text:
What are the disadvantages of forbidding flights to and from the African Ebola region?
After looking through the available Stack Exchange sites, this one seems to come closest to the appropriate place to ask...
Popular opinion, including my own, is that banning flights to and from the Ebola-ridden portion of Africa would protect us overall. I understand it would increase pressure on that region, making it more chaotic and less conducive to tracking people, so that eventually it could "explode uncontrollably" out of that region in a year or whatever time frame. Sanjay Gupta explains this briefly in Jon Stewart's (at points hysterical) report.
The disadvantage of allowing free travel to and from these regions, as I see it, is that the disease spreads much much faster, and to many many more disparate locations. This is because of the variety of places where each passenger comes from. And also the flight crew and plane itself, which affects all future passengers.
I'd appreciate more educated opinions. I'm far from it, regarding these issues, as are many Americans.

The main disadvantage is that you will not get aid into the region which is extremely urgent.

I suspect that the main issue is the balance between containment (might favour closing borders) and control of people that enter the country (might favour allowing controlled airtravel). It has been argued that banning flights will lead to more people entering the country illegaly, which means that they cannot be screened for the disease in the same way as airtravellers. However, much of this also deals with politics, trade etc. From a biological viewpoint the issues should mainly be routes/vectors of dispersal and identification/containment of infected individuals.

The question is if this would help. I doubt it, since people which are infected, but have not yet developed symptoms (meaning they are not contagious), can travel via land across borders. This will probably slow the spreading down but it will not prevent it completely.

Well, it seems prudent to at least have flights from these locations limited to highly-prepared sections of the airport. It would also make sense to permit them to land only at specific airports. In the dead center of JFK is probably not a good idea.

Having them separated at the airport only gives you better options in separating out passengers that started showing symptoms while on board. Infected passengers without symptoms could still change to another plane afterwards, that will not be tracked as it did not depart directly from the Ebola region.

:)  https://uk.news.yahoo.com/ebola-us-restricts-air-travel-africa-160416055.html

I think the disadvantages are mostly economical in that region and so they has nothing to do with epidemiology. Possibly a long term effect can be, that the economy of the region turns from bad to worse, which can affect the healthcare too, but that's just speculation.
The advantages are obvious, ebola is quarantined at some level, so these measures prevent or at least slow down its spread around the world.


text:
Can Hepatitis be caused by Bacteria?
There are many information about viral hepatitis. But it is interesting for me, can bacteria cause the hepatitis too?

Short answer: Yes , they can. Have a look at this Wikipedia article.

@Chris - I would disagree; I couldn't find any mention of hepatitis from bacteria in your linked source. Can you please elaborate?

Look under causes, there you will find the following: "Less commonly some bacterial, parasitic, fungal, mycobacterial and protozoal infections can cause hepatitis." Since a Hepatitis only describes the inflammation of the liver, anything what can cause this causes a hepatitis. You could also have a look here.

Hepatitis just means liver inflammation. The word per se does not indicate any causative agent.

Hepatitis is a condition of the liver where the cells of the liver organ are inflamed. Most often it is caused by a viral infection, hepatitis A, B and C are all viral forms of the disease.
Bacteria (and Fungi) can cause hepatitis of the liver, and two examples would be the Staphylococcal and Streptococcal bacteria. These can directly infect the liver, and are also responsible for some inflammations in other tissues of the skin and heart and elsewhere.
Prolonged alcohol abuse is another cause of hepatitis (as well as cirrhosis) and is not associated with bacteria virus or fungi, but instead from a damaging effect on the liver.

Helicobacter hepaticus is suspected to cause hepatitis.

Thanks @inf3rno you could add that in as a second answer

I don't want to, I don't think it is enough for an answer, maybe to an edit...

http://europepmc.org/abstract/MED/11677423

Hepatitis has two definitions: inflammation of the liver in general, or inflammation of the liver due to one of several viruses.  The viruses are, of course, viral.  However hepatitis can also mean the symptom of an inflamed liver.  That symptom can be caused by bacteria.

The suffix '-itis' (-ῖτις, in ancient greek) usually is added to a word to represent a pathological condition called inflammation.
So, haepatitis (or hepatitis) means generically inflammation of liver (ἧπαρ épar, in ancient greek).
Usually it is  caused by viruses  such as HAV, HBV, and HCV.
An haepatitis can be due also to  toxic agents or be autoimmune .
But, whaterver it is the cause of inflammation of liver cell, it is called haepatites; even if it is caused by less common pathogens as bacteria; protists like T Gondii ; minor hepatotropic viruses, like EBV, CMV, and herpetic viruses in general; fungi, or protozoa and other parasites.
Bacteria can cause haepatitis, examples would be the Staphylococcal and Streptococcal haepatitis.
Ever the excessive intake of table salt (Na-Cl) or cronic alcoholism may cause  haepatitis or even a liver's cirrhosis.
So, though it is less common, but bacteria may cause haepatitis.

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text:
How many cells are there in the apical meristematic tissue?
How many cells are there in the apical meristematic tissue?
Looking at this picture...

, I would tend to think that there are few hundreds cells in the meristem tissue. But I guess this is a picture of a root tip and the answer will be much different if we look at big branches and big trunks of roots. Also, the answer will probably differ between monocots and eudicots.
Roughly speaking, how many cells are there in different apical meristematic tissues (root, branches, trunk, different species)?

Meristem size is a very controled, highly genetic feature. It doesn't change between big or small branch/root (The SAM and RAM are obviously different).
There are very levels of potency in the meristematic tissue, so you should explain more which section of the meristem is of interest.
SAM (shoot apical meristem)
In *Arabidopsis thaliana* there are 9 long-lived meristematic cells, 3 in each lineage (L1, L2, L3) (https://www.sciencedirect.com/science/article/pii/S0012160609013840)
But the whole meristem is somewhat larger. If you consider the organizing center and cells that react to wushell by creating CLV1, CLV3 you get a few dozens.
If you consider cells that express miR156, miR172 or AP2-like genes you can get a few hundereds.
The scale is similar between species but the number and genes used to asses it vary.
RAM (root apical meristem)
I know less about the RAM but we can consider there the Quiescent center and also the Intial cells togheter called the promeristem.
THe Quiescent center consists of 10-20 cells and there is one (sometimes more) initial per file of cells in the root giving 20-30 cells in the promeristem.
The meristematic zone is somewhat bigger than the promeristem but the cells are pluripotent with relative small mobility.
 Roughly speaking
The most meristematic zone of each meristeme has no more than 50 cells.
The full area considered a meristeme can have a few hundered cells, depending on the research goal.

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text:
How long does the Ebola virus remain infectious on contaminated items or surfaces?
I'm sure there will be variation depending on what the contaminated item or surface is made of - linens, I could imagine, would remain dangerous for longer than a door-knob. But if the items are not decontaminated in some way, how long can the virus survive outside a host?

This really depends on the environment, one study (listed below as reference 1) found that the Ebola virus can survive under ideal conditions on flat surfaces in the dark for up to six days - see the figure from the same publication.

However, the virus is quite sensitive to UV radiation (see reference 2 for all the details) and most viral particles are likely to get inactivated within relatively short time. It might still be possible to get positive tests for Ebola from really sensitive PCR-based tests, but these are most likely not infectious anymore. The CDC lists common bleach (or any other routinely used disinfected) as a good way to get rid of Ebola viruses.
References:

Persistence in darkness of virulent alphaviruses, Ebola virus, and
Lassa virus deposited on solid surfaces
Sensitivity to ultraviolet radiation of Lassa, vaccinia, and Ebola
viruses dried on surfaces

From how many particles does it cause disease? (I forgot the exact term. :S)

Using % and log on the same graph... sigh ...

I found this safety sheet in the topic.

SECTION IV – STABILITY AND VIABILITY
DRUG SUSCEPTIBILITY: Unknown. S-adenosylhomocysteine hydrolase
  inhibitors have been found to have complete mortality protection in
  mice infected with a lethal dose of Ebola virus (30).
DRUG RESISTANCE: There are no known antiviral treatments available for
  human infections.
SUSCEPTIBILITY TO DISINFECTANTS: Ebola virus is susceptible to sodium
  hypochlorite, lipid solvents, phenolic disinfectants, peracetic acid,
  methyl alcohol, ether, sodium deoxycholate, 2% glutaraldehyde, 0.25%
  Triton X-100, β-propiolactone, 3% acetic acid (pH 2.5), formaldehyde
  and paraformaldehyde, and detergents such as SDS (20, 21, 31-34).
PHYSICAL INACTIVATION: Ebola are moderately thermolabile and can be
  inactivated by heating for 30 minutes to 60 minutes at 60ºC, boiling
  for 5 minutes, gamma irradiation (1.2 x106 rads to 1.27 x106 rads),
  and/or UV radiation (3, 6, 20, 32, 33).
SURVIVAL OUTSIDE HOST: The virus can survive in liquid or dried
  material for a number of days (23). Infectivity is found to be stable
  at room temperature or at 4°C for several days, and indefinitely
  stable at -70°C (6, 20). Infectivity can be preserved by
  lyophilisation.

2010 - Free Safety Data Sheet Index - Ebola virus

However there are no references on the site, so I checked the data provided. According to scientific articles it is trusty, however these articles are related to not the current West African strain, so it can be slightly different.

1982 - Inactivation of Lassa, Marburg, and Ebola viruses by gamma irradiation.

Clinical specimens from patients infected with Lassa, Ebola, or
  Marburg virus may present a serious biohazard to laboratory workers.
  We have examined the effects of heat, alteration of pH, and gamma
  radiation on these viruses in human blood and on the electrolytes,
  enzymes, and coagulation factors measured in laboratory tests that are
  important in the care of an infected patient. Heating serum at 60
  degrees C for 1 h reduced high titers of these viruses to
  noninfectious levels without altering the serum levels of glucose,
  blood urea nitrogen, and electrolytes. Dilution of blood in 3% acetic
  acid, diluent for a leukocyte count, inactivated all of these viruses.
  All of the methods tested for viral inactivation markedly altered
  certain serum proteins, making these methods unsuitable for samples
  that are to be tested for certain enzyme levels and coagulation
  factors.

1984 - Physicochemical inactivation of Lassa, Ebola, and Marburg viruses and effect on clinical laboratory analyses.

Ebola, Lassa, Venezuelan equine encephalitis, and Sindbis viruses were
  dried onto solid surfaces, incubated for various time periods under
  controlled conditions of temperature and relative humidity, and
  quantitatively eluted from surfaces, and viral titers in the recovered
  samples were determined. The viral inactivation kinetics that were
  obtained indicated that viral resistance to natural inactivation in
  the dark follows (in decreasing order of stability) alphavirus > Lassa
  virus > Ebola virus. The findings reported in this study on the
  natural decay in the dark should assist in understanding the
  biophysical properties of enveloped RNA viruses outside the host and
  in estimating the persistence of viruses in the environment during
  epidemics or after an accidental or intentional release.

2010 - Persistence in darkness of virulent alphaviruses, Ebola virus, and Lassa virus deposited on solid surfaces

Our study has shown that Lake Victoria marburgvirus (MARV) and Zaire
  ebolavirus (ZEBOV) can survive for long periods in different liquid
  media and can also be recovered from plastic and glass surfaces at low
  temperatures for over 3 weeks. The decay rates of ZEBOV and Reston
  ebolavirus (REBOV) plus MARV within a dynamic aerosol were calculated.
  ZEBOV and MARV had similar decay rates, whilst REBOV showed
  significantly better survival within an aerosol.

2010 - The survival of filoviruses in liquids, on solid substrates and in a dynamic aerosol

Any explanation about downvote?

What does  found this safety sheet in the topic mean? Link?

@not2qubit I wrote a quote and a link right below that.


text:
How does high-fidelity of DNA replication depend on the formation of hydrogen bonds?
Replication has an error rate of less than 1 in 100 million. DNA polymerase forms H-bond with the H-bond acceptor atoms in the minor groove. <-- enhance fidelity here?
Binding of the triphosphate group to the active site of DNA polymerase triggers a conformational change. Changing a conserved Tyr residue increases the error rate by 40 fold.
I don't quite understand the above two statements. Can anyone explain in detail to me? Thanks!

Where do these statements come from? Can you post a link to the source?

it comes from my lecture note. Maybe similar statements can be found from here. The lecture quotes this from this reference book link

There's a few probs with this question one is h-bond acceptor- what is that? Then w the tyr residue are you talking about the polymerase? I have a feeling your instructor is using this mediocre example to explain to you: the structure of dna, and the fact that aa sequence determines over protein structure which determines protein function. I'm gonna post some info on  high fidelity pol but it's not going to completely answer your question cause I believe, respectfully, there could be some errors in it.

DNA polymerase must catalyse the addition of 4 different nucleotides to the growing strand. This means that it cannot directly determine which base to incorporate at a specific point (how would it 'know' which base to incorporate and how it would it change its specificity for different bases). This means that the specificity for which base pair to incorporate is dependent on the template DNA strand.
Correct Watson-Crick base pairing (that is, hydrogen bonding) between the template strand and the nucleotide to be incorporated triggers the closing of the finger domain of DNAP around the primer-template junction and positions the latter in the optimal position for catalysis (with the $\ce{\alpha-PO_4}$ of the incoming nucleotide near the $\ce{3'-OH}$ of the primer for a nucleophilic attack catalysed by two $\ce{Mg^{2+}}$ ions). This is where the conserved tyrosine residue you mentioned comes into play. An incorrectly paired nucleotide will not trigger this conformational change and will not be positioned optimally, thus catalysis is less likely.
Furthermore, the DNA polymerase makes contacts with the minor groove of the primer-template junction through hydrogen bonds. This interaction is not base-specific (all Watson-Crick base pairs have he same pattern of hydrogen-bond acceptors in the minor groove) but only occurs when the correct nucleotide is incorporated, thus stabilising the complex.
Finally, discrimination between ribonucleotides and deoxyribonucleotides is done by steric exclusion of the $\ce{2'-OH}$ by amino acid residues in the binding pocket.
These factors can be thought of as kinetic proofreading as they simply slow down the reaction rate and provide time for an incorrectly paired nucleotide to dissociate. However, they can still be incorporated and many DNA polymerases have a $\ce{3'->5'}$ proofreading exonuclease that can remove incorrectly paired nucleotides. This proofreading is again mediated by interactions between the DNAP and the primer-template junction (ie hydrogen bonding with the minor groove). A weakened interaction due to an incorrectly paired base reduces the affinity between DNA and the catalytic site and increases the affinity between DNA and the proofreading site (because it has a preference for cleaving ssDNA from the 3' end).

This is really helpful and detail. Now I understand!

I would upvote this over my own , good info

High-fidelity DNA polymerases have several safeguards to protect against both making and propagating mistakes while copying DNA.
Such enzymes have a significant binding preference for the correct versus the incorrect nucleoside triphosphate during polymerization.
If an incorrect nucleotide does bind in the polymerase active site, incorporation is slowed due to the sub-optimal architecture of the active site complex. This lag time increases the opportunity for the incorrect nucleotide to dissociate before polymerase progression, thereby allowing the process to start again, with a correct nucleoside triphosphate (1,2).
If an incorrect nucleotide is inserted, proofreading DNA polymerases have an extra line of defense
The perturbation caused by the mispaired bases is detected, and the polymerase moves the 3´ end of the growing DNA chain into a proofreading 3´→5´ exonuclease domain. There, the incorrect nucleotide is removed by the 3´→5´ exonuclease activity, whereupon the chain is moved back into the polymerase domain, where polymerization can continue.
From: New England biolabs:
https://www.neb.com/tools-and-resources/feature-articles/polymerase-fidelity-what-is-it-and-what-does-it-mean-for-your-pcr

Both the sentence can be understood from the below explanation.
In a newly synthesizing DNA strand, the DNA polymerase forms extensive hydrogen bonds with the newly added base everytime a new nucleotide is added. (First sentence) Polymerase also forms bonds with the DNA backbone of phosphate and sugar. (Second sentence)
The first sentence talks of how polymerase will form bonds via the minor groove of the newly synthesized DNA. Second sentence talks about the changing of an amino acid from the DNA polymerase (which is important for forming bonds with DNA backbone). This changing of amino acid will cause error in the nucleotide added (as the Polymerase is not positioned properly which you will understand in the following explaination)
These bonds of polymerase and bases along with the bonds between the DNA backbone and polymerase position the DNA polymerase.
When a newly added nucleotide is correctly base paired, the structure of the paired bases will be such that the bonds formed between polymerase and base will allow DNA polymerase to be positioned for the addition of next new nucleotide.
If a incorrect nucleotide was added the DNA polymerase positions such that it's exonuclease site is at a position to catalyse exonuclease activity.
Thus, the hydrogen bonds between the base and Polymerase is needed for correct positioning of polymerase to either allow the next nucleotide to be added (if correct base was added) or allow exonuclease activity of Polymerase (if an incorrect base was added). This will help in proofreading and thus provide high fidelity.

authors: Михайло Олександрович Іванцов


text:
How does protein denaturation work?
I was wondering how protein denaturation works.

Are there covalent bonds, such as disulfide bridges involved, or is it based purely on non-covalent bonds such as hydrogen bonds? Why is denaturation irreversible in most cases if only non-covalent bonds are involved?
Is it possible to denature protein by rapid changes in electromagnetic field or pressure? (The articles I have read so far mention only stress factors like sudden pH, osmolarity, temperature changes...)
How can I protect a protein against denaturation? e.g. in PCR we use a heat resistant DNA polymerase, so certain amino acid sequences might protect against heat denaturation, but I need reassurance about this.

I investigated the topic too, so here is my answer.
To understand thermodinamic stability of water solved globulins or membrane proteins (all of them proteins hereafter) we have to understand protein folding. Proteins have a 3d structure (composed by their primary, secondary and tertiary structures). The structure of the proteins is constantly changing between the folded and unfolded states. The folded state has a lower free energy while the unfolded state has a higher. Between them there is a free energy barrier which determines the speed of the folding on a specific temperature.
Changing structural on environmental factors can affect these free energies and can shift the equilibrium to the unfolded state. The unfolded protein can suffer irreversible changes (aggregation, disulphide exchange, proteolysis, irreversible subunit dissociation, chemical degradation, etc...), so the denaturation of the protein can be reversible or irreversible.
Note that this is a very simplistic view, I think there are different degrees of unfoldedness, and so different things can happen when the protein is in one of these. For instance by a low degree of unfoldedness misfolding can happen which results a stable, but inactive folded state without coagulation (this can be more or less reversible). By a higher degree of unfoldedness coagulation can happen.
Folding mostly depends on one simple rule: all of the hydrogen bonds have to be satisfied, because a non-satisfied hydrogen bond has a very high energetic cost. The proteins have polar surfaces, which form hydrogen bonds with the water, and one or more apolar center, which have inner hydrogen bonds as backbones. Burial of an unpaired polar amino-acid (e.g. non-satisfied hydrogen bond) is very destabilizing and so it is non-existent in natural working proteins. Other factors, like salt bridges, aromatic-aromatic interactions, disulphide bonds, etc... can affect the stability as well, but hydrogen bonds and hydrophobic interactions are the major factors. The weights of these two major factors is most likely protein dependent (a study suggested 75% and 25%, while another 40% and 60%).
The backbone hydrogen bonds are usually most stable around room temperature, so the lowest free energy and the maximum stability is around 20°C by most proteins and both heating and cooling lowers the stability and can lead to denaturation. High temperatures (>80°C) can cause covalent degradation, and so irreversible denaturation. Pressure has similar effect on the hydrogen bonds and the stability as cold denaturation.
The osmolyte cosolvents like urea or TMAO contribute differently to the free energy of the folded and unfolded states and so shift the equilibrium between them. for example urea can cause denaturation, while TMAO protects the protein from denaturation. I think it is evident that changing pH and saltiness has strong effect on the charges of the amino acid side chains, and so the hydrogen bonds and the stability.
Both ultrasound and pulsed electric field (PEF) can cause denaturation. The effect seems strongly depending on the parameters of ultrasound/PEF and the type of the protein. Interesting that PEF can increase the enzyme activity too. It is hard to find studies about the denaturation mechanisms by these methods.
If we want to increase the protein stability, the method we choose can depend on what we want to protect the protein from. One or more methods from the following list can help to increase the stability:

increase of compactness and better packing (minimalization of surface/volume ratio)
increase of electrostatic interactions (formation of additional ion pairs, e.g. more glutamic acid)
additional hydrogen bonds
additional disulphide bridges
increasing hydrophobic interactions (greater proportion of buried hydrophobic residues)
change protein microenvironment (use osmolytes, change pH, saltiness)
glycosylate the protein surface
decrease chain length
change surface amino-acids (the effect can be completely unpredictable, but there are surface residue patterns with known effect on stability; add more ionisable amino acids to the surface; bury hydrophobic residues; etc...)
protein fixation can change the stability as well

References:

Thermodynamic stability of a protein that unfolds and refolds rapidly,
  reversibly, cooperatively, and with a simple, two-state mechanism. The
  easiest proteins in which to study folding and stability are those
  that exhibit this sort of rapid reversibility. Both experimental
  design and also theoretical treatment of data are simplified by
  reversible systems. Thus, it is no surprise that most of the
  literature reports about stability discuss this type of reversible
  system. The stability of the protein is simply the difference in Gibbs
  free energy, dG, between the folded and the unfolded states. The only
  factors affecting stability are the relative free energies of the
  folded (Gf) and the unfolded (Gu) states. The larger and more positive
  Gu, the more stable is the protein to denaturation.
If a protein unfolds reversibly it may be fully unfolded and inactive
  at high temperatures, but once it cools to room temperature, it will
  refold and fully recover activity. In the case of irreversible or
  slowly unfolding proteins, it is kinetic stability or the rate of
  unfolding that is important. A protein that is kinetically stable will
  unfold more slowly than a kinetically unstable protein. In a
  kinetically stable protein, a large free energy barrier to unfolding
  is required and the factors affecting stability are the relative free
  energies of the folded (Gf) and the transition state (Gts) for the
  first committed step on the unfolding pathway. Irreversible loss of
  protein folded structure is represented by: F <-> U -> I, where I is
  inactive due to aggregation, disulphide exchange, proteolysis,
  irreversible subunit dissociation, chemical degradation, etc...

1996 - The Source of Stability in Proteins
2009 - Charge–charge interactions in the denatured state influence the folding kinetics of ribonuclease Sa
2006 - Why Are Proteins Charged? Networks of Charge–Charge Interactions in Proteins Measured by Charge Ladders and Capillary Electrophoresis

Evidence from proteins and peptides supports the conclusion that
  intrapeptide hydrogen bonds stabilize the folded form of proteins.
  Paradoxically, evidence from small molecules supports the opposite
  conclusion, that intrapeptide hydrogen bonds are less favorable than
  peptide–water hydrogen bonds. A related issue—often lost in this
  debate about comparing peptide–peptide to peptide– water hydrogen
  bonds—involves the energetic cost of an unsatisfied hydrogen bond.
  Here, experiment and theory agree that breaking a hydrogen bond costs
  between 5 and 6 kcal/mol. Accordingly, the likelihood of finding an
  unsatisfied hydrogen bond in a protein is insignificant. This
  realization establishes a powerful rule for evaluating protein
  conformations.
In their description of the alpha-helix, Pauling et al. (1951)
  asserted that the energy of the peptide N–H• • •O=C hydrogen bond was
  of order -8 kcal/mol, and that “such instability would result from the
  failure to form these bonds that we may be confident of their
  presence.” Pauling’s earlier estimate of the total protein hydrogen
  bond energy was -5 kcal/mol (Mirsky and Pauling 1936). From solution
  studies of urea dimers, Schellman estimated that an intrapeptide
  hydrogen bond would be enthalpically favored over a peptide–water
  hydrogen bond by ~1.5 kcal/mol (Schellman 1955). These and similar
  early studies led to the conclusion that the peptide hydrogen bond is
  a significant factor in stabilizing protein conformations.
This view was to change dramatically following a famous review by
  Kauzmann (1959), who invoked the thermodynamics of small model
  compounds to argue that stabilization of the folded state of a protein
  is due almost exclusively to the hydrophobic effect. Soon after
  Kauzmann’s proposal, Klotz and Franzen (1962) determined that the
  enthalpy of the interamide hydrogen bond of N-methyl acetamide in
  water was zero, and concluded that “the intrinsic stability of
  interpeptide hydrogen bonds in aqueous solution is small.” Similarly,
  hydrogen bonding involving another small molecule,
  epsilon-caprolactam, in dilute solution was shown to be negligible
  (Susi and Ard 1969). Kauzmann’s proposal, bolstered by these later
  studies, led to the widely held view that the hydrophobic effect makes
  the major energetic contribution to protein stability, with hydrogen
  bonds contributing little, or perhaps even opposing, the folding
  process. See Baldwin (2003) for a recent discussion of these issues.
Protein hydrogen bonds are ubiquitous, directional, and largely local,
  partitioning the polypeptide chain into alpha- and 3_10-helices,
  beta-sheet, and beta-turns. Together, these hydrogen-bonded backbone
  structures account for at least 75% of the conformation, on average,
  with remaining residues participating in both additional
  intramolecular hydrogen bonding and hydrogen bonding to water.
  Unsatisfied backbone polar groups are energetically expensive, to the
  degree that they almost never occur.
Force measurements between surfaces functionalized with lipids having
  hydrogen bonding headgroups (NTA, A, T, and MeT lipids) lead to a
  reproducible value of the energy of a single hydrogen bond in pure
  water: ~0.5 kcal/mol. It shows that it is energetically more favorable
  for the headgroups to make hydrogen bonds with each other than to make
  hydrogen bonds with water molecules. This is coherent with past
  studies made on proteins stability, which showed that intramolecular
  hydrogen bonds in a folded protein are energetically more favorable
  than bonds with water molecules in an unfolded protein with an average
  stabilization of ~1 kcal/mol per intramolecular hydrogen bond.

1996 - Forces contributing to the conformational stability of proteins.
2005 - Do all backbone polar groups in proteins form hydrogen bonds?
2011 - Backbone-Driven Collapse in Unfolded Protein Chains
2006 - Hydrophobic collapse in (in silico) protein folding
2002 - Thermodynamic Consequences of Burial of Polar and Non-polar Amino Acid Residues in the Protein Interior
2003 - Thermodynamics of Heat Activation of Single Capsaicin Ion Channels VR1
2003 - Temperature Range of Thermodynamic Stability for the Native State of Reversible Two-State Proteins
2009 - Protein Cold Denaturation as Seen From the Solvent
2010 - Construction of Peptoids with All Trans-Amide Backbones and Peptoid Reverse Turns via the Tactical Incorporation of N-Aryl Side Chains Capable of Hydrogen Bonding
2002 - Energy of Hydrogen Bonds Probed by the Adhesion of Functionalized Lipid Layers
2012 - How, when and why proteins collapse: the relation to folding
2011 - Inversion of the Balance between Hydrophobic and Hydrogen Bonding Interactions in Protein Folding and Aggregation
2011 - Membrane protein folding: how important are hydrogen bonds?

The main determinant of cold denaturation tendency is likely the
  stability decrease of backbone hydrogen bonds at low temperatures,
  which in turn is affected by the packing manner of the hydrophobic
  core cluster
Using a newly developed pressure cell, we have now mapped pressure-
  and temperature-dependent changes of 31 hydrogen bonds in ubiquitin by
  measuring HBCs with very high precision. Short-range hydrogen bonds
  are only moderately perturbed, but many hydrogen bonds with large
  sequence separations (high contact order) show greater changes. In
  contrast, other high-contact-order hydrogen bonds remain virtually
  unaffected.
We study the stability of globular proteins as a function of
  temperature and pressure through NPT simulations of a coarse-grained
  model. We reproduce the elliptical stability of proteins and highlight
  a unifying microscopic mechanism for pressure and cold denaturations.
  The mechanism involves the solvation of nonpolar residues with a thin
  layer of water. These solvated states have lower volume and lower
  hydrogen-bond energy compared to other conformations of nonpolar
  solutes. Hence, these solvated states are favorable at high pressure
  and low temperature, and they facilitate protein unfolding under these
  thermodynamical conditions.
We further find that it is the changes in hydrophobic hydration with
  decreasing temperature that drive cold unfolding and that the overall
  process is enthalpically driven, whereas heat denaturation is
  entropically driven.
As a consequence of a weaker penetration upon pressurizing, it was
  found that the pressure-denatured state was partially unfolded
  compared with the heat-denatured state. The mechanism of pressure
  denaturation was related to the disruption of the hydrogen-bond
  network of water onto a set of clusters characterized by strengthened
  O – H interactions, inducing a hardening of protein dynamics. The
  mechanism is opposite to that observed upon heating, i.e., the
  softening of the hydrogen bond network of water inducing a softer
  protein dynamics.
We can conclude that the main driving force of protein denaturation at
  high pressures is the decrease of the hydrophobic effect as a
  consequence of the changes in water structure, without contradicting
  any of the current theories on the hydrophobic effect.
For the pressure denaturation the weakening of the hydrophobic
  interaction between the bulky side chains is found to be crucial at
  lower temperatures, leading to an apparent destabilization of the
  folded backbone structure at elevated pressures.

2013 - Molecular dynamics simulation indicating cold denaturation of beta-hairpins.
2012 - Cold-Induced Changes in the Protein Ubiquitin
2008 - Microscopic Mechanism for Cold Denaturation
2009 - Hydrophobicity at low temperatures and cold denaturation of a protein
2012 Key stabilizing elements of protein structure identified through pressure and temperature perturbation of its hydrogen bond network
2012 - Unifying Microscopic Mechanism for Pressure and Cold Denaturations of Proteins
2012 - Role of Hydrophobic Hydration in Protein Stability: A 3D Water-Explicit Protein Model Exhibiting Cold and Heat Denaturation
2011 - Molecular mechanisms of the anomalous thermal aggregation of green fluorescent protein
2011 - Analysis of the Mechanism of Lysozyme Pressure Denaturation from Raman Spectroscopy Investigations, and Comparison with Thermal Denaturation
2008 - Cold- and Pressure-Induced Dissociation of Protein Aggregates and Amyloid Fibrils
2009 - The Behavior of the Hydrophobic Effect under Pressure and Protein Denaturation
2004 - Reversible Temperature and Pressure Denaturation of a Protein Fragment: A Replica Exchange Molecular Dynamics Simulation Study

It is found that the energetics involving backbone hydrogen bonding
  controls these shifts in protein stability almost entirely, with
  osmolyte cosolvents simply dialing between solvent-backbone versus
  backbone-backbone hydrogen bonds, as a function of solvent quality.

2008 - Structure and Energetics of the Hydrogen-Bonded Backbone in Protein Folding
2008 - Urea, but not guanidinium, destabilizes proteins by forming hydrogen bonds to the peptide group
2011 - Backbone and Side-Chain Contributions in Protein Denaturation by Urea
2009 - On the mechanism of SDS-induced protein denaturation
1995 - Hydrogen Bonds and the pH dependence of Ovomucoid Third Domain Stability
2004 - Effects of Chaotropic and Kosmotropic Cosolvents on the Pressure-Induced Unfolding and Denaturation of Proteins:? An FT-IR Study on Staphylococcal Nuclease
2002 - The hydration structure of guanidinium and thiocyanate ions: Implications for protein stability in aqueous solution

Overall, the sonication process had little effect on the structure of
  proteins in WPC solutions which is critical to preserving functional
  properties during the ultrasonic processing of whey protein based
  dairy products.
The data presented here suggest that among proteins of fibrinolytic
  systems, the fibrinogen is one of the most sensitive proteins to the
  action of ultrasound. It has been shown in vitro that ultrasound
  induced fibrinogen aggregates formation, characterized by the loss of
  clotting ability and a greater rate of plasminolysis than native
  fibrinogen in different model systems and under different mode of
  ultrasound treatment.

2011 - Effects of ultrasound on the thermal and structural characteristics of proteins in reconstituted whey protein concentrate
2011 - Effects of low frequency ultrasound on some properties of fibrinogen and its plasminolysis

The results obtained with the different experimental protocols
  indicate, however, that the conformational equilibrium of GrpE is
  insensitive to electromagnetic fields in the tested range of frequency
  and field strength.
Effects of pulsed electric fields (PEF) treatment (0–547 µs and 0–40
  kV/cm) on physicochemical properties of soybean protein isolates (SPI)
  were studied. Solubility, surface free sulfhydryls (SHF) and
  hydrophobicity of SPI dispersions (20 mg/ml) increased with the
  increment of the PEF strength and treatment time at constant pulse
  width 2 µs, pulse frequency 500 pulse per second (pps) and sample flow
  rate (1 ml/s). When the PEF strength and treatment time were above 30
  kV/cm and 288 µs, solubility, surface SHF, and hydrophobicity of SPI
  decreased due to denaturation and aggregation of SPI by hydrophobic
  interactions and disulfide bonds. Size-exclusion chromatography and
  laser light scattering analyses demonstrated further that stronger PEF
  treatment-induced dissociation, denaturation and reaggregation of SPI.
  Circular dichroism analysis showed that PEF treatment did not produce
  significant secondary structure changes of SPI.
A compact and low cost bench-top, pulsed electric field treatment
  system was designed and developed. The unit consisted of a
  high-voltage pulse generator (? 30 kV) and a treatment chamber with ?
  148 ml capacity. Over the set-up voltage range of 4–26 kV, 30 pulses
  (with instant charge reversal) were applied to eight different enzyme
  solutions using a 0.3-cm electrode distance, a 13–87 kV/cm field,
  0.5-Hz pulse frequency, 2-µs pulse width and 20 °C process temperature. For some enzymes, activities were reduced after the pulse
  treatments: lipase, glucose oxidase and heat-stable ?-amylase
  exhibited a vast reduction of 70–85%; peroxidase and polyphenol
  oxidase showed a moderate 30–40% reduction whereas alkaline
  phosphatase only displayed a slight 5% reduction under the conditions
  employed. On the other hand, the enzyme activities of lysozyme and
  pepsin were increased under a certain range of voltages. Electric
  pulse profile (instant charge reversal) played a very important role
  in reducing the activities of various enzymes.
Effects of high-voltage pulsed electric field (PEF) on native or
  thermal denatured enzyme activities were studied. When PEF was applied
  to various native enzymes, 105–120% of initial enzyme activities were
  observed after PEF treatment. It was suggested that an activation of
  enzyme would be possible by PEF treatment. We attempted a refolding of
  thermal denatured enzyme by using PEF. When PEF was applied to
  denatured peroxidase, enzyme refolding was accelerated in PEF and 60%
  of initial activity was observed after 12 kV/cm and 30 s of PEF
  treatment although spontaneous refolding of this enzyme resulted in
  40% of initial activity. On the other hand, when PEF was applied to
  thermal denatured lactate dehydrogenase (LDH), further PEF-induced
  inactivation was observed. It was suggested that the influence of PEF
  is dependent on the type of enzyme.

2014 - Real-time assessment of possible electromagnetic-field-induced changes in protein conformation and thermal stability
2007 - Effects of pulsed electric fields on physicochemical properties of soybean protein isolates
1997 - Effects of high field electric pulses on the activity of selected enzymes
2007 - Influence of pulsed electric field on various enzyme activities

In halophiles, protein stability and function are maintained by
  increased ion binding and glutamic acid content, both allowing the
  protein inventory to compete for water at high salt. Acidophiles and
  alkalophiles show neutral intracellular pH; proteins facing the
  outside extremes of pH possess anomalously high contents in ionizable
  amino acids.
These facts suggest that globular proteins should be maximally stable
  around room temperature. Twenty-six of these are unique, and 20 of the
  26 are maximally stable around room temperature irrespective of their
  structural properties, the melting temperature, or the living
  temperatures of their source organisms. Their average temperature of
  maximal stability is 293 ± 8 K (20 ± 8 °C).   The average energetic
  contribution of the individual amino acids toward protein stability
  decreases with an increase in protein size.
Analysed in terms of their effect on the protein structure, the ways
  in which thermophilic organisms obtain relative stabilization of their
  proteins can be classified as follows:

increase of compactness and better packing
increase of electrostatic interactions
additional hydrogen bonds
additional disulphide bridges
increasing hydrophobic interactions
protein microenvironment
glycosylation

The rational modification of protein stability is an important goal of
  protein design. Protein surface electrostatic interactions are not
  evolutionarily optimized for stability and are an attractive target
  for the rational redesign of proteins. We show that surface charge
  mutants can exert stabilizing effects in distinct and unanticipated
  ways, including ones that are not predicted by existing methods, even
  when only solvent-exposed sites are targeted. Individual mutation of
  three solvent-exposed lysines in the villin headpiece subdomain
  significantly stabilizes the protein, but the mechanism of
  stabilization is very different in each case. One mutation
  destabilizes native-state electrostatic interactions but has a larger
  destabilizing effect on the denatured state, a second removes the
  desolvation penalty paid by the charged residue, whereas the third
  introduces unanticipated native-state interactions but does not alter
  electrostatics. Our results show that even seemingly intuitive
  mutations can exert their effects through unforeseen and complex
  interactions.
These results suggest that surface charge-charge interactions are
  important for protein stability and that rational optimization of
  charge-charge interactions on the protein surface can be a viable
  strategy for enhancing protein stability.
We have discovered a novel property of single-walled carbon nanotubes
  (SWNTs)their ability to stabilize proteins at elevated temperatures
  and in organic solvents to a greater extent than conventional flat
  supports. Experimental results and theoretical analysis reveal that
  the stabilization results from the curvature of SWNTs, which
  suppresses unfavorable protein-protein lateral interactions. Our
  results also indicate that the phenomenon is not unique to SWNTs but
  could be extended to other nanomaterials. The protein-nanotube
  conjugates represent a new generation of active and stable catalytic
  materials with potential use in biosensors, diagnostics, and bioactive
  films and other hybrid materials that integrate biotic and abiotic
  components.
The main chain to side chain salt bridge between the N-terminus and
  Glu 14 was, however, found to stabilize PFRD-XC4 by 1.5 kcal mol-1.
  The entropic cost of making a surface salt bridge involving the
  protein's backbone is reduced, since the backbone has already been
  immobilized upon protein folding.

2000 - Stability and stabilization of globular proteins in solution
2002 - Maximal Stabilities of Reversible Two-State Proteins
2014 - Enzyme Thermostabilization: the State of the Art
2012 - Rational modification of protein stability by targeting surface sites leads to complicated results
2012 - Disulfide Bonding in Protein Biophysics
2011 - Methanol Strengthens Hydrogen Bonds and Weakens Hydrophobic Interactions in Proteins – A Combined Molecular Dynamics and NMR study
2011 - Contribution of Hydrophobic Interactions to Protein Stability
1997 - Protein thermal stability, hydrogen bonds, and ion pairs
2005 - Thermal stability of proteins.
2004 - Protein structure, stability and solubility in water and other solvents.
2000 - Rational Modification of Protein Stability by the Mutation of Charged Surface Residues
2006 - Protein Stability and Surface Electrostatics:? A Charged Relationship
2003 - Contribution of Surface Salt Bridges to Protein Stability: Guidelines for Protein Engineering
2000 - Influence of Sucrose on the Thermal Denaturation, Gelation, and Emulsion Stabilization of Whey Proteins
2006 - Increasing Protein Stability through Control of the Nanoscale Environment
2000 - Contribution of Surface Salt Bridges to Protein Stability
2003 - Elastic coupling of integral membrane protein stability to lipid bilayer forces

This is an impressive list of references, but how many of these are available to the general public outside an university?

@Chris I think about 5-10% (bigger libraries usually have access to scientific articles as well). I too don't have access to the full text, just the abstracts in most of the articles, but it is usually enough to add one or more important sentences to my post. It is pretty hard to collect the information this way (as you can see I used around 30 references for a single page). Reading books is not enough either if you want to be up to date... :S

Longest Biology.SE answer! Good job!

@TanMath Actually 5/10 is mine answer from your list. Does not matter. I just like using long quotes and lots of references.

Really the question how does protein folding work?  But let me answer your questions...
1) Very few proteins have disulfide bonds (usually secreted proteins) or really any covalent bond stabilizing the amino acid chain beyond the bonds that make up the polypeptide itself.  Denaturation is only reversible in relatively few cases in fact.  A few proteins, usually very small ones can be nursed back into a native folded state from an unfolded one, and then only a percentage of the sample will reattain the folded state.
2) Sure.  In fact pressure changes the hydrogen bonded structure of the water and also therefore the thermodynamics of protein structure and has been used to study protein folding. Generally the electomagnetic field does not affect the state of the protein fold.  I cite the fact that many many proteins have been studied via nuclear magnetic resonance, in which the proteins have been inserted into some of the most powerful magnets that can fit into a reasonably sized room.   That is not to say that the protein function might not be affected by such a field.  I'm sure by the time the field is large enough to ionize water or the peptide change you would see something... so you can always push things too the breaking point.
3) Many proteins from thermophilic organisms are more resistant to denaturation and companies actually engineer proteins to be resistant to all sorts of outrageous conditions and still be folded and functional.  Laundry detergent is full of crystallized enzymes that will sit happily in detergent for a long time.  I don't even know if these products have a shelf life.
Overall proteins are vulnerable to denaturation for a good reason- the cell degrades them when it doesn't need their function and can recycle them for their component amino acids. If they were all this robust the cell would starve to death quickly.  If there is a biological role to a protein that is denatured and then refolds itself it is only for extremely rare situations.  Proteins for the most part don't fall apart once they are folded and if they do, they are done.
Some possible exceptions: some antibiotic peptides which fold into pores that kill their targets and the amyloid plaque which takes on a different fold when in the brain which is associated with - but may not cause - Alzheimer's.

Some RNAse enzymes are capable of renaturing, makes it annoying to get rid of them.

"Very few proteins have disulfide bonds or really any covalent bond stabilizing the amino acid chain " - can you add some reference about this? e.g. insuline, egg yolk proteins, gluten, hair proteins contain disulfide bonds. I guess every protein with multiple cys can and maybe does have that, so I don't think it is rare. This part of question was about: do primary bonds form by denaturation or not? If not, then why is it irreversible? I don't think you can explain that only with secondary structural changes. e.g. by egg yolk it becomes white, so I guess there is protein aggregation involved.

"Generally the electomagnetic field does not affect the state of the protein fold. " I hardly believe that, afaik based on the pH amino acids can have negative or positive charges, so the EM field can pull one end of the protein chain and repel the other end, but I think most of the proteins are not affected, because there is an even distribution of +/- charged amino acids along the chain. But that's just my theory. I can accept this part of your answer.

"companies actually engineer proteins to be resistant to all sorts of outrageous conditions" - That part of the question was about how to engineer such proteins in theory. I suspected, that the technology already exists.

added references. i misunderstood what you meant by electromagnetic field.  the specific arrangement of charges can be quite important to a protein... usually this is seen as direct couloumbic repulsion or complementarity.  most of the long range electrical fields from protein charges affect how proteins interact with each other.  a harder question to answer definitively.

i could go on about protein engineering. heres an example refrerence http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2242557/

+1, I think this is a good answer, but it was too basic for me. Btw. I hate to accept my own answer. :S

Are you taking in an in vitro context for preventing protein denaturation after protein isolation from for example E. coli or are you more worried about proteins in the context of the whole cell?
I'm no expert in the protein folding/conformation studies but from laboratory based prospective if you want to achieve denaturation for experimental purposes, you treat your samples with SDS and high heat (~ 100 oC for 10 min) to eliminate H-bonds and to get rid of disulphide bonds, you use a reducing agent such as beta-ME or DTT, which is commonly found in molecules such as Ab or cell surface receptors such as EGFR so obviously for western-blot experiments which you need your disulphide bridges to be preserved you do not use reducing agents but you still heat your samples and treat with SDS to get rid of the hydrogen bonds and linearalise your protein.
Based on this study, which used BSA and β-lactoglobulin, denaturation caused by high pressure is similar to that caused by the cleavage of hydrogen bonds with urea or guanidine hydrochloride so, yes, rapid changes in environmental conditions can have denaturing effects similar to chemical based agents.
If you are trying to prevent protein denaturation in a whole cell, then you need to treat them with cryo-preservation media containing usually 10% DMSO such as this. If you are working just with proteins alone, the best method is to work with your samples freshly prepared (lysed etc) and when isolating your proteins for future used, snap freeze them in liquid nitrogen and store at -80 oC. If your proteins are attached to beads such as GST-tagged proteins, then store your beads in a buffer congaing glycerol and put at -20 oC. I use 50% glycerol (v/v) and it works well for me! If however this response does not answer your particular question or concern, please edit and elaborate on what exactly you are worried about in your line of work and I shall modify my response accordingly. Hope this helped in some way!

Thanks you answer it was interesting. +1 I am not worried about anything, I just want to learn more about the details of how denaturation works. I want to refresh my memory about bioengineering, I skipped the last 3 years, since I learned software engineering. Instead of relearning the whole stuff I thought it would be better to ask more detailed questions about one or more topics... I meant in vitro proteins, for example egg white, etc..., and it was a theoretical question, but it was good to see some laboratory practices again. Just be careful with mercaptoethanol, it can cause cancer! :-)


text:
Why is gynodioecy common and androdioecy rare?
Gynodioecy is when a population features individuals that produce both male and female gametes and individuals that produce just female gametes. Androdioecy is when a population features individuals that produce both male and female gametes and individuals that produce just male gametes. The former is "not uncommon" and the latter is "virtually unknown."
Charlesworth 1991 states that this is common because cosexual populations would normally evolve a male sterile mutation first, causing gynodioecy, and then female sterility mutation(s) will build up leading to dioecy.
Why should it be so much more common for male sterility mutations to evolve first?
(I think the answer lies within articles cited in the above paper, Charlesworth & Charlesworth 1979 Proc R Soc B, and 1987 Evolution which I'll try to read this weekend, if it is I'll post a self-answer but in the mean time...).

I think the short answer is along the lines of: Because ovules represent the limiting factor while there are plenty of pollen grains. Males have a hard time surviving in a androdoiceous population while female might be able to survive in a gynodioceous if it spares enough energy (by not producing any pollen grains) to create ovules. One advantage for a female of not being hermaphrodite compare to other individuals in the population is that it won't lose ovules to produce inbred offspring by selfing.

That's what I had interpreted it as


text:
Alternatives to trypsin for cell detachment?
I have ran out of trypsin and need to passage my cells (immortalized chondrocytes, C28/I2) today or tomorrow. I have been out of town and forgot to order more trypsin.
I was wondering if there are any alternative, "homemade" ways to detach cells. Googling this results in a lot of commercially available detachment solutions. I may or may not have a cell scraper available, but I have never tried it. I have hyaluronidase and I was thinking that might work.

Do you use flasks or plates? And how strong do your cells attach?

My cells are in a T75 flask. They attach moderately strongly.

You could try to knock them off the plastic. To do so, you take the flask with medium in one hand and knock it gently 4 or 5 times against the palm of the other hand. The cells should come off then and can be centrifuged down to separate from the medium. Alternatively you could replace the medium first and then knock them off.

It is simple - and more gentle (even though the handling seems a bit rough) for some cell lines than trypsination.

EDTA can work for some cells. I forget what concentration to use.

Most chealating agents will work. Important to rinse off your cells in Ca and Mg free buffer

Lets make this a proper answer: There are a few possibilities to detach adherent cells without Trypsin.
PBS/EDTA: Integrins and Cadherins play an important role in the adhesion and also in maintaining cell-cell contacts. These function of these proteins depends on Calcium2+ ions, so EDTA will chelate them and make them unavailable. First remove the culture media, rinse the cells with warm PBS to get rid of most ions and then incubate them for 5 min (the time needs to be optimized for each cells line) in PBS with 10mM EDTA in it. The cells either detach themself, can be washed of the surface with a pipette or can be gently knocked off the surface (this works only in tightly closing flasks). Centrifuge the cells shortly to pellet them and get rid of the PBS/EDTA and take them up in fresh medium.
Wash cells of the surface: Some cell lines are so loosely attached (which makes working with them pretty hard), that they can simply be washed off the surface. To do so, use the pipetboy to get some medium and then pump it out again against the cell layer. You can see the cells disappearing from the surface and the medium (or the PBS) get more cloudy.
Knock off cells: To do so, you take the flask with medium in one hand and knock it gently 4 or 5 times against the palm of the other hand. The cells should come off then and can be centrifuged down to separate from the medium. Alternatively you could replace the medium first and then knock them off. This method is not recommended for very sensitive cell lines.
Besides these methods, there are a number of commercial products available which claim to be better than the classical Trypsin/EDTA method and to be less harmful for the cells. Since I haven't tested them, I cannot say anything about them. In my experience Trypsin and the methods described above work perfectly.

Addition to what Chris already said:
Papain can be used for cells sensitive to trypsin (neurons etc)
Collagenase  can be used for certain cells where trypsin is ineffective (Accutase is a commercially available enzyme mix(?) which has collagenase activity)
Hyaluronidase - I don't know where it is specifically preferred but it is used.
Pronase and Proteinase K - Can be used to disrupt tough tissues. I have used them mostly to dechorionate zebrafish embryos.
See this documentation by Sigma-Aldrich on cell disruption enzymes.


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

Can you define some of those acronyms? I'm assuming ECM is extracellular matrix, and HA is hyalauronic acid, but I could be wrong, and I could have spelled hyalauronic wrong.

Yes, sorry---ECM = extracellular matrix, HA = hyaluronic acid.  I know that a typical hematoxylin and eosin stain (H & E) will pick up things that are negatively charged, such as HA, but how can you fix cells without disrupting the ECM?  Also, I was wondering if methods exist to analyze cell ECM production via fluorescence or some other method that utilizes a probe that I could observe with a microscope.

Interesting question. Afaik ECM is much more than just HA, it contains chondoitin and other glucoseamine related stuff as well. Some of them is capable to regulate immune reaction, for example chondroitin-sulfate can reduce TNFa production and so inflammation by arthritis.

http://www.naturebiotech.com.tw/Fluorescent%20ECM%20Proteins.pdf
I guess this study uses the same stuff: http://figshare.com/articles/Degradation_of_fluorescent_ECM_networks_by_SPARC/404676 it is probably possible, but I never worked with ECM.

There have got to be some antibodies against ECM components you could use for immunohistochemical labeling.

Different components of the ECM can be stained differently but since you asked about hyaluronic acid (HA) I'll limit my answer to its staining.
See this paper. They use Hyaluran Binding Protein (HABP) as a specific probe for HA.

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

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

The book "Basic Histology" by Junqueira and Carneiro acknowledge the problem in histologic fixation of ground substance. They recommend freeze drying in liquid nitrogen and  then removing water by high vacuum at a temperature of -30 celcius, which will cause sublimation (ice-->vapor). Then fixing the sample with a nonpolar solvent. Afterwards you can use stains like PAS technic.
I've never done this, I'm just copying from the book. If you already happen to have liquid nitrogen, high vacuum, and PAS in your lab this might be cheaper than HABP.


text:
Nystagmus drug FDA approval?
Congenital Nystagmus is an eye focusing disorder. It happens in manuals. Wikipedia lists several treatments on its page. Are any of those FDA approved for human use of that disease.

drugs found to be effective against nystagmus in some patients include memantine, levetiracetam, 3,4-diaminopyridine, 4-aminopyridine, and acetazolamide.
  -wiki

googling for the drug name will tell you if it's available. Based on my 4 seconds of research, the first two are.

@MattDMo no sir i think you're mistaken. would you share your keywords so that i can examine the results and validate that nystagmus is an approved condition of treatment.

the links i found said otherwise: Curbside Consultation in Neuro-ophthalmology: 49 Clinical Questions

The mainstay of therapy is pharmacologic and several good options exist for [acquired pendular nystagmus] treatment. Gabapentin has a very tolerable side effect profile a large dosing range and its beneficial effects in suppressing oscillopsia and dampening the nystagmus waveform in APN have been demonstrated in a double-blind controlled trial. (non FDA approved use)

"Available" is different from "FDA approved for this use." Memantine (Namenda) and Levetiracetam (Keppra) as well as gabapentin (Neurontin) are most certainly available to be prescribed for whatever by any doctor, but I doubt any of them is approved for nystagmus. (I don't know for sure, just pointing out this discrepancy in usage.)


text:
About the plight of Elephants and efforts to conserve them?
Poachers are only after the ivory horns right? I read this story from the New York Times ( I think) of saving a Rhinocerous by some Park Rangers and a Vet. ( forgive spelling) ; they tranquilized the Rhino and took its horn off so it wouldn't be killed. I know Rhinos need their horns so maybe a hard plastic 'prosthesis' could be put in its place. Maybe the 'prosthesis' could be colored yellow or have some markings on it so any poacher would know it's fake. Of course this could all be done for the elephant too.
Could this be a feasible way to save Elephants or Rhinos??

YOU mean their tusks right? And the Rhino horns can be so replaced also. But the non-valuable replacements would have to be marked or visibly different from 'regular' horns or tusks.

I don't think this is really answerable one way or the other.  Poachers may not look carefully enough to see what they are aiming at, or worse, the yellow horn might attract more predators.  Failing that anyone's actually studied this issue, the answers are just going to be a matter of opinion.

Rhinos and elephants don't really suffer badly from predation, there's not much that will try to take one down, so the colour wouldn't matter that much - the main issues are poaching and habitat loss.

Dehorning of rhinos has been tried with limited success. Poachers have killed dehorned rhinos anyway, either out of spite or to avoid tracking worthless prey in the future. There is the problem of anesthesia (always a risk) and the fact that rhino horns are usually not destroyed but saved in the event of decriminalization. But at least horn grows back.
Considering the strength of horn and ivory, and the force applied in their use, plastic would not be of much use to them (especially elephants with long tusks).

They are used for digging for water, salt, and roots; debarking or marking trees; and for moving trees and branches when clearing a path. When fighting, they are used to attack and defend, and to protect the trunk. - Wikipedia

To detusk elephants would be akin to declawing a lion, though much more dangerous and painful. Though this might help prevent poaching, the future of these animals lies in prevention.

So is doing nothing an option? You admit de-horning might prevent poaching , using ANESTHESIA to remove tusks.If not then to remove a tusk why not use a harmless dye to make it look ugly and not marketable.

If de-horning is painful of course forget about it , but dying the horn is still an option. Forgive my impudence , I just get tired of most of my suggestions being shot down.

I apologize again. How was I belligerent ,  I just capitalized the word anesthesia; and people have talked about removing tusks for a while and I never heard about the ineffectiveness of anethesia so I just thought I was being talked down to again.

One could also save Tigers by spraying their coat with harmless indellible ink that makes any market value poor to poachers.

In todays Globe and Mail (I bought this paper in Ontario , Canada ) there is an article  with a picture of Dr. Marius Kruger , in Kruger National Park trying to move a Rhino out of a high risk area. Trying to move these Rhinos seems like a lot of effort. Maybe just using an indellible dye or some kind of harmless dye that ruins the 'medicinal' quality of the horn might help.

Is there a harmless dye or some substance that could be 'absorbed' by the Rhino horns that would make its medicinal value worthless?

@user128932 - none of the biological dyes that I can think of would penetrate the outer layer of horn, sorry. Eventually they would wear off as well, I think, from friction.

What about injecting a dye further in?

You can't inject rhino horn. You might be able to drill into it, but that might damage the pulp or open it to infection, and there's always the risk of anesthesia. But it's good to see someone working on a way to save rhinos. Keep thinking 'outside the box'! :-)


text:
Regarding benign tumors and what 'stops' them
Benign tumors can grow to dangerous size yet are they capable of metastisizing ; if not what stops this? Also with a benign tumor if you call its cells 'near' its edges its tumor 'cell wall' I was wondering if the cells in its Tumor Cell Wall still have apoptosis mechanisms in them that function?

If tumors metastasize, they are not benign.

Afaik they still have apoptosis, but they slowly develop a resistance to signals which can trigger it. That's why they need stronger signals to stop proliferating than normal cells .

How do benign tumors develop a resistance to signals that can trigger apoptosis? If a benign tumor has stopped growing would this mean it has some active apoptosis mechanisms?


text:
Are there organisms that have incorporated plastic into their lives?
Are there organisms that have incorporated (manmade) plastic into their lives in any way? Either in their diet, or as a part of their body?

What do you mean by "plastic"? Manmade, oilbased plastics?

@Chris Yes, Manmade plastic.

It's not appropriate as an answer given the 'manmade' specification, but I have to mention the bee genus Colletes ('polyster bees') here, since they actually make their own plastic: http://www.scientificamerican.com/article/from-pollen-to-polyester/ (and http://opus.bath.ac.uk/31888/). Thanks to @george-law for drawing my attention to these in his answer here: http://biology.stackexchange.com/questions/47898/bee-identification

Biodegradable waste is a type of waste which can be broken down, in a
  reasonable amount of time, into its base compounds by micro-organisms
  and other living things, regardless of what those compounds may be.

from wikipedia

So yes, there are microbes which are capable of biodegradating manmade plastic. It depends on plastic types.
If you meant creating new pathways to biodegradate non-biodegradable plastics, then I don't think so. My opinion that by some of those plastics there are theoretical barriers (e.g. energy barriers or toxic byproducts), and by some of them evolution might create a pathway in time (I don't think in our lifetime, but nothing is impossible).
There are microbes which build plastics to store energy. They are just polymers like starch or cellulose (sugar polymers), with different building stones... Afaik the first biodegradable plastics came from here, but so they were very expensive. Nowadays we don't need microbes in the polymerization process, e.g. we can create polylactic-acid without the presence of microbes.
edit:
I have found an interesting article in the topic.

Now, for the first time, researchers have found detailed evidence that
  bacteria in an animal’s gut can safely biodegrade plastic and
  potentially help reduce the environmental impact of plastic in
  landfill and elsewhere. The animal in question? The humble mealworm –
  which turns out to be not so humble after all.
Researchers led by Stanford University in US and Beihang University in
  China found that the mealworm – the larval form of the darkling beetle
  – can safely subsist on a diet of Styrofoam and other kinds of
  polystyrene, with bacteria in the worm’s gut biodegrading the plastic
  as part of its digestive process. The findings are significant because
  it was previously thought that these substances were non-biodegradable
  – meaning they ended up in landfill (or worse, our oceans, where
  they’d accumulate for decades).

ScienceAlert - Scientists find worms can safely eat the plastic in our garbage

I don't know if this qualifies as "incorporated ... into their lives", but Hermit crabs use all sorts of man-made materials as housing/protection. If you do a google image search on "hermit crab plastic you will see many examples, including plastic waste.
There are also other animals that use random materials that are lying around to construct housing/cases, and I can imagine that e.g. Trichoptera larvae will occationally include pieces of plastic in their cases. At least they will use gold and pearls (when not given an option). However, these are not really examples of species that have adapted specifically to plastic to use it as a resource.

One example: The Satin Bowerbird (Ptilonorhynchus violaceus).
The males of this species build structures out of sticks (suprisingly called bowers) that they decorate with blue items to attract potential mates. Recent research has shown that the males have began incorporating plastics into these structures for courtship.
A google image search can confirm pictures of this. In this study: "Sexual selection drives rapid divergence in Bowerbird display traits"
researchers provided the birds with square plastic tiles, that were ultimately incorporated into bowers.


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What is the mechanism of reflex arcs?
When a reflex arc occurs the signal from the receptor passes straight to the motor neuron instead of being passed onto the brain.
This is a rather simplistic explanation, I was hoping to make it more detailed. How does the body know when a threshold, heat for example, has been crossed and what mechanism is able to activate the reflex?
Also where does this occur, in the receptor or the spine?

Please, see reflex arcs in the books Pocock et al. and Costanzo et al. Review Guyton if necessary. Very well written. Susan coverers only some arches. Would like to see some of your work to answer this question.

Withdrawal reflex
You asked specifically about the withdrawal reflex and the receptors that trigger this. The initiation of the reflex arc is determined at the level of the nociceptors (pain-transducing receptors) in the epidermis. For the most part, these are part of “free” (not encapsulated) nerve endings of sensory fibers. These fibers course within spinal nerves whose cell bodies are located in the dorsal root ganglia adjacent to the spinal cord. There are two types of nociceptive endings:

mechanical: with parent fibers Aδ

transduce severe mechanical deformation

polymodal: with parent C-fiber units

transduce heat, cold, irritant signals

This picture shows free nerve endings in the epidermis. The boxed portion of the big picture is expanded in the bottom right.

The withdrawal reflex initiated by these receptors is mediated by a polysnaptic (multiple neurons) arc. The sensory neuron synapses with interneurons in the spinal cord.1 Some of these use glutamatergic connections to activate appropriate muscle groups mediating withdrawal. Others inhibit the reciprocal muscle groups (reciprocal inhibition) to allow this movement to be unimpeded.
Here is a cartoon diagram showing the spinal components of the reflex arc in a cross-sectional level of the spinal cord. Notice the interneuron between the sensory and motor neurons (although it's not labeled as such here):

Stretch reflex
In order to provide a broader picture of the basic principles involved in spinal reflexes, it's helpful to also mention the stretch reflex. This is perhaps the quintessential reflex arc because it is monosynaptic, exemplified by the patellar tendon reflex. The stretch reflex is fast, with a latency (stimulus–response interval) of about 15–25 ms (contrast the polysynaptic withdrawal reflex with latency ~70-100 ms.)
The stretch is initiated at the Golgi tendon organs. These are found at the junction between muscle and tendon. The (Ib) nerve fiber splays out and intertwines with tendon fiber bundles. The  nerve endings are activated by the tension of muscle contraction (either passive (as when the patellar tendon is tapped), or active (as during voluntary movement). The afferent sensory neurons directly excite homonymous motor neurons  (i.e. motor neurons supplying the same muscles), and inhibit (via interposed “Ia internuncials”) the antagonist muscles.
I have limited the discussion here to the withdrawal reflex you asked about and another basic spinal reflex arc as an illustration of principle. There are many other, mostly more complex reflex arcs that are beyond the scope of this answer, but I highly recommend checking out a neuroanatomy or neurophysiology textbook such as the one I've listed below if you'd like more information.

Note

1. Although the discussion here is limited to the anatomy of the reflex arc, there are additional synapses within the spinal cord that connect with ascending circuits, as described in the section about afferent neurons of spinal nerves in another answer. Some of these tracts end up at the cortex and are the basis for conscious perception. However, note that this process is multisynaptic and takes longer. The beauty of the spinal reflex arc is that it does not require information to travel all the way up to the brain and back down, which would slow down the response considerably. Practically, this means that you will pull your hand away from a hot stove before you have conscious sensory awareness of the burn.

Reference

Apart from linked article and images with sources below, all information is summarized from:

MJ Turlough FitzGerald,  Gregory Gruener, Estomih Mtui. Clinical Neuroanatomy & Neuroscience © 2012, Elsevier Limited.

Image 1 from: http://en.wikipedia.org/wiki/Free_nerve_ending

Image 2 from: http://www.tutorvista.com/content/biology/biology-iv/nervous-coordination/natural-reflex.php

Dear Susan, thank you ever so much to get back to me, this is wonderfully written and informative. So you say that the nociceptors in the epidermis trigger the reflex arc.
How is there response different to stimulating reflex arcs and how is this message passed through the nervous system to the spine so that the message gets sent to the effector, as well as the brain?

@Freeman - I tried to clarify these points in the answer. Let me know if that helps.


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Lateral corticospinal tract and termination
I'm studying the motor pathways of the brain and I'm a bit confused about how the lateral corticospinal tract descends.
From Neuroanatomy: Text and Atlas by Martin, J. H., 4th edition, right before Figure 10-4:

Some of these [terminating] axons descend ipsilaterally; many descend
  contra-laterally and re-cross midline within the gray matter in lamina 10.
  The function of these ipsilateral axons is not well understood.

I understand that the axons cross over at the Pyramidal decussation, but this paragraph is really confusing me. What descent is being referenced here? Is it descending in the spinal chord? Alternatively, is the paragraph implying that some axons don't decussate in the pyramidal decussation?

Can you provide a page number and tell us what edition of Martin you're using?

@Susan Fixed. Unfortunately, I can't give you a page number because I'm using the Kindle edition of the textbook. I tried to give the most accurate reference I could.

The answer ends up being on the next page when discussing the ventral corticospinal tract.

Many ventral corticospinal tract axons have branches that decussate in
  the spinal cord, similar to the re-crossed lateral coticospinal tract
  axons described earlier.

In other words, some axons of the lateral corticospinal tract ignore the pyramidal decussation, join the anterior corticospinal tract (which then synapses bilaterally later at the spinal commissure).


text:
What are the genus and species name of different breeds of dog?
Can you refer me to a good source containing the genus and species name of different breeds of dogs?

Why in "Can any species be bred selectively/engineered to become as diverse looking as dogs?" is link provided to "not scientific" list of dog breeds?

Why in "Can any species be bred selectively/engineered to become as diverse looking as dogs?" is link provided to "not scientific" list of dog breeds?

All the different breeds of dogs - from Irish setters to greyhounds - are all part of the same species, canis lupus familiaris. The common, domesticated dog is actually a subspecies of the grey wolf. The different breeds do have different genetic characteristics (just as humans have, say, different eye or hair colors), but they're a all one and the same. The different names for different breeds are not like the scientific classifications of organisms via domain, kingdom, etc. They're just our choices.

References:

http://www.vetinfo.com/scientific-name-for-dogs.html
https://en.wikipedia.org/wiki/Dog_breed#Description
https://en.wikipedia.org/wiki/Subspecies_of_Canis_lupus
http://www.choosing-a-dog-made-easy.com/dog-types.html

All breeds of dogs are members of the same (sub) species: Canis lupus familiaris. "Breeds" of dogs are not scientific designations but are collections of traits recognized as unique by different breeding organizations. As such, certain breeds are recognized as unique in some organizations do not exist in others (see here for examples).

Ahh, didn't see your answer. Sorry about that.

@HDE226868 Don't be sorry. Multiple answers are encouraged, and improves the quality of the site.


text:
Why do we need red blood cells?
From what I know, the main function of red blood cells (RBCs) is hemoglobin transport. So, why do we need cells packed with hemoglobin: why can't it travel freely in the bloodstream?
My own thoughts were:
1) Having hemoglobin packed into cells means it can be released where it's most needed. For example, when we are exercising, our muscles need more oxygen, so more erythrocytes release their oxygen in the muscle tissue.
2) The diameter of a capillary is much bigger than a single protein molecule's diameter, but comparable to a cell's diameter. So, when cells are traveling through a capillary, all of them are close to its walls. However, when free molecules are traveling through it, some of them are close to the walls, while the others are in the "middle". I figured, those in the "middle" can't exchange oxygen with the surrounding tissues. So, red blood cells make gas exchange more effective.
Do you think any of this makes sense? Why in reality do RBCs exist?
Any insight or book recommendations would be very appreciated:)

#1 doesn't make sense. Whether in cells or not in cells, O2 binding to Hg depends on O2 concentration in solution. #2 doesn't make sense, but you are close to the interesting idea "having objects with diameter close to the blood vessel has unique and desirable hydrodynamic properties", but I would suspect it's more that capillaries evolved to track particle size, not the other way around. A useful insight would be to look at closely related animals with and without RBCs. Also, consider nucleated bird RBCs.

If you want a good look at why free hemoglobin is a bad idea, read an article about transfusion reactions (hemolysis) and the organs it damages.

Hemoglobin molecules used to manufacture these products are not
  contained by a red cell membrane, and when released into the
  vasculature, these molecules rapidly scavenge nitric oxide.This can
  result in systemic vasoconstriction, decreased blood flow, increased
  release of proinflammatory mediators and potent vasoconstrictors, and
  a loss of platelet inactivation,17- 20 creating conditions that may
  lead to vascular thrombosis of the heart or other organs. This
  mechanism has recently been shown in preclinical models to be
  responsible for injury during hemolytic states, in which hemoglobin is
  also released into the circulation.21
Unlike naturally occurring hemoglobin, manufactured cell-free
  hemoglobin-based blood substitutes (HBBSs) can be chemically altered
  to theoretically minimize such toxicities. It has been postulated that
  cross-linking, polymerization, or pegylation of hemoglobin will create
  larger, more stable HBBS molecules, preventing extravasation and
  thereby leading to a reduction in toxicities related to nitric oxide
  scavenging. At least 1 manufacturer has also chemically increased the
  affinity of its HBBS for oxygen (lower P50, the partial pressure of
  oxygen required for 50% hemoglobin saturation) to decrease arteriole
  oxygen transfer and thereby potentially eliminate untoward
  cardiovascular effects.

2008 - Cell-Free Hemoglobin-Based Blood Substitutes and Risk of Myocardial Infarction and Death

So cell free hemoglobin is toxic. As you can see this toxicity can be reduced in other ways too, so it seems like there is an evolutionary pressure in the direction of having blood cells, maybe it is simpler this way. To answer the other question, I think there can be free HGB in the blood when blood cells fall apart because of an infection e.g. malaria, etc...

Hemolysis in falciparum malaria results in NO quenching by cell-free
  hemoglobin, and may exacerbate endothelial dysfunction, adhesion
  receptor expression and impaired tissue perfusion. Treatments that
  increase NO bioavailability may have potential as adjunctive therapies
  in SM

2008 - Relationship of Cell-Free Hemoglobin to Impaired Endothelial Nitric Oxide Bioavailability and Perfusion in Severe Falciparum Malaria

Btw. I agree with rhill45, I think too that it is easier to regulate O2 and CO2 exchange if you have a specialized cell type, so it might have regulation purposes. It can have recycling purposes either, because it is hard to distinguish between old (damaged) and new HGB when they are in a cell-free form. This problem probably can be solved by destroying only glycosylated hemoglobin, but I guess it is much easier to filter out the old RBCs in the spleen...

In the process of maturation, a basophilic pronormoblast is converted
  from a cell with a large nucleus and a volume of 900 fL to an
  enucleated disc with a volume of 95 fL. By the reticulocyte stage, the
  cell has extruded its nucleus, but is still capable of producing
  hemoglobin.

according to wikipedia (without citation).

Other sources claim the same, with the extension that this period lasts only for a short time, because the cell soon loses its mRNA and so it stops producing HGB. So according to these articles RBCs create the HGBs in the early stages of their life. (I did not find a real scientific article about this, but I can accept this theory.)
According to Chris this toxicity is just a protection mechanism, so I dug deeper.

Bacterial virulence is greatly enhanced by freely available iron, such
  as that in fully-saturated transferrin or free haemoglobin. Following
  trauma a fall in tissue Eh and pH due to ischaemia, plus the reducing
  powers of bacteria, can make iron in transferrin freely available and
  abolish the bactericidal properties of tissue fluids with disastrous
  results for the host. Hyperbaric oxygen is a possible therapeutic
  measure that could restore normal bactericidal systems in infected
  tissues by raising the Eh and pH.

2006 - Iron and infection: the heart of the matter

Iron lies at the center of a battle for nutritional resource between
  higher organisms and their microbial pathogens. The iron status of the
  human host affects the pathogenicity of numerous infections including
  malaria, HIV-1, and tuberculosis.

2012 - Hepcidin and the Iron-Infection Axis

So RBCs protect the iron against microbial pathogens, that's their key role. I think every other related problem, like O2 release regulation, free HGB toxicity, HGB recycling, etc... can be solved with free HGB as well, so most probably iron protection is the evolutionary pressure to store HGB in blood cells instead of letting it be in the blood in a cell free form. It's funny that every single book gets this wrong, and they claim that carrying oxygen is the most important role of this cell type, while they aren't mention anything about iron protection... :-)

One point of free hemoglobin in the blood being toxic is the fact this happens when red blood cells get damaged, which is obviously not a good thing. So this is a protective mechanism as well.

Hmm interesting theory. RBCs might be protecting the Fe from infectious microbes. I heard a theory that by infections the human body clears up Fe from blood, because microbes need Fe for multiplication, creating metalloproteins etc... I never investigated... :-)

@Chris thanks, this iron theory seems like really true.

Oh wow, thank you for your response. The 'iron protection' reason is a beautiful explanation :) I wonder if there are any other proteins with iron incorporated and whether they are protected as well, I'll try to look into it

@Eva Ofc. there are, e.g. transferrin, but by infection they are cleared from the blood (hepcidin regulates their level), but HGB cannot be removed, because it is the oxygen carrier, so you would drown in the lack of HGB...

This is not a topic I know well, and the answer clearly contains lots of useful information. However, I find this answer really problematic since it is filled with teleological arguments in relation to evolution, e.g. "...why evolution created this cell type..." and "...creating a new cell type was the easiest way to the evolution..."  This is simply not how evolutionary processes work, and even if this is not intentional, it can still cause a lot of confusion.

@fileunderwater Yes you are right, I weren't accurate. I meant that there is an evolutional pressure to store the HGB (and iron) in blood cells instead of let it run in a cell free form in the blood stream. Is this acceptable for you?

@inf3rno Yes that would be better, to remove the appearance of evolutionary purpose and that evolution is actively searching for "easy" solutions.

@Eva http://www.ncbi.nlm.nih.gov/pubmed/15095784
There are RBC derived vesicles. This study estimates that RBCs lose about 20% of HGB during their lifetime (120-150 days) by creating vesicles. These vesicles have a short lifetime, they are degraded by the liver. Another article in the topic: http://journal.frontiersin.org/Journal/10.3389/fphys.2013.00365/full . So there is always HGB in blood, but I don't think it is relevant by respiration, it is just part of the degradation process.

@Eva Note that vesicles have phospholipid membranes just as cells do.

@inf3rno- Do you think Hemophilia is a beneficial mutation?

@TheVoid I don't know of any reason because of hemophilia could be beneficial. By some of the heritable diseases there are hypotheses that the mutations had advantages at some time during our evolution. E.g. the sickle cell anaemia point mutation was beneficial when malaria was more common. https://en.wikipedia.org/wiki/Human_genetic_resistance_to_malaria#Sickle-cell If you find a similar selective pressure by hemophilia, then it can be a possible cause of the mutation.

@inf3rno- I know i'm getting off topic but DVT is one of the highest causes of death, So could a Hemophiliac die of DVT? Im asking because you seem to have a interest in hematology.

@TheVoid They could, but it is very rare. http://www.ncbi.nlm.nih.gov/pubmed/12945884 So yes, this can be a selective pressure, which can make these kind of mutations more widespread/prevalent. I don't know which would the proper word here, since it is still rare. And most probably it is rare, because its costs are higher than its benefits.

This is a well worded question. There are more reasons than the following but the most apparent is hemoglobin production and its transport. The erythrocyte is a cell whose structure is optimal for its function-the production and transport of hemoglobin.
It lacks a nucleus and organelles so that it can devote almost 100% of its energy to hemoglobin production. It has this  bi-concave disk shape to increase its surface area thus increasing the exposure of hemoglobin to oxygen and CO2.
It's a small and flexible cell allowing them to easily maneuver the capillaries (where they work).
Because it's anuclear it has a short lifespan but they are rapidly produced and regulated by erythropoietin.
In order for tissues to receive oxygen and rid themselves of carbon dioxide there needs to be an orderly transfer and movement of hemoglobin from the tissues to the lungs and back-and-forth. Without this cycling of hemoglobin on the erythrocyte the protein would move more in the body through diffusive means. This would not promote the required segregation of oxyhemoglobin in the tissues and carbaminohemaglobin in the lungs.
Check out any edition of Anatomy and Physiology by Marieb. All editions have an entire chapter related to the subject

Thank you for your answer! I didn't know that hemoglobin is synthesized in RBCs, it makes more sense now. However, I still have a question: how do red blood cells help segregation? When gas exchange happens, is hemoglobin free in the tissue or still actually inside a cell?

Cause the hg is on the rbc, wherever the rbc is the hg is. Only the rbc can effectively be circulated, if was just swishing around the body too much hg would diffuse where it not needed  in respect to oxyhemoglobin and carbonMinohemoglobin

Do you have any references for this? It seems unlikely to me that a red blood cell can produce haemoglobin without DNA or RNA (once it's degraded).

It's not an easy concept because you have to think of the requirements of the whole organism additionally the requirements of specific regions of the body tissues versus Lungs.

Your claim about diffusion is interesting but, again, do you have a reference?

Check that text out most of what I learned is from there

It's not degraded it has ribosomes it produces hemoglobin

So, hemoglobin is actually NEVER free in the body? (In normal circs, of course)

Never say never look up what a contusion is and where bilirubin comes from

These are good new questions your asking

Okay, I think I understand it better now, thank you!

This is not an answer to the question, but tangent comments that might be useful for how you look at the problem (and too long for a comment). First, for a question like this it is useful to look at other solutions to the same problem. For instance, the second most common molecule for oxygen transport is Hemocyanin, and this is not bound to cells but is directly suspended in hemolymph (arthropod/mollusc "blood"). So specialized cell types for oxygen transport is not a necessity for effecient oxygen transport in rather advanced organsism. So your question; "why do we need cells packed with hemoglobin: why can't it travel freely in the bloodstream?", while being true for humans and other vertebrates, is not true for oxygen transport in all "complex" animals.
Second, while there seems to be good reasons for why hemoglobin is bound in RBC, you should at least entertain the idea that the cause of RBC-bound hemoglobin in vertebrates is an evolutionary contingency (i.e. a random historical event). Evolution is always constrained by previous evolutionary history, and the reason that all vertebrates (+ a number of other organsisms) share RBC-bound hemoglobin may simply be that they share a common ancestor. This does not mean that it lacks advantages, but it also means that it might be misleading to search for the reason for RBC-bound hemoglobin in a particular species. For some background on evolutionary contingencies and many useful references in the intro, as well as an interesting experiment to test for contingencies, you can have a look at Blount et al. (2008) (part of Lenski's Long-term Experimental Evolution project).

I remember going to a chemistry lecture which mentioned this (the lecture was on blood transfusion in general).
The main reasons are:
1) Hemoglobin is toxic to the human body: Hb in RBCs is a tetramer, but in the plasma it breaks into two dimers --> toxicity in the kidneys. Hb needs modification by cross-linking or recombination. Wikipedia states that this is Acute Tubular Necrosis.
2) Hb in plamsa decreases osmotic pressure
3) Hemoglobin removes the NO from the vessel walls causing vasoconstriction, shrinkage of the vessels.  --> this was the main focus of the chemistry lecture; there was a lot of talk about free radicals and stuff but I've unfortunately forgotten the details
I've also searched a bit on the web and some people (one yahoo answers) confirm rhill45's answer.
I think searching failed blood transfusion products (people have tried transfusing Hb directly) will be of great help.

Could you please add some references to support your response!

for 1) and 2) http://www.chm.bris.ac.uk/motm/mpg/whymod.htm
for 3) I got the info. from a chemistry lecture I attended, so it's just personal notes

See one of my references. It writes the exact same thing that Hg binds to NO. Removing NO from blood is a problem because NO is a gasotransmitter causing vasodilatation. So having less of it causes vasoconstriction. https://en.wikipedia.org/wiki/Gaseous_signaling_molecules#Nitric_oxide


text:
A good introductory book to histology?
Like the title says, I am looking for a good introductory text to histology. It would ideally cover

sample preparation
microscopy
staining, and
several example experiments

Suggestions?


text:
Like size and colour constancy, why does the brain not maintain focus constancy?
I have progressive myopia. I grew up with perfectly normal eyes but slowly started getting myopic.
The thing is, my brain knows (or should know) what the world looks like -- it knows that far away objects do not suddenly blur. So when the input from the retina changes, why doesn't the brain correct it in perception?
I'm assuming here that this should work by the same principles as size and colour constancy. In both cases the input from the retina is different but the brain doesn't perceive it as an actual change in size or colour.

The input is a blurry signal, what shall the brain do with it?

Interesting question. I concur with @Chris. Color constancy and size constancy are neural mechanisms and can therefore be imposed on visual input from the retina. In contrast, a blurry input cannot be neurally improved. As an analogy: Visual perceptions are processed and rendered by the brain and therefore represent "photoshopped" perceptions. In other words, perceptions are subjective representations manufactured by higher-level visual processing. However, focus is determined by optics. An out-of-focus picture, to push the analogy, cannot be fixed by fotoshop, nor the brain.

Ps: sorry to hear about your visual disorder. Good luck.