text:
What happens to drug metabolism when CYP450 enzymes are presented with two substrates
What happens when two substances, both substrates for Cytochrome P450 metabolism, are both present in the bloodstream?
For example, with sertraline and cannabidiol (CBD), if someone took a sertraline tablet and later used CBD, how does the presence of two CYP substrates affect drug metabolism? Does one drug inhibit the metabolism of the other? What happens to blood levels of the drugs? Does the order of administration matter?

If you want to ask the question about two specific substances and one specific enzyme, you should edit the title of your question to make that clear. If you are asking about the broader biochemical principle then you should edit the body of your question to make that clear.

Welcome to SE Biology. As a new user you should take the tour and read the help on asking good questions, where you will see that you are expected to demonstrate that you have researched a question before posting. This question can be answered by an understanding of the basic principles of enzyme action. Read, for example, this section of Berg et al. online, paying particular attention to the meaning of Km. Oh, and what is CBD? Don't tell me, edit your question.

@David Km? I think you're overly simplifying this question, as if you are pointing someone asking about events at relativistic speeds towards Newton's laws. The whole point is that this is a case where MM kinetics don't necessarily apply (I don't know about the specific example OP references, but I am thinking of liver enzymes like this one ).

@BryanKrause  The etermal question — what does the poster already know? I would assume from the terminology of "take priority" and "take over" in a question written in reasonable English that the poster is unaware that different substrates for an enzyme can have different affinities. Likewise his reference to x mg of one substrate but an unspecified amount of the second suggests he is unaware of the effect of concentration (and relative concentration of substrate). But I may be wrong.  Let him tell us.

@David I agree that the language is a bit sloppy, but it seems like OP is coming at this with some knowledge of medical implications of pharmacology rather than biochemistry and I think this question is better researched than you are giving credit for.

@BryanKrause and David honestly, this sounds very much to me like someone who is asking "Can I take my antidepressant and cannabidol together, and if so, how?"

I edited to, I think, maintain the kernel of the on topic question. It seems to be about CYP activity specifically (vs. other classes of enzymes). I kept the CBD/Sertraline example because it limits the teaching points (from my perspective), mainly, to: there are many CYP enzymes, they are promiscuous, and this isn't the only thing to consider when evaluating drug-drug interactions.

I think the OP is asking the following:

If an enzyme is not specific one substrate, but is simultaneously presented with a pair of substrates, which one 'wins' and how do we decide?

For example, if an enzyme is presented with a racemate such that the D-form has a 10-fold lower $K_m$ than the L-form, but the L-form has a 5-fold higher $k_{cat}$, which one is preferentially metabolized, and how do we decide?
It was Fersht who first provided the definitive answer, at least for single-substrate enzymes (Fersht, Enzyme Structure and Mechanism, 1977; see also here)

The kinetic parameter determining the specificity for competing substrates is neither $K_m$ nor $k_{cat}$, but the (so-called) specificity constant: $$\frac{k_{cat}}{K_m}$$

If it assumed that both substrates, considered in isolation, obey the Michaelis-Menten kinetics, then it is very easy to derive (starting with the ratio of the respective Michaelis-Menten equations) the following expression for the initial velocities when both substrates are present simultaneously.
$$  {
  {{{v_{i}^1}}\over{v_{i}^2}}} =  {{{{k_{cat}^1}}\over{K_{m}^1}[S_1]}}  \times{{{{K_{m}^2}[S_2]}\over{k_{cat}^2}}} \ \ \ \ \ (1)$$
(The equation is derived by, among others, Cornish-Bowden (2004, pp 36-39):
If $V_{max}$ is preferred to $k_{cat}$:
 $$  {
  {{{v_{i}^1}}\over{v_{i}^2}}} =  {{{{V_{max}^1}}\over{K_{m}^1}[S_1]}}  \times{{{{K_{m}^2}[S_2]}\over{V_{max}^2}}} \ \ \ \ \ (2)$$
${{k_{cat}}}\over{K_m}$ has units of a second-order rate constant and, giving it a symbol (${k_{1}^{\prime}}$ for $S_1$ and ${k_{2}^{\prime}}$ for $S_2$) to reflect its status as a fundamental kinetic constant and not just a ratio, allows the following equation to be written:
$$  {
  {{{v_{i}^1}}\over{v_{i}^2}}} =  {{{{k_{1}^{\prime}}}\over[S_1]}}  \times{{{[S_2]}\over{k_{2}^{\prime}}}} \ \ \ \ \ (3)$$
This equation provides the answer to the OP question. For the racemate described above, we need only calculate the ratio of the specificity constants to get the answer:
$${
    {
     {
      {v_{i}^{D_{form}}
     }
     }\over{
             v_{i}^{L_{form}}}
            }
    }   =
{
    {
     {
      {k_{D_{form}}^{\prime}\times{[D_{form}]}
     }
     }\over{
             k_{L_{form}}^{\prime}}\times{[L_{form}]}
            }
    } = {
    {
     {
      {k_{D_{form}}^{\prime}
     }
     }\over{
             k_{L_{form}}^{\prime}}
            }
    } =  2 \ \ \ \ \ (4)$$
Much could be written about the specificity constant (diffusion control, enzyme 'perfection', Haldane relationships), but I'll make just one. Considering the single-substrate Michaelis-Menten enzyme, the following holds AT ALL SUBSTRATE CONCENTRATIONS
$$  {
  {{{v_{i}}}}} =  {{{{k_{1}^{\prime}}}}[{S_o}][E]}   \ \ \ \ \ (5)$$
When $S_o$ is very low, $[E]$ = $e_o$ (approx) and the following may be written (where,unlike $[E]$, $e_o$ is usually known or may be determined)
 $$  {
  {{{v_{i}}}}} =  {{{{k_{1}^{\prime}}}}[{S_o}]e_o}   \ \ \ \ \ (6)$$

But it is Eqn (5) that is the important one: $k^{\prime}$ (the so-called specificity constant) may be thought of as the second-order rate constant governing the combination of ('free') enzyme with substrate at all substrate concentrations, not just when $S_o$ << $K_m$

Much could be written about this as well
Definitions
I think it is reasonably obvious what everything means. Nevertheless, here is a list:

$K_{m}^1$  is the Michaelis Constant for substrate 1
$K_{m}^2$  is the Michaelis Constant for substrate 2
$k_{cat}^1 $ is catalytic constant for substrate 1
$k_{cat}^2 $ is the catalytic for substrate 2
$V_{max}^1 $ is the maximum velocity for substrate 1
$V_{max}^2 $ is the maximum velocity for substrate 2
$k_{1}^{\prime} $ is the specificity constant for substrate 1
$k_{2}^{\prime} $ is the specificity constant for substrate 2
$v_{i}^{1} $ is the initial velocity due to substrate 1
$v_{i}^{2} $ is the initial velocity due to substrate 2

Reference

Cornish-Bowden (2004) Fundamentals of Enzyme Kinetics 3rd Edn. Portland Press (London)

You really think? If only questions on SE Biology were at that level. To avoid your answer going to waste I’d edit the question drastically so there is no doubt your answer fits. If the poster doesn’t like it he can always revert, but his lack of response to comments suggests this unlikely.

I enjoyed this answer. I'd be curious to see your thoughts about how well this applies to drug metabolizing CYPs in vivo, given their particular properties.

FYI I've edited the question to, I think, let the useful pharmacology question be more clear. Along with @David, I'd encourage you to edit the question as well, since you saw a useful biochemistry question in it.

What are CYPs? How are they different from other enzymes?
Cytochrome P450 enzymes (CYPs) are a large family of enzymes involved in the metabolism of many endogenous and exogenous compounds (including typical dietary substances and pharmaceuticals). There are many different CYPs, each individual CYP form can metabolize many different compounds, and a single compound is typically metabolized by more than one CYP, sometimes at the same site, sometimes at multiple sites, sometimes in an ordered sequence, and sometimes not. This promiscuity in substrate/enzyme interaction is in contrast to most human enzymes, which are highly specific. Its cost, though, is efficiency.
CYPs and drug-drug interactions
CYP effects are an important subset of drug-drug interactions, but this is typically not described in terms of race conditions. Perhaps this is because of the particular relationship between enzyme and substrate. In addition to being metabolized by CYPs, many drugs and dietary substances can inhibit some CYP forms and induce others (including forms that do not metabolize the substance itself).
To answer the particular question about whether the order of administration matters, while inhibition is typically at the level of protein interaction, induction involves gene interactions. Because induction involves gene interactions, induction results in interactions that do not depend on both drugs being available to CYP at the same time. This means that (for induction effects) neither changing the order of administration or staggering doses will prevent the interaction. Generally, those examples of drug-drug interaction that are readily prevented by dose order involve pharmacodynamic interactions, i.e., interactions at the drug's intended molecular target.
Is this all you have to consider when evaluating for a potential drug-drug interaction?
For emphasis, I'll say it again: CYP effects are an important subset of drug-drug interactions. There are many things to consider when evaluating the effect of polypharmacy.
Further reading
You can read about this in Goodman & Gilman, the Pharmacological Basis of Therapeutics. Ch 6 has a good subsection about CYP metabolism in general, with specific discussion about the metabolism of different compounds in other chapters. Most good basic pharmacology textbooks will cover this, but I think G&G does a particularly good job. Full prescribers information on any drug will include information on CYP450 metabolism, inhibition, and induction.  You can look at wikipedia, but this is not the best wikipedia article I've read.
So what about sertraline and CBD?
I am not going to make a statement about whether a particular combination of drugs does or doesn't interact, if only to encourage anyone with a drug-drug interaction question TALK TO THEIR DOCTOR, or whoever prescribed your medication. Different jurisdictions have different laws about CBD, but doctors are not law enforcement officials. You can and should tell him/her about everything you take.

If you think that this is a personal medical question (that hadn’t occurred to me), surely you should vote to close.

@David as, alas, we often see, it seems to me like there is one  question in the text of the OP/post (not personal medical) and another question in the mind of the OP/poster, but the OP/poster hasn't engaged with the comments. I tried to answer the text of the question, and only because there was excellent information in another answer.


text:
Pipetting damage to cells
I'm curious how much damage is potentially inflicted by shear stress by pipetting. I know that syringes used for stem cell injection can cause a lot of damage. However, to what extent does this happen with P20 and P200 pipette tips? Understandably the shear modulus of bacterial cells is significantly different from that of cancer cells, which will be different from that of stem cells.

It might be possible to compare P200 with P20 on the cheap (anybody up for a crowd-sourced experiment on HeLa or E. coli?), but I suspect you actual question asks for absolute numbers, and is therefore almost impossible to answer. It is hard to envisage any non-pipette method to deliver 100% viable cells, and even harder to think of alternatives (measure free DNA after pipeting? how can that be converted to cell counts?). User137 suggests something decent, but still short of absolute. In the absence if evidence, all the answers you will receive are bound to be speculative "expert opinion".

This is an excellent question, I have been training people to culture cells for about 12 years and students have a hard time grasping this and appreciating the importance etc.
What cells are usually experiencing during pipetting is analogous to a crowd of people trying to fit through the doorway of a building. Shearing during pipetting  is certainly a legitimate concern in cell culture. You will notice its negative effect on viability most explicitly when pipetting cells in freezing
 medium (containing DMSO) following a thaw. Until their DMSO concentration drops their membranes are weaker & more fluid. That's why you pipette the frozen cells drop-wise to the fresh medium, to be especially gentle at this point.
Prokaryotic cells such as the above mentioned TOP10 cells are treated with Calcium chloride and glycerol which has essentially the same effect on their walls and membranes. Hence pipetting should be delicately performed after thawing these cells as well.
With that being said, if you compare the sensitivity of prokaryotic and eukaryotic cells to shearing, eukaryotic cells are profoundly more sensitive.
For individuals using competent bacteria for sub-cloning and other routine uses, killing a small percentage of of your cells is not that important. However if you are using the transformation to generate cDNA libraries it's very important that you have a titer sufficiently representing the transcriptome the library is composed of.
In these instances using a more premium competent cell, adhering to correct temperatures and minimizing pipetting is essential. This is why many are taught to swirl the DNA the with the competent cells, rather than the harsher alternative: pipetting up-and-down.
The four most important factors that contribute to cellular shearing are, and in order form most to least contributory:

Diameter of the bore in the pipette tip, the smaller the more shearing.
Speed at which the suspension is passing through the opening of the tip. The faster the more damaging.
Size and rigidity of the cell. Larger cells are more prone to damage.  Cells with a murein wall are less prone to damage.
Concentration of cells. Cultures that are more concentrated are more prone to damage.

Because the make up if the cell itself is so influential on the amount of damage, and because of the enormous variety of cells; designing a representative experiment to assess damage would be very difficult and  laborious.
Finally,  the variety of tips and seriologicals is also enormous. However if one were to attempt to assess this it could be done:
Choose a representative variety of cell lines, choose a representative variety of pipettes. One would probably want to use a robotic pipette to be able to  evaluate incrementally assigned speeds and pressures. Look at different culture concentrations,  phases of the growth curve, time between pipetting and analysis, distance between the exiting fluid and the culture etc, etc.
I think a very successful analysis method would be using propidium iodide and FACS.
After your experiment which will cost a lot of time and $, I think you will find common sense rules: keep pipetting to a minimum and use wider tips whenever possible.

Good point Here I will  rephrase as it seems to be getting quite a number votes

Won't the material with which the pipette is made affect the cell too? I would imagine cell membranes having different affinity to different materials

@CRags certainly yes but really minimal.

It's an easy experiment to do. Take your cells aliquot them into 10 microfuge tubes, and pipette each suspension increasing amount of times, stain with trypan blue and count.
The most important factors will be which pipette-type you use; I would expect a p1000 to cause more damage then a p200 then a p20 due to velocity of the fluid. Also the most important factor will be the skill of the scientist, if you pipette slowly it should decrease stress as opposed to pipetting quickly.
In my experience it depends on the pipette-type and the skill of the operator. The only way to answer this for you is to try it empirically.

Well, then that will heavily be based on operator error. Anecdotally, I've heard that it is the other way; a P1000 would causes less damage than a P20.

Artem is right: the only way to say is empirically. The P1000 will influence the cell damage likely because of the velocity. In contrast, the P200 and P20 could give some damage due to the narrow tip hole.

Give it a try and post the results. I do believe that operator skill is the single most important factor.

We used to use a peristaltic pump to plate HepG2 cells into 384 and 1536 plates. When we moved to primary hepatocytes the pump killed too many and had to move to hand plating with an 8 channel pipette. So cell type matters a lot.

Anecdotally I have not observed any cell death upon pipetting of E. coli DH5alpha or TOP10, however as competent cells, mixing by pipetting up and down is discouraged due to the compromised cell wall.

Good pointIt's pretty hard to kill bacteria mechanically  period, the competent cells are more sensitive though and concern comes when  building cDNA library's mostly as you need a very representative number of colonies

Shear stress $\tau$ in this small sizes is usually measured in dyne/cm2 or N/m2 = Pa. The equations betweeen them: $1dyn/cm^2 = 10^{-5}N/cm^2 = 0.1N/m^2 = 0.1Pa$.
What kind of damages zygotes can suffer by pipetting?

Using scanning electron microscopy, we found open holes on the surface
  of lysed eggs, indicating failure of the plasma membrane to reseal
  after microinjection. No holes were seen in unlysed eggs, but many of
  them had membrane alterations suggestive of healed punctures.

1987 - Zygote viability in gene transfer experiments

Even a small 1.2 dyn/cm2 shear stress induces apoptosis by pipetting zygotes. So zygotes have their critical shear stress level by 1.2 dyn/cm2 and pipetting involves greater forces than 1.2 dyn/cm2.

Shear stress at 1.2 dynes/cm2 induces stress-activated protein
  kinase/jun kinase phosphorylation that precedes and causes apoptosis
  in embryos (Xie et al., 2006b, Biol Reprod). Pipetting embryos is
  necessary for many protocols, from in vitro fertilization to
  collecting embryos prior to analyzing gene expression by microarrays.
  We sought to determine if pipetting upregulates phosphorylated MAPK8/9
  (formerly known as stress-activated protein kinase/jun
  kinase/SAPK/JNK1, 2). We found that phosphorylated MAPK8/9, a marker
  of MAPK8/9 activation, is upregulated in a dose-dependent manner by
  pipetting.

2007 - Pipetting causes shear stress and elevation of phosphorylated stress-activated protein kinase/jun kinase in preimplantation embryos

The critical shear stress level is somewhere between 0.01 and 1000 dyn/cm2 by animal cells depending on the cell type and species. (I think the average is somewhere about 50 dyn/cm2, but it is very hard to differentiate between articles mentioning critical shear levels and most lethal shear levels, so the range and the average might be lower.) The death constant (1/h) increases exponentially by increasing the shear stress.

An apparatus for the detailed investigation of the influence of shear
  stress on adherent BHK cells was developed. Shear forces between 0.0
  and 2.5 N m−2 were studied. The influence on cell viability, cell
  morphology, cell lysis, and cell size was determined. Increasing shear
  forces as well as increasing exposure duration caused increasing
  changes in cell morphology and cell death. A “critical shear stress
  level” was determined.

1992 - Determination of a “critical shear stress level” applied to adherent mammalian cells

Shear stress related damage to a mouse hybridoma was examined by
  Abu-Reesh and Kargi under laminar and turbulent conditions in a
  coaxial cylinder Searle viscometer. Cells were exposed to 5 to 100
  N/m2 shear stress levels for 0.5 to 3.0 h. At a given shear stress and
  exposure time, turbulent shear was much more damaging than laminar
  shear as also reported in the past for protozoa and plant cells. Under
  turbulent conditions, damage occurred when shear stress exceeded 5
  N/m2. Respiratory activity of the cells was damaged earlier than the
  cell membrane, thus implying transmission of the stress signal to the
  interior of the cell. Cell damage followed first-order kinetics both
  in laminar and turbulent environments. For turbulent shear stress
  levels of 5 to 30 N/m2, the death rate constant (kd) increased
  exponentially with increasing stress level; the kd values varied over
  0.1 to 1.0 1/h.

2001 - Hydrodynamic Damage to Animal Cells

Subconfluent endothelial cultures continuously exposed to 1–5
  dynes/cm2 shear proliferate at a rate comparable to that of static
  cultures and reach the same saturation density (≃ 1.0–1.5 × 105
  cells/cm2 ). When exposed to a laminar shear stress of 5–10 dynes/cm2
  , confluent monolayers undergo a time-dependent change in cell shape
  from polygonal to ellipsoidal and become uniformly oriented with flow.
  Regeneration of linear “wounds” in confluent monolayer appears to be
  influenced by the direction of the applied force. Preliminary studies
  indicate that certain endothelial cell functions, including fluid
  endocytosis, cytoskeletal assembly and nonthrombogenic surface
  properties, also are sensitive to shear stress. These observations
  suggest that fluid mechanical forces can directly influence
  endothelial cell structure and function.

1981 - The Dynamic Response of Vascular Endothelial Cells to Fluid Shear Stress

Shear stress above 0.25 dyne/cm(2) resulted in dramatic loss of
  podocytes but not of proximal tubular epithelial cells (LLC-PK(1)
  cells) after 20 h.

2006 - Podocytes are sensitive to fluid shear stress in vitro

A series of careful studies has been made on blood damage in a
  rotational viscometer. Specific attention has been focused on the
  effects of solid surface interaction, centrifugal force, air interface
  interaction, mixing of sheared and unsheared layers, cell-cell
  interaction, and viscous heating. The results show that there is a
  threshold shear stress, 1500 dynes/cm2, above which extensive cell
  damage is directly due to shear stress, and the various secondary
  effects listed above are negligible.

1972 - Red Blood Cell Damage by Shear Stress

The shear stress threshold of some dinoflagellates (microalgae) is
  even lower than that of erythrocytes (0.029 N/m2). For example, a
  continuous laminar shear stress level of only 0.0044 N/m2 (equivalent
  to a shear rate of 2.2 1/s) has proved lethal to the dinoflagellate
  Gonyaulax polyedra.

Upstream Industrial Biotechnology

Other cell types are not necessary as sensitive as animal cells and they don't necessary react with apoptosis (about 10 dyn/cm2) to shear stress, so you have to use necrotic (about 5000 dyn/cm2) forces to destroy them :
cell type                       size                shear sensitivity
microbial cells                 1-10μm              low
microbial pellets/clumps        up to 1cm           moderate
plant cells                     100μm               moderate/high
plant cell aggregates           up to 1-2cm         high
animal cells                    20μm                high
animal cells on microcarriers   80-200μm            very high
fungi cells                     2-10μm              moderate/high

Table 1 - shear sensitivity by cells types
Bioprocess Engineering Principles: table 8.6 - Pauline M. Doran
1996 - Role of hydrodynamic shear in the cultivation of animal, plant and microbial cells
1988 - Effect of shear on the viability of plant cell suspensions
2004 - A quantitative analysis of shear effects on cell suspension and cell culture of perilla frutescens (plant) in bioreactors
2009 - Shear Sensitivity - the full text probably contains all the numbers

Results show that Chinese Hamster Ovaries and Human Embryonic Kidney
  cells will enter the apoptotic pathway when subjected to low levels of
  hydrodynamic stress (around 2.0 Pa) in oscillating, extensional flow.
  In contrast, necrotic death prevails when the cells are exposed to
  hydrodynamic stresses around 1.0 Pa in simple shear flow or around
  500 Pa in extensional flow.

2009 - Induction of mammalian cell death by simple shear and extensional flows

The shear sensitivity is not determined only by cell type and species, there are many other factors involved:

type of cell and species
composition and thickness of cell wall when present
size and morphology of cell
the intensity and nature of shear stress, whether turbulent or laminar, or associated with interfaces (e.g. during bubble rise and rupture)
growth history, both short-term (e.g. starvation) and long term adaptation
growth medium (trace elements, vitamins, carbon and nitrogen sources)
growth rate
growth stage
type and concentration of shear protective agents if present

Cells can be very sensitive to shear stress caused by turbulent flow, while not so sensitive to shear stress caused by laminar flow.

On the basis of laminar flow viscometriy measurements, a critical
  shear stress level of 80-200 N/m2 has been suggested for Morindata
  citrifolia cells.
... while for Daucus carota a shear stress level of 50 N/m2 has been
  associated with cell damage. In other study, carrot cells in a laminar
  flow Couette viscosimeter lost the ability to grow and divide in the
  shear stress range of 0.5-100 N/m2. The intracellular enzyme activity
  was impaired at shear stress levels above 3000N/m2, but significant
  lysis did not occur until a shear stress level of 10.000 N/m2 applied
  over a prolonged perioud (>1h).
In contrast to the behavior in laminar flow, the cells were quite
  sensitive to turbulent impeller agitation. Impeller tip speeds of ~1.1
  m/s lysed a significant proportion of the cells within 40min.

Cell and Tissue Reaction Engineering
Upstream Industrial Biotechnology

The bubble damage is severe (1000 cells by a single 3.5mm size bubble) because of the cell adherence to the interface of the bubble and the strong forces involved (>1000 dyn/cm2 by stirred bioreactors). The adhesion and so the damage can be reduced with surfactants.

2004 - Quantitative studies of cell-bubble interactions and cell damage at different pluronic F-68 and cell concentrations.
2004 - Surfactant Reduction in Embolism Bubble Adhesion and Endothelial Damage

It is proposed that when cells are either attached to, or very near, a
  rupturing bubble, the hydrodynamic forces associated with the rupture
  are sufficient to kill the cells.
All experiments were conducted with Spodoptera frugiperda (SF-9)
  insect cells, in TNM-FH and SFML medium, with and without Pluronic
  F-68. Experiments indicate that approximately 1050 cells are killed
  per single, 3.5-mm bubble rupture in TNM-FH medium and approximately
  the same number of dead cells are present in the upward jet. It was
  also observed that the concentration of cells in this upward jet is
  higher than the cell suspension in TNM-FH medium without Pluronic F-68
  by a factor of two. It is believed that this higher concentration is
  the result of cells adhering to the bubble interface. These cells are
  swept up into the upward jet during the bubble rupture process.
  Finally, it is suggested that a thin layer around the bubble
  containing these absorbed cells is the “hypothetical killing volume”
  presented by other researchers.

1994 - Quantification of damage to suspended insect cells as a result of bubble rupture

For a hybridoma line, reported that exposure to laminar shear stress
  (208 N/m2) in unaerated flow in a cone and plate viscometer led to
  substantial loss in cell count and viability within 20 min. At a
  constant 180 s exposure, increasing shear stress over 100-350 N/m2
  linearly enhanced cell disruption, with >90% of the cells being
  destroyed at 350 N/m2 stress level. Shear stres levels associated with
  bubble rupture at the surface of a bioreactor may range over 100-300
  N/m2. These values are remarkably consistent with shear rates that
  damaged hybridomas in unaerated laminar flow experiments.

Upstream Industrial Biotechnology

Smaller hole pipettes cause more damage.

We also examined aspects of the gene transfer procedure that might
  influence survival such as the size of injection pipettes and their
  taper relative to zygote diameter, possible toxicity of the injection
  medium, the timing of injection, and immediate vs. delayed pipette
  withdrawal. The only factors that significantly affected cell
  viability were pipette size and taper, and timing of injection in
  relation to first cleavage. This suggests that zygote viability
  correlates inversely with the size of the hole produced by the
  injection pipette and that damage to the membrane is less successfully
  repaired as the fertilized egg readies itself for division.

1987 - Zygote viability in gene transfer experiments

It is hard to find anything about the level of shear stress by pipetting. It can be certainly more than 1 dyn/cm2. It has a short duration (at most a few seconds). I think the following factors can influence the shear stress levels by pipetting:

pipette type
flow speed (faster flow can be more likely turbulent)

negative pressure by suction
hole size (bigger hole can reduce flow speed)
liquid viscosity

bubble formation

Probably more factors are involved but I am not a pipetting expert. ;-) I agree with the others, it surely depends on the personal skills e.g. an amateur can create huge bubbles by pipetting, which can kill a lot of cells by formation and disruption...
I agree with Artem that this is an experiment to do especially if the result is important for you. What you need to create a model about pipette damage, are the shear stress levels by pipetting and the critical shear stress levels of the cells. I think it is hard to design and experiment in which you can measure the shear stress levels in your pipettes and there is no flow model for pipetting as far as I know, so it can be a good topic for a thesis or a diploma work.

I know this is a two-year-old thread, but I though I would post this anyway in case someone else is searching for this answer like I was tonight. This article cited below doesn't discuss pipette tips vs needles specifically, but it does discuss the difference in effects of tapering vs cylindrical needles on cell damage. Unfortunately, the math in the paper is a bit beyond me (I'm a doctor, not an engineer, and they didn't cover this stuff in medical school), but they found that with cylindrical needles result in approximately 5x the amount of cell death compared to a tapered needle at any given flow rate, and approximately 6-8x the amount of cells damaged. This was likely due in part to the need for higher pressures to increase flow rates in cylindrical needles compared to tapered needles and variations in shear due to the geometries. While a tapered needle is not identical to a plastic pipette tip, the geometries are comparable.
Biotechnol Prog. 2011 Nov-Dec;27(6):1777-84. Effect of needle geometry on flow rate and cell damage in the dispensing-based biofabrication process. Li M1, Tian X, Schreyer DJ, Chen X.
http://onlinelibrary.wiley.com/doi/10.1002/btpr.679/full

I have a real life biological example.
simplified experiment setup:
ex vivo purified B cells undergo 3 washes in PBS (spin and resuspend), then they are incubated in vitro for 24 hrs and analyzed by flow cytometry using Acqua Zombie and PI for dead cell exclusion.
Experiment 1: pipeting after washes using 1ml tip
Experiment 2: pipeting after washes using 10ml pipette
Cell survival as analyzed by flow cytometry:
Experiment 1: 9.96%
Experiment 2: 43.9%

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text:
Are there any plants that retrieve energy from the wind?
Many trees grow in windy places, but appear to have adapted to this by developing characteristics that provide resistance to wind.
Are there any plants that appear to have been selected for the ability to obtain appreciable amounts of energy from wind, apart from propagation of spores and seeds?

Does this answer your question? Are there known life forms that are able to transform mechanical energy into chemical energy?

Worldbuilding has a version of this question, for your interest.

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text:
Why are my faeces black in color after eating Oreos
Why are my faeces black in colour the morning after I eat some Oreos?
Day 1 : Eat a handful of Oreos & the next morning your stool is black.
Day 3 : Eat a handful of cocoa flavored biscuits & the next morning your stool is normal.
Day 5 : Eat a handful of Chocolates & the next morning your stool is normal.
I'm aware of the beetroot digestion story, and how it doesn't happen to everyone. What is surprising in the case of Oreos is that it just takes a
handful of Oreos to turn the stool black. But with any other biscuits or chocolates, my faeces are normal.
I don't have anything other than anecdotal evidence but a lot (NOT ALL) of my friends have had similar experience. Just Googling "Black stool after eating Oreos" & I see a lot of people (not all) having similar experience. Do note that to my knowledge it doesn't affect my body in any way.
Why is that the case? Why doesn't it happen to everybody?
What ingredient in Oreos makes it happen? What is the physiological underpinning?
Asking this question with curiosity than caution. Looking for biological/biochemical perspective.

@jreut sorry, i didnt understand what you are trying to suggest. Are u offended by my little not-so-funny joke at the end. Should i rephrase the question. Was my question unclear?

its based on the food coloring so
the food coloring is black so then it caused by that and the choclate just don`t to much oreos

This is a perfectly reasonable question based on a self-adminstered (human) trial. Morever, the proposer bases their observations not on one subject but several reports. The impromptu survey of friends etc. is also acceptable. By the way, self-reported intakes/output records are an accepted method in nutrition research.
My 2-year-old child exhibited the symptoms described above, after consuming two Oreo biscuits in the afternoon. That evenings soiled nappy (diaper) revealed a dark but otherwise well-textured stool. When my concerned partner brought this to my attention, it immediately reminded me of the use of carmine red and related food dyes for the measurement of gastrointestinal transit times. The principle here is that the dyes are not absorbed in the gut, so the time from consumption to excretion gives a measure of bowel function. Short transit time means no constipation and is considered a sign of great bowel function.
Based on the observations reported for Oreos, my educated guess would be that Oreo products contain miniscule amounts of non-absorbed colorants - something that is generally regarded as safe. Self-reported symptoms are generally considered valid by health professionals. I am still intrigued by the Oreo colouring puzzle, as this colourant must be natural.

Transgenics are also "generally regarded as safe", "because they contain DNA and our species has always eaten DNA". Just a comment.

I agree the question is reasonable, but I don't think you've answered it in any meaningful way. You've provided more anecdotal evidence which OP already has, brought in the example of beetroot (also raised by OP). The answer essentially here is "non-absorbed colorants" which isn't specific enough for me!

According to this site there is something called black cocoa powder, a particularly dark product referred to as an ultra-Dutch processed cocoa powder. The site recommends this for anyone trying to reproduce the colour of Oreos, claiming that it acts more as a colouring agent than a flavouring agent.
The site also recommends two commercially-available products so now you should be able to do a real experiment by baking two batches of cookies that differ only in whether they contain this. Then you can report back here, but maybe this time with photographic evidence.

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Can the mating of a couple with Rhesus positive and negative blood types result in miscarriage?
Can the combination of $+ve$ and $-ve$ blood groups of a couple be a cause of miscarriage in pregnancy?

I have added the qualification of Rhesus to the question, without which it is incomplete. Anyone can suggest an edit to a question. Please do so if you want to improve this SE.

I want to know can +ve and -ve blood group of a couple could be a cause of miscarriage in pregnancy?

Yes. In extreme cases, it can. You are talking about Rh Incompatibility, and can become a big issue when the mother has Rh(-) blood and the father has Rh(+) blood (such as the case with your cousin and his wife).
What could have happened (but definitely won't say for sure) is that your cousin's wife had a natural miscarriage which exposed her to the Rh proteins of the child, and then the subsequent pregnancy had complications due to the previous exposure and mother's development of antibodies which lead to the second miscarriage. However, I am not a licensed physician and you should consult a physician before pursuing any sort of treatments!!!
Rh factor is the presence of surface proteins on Erythrocytes (Red Blood Cells or "RBC"). If Leukocytes (White Blood Cells - most commonly reported as "T-cells") encounter Erythrocytes that do not share the Rh factor of their host, then they can develop antibodies to it - which help identify Antigens (foreign proteins and molecules). Once the Antibodies have been generated the Immune System can attack any foreign Erythrocytes.
In this way, the mother's Immune System can actually attack the RBCs of her child.
You can find out more here: http://kidshealth.org/parent/pregnancy_center/your_pregnancy/rh.html
And a few select quotations:

Rh incompatibility usually isn't a problem if it's the mother's first pregnancy because, unless there's some sort of abnormality, the fetus's blood does not normally enter the mother's circulatory system during the course of the pregnancy...
...Other ways Rh-negative pregnant women can be exposed to the Rh protein that might cause antibody production include blood transfusions with Rh-positive blood, miscarriage, and ectopic pregnancy...
...Rh antibodies are harmless until the mother's second or later pregnancies. If she is ever carrying another Rh-positive child, her Rh antibodies will recognize the Rh proteins on the surface of the baby's blood cells as foreign, and pass into the baby's bloodstream and attack those cells. This can lead to swelling and rupture of the baby's RBCs. A baby's blood count can get dangerously low when this condition, known as hemolytic or Rh disease of the newborn, occurs.*

And you are correct that there is a treatment via injection, but the Doctor is also correct in that administering it past the first pregnancy does little for future fetuses:

Today, when a woman with the potential to develop Rh incompatibility is pregnant, doctors administer a series of two Rh immune-globulin shots during her first pregnancy. The first shot is given around the 28th week of pregnancy and the second within 72 hours after giving birth. Rh immune-globulin acts like a vaccine, preventing the mother's body from producing any potentially dangerous Rh antibodies that can cause serious complications in the newborn or complicate any future pregnancies.

And the ultimate effects of missing the shots and having very unfortunate luck:

Rh incompatibility rarely causes complications in a first pregnancy and does not affect the health of the mother. But Rh antibodies that develop during subsequent pregnancies can be potentially dangerous to mother and child. Rh disease can result in severe anemia, jaundice, brain damage, and heart failure in a newborn. In extreme cases, it can cause the death of the fetus because too many RBCs have been destroyed.

Is there a cure? No. Once the antibodies have been developed, the Rh(+) protein is known to the mother's Immune System. Nothing short of wiping out the mother's Immune System would act as a cure.
However, in extreme cases, there are treatments:

If a doctor determines that a woman has already developed Rh antibodies, then the pregnancy will be closely monitored to make sure that those levels are not too high. In rare cases, if the incompatibility is severe and the baby is in danger, a series of special blood transfusions (called exchange transfusions) can be performed either while the baby is still in the uterus or after delivery.

But don't fret yet!
Rh surface proteins are determined by genetics, and each time a child is conceived there is a chance that the Rh protein will be (-) if the exact genotype of the (+) parent allows it. So if your cousin's wife were to get pregnant again (and each time she does) it's a chance that the Rh Incompatibility (aka - "Hemolytic Disease", aka - "Rhesus Disease") won't show up.
So there are some reasons to stay positive.

I would add one more thing - generally the longer they wait before trying again, the better chances fo a Rh+ foetus. Memory cells slowly die and in my country 5 years after last pregnancy with problems a Rh- woman's pregnancy is considered normal risk. Still - a specialist will tell you more and help your sister.

Ehh... Memory cells do slowly die, but they can last for up to 40 years. Though if the response wasn't strong to begin with, I suppose the level of CD4 cells could be relatively low.

As an addition it's worth pointing out that the timing and number of Anti-D antibody injections given to the mother varies, in the UK I believe it is at 28 and 34 weeks during pregnancy, soon after delivery then regular injections until the Kleihauer test comes back negative for foetal cells in the mother's bloodstream.

Sometimes If the pathology (Rh incompatibility) was diagnosed, the hormone progesterone is applied, functioning as a protection for the embryo and preventing pregnancy loss. Anyway, you should consult a physician first.

To add a more concise answer:
Yes, the conflict between positive and negative Rh (Rhesus) blood groups can cause miscarriage.
The genetic makeup decides whether red blood cells (RBC) carry a specific surface protein known as Rhesus factor (Rh). If your own RBCs do not carry this protein (Rh-), your body will consider it (or RBC carrying it) a foreign substance and treat it like anything foreign - the immune system will respond and eliminate it, just like an infection.
If a Rh- mother has a child whose RBC are Rh+ (which is possible even if only one parent was Rh+), the mother's body will develop an immune response against the baby's blood itself.
This includes the immune response's memory: just like it remembers the "fake" infection from a vaccine to protect against a real disease, the immune system will remember the Rhesus protein, so if future pregnancies develop babies with Rh+ blood, the reaction will be more severe.
See also Wikipedia on the Rh factor and Miscarriage due to Rh factor.


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What determines the fate of a cell with respect to differentiation?
I have been reading about Townes and Holtfreter's work in 1955, in which cells are dissociated from a blastocyst in an alkaline solution then mixed together and spontaneously reaggregates based on type, so epidermal cells around the outside and neural plate cells in the middle.
I understand enough about cell adhesion to understand why the cells will seem to attract cells of their own type, but would like to know how they can initially detect what to become and where they are needed in a specialised form, without something acting like a brain telling them what to become and where to go.
If the selection from the available types is random, as I suspect, what happens to blastocysts with too much epidermal tissue or vice versa? I'm struggling to imagine how organisms like this can develop without something taking the lead and actively coordinating what goes where.

Cell differentiation, cell fate and cell mapping is an interplay of accessible evolutionary strategies/programmes and responses to dynamic environmental cues such as specialized hormones (e.g. morphogens) and physical parameters and constraints. That is putting it very broadly. It is a complex issue, if L. Wolpert's PLOS assays are any indication. I compiled a few links to get you started.
Specifically, reappraising the topic of your cited classical experiment are R.Moore et al:

The classical cell sorting experiments undertaken by Townes and
  Holtfreter described the intrinsic propensity of dissociated embryonic
  cells to self-organize and reconcile into their original embryonic
  germ layers with characteristic histotypic positioning. Steinberg
  presented the differential adhesion hypothesis to explain these
  patterning phenomena.....

(Source: Robert Moore, Kathy Q. Cai, Diogo O. Escudero, Xiang-Xi Xu, Cell Adhesive Affinity Does Not Dictate Primitive Endoderm Segregation and Positioning During Murine Embryoid Body Formation, Genesis. 2009 September; 47(9): 579–589)
Regarding: ...without something taking the lead and actively coordinating...
On a hunch that you are not talking about complexity, attractors and polarity, I would like to share a few words. You may completely disregard them if you'd like.
My personal experience (from my country) is that few biologists delve into "that" branch of EvoDevo, because a profound understanding involves calculus, modeling and a knack for theoretical biology. Yet, afaik few struggled comprehending the evolutionary logic of making an organism based on Albert's book chapters alone.
See:

Reaction–diffusion system
Cell fate determination
Fate mapping
Asymmetric cell division
Pattern formation
Alberts Molecular Biology of the Cell describes this very well (can be accessed online for free)

I personally recommend G.Müller's authored/coauthored papers:
(open access)
http://homepage.univie.ac.at/gerhard.mueller/publications-papers.html
Disclaimer: I am not specialized in the field of EvoDevo or Theoretical Biology.
Views expressed here are my own.

I would like to add to Lo Sauer's nice answer but give a slightly different perspective.
What you referred to as the "brain" of the cell, is mostly its regulatory program. An abstract way to think about the regulatory program is like a computer, or mathematical function, which gets input (in the form of signal molecules inside and outside the cell) and calculates an output (behavior - which genes/proteins to activate, for example) based on this input. This is usually how cells make decisions, both in differentiation and when reacting to the environment.
Of course the really interesting part is how the regulatory program is implemented. It seems that most of it is encoded in the DNA, although there is also a significant role for epigenetics factors (non-DNA factors that are inherited from the zygotes). As you can imagine this regulatory program is highly complex and is being studied by many groups, mostly using genomic experimental and computational techniques. It is currently far from being understood at a comprehensive level.
You can read about specific simple examples in some of the places Lo Sauer mentioned, for example Drosophila embryo segmentation/pattern formation.


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Why do alpha-gal allergies only occur after a tick bite if alpha-gal is already present in red meat?
I just read an NPR article about allergies to red meat being caused by tick bites. That stood out to me because I thought allergies are triggered by an initial exposure to some allergen. In this case, the allergen is alpha-gal, a disaccharide found in cell membranes of most mammals; humans and apes are a notable exception. The article explains that ticks might cause this allergy by transferring alpha-gal from other animals to us when they feed on our blood.
However, we also are exposed to alpha-gal every time we eat red meat. How are we protected from allergic reactions when we eat red meat but not when we eat peanuts? Why does that protection fail after alpha-gal is exposed to our bloodstream?

Please give the full chemical name for the compound you refer to as alpha-gal. This is not a common abbreviation.

@David Gal is the standard abbreviation for galactose, per IUPAC.

@canadianer — The question referred to alpha-gal which is not, but in any case glc is the IUPAC abbreviation for glucose but it would be strange to use this. My point is that for optimal communication (and especially in titles) abbreviations should only be used if they are widely known (that is what I had intended) and really necessary.

@David the allergy itself is known by clinicians as alpha-gal syndrome. A common (but unclear) name would be meat allergy. I think the title is clear to people that are familiar with it.

In order for the immune system to respond to an antigen, beyond recognition of that antigen, there needs to be a signal that there is something wrong. Co-stimulation can take a few different forms, but it requires the involvement of more than just one arm of the immune system, and generally helps prevent our immune system from what I like to call the Dr. Strangelove effect (a psychotic lone general can just decide that there is a problem and launch an attack). Here, costimulation might be from (or downstream of) the tick bite and other invaders associated with the tick bite, or from an allergy to peanuts. You can read about this in the first chapter of Sompayrac's How the Immune System Works, as well as the first chapter of Abbas Basic Immunology.

Does the immune response also vary by the route that the antigen enters the body? I'm speculating here, but if the GI tract is less prone to triggering immune responses, that could explain why we're okay with eating alpha-gal but not if alpha-gal gets in our blood. While it's possible that the tick bite itself is a source of some costimulating substance, I also read that immune responses against alpha-gal may also play a role in rejection of pig tissue implants. I can't imagine that a similar response would occur if we ATE that tissue.

@BatWannaBe yes, mucosal exposure is less immunogenic, and eating pork is different from having a porcine valve. Costimulation is a requirement, though, however the antigen is introduced.

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What is protein secondary structure?
Could someone please clarify what is protein secondary structure:
https://en.wikipedia.org/wiki/Protein_secondary_structure
I believe I understand the primary structure, I am not sure what's the difference between secondary and tertiary structure. Tertiary structure seems to be 3d structure of a polypeptide but I am not at all clear about the secondary structure.

Can you clarify your question? what do you know about protein secondary structure and what are you having a hard time understanding?

@DanHall I am studying the structure of protein and while I believe I understand the primary structure, I am not sure what's the difference between secondary and tertiary structure. Tertiary structure seems to be 3d structure of a polypeptide but I am not at all clear about the secondary structure. Does this help?

edit your question to include that  :)

Proteins are made up of long chains of amino acids covalently joined together. The order of amino acids is the primary structure of a protein. In physiologic conditions, these long chains of amino acids fold into three dimensional shapes. The terms secondary and tertiary structure are used to refer to specific aspects of the three dimensional shape.
tl;dr what's the difference?
Both secondary and tertiary structure refer to the three-dimensional shape of a protein. Secondary structure is the regular repeating patterns, generally stabilized by hydrogen bonds between the NH and CO groups of the peptide backbone. Tertiary structure can be thought of as the way secondary structural elements fold together to create the overall shape of the protein.
Secondary structure
Secondary structure refers to regular repeating patterns stabilized by hydrogen bonding between the NH and CO groups of the peptide bond. Typically textbooks will focus on the $\alpha$-helix and the $\beta$-sheet.
Berg biochemistry has some useful diagrams demonstrating these secondary structures. The first is an $\alpha$-helix. The side-chains are represented by green balls here. Notice the orientation of the NH and CO groups, which stabilize this structure:

The $\beta$-sheet forms a very different secondary structure, but it's also stabilized by hydrogen bonding between NH and CO groups of the peptide bond.

Tertiary structure
Tertiary structure is the larger three-dimensional structure of a protein in its environment. It can be useful to think of tertiary structure as the way different secondary structural elements fold together to form the full, active protein. Notice in this figure, also from Berg, the way the elements of secondary structure (the $\alpha$-helices) fold into an overall three dimensional shape that can nicely cradle the heme group.

Secondary structure proteins are repeating chains of alpha helixes and beta sheets like spider silk.
Tertiary structure proteins are globular proteins, like enzymes.

All proteins have both secondary and tertiary structure in physiologic conditions. These terms do not refer to different proteins. They refer to different aspects of their structure.


text:
Can a vaccine or antidote be administrated via gases or sprays?
On TV or in movies a gas or spray containing a vaccine/cure/antitoxin is released and everybody is saved. Is this something plausible in real life? Specific examples would be appreciated.

Yes. This has been possible since the 1990's. In the US recently, the flu vaccine was recently offered as a nasal spray.
There is current research being done to aerosolize several vaccines. Public health officials have an interest in this method due to it being less expensive to produce, more people can receive the vaccine in a shorter time frame, and less need for infrastructure.
In India, they have started to give children aerosolized versions of the Measles vaccine. From research published in 2015 in The New England Journal of Medicine, scientists were reviewing how effective the aerosolized version is against the vaccine given subcutaneously. Even though the group's statistically analysis of the children's seropositivity, a method derived from previous studies, demonstrated  the aerosol vaccine was statistically "inferior" to vaccines given sub-q. However, both groups of children had the same protection from the Measles.
https://www.nejm.org/doi/full/10.1056/NEJMoa1407417
https://www.ncbi.nlm.nih.gov/pubmed/12656420
https://www.jimmunol.org/content/196/12/5014

There are a number of currently used aerosolized vaccines throughout the world. Generally, these are studied and administered in single individual doses. There are advocates for the use of larger, sealed exposure chambers for rapid administration of vaccines to large numbers of people, possibly in the field, for example in a tent like this figure from the earlier linked reference.

The primary barriers for a general release of a vaccine or other medication as, e.g., an aerosolized spray, would be ethical (difficult to get consent from all potential exposed individuals) and dose related (difficult to ensure a specific safe and effective dose).
The closest natural experiment I'm aware of would be the use of live attenuated Sabin oral poliovirus vaccine. Unlike other currently used vaccines, the Sabin vaccine is transmissible. In developing countries, vaccine is transmitted from vaccinated individuals to un-vaccinated individuals through the fecal contamination of food and water, using the same route that wild type poliovirus is transmitted. This can result in extending immunity beyond those who directly receive the vaccine. You could conceptualize this as blanketing a local population with vaccine. It's not without problems, though, because in cases where the overall initial vaccine coverage is low, circulation of the vaccine can eventually result in reversion of the reservoir of previously non-virulent (attenuated) vaccine to a virulent type. This is how you get vaccine derived polio outbreaks, and one of the reason not to use transmissible viruses as vaccines.


text:
How are we able to selectively inflate our cheeks?
First an observation - I noticed that I can not inflate my cheeks with my mouth open. This means that inflating cheeks is not a muscle property and that only pressure of air from lungs trapped inside my closed mouth is responsible for any inflation. Also, once inflated I can move my tongue anywhere and still retain the inflation. This means that tongue is also not responsible for air regulation inside mouth.
Moving on, we all know that we can either inflate both our cheeks, or we can inflate only cheek from one side or we can inflate *portion of face between lips and chin* (I don't know what it is actually called). Put simply, we have complete control over which part of my face would I like to inflate.
I don't understand how this is possible without muscle control? Air has tendency to occupy all space therefore my entire cheeks should get inflated without me having any control whatsoever, but as it turns out I can control and redirect the air to apply pressure only at a particular cheek without any help from tongue. How?

Why have you concluded that not being able to inflate your cheeks with your mouth open means the muscles of your mouth and face are not involved in control the space available for inflation?

I was convinced that facial muscles could only produce inflation and not contraction (mostly because we never feel contraction). A naive conclusion on my part as evident by Bryan's answer.

Muscles can only "pull" never "push" - that's just how they are organized at a molecular level. We can only push things because we use joints as levers: if you "pull" on the outside surface of your arms, you can push things out with your hands because that pull acts to extend the forearms.
It's not really possible to puff out your cheeks with muscle, because there is nothing floating in the space outside your face to pull against. Your cheeks puff up a bit when you smile, but I think you will agree that's a completely different type of "puffing" and comes from gathering up a bunch of tissue.
However, it's fairly simple to contract muscles in your face (specifically the buccinator) to prevent a cheek from bulging out by tightening the muscles in the cheek. The air pressure you are producing is pretty minimal, so it doesn't take much strength. The cheek bulges out when the muscles are relaxed, and doesn't bulge when the muscles are contracted.

Perfect. Just one follow up. When my mouth is closed and cheeks not inflated, are my cheek muscles still contracted? I ask this because when I then attempt to inflate my one cheek I do not notice any significant feeling on my other cheek of contraction or whatever. Is it because muscle contraction is so insignificant that I did not feel it, or because my facial muscles were already contracted before I attempted inflation.

@Sarthak123 I think you would get your answer reading about muscle tone. In general, though, you don't really feel muscle contraction except when it is unusually forceful (especially a cramp), and even then you may also be feeling the movement of other tissues rather than the force of the muscle itself. Think especially about all the muscles in your back and core that maintain your posture: you probably don't ever notice them and they are doing a lot more work than your cheek muscles would be.

While it's true that we don't have facial muscles to actively move our cheeks, we DO have muscles to put them under tension (I don't which specific ones that are though).
If we apply both air pressure from our lungs and tensions to (selected) cheeks, we can thereby control which regions to inflate.
As an anecdotal note: building up and using this tension is especially important for musicians playing wind instruments


text:
Normalise protein database domain-wise
Suppose we've collected a big (hundreds of thousands) library of different protein sequences with certain features. Then we want to use this data base to train a classifier. And for several statistical reasons we want different functional domains to have somewhat equal frequencies in the data base to reduce domain-specific bias. The straightforward way to achieve this is to use structural information from UniProt and the like, but many proteins don't have any verified structures and de-novo structure prediction might take ages to compute. Alternatively we can perform sequence clustering and pick an even number of sequences out of each cluster. We can either apply a local-alignment based clustering algorithm with ~35% identity threshold or use some sort of hidden Markov model to cluster by profile. What do you think? How biologically relevant this might be? Can this simple clustering based approach help normalise the library to some extent?

Biologically relevant for what? If you told us what are the "statistical reasons" or why would you want that we might be able to help. I understand the question but I have no idea what would you want to get rid of some data just to have a "non-biased database".

@Athe We are working on a prediction tool that can get biased due to overrepresentation of specific functional domains in the data set. I'm sorry, but that is as much as I can tell due to information policies in my lab. The sole question can be put in a single sentence: "Is sequence clustering sufficient to normalise the library domain-wise?"

Any bias you will get will be the result of a deeper knowledge on certain structures or domains, rather than because of your database. Anyway, if you had a biased database that wouldn't mean you identified wrongly the proteins, but rather that your ability to identify proteins would greater when dealing with certain stuff.

@Athe basically, we want to compare the performance of biased and unbiased classifiers. It's likely that an unbiased classifier will fare better with new data on poorly studied proteins.

@EliKorvigo If I have understood your question: I am wrestling with a similar problem, and this is why clustering is useful. Generally, clustering reduces over-representation of a group. What it cannot do is increase underrepresented elements, which in databases is a big problem. Over/under-representation is likely due to the element being over/under-studied (often because of "fashionable" subject area, or experimental difficulty) rather than biological significance.

@James good to hear from you. I've been working on this ever since. Regretfully, clustering based on sequence alignment is of little use for complicated/modular objects such as proteins.


text:
Mouse H2 allele sequences
I've been trying to find complete sequences of mouse (Mus musculus) MHC H2 locus haplotypes for quite some time now with limited success. The EBI IMGT database has a table of mouse H2 haplotypes, yet IMGT only provides haplotype sequences for human HLA genes via an FTP sever. I've found similar data for several other species at EBI's IPD-MHC, but Mus musculus is not on the list. The MGI database provides access to H2 SNPs, but I haven't found a mapping from SNP combinations to reconstruct happlotype sequences given reference genes.

Are you after amino acid or gene sequences?

@David I'm looking for nucleotide sequences: "I haven't found a mapping from SNP combinations to reconstruct happlotype sequences given reference genes". Protein sequences are readily available in the UniProt database.

I have also hit this issue. I was interested in full length amino acid sequences for the classical class I mouse MHC alleles. I was able to find a number of them on uniprot but not all. Here is my list below. Interested if anyone knows additional sequences to extend this:
H-2 D

H-2 Db
H-2 Dd
H-2 Dp
H-2 Dk
H-2 Dq

H-2 K

H-2 Kb
H-2 Kd
H-2 Kk
H-2 Kq

H-2 L

H-2 Ld
H-2 Lq

Seems a useful answer to me, but I wonder whether the poster wanted gene or protein sequences. He didn’t say.

Thank you for your effort. I've been using these UniProt protein sequences myself, but the question is about nucleotide sequences. Those are harder to find.

MGI database may give you some help about Mouse H2 complex full length sequence.
https://www.informatics.jax.org/quicksearch/summary?queryType=exactPhrase&query=H2&submit=Quick%0D%0ASearch


text:
Flower identification: Moscow, Russia
I found this plant near the MSU, Moscow, Russia. Could someone help me to identify it?

Look into species in the Caprifoliaceae family, for instance species in the Knautia genus. The flowers and leafs in your pics look very similar to these.

It looks very similar to Cephalaria gigantea.


text:
Can two Hfr strains of E. coli conjugate?
Genetics textbooks (and some internet searching) yield abundant examples of Hfr strains conjugating with F- cells, but these sources are surprisingly silent regarding the results of an Hfr encountering another Hfr strain. Will conjugation occur in both directions, or will it not occur at all? Similarly, can F+ cells conjugate with other F+ cells?


text:
What determines which strand of DNA is transcribed by RNA polymerase?
DNA has two strands. How does the machinery of RNA transcription determine which one to transcribe?

I'll keep this short and simple. The direction of transcription (which determines which strand is used as the template) is controlled by the promoter, which is a region of specific DNA motifs at the 5' end of a gene. RNA polymerase binds to the promoter, which orients it on the correct strand and in the correct direction, after which it can proceed to transcribe the gene.

That great little animation is from this website.

To add to canadianer's answer, in fact genes can be found on both strands of the DNA in most eukaryotic cells, in the sense that the sense and anti-sense strands are not always the same strand. The direction is therefore completely determined by the promoter. Furthermore, there are bidirectional promoters.

This is interesting +1!! Can you add a reference to the sense/anti-sense being not confined to a particular strand?

@AliceD I'm pretty sure that he/she is just referring to the fact that, along an entire chromosome (which has two strands), some genes will be found on one strand and some on the other. The terms sense and antisense are relative to a specific gene, not an entire chromosome. Sometimes, uncommonly, two genes will overlap on opposite strands at the same loci.

@AliceD that would be pretty much any genome paper or undergraduate text book, really.  For a visual overview, have a look at this. You'll see genes in both directions, so on both strands (the direction is given by the arrows in the lines representing the genes).

@terdon, gosh I feel kind of..  erm,... dumb, but I have struggled with this concept for years. Thanks!!

@AliceD good grief, when did not knowing something not directly related to your field become a reason to feel dumb? Did I miss a meeting? My PhD was on gene prediction and genome annotation, so this is my bread and butter. Just don't ask me to describe the Krebs cycle :)

@terdon I have a BSc in Biochemistry. I left the field a decade ago and went into neuroscience. Honestly, I have struggled with this since the first time I started learning about DNA. It all didn't make sense. I honestly thought there was one coding strand, and the other was just a backbone for chemical stability..:-/ This post has enlightened me for sure. It all fell in place. Just here.


text:
Are there animal species who would sacrifice their lives to save their offspring?
In the comment section of YouTube animal videos, there are people who say that animal mothers love their offspring very much as if human mothers do. But are there actual animal species whose parents are willing to lose their lives to save their offspring's lives?
Thinking purely in the perspective of spreading its genes more, it seems to me that it will be better to save the parent's own life and produce more offspring in the future than losing his or her life to save current batch of offspring, so I cannot think animals have that much "love" for their offspring, but it could be wrong.
Also, exclude the species that reproduce and automatically die afterwards, like salmon.

Why exclude the species which are the clearest examples of the circumstances you describe? Especially because I'd wager that a majority of animal species follow that pattern.

Is it actually true that human parents are willing to sacrifice their lives to save their children? It's a saying that gets a lot of advertisement, but does data actually back it up?

animals are willing to kill to save their offspring and are at the risk of getting killed by doing so.i think that it is fairly close to sacrfice their life?

The pelican is often used in Christian symbolism because of the belief that a mother pelican will kill herself to feed her brood. However, I'm having trouble finding any zoological / scholarly sources that confirm or refute this phenomenon.

In support of the other side of the argument, pelicans have been observed cannibalising their own chicks.

"Thinking purely in the perspective of spreading its genes more, it seems to me that it will be better to save the parent's own life" My understanding is that this tends to be the case not that long ago when people had many more children than they do now and infant mortality was much higher. At that time, it was arguable that losing your spouse was more traumatic than losing your child. Also social insects routinely sacrifice themselves to save their progeny.

@trondhansen Yeah, tell me an example of a species that actually takes very real danger to its own life to save its children.

@DKNguyen The social insects example, I think, is not applicable here, because they are not parents but copies. That is, the individual who sacrifices itself have the same genes as the ones that it saves. I was talking more about parents whose children have only 50% of one parent.

Large herding animals do this all the time. Surround the weak and young

Plovers fake injury to draw predators away from their nest, drawing the attention/interest of the predator to themselves. Parents die trying to save their kids somewhere in the world all the time: parents drown holding the child above them, push their kids out of the way of oncoming traffic, mothers forgoing chemotherapy while pregnant and allowing the cancer to advance and become fatal, etc. Animals may not love their offspring in the same way, but they do love them (read Jane Goodall's work.) But I suspect you'll reject any answer just for the sake of argument.

@anongoodnurse Brings up a thought...you probably need to look at animals that live in communities and can rear the orphaned offspring. The parent sacrificing itself to save an offspring is pointless if all the offspring die. I am unsure if a single parent could do the job unless that was the normal arrangement for that animal, but in that case it is also less likely, though not impossible, that the non-caregiving parent would be around to sacrifice itself in the first place. If just you and your 5 year old live in an isolated cabin in the woods, it is quite pointless to sacrifice yourself.

Which also brings up the fact that dying in an attempt to save your offspring is not the same as willingly sacrificing yourself so your offspring lives on. In that respect, it may be impossible to know what an animal's intentions were because you do not know how they think since you are not that animal.

For the human side, if wikipedia is to be held reputable in that matter (1 and 2), filial infanticide has been observed in humans as a form of population control in situation of scarcity. It was quite common, it was transversal to all cultures and it had been there since before the invention of agriculture. Concerning sex-selective infanticide, I take the liberty to remark that a reasoning like "I can raise another two sons, but not a second daughter" is a rather sophisticated take on scarcity.


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Why do Type II Restriction Endonucleases cleave at palindromic sequences?
Type II Restriction enzymes usually cut only at palindromic sequences. Is there any specific reason for that? Is there any advantage for bacteria if they cleave phage DNA at this type of sequence?

First, not all restriction enzymes cut at palindromic sequences.
A lot of them do though, simply because it is more effective. Recognising a palindromic sequence enables them to cut both strands of DNA at the "same" site, because the strand will have the same sequence only in different directions at that site.
See Wikipedia for example.

Of course..you are right but what advantage did a bacteria have by evolving such enzymes (which cut at palindromic sites)?

That it's going to cut both strands. So it is more efficient.

Yes you are right.Many of the bacteriophages are double stranded. Thanks :)

Short Answer

The palindromic symmetry of the restriction site allows a dimeric
  enzyme to bind the DNA in a manner that bends the double helix in a
  way that facilitates the endonuclease reaction.

More Detailed Answer
The ‘palindromic’ nature of the recognition/cleavage site of restriction endonucleases, such as EcoRV (illustrated here) results in a form of symmetry (A) that allows a dimeric enzyme — that forms a tunnel — to bind symmetrically at that site in the DNA (B).

This binding causes the DNA to bend (C) bringing a catalytic magnesium ion into a position in which it can interact with phosphate of the phosphodiester bond that is being cleaved (D). (The dimeric nature of enzyme allows force to be exerted at two points, to produce the bend. Compare bending a thin pipe over one’s knee, applying equal force with both hands.)

Methylation of the adenine nucleotide in the recognition sequence prevents hydrogen bonding of the enzyme to the DNA. DNA lacking the recognition site is not cleaved by the restriction enzyme because it does not bind specifically to the protein so that the magnesium ion remains too far away.
Reference
This answer is based on chapter sections 9.3.2 and 9.3.3 of Berg et al., which is available online at NCBI Bookshelf and is well worth reading in full. There is also a PDB Molecule of the Month item on this, although unfortunately the bending of the DNA is not apparent in the images there.
Comment on Last Two Sentences of Question
There is no particular “advantage for bacteria”  other than “it works”.  So I think the last sentence is looking at things from the wrong perspective.

This late answer was provoked by a recent duplicate question. I felt that none of the answers to the original or duplicate covered the reason why the recognition by an enzyme dimer was important to the cleavage.

These REs, that recognize palindromes, are mostly homodimers and hence the same sequences (for each monomer)for recognition, only they are reversed. This explains the palindromes.


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How does the hydrophobic amino acid fuse the corona virus with the host cell membrane?
I am reading the article How the coronavirus infects cells — and why Delta is so dangerous.
It describes the fusion process of the virus into the host cell as follows right above an animation demonstrating the process.

First, TMPRSS2 cuts a site on the spike’s S2 subunit8. That cut
exposes a run of hydrophobic amino acids that rapidly buries itself in
the closest membrane — that of the host cell. Next, the extended spike
folds back onto itself, like a zipper, forcing the viral and cell
membranes to fuse.

Is the hydrophobic property of the hydrophobic amino acid crucial for the burying into the closest membrane and folding back onto itself? What is the physics of this mechanism?

The way you pose your question is problematic. First you appear to be asking two questions, one of which you demand to be answered with “detailed physics”. If that is so you would seem to be posting on the wrong site, although another interpretation is that you require an explanation of the “hydrophobic effect” — chemical thermodynamics of proteins, covered in the introductory chapters of biochemistry texts such as Berg or Lehninger. If this is the case (and the obviousness of the answer — yes the hydrophobic nature is crucial — suggests so), your question comes under the category “homework”.

Your second question, which, if valid for this site, needs to be posed separately. Again, it is not sure whether you are familiar with proteolytic enzymes in general (use of the word "cut" suggests perhaps not) and the frequent activation of proteins by hydrolysis of peptide bonds. Even if you are, the phenomenon is widespread in RNA viruses because of their tendency to synthesize polyproteins (for reasons discussed elsewhere on this site). There are numerous articles on the effect of proteolysis on Covid spike protein, suggesting you are not searching in an appropriate manner. Why not?

As you hace accepted an answer that only addresses one of the questions, and as the second should have been posted as a separate question I have edited your question and removed it. I have also cut unnecessary material about homework questions etc. as this has been addressed and is not part of the question.

Hey, @David--while I appreciate the edit to remove the close vote discussion from the question, I disagree with removing the part about the cleavage initiating the process. The answer does address this (see paragraph beginning: "The cleavage of spike is crucial..."). While the asker did write separate sentences ending in question marks, they both describe the same process, as fusion does not happen without cleavage. The original way the asker formatted the question (without the ordered list) makes the most sense to me.

Happy to discuss this further in chat if you disagree! Just ping me and I can jump in. Will not edit in case you want to chat.

@David: Actually I was planning to say things along the same line as Luigi several days ago but had been really busy. I will raise my objection in details later.

@Luigi — I am away and only checking SE to respond briefly to direct messages. As far as I recall the first part of the question requires an answer that relates to the precise molecular details of proteolytic cleavage on the structure of the spike protein, an answer in which the latter is represented by a triangle does not do. Nor do I see anything in your answer that would seem irrelevant to the question as abbreviated. If you go ahead regardless I feel that will only diminish your answer, but on your head be it.

Interesting question! Yes, the hydrophobic amino acids are very important; they facilitate interaction with the hydrophobic (inner) portion of the lipid bilayer. A useful review focusing on the bilayer side that I'll reference throughout this answer is here: Mechanics of membrane fusion, doi: 10.1038/nsmb.1455.
(a) shows a model of two lipid bilayers fusing (minus protein contributions). Essentially, the spike makes this process thermodynamically favorable.

The hydrophobic residues are key because they are what enables the other end of the spike protein to interact with and deform the cell membrane. Here's a model of protein-mediated fusion from that same review (they emphasize that the deformation is key):

The cleavage of spike is crucial to initiate this process because the hydrophobic residues are not accessible/cannot interact with the cell membrane unless the spike has been cleaved. This works to the advantage of the virus, since if the spike is close enough to be cleaved by TMPRSS2, it's close enough to stab the membrane of the correct cell. A virus with hydrophobic residues that are always ready-to-go, in comparison, would likely fuse with a lot of random/off-target membranes of cells or vesicles that would not be permissive to viral replication.
Mechanisms of membrane fusion disparate players and common principles is a review paper.
A detailed discussion of the physics of this process is beyond the scope of this site, but here are some potential starting points (disclaimer: I am not a physicist):

Mechanics of membrane fusion/pore formation
Membrane tension and membrane fusion
The hydrophobic force: measurements and methods
Reconciling the understanding of ‘hydrophobicity’ with physics-based models of proteins

+1 and accepted. This is exactly the kind of answer I am looking for! Much appreciated!

I added one more physics reference that is more recent. Hope you do not mind.

(+1) But to avoid confusion: if we consider the lipid membrane a bilayer, the interaction is with the hydrophobic portion of the outer layer of the bilayer? (And this is due to the 'oil in water' (or hydrophobic) effect)

Release of S1 trimer should be what allows conformational changes of S2 whose transition to lower energy state curves the membranes (assuming the fusion peptide anchored into the host membrane). https://www.pnas.org/content/114/42/11157 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7112261/ There is more than one spike trimer involved, curving the membranes at different points together induces a hole and fusion of the two membranes. But it is very difficult to be sure because CryoEM doesn't fit well with membrane stuffs and conformational transitions. @Hans

@reuns: I appreciate your technical point. Let me read the paper you link to and respond later.


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What is the most basic organism to respond to Classical conditioning (capable of learning)?
I have been doing some reading of Classical conditioning which is considered to be an indication of animal's ability to learn...
Before this I considered insects to be machine like - devoid of any sort of 'thinking' just doing things that evolution 'made' them to do to survive...
However I have found that cockroaches and even fruit flies could be conditionally trained...
Which made me wonder What would be the least complex species that respond to classical conditioning?
I have also read this question about single-celled organisms capable of learning and I don't think that this 'cuts it'... this is nothing more than chemical response... however classical conditioning is different and in my opinion certainly does indicate ability to learn...

It's not clear what you mean by "first"? Earliest in evolutionary time?

@kmm Hi kmm, I am looking for the 'most basic' one, but I think that acquiring ability to learn was so advantageous that it will be same ancestor for all of us that got this ability, so evolutionary 'first' should be the same...

C. elegans, with only 302 neurons, is reportedly capable of both learning and memory, e.g. http://learnmem.cshlp.org/content/17/4/191.long so very simple nervous systems are capable of it.  Don't know how you would determine which was first in evolution, as behavior doesn't fossilize well :-)

@jamesqf Wow! Could you post it as answer please I would like to accept it... I am sure that first ancestor is long gone....

I changed your question to ask about the least complex as opposed to the first since the "first" doesn't really mean anything (see, for example, here).

While we all have a vague intuition of what is a complex and non complex organism, the term complexity is not well defined. I would guess that the accurate definition would matter little to the purpose of the question though

@Gerardo Furtado: Actually that nematode is argually more evolved than a human (or just about any vertebrate), because evolutionary time should be measured in generations, not years.

@Gerardo Furtado: I didn't read it.  It seems a fairly obvious conclusion from the mechanism of evolution.

@GerardoFurtado obviously, the whole idea of "more evolved" doesn't make any sense. However, if you were to use the term, the only reasonable definition for "more" or "less" evolved would be "has gone through fewer or more generations". By that measure, nematodes are indeed "more evolved" for whatever that's worth. Relevant Q&A: https://biology.stackexchange.com/q/832/1306

@GerardoFurtado good grief, relax! Please read what we are saying, my comment (and my answer in the linked post) are saying precisely that the whole idea of "more" or "less" evolved is nonsensical. However, if you were to use those silly terms, the only way they might make sense is in terms of generations. And with all due respect, get off your high horse. We're all experts here and have been working for just as long as you have.

Very simple nervous systems are capable of learning  C. elegans, with only 302 neurons, is reportedly capable of both learning and memory.  There is a fairly large literature on the subject, as C. elegans is a popular research subject - a Google Scholar search gives about 40K hits, e.g. http://learnmem.cshlp.org/content/17/4/191.long
We have to remember that small is not necessarily primitive: the C. elegans nervous system (like every other one in existence today) has been optimized by millions of generations of evolution to do what C. elegans needs in order to survive.
Actual evidence of learning in nervous systems in the distant past is rare.  It's behavior, and behavior doesn't fossilize well :-)  Actual nervous systems apparently don't fossilize all that well, either.  The earliest well-preserved example I could find was this http://www.cam.ac.uk/research/news/520-million-year-old-fossilised-nervous-system-is-most-detailed-example-yet-found from 520 million years ago.  But since learning would give a creature a survival advantage, I'd guess that it evolved fairly early.


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Can antimicrobial peptides be called antibiotics?
Antibiotic peptides are present in almost all multicellular eukaryotes. So can they be called antibiotics ? ( which are usually defined only for fungi and bacteria )

Antibiotic peptides are definitely antibiotics.  They are often referred to more specifically as peptides because the fact implies that they are less toxic and conveys some important understanding of how they work.  Not sure if they all form pores in the target cell, but that's how magainins work.


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Is plaque formed even if you do not eat anything?
Some people report that their gum and dental health improves when they are fasting. Many forums contain crazy amounts of misinformation and claims which are unsupported by serious scientific research, so many people attribute various effects of fasting to their body being "purged of toxins" and all sorts of other nonsense.
I have noticed one of these effects on myself when I'm fasting - my teeth get somewhat sticky in the evening. The same effect is reported by many people on the aforementioned forums. On normal days when eating food, this does not happen.
It's pretty certain it's not some sticky toxins being excreted by the teeth. So what is it? I strongly suspect that it's just normal plaque, which would otherwise be abraded by chewing on food. But I always assumed that plaque is formed by food remains in the mouth, so it leads me to the question:
Is plaque formed even when one does not eat any food?
Citations of scientific literature are welcome.

But I always assumed that plaque is formed by food remains in the mouth

It's not surprising that you'd have this assumption. The clinical term, dental plaque, refers to soft deposits on the teeth. While is often described to the lay public in connection to eating (without brushing), it is not food, or the remains of food, it is a biofilm. Biofilms are complex masses of bacterial colonies in a gel-like matrix produced by those same colonies. The matrix typically, helps the colonies adhere to some surface and protects them from external threats.
Good supporting electronic references of what, exactly, a dental biofilm is and how it impacts the health of your mouth and body are behind a paywall, but you may be able to access them at your local public or school library. Socransky and Haffajee have a good review in Periodontology. You can find it on Pubmed (behind a paywall).
As you suspected, not eating does not prevent plaque formation, but it is not because your teeth are excreting sticky toxins. Your mouth is full of bacteria, most of which lives peacefully without causing any problems. They're the ones that make the plaque, and they will make it whether you eat or don't. Whether or not those bacteria are more likely to cause problems (e.g., cavities and gum disease) if you fast is a question for future research.
There is some evidence that the bacterial composition in the mouse gut changes when they fast, and that obesity is associated with periodontal disease in humans. There is some interesting evidence in support of effects of intermittent fasting that would make it reasonable to ask a research question about the impact on dental caries and periodontal disease, but that evidence isn't enough to support fasting as a treatment for any disease.
tl;dr
Plaque is (caused by) bacteria, not food. It's produced whether you eat or not. Fasting is certainly not an approved treatment for periodontal disease or cavities, and I'm not aware of any direct evidence supporting it.


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Vibrio vulnificus from liquid soap
At some point between 2002 and 2006 I attended a departmental seminar in the UK on Vibrio infections, and particularly on the (then relatively unheard of) V. vulnificus, which causes necrotizing wound infections and septicemia when it enters open wounds. The speaker discussed two case studies: the first was of a case (possibly a cluster of cases) in a garage, I think in Australia, where the workers repeatedly topped up a liquid soap dispenser from a big bottle rather than replacing the bottle, and it had at some point become contaminated with V. vulnificus, which had survived in the soap, and infected an individual who went to wash their hands because they cut themselves.
The second case, which I only mention because it was part of the same talk and I have a suspicion the seminar speaker (whose name I can't remember) might have written papers on both, was about the rise in V. vulnificus cases in the Middle East (Israel, I think) which arose from a new trend for fish markets offering live fish in tanks at market rather than transporting them for a few hours on ice before sale (which was previously killing the bacteria, which occurred fairly ubiquitously in Israeli fish farms due to the high water table and high groundwater salinity).
This was a great seminar with two great stories that illustrate the ecology of Vibrios and I'd love to have sources for either, but particularly the first one. However, I can find no mention of either in the literature. Can anyone help?

The Isreali outbreak (associated with changes in fish marketing) was reported in Lancet a few times. It was particularly important for identifying biogroup 3. I hope that might be helpful, but I'm not sure it will be. Since it was an important epidemic, I wouldn't be surprised if it was discussed in a visiting lecture by someone who wasn't part of the Isreal Vibrio study group.
I'm not aware of a soap dispenser case for V. vulnificus, but soap dispensers have been implicated in the transmission of other pathogens. Could it have been some other halophilic bacteria, possibly another Vibrio?


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How can we smell odor direction if we breathe through one nostril at a time?
It's known that humans breathe mostly through one nostril at a time. How can we then perceive the direction the smell is coming from? Some articles claim similarity between olfactory and auditory directional perception:

The direction of a sound source can be determined binaurally by using
  the time difference and the loudness difference of the sound waves
  arriving at the two ears. Similarly, the direction of an olfactory
  source can be determined by using the time difference and the
  difference in sensation magnitude of the olfactory stimuli between the
  two nostrils as the air surrounding the odorous object is inhaled.
  Time differences of the order of 0.1 msec can be recognized—a value
  similar to that found in hearing.

However, that explanation runs afoul of breathing mostly through only one nostril at a time because at least the difference in sensation magnitude of the olfactory stimuli should depend heavily on which nostril is 85% shut and which one is wide open.

HI Michael. I think your question can be solved by re-reading the source you interpreted to mean humans only "use" one nostril at a time.

@DeNovo, if you barely breeze through the 85% closed nostril you are unlikely to smell through it with the same intensity as through the open one. That makes it unlikely that you can use at least the difference in sensation magnitude of the olfactory stimuli between the two nostrils as the air surrounding the odorous object is inhaled part of the suggested mechanism of directional olfactory sense.

I believe both the low flow and high flow nostril are used to detect smells in a given cycle. I think your question could be improved by changing "use one nostril at a time" to "breathe from one nostril at a time", since you're saying "Its known..." It is not known that humans only detect smells from one nostril at a time.

Good edit, and I think this is a very interesting question. I just edited myself to change breeze to "breathe", which I think is what you meant. Feel free to roll back if i misunderstood. I don't have electronic access to the physiology study from the 60s you referenced, but I am very curious as to whether they took this into consideration.

my guess is that it requires detecting differences in concentration by turning your head.

A more recent (and complete) article: https://www.nature.com/articles/srep05796


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What is going on with these buccal epithelial cells?
A pooled saliva sample from a 70 year old male. What is happening with these cells?

Are these cells undergoing normal apoptosis?
In the video, the cytoplasmic movement looks liquefied and jelly-like (A).
B looks more granular, with small vacuoles that seem to have bacterial activity in them (what could this be?).
Elsewhere in the sample were completely detached, intact nuclei.
Could this be indicative of diabetes? http://www.jdrntruhs.org/temp/JNTRUnivHealthSci1133-9277352_023437.pdf

The cell you've marked "B" is dead, as is common in cells in a saliva sample. The particular path to cell death is very hard to say with an unstained light micrograph, but the fact that you have a dead blebby cell in a saliva sample is not diagnostic or indicative of anything.

If there is a relatively high abundance of them in saliva, could it be indicative of oxidative stress/lipid peroxidation/ROS?

@SMc The count of dead/live buccal cells in saliva is not useful diagnostic information

Thanks. Could you share what signs in a stain might indicate a particular path to cell death?

@SMc generally, you'd at least want an H&E stain to help identify the eosinophillic and basophillic elements. You can read more about a variety of different ways pathologists identify different pathways to cell death here

Thank you very much for the info and link, exactly what I didn't know I needed. Much appreciated!


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Ascending loop of Henle
When ions diffuse out passively or are actively transported out of the ascending loop of Henle, do those ions just hang around or do they go into the circulatory system and leave the kidney.
I ask because I know the medulla must stay salty but I always assumed that those ions were then entering blood vessels for another purpose.

Do ions in the medullary interstitium just hang out, or go into the circulatory system and leave the kidney?

Both!
You've grasped one of the fundamental principles of the renal physiology -- the medulla must stay salty. Lets start there and see if we can't work out what happens.
As the filtrate flows through the tubule, solutes are removed from the lumen at the thick ascending limb and added to the medullary ECF. This concentrates solutes in the medulla, producing the corticomedullary gradient (the medulla must stay salty). This is called countercurrent multiplication, and explains how such a large osmolar gradient occurs between the cortex and the medulla.
At steady state, with an established corticomedullary gradient, what happens? Solutes continue to be reabsorbed by the tubular cells in the thick ascending limb. In order for it to be steady state, each ion reabsorbed into the ECF needs to go somewhere. One of three things could happen to these ions:

Secretion or diffusion into the collecting duct (and excretion as urine)
Diffusion into the cortex (dissipating the corticomedullary gradient)
Diffusion into the capillaries in the medulla, the vasa recta (exiting the kidney through the renal vein)

In fact, all of these things happen to a certain extent.
Secretion and diffusion into the collecting duct (1) are regulated by changes in the expression of pumps and channels. Diffusion into the cortex (2) is kept to a minimum by diffusion into the vasa recta (3), what we call countercurrent exchange.

I always assumed that those ions were then entering blood vessels for another purpose.

So this does happen, but remember, the main reason for concentrating solutes in the medulla is so that the kidney can, if it needs to, excrete a very concentrated urine. Ions enter the blood vessels for the same purpose, in order to prevent them from diffusing back to the cortex, dissipating the corticomedullary gradient.
The concepts of countercurrent multiplication and countercurrent exchange were proposed in the 1940s and supported by a series of experiments in the 1950s. The landmark 1959 paper by Gottschalk and Mylle in The American Journal of Physiology was reprinted in 1997 by JASN and available for download without a paywall. It's an excellent read! As they predicted, we've learned a lot more, but this model still holds up, and is what we teach in renal physiology to this day.
This is their figure: