit of information is!

@tyersome Can you prove my claim wrong? After all, you say it's NOT true.

BTW: It is not called junk DNA, it is called non-coding DNA.

And? What do you want to tell me with this comment? Non-coding and junk is distinctively different. One doesn't code for proteins but contains a lot of regulatory (for example) information, the other one implies that it can be removed which it cannot. The term "junk" has no scientific basis.

That means the more non-coding DNA, the more complex the species. Or am I wrong here?

I have edit(ed?) the question. But before I submitted my question I was at risk to be blocked, so was to read!!!

In science it is generally expected that you do some research before making a claim, editorial articles are not research. there is a wonderful tool called google scholar that lets you search actual sources. https://scholar.google.com/

@john What can I do to improve my question? I've done it a zillion times now. Why can't I ask questions anymore? On which grounds has my privilege been taken away, though I think I know...

non-coding, information-rich, DNA

Since noncoding DNA contains many long repeating sequences repeated thousands or even millions of times, it is not necessarily information rich, and is often extremely low entropy.

Does human DNA contain that much (the most) non-coding parts?

No. The human genome is a midsized genome by eukaryotic standards, so it's not going to contain the most of almost anything because it isn't large enough. To put into context, the wheat genome has ~6 times as much noncoding DNA as the entire human genome. Then there is the lungfish, which could fit as many again copies of the wheat genome into it's noncoding DNA:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5718017/#Sec1title

Could it be that this huge amount is what makes us "free"? That thát's the reason why we differ from other species in an obvious way?

Our genomes are very average for eukaryotes, so not likely.

Has there any research been done to answer my claim?

Yes. The puzzling lack of correlation between genome size and organism complexity was an unsolved mystery in biology for about half a century. It was eventually resolved when high throughput sequencing combines with bioinformatics revealed that the actual information required to build an organism is very low compared to the typical size of a genome, and so factors other than information content drive genome size.
Also as an aside since I saw this in the comments: since a BP can have 4 values, it can store 2 (not 1) bits of information. Most BPs store less however because they are not random.

What about the length of human DNA? In comparison to other species?

Each base pair is 0.34 nm long. 3 billion * 0.34nm = 1 m per copy and you have two copies. You can do the math for other species.


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Does my reasoning about the first emergence of proteins make any sense?
In order to make proteins, a cell uses ribosomes, which itself is a structure made out of proteins. The first ribosome couldn't have been created with the help of ribosomes though, as the ribosomes weren't there yet! So where did the first proteins came from? Before the advent of ribosomes, which, when they arrived on the scene (in some primitive form), subsequently could be used to make increasingly complex proteins.

In prokaryotes, ribosomes are roughly 40 percent protein and 60 percent rRNA. In eukaryotes, ribosomes are about half protein and half rRNA. Ribosomes are usually made up of three or four rRNA molecules and anywhere from about 40 to 80 different ribosomal proteins.

Amino acids were abundantly present though before ribosomes came into existence. Most of them were left-handed as is life itself (look at the Softenon babies). You can compare this with the matter-antimatter problem in physics (which is not really a problem in my theory, but I won't bother you with that sh*t). A scenario to achieve is easy to come up with.
While competing-self-replicating molecules were present too, they could make good use of them. A rudimentary ribosome emerged (with earlier formed proteins, by accidentally combined amino acids so these proteins came first, actually).
Behold the creation of life! Once started life exploded, leading to us (some say that there is some kind of hyper evolution going on: the rise of the robots with no ticker, no tears, no feelings but a high calculating power).
Is my reasoning reasonable?

You raised what appears to be a similar point four years ago: Was there originally a non-ribosomal way of synthesizing proteins?. I am not sure what your actual question is this time. You do not seem to elaborate on your title and just state that proteins could have been formed from amino acids.

I'm asking now if they could have emerged by accident, just as amino acids did. Ain't it probable that in a soup full of amino acids these amino acids will react with each other to form a big collection of protein?

Before the question can be addressed I think you need to clarify or revise the statement “:…proteins, one of which could have been primordial life”. How can a protein be life?

@user1136 You can reduce and reduce, so the final question is: where did it all come from? Where there rishons, curved spacetime, inflation, singularities first? Where did they come from? Why is there anything at all? Why isn't there nothing?

If you wait long enough, amino-acids will combine to get the right proteins. Self-replicating molecules can use them.

@user1136 The answer can be connected with the fact that Nature (in physics) is left-handed. Only left-handed neutrinos exist. But I question this. It could be that the asymmetry originated just by accident. There are many scenarios to make this happen. Right hands don't fit in lefthand gloves.

Fred Hoyle thinks that matter is continuously created and the Universe is eternal, so no need for a cause. Panspermia, hmmmm....I would like to live there for certain! Maybe...

@user1136 You can see it as how the asymmetry between matter and anti-matter occurs in the early Universe,. For sure there is a similar mechanism is at work. between left and right-handed molecules of life.

Don't you mean "Lucifer's Legacy"?

why would proteins form without ribosomes?

@John Wasn't there an abundance of amino acids, prior to life? Amino acids were formed in a lab once. Why shouldn't proteins form?

Now you have changed your question to the merely asking whether a theory you propose is reasonable your question is clearly off-topic for this list and I have voted to close it on this basis.

@David Fair enough. But why am I not allowed to ask questions anymore? I did edit my questions, so is there still a reason for not being allowed to ask a question?

If you are being prevented from asking questions this must be a decision of one of the moderators. I am not a mod, just a list member able to cast a vote. You can ask on meta.

@David Good suggestion! Thanx. ;-}

I would also say that your "question",  though not a question, could be posted as your own answer to your original question. To amplify the reason I think it is not a question in terms of SE Biology, I would say that it comes in this category of subjective questions of the sort "…am I right?".

As their name suggests, the majority of a ribosome's structure and function come from ribonucleic acid (RNA), not protein. While ribosomes are about 35%-40% protein on average, a majority of ribosomal proteins are not essential for the catalytic functions of the ribosome, and none are in direct contact with the catalytic reaction site where peptide bonds are formed. Thus, it's hypothesized that the earliest ribosome analogs consisted entirely of RNA in what some might consider a pre-biotic RNA world.
In this "RNA World" framework, it is posited that other macromolecular structures, like proteins, DNA, and lipid membranes all arose after the existence of some primitive form of self-replicating RNA molecule.
References:
Khaitovich, Philipp, et al. "Characterization of functionally active subribosomal particles from Thermus aquaticus." Proceedings of the National Academy of Sciences 96.1 (1999): 85-90.
Nissen P, Hansen J, Ban N, Moore PB, Steitz TA. The structural basis of ribosome activity in peptide bond synthesis. Science. 2000;289(5481):920-930. doi:10.1126/science.289.5481.920
Davidovich, Chen, et al. "The evolving ribosome: from non-coded peptide bond formation to sophisticated translation machinery." Research in Microbiology 160 (2009): 487e492.

I think you will find a similar RNA world answer to the poster’s previous question. This present question is either a duplicate, and should be ignored, or deserves an answer either criticising the poster’s proposal or explaining the views of those who have considered the nature of early proteins. You may not be aware that there are some eminent scientists that argue against the RNA world, and even if you accept it there are problems about the appearance of proteins.

It's pretty obvious that the prebiotic world consisted of lf-replicating molecules. These molecules slowly merged with proteins to make ribosomes fit for producing proteins. Life got started!

Bacterial ribosomes stripped of their proteins still function. they are slower, more error prone, and breakdown faster but they still function. proteins are not needed for the creation of proteins. http://uu.diva-portal.org/smash/get/diva2:408601/FULLTEXT01.pdf

I edited fro upvoting so I could upvote and accept.


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Cuckoo interbreeding between those with different host species
Whilst there are many (~150) species of cuckoo, it sounds like in the UK there's only 1 (Cuculus canorus).  However, this 1 species specialises depending on their host species/environment; e.g. their eggs look like one of their four different host species (dunnock, meadow pipit, pied wagtail, and reed warbler).
I'm led to believe that the cuckoo will use the same host species as their parents, as their eggs have evolved to look like 1 of these particular host species, rather than some decision on the bird's part when laying the egg, or environmental factors (e.g. influence of a marshland diet) influencing the egg's camouflage.
Does this mean that the cuckoo is going through divergent evolution, leading to speciation?
Also, do we ever see interbreeding between different "strains" of cuckoo, and does this have a negative impact on "egg camouflage", or is this trait controlled by the genes of only one of the parents, thus avoiding this risk?

You may find this article helpful: https://phys.org/news/2014-11-egg-colours-cuckoos-masters-disguise.html

Thank-you; so it seems that in the case of at least one cuckoo species (from Aus) the cuckoo is a generalist, so the per-host-species-speciation isn't a concern.


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Defining: Evolutionary (quantitative) Genetics and Population Genetics
How do we define the fields that are Evolutionary (quantitative) genetics and population genetics. What set these two fields apart? Can you try to provide definitions?
To my intuitive understanding, I'd tend to think that population genetics is a subfield of evolutionary genetics.

According to Hartl & Clark on population genetics:

"Population genetics deals with Mendel's laws and other genetic
  principles as they apply to entire populations of organisms.... also
  includes the study of the various forces that result in evolutionary
  changes in species through time."

According to Conner & Hartl also on population genetics:

"Population genetics is the study of naturally occurring genetic
  differences between organisms; these differences are called genetic
  variation. Genetic variation is important because it is the raw
  material for evolution... to understand the purview of population
  genetics, we need to have a better understanding of populations and
  genetic variation"

According to Conner & Hartl on quantitative genetics:

"Most phenotypic traits do not fall in to distinct categories, but
  rather are continuously distributed... These traits are called
  quantitative or metric traits because they need to be measured not
  just scored."

According to Falconer & Mackay on quantitative genetics (my personal favourite book on quant gen, which spends the first 5 chapters going through population genetics):

"Quantitative genetics is concerned with the inheritance of those
  differences between individuals that of degree rather than of kind,
  quantitative rather than qualitative.... It is nevertheless a basic
  premise of quantitative genetics that the inheritance of quantitative
  differences depends on genes subject to the same laws of transmission
  and having the same general properties as the genes whose transmission
  and properties are displayed by qualitative differences.
  Quantitative genetics is therefore an extension of Mendelian genetics, resting squarely on Mendelian principles as its
  foundation."

Personally I would say that evolution is inescapably a population genetics process and (virtually) no study of it can be done without some understanding of population genetic principles. Many evolutionary genetics problems can be best dealt with using quantitative methods, and quantitative genetics is an extension of population genetic principles. Population genetics relies on selection, drift, mutation and gene flow - these are all key quantitative genetics.
Population genetics study focuses then on the four basic principles above from a (simplified) Mendelian view, while quantitative genetics deals with more realistic evolutionary genetic phenomena by allowing for, and assessing, genetic variance from many loci influenced by additivity, dominance, and environmental factors. Both fields are studies of evolutionary genetics, population genetics can be studied whilst ignoring quantitative genetics, but quantitative genetics relies on population genetics principles so I would call it an extension of - but not sub-field - of population genetics.


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Assumptions of Hamilton's rule
Which elements of the following list are  assumptions of the Hamilton's rule?

Population structure (non-panmictic population)
Additivity

= Fitness of the heterozygote equals the mean of the fitnesses of both homozygotes

No epistasis or pleiotropy
Stable population size
Inifinite population size
Sexual reproduction
Selection on diploids or selection on haploids
Recombination (cross-over)
Mendelian segregation
Iteroparous population
smooth fitness landscape
mutation rate is high enough

Are there assumptions of Hamilton's rule that are not listed above?

A paper detailing the controversies about the assumptions of kin selection can be found here: http://onlinelibrary.wiley.com/doi/10.1111/j.1420-9101.2011.02236.x/pdf

Unfortunately, the answer depends completely on how stringent you are with "Hamilton's rule". If you just mean the equation $r \geq c/b$ then it is important to look at modern usages. In modern usage, all three of the terms $r$, $c$, and $b$ can be arbitrarily complicated. My favorite examples include when $r$ takes into account spatial structure saying that an agent near you is more "related" than a genetically identical agent far from you. Assumptions like that are a must, if you want to look at things that much of modern research is concerned with.
For this "most general" interpretation of Hamilton's rule, only one property is required and this property does not appear on your list: linearity. Note that this is not the same thing as the additivity you describe. Linearity means that your equations for small changes in proportions are linear in fitness: i.e. $\dot{p} = pf(E)$ where $E$ is some description of the environment, and $f$ is a linear function of the variables of interest (I used a continuous or large-population limit here, but similar things hold true for distributions over discrete populations).
Note, that in the above general and super-vague use of Hamilton's rule, the rule itself is not a biological observation but a simple fact of linear algebra. Of course, if you want to get linearity out as a consequence of some biological assumption, then the most common way to do this is by assuming weak selection.
If you put restrictions on what kind of features of the population, interaction, and environment structure $r$, $c$, and $b$ are allowed to incorporate then this will result in biological theories which will be mathematically true under only some of the assumptions you list. The subset of required assumptions will depend on what specific restrictions you place on $r$, $b$, and $c$.
There are no standard assumptions accepted on these parameters, so (unsurprisingly) I can't answer your question further without more specification on your part.

authors: ⵜⵓⵊⵢⴰ ⵜⵉⵣⵉ ⵓⵣⵣⵓ


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What's the mechanism or structure responsible for new species genetic code generation?
I always had this question in mind. I think, If humans find answer to it then we can trigger the next evolution of human specie.
What is the mechanism or structure responsible for evolution ? I don't mean the nucleus and the genetic code. because it's the consequence (the result) of evolution.
I mean all that I found right now as studies materials, treat only the consequences of the evolution, similarities between ancestors and descendants..etc
But what process triggers this evolution ?
For example, the birds ancestor (which couldn't fly ), how did his cells generate genetic code to build new proteins needed to build new protein structures and organs and also to keep this evolution's result for next generations ?
Is there any current research on this matter ?

Thank you All for your explanation, but they treat only the case when there is only a certain length ADN chain and this chain will change in time to produce let's say "more effective population ".
but if we say that all the species came from one cell. than this cell had necessarily less ADN then we have now (for ex: it doesn't have yet ADN to code for hemoglobin and other complex proteins)
So my question was Where did the new ADN came From ?
This question came to me, when we were studying bacteriology and one bacteria had all my attention, it's the staphylococcus, they produce a coagulase that trigger the coagulation process to stop the blood stream so the phagocytes and immune cells can't reach there position.
Random mutations ? well random process can have some result in variation and deletion of existing species, but not in building new ADN chains.
don't tell me that the staphylococcus acquired the ability to produce this protein randomly, because if we do some math, the ADN is a base 4 code (there is 4 bases) and to produce an amino acid we will need 3 bases, so for 30 A.A protein we have only one chance in 4 power 90 without adding the random length and the random 3 dimensional structure, I know, even if there is billions of staphylococcus that will mutate all the time there will be nearly 0 chance to produce a protein that can action exactly with the prothrombin.
that's only for one protein.
I Know I have moderate knowledge in biology but I don't believe that errors in a code (mutations) can make it "better" or produce functioning mechanisms that can interact with other organisms, because if we say so, then we are just insulting our intelligence as human being, because we are saying that random process is making organisms that we, with our brain can't reproduce, the proof is we are still using antibiotics and didn't make our immune system more effective.

On a cellular level, Meiosis is the mechanism that creates genetic diversity in gametes.  Sexual reproduction, though, is the largest contributing factor to diversity and the catalyst of evolution.

Thank you for your comment MG_MD, I agree with you that  Meiosis and Sexual reproduction contribute to diversity. But not necessarily to evolution because we all know that these two processes use what's already existing of genetic material (from parent cells), but a new specie need new genetic code to evolve. so My question is, what  mechanism or structure that builds or generate this new code ?

The mechanism is simply random changes.  If the changes are neutral or beneficial, they stick around.  If they are seriously detrimental, the changed creature doesn't survive to pass on the changes.

It is one of those times when I would love to be allowed to down vote comments!

Evolutionary biology is a large field of research that investigate the mechanism that dictate evolutionary processes. There are hundreds of papers published each month on evolutionary biology and the question is therefore way too broad.

You might want to attend an introductory course to evolutionary biology such as the free online course Understanding Evolution by UC Berkeley. You seem to be particularly interested to mutations.

Okay so what I am interested in, are the insertion mutations (adding code to ADN) because they are the only mechanisms that can explain the new specie capabilities ex : from non flying to flying there must be new ADN fragments that will code for the wings and feather ...etc

First, I don't think that the code insertion that caused evolution was random.
For the simple reason that there is the Proofreading mechanism for the ADN (error-correcting processes). I mean a mutation (or billion of mutations) that happened randomly even for billions of years can't lead to produce something that prevents other future mutations.
if the evolution happened , then it happened outside of the ADN or ARN by inserting new code fragments to acquire new species features, so my question is what is and what caused this process ?

@Allad1n Your questions are very very basic questions in evolutionary biology (no offense) and you will get all the info you need by following the links I gave you. It will take you a few hours and you will have a much better understanding of what evolution is about (and about the role of mutations in evolution). Your question for the moment is just too broad for a StackExchange post.

I think one of the elements you are missing is that many mutations do change the size of the genome. If you follow up with the references @Remi.b has provided you'll learn about insertions, deletions, translocations, aneuploidy, and mobile genetic elements. You may be familiar with conditions like Down's syndrome which is the duplication of an entire chromosome. Both replication and proofreading are imperfect processes, they are good enough to make changes very slow, but they don't entirely prevent change.

@Allad1n I added a small paragraph on mutations that increase/decrease the amount of DNA.

@Allad1n You say I Know I have moderate knowledge in biology but I don't believe that errors in a code (mutations) can make it "better" and it sounds extremely opinion based rather than evidence based. Do not believe! Investigate the question (Understanding Evolution UC Berkeley).

I strongly advice to have a look at an introductory source of information on evolutionary biology (such as Understanding Evolution by UC Berkeley). It will give you much more information.
Locus and Allele
Here are two definitions to start with:

A locus is a location on a chromosome. This location can be of any size. It can be a single nucleotide, a codon, a whole gene or even longer.
An allele is one variant at a given locus. When considering relatively short loci (say 1 nucleotide or 1 base pair (bp)), then the majority of loci have only one allele.

What is evolution?
Evolution is defined as any change in allele frequency in a population over time.
There are a number of "forces" that affect evolutionary processes. I picked the 3 most commonly considered: Mutations, Natural Selection and genetic drift
Natural Selection
Natural Selection is the process by which variants of genes called alleles are selected and therefore increase in frequency. This selection result from a differential reproductive success.
Natural selection occurs whenever the three following conditions are respected

Individuals in a population varies in terms of a given trait
This trait has some (additive) heritability. Here is one of the several posts that explain the concept of heritability. It might be slightly a post that is a bit advanced for you though but shortly speaking it means that offspring are more similar to their parents more than they are to other non-kin individuals in the population.
The fitness varies (not necessarily linearly) as the trait varies.

Simple example:

In a population, there are blue pens and red pens
Reproduction is asexual and blue pens create other blue pens while red pens create other red pens.
blue pens make more offspring than red pens.

In such situation natural selection occurs yielding the frequency of the blue pens to increase in the population while the frequency of red pens will decrease.
You may want to have a look at this post (although it might be too advanced) to understand the concept of heritability.
Mutations
In the broad sense mutation is any change in the DNA sequence. Some changes are more likely to happen that other but in any case the likeliness of these changes to happen is not dependent on the consequence they will have on the phenotype (shortly speaking, phenotype is how an individual looks like) and on the reproductive success. So mutations occur randomly and the specific mutation that would be needed in the population may not occur. Therefore saying, if a trait is needed (in the sense of "if a trait would be beneficial"), then a mutation will occur to make this trait existing is wrong. Note that most mutations are deleterious (decrease the reproductive success) while few of them are beneficial (increase the reproductive success) and those that are beneficial are more likely to raise in frequency in the population.
Mutations can be a simple a "small change" such as nucleotide substitution, an nucleotide insertion and deletion or can be a "bigger change" such as a chromosomal duplication/deletion, a whole genome duplication and the duplication/deletion of a long sequence.
Mutations create the genetic variance on which natural selection selects the best variants. As a consequence natural selection decreases the genetic variance while mutations increases genetic variance.
Genetic drift
If the change in frequency of mutations would depend exclusively on natural selection, then I would not have said before that a beneficial mutation is more likely to raise in frequency but I would have said that a beneficial mutation will raise in frequency deterministically. An intuitive explanation of what is genetic drift can be found on this post. It will also allow you to understand why small population undergo more random change in frequency of their genes than are big population.


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Question about DNP derivatives of amino acids (specifically epsilon-DNP-lysine)
I have a pretty basic biochemistry question but am having trouble finding the answer to it:
Normally, 1-Fluoro-2,4-dinitrobenzene (DNFB) reacts with just the amino terminus of amino acids. However, with lysine, DNFB can react in two places (at the amino terminus and to the epsilon amino group). The DNP derivative of lysine is referred to as "epsilon-DNP-lysine".
Does "epsilon-DNP-lysine" refer to a product where the DNP is bound only to the epsilon amino group (but not to the amino terminus), or does it refer to a product where DNP is bound simultaneously to the epsilon amino group and to the amino terminus?
Also, can the same thing happen with other amino acids that have an amino group in the side chain? i.e. can there be epsilon-DNP-arginine, for instance, or is this behavior unique to lysine?

Cross posted on chemistry: http://chemistry.stackexchange.com/questions/46359/question-about-dnp-derivatives-of-amino-acids-specifically-epsilon-dnp-lysine


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Has anyone used Crispr/Cas to induce a knock-in in MEF cells?
Does anyone have experience with the CRISPR/CAS9 platform performed on MEF? Or does anyone recall any relevant articles?

Is this the paper you are looking for? http://genesdev.cshlp.org/content/27/23/2602.long

From this paper:

We chose to test for Cas9-driven targeted mutagenesis on the
  endogenous Trp53 gene in mouse embryonic fibroblasts (MEFs), a cell
  line in which the biology of p53 has been thoroughly characterized and
  where the gene is structurally intact.

Furthermore:

Seventy-two hours post-transduction, cells were cultured in the
  presence or absence of Nutlin-3a, a specific inhibitor of the MDM2–p53
  interaction (Tovar et al. 2006). Cells were scored for the fraction of
  GFP+ cells after 4 d of Nutlin-3a exposure using flow cytometry (Fig.
  2B). Nutlin-3a potently activates a p53-dependent anti-proliferative
  cellular response, which strongly and specifically selects for any
  cells with disrupted Trp53 function (Efeyan et al. 2007). Much like
  MLP-p53.1224 infected cells, the pQCiG-p53 GFP+ cells were rapidly
  enriched for in the presence of Nutlin-3a, suggesting that
  CRISPR-mediated gene disruption had initially occurred in at least a
  proportion of the initial Cas9-expressing cells.


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How do bats manage lymph fluids?
We all know that bats hang upside down to sleep. I was watching some sleep for a while, and they don't move much while asleep.
If I fall asleep sitting in a chair my lower legs will swell. Lymph fluids in people are mostly moved by muscles in the limbs of the body.
It would seem like a sleeping bats lymph fluids would gather at or near the head, chest and lungs.
How do bats manage lymph fluids?


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What chemicals can be detected in sweat?
This question came to mind after reading this article. The article speaks of inducing sweating to determine, by a roundabout fashion, the amount of salt therein. I'm no medic but I find myself wondering whether sweat may be used directly to measure any other chemicals secreted by the body.
For instance:
If one's kidney/liver were to suffer some malady would the body attempt to discharge some additional waste through one's sweat
What chemicals may be detected by analysing sweat?

I recently watched a documentary in which a team demonstrated a type of sensor that would compute blood sugar levels from sweat, which was pretty neat. I guess a lot of stuff is leaked out that way.

@Polynomial: Just the kind of answer I hoped to have. If you would post it as an answer I can atleast acknowledge the effort.

Cystic fibrosis diagnosis. Here is a link to a paper describing the use of β-adrenergic sweat secretion as a diagnostic test for cystic fibrosis.
Anti-cancer therapy and its effectiveness. This report seeks to determine the levels of the anti-cancer drug sunitinib and its active metabolite N-desethylsunitinib in sweat.
I'll add others later.
Here's a 2004 study looking at a particularly unpleasant sulfury compound produced by bacteria in contact with sweat. It's interesting that the enantiomer of the malodorous compound had a grapefruit-like smell.
This paper puts forth the idea that sweat, which contains lactate, lactic acid, urea (of course) and amino acids, can be used in forensics.

I can't provide any real technical details, but I recently watched a documentary in which a team demonstrated a new type of blood sugar sensor that could be simply swabbed against sweat. They were trialling it as a non-invasive option that paramedics could carry, for use on unconscious patients as a means of checking for signs of diabetic shock. They mentioned that it only required a minimal sample; a swab of the palm of the hand was sufficient to gain a decent reading.
I'm unsure as to the mechanism of the device - it could well have been direct measurements of sugars or sugar by-products in the sweat, or it could have been looking for other chemicals associated with abnormal blood sugar levels.

What was the documentary called?

I honestly can't remember. I believe it was a BBC Horizon episode, but I may be wrong.


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Why does Helium make your voice change?
When we breathe in helium and then speak, our voice changes drastically. Does it happen only due to helium or can happen if we use other gas? What factors of the gas does our voice depend on (like density, temperatue etc.)

Helium is not as dense as air, and when your vocal cord vibrate with the helium, it vibrates at a higher frequency, making your voice higher. sulfur hexafluoride Is Denser than air, making your voice deeper.


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What is a good non-fluorescent DNA dye?
Can anyone suggest a dye which specifically targets DNA, but is not fluorescent? We plan to mark DNA before observing it with RAMAN-Spectroscopy. Because of the weak signal, even a low emission would disturb the reading.

I don't understand why you want to dye the DNA at the same time as performing the Raman spectroscopy, anything else you put in your sample will interfere in some way during your measurements, I assume. Does the dye need to be specific for DNA, or is a general nucleic acid dye enough? Should it be a non-covalent dye or something your want to specifically attach to a certain position in your DNA?

The Dye is needed to know where to aim. The Signal form the dye can be subtracted by measuring it without DNA. The main thing of importance is that the Signal is not so strong that it overshadows the DNA signal.

One option is to use biotin labelling. Most molecular biology supply companies do kits for this, and supply biotinylated nucleotides.

I accepted your answer, but I don't really know how well it would have worked, as the experiments were never performed after all. (It was a colleagues project, not mine)

Methylene blue? Certainly not as sensitive or specific as other options but it's cheap and does not fluoresce.


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What is this tiny jumping cocoon?
I found this little jumpy cocoon thingie clinking approximately once every 4-5 seconds inside a metal lid. It's been jumping inside there for about a day since I first found it like that. It has a tiny flat mark on one of its sides which suggests that's how it initially stuck itself to something, and then got unstuck. What is this thing?
Here's a short web vid of it: https://giant.gfycat.com/IcyHarmfulCentipede.webm
And here's a static pic:

Update:
It stopped jumping around after about 1.5 days since I found it, and we decided to carefully cut it open with a paper knife. Inside was a white grub with a tiny orange dot on one of its ends, all foldy like a bendy part of a cocktail straw. It was still at first, but we sprayed it with water and put it on a leaf. It started moving around slowly, and looked like it was soaking up water. When we checked up on it later, it had disappeared and probably crawled away somewhere. Unfortunately, I didn't take any pictures of that, so it could have been anything.

excellent video!  I look forward to learning the answer.

@Will I posted an update.

Where in the world are you?

This was found in Russia, near Moscow.


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Effect of cellular phone towers on human health
We live in world of mobiles, tablets, PCs and other electronic gadgets. We are continuously exposed to radio frequencies and other cellular frequencies. Generally, all of these waves are very low energy / long wavelength (which makes them non-inonizing). This makes them less probable agents to cause any health problems.
I have been searching for potential effect of cellular phone towers on human health. Towers will emit large number of such waves due to our daily usage of electronic devices. The International Agency for Research on Cancer (IARC) has reported cumulative radiofrequencies are categorized as class 2B (possibly carcinogenic to humans). Does this mean people living near cellular phone towers are more prone to health hazards?
I was searching for scientific reports to support or deny any claim made here. I checked the FDA website for guidelines:

Under the law, FDA does not review the safety of radiation-emitting consumer products such as cell phones and similar wireless devices before they can be sold, as it does with new drugs or medical devices.... FDA shares regulatory responsibilities for cell phones with the Federal Communications Commission (FCC)

However, the FCC guidelines state:

The FDA, which has primary jurisdiction for investigating mobile phone safety, has stated that it cannot rule out the possibility of risk

And there are lot of other links to other organizations. I couldn't find any citing of scientific paper. This, again, made me confused as to whether cellular phone towers are safe for people living around them? How does the 'non-thermal' effect of this radiation work? There are few reports (like this and this) which I found but they didn't seem convincing.

I suggest using Google scholar search to find a review paper which will summarise studies done in the area before. If you want to save time you can answer your question by reading the abstract and the conclusion. Good luck!

Well.. I don't know why you tagged this question with [tag:cancer]. Microwaves can have some harmful effects but carcinogenesis is not one of them. MW do not have enough energy to cause electronic transitions that can cause DNA damage or produce free radicals.

Possible duplicate of http://biology.stackexchange.com/q/36394/3340

@WYSIWYG I used cancer tag because only health hazard I was able to find with reliable source is "possibly carcinogenic" remark from IARC (as mentioned in question). Also I know that companies requires NOC (No objection certificate) from radiologist or radio oncologist.

Possible duplicate of http://biology.stackexchange.com/q/39422/3340 as well

C'mon, how is that duplicate? There discussion is about different kinds of radiations.


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Definition of Linkage Desiquilibrium (LD)
According to wiki, linkage disequilibrium $D$ equals
$$D = x_{11} - p_1\cdot q_1$$
where:
$$
        \begin{matrix}
        \text{Haplotype} & \text{Frequency}\\
        A_1B_1 & x_{11}\\
        A_{1}B_{2} & x_{12} \\
        A_{2}B_{1} & x_{21} \\
        A_{2}B_{2} & x_{22} \\
        \end{matrix}
$$
and
$$
        \begin{matrix}
        \text{Allele} & \text{Frequency}\\
    A_{1} & p_{1}=x_{11}+x_{12} \\
    A_{2} & p_{2}=x_{21}+x_{22} \\
    B_{1} & q_{1}=x_{11}+x_{21} \\
    B_{2} & q_{2}=x_{12}+x_{22} \\
        \end{matrix}
$$
According to Hartl and Clark, linkage disequilibrium $D$ equals:
$$D = x_{11}x_{22}-x_{12}x_{21}$$
Question
Can you please prove that these two formulations of linkage disequilibrium are equivalent (assuming that they are equivalent)? If they're not… Do we use different definitions? What are their respective meanings?

none of your references seem to have links?

Yeah, where are the links?

Thanks for noticing. don't know what happened to them. I added the links.

Just need to solve the equation. p1 = X11 + X12; q1 = X11 + X21; 1 = X11 + X12 + X21 + X22.
D = X11 - (X11 + X12) * (X11 + X21)
D = X11 - (X11X11 + X11X21 + X11X12 + X12X21)
D = X11 - X11X11 - X11X21 - X11X12 - X12X21
D = X11 * (1 - X11) - X11X21 - X11X12 - X12X21
D = X11 * (X11 + X12 + X21 + X22 - X11) - X11X21 - X11X12 - X12X21
D = X11 * (X12 + X21 + X22) - X11X21 - X11X12 - X12X21
D = X11X12 + X11X21 + X11X22 - X11X21 - X11X12 - X12X21
D = X11X22 - X12X21
Sorry for the very long answer, but I thought it would be more clear if I wrote everything out.


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Help analyzing SDS-Page gel
In this experiment, we transformed a truncation of the NFAT protein sequence into a plasmid vector to be expressed in E.Coli as a fusion protein with GST.  We also attempted to transform the normal plasmid without NFAT so that we could get GST alone.  After growing up these colonies and selecting positive colonies, we lysed the e.coli.  We collected some of this lysate for SDS-PAGE.  We then put the lysed GST and GST-NFAT solutions in separate columns with glutathione beads.  GST binds glutathione.  We washed the column and collected some of the wash for SDS-PAGE.  Finally, we eluted the GST and GST-NFAT off the column and saved some for SDS-PAGE.
I have attached a picture of a successful version of the SDS-PAGE.
You want to direct your attention to the first lane, the Molecular Weight Marker (MWM).  The rest of the lanes should be interpreted in sets of 3.  The first of the three is the crude lysate, the second of the three is the first wash, and the last is the eluted protein of interest.  The important lanes for my analysis are 8-10 and 11-13.
I will explain what I know from this SDS-PAGE gel so far.  I know the weights of the different bands in the molecular weight marker because I was given a copy of the different proteins in the marker.  From this information, I was able to confirm that I isolated my protein of interest in lane 13 and isolated GST-alone in lane 10.  I also understand the reason why the lysate lanes are darkest, followed by the wash lanes, and then very clean protein of interest lanes.  Also, note that the marker and the elution lanes were loaded with 10 microliters while the other lanes were 2 microliters each. However, there are some things that I do not understand from the gel.
(1) Why are the bands so diffuse/low resolution.  I imagine it may be overloading the wells, but I am not convinced because I followed a set procedure.
(2) Why is there large amounts of streaking, especially in lanes 5, 8, 9, 10, and 11.
(3) I isolated my protein of interest because it was a fusion protein with GST (or just GST alone), and then eluted the protein off the glutathione beads via excess glutathione wash.  Theoretically, the lanes for the elutions should be free of everything except the protein of interest and glutathione then.  This mostly holds true for lanes 4 and 9, which should only have GST and glutathione.  However, lanes 7 and 13 should only have GST-NFAT and glutathione.  The lanes are not as clear however and seem to have stained numerous other proteins.  What is going on?
(4) I was told by a professor that the second band in lane 13 (the GST-NFAT lane) was a degredation product.  How can this be?  The band does not correspond to the weights of NFAT alone or GST alone.  Also, if the NFAT-GST was degraded, wouldn't there be two bands of degredation product?
(5)  Why do the GST-alone lanes have what looks like doublet-bands?  (Lanes 4, 10).
(6)  If we eluted the proteins of interest with excess glutathione, which has a very low molecular weight, why doesn't it show up on the gel?  Is it possible that it ran off before everything else?
(7)  I have a list of the weights of the bands of the molecular marker.  Yet, there is an extra band at the bottom that does not show up on my list.  Is it possible my list is incomplete, or is there something else happening?
Finally, I have attached a picture of a failed SDS-PAGE gel.
The only thing that I definitively know was a source of error is the fact that my buffer level fell during the run (due to a leak).  The results of this gel are accurate (Lanes 2-7 correspond to lanes 8-13 on the above gel, and the results are almost identical) yet the gel turned out horribly.  How can the buffer falling cause this result?  Or is there something else that may have contributed to this weird pattern?  Finally, the lanes are not as distinct in this gel as the first gel, yet the same comb, and thus the same size and spaced wells were used.  So why was there so much bleed between lanes/ lack of space between the lanes?
Thanks in advance for any help.

These are a lot of questions and there is still some information missing to give you at least some answers. 1. Which molecular marker did you use (it would be at least important to know the bands), it would be even better if you could number lanes and buffer in the gel. 2. What did you put in which lane? 2-4 is crude lysate, 5-7 the first wash, 11-13 the elution, but what is in 8-10?

Here are some thoughts based on my own experiences purifying many proteins and running many SDS-PAGE gels:
(1) Resolution--how fast did you run this gel? Often if you run at higher than say 150V or so you can get bands that look like this. The resolution could also be related to..
(2) I would bet the streaking is due to salt in the sample--a lot of the time lysis/wash/elution buffers can have upwards of 500 mM or 1 M salt, and this invariably causes streaking. Load less sample in these lanes and keep the total volume the same to dilute the salt below 250 mM at least. Other things in your buffers could be causing the streaking, but salt is the most common (let us know the composition of your lysis/wash/elution buffers).
(3) Your purification of GST alone looks very good--often your preps will look much more like the lanes you have indicated, which are not entirely clean. This is quite common for a one step purification--often you need 2-3 for certain proteins to completely remove contaminants. There are several possible sources of these bands:

Endogenous proteins: Many bacterial proteins will non-specifically stick to the beads (this is why we wash), but even thorough washing can still leave some contaminants. These proteins also could be bound to your protein of interest and are co-eluted off of the resin.
Truncation products: Depending where your tag is (let's sat it is on the N-terminus), you can sometimes get incomplete translation products--they have the tag, but they are not full length proteins. These will still bind and elute from the beads because they have retained the tag. Ignore this point if you tag is on the C-terminus, as in that case the tag will only be on full-length protein.
Degradation products: This is related to your later questions--often during the purification your protein will be degraded by bacterial proteases. Did you include a variety of protease inhibitors in your lysis buffer? Keeping all of your samples on ice is also important for this reason.

(4) Understand that degradation products do not mean you get only your protein and the fused GST--they can be a variety of truncations due to degradation by proteases.
(5) I would bet this is just due to your running conditions or the salt in your samples. I think this is probably actually your single GST band.
(6) Glutathione will not show up on the gel--it's formula weight is about 300 g/mol if I recall meaning it's about 300 Daltons, so much smaller than anything that you'll retain on the gel. Further, remember than your stain is for proteins--Coomassie blue binds basic residues on proteins.
(7) I'm not sure which band you are referring to, but I think the very bottom band in your marker lane is simply the dye front. It could also be a degradation product of a protein in your ladder.
As far as the second gel goes--it is all due to the buffer level falling during the run. Without buffer covering the top of the gel there is no current flowing. Probably as the leak was occurring you had uneven distribution of the buffer. Strange things can happen when this occurs (unscientific, I know).

Thank you for your detailed analysis.  I have taken the information and used it to help me understand my gel more.
(1) I ran the gels at 120V through the 4% stacking layer and then 200v through the 12% resolving gel.
(2) I will look more into the salt composition and report back.
(3) I still do not understand why the GST alone lanes were more free of extraneous proteins than the GST-NFAT lanes.
(4) If a protease degrades a protein, would there not be two resulting products?  Yet there is only one extra band.
I attached a labelled gel to make things more clear.  Thanks for the response!

Definitely your streaking and resolution is due to the voltage you used--I usually do 80V for the stacking and 120V for the separating. You still get enough information running it that fast, but not great pictures (as you can see!). As for the extra bands--again these could be bacterial proteins bound to your protein (especially chaperones). I think this is the most likely issue--you can increase your washes to try and clean it up. The GST prep might be more pure because you have more GST than GST-NFAT--it could be fully saturating the beads, preventing bacterial proteins from binding.