Cousin Marriage from genetics point of view In most societies marriages between cousin are viewed negatively, due to a fear of "bad genes".
But lets say I am a girl and I marry the son of my mother's brother (i.e. my uncle), than there is no gene similarity.
Then I have two X-chromosomes, where one came from my father and the other one from my mother. My cousin (the son of my uncle) will have one Y-chromosome from his father and one X-chromosome from his mother (wh o is unrelated to me). My mother will also not be a carrier of my cousins Y-chromosome (since she is a female).

Does this all mean that this particular cousin marriage is unproblematic, and no different than a marriage between completely unrelated people?

The problem is that humans have 22 other pairs of chromosomes than just the sex chromosomes X and Y. Reproducing with your cousin (the son of your mother's brother is the son of your uncle which means your cousin) is generally looked down upon because of inbreeding.

Here's how it breaks down. Your mother and her brother (your uncle) each received 50% of their genes from your grandmother, and 50% from your grandfather. You received 50% of your genes from your mother and the other 50% from your father, who presumably is unrelated to the family. Therefore, you received 25% (50% of 50%) of your genes from your grandmother, and 25% from your grandfather. The same is true of your cousin - 25% from grandmother, and 25% from grandfather. The chances of some of your 25% and his 25% overlapping are rather high (for any one allele of a gene, it has a 1 in 4 chance of being the same as the cousin's). Combine that with 19-20,000-something genes, and that's a lot of overlap.

The problem with overlap/inbreeding is that any "hidden" (recessive) alleles may become homozygous. This may not be a problem for some genes, but a rather big problem for others (see my previous answer about Hunter Syndrome for an example.) There is a real potential of serious genetic diseases in any children resulting from such a relationship, which of course isn't fair to them.


What is the difference between fixation and loss of alleles in a population? When running a simulation in PopG, with parameters:

Population size: 100
AA fitness: 1.0
Aa fitness: 1.0
aa fitness: 1.0
Mutation A to a: 1.0E-6
Mutation a to A: 1.0E-6
Migration rate between populations: 0.001
Initial frequency of A: 0.5
Generations to run: 1000
Populations evolving simultaneously: 100
Random number seed: autogenerate

I get a result of 20 populations being fixed and 10 populations being lost. Obviously, as this is a simulation, these results will vary each run; but what I am having trouble understanding is are lost populations just fixation of the recessive a allele?

Yes, 'lost' seems to be referring to fixation of the a allele in this program, where the statements 'fixed' and 'lost' are specifically referring to the A allele. Conceptually, 'fixed' and 'lost' are describing the same thing in this particular case ( since you only have two alleles in the population) - the loss of one allele in a population.

  Note that once the plot of the gene frequency curves reaches the right-hand side of the graph, the program prints there the number of populations that fixed for the A allele (ended up with a frequency of 1.0) and the number that lost this allele.

(my emphasis, from http://evolution.gs.washington.edu/popgen/popg.html)


Functional role of voltage-gated potassium channels Having better learned here how action potential creation works in some detail, I'd like to pin down the functional role of voltage-gated potassium channels: they mainly shorten the time it takes the neuron to get back to rest potential. Without potassium channels, the sodium ions that entered the neuron through a sodium channel would slowly diffuse away (electrotonically) and the sodium potassium pumps reset the potential. With potassium channels, this process is drastically accelerated (by quickly moving positively charged ions out of the neuron in situ). Without potassium channels, an action potential would be created nevertheless by the sodium channels alone, i.e. a peak of 40mV would be generated (equally fast!), but it would decay much slower, not yielding a pronounced peak.

  Would you agree that this is a correct description of the main
  "purpose" of potassium channels involved in producing action
  potentials?

In any case, potassium channels seem to  work equally well when their "closing" potential would not be -80mV, but e.g. -70mV, i.e. the resting potential. But because it's -80mV the potassium channels produce an afterhyperpolarization. My second question is:

  Does afterhyperpolarization play a ("positive") functional role,
  too, or is it just unavoidable? If so: Which "negative" and
  undesirable effects might it have? (In some respects it might
  have been better, if there was no afterhyperpolarization.)

The meaning of reversal potential

Ion channels do not themselves have reversal potentials except for via a weighted average of the ions that they conduct. The reversal potential for a given ion is given by the Nernst equation and besides physical constants is a function only of the relative concentrations of ions inside and outside the cell.

The equilibrium potential of the whole cell is given by the Goldman equation, which is similar to the Nernst equation but covers any number of ions. Note that you can also calculate a "reversal potential" for a channel using the Goldman equation by considering all the ions that a given channel will conduct.

The reason that a cell's equilibrium potential at rest is not equal to the potassium reversal potential is because cells are not permeable only to potassium at rest; although potassium dominates, there is some conductance to other ions, which depolarizes the cell slightly.

There is no way for a potassium-selective channel to have a reversal potential any different from the potassium reversal potential, unless it were to be permeable to other ions as well.

What would happen if there were no potassium channels?

If there were no potassium channels at all, cells would rest near 0 mV, give or take a few mV. The "leak" channels that allow cells to rest at a negative potential are primarily potassium channels. However, it seems like your question is mostly directed towards voltage-gated potassium channels.

What would happen if there were no voltage-gated potassium channels?

As you suggest, cells would repolarize much more slowly. However, your question still has inaccuracies.

1) This repolarization would not be from sodium diffusing away, it would be from potassium leaving the cell through leak channels.

2) The sodium-potassium ATPase is not directly responsible for the membrane potential or for repolarization in an action potential. Ion concentrations change very little during an action potential. The thing that changes is the permeability to different ions. The sodium-potassium ATPase is important, however, for maintaining the relative inside concentrations of sodium and potassium ions over the long term.

In addition, as you also suggest, there would be no afterhyperpolarization.

Is there a purpose to the afterhyperpolarization? Is it just unavoidable?

There is somewhat of a purpose. Although the afterhyperpolarization isn't strictly necessary to get action potentials to fire, there are some hyperpolarization-activated channels in some cells, and in all cells the hyperpolarization facilitates the removal of the inactivation block of sodium channels. In general words, it serves as a bit of a 'reset signal' beyond mere repolarization.

However, the afterhyperpolarization is also pretty much unavoidable without a very fine-tuned engineering of the repolarization process (you would need to rapidly close potassium channels as they approached rest, which would also slow down the return to rest).

Overall, this material would be well-covered in an introductory neuroscience textbook. My personal recommendation is Purves:

Purves, D., Augustine, G. J., Fitzpatrick, D., Hall, W. C., LaMantia, A. S., McNamara, J. O., & White, L. E. (2014). Neuroscience, 2008. De Boeck, Sinauer, Sunderland, Mass.

(any other edition is fine, too, and there a lot of other good alternatives as well)


Approximate Cell Doubling Time? If I know it takes 12 min to occur in mitotic fibroblast cells and I count there are 32 dividing cells in the microscope slide out of a total population of 32034 cells, how do I calculate the approximate doubling time in hours?

My colleague says it should be around 200 hours. But I don't understand how they reached to this conclusion, can anyone explain this to me please?

Thanks


Is the number of protons in the mitochondrion sufficient for ATP synthesis? If the proton concentration in the mitochondrial matrix (based on its pH) is multiplied by its volume, the total number of protons in somewhere in between 2 and 8.

  My question is whether this is sufficient for ATP synthesis, if 2–3
  hydrogen ions are required for each molecule of ATP synthesized.

My calculation is as follows:

pH = –log[H+]

The pH of the mitochondrial matrix is ca. 8. Thus, [H+] = 10-8 M (moles per litre).

If the mitochondrial volume is 0.2 μm3 this is equivalent to 2x10-10 μl = 2x10-16 litre

Using Avagadro’s number as 6x1023 it follows that:

Total number of protons in the matrix of a mitochondrion = 10-8 x 2x10-16 x 6x1023

= 1.2 (although other figures may give a value as high as 8).

If a pH of 6.8 is considered for the inter-membrane space along with a 0.1 fl volume, the number is 6.7 protons.

I found a paper where the question is adressed. First, the definition of pH at very low volumes is challenged, along with its measuring techniques. Second, it proposes novel mechanisms for proton availability in such situations.
(http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0045832)

The question, as amended, can be summarized as:

  If there are 2–8 protons in the mitochondrial matrix (as calculated
  from a pH of 8) is this sufficient for ATP synthesis, if 2–3 hydrogen
  ions are required for each molecule of ATP synthesized?

The initial deficiency in the argument was that it did not consider the inter-membrane space, and my answer was:

According to the generally accepted Mitchell Hypothesis, the generation of ATP in the
mitochondrion is due to an electrochemical gradient between the
mitochondrial matrix and the inter-membrane space.
This gradient is predominantly a pH gradient — the [H+] is
higher in the inter-membrane space than in the matrix
The flow of protons down this gradient is responsible for the
production of ATP.
The H+ gradient is maintained by protons being pumped across the inner mitochondrial membrane by the flow of electrons through the electron transport chain. (i.e. The H+ concentration is kept low in the matrix and high in the inter-membrane space, even though protons are continually flowing into the matrix.

i.e. For ATP synthesis to occur there is no requirement for a high steady-state concentration of hydrogen ions in the mitochondrial matrix — quite the opposite (as is reflected by the pH 8). A relatively high concentration of hydrogen ions is only required in the inter-membrane space — as is indeed found.

The amended question assumes a pH of 6.8 for the inter-membrane space, and calculates 8.9 protons to be in this compartment.

The poster still does not state specifically what the problem is — there is still a concentration gradient of hydrogen ions, and a vast body of experimental evidence shows that it is this gradient of hydrogen ions that drives ATP synthesis.

So the implied question does not seem specific to ATP generation, but to the concept of pH in cellular compartments of small volume. There is obviously something wrong here, and the paper quoted — which addresses this question — suggests some possible explanations:

That the pH measured is incorrect because of the methodology
That the hydrogen ions are not free but associated with negatively charged species (possibly phosphate ions) from which they may be released, as required.

The latter point had occurred to me before reading the paper. In summary:

The steady-state hydrogen ion concentration gradient is sufficient to drive ATP synthesis, with many hydrogen ions at any time passing through the membrane in one direction or another.
Many of the hydrogen ions in both compartments will be buffered in a manner that allows there release
The naive calculation is likely to be an underestimate because the pH in the inter-membrane space may be much lower.

If I were an ox-phos person I would know how many molecules of the ATP synthase complex there are per mitochondrion and the number of protons pumped into the membrane space per unit time. Such information would, presumably, bear on the problem.


What is the advantage of using starter cultures for growing bacteria? Many DNA isolation and protein expression protocols contain instructions to use a starter culture of E. coli that is then used to inoculate the main culture.

What are the advantages of using starter cultures compared to just let the bacteria grow in the same medium for a longer time? When should one use starter cultures and when can one safely skip that first culture?

Growth can be quite slow for some species under certain conditions when the concentration of cells is too low. Log-phase growth is powerful, and so one would like to keep cells in this state for the experiment at hand. Different genes are expressed then compared to a stationary phase.

In addition, you'd like your culture to out-compete a contaminant if there is one. That is more easily accomplished with a starter culture, which is then used to inoculate a larger culture for scale-up. Inoculating directing into the large-sized flask may allow your bacteria to enter a stationary phase, thus giving an opportunity for other species to out-compete your bacteria.


Would a plant need light if the chemicals gained by photosynthesis were given through the roots or as a foliar spray? If you took the chemicals a plant gains through photosynthesis and put it through the plants' roots or by injection, or used as a foliar application for intake through the stomata, would the plant need light? If not, how would it respond to the treatment?

Not exactly the same thing, but a species of algae has been genetically altered to allow it to  uptake glucose, bypassing the need for photosynthesis: http://www.unisci.com/stories/20012/0615013.htm


Heritability of trait stronger from one sex over another? Given a trait that can be expressed (and measured) in both parents (e.g weight, height, strength, speed), are there ever traits in the child that correlate better with one sex parent than the other? If so, can you give some examples. This could be in any species.

It has been shown in Drosophila that cross-sex heritability is low for lifespan, where within-sex heritability was three times greater than cross-sex heritability. This means that, sons more closely resemble their fathers and daughters more closely resemble their mothers. This could be considered one such example, if you consider the trait to be a sex-specific thing, i.e. that fathers have a greater influence on lifespan in sons than mothers do.

In humans (and numerous other species, e.g. Indian Meal Moth), it has been shown that several traits have small cross-sex genetic correlations, suggesting that (in such traits) the parent of the same sex is a better predictor of a child's trait value.

It is common (in quantitative genetics circles) to consider homologous traits in two sexes as separate traits (e.g. male lifespan and female lifespan are separate traits), and analyse them in a multivariate framework such as a G-matrix. They often have some genetic covariance between the sexes because of pleiotropy and linkage disequilibrium (though covariance by LD is generally more transient: see books on quantitative genetics by Lynch & Walsh, Falconer & Mackay, or Roff, for more reading).


How does cell detect if a RNA polymerase II is stalled during transcription and in turn deploy the proper transcription-coupled repair factors? When a segment of the template strand of DNA is damaged due to factors such as UV radiation, a lesion is created that would effectively block the passage of RNA polymerase II during transcription.

When such stalling occurs, a mammalian cell would usually deploy various transcription-coupled repair factor, such as the XP group of proteins to give provide a proper basis of the lesion and to orient other enzymes in. The endonuclease would cut out the damaged bases, and the DNA polymerase and DNA ligase would, respectively, add the new bases and correctly anchor them onto the template strand.

I fully realize that during the process in which the RNA polymerase II was stalled to the arrival of the transcription-coupled repair factors, some sort of cell signaling must have occurred. However, I could not find any sources that would tell me the specificity of such phenomenon. Therefore, I hope this forum could explain such matter.

Thank you very much!

The beauty of RNA polymerase II is its faculty to act like a sensor towards damage to genetic data. The response of the RNA molecule is variable on the type of DNA lesion which presents itself.
DNA lesions may be a consequence of ultraviolet radiation, or through the metabolic by-products of oxidative free radicals. These specific faults within the lesion, it is hypothesised, are respectively detected by the RNA pol II molecule by interaction with its active site.

Some examples of different genetic damage to bases

In the example you provided, namely, RNA is limited fully or partially from transcription elongation, this is detected as an inhibition of the active site. This could be caused by presence of cyclobutane which distorts the shape of the DNA molecule such that it prevents further RNA synthesis.

Therefore, in the incident that RNA pol II is fully stalled, the first co-factor to commence the signalling process is Transcription factor II H, which repositions the polymerase molecule away from the site of damage. Although it is not fully known, this allows the XPG, having certain endonuclease properties  to excise the faulty bases (thymine dimer, for instance).

In order to fully repair the molecule, DNA polymerase uses translocation to reinsert the correct complementary bases. PCNA, proliferated cell nuclear antigen, may be used as a DNA clamp to increase the processivity, ability for multiples catalyses without leaving the substrate, of DNA polymerase. Then protein complexes XPD operates as a ligase.

Therefore TC-NER, transcription-coupled repair, is believed to begin at a blockage of the active site of RNA pol II!

Best regards
More information regarding this hypothesis and function may be found from: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4984683/ and https://www.ncbi.nlm.nih.gov/pubmed/11245433


Recent classification for parasitoid (ecological relationships) I'm about to present an exam about ecological interactions in biological control. Although the position of some groups is clear, in the case of parasitoids they are included sometimes as predators, some others as parasites, while sometimes they are included like an own group. For example, in this paper they
 are included as parasites, but I wanted to know if there is a more recent reference or classification for these groups (Trophic strategies,
animal diversity and body size Kevin D. Lafferty and Armand M. Kuris).

I think the wikipedia article defining parasitoids has it right on this one. The term is, and should be flexible and it's definition defined by context. i.e Case by case definitions are made obvious in the literature.

  Patently there is no point to trying to draw arbitrary lines of distinction between such vague, and often variable, life histories. In each ecological or ethological study, the terms applied should reflect the facts in the contexts relevant to the matter in question. Such studies need not in all cases use the identical terminology, and there is no reason they should.

This means that you should always describe the life cycle even if you call the organism a parasitoid. There is too much variation between seemingly similar organism life histories to use a strict and specific term.

For those struggling to see the link from the question, they suggest a parasitoid can be measured as a parasite that reduces host fitness to zero:

  ... they are also quite different from these other parasites,
  in that, similar to a predator, they must kill their host.

A recent (2015) review on Whiteflies refers to Hymenoptera as parasitoids of Whiteflies because the Hymenoptera are parasitoids as larvae as they kill the Whiteflies and then become free-living adults.


Identification of a Lepidopteran I’m afraid the quality of the television picture below isn’t very good, but can anyone identify this moth? It was one of those that invaded the pitch at the Euro Final in Paris on 10th July 2016.

I couldn't really be completely sure by this picture alone so I did some searching around and turns out it is a Autographa Gamma(Silver Y)


DNA length and annealing kinetics I have a mixture plasmids and undesired short linear fragments that share the same sequences. During denaturation and annealing, I would like the plasmids to 'find each other' before annealing to the shorter linear fragments. Assuming the concentration of shorter fragments is significant, is there a temperature profile to bias towards re-annealing of longer DNA?

More specifically, this is for a variation of the Surveyor Mutation detection assay, where re-annealed DNA with mismatches are digested, leaving non-mutant DNA intact. I would like to keep non-mutant plasmids for E. coli transformation. However, some linear fragments  ~10-50% of the length of the plasmid have escaped exonuclease treatment and would compete with the plasmids during annealing.

Short answer is that higher temperature favors annealing of longer sequences. There are number of ways to calculate melting temperature, but all of them produce similar results: longer polymers require more thermal energy to melt. Hence, quick cooling from higher (say, from 95C thermocycler can cool in 10-12 sec) to RT/4C will favor re-annealing of circular strands. Slower cooling should allow more ssDNAs to bind.

But again, if end goal is to select for circular dsDNA, simple transformation should take care of that.


How Common are Paraneoplastic Syndromes in Cancer Patients? I recall reading around one in four cancer patients will suffer a paraneoplastic syndrome during the course of their illness but I can't find where I read this and I can't find any reliable sources to back this up.

The incidence of paraneoplastic syndromes appears to be variable and dependent on the kind of cancer. Estimates by Baijens and Manni (2006; Eur Arch Otorhinolaryngol 263: 32–36) are 1% to 7.4% of all cancer patients, however they are citing Gulya (1993; Laryngoscope 103: 754–761) and Zuffa et al. (1984; Neoplasma 31: 231–236) for the data.

Pelosof and Gerber (2010; Mayo Clin Proc 85: 838–854) make the particularly salient observation that

  As patients with cancer live longer, and as diagnostic methods
  improve, this prevalence will likely increase.


Acidity and Alkalinity of Foods Some foods leave an acidic effect on the body such as meat and dairy, while others leave an alkaline effect, like vegetables. However, are these effects significant enough to greatly alter the blood pH that seems to be strictly monitored by the kidneys, which keep it around 7.4?

Extracellular acid base homeostasis in human physiology is maintained primarily by the bicarbonate buffer, as regulated by both the kidneys and the lungs (and to a certain extent, the intracellular phosphate buffer). Outside of illness or injury, (arterial) blood pH is kept between 7.35 and 7.45. There is an excellent review of acid base homeostasis in Pubmed central that covers these points. Be aware before diving in, though, acid base homeostasis is one of the most complicated topics in human physiology.

As discussed in the reference above, a healthy pair of kidneys can usually compensate for a dietary acid or alkaline load. In these cases, what changes is not your blood, but your urine. There, is, though, some evidence that high blood pressure, diabetes, and possibly poor bone health may be associated with a chronic dietary acid load. Though an alkaline diet is being investigated as a treatment for chronic kidney disease, it is not currently approved for the prevention or treatment of any disease in the US.


Help identify this insect with a fan tail I am trying to identify this creature... I took the shot in Medellín, Colombia. It is about 1cm in size.

This is the nymph stage of a planthopper, an insect in a suborder of the hemipterans.

The "fiber-optic-like" tail is actually made out of wax! From Wikipedia

  Nymphs of many [planthoppers] produce wax from special glands on the abdominal terga and other parts of the body. These are hydrophobic and help conceal the insects. Adult females of many families also produce wax which may be used to protect eggs.

The fact that there are about 12,5000 species of planthoppers and I am fully unfamiliar with the fauna of Colombia, I can only provide a quick image confirming that it is a planthopper. (Perhaps you have a field guide or key available to you to help ID to genus or species)

 Credit: Malcolm Burrows, source

You can find an aditional image of a species more similar to yours here.


What are the differences between G+ and G- bacteria? The distinction between Gram-positive and Gram-negative bacteria is based upon the Gram staining method, that reflects the bacterial wall physical properties.
However, this classification involves also a large number of differences between them. For example, the endospore formation usually occurs in Gram-positive bacteria and also the quorum sensing mechanism is different.

So what are those differences? Which of them are due to the cell wall thickness and membrane(s) composition and which instead to evolutionary divergences?

I didn't know there were distinct differences between gram-positive and gram-negative bacteria when it came to quorum sensing, but it seems as though there are:

  In gram negative bacteria, acyl-homoserine lactone type molecules serve as the main signalling molecules while lipid, peptide, and amino acid based signalling molecules infrequently serve as signalling molecules. Furthermore, in gram-negative bacteria, there is one well conserved mechanism for controlling quorum response. Gram-positive bacteria, on the other hand, use peptides or modified peptides as the primary means of signaling; and also differing from gram-negative bacteria, there are several different mechanisms found within the class which are used to gain quorum responses.

Source.

In G+ bacteria, the two main quorum sensing mechanisms are apparently as follows:

Two-component signal transduction, in which the peptide signal works by binding to a sensor protein, histidine kinase, located in the cell membrane of the bacterium. The activation of the histidine kinase leads to phosphorylation of response-regulating protein, and interaction with another regulatory protein facilitates transcriptional activation.
Internalization, in which the signal molecules are transported into the responder cell to interact with intracellular effectors.

G- bacteria on the other hand, synthesize autoinducers, effector molecules that can diffuse freely through the cell membrane and trigger cell response when a certain concentration threshold is reached. I do not know how or if these differences are related to cell wall structure.

When it comes to endospore formation, all I know of the difference between the two is that this is by far most common in gram-positive bacteria.


Why do cells vary in shape and function when they have the same genome and the same organelles? Why do cells vary in shape and function when they have the same genome and the same organelles. For example: why do all cells have nuclei but red blood cell's don't; why can't the cells of a eye perform the function of the tongue; and the list goes on and on. If you say it is because of gene regulation, so then how does the RNA know to transcribe the specific genes that are necessary to that particular cell?

Because cells are not only characterized by by their genetic material and other interior components, but also by the genes they express. Cells have to fulfill multiple different functions to be able to build complex multicellular organisms. Differently expressed genes lead to different proteins made in the cell, which leads to different morphology, shape or function. For example melanocytes in the skin are highly specialized cells which mostly make the pigment melanin. Plasma cells on the other are highly specialised for making antibodies.

It is all about regulation of genes. The RNA doesn't know or transcribe anything -
the DNA is trancribed into the mRNA (which is then further processed) and finally translated into proteins. Cells develop from precursors which proliferate and finally differentiate into highly specific cells. This progress is controlled and activated by specific transcription factors and growth factors. For example: pigment cells only develop, when a specific transcription factor is present. When this factor cannot be expressed, these cells do not develop at all.

This developmental process is shown schematically in the figure below (the figure is from the NIH website on stem cells):


Chromosomal translocation notation A reciprocal translocation is denoted for example: t(4;12)(q32;q24) indicating that q32 on chromosome 4 being swapped with q24 on chromosome 12 if I understand this correctly.

My question is: How do I know whether this is a balanced or an unbalanced translocation?

This translocation is balanced: if it was not there was a specific sign for specific unbalanced event, for example "del" for deletion or "+" and "-" signs etc.


Protein structure prediction from amino acids sequence Information given at this resource https://predictioncenter.org/ is close to impossible to digest (as with everything in this field), so if anyone could tell me what is the accuracy we can predict tertiary protein structure now - I would be grateful.

Also would love to hear your thoughts on 'why a cell can make exactly the same protein structure thousands of time using known to us physical laws, but we have to guess it using machine learning'? Why is it difficult?

what is the accuracy we can predict tertiary protein structure

That depends on the protein.  If the primary sequence closely matches the sequence of a protein for which the structure is already resolved, then template-based methods to model 3D structure can be used (a.k.a homology modeling).  These methods tend to be accurate, as assessed by template-modeling score, though crystal structure confirmation is only available for a minority of models (1%, per this 2010 paper).
For proteins without structurally-resolved homologs, ab initio folding is often used, which relies on molecular mechanics assessment of iterative peptide chain folding to find structures that minimize the Gibbs free energy. Popular software for protein molecular mechanical modeling include CHARMM and AMBER.  Ab initio methods are computationally intensive and are more difficult to validate.

'why a cell can make exactly the same protein structure thousands of time using known to us physical laws, but we have to guess it using machine learning'? Why is it difficult?

It's hard to know all the cellular factors present when a particular protein is synthesized and how those factors affect the folding of the protein.  What is the temperature and pH proximal to the ribosome?  Are chaperone proteins involved?  Is the lowest-energy structure the true structure, or does the native structure fall in a local, stable minimum with a functional potential selected by evolution?  A good discussion of that last point can be found on Quora.


Which three functional groups are found in the general structure of amino acids? Yes, I know, not two, but THREE.

EDIT: Yes, sorry but I did quite a bit of research, searching my notes and textbook for the answer, but all I could find was TWO functional groups as a opposed to the three my guide said there should be. Trust me, I looked quite a bit and there were many conflicting sources with different answers.

Amine, alkyl, and carboxylate.

I'd guess the part that you're having trouble on is that the alpha carbon in the center of the generic AA structure is part of an alkyl functional group
Edit
The original answer that I gave might have been too clever for its own good. Depending on how one looks at the question, the third functional group could instead be the functional group of the particular side chain, i.e. for Alanine it would be a methyl group, for Tryptophan it would be an indole group, etc.


Does the term "fitness advantage" or "fitness disadvantage" make sense? Same for the terms "selective advantage" and "selective disadvantage" which I intend to use synonymously.  There are usages of each on Google Scholar, but do evolutionary biologists understand what is meant?

What is unclear to you?

If you could highlight what is unclear to you, or what exactly are the semantic issues in your opinion, that would help to really address your misunderstanding. In absence of that, I will just give you a general explanation of their meaning.

What does 'fitness advantage' mean?

If a group of individuals has a fitness advantage, it means that this group of individuals has a higher fitness over some other group of individuals. The other group, then has a fitness disadvantage.

Natural selection

If we grouped these individuals based on genetics, then the genotypes having a fitness advantage will likely raise in frequency in the population. If we used phenotypic trait to group individuals and if the trait is heritable, then the frequency of these phenotypic traits is also likely to raise in frequency in the population.


Edman method to identify peptides with Phenylisothiocyanate (PTH) We all know that in this method the PTH reacts with the first amino acid (aa) from the N-terminal to the peptide and separates from it giving PTH-aa so that we can know the amino acids sequence in the peptide.

The question is what prevents the PTH from reacting with the second amino acid after it separates with the first amino acid in the same time and phase? Because if it does we can't distinguish between the first and second amino acid residue in the sequence.

The short answer is that the Edman degradation is a multi-step process. The Wikipedia page has a decent picture of the mechanism. In practice, the peptide is reacted with phenylisothiocyanate (PTH) under mildly basic conditions to give a thiourea, which is stable. The excess PTH is separated from the thiourea intermediate. The thiourea is then treated with acid to cleave the N-terminal residue from the peptide. The PTH is no longer present, so there's no concern about reacting with the second residue.


Bugs' love for light Do bugs love light bulbs because they resemble the stars or is it the sun? How do they sense the bulb? What is the purpose of this "brightophilia" that has evolved in insects?

I think the answer to your question is relatively unknown. The answer I have heard the most often, which is largely the most accepted, is that many insects orient themselves in space using light. So if they are flying at night, the soft light of the moon tells them which relative direction they are going. Light bulbs end up confusing them, because they think they can orient themselves to it, but they are wrong.

http://www.npr.org/templates/story/story.php?storyId=12903572

Additionally, insects do have very similar photoreceptors as humans and vertebrates. Fruit fly eyes are a major research topic because of the similarity of the photoreceptor proteins as well as the amazing genetics that can be done.


SNP genotyping using PCR I read this wikipedia article on SNP genotyping and wasn't able to understand this part :

  In examining the results, if a genomic sample is homozygous, then the
  PCR products that result will be from the primer which matches the SNP
  location to the outer, opposite strand primer as well from the two
  opposite, outer primers. If the genomic sample is heterozygous, then
  products will result from the primer of each allele to their
  respective outer primer counterparts as well as from the two opposite,
  outer primers.

Can anyone explain this ?

Valid XHTML http://nar.oxfordjournals.org/content/29/17/e88/F1.large.jpg.
Figure 1. Schematic presentation of the tetra-primer ARMS-PCR method. The single nucleotide polymorphism used here as an example is a G→A substitution, but the method can be used to type other types of single base substitutions. Two allele-specific amplicons are generated using two pairs of primers, one pair (indicated by pink and red arrows, respectively) producing an amplicon representing the G allele and the other pair (indicated by indigo and blue arrows, respectively) producing an amplicon representing the A allele. Allele specificity is conferred by a mismatch between the 3′-terminal base of an inner primer and the template. To enhance allelic specificity, a second deliberate mismatch (indicated by an asterisk) at position –2 from the 3′-terminus is also incorporated in the inner primers. The primers are 26 nt or longer, so as to minimize the difference in stability of primers annealed to the target and non-target alleles, ensuring that allele specificity results from differences in extension rate, rather than hybridisation rate. By positioning the two outer primers at different distances from the polymorphic nucleotide, the two allele-specific amplicons differ in length, allowing them to be discriminated by gel electrophoresis. (http://nar.oxfordjournals.org/content/29/17/e88/F1.expansion)


How verified experimentally is the Marginal Value Theorem for viruses? Reading some Stanford notes on R0, they get to MVT and optimal virulence:

  Consider a directly-transmitted infection from which there is no recovery (e.g., Herpes Simplex). The population experiences a baseline mortality rate, µ, and a disease-induced mortality δ. [Then the SI model]

  ds/dt = −βsi − µs
  di/dt = βsi − (µ + δ)i,

  Figure 4: Marginal value theorem for optimal virulence. The ESS [evolutionarily stable strategy] virulence occurs where a line
  rooted at the origin is tangent to the curve that relates β to δ. Two curves are depicted. The
  first curve shows a pathogen in which transmissibility increases relatively rapidly with mortality.
  Point A indicates the optimal balance between β(x) and δ(x) under this case, and the optimal
  virulence is indicated x∗
  . For the second curve, relative transmission is less efficient. Therefore,
  the tangent line from the origin to the curve hits further out (B) along the mortality axis and
  the optimal virulence is higher (x∗∗).

Wikipedia has a page on MVT but it doesn't discuss viruses/virulence at all (although it has some criticism of MVT from other angles/domains). So, how verified experimentally is MVT for viruses?

I'm not an expert but it seems purely theoretical. There are some fairly basic criticisms that can be made of this model. First it assumes that viruses tend to optimize propagation, a perfectly reasonable assumption. The clear prediction is that propagation rate should be inversely related to mortality rate. Quickly checking a list of the most common viruses shows you that this relation is not that strong, if there at all. The second issue is that R0 is a very abstract measure. Viruses do not propagate in a straightforward manner. Rabies relies on animals biting each other, HIV sexual contacts, etc. On average each virus will still have an R0, but I'm not sure it is so sensible to assume it will trade-off with mortality as it relies on the animals behavior (although with rabbis for example the animal behavior is actually modulated by the virus itself to increase propagation). Lastly epidemics usually start with a zoonotic disease randomly mutating and jumping species. They often have quite different effect on different species so here again I am not sure it is completely reasonable to assume that the mortality rate of a virus will tradeoff with infection rate.

It's still a useful tool to think about how viruses should behave. As you noted there also are criticisms about the MVT to describe animal foraging. But mathematically, under some assumptions, it is the optimal solution. So any deviation you see from that tells you your assumptions were wrong.


Do recessive alleles really exist? This question may seem illogical to some, but I seriously have this doubt. I searched google for some proofs but they were extremely complex and I couldn't understand anything.

I was just wondering whether we really have recessive allele or not? Is it like there are only dominant allele present, and when dominant allele isn't present we consider it recessive.

Is it like there is a place reserved for dominant allele and if that place is empty it turns out to be recessive.

Although this thought is vague but then if you take this example, it probably would make sense:
Let's say there are two allele : T and t for tall and short respectively. Now, because TT, Tt, tT are tall, they all lead to the formation of specific hormone due to the presence of dominant allele. But the plant with genotype tt is short, hence the "extra" hormone for "excessive" tallness is missing in tt plant because the dominant gene isn't present. Can we say that that place for two allele (dominant allele) is actually empty in the plant with genotype tt?

This is a good question. Firstly, let's get the terminology straightened out: The terms recessive and dominant are not actually used to describe genes, but rather alleles. The term allele is used for alternative forms of the same gene.(1) Many genes have two or more alleles, and some genes have alleles that can be described as dominant or recessive.

It is also useful to be familiar with the terms genotype and phenotype. Genotype refers to the form of the genetic material (DNA), while phenotype refers to the observed effect of the genotype.

Secondly, it's important to realize that the concept of "dominant" and "recessive" is a human-made abstraction. The concept of dominant and recessive genes were invented (or discovered, if you like) before we reached a good undertanding of how genetics works at the molecular level. Thus, genetics in the early days had a much cruder understanding of how different phenotypes depend on the genotype.

The dominant/recessive concept is useful in cases where there is a limited number of possible allele pairs and one or several alleles can mask the effect of other alleles. This is a very limited set of cases. Many genes have many different alleles, and it's hard to account for all of them. Many alleles also do not have a clear observable effect, in which case any "masking" effect is not prominent. To quote Wikipedia (2):

  The most common basis of dominance and recessiveness is that the
  dominant allele codes for a functional protein and the recessive
  allele for a mutant, non-functional protein.

A further important point is made in the following passage:

  Dominance is not inherent to an allele. It is a relationship between
  alleles; one allele can be dominant over a second allele, recessive to
  a third allele, and codominant to a fourth. Dominance should be
  distinguished from epistasis, a relationship in which an allele of one
  gene affects the expression of an allele at a different gene.

Let's consider your example: A single gene with two different alleles, T and t. Let's assume the T allele codes for a more powerful version of the growth hormone than the t allele, or that the t allele produces a non-functional hormone. Furthermore, we assume that production of the T hormone from a single allele is enough to make the plant grow tall, and that production of T or t from a second allele has no further effect. Then, we can say that the T allele masks the effect of the t allele. However, as you can probably imagine, one allele fully masking the effect of another is rather rare. So recessive/dominant allele pairs are rather the exception than the norm.

Thus, the that place for the two alleles in the genome of the plant is definitely not empty. Note that a mutation could in principle cause one of the genes to be deleted in its entirety from one of the chromosomes of the plant during reproduction. The "place" for the gene on that chromosome would then indeed be empty. This has nothing to do with how dominance and recessiveness usually works, except that a recessive gene could become expressed if the dominant allele is deleted.

So, at the molecular level there is no concept of recessive or dominant alleles. Some genes have allele pairs that can be described as dominant/recessive in relation to each other, most others do not. The effect of different combinations of alleles determines whether the relationship between the alleles is described in terms of dominant/recessive.


A possible cause of autoimmunity I read that

  Doherty and Zinkernagel found that MHC- heterozygotes present more
  antigens to the immune system than homozygotes; yet, the infected
  heterozygous mice in their experiment all died, apparently from
  overresponsiveness.

Can MHC-heterozygotes be more susceptible to autoimmune disorders and allergies because there is a tendency of over responsiveness ?

It looks moderately muddled, but perhaps.  This paper1 is a good place to start; it's free and the intro lists a number of more recent studies.  That study found a connection to lifetime reproductive success in sticklebacks (a fish) with intermediate MHC diversity.  This 2007 study in mice2 is a particularly nice one, dealing with a inbred line outbred to wild mice, finding again, no advantage to heterozygotes.  There are others, but most deal with the concept descriptively (self-delighting in their continued refutation of a commonly-held belief) or predictively (such as this from PNAS in 19923 or a 2009 review4) but specific and proven reasons are sparse.

The general feeling is that it may remain unclear what sort of genetic interactions are involved in MHC (additive effects, overdominance, etc.) but it is probably also complicated due to the nature of immunology.  For example, a paper from 20035 points out that in an immunological response, only a few peptides dominate the response; there may be no real advantage to having extra ones if they are unused, and having those others around might dilute the useful response (That paper also takes an interesting view of serial infections, and shows that heterozygotes are indeed advantaged during coinfection).  The above PNAS publication3 gives the idea, which the stickleback paper1 recapitulated, that if more alleles are present, more T-cells will be self-reactive and will therefore be purged, resulting in an overall decreased T-cell availability.

Other hypotheses are present in the review4 I mentioned, such as perhaps positive selection efficiency is not MHC-diversity dependent whereas negative selection is, or indeed increased autoimmune reactions as you guessed.  My guess would be some combination of the above, with selection for heterozygotes being favored in the real world for multiple and repeated infections but certain specifics resulting in a homozygote preference, of which autoimmunity is likely playing a role.


Are there other mechanisms for mutation besides imperfect DNA replication? I was reading http://www.askamathematician.com/2012/05/q-is-quantum-randomness-ever-large-enough-to-be-noticed/ and saw:

  [...] the evolution of entire species can be changed by a single
  mistake in the replication of a strand of DNA (this is one mechanism
  for mutation).

... implying other mechanisms for mutation exist. Do they?

Absolutely. Ionizing (X-rays, neutrons, electrons, heavy ions) and non-ionizing radiation (UV), chemicals, etc. are able to induce DNA Damage, which is then imperfectly repaired. So it's not an issue of imperfect replication, but also of imperfect damage repair.


How to generate simulated mass-spectrometry data for phosphorylated proteins? I am trying to generate simulated MS data (Top-down and Bottom-up) for phosphorylated protein such as platelet-derived growth factor receptor (PDGFR-B). There are 10 tyrosine sites which are phosphorylated. Could you kindly tell me if there is any good software application to help me do that?

Also, how can I include in the input file (FASTA) that there are 10 modification sites on the protein sequence?

What are the parameters required to be set for top-down and bottom-up MS separately?

I know this is a two years old question... but I recently developed a web application which could be useful for you:
Prot pi

The Protein tool lets you simulate the mass spectrum of the intact protein, while the Peptide tool gives you the fragment ions of peptides. Modifications can easily attached to every site you want.


Insect identification request I live in France. I've just found several (8) of these in my living room, close to an oak cupboard and my Christmas tree, a cut Abies nordmanniana (supposedly grown in France).

Their body is around 5 mm (1/5 in) long. On the tissue they walk easily (1st picture), but on the glass of the jar they can't even stay upright and fall upside down (2nd picture).

(At first I was afraid they would be woodboring insects, which I've never seen, but WP taught me the latter are beetles, and these beasts aren't beetles, right?)

EDIT -- I think this is actually a black stem aphid (Cinara confinis) [see below]

I think these are Hemiptera, and I doubt they are pests. They probably came from the christmas tree (which usually brings hundreds of arthropods into your house). It is a bit hard to see from your pictures (blurry, no clear underside), but my initial guess would be a nymph from Hemiptera (True bug), for instance from the Coreidae family (look at a google picture search at nymphs for some examples). An alternative could be nymphs from Psocoptera), which can look a bit similar. A clear difference between them is in the mouthparts, where Hemiptera have a rostrum (a "straw", sucking mouthparts), which should be seen from the ventral side, while Psocoptera has biting mouthparts. Your second ventral picture seems to show a long rostrum along the underside, which would point directly at Hemiptera. I don't know of any indoor Hemiptera pests (except ones that might attack house plants), but I might be mistaken.

This is just shown as an example, and is not likely to be the correct species, but here are the nymph stages of the common Coreus marginatus, just for comparison:

(from http://www.ukwildlife.net/heteroptera/coreidae/coreus_marginatus.html)

Here is a picture clearly showing the rostrum (see arrow):

(from http://www.fao.org)

Another possibility could be that they are aphids. This is still within Hemiptera (but not Heteroptera), and they also have a rostrum. Aphids have a pair of "tubes" (cornicles) coming out of their backs where they can extrude defensive compounds, and your first picture shows something that might be cornicles (the pointy things towards the back). However, to me, they seem to lie towards the side and look like the type of spikes or thorny sides that many Heteroptera have (a suborder of Hemiptera). Your individual also seems to have flattened edges of the hind body, which e.g. many Coreidae have. Again, clearer pictures would separate these possibilities. It would also be useful to see the number of antennal segments clearly.

EDIT
That said, I looked at some pictures of aphids living on coniferous trees and they can be fairly similar to your specimen. I actually think Cinara confinis is very likely (or another species in the same genus). This species is circumpolar, found in France, and often lives on Abies:

(source: free.fr)

(Cinara confinis, both pictures from http://aesgsf.free.fr/V5/hemipteres-divers-de-picardie-hemiptera-cinara-confinis.html)


Is it purely the nervous system causing vaginal lubrication (arousal)? My girlfriend was watching some documentary on TLC about a paralyzed woman getting pregnant. I believe that woman still has some feeling, as she spoke about feeling the effects of a bladder inflamation. So supposedly, her brain could fire up her vagina to get ready for sex (in the sense that it gets lubricated and the labia get swollen).

But suppose a woman is paralyzed so they have no nervous connection from the brain to the vagina (or vice versa). Could she still be aroused in the sense of swollen labia, etc? (Presumably via some hormonal system?)

There is a good open access review about the effects of different hormones on sexual arousal. In most instances, the hormone is acting on the brain, which signals the information to gonads and genitals via nerves (i.e., the hypothalamic-pituitary-gonadal axis). However, in a study in which I have participated, we found a more direct and probably ancient signaling pathway where the mouse liver, in response to protein intake, was sending a permissive signal to the uterus for reproduction. Whether this holds true for vagina lubrication was not investigated, but I would be optimistic that mechanisms other than nerve communication could play some roles.


What dangers would the wireless transmission of power through microwaves pose to living organisms? If we were one day able to harness the power of "wireless electricity", and INTEGRATE it into society, what disadvantages and/or dangers to living organisms would become relevant at that point? To my understanding, the power would be transmitted through microwaves, which may or may not be correct.

The example I will use in regards to "wireless electricity", would be... The transmission of power from one source to another without the need for power cords, or power lines.

One such instance, according to "http://phys.org/news/2015-03-japan-space-scientists-wireless-energy.html", states "The idea, said the JAXA spokesman, would be for microwave-transmitting solar satellites—which would have sunlight-gathering panels and antennae—to be set up about 36,000 kilometres (22,300 miles) from the earth."

Whether wireless power transfer is safe depends on the type of power transfer. Inductive coupling is generally safe, but only works across small distances (i.e., millimeters to centimeters). The other option is far-field or radiative technology, where either visible light (from lasers) or microwaves are used. The latter has not been applied much, some uses have been found in space technology. Their safety in general will depend mainly on the power being transmitted. For example, a laser can be destructive if it is powerful enough.

I will focus on inductive coupling, because it is not only safe, it is commonplace. The prime example being cochlear implants. Cochlear implants are basically electrode arrays implanted in the inner ear to directly electrically stimulate the auditory nerve in deaf people where the hair cells have degenerated (or were never there). The implant is powered by an external battery worn behind the ear. It is coupled to a head-worn external coil that wirelessly transfers the power needed to drive the implant to an internal, surgically implanted coil. I'm not entirely sure about the exact numbers, but more than 100,000 folks around the globe have received one or two cochlear implants.

Cochlear implant showing the external and internal coil to transcranially transmit power to the implant.Source: Extreme Technology

Very similar technology is used in retinal implants. Retinal implants electrically stimulate the degenerate retina to [partly] restore vision in the blind. For example, the Argus II deploys an external coil mounted on a pair of glasses that wirelessly couples to a surgically implanted coil in the eye to power the implant. Being newer technology, there are not more than two hundred or so people implanted worldwide as we speak, but this number will definitely sore in the near future, all, or at least many relying on wireless power transfer.

Schematic of the Argus II retinal prosthesis showing the wireless link. Source: Ars Technica.

These examples may not be exhaustive. For example, transcranial magnetic stimulation of the brain is another example of wireless energy transfer across the skull, making use of magnetic induction to stimulate the cortex. However, these examples do show that medical bionics is already making use of wireless power transmission technology.


Is it possible to give a person an allergic reaction in a very specific place? Can I give a person an allergic reaction at a very specific spot in a tissue?
And if so, how accurate can i get?

Depends on the kind of allergic reactions you want to create. If your target tissue is skin epithelium sure you can.

That's actually the way the skin allergy test is all about: The physician tries a wide variety - last time I did it were 28 well known kinds - of substances in liquid form (drops). If an allergic reaction is caused, the physician takes note. Even very small quantities can cause allergic reactions.

These tests are usually made in a secured environment (physician's office, hospital, etc) at a very low level which most of the times, if result is positive will cause just an irritation. The level of irritation will be self-explanatory, so even a non trained patient can understand what is going on.

Not sure if that what you were asking though.

Best Regards,

pa


Would two species of yeast with similar genome sizes have the same number of genes or chromosomes? Similar organisms generally have similar genome sizes. Given this, would two species of yeast have the same number of genes and chromosomes?

Edit: Fixed with thanks to @daniel-standage

This question appears to start from the premise that different species of yeast are closely related, but they aren't. Saccharomyces cerevisae and Schizosaccharomyces pombe, both Ascomycetes, are thought to have diverged at least 300 million years ago (c.f. the mammalian divergence from other vertebrates was about 200 million years ago).

S. cerevisiae has a genome size of 12.1 Mb, with 5821 protein coding genes (plus another 786 dubious ORFs) spread over 16 chromosomes.

S. pombe has a genome size of 12.6 Mb with 5124 protein coding genes on just 3 chromosomes.

Filamentous fungi have larger genomes and gene numbers. From memory, Aspergillus nidulans has 8 chromosomes and over 9,000 protein coding genes. So, the similarity in gene numbers in the two yeasts probably reflects their broadly similar lifestyles.


Can any one explain me the structural difference between Proteins and Peptides? I have read in books that Proteins and Peptides are fundamental components of cells which carryout important biological functions.Can any one explain me the structural difference between Proteins and Peptides?

In terms of structure: both are composed of amino acids.

A peptide is when at least two amino acid are linked together.
A protein is composed of multiple amino acids and have a secondary, tertiary and even quaternary structure.

In terms of function: larger molecules have more complex functions.

Peptides can act as a intracellular or extracellular ligands which will activate a signal.

Proteins have a large array of functions (enzymatic, structural, receptors etc)

This article explains in more details the differences in proteins structure and functions:https://en.wikibooks.org/wiki/Structural_Biochemistry/Proteins


Why doesn't enzyme reaction rate rise linearly with substrate concentration? This is the graph of the Michaelis-Menten equation which describes the relationship between reaction rate and substrate concentration:

I don't understand why it is hyperbolic. Intuitively, I would think that it would be linear.
Here is my logic for a specific scenario:
Let's say enzyme $E$ converts substrate $S$ at a rate of $1 S$ per second. Now let's say we have a container with 1000 enzyme E's. And there is a tube connected to the container that pumps in $10 S$ per second.
Logically, in the one second, all 10 substrates should be catalyzed. The rate of reaction would be $10/s$. Now if we increase the pump to 500 substrates per second, you would think that all 500 substrates would be catalyzed in one second, making the rate $500/s$. Thus, a linear relationship.
The formula for rate of enzyme-substrate complex formation is also linear:
$$\frac{d[ES]}{dt} = k[E][S]$$
What am I missing here? I am looking for a mechanistic explanation (diffusion, dissociation, etc)
Edit: I've done some more thinking and I have a potential explanation. Could it be that, as the concentration of substrate goes up, the probability of a substrate interacting with an unbound enzyme goes down.
In my scenario, the first substrate has a 1000/1000 chance to find a free enzyme, the second substrate has a 999/1000 chance of finding a free enzyme, etc.

Disclaimer
This answer is a conceptual explanation, as appears to be the request, rather than a repetition of the derivation of the Michaelis–Menten equation, which I feel inappropriate, partly because it can be found elsewhere, e.g. in Wikipedia and Berg et al.. I appreciate that, like the derivations on which it is based, some of its assumptions do not always hold, or do not hold for all enzymes, and that some with an expert knowledge of enzyme kinetics will feel that it would be better to say nothing than present a conceptual simplification. Although I welcome corrections — I am not an enzymologist — but disagree with this point of view.
Summary
The reason that increasing the substrate concentration of an enzymic reaction does not increase the reaction rate beyond a certain maximum (Vmax) is that the reaction rate is dependent on the concentration of enzyme-substrate complex, not its rate of formation. Increasing substrate concentration only affects the reaction rate in so far is it affects the proportion of enzyme molecules involved in enzyme–substrate complex, which reaches a maximum when all of the enzyme is in such complexes.
More detailed explanation
The question presents a rate constant for only one of the reactions involved in an enzyme-catalysed reaction. In fact there are four that must be considered: the forward and backward reactions for the formation of a complex, ES, between enzyme (E) and substrate (S); and the forward and backward reactions for the formation of product (P).

The Michaelis–Menten treatment considers the initial velocity of reactions, at which time little product has formed so that it is assumed that the back reaction from product can be ignored, simplifying the situation to a consideration of the rates of three reactions:

A key assumption — the steady state assumption — in Michaelis and Menten’s original derivation is that there is that there is a considerable excess of substrate over enzyme so that the substrate is in instantaneous equilibrium with the ES complex. So, in effect, at a particular concentration of substrate the concentration of ES is constant. The implication in the question that the rate of formation of this complex would determine the reaction rate is incorrect.
The rate of the reaction depends only on the ES concentration and k2, the rate constant for the formation of products, also known as kcat, which is a characteristic of any enzyme and can be thought of as representing its catalytic capability:

d[P]/dt = kcat[ES]

What the substrate concentration does affect is the position of equilibrium for the formation of ES from E and S, i.e. how much enzyme is converted into complex. However there is obviously a maximum, approached asymptotically, equivalent to the total enzyme present. This explains† the hyperbolic nature of the curve for reaction rate.
The concentration of substrate needed to reach this saturation (more easily measurable as that to achieve half maximum initial velocity) is another characteristic of the enzyme (and substrate) and can be thought of as reflecting the affinity of the enzyme for substrate (the dissociation constant). The hyperbolic nature of the rate curve is similar to that for binding of small molecules to non-catalytic proteins such as the oxygen-carrier, myoglobin, and hormone receptor proteins.
Just as not all proteins in this latter class (e.g. haemoglobin) show simple hyperbolic binding of their ligand, so not all enzymes (e.g. allosteric enzymes) show hyperbolic kinetics. But that’s another story, which has been told many times on this site.

† I have given a more extensive explanation of the hyperbolic nature of the curve in an answer to a previous question, which I must admit I had forgotten about.


How is the renal osmotic gradient maintained even though the blood osmolarity changes? I am a high school student and I am a little confused in 2 things related to our urinary system:

We know in our kidneys a countercurrent mechanism exists due to which there is a steep gradient of osmolarity is observed as we go deep inside the medulla and due to which water gets reabsorbed from the descending limb of Henle's loop into the ascending limb of vasa recta but due to the countercurrent of vasa recta osmolarity of blood doesn't changes but as collecting duct descends deep into the medulla it also loses water. Where does this water get drained? Does it get absorbed into a blood vessel? I don't think so because if the blood  is also moving down with the collecting duct then it should also lose water as osmolarity increases as we go down.

We know that ADH increases the water reabsorption from the distal parts of nephron via aquaporins but if more aquaporins are there the collecting duct should pass urine of 1200mosml osmolarity, shouldn't it? and in that case will the concentration gradient in the medulla be maintained? if yes then how?  I am not able to imagine how our kidney would behave if blood of increased osmolarity get into it.

The water doesn't get drained.  As blood flows down a vas rectum, in any given section of the arteriole the tonicity is slightly higher outside the arteriole vs inside the arteriole.  This results in a small amount of water flowing out of the arteriole to attempt to equilibrate the osmolarity.  But before this has even finished happening, the blood has flowed down another quarter of a millimeter (or whatever) where the tonicity is even higher outside the arteriole.  In other words, down the entire vas rectum the water is flowing out.  But when the vas rectum comes back up, the situation is reversed, so the same quantity of water ends up diffusing back into the blood vessel.  Thus the osmolarity at any given level of the medulla remains constant.

Correct, the maximum osmolarity of urine is 1,200 mosm/L.  The concentration gradient in the medulla will change very slightly (temporarily), but don't forget that even as the urine in the collecting tubule is being concentrated to that maximum concentration, the whole process of creating the concentration gradient is actively happening in loops of Henle all around the collecting duct.  So even if the initial effect of having a bit more water in the medulla from the collecting tubule would be to slightly lower the extracellular osmolarity, in the grand scheme of things it changes nothing since the rest of the nephron is still actively creating an effective osmolarity gradient.

References

Any physiology textbook... for instance (among others), I have Human Physiology, from Cells to Systems - in the First Canadian Edition it's pp. 553-63.


Can primary tumor cells grow in 2D culture? Is it possible to expand primary tumor cells in 2D culture? Are they adherent cells? Do you have any experience especially with culturing non-small cell lung cancer in 2D?
Thank you.

Short answer: Yes, this is possible, it is the way most (cancer) cell lines have been generated.

Long answer: Culturing cells from tumor tissues is done in labs, especially, if you don't want to rely on the often very old cultures used in the labs. Many of these where started in the 1970s and are strange in many ways, e.g. contain many chromosomes multiple times. I have routinely isolated new cell lines from melanoma tissues (mostly metastases from different organs), but the general procedure is the same for other tumors as well.

To isolate cells from a tumor, you first wash the tumor sample to get rid of the blood. Then you cut down the tumors into small pieces using a scalpell, before adding a mix of enzymes like Collagenase, Dispase and Hyaluronidase to dissolve the tissue further in order to get a single cell solution. After the incubation with the enzymes the suspension is passed through a cell strainer to remove all remaining bigger cell aggregates and tissues residues and centrifuge the cells down. They are resuspended in an appropriate medium for the cell type and seeded to an appropriate plate/flask. For our samples this was typically either a 35mm plate (or a 6 well plate, which has the same area per well) or a T25 flask. Most cells from such isolations grow adherent, but sometimes you can observe cells, which do not adhere to the surfaces.

The procedure itself is not very complicated, but needs optimization. Depending on your tissue, the enzyme cocktail can be varied, as well as the length of incubation and the incubation time in this step. Then different plate/flask surfaces can play an important role, also the medium composition.

When we started doing this work in the lab, about 1 in 10 attempts was successfull, after optimization we went up to 6-7 of 10. What is important to take into account is, that the cells change during incubation and adapt to it. This means you need to question yourself, how good of a model they can be and need to be. If you need our detailed protocol, let me know, I can post it somewhere.


How does the counter current mechanism concentrate urine? The movement of ions like sodium into the interstitial space causes water to passively diffuse out the descending loop of Henle. How does this concentrate the urine? The solvent is removed at one place, and the solute at another. Shouldn't the concentration remain the same? Or does the removal of a little solute remove a lot of solvent? Why?

Have a look at this figure (from here):

In the descending loop the NaCl concentration is lower than in the surrounding tissue which leads to a passive water transport along the gradient, which leads to a concentration effect. In the ascending loop then NaCl is actively transported out of the loop which then prevents the diffusion of water back into the loop.

In the collecting tube water is actively transported out leading to an even higher concentration effect. A nice animation of this can be found here.


Can rats pass on memories of a maze to their offspring? A friend of mine told me once about a documentary movie he saw some years ago. On this movie he saw scientists talking about particular experiment. This experiment involved rats and probably electrical traps. The rat had to get to the cheese, there were traps on the shortest route to it, and obviously it got shocked few times. What is interesting is that my friend says that when they took its offspring (probably born later) they avoided those traps.

I'm aware that its not how "genetic memory" works. Its not memory of individual, but of species (so it requires evolution). This is what I'm trying to explain to him, but he says "he knows what he saw".

Anyway maybe someone here is aware of such an experiment. I believe that he is wrong about something (or conclusions drawn where changed later), so I would like to find out more about it.

To sum up:

Its not Tryon's Rat Experiment
It involved: rats, traps (probably electrical), more then one path to cheese, rat's offspring and some sort of memory/learning amongst rats.

The phenomenon you're talking about was a fad in the 60's, called 'interanimal memory transfer'. It started out when James McConnell performed a later-discredited experiment in which he found that if you chopped up flatworms which had been exposed to some stresses, and fed them to other unexposed flatworms, the unexposed worms became wary of the source of stress quicker after eating their dead companions. He jumped to the conclusion that a 'memory molecule' was being transferred, and that the cannibal worms gained the food worms' memories of the stress.

People then started looking to see if they could:

repeat the experiments
find the same phenomenon in other animals

In the first case, nobody could replicate the experiments in worms, but because McConnell was such a PR genius he managed to convince the public that his results were valid (see Rilling, 1996 for more on this).

In the second case, Frank et al. (1970) and others tried working with rats - I think this is the experiment you're talking about in the question. They found various interesting results including that if you trained rats to run through a maze by using particularly stressful negative reinforcement (like electrocution), then those rats' children would be able to learn the new maze much faster. However, Frank et al. didn't make the same mistake as McConnell - first of all they wondered if the parent rats might be leaving a scent trail. So they used duplicate mazes with the exact same design, putting the children into clean mazes. The children of adults who had already learned the maze continued to outperform the control rats - the explanation was not scent trails.

Next they wondered whether it might be that the second generation rats had been born with a higher wariness as a result of the stress their parents suffered; i.e. it could be a hormonal transfer from mother to child (e.g. cortisol, the stress hormone).

Frank et al. tested their hypothesis by torturing some rats for a while (rules about animal welfare were not strict in the 70's). They would lock some rats in a small jar and bash them about for a long time, then kill them, chop them up, and take out their livers. They fed the livers to other rats, and found that after eating the livers the other rats learned the maze much faster. They interpreted the results in what now seems a sensible light: the stressed rats were producing high concentrations of a stress-signalling molecule. When those rats either had children or were fed to other rats, they passed on high doses of the stress molecule. This raised the alterness and wariness of the receipient rats so that they were much quicker to learn which parts of the maze were dangerous.

There is no evidence that the child rats actually 'remembered' the maze - they still had to find their way around, but they were extremely wary of the electrocution plates and so avoided them, finding the safest way to the end. This is not a case of genetic memory.

 Frank B, Stein DG, Rosen J. 1970. Interanimal “Memory” Transfer: Results from Brain and Liver Homogenates. Science 169: 399–402.
 Rilling M. 1996. The mystery of the vanished citations: James McConnell’s forgotten 1960s quest for planarian learning, a biochemical engram, and celebrity. American Psychologist 51: 589–598.


What are the teeth of the viperfish composed of? One of the viperfish's (genus Chauliodus) most unique traits is the transparent, needle-like teeth. Some other abyssopelagic fish (e.g. certain angler fish) have similar teeth. I'm curious as to what these teeth are actually made of. They clearly aren't made of bone, and from what I can tell from various fish skeletons, they decay fairly quickly with the rest of the fish.

They are not unique

The are made of enamel and dentine just like ours, Even the enamel in human teeth is translucent. Note viper fish are tiny so their teeth are likewise very small, so they can look transparent just by being translucent an small. Hydroxyapatite, the mineral enamel and dentine are made of is translucent. the difference is in the crystal structure,(teeth or often porous which leads to more scattering and less transparency similar to why dry paper is white and wet paper is translucent (also true of teeth)). Impurities or more precisely what else is present in the enamel and dentine are present has an effect as well, as teeth are not just hydroxyapatite.

Source for the composition of teeth.

source for the translucency and microstructure of teeth

Source discussing how translucency changes with mineralization in cow teeth.


For emphysema, which of the respiratory volumes is affected? It could be the tidal volume because it affects how a person inhales and exhales normally.
It could be the residual volume and functional residual volume, because it increases its amount. Because it traps air.
On the other hand it also affects the Forced vital capacity because it decreases the amount of air that can be forcibly exhaled immediately after one inhalation.

To learn obstructive/restrictive lung diseases, I find it easiest to think in extremes at first, with vivid descriptions of why.  So in obstructive lung diseases, like COPD/emphysema:

Total volume increases because so many of the walls of the alveoli have been destroyed, they are like giant floppy bags instead of nice firm bubbles.  There's more empty space, and total volume is therefore increased.

Reserve Volume and End Respiration Volume increase because these alveoli are large and stretched and floppy and can't push as much air out, even when you try.  (Decreased elastic recoil.)  They also flop shut often before the air is expelled - trapping air in.

Tidal volume may not change at all, but it takes longer to exhale than with normal lungs.  That is why FEV1 and FVC are lower, for the same reason.

Residual volume


Are Gram negative bacteria classified as such because of their negative membrane potential? Does the membrane potential usually quoted for Gram negative bacteria (e.g., E. coli) refer to the potential across both membranes? - If yes, then does the potential fall more over the inner or outer membrane? Are there any studies that estimate/measure the relative fraction for each membrane?

I assume that the measurements of potential are usually carried out by inserting an electrode inside the cell and measuring the difference with the outside, this would make the answer to the first question yes.

Short answer
The distinction between Gram positive (Gram+) and negative bacteria (Gram-) has absolutely nothing to do with membrane potentials; it is all about the Gram staining procedure.

Background
The Gram staining was named after the Danish bacteriologist Hans Christian Gram, who originally devised it in 1882 (Gram, 1884). Gram staining is a common technique used to differentiate two large groups of bacteria based on their different cell wall constituents. The Gram stain procedure distinguishes between Gram+ and Gram- groups by coloring these cells violet or red, respectively (Fig. 1).

Gram+ bacteria stain violet due to the presence of a thick layer of peptidoglycan in their cell wall, which retains the crystal violet these cells are stained with. Gram-, on the other hand stain red, which is attributed to a thinner peptidoglycan wall, which does not retain the crystal violet during the decoloring process.

Gram staining procedure
The procedure involves staining the cells with a crystal violet dye. Next, an iodine solution (iodine and potassium iodide) is added to form a complex between the crystal violet and iodine, which is insoluble in water. Then, a decolorizer, such as ethyl alcohol, is added to the sample, which dehydrates the peptidoglycan layer, shrinking and tightening it. The crystal violet-iodine complex is not able to penetrate this tightened peptidoglycan layer, and is thus trapped in the cell in Gram+ bacteria. In Gram- bacteria, however, the thinner peptidoglycan layer does not retain the crystal violet-iodine complex and the color is lost. Lastly, a counterstain, such as the weakly water soluble safranin, is added to the sample, staining it red. Since the safranin is lighter of color than crystal violet, it does not disrupt the purple coloration in Gram+ cells, but it does stain the decolorized Gram- cells red.

Fig. 1. Gram+ bacteria (left) and Gram- on the right. source: Lab Tests Online

Reference
- Gram, Fortschritte der Medizin (1884)


Action Potential Distribution On Synapses This is a biology+physics question. Since there is no biology section, I am asking here.

In brain, when a neuron reaches to threshold value, it fires an action potential. In most graphics, that is shown as 40 mV. An example is

Neuron's this potential reaches to all synapses where this neuron is connected to, and chemically transferred to other neuron and transformed into electric charge again.

My question is, because in artificial models not shown, if that whole 40 mV is distributed to those synapses according to synapse strengths, or do all synapses take a total 40 mV which is like creating a potential while it is not there?

Another small question is if the collected potential is stored in neuron if it cannot reach to threshold value like a capacitor in circuit?

I think you are really wondering how axonal morphology affects the voltage along the axon. The short answer to your question is that each synaptic terminal sees the same voltage because that voltage is generated "fresh" at each site. This has nothing to do with synaptic strength, which determines the amount of voltage deflection in the postsynaptic terminal but not in the presynaptic terminal.

The axon has two major properties that allow for this even activation across its branches. First, as @Armatus said, the axon is an active structure, meaning that the action potential (AP) regenerates as it travels along the axon. This means that there is essentially no decay of the voltage as the AP propagates.

Second, the axonal geometry appears to be carefully regulated. As you seem to have guessed, there has to be sufficient current flow to activate an action potential in the neighbouring patches of membrane or else there is a propagation failure and the AP stops. This is a problem at axonal branch points (see Box 1 in Debanne, 2004), where the diameters of daughter branches have to be correctly sized so that there is little or no extra electrical load. (For instance, if one branch stays the same size as the mother, the other branch is an extra load that will "steal" current and leave less current travelling down the mother branch). Recent work using voltage-sensitive dyes have shown that in mammalian neurons, in practice, propagation failures are rare (Foust et al, 2010). This suggests that there is fine regulation to ensure that the geometry is "just right." (Those "just right" rules are basically governed by cable theory, which I've previously described here.)

To your last question, yes, there is time-dependent decay of subthreshold potentials because the membrane is a capacitor (~1 uF / cm^2). I wouldn't call this "storage" exactly, but it does work just like a capacitor in a circuit. Many people think of the membrane as a capacitor and a resistor in parallel.

Debanne, D., 2004. Information processing in the axon. Nature Reviews Neuroscience 5, 304–316.

Foust, A., Popovic, M., Zecevic, D., McCormick, D.A., 2010. Action Potentials Initiate in the Axon Initial Segment and Propagate through Axon Collaterals Reliably in Cerebellar Purkinje Neurons. J. Neurosci. 30, 6891–6902.


What is the classification for animals with full tube digestive tracts? What is the formal name for animals with full digestive tracts, by which I mean a mouth and an anus, and what is the classification for animals that have a single hole for exchanging food and waste?

Animals with a single hole do not form a monophyletic group: metazoa > eumetazoa >bilateria almost all have separate mouth and anus (except notably flatworms which is one reason it does not form a monophyletic group).

As species are not grouped in monophyletic groups by what they don't have (eg. invertebrates do not form a monophyletic group while vertebrates do) there is no particular group. Eumetazoa before the bilateria have a single mouth-anus.


Why is knowledge of bacterial pathogenesis important? Why is knowledge of pathogenesis increased more and more for common bacterial pathogens? Most of these studies lack a near application in disease control such as vaccines or antibiotics.

Examples:

Studies on the interactions of Haemophilus parasuis with porcine
epithelial tracheal cells: Limited role of LOS in apoptosis and
pro-inflammatory cytokine release
Sialic acid in the lipopolysaccharide of Haemophilus influenzae:
strain distribution, influence on serum resistance and structural
characterization

Because it is first important to understand a mechanism before you can think about using it for drugs. Take melanoma for example: A large subset of melanoma has a mutated and constitutive active BRAF kinase which permanently signals towards the nucleus and thus deregulates gene expression. Once this mutation was found it was possible to design inhibitors which only work on this specific mutation, which are available in the clinic today.

The same is true for example for activity of antibiotic on bacteria and the fight against resistance. Once it was known that the enzyme beta lactamase inhibits beta lactam antibiotice (penicillin or ampicillin for example) it was possible to find an inhibitor of the enzyme. The clavulanic acid works as a specific inhibitor and has been added to beta lactam antibiotics subsequently to overcome resistance. The same is true for changing antibiotic molecules chemically so they evade the established resistance mechanisms.

The contributions of basic research is the basis for applied research and drug design. Without them, this wouldn't work. Besides that it is also the curiosity of humans which drives science - without having any particular application in mind. These often come much later.


Can somebody identify this insect? It has transparent wings which covers the body like an armor. It has shining red orange colour.

I found it in the western ghats of kerala.

This is a tortoise beetle, a coleopteran from the Family Cassidinae.

According to the Queensland Museum:

  tortoise beetles are quite distinctive because they’re actually quite flattened and their wing covers are expanded around the edges. So the wing covers are the hard forewings that protect the hind wings in beetles and because they’re spread out at the sides, they look somewhat like a turtle or a tortoise. So that’s how they get their common name.

There are many beautiful specimens, like these:

Your photo is not exactly the best one, but based only on it I'd say that your specimen is a golden tortoise beetle (Aspidimorpha sanctaecrucis):

Here is another image of it, even more similar to your specimen:


What is the difference between natural selection and adaptation? From what I've read it seems that the only actual difference is that creationists use adaptation and people who believe in evolution use natural selection. But otherwise, from my understanding, the two terms are synonymous. Is that correct?

Natural Selection

Natural selection is the differential in survival and/or reproductive success among different individuals. As such, natural selection also refers to the process by which genotypes associated with greater fitness increase in frequency in the population through time.

More information on wikipedia > Natural Selection

Adaptation

An adaptation (or an adaptive trait) is a trait with a functional role that evolved (and is maintained) by means of natural selection.

More information on wikipedia > adaptation

Usage

Both the terms adaptation and natural selection are extensively used in science (and none of them come from the creationist religious belief). Their definitions are related as one is causing the other but these terms are not synonyms.

Further information

As the question is very introductory in the field of evolutionary biology, you might want to have a look at an introductory course to evolutionary biology. Evolution 101 (a.k.a. Understanding Evolution) by UC Berkeley is short, concise and very accessible even for those that have little a priori knowledge in biology.

Side Note

You said "believe in evolution". It is of course a common phrasing from the creationist ideology. Evolution is a theory (a theory is very different from a hypothesis see this answer for more information) and therefore, the phrasing "to believe in evolution" sounds quite wrong as it wrongfully suggests evolution is a thing on which we could legitimately have different opinion about its existence.


Anti-parallel DNA code operons Coming from a software engineering standpoint, suppose I have a string of code like so:

... 5'-ATAGAC-3' ...

... 3'-TATCTG-5' ...

Assume the above code is part of a larger segment. Now, reading from 3' to 5', the promoter and operator would be somewhere before the structural gene on the 2nd stand:

(Promoter) (Operator) ... 3'-TATCTG-5' ...

Where would it be on the first strand? From what it looks like, the first strand codes for a completely different protein than the second stand:

... 5'-ATAGAC-3' ... (Operator) (Promoter)

Yet, the two strands are complementary.

In your example, yes the two strands do code for different proteins. However, biologically this generally doesn't occur. I say generally because I don't want to rule it out definitively but I don't know of an instance where both strands at a given locus code for a protein and, where it does occur, it is often used as a criterion for annotating one of the elements as dubious. Along with that, there would be no promoter immediately 5' to one of the strands. Even if it does occur biologically, each strand would code for a different protein and would be a different gene.

In any gene, one of the strands is identical to the RNA transcript (before processing and with T instead of U). This is called the coding or sense strand and runs 5' -> 3'. The other strand is used as a template by RNA polymerase (RNAP) to polymerize the RNA transcript. It runs 3' -> 5' and is called the template or antisense strand.

Also, a note on promoters: promoter consensus sequences by convention are given on the sense strand. However, as far as I know, transcription initiation factors recognize the base pairing between both strands in the major groove of dsDNA because they must bind before promoter melting occurs. Thus, I wouldn't say that a promoter exists only on the template strand.


What kind of species is this? Does anyone know what this is? It is seen in France. It looks like it has eight legs and is about 8-10 cm long.

It is a longhorn beetle, family Cerambycidae. Two of the "eight legs" are antennae. It looks a lot like the one pictured here: https://hiveminer.com/Tags/cerambycidae%2Cfrance


Confused about plant phyla My kids and I are doing a fun project collecting pictures of life in parks and national parks around us. We are trying to classify what we find down to genus and species.

However, I'm confused about what the plant phyla are. With animals, it is pretty clear (e.g. arthropods, chordates), but I don't understand what they are for plants. I see informal groupings and divisions, but not what phyla.

Phyta means plant... The different 'phytae' mark different levels in the taxonomy...

Example:

Streptophyta from the Greek strepto, for twisted, i.e., the morphology of the sperm of some members and phyta (plant), a group including land plants and some algae

Embryophyta - land plants

Tracheophyta - vascular plants (from Ancient Greek τραχεῖα (trakheîa, “windpipe”) + -ophyta)

To answer your question... Phyta is a part of many plant taxonomy levels... It is not one type of plant but it marks the membership of a group to the kingdom of plants.


Why Do Most Humans & Cats Have Blue/Bluish Eyes At Birth? I've read that the eye color at birth for most humans and for cats may not always be the the true genetic color at first. This is due to the lack of melanin in the iris. This makes sense as there is no light in the womb to stimulate the production of melanin.

My question(s) though is:

Why does the lack of said melanin produce a blue/bluish colored iris?
Why is it not say green, red, clear, etc?

The blue colour is an example of structural colour, caused by light interacting physically with something. Some examples of structural colour are the iridescence of insect wings and body surfaces (usually caused by repeating chitinous structures), and of certain birds feathers, as well as the non-iridescent colours of the blue and yellow macaw.

In the case of the eye it is the stroma of the iris that is responsible. This is a network of fibrous tissue which scatters light. When light is scattered in this way (Rayleigh scattering) it is the short wavelengths which are most scattered. So when you look at the sky (away from the sun) you are seeing diffuse blue light created by this scattering in the atmosphere. In the case of the iris what you are seeing is light reflected from the eye being scattered within the iris, creating the diffuse blue colour. As you say in the question, everything else is down to melanin.


Diffusion coefficient of cells in blood? What's the diffusion coefficient of white cells in blood?
Is it well defined, or are cells too large and few as to be treated as particles in this context?

P.S. I have tried to look this up, but what I find inevitably is about diffusion coefficients of molecules inside cells, which is not what I want.

Cells absolutely can be considered as diffusing objects.  However, the origin of the "diffusion" can be very different than for, say, a bead in water.  The reason is that the thermal motion that creates the diffusion of a micron-sized bead can be much less important for a (large) cell.  For instance, the diffusion coefficient due to thermal forces of a sphere in a fluid with viscosity $\eta$ is
$$D_{therm} = \frac{k_B T}{6 \pi \eta R}$$
where $R$ is the cell radius (this is the "Stokes-Einstein" result).  For a white blood cell (say 10 microns in radius), this would - assuming blood is at least as viscous as water - lead to thermal diffusion coefficients around 1 microns$^2$/hour- i.e. we would need many many hours for a cell to travel its own diameter.  This result neglects a bunch of complexities - blood is not perfectly viscous, there is a really high density of red blood cells in blood, etc... but the basic result is that the thermal buffeting that drives the diffusion of a colloidal bead is not enough to drive a cell.
However, cells are not passive beads!  They crawl, both randomly, and (as cancerconnector notes), in response to signals like chemical gradients.  If a cell crawls with a speed $v$ and maintains its orientation over a time $\tau$, it's reasonable to describe its motion (over times much longer than $\tau$ as being diffusive with an effective diffusion coefficient
$$D_{motility} = \frac{1}{2} v^2 \tau$$
which you can get mostly from dimensional analysis, or more rigorous models.  For white blood cells, $v$ is on the order of microns/minute - at least when measured on slides - it might be different in the body.  $\tau$ is a few minutes, so $D_{motility}$ is on the order of many microns$^2$/minute - orders of magnitude faster than mere thermal diffusion.
A good introduction to modeling of this question is probably chapters 9-11 of Leah Edelstein Keshet's "Mathematical Models in Biology" and she cites some classic Lauffenberger papers on macrophage response, etc.  You may have access to this online: http://dx.doi.org/10.1137/1.9780898719147
Also, note that everything I've said so far neglects blood flow - if this is important in your problem (which will depend on the context), things can get more complex (have to include flow in your diffusion equation).  But using diffusion equations to model the spread of randomly motile cells is a very common approach, and there is a lot of literature on it!


Does a gene that regulates itself necessarily be a transcription factor? I am not a biologist, so please pardon the overly noob question. Some genes are transcription factors (TF) and regulate other genes. My question is: if a gene is NOT a TF gene, can it regulate itself? E.g. given a system of 3 genes {g1,g2,g3} where only g1 and g2 are TF, then in a gene regulatory network, what are ALL possible parental sets of g3 (where in this GRN, you put a directed edge from the regulating gene to the regulated gene)? Will it be {{g1},{g1,g2},{g2},{}} or {{g3,g1},{g3,g1,g2},{g3,g2},{g3}}

First of all you need to clarify what exactly is the output that needs to be regulated. We often say regulation of expression of a gene but what expression ultimately leads to is the activity of the gene (whatever it might be: enzyme based catalysis, cytoskeletal rearrangement, response to an extracellular signal). Activity of course depends on the expression level of the gene but it also depends on other factors such as covalent modifications, interactions with other genes (like dimerization) etc. Moreover, for genes which code for proteins, expression also has two stages.

Coming back to your question:

  If a gene is NOT a TF gene, can it regulate itself?

Yes it can. There are many modes of gene activity regulation as I already mentioned. Examples where a non-TF gene can regulate itself:

Feedbacks in cell signalling which happen via activity modulation by protein phosphorylation [1].
Regulation via post-transcriptional regulation via RNA binding proteins (RBP) or regulatory RNAs such as miRNA. MAPK signalling pathway has a feedback via the RBP, Rnc1, which upon phosphorylation binds to and stabilizes the Pmp1 mRNA. Pmp1 is a phosphatase which dephosphorylates Rnc1[2]. This loop contains regulation by both post-translational modification and post-transcriptional mRNA stabilization. There are many other examples involving RBPs. An miRNA, let-7 is post-transcriptionally regulated by Lin28 (promotes degradation) which in-turn is post-transcriptionally repressed by let-7 [3].

There are many examples of metabolic feedbacks too which operate via allosteric regulation of the enzyme activity.

If you are only interested in regulation of gene expression then you can ignore phosphorylations and allosteric regulation but there are several examples of post-transcriptional regulatory interactions which also contain feedbacks.

References

Dougherty, Michele K., et al. "Regulation of Raf-1 by direct feedback phosphorylation." Molecular Cell 17.2 (2005): 215-224.
Sugiura, Reiko, et al. "Feedback regulation of MAPK signalling by an RNA-binding protein." Nature 424.6951 (2003): 961-965.
Rybak, Agnieszka, et al. "A feedback loop comprising lin-28 and let-7 controls pre-let-7 maturation during neural stem-cell commitment." Nature Cell Biology 10.8 (2008): 987-993.