text:
Photosynthetic Pigments vs. Chloroplasts
What is the difference between Photosynthetic Pigments and Chloroplasts? I know plants have both but Prokaryotes (Bacteria and Archeae) only have the former.

Photosynthetic pigments are the chemicals which take part in photosynthesis, in particular they are they ones which absorb photons and fluoresce (emit photons of a different wavelength) or emit electrons. Pigments are molecules, and chlorophyll is a key example. These pigments are required for photosynthesis to take place, as they generate the electrons which create the electrochemical gradients which power photosynthesis, thus all photosynthetic organisms will have photosynthetic pigments of some kind.
Chloroplasts are membrane-bound organelles in plant cells, made up of many hundreds of thousands of molecules including pigments. Plant photosynthesis takes place on their internal membrane, the thylakoid. Specifically, the thylakoid membrane of chloroplasts is the membrane across which the aforementioned electrochemical gradients are created in plants.
Chloroplasts originated from a free-living bacterium, probably a cyanobacterium, entering a eukaryotic cell. So prokaryotes don't have them because the chloroplast endosymbiosis event was one way in which plants diverged from their non-plant ancestors. So you can think of a cyanobacterium as a free-living chloroplast - they have their own internal membranes similar to the thylakoid across which electrochemical gradients are created for photosynthesis. Conversely, you can think of a chloroplast as a small cyanobacterium living symbiotically inside a plant cell.


text:
Which strains of C. diphteria are causing Diphteria toxin?
I got this question:
Diphteria toxin is produced only by those strains of C. diphtheria that have which of the following characteristics?

Encapsulated
glucose fermenters
lysogenic for b-prophage
only mitis-strains
sucrose fermenters

I think the right answer is lysogenic for b-prophage, since Freeman found out that toxic gene is encoded by lysogenic phage infecting all toxigenic strains in 1951.
However, I am not sure what "b-" means in "b-prophage".
Which part is "b-" in Prophage?

Real simple: Beta!  Often called "phage beta" b-prophage is a more modern way to write it.  I knew that one off the top of my head, but I like to refer the general public interested in bacteriology to Tadar's online text.
It's nicely done, and I wish that it had been around when I was studying bacteriology.
Specific to your question:

Hence, Corynebacterium diphtheriae can only produce the toxin
  responsible for the disease if it carries a temperate virus called
  phage beta. Only lysogenized streptococci  produce the erythrogenic
  toxin (pyrogenic exotoxin) which causes the skin rash of scarlet
  fever; and some  botulinum toxins are synthesized only by lysogenized
  strains of C. botulinum.

source: Stack Exchange

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sort: votes


text:
Why do 6-8% of diphtheria patients do not develop natural immunity after being affected?
I am thinking of why some patients do not have natural immunity after exposure to the A-B toxin of diphthria.
I think the A-B exotoxin is the key factor causing this disease and should trigger memory cells to form.
DT has both local and systemic effects.
Locally, its action on epithelial cells leads to necrosis and inflammation, forming a pseudomembrane composed of a coagulum of fibrin, leukocytes and cellular debris.
Absorption and circulation of DT allow binding throughout the body.
Local effects produce pseudomembrane.
The major impact of transduction in pathogens is the introduction and stable inheritance of virulence genes such as those coding for toxins.
C diphtheriae is lysogenic with a phage containing the diphtheria toxin gene.
Diphtheria toxin is produced by C diphtheriae only when infected with a bacteriophage that integrates the toxin-encoding genetic elements into the bacteria
The toxicity for intact cells depends on toxin binding and uptake.
In other words, the net effect of the toxin depends on the function of the target protein and the function of the cell.
B subunit binds to receptors that regulate cell growth and differentiation, thus exploiting a normal cell function.
A subunit inhibits protein synthesis.
B subunit binding determines cell susceptibility.
Absorption and circulation of DT allow binding throughout the body.
I think this uptake does not occur sufficiently with patients without natural immunity stimulation.
I think the reason for no natural immunity for some patients after toxin exposure is that the host does not stimulate enough adaptive immunity and no memory cells are built.
Again, this is because the bacteria has little invasive capacity.
Diphtheria is due to the local and systemic effects of DT with potent cytotoxic features.
The uptake of the toxin varies also among some patients.
So other patients have probably more local effects.
This would explain partially why the adaptive immunity is not triggered.
Diphtheria toxin is antigenic itself.
So it can stimulate the production of protective antitoxin antibodies during natural infection.
In those patients without development of natural immunity, A subunit fails to bind EF-2, probably.
One reason is that the toxin does not get into bloodstream in 6-8% cases, and so natural immunity is developed.
So there is too low effective dose of diphtheria for some patients to invade the epithelium and trigger the adaptive immune response and create memory cells.
Sources: Murray Microbiology, Sherris Microbiology and Jawetz Microbiology.
Why do 6-8% of diphtheria patients not develop natural immunity after being infected?

Couple of quick thoughts. Extoxins by definition are secreted, and making antibodies to them can be great to limit their toxic effects, but does little to diphtheria, which is what you would want to remove if it's being pathogenic.  I'm going to have to look more into the lit to see if it seems host or path specific.

@Masi Do you have a source for the 6-8%?

There are two other, but rather exotic possibilites which explain why people do not develop immunity after an diphtheria infection. These are unlikely to get to 6-8% of the cases which @Masi writes, but I am missing the reference here.
The first possibility are people with chronic renal failure. They have problems with their immune responses since their antigenpresenting cells do not get the necessary co-stimulatory signal by the T-cells. See this paper. People with other problems in their T-cells or the co-stimulatory signal would have this problem, too. See this article.
The other possibility would be the distribution of the antibodies. The diphteria toxin is made out of two subunits, A and B. B is important for making the way of A into the cell, A gets cleaved in this process and fully active. When the antibodies made in the process are mostly against A (and then against parts, which change their conformation after the cleavage), this antibodies are mostly useless to fight the toxin. See this paper.
One (but is complete speculative) possibility is on the toxin itself. It could be possible, that some people are more sensitive to the diphtheria toxin, so that the amounts necessary for the negative effects are too small to trigger an adequate immune response. This is known for the tetanus toxin, where even a survived infection doesn't provide immunity (except when people are vaccinated afterwards) as the toxin is so toxic, that it doesn't trigger the immune system. The caveat is, that the diphteria toxin is about 3 orders of magnitude less toxic than the tetanus toxin.

may I ask if there are really no survivors of tetanus whatsoever, that become immune ? Even if they are not immune, do they have antibidies for some time ? I would expect this to happen as a stochastic effect. I only know - actually from antivaxers, but the sources seem legit - that there are some unvaccinated people, especially children, who have antitoxin antibodies without a known history of tetanus.

@Barbara As I explained above, survivors do not become immune because the tetanus toxin is so toxic, that the amount necessary to poison a person (we are talking about an LD50 of 2.5-3 ng/kg) will not trigger an immne response. Can you please cite the source?

Naturally acquired immunity to tetanus toxin in an isolated community.
H Matzkin, S Regev
Infect Immun. 1985 Apr; 48(1): 267–268.
PMCID: PMC261948

[Naturally acquired tetanus antitoxin in the serum of children and adults in Mali].
Ehrengut W, Sarateanu DE, AgRhaly A, Koumaré B, Simaga SY, Diallo D.
Immun Infekt. 1983 Nov;11(6):229-32. German.
PMID: 6680401

Naturally acquired antibodies to tetanus toxin in humans and animals from the galápagos islands.
Veronesi R, Bizzini B, Focaccia R, Coscina AL, Mazza CC, Focaccia MT, Carraro F, Honningman MN.
J Infect Dis. 1983 Feb;147(2):308-11.
PMID: 6827147

Response to single dose of tetanus vaccine in subjects with naturally acquired tetanus antitoxin.
Dastur FD, Awatramani VP, Dixit SK, D'Sa JA, Cooverji ND, Anand MP.
Lancet. 1981 Aug 1;2(8240):219-22.
PMID: 6114281

New concepts on tetanus immunization: naturally acquired immunity.
Veronesi R, Cecin H, Corrêa A, Tavares J, Moraes C, Bertoldo OJ.
J Hyg Epidemiol Microbiol Immunol. 1975;19(1):126-34.
PMID: 1092755

Just wanted to add that this is a common problem with vaccines.

...consider an actual measles outbreak in Colorado in December 1994.5 Out of 625 children exposed to the disease, 17 got measles. Of those 609 who had previously been vaccinated, only 10 (or 1.6%) developed measles. Of the 16 children who were not immunized, 7 (or 44%) developed measles. Thus, the risk for immunized children was less than 2% while the risk for unimmunized children was 44%.

Most vaccine development struggles to reach high immune efficacy; You usually can't just inject some dead bacteria or virus and expect to get an immune response.
In particular I think there has been adaptations in the immune system to DT such that it tends to stimulate an immune response.  This is pretty much a reaction to the peptide sequence itself.  We know this because since the 1980s there has been concern that the live toxins in DPT vaccines might be causing health problems with young children.  (They don't).  As such, acellular vaccines were developed where just a few proteins were included - the cell was not used, and DT was produced where only a fragment was added or the toxin was rendered inactive by mutagenesis. DT is such a reliable component that by itself it can illicit an 88% immunity rate.
These DT fragments are formulated with other bacterial components to create new vaccines.
The failure of the vaccine on occasion is most likely the result of individual variations in immune loci. The immune system is highly complex and also highly variable from individual to individual even amongst close relatives.  their immune activation or their defenses (complement and immunoglobin pathways) may make some individuals more susceptible to diphtheria than others.
The science of vaccine formulation is highly empirical; I don't think it is understood why some molecules evoke a broadly distributed reaction and others do not.  Even so the diphtheria toxin is one of the more universal immune stimulants known.  I don't think that a completely universal adjuvant (something added to a vaccine to stimulate an immune response) is known.

This is a common problem with vaccinations, they have no 100% succes rate. For the diphtheria number Masi mentioned it would be interesting to know if these are immunized and so on...

expanded answer

In this article they look at the development of natural immunity to diptheria in those who were vaccinated. I could not find any studies on people who had acquired it naturally.
http://www.sciencedirect.com/science/article/pii/S0264410X97001485
They found that the development of immunity to diptheria vaccine depended on several factors:

Time lapsed since last vaccination
Females had lower immunity rates
Number of previous vaccinations
Last vaccination within the first 3 years of life
Age

What this may mean for individuals who are affected is that similar factors could play a role preventing them from acquiring immmunity to diptheria. Indeed, some of the factors like last immunization and number of vaccinations are logical since diptheria may evolve or there may be different strains so the body needs to have the lastest antibodies for immunity.

All the points above are interesting, but they are only important for answering the question why people get diphtheria and not why they are not developing immunity after having the disease. Evolution of strains is not a problem, since the vaccine is directed against the toxin and not against some fast changing component. Otherwise we would need a new vaccination every year (or at least every few years) which is not the case.

The question asks why do some people not develop immunity. My answer consists of reasons why this may be the case-- at the macro level (for vaccinations). I did not go into molecular mechanisms of why diptheria does not result in immunity in the 6-8% because I could not find any references in the literature. If you imagine the evidence that would need to be gathered to establish this, you would realize this is a tall order. Evolution of strains is documented in the literature -- see this article for insight http://jid.oxfordjournals.org/content/181/Supplement_1/S168.full .

Thats why I asked Masi for the reference on this quote. There are some possible mechanisms why people are not developing a immune response, I will write about this later. The evolution of the strains is obviously not causing problems, the vaccination seems to work.

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text:
What do sharks not like the smell of?
I was reading about the sharks strong sense of smell ( Shark senses - @EnhancedLearning.com ) and wondered if any research has been done into what they don't like the smell of?
Is there any material that they don't like being near and would stay away from?

Could you provide a link to what you were reading?

Shark senses-@EnhancedLearning.com . Maybe they could mix a deterent into surfboard wax or wetsuits (:

I don't think one can easily determine what smell sharks don't like. You know, you can't easily find whether a shark turned around from something because it didn't like its smell or it wasn't interested in it, especially tiger sharks ;)

@another'Homo sapien' , if I could name one I wouldn't need to ask the question? With the advances in biotechnology and other areas in recent decades it is more than possible that we could make something that deters sharks, I think to say it doesn't exist or can't be done is very narrow minded (with all due respect it's figure of speech) .

There could be a marine creature that contains something that makes the sharks not like to eat them or see them as a snack.

@another 'Homo sapien' I was just guessing with the puffer fish I , agree this is going a bit off topic from the O.P, thank for the input anyway (:


text:
Why are nucleic acids negatively charged at physiological pH?
Why do nucleic acids and mononucleotides have a negative charge physiological ph?

Are you asking about nucleic acids or nucleotides?

This sounds like a homework question. Have you tried looking at the structure of a nucleotide?

http://www.tud.ttu.ee/im/Tonu.Reintamm/shabarova/4.1.html

The phosphate group/s present in the mononucleotide or nucleic acid result in the structure having an overall slightly negative charge.
Positively charged proteins that are also present in the cell such as histones help to keep the negatively charged nucleic acid stable 'in vivo'.


text:
Alternatives to PCR
PCR uses cycles of heating and cooling to denature the strands, calling for special thermostable DNA polymerases. In a cell, during replication, Helicase unwinds the DNA without the requirement of heat. Can Helicase be used instead of the heat cycling to achieve single stranded dna? Would that eliminate the need for heat cycling, and hence special thermostable polymerases?

The temperature is cycled because we want to control the reaction. We control the reaction to multiply the DNA to the levels required. Thirty to forty cycles are usually good enough. You can't control helicase in the same way. So, no, helicase cannot be used instead.

Edited after clarifications in question,
Let's start with normal functions of both enzymes. Helicases separates DNA strands while polymerase synthesize DNA strands as shown in the following figure. (Image Source: Wikimedia Commons)

Watch this animation, it will clear your doubts about function. However, RNA polymerase does have both activities.
In cells, helicase action is required to separate DNA strands. After that only polymerase can act. During PCR, separation of strands is done by increasing the temperature. This process is called DNA melting. This temperature is generally very high, around $90^oC$ to $100^oC$ depending on your sequence. At this temperature many proteins will not function, hence you need thermostable polymarase. About 40 years ago, such an enzyme was discovered from extremophiles (Chien et al 1976). Now it is commercially available as Taq polymerase. These enzymes are recombinant proteins with a few mutations which have also increased its yield and stability (Villbrandt et al 1997).
Now coming to your main question (Which I think I understood correctly this time).
The concept you are asking about has already been successfully tested in RNA detection. Researchers have used "Isothermal reverse transcription thermophilic helicase-dependent amplification"(Goldmeyer et al 2007). They used not only helicase but also reverse transcriptase (because they were detecting RNA). The following image (taken from the paper) shows the main steps in this process. Circles indicate DNA polymerase, squares indicate reverse transcriptase, and triangles indicate helicase.

Quoting from the paper (bullet points are mine),

Arrows indicate specific primers, circles indicate DNA polymerase, squares indicate reverse transcriptase, and triangles indicate helicase. The first-strand cDNA is first synthesized by a reverse transcriptase

(steps 1 and 2). The RNA-DNA hybrids from the reverse transcription are then separated by UvrD helicases generating single stranded (ss)
  RNA and DNA templates
(steps 3 and 4). The ssRNA enters next round of RT reaction
(step 5-a) generating more first strand cDNA. The ssDNA was converted into double-stranded DNA by the DNA polymerase
(step 5-b) and amplified concurrently in the tHDA reaction
(steps 6 through 9). This process repeats itself to achieve exponential amplification of the RNA target sequence.

I think you misunderstood the question: it wasn’t asking whether a helicase could substitute a polymerase in the PCR, but whether it could substitute the heat cycling.

Thank you for the answer, but Konrad Rudolph is right.I meant to ask if the heat cycles could be avoided altogether.

Ah, ok. I will edit answer accordingly. Now wording is better and with more clarity.

CubeMaker, @KonradRudolph, check now. I have edited answer. I guess this is what you are looking for.

Isothermal DNA amplification technologies have been developed. You do not need thermal cycling to amplify DNA fragments by this method.
http://www.ncbi.nlm.nih.gov/pubmed/17720718


text:
Calibrating Motic Camera to Stage Micrometer
Whilst calibrating my Motic Microsope's camera, I am able to calibrate the 10x object lens against the stage micrometer accurately.  However when I calibrate (using the Motic 2.0 Plus software) the 40x object lens, it always sets the ratio incorrectly.
For example, in the calibration panel, I load a photo of the scale that I took and then I draw the circle so that it measures the pixels both in height and width and then I tell it that the circle is 10 µm.  But it doesn't seem to get the ratio correct.  When I did this for the 10x lens it worked perfectly.
So I took a photo of the scale with the 40x object lens and then went to calibrate that.

Here you can see how the calibration is performed: you position a circle over the photograph and tell it the size in µm (it's rather large, sorry):

Here you can see the measuring line out of whack.  It gives me 8 µm for a length that should only be 4 µm.

Am I missing something?

The way I solved this was by using the scale line method.  First, I understand that each division on the stage micrometer is equal to 10 microns.  Then, using my photograph of my stage micrometer and the Motic software on my computer,  I draw a horizontal line over oh, say, 3 divisions and tell it that this distance (measured in pixels) is equal to 30 microns.
Now, using the same method, this is also possible:
I found another Windows program called Meazure which you can use in the same fashion without any special microsoft software.  For this I use XnView to open the photograph of my stage micrometer, set the zoom to 100% and then draw a straight line over oh, say, 3 divisions.  Then I see how many pixels long that is.  Then I tell Meazure that this many pixels is equal to 30 microns.  Now I can measure, in XnView, any image taken by the microscope's camera - I just have to remember to assure the view is exactly the same.
The Meazure program is very nice and easy to use, and I actually prefer it, although the Motic software provides labels and such that are useful.

It looks like the shape is an ellipse rather than a circle. The ellipse has major and minor axes, which are described in terms of half-axes (177 and 175 pixels respectively). Is it possible the software is incorrectly using the half-axis measurements, whereas when you draw a perfect circle it will correctly use the diameter? This is consistent with the x and y scale numbers being different from each other.
So I would suggest re-calibrating with a perfect circle.
Hope this helps.

When I calibrate, should I calibrate to the edges of that black box?  It's supposed to represent 4µm.  If they were tick-marks I would think to measure to the insides...  It's kind of confusing.  Do I count the tick mark or not? Or do I measure to half of it?

With my own calibration slide that has a linear scale (like a ruler), I measure from the left side of one tick mark to the left side of another one.  I'm not familiar with your calibration slide, so I don't know what the outer lines represent. Do you have any documentation or are there other areas of the slide that are more clearly labeled?

My Mycologist says that it's supposed to be 10 microns from one tick to the next - whether left to left as you say (which is easy to see - thanks!) or from half to half of the tick.  So I tried this by capturing the scale with the 10x lens and calibrated four ticks to be 40 microns.  But when I measure from tick mark to tick mark I get 18.10 microns.  I'm still missing something.

My Stage Micrometer has five calibrators: a circle at 1.5mm, a circle at 0.6mm, a scale cross (1 DIV=0.01mm), a tiny circle at 0.15mm and a circle at 0.07mm.  Should I be using a particular one of these?

Okay, I think I've got this.  Instead of calibrating by drawing a circle over the scale cross, I used a different calibration setting where I just drew a straight line vertically and a different line horizontally.  with my Mycologist's directions that each length between tick marks = 10 µm I am now able to come up with correct dimensions.  Thanks for your time and attention!  Should I post this as it's own answer, or should you update yours to match so that I can accept a solution?

Great to hear that you solved it! I'm not a Stack Exchange expert, but I think the solution you found is different from my original idea. So for me, it makes sense for it to be its own answer.


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What is the subcellular location of synthesis of non-essential amino-acids?
What is location of non-essential amino acids synthesis in a cell? Is it some specific organelle? And what is the gene driver behind this?
I thought the whole point of DNA is coding for how to synthesize proteins and that it is the mechanism of genes expression. Triplets of nucleotides are codes of amino acids and that is the granularity that cell works with.
Now it turns out cells knows how to synthesize more than half of the 20 amino acids, in humans, and I do not see, in the web, good texts of how it is done, where, and how that is coded.
Thank you for helping to shed some light.

This is a very basic question, the answer to which is easy to find on the internet. Did you search Wikipedia for Essential Amino Acids or Amino Acid Synthesis? If that is insufficient and you need a biochemical text book chapter, Berg et al. on NCBI Bookshelf should be your next port of call. The specific section is in Chapter 24. Your expression "gene driver" is unclear to me. Read the chapter and then explain any further questions.

Hardly it is a basic question, David. I did go through the wikipedia articles but I did not manage to answer the title question. I am a computer programmer, I have no formal education in molecular biology.

Consider the response if I posted a question on Stack Overflow asking what a “for loop” was (for). Not only would I be posting a basic question to the wrong sort of site, but I would have shown a singular lack of initiative or aptitude in using the resources of the internet.

You are showing a lack, that is sure. Quite singular

I think you are almost right. DNA (in the nucleus) is transcribed to mRNA, and protein synthesis occurs on ribosomes where the the sequence of bases in the mRNA is translated into protein. Ribosomes are located in the cytoplasm or attached to the endoplasmic reticulum. (The 'mRNA story' is well told in Who discovered mRNA?)
But there is also another type of RNA that is critical to protein synthesis, and that is transfer RNA (tRNA): each amino acid is attached to an 'adaptor' molecule (tRNA) and it is this form of the amino acid that is used by the ribosome. It is the adaptor molecule (a tRNA 'charged' with an amino acid) that contains the anti-codon, which base-pairs with the mRNA during protein biosynthesis.
In order to carry out protein biosynthesis, the cell needs a supply of amino acids, the 'building blocks' of proteins. It is here  your thinking (maybe) is a little confused? The building blocks may come the digestion of protein in food, or they may be synthesized by the organism. If they can be synthesized 'de novo', perhaps starting from a glycolytic or Krebs cycle intermediate, they are (usually) considered non-essential. What amino acids are considered essential or non-essential depends on the organism. Humans, for example cannot synthesize 'de novo' the aromatic amino acids Phe, Tyr or Trp, but we can convert Phe to Tyr.  E.coli, on the other hand, can make all three of these amino acids from simple building blocks, but cannot convert Phe to Tyr (see Miller & Simmonds). Thus Tyr is considered non-essential for humans (provided that an adequate supply of Phe is available).
The biochemical pathways leading to amino-acid biosynthesis are usually quite complex, with the involvement of many gene products (enzymes). The story of amino acid biosynthesis is well told in Umbarger(1978):Amino Acid Biosynthesis and its Regulation.

There are several enzymes involved in amino acid biosynthesis. These some of thse enzymes are encoded in the human genome. You can check out KEGG for a detailed pathway in different organisms.

The green arrows denote reactions (and enzymes) that are present in a given organism (Homo sapiens, in this case). If you click on the arrows you can know the details about the enzyme.
These enzymes are present in the cytoplasm as well as in mitochondria. Moreover, the reactants for synthesis of certain amino acids are produced in mitochondria (TCA cycle intermediates). See this article on the role of mitochondria in amino acid metabolism.

  Overview of the amino acid metabolic network in human mitochondria. Shaded areas represent the cytoplasmic segments of the pathways.

I lack chemistry knowledge in order to understand the answer fully. Thank you for answering - it gives some key hints and introductions to the topic and has quite good links. One thing perplexies me still - enzymes are transcribed & translated from DNA which are to participate in non-essential amino acids sythesis, but for the translation you need amino-acid building blocks. So it might happen the same amino acid is needed,which is then a recursive task? Seems I have to read more to understand,I am also a layman in molecular biology

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text:
How many different species have existed on Earth?
NOTE: Someone else asked this same question a few years back, but it was incorrectly marked as a duplicate and so the question may not have been answered satisfactorily. I'm asking it again, in hopes of getting a stronger answer (if there is one). Please do not mark as a duplicate; I really appreciate it!
(Original question: How many species have existed on earth?, incorrectly marked as a duplicate of: How many organisms have ever lived on Earth?)
QUESTION: How many species have ever existed on Earth, throughout the entirety of Earth's history? For clarity, I'm not asking about the number of individual organisms (answered in 2nd link above), nor about the number of living species estimated to exist today (also cited in an answer in the 2nd link above). All species, ever (never answered in any link, to my knowledge).

Species are not countable in time.

Not an answerable question.  The problem, besides the obvious one of lack of data (no one really knows how many species exist today, let alone in the distant past), is that the idea of species is a human construct,  For instance, are wolves & coyotes different species?  They have different names, but have interbred to produce the coywolf.  Or all the fossils of pre-humans that keep getting dug up: are they all really different species?  Then when you get into microorganisms and things like horizontal gene transfer, the species line gets pretty blurry...

I was only wondering if there was a ballpark figure, out of curiosity. I know there is no perfect way to answer the question, given the subjectivity of what constitutes a "species", and the incompleteness of the fossil record (and impossibility of many types of organisms being fossilized to begin with). I am not that strong in this particular branch of biology, so I posed the question. If there's no answer, there's no answer, and that's fine (once again, I wasn't sure since the previous asking of the question was shot down).

From Raup (1986).

Up to 4 billion species of plants and animals are estimated to have
  lived at some tlme m the geologic past (2), most of these in the last
  600 million years (Phanerozoic time). Yet there are only a few million
  species living today. Thus, extinction of species has been almost as
  common as origination.

I am not sure how exactly has it been estimated. Read the paper for more details.
In 1991, Raup comments:

Countless species of plants and animals have existed in the history of
  life on Earth. Estimates of the total progeny of evolution range from
  5 to 50 billion species. Yet, only an estimated 5 to 50 million
  species are alive today – a rather poor survival record. With, at the
  most, only one in every thousand species surviving, what happened to
  the others?

Mora et al. (2011) predict ~8.7 million extant eukaryotic species. So I would guess that there are >5 billion (extinct + existing) species on earth.
I guess there will be many more prokaryotes. We don't know anything about ancient prokaryotic species because there are no fossils records. I would say that it would be nearly impossible to estimate the number of prokaryotic species: even now we do not have a very reliable method of typing microbial species (people mostly rely on 16S rRNA sequencing). See What defines a microbial species?

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text:
Where are Opsonins produced?
I read that opsonins are a type of antibody that play a vital role in chemotaxis and phagocytosis in general. The fact of them being antibodies though, got me confused. Antibodies are, to my knowledge (however inadequate it may be) , released by plasma cells after macrophages present antigens. Yet my book says that pathogens are covered in antibodies (opsonin) which help the macrophage initiate phagocytosis. How can antibodies (opsonin) be present before the APC Present the antigens to activate the production of antibodies?
P.S.: I'm a college student so there's probably a lot of things I'm missing out on. Please do fill me in :)

Did you check wikipedia on opsonins? For a more authoritative reference see this and this.

Yeah i tried, and cheers for the other two links, but i still can't find a clear citation of a source. Found what they do and how they work but not where they are produced. FYI by where i mean what produces them. Probably shouldve clarified that sorry.


text:
Does someone know of a website that keeps track of a species population?
I am planning on doing some math on population growth, but I need a reliable source of data on population growth of some species over time. Does anyone know of a resource (website/publications/public repository) that has such information?

Why a website rather than a publication who kept track of population size over time? What kind of population dynamic are you looking for (exponential growth, logistic growth, stable population size, decreasing population size, ...). Any species of preference?

A publication or such would work, as long as I can get my hands on it. I prefer logistic growth, but the others would do just fine as it does not really influence my purpose.

Humans are currently going through a logistic looking growth, where the peak of growth (growth of $r$) has been reached in the 1970s. Those would be easy data to find and always pleasant to play with.

How about human?
You will find the data of human population growth on the webpage "Our World in Data". Scroll to the second graph, click on the tab "data" and download the .csv file.
Just google for any specific species of interest
Otherwise you can just google things of interest. Look for large emblematic mammals or commercially important species.

If you google "bald eagle population growth", you will easily find these data.
If you google "moose growth population breeding pairs", you will find these data.
If you google "killer whale population growth", you will find these data.
If you google "tuna population growth", you will find these data.

COMADRE
COMADRE is a database of animal matrix population models. It can be of interest to you.

Can we ask for resource names on Biology SE like the one asked here?

I think you can, yes. As long as what you're looking for is well defined. I am a bit confused by your comment. Are Anonymous and BrianBlumberg the same person or did you forget the hyperlink on the word "here"?

No, that is not me. Thanks for the information.  Do you know of other sources which provide information on the population number of other species/organisms?

@BrianBlumberg Please see edited answer.


text:
Are there eukaryotes with fully working mitochondria but without mitochondrial genes?
Are there eukaryotic organisms with fully working mitochondria that do not have genes in the mitochondria?  By fully working, I mean ones which can carry out oxidative phosphorylation, unlike reduced mitochondria like organelles such as mitosomes in Giardia lamblia.
Is it possible to transfer all mitochondrial genes to the nuclear DNA and still have fully-functioning mitochondria?

No there aren't any organisms with fully functional mitochondria which (the latter) do not retain the minigenome.
On whether it is theoretically possible to transfer all the mitochondrial genes to the nucleus:
Perhaps it is possible and mitochondria may work just like lysosomes and ER, but I think that the responses will be greatly delayed. At present there are no mathematical models that can provide a better understanding of that possibility. Nonetheless, some studies have shown that chloroplasts and mitochondria also have redox dependent gene regulation by which the expression of some components of the ETC is regulated by the redox state of the quinone. This helps in optimization of the ETC; if all genes were in the nucleus then this would not be possible. This pheonomenon is, however, better studied in chloroplasts. See this review.


text:
Conifer with red fruit
What kind of conifer is this?

Red fruit
Broad needles; not clusters
12 feet tall; north wall of apartment building
East of Toronto, Ontario
September 20, 2022
Hint: click the photos a couple of times to zoom in

Street view 2009:

Street View 2021:

You shouldn't eat anything that you've not identified with 150% certainty, which means this comment is technically not required. Still: the entire yew bush is poisonous.

Yew trees grow to 5000 years old and have been associated with cemetaries since pre-christian times. https://www.google.com/search?q=very+old+yew+tree&sxsrf=ALiCzsbCzlHolFTxlVLfuPM94rWqDyOrFg:1664074956444&source=lnms&tbm=isch&sa=X&ved=2ahUKEwjH-aGl-q76AhW-X_EDHZYJAsUQ_AUoAXoECAEQAw&biw=1366&bih=620&dpr=1.88

The basic appearance is consistent with the family Taxaceae, commonly known as the Yew family. Primary indicators are the relatively distinctive shape and color of the arils (the red fleshy bits around the cones, which are actually technically not fruit), the fact that it’s a shrub, the fact that it was seen in Ontario (correct climate for most Yew species), and the fact that it’s being used as a decorative plant (Yews are very popular as decorative shrubs in that region of North America).
We can eliminate most of the genera relatively quickly:

Pseudotaxus has only one species, which has white arils instead of red.
Austrotaxus has only one species, which has a rather distinctively different aril than what is seen in the picture.
Cephalotaxus species also have a rather distinctively different aril than what is seen in the picture.
Amentotaxus species have rather distinctively different leaves (they’re much larger, among other differences).

That just leaves us with the genera Toreya and Taxus, which account for most of the species of Yew globally. A Toreya species is not particularly likely, as they are not generally used much in that part of North America as decorative plants, which just leaves Taxus.
My first guess given the region and apparent lack of male cones would be Taxus canadensis (the Canadian Yew), but the stated height and growth habits seen by comparing the 2009 and 2021 pictures don’t quite agree with that (T. canadensis generally does not get much more than 2.5 meters (about 8-9 feet) tall, and tends to grow out much more than up.
More likely, it’s a hybrid of T. canadensis and T. cuspidata (the Japanese Yew), which is a relatively common variety used as a decorative plant in the Midwestern and North Eastern US, as well as South Eastern Canada.

As a side note, irrespective of what exact species this is, be careful around it. All parts of every species in the family Taxacae except for the arils are highly toxic to humans year round. Yew poisoning can easily be lethal, and currently has no known antidote (though in theory most of the symptoms are treatable).
Touching the plant is fine, but you should be careful handling any clippings or sawdust from cutting it, and definitely do not eat any part of it (the arils are theoretically fine to eat, but the seeds they surround are actually the most toxic part of the plant, so it’s generally not worth the risk).

We used to taste the arils (pericarp) quite commonly. They are safe. Some people also made a jam from them, but I would not recommend that.

I remember a funeral parlor surrounded by yew shrubs that my siblings and I passed on our way walking to and from school. I ate these berries by the literal handful every day they were available; my mother had told me it was fine as long as I was sure to spit out the seeds. I was never poisoned that I know of, so I think you might be overcautious. (I tended to listen to my mother.)

@anongoodnurse its not over caution, Taxine alkaloids is very lethal, and rapid acting if you failed to spit out the seeds you would have died. https://en.wikipedia.org/wiki/Taxine_alkaloids

@John - But I'm not dead, am I? My siblings also ate the fruit of the yew shrubs we passed. Surely if it were as toxic as you imply, one of us must have become sick, yet we never did, and we're all alive save one who died of war-related injuries. I'm not advocating eating the seeds or chewing on any other part of the plant. Not advocating anything at all. Just relaying my experience with yews.

From what I've seen here, in Europa, this definitely looks like some kind of Taxus_baccata (Taxaceae family).
It most probably is a Taxus canadensis in Ontario. Also know as (local names): Canada yew, American yew, ground-hemlock, if du Canada, sapin trainard.
As it's always hard to tell based on photo that we didn't take ourselves, the best you can do is to compare its features with an identification key (either numerical/book).
The best online definition that I found for this species is:

Shrubs to 2 m, usually monoecious, low, diffusely branched, straggling, spreading to prostrate. Bark reddish, very thin. Branches spreading and ascending. Leaves 1--2.5 cm ´ 1--2.4 mm, pale green abaxially, mostly without cuticular papillae along stomatal bands, dark green to yellow-green adaxially, epidermal cells as viewed in cross section of leaf wider than tall or ± isodiametric. Seed somewhat flattened, 4--5 mm. 2 n = 24.
Provided by: [A].Flora of North America @ efloras.org
Straggling shrub with ascending or rarely erect stems to 2 m; lvs 1–2 cm × 1–2 mm, abruptly narrowed to a sharp point, attached by the shortly petiolar base to a decurrent sterigma on the twig; scales of winter-buds keeled, ± acute; fleshy seed ca 5 mm; 2n=24. Coniferous woods and bogs; Nf. and Lab. to Minn. and se. Man., s. to Va., Ky., and Io.
Provided by: [B].Manual of Vascular Plants of Northeastern US and Canada

Source: http://www.worldfloraonline.org/taxon/wfo-0000459412
See also:

http://www.efloras.org/florataxon.aspx?flora_id=1&taxon_id=233501254
http://sweetgum.nybg.org/science/vh/specimen-list/?SummaryData=taxus+canadensis
http://www.theplantlist.org/tpl1.1/record/kew-2521219

Source: Arbustrum Americanum : The American grove, or, An alphabetical catalogue of forest trees and shrubs, natives of the American United States, arranged according to the Linnaean system : containing, the particular distinguishing characters of each genus, with plain, simple and familiar descriptions of the manner of growth, appearance, &c. of their several species and varieties. : Also, some hints of their uses in medicine, dyes, and domestic oeconomy (Marshall, Humphry, 1722-1801) DOI: https://doi.org/10.5962/bhl.title.68506
Available at: https://www.biodiversitylibrary.org/bibliography/68506 or: https://collections.nlm.nih.gov/catalog/nlm:nlmuid-2562033R-bk

What is the principle difference to Taxus baccata? And I find the statement confusing. First saying that it is a kind of T. baccata and then that it is T. canadensis. Perhaps you meant Taxus baccata s.l. or agg.?

"Taxus baccata L., known as European or English yew, is a conifer native to Europe." > https://forest.jrc.ec.europa.eu/media/atlas/Taxus_baccata.pdf
I don't know enough its spread outside Europe to make an assertion about its presence in Ontario actually.

I do not think the natural spread is too relevant. The shrub is likely to be cultivated.  I only know the European one. But I was mainly pointing to the confusing statement in the first sentence.

authors: Vladimir F Героям слава


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Ontario plant with 3-5 leaflets per compound leaf
This plant has 3-5 leaflets per compound leaf. It caught my eye because, at first, I thought it resembled poison ivy. But I don't think it's poison ivy.
What species is it?

Date: May 11, 2024
Location: Norwood, Ontario, Canada; full shade along forest trail edge
Height: 1 foot
Description: New leaves looked somewhat greasy, dark green/dark red, compound, serrated, opposite

Unfortunately, I can't go back to get clearer pictures.

This appears to be Aralia nudicaulus, wild sarsaparilla. It has a main stem that branches in three, with compound leaves with 3-5 (7) serrate leaflets. It occurs in your area.

From Wildflowers of Ontario

Thanks! "Because it sometimes grows with groups of 3 leaflets, it can be mistaken for poison ivy; the way to tell the difference is that Wild Sarsaparilla lacks a woody base and has fine teeth along the edges of the leaves." https://en.wikipedia.org/wiki/Aralia_nudicaulis

This is almost certainly poison ivy. When you said the leaves had a greasy feel, alarm bells started ringing and I hit up Google, and the images I got for poison ivy bore a very close resemblance to what you have here. Quite frankly, I'm surprised you didn't get a rash from a an exposure 12 days ago...

The Wikipedia page for Toxicodendron radicans (eastern poison ivy) says, "Leaflet clusters are alternate on the vine." Whereas the leaflet clusters in the photos above are opposite. So I don't think it's poison ivy.

Please do not use this site for simple guessing. If you are unsure of something, it is good to make that explicitly clear. Though, whether you know the answer confidently or not, adequate cited support needs to be provided. Your answer is incorrect -- see here for a previous SE post about poison ivy.


text:
Cedar-like conifer near Kaladar, Ontario
What species of conifer is this?

Cedar-like leaves
Rocky terrain near Kaladar, Ontario
Sept 29, 2022
Approx 15 feet tall; approx 6 inches DBH

Certainly looks like the Eastern Red Cedar, Juniperus virginiana.  They are very fond of disturbed areas and can be any where from a scrubby bush to a decent tree.  Wikipedia has more info.  Your location is a little north of the distribution maps, but not much, and it is warmer these days...


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What causes plants in the prunus genus to reach anthesis?
In a related question, I ask how to trick fruit trees into flowering later in the spring by prolonging frozen ground conditions.
However, I'm starting to realize that I don't actually understand what triggers plants to flower in the spring in the first place. Possibilities include:

Photoperiodism
Air temperature
Soil/root temperature

It seems to me that this is a simple enough question. I'm guessing that plants in a certain genus would have a fairly specific genetic program that would stipulate when they should flower.
For example:
If root temperature is greater than X (for greater than Y duration), and daylength is greater than Z, then initiate flowering.
I'm not looking for the specific values (example x = 10 degrees C); the values would likely vary by species or even by plant. I'm just wondering what the primary variables are.

An answer provided by the University of Guelph Plant Sciences Department (they specialize in Malus):

Flowering of Malus and Prunus is driven primarily by air temperature. Provided sufficient winter chilling has accumulated for a given cultivar, tree growth and bud development will advance when air temps are above approx. 5 degrees Celsius. This process is irreversible. Once enough heat units (degree days) are accumulated, the flowers will open.
Flowering is a complex physiological process within the plant, driven by temperature. Photo-period likely does not play a large role in Malus.

Here’s how it works. Every morning when the sun breaks over the horizon — no matter what time of year it is — a clock starts ticking inside the trees. After a specific number of hours, the plants’ cells start producing high levels of a molecule known as the FT protein. This protein is responsible for initiating processes that help the plant grow.
But the FT protein has a curious property: In the absence of sunlight, it curls up and dies. So when the sun sets, it degrades rather quickly and becomes useless to the plant.
Nilsson thinks this peculiarity is the key to the seasonality of certain flowering plants, including most trees that blossom in the spring.
If a plant is genetically programmed to produce lots of FT protein starting, say, 13 hours after dawn, the molecule will be abundant during the last few hours of daylight in the longer days of summer. And those few hours are enough to kick-start crucial growth processes. So the cherry trees do most of the heavy lifting for the spring festival — bud and flower formation — way back in the summer and early fall.
As autumn progresses and the days shorten, that same 13-hour clock — the number of hours will vary by species and even by individual plant — means that the FT protein will be produced in darkness, and it will degrade before it can work its magic. The trees take this as a signal to drop their leaves and stop generating new buds.
When winter arrives, day length and temperatures both reach their annual nadir. At this point, the plant goes through vernalization, a dormancy period that has enormous importance in protecting the trees, for reasons explained below.
In springtime, one might imagine that the FT protein process would reverse: The days get longer, the FT protein is produced during daylight hours, and the plant kicks off its growth process. Surprisingly, that’s not what happens.
While the cherry trees recognize the arrival of winter by sensing a decline in daylight, they detect the arrival of spring based on temperature. They wait for what’s called a “temperature sum”— basically a bunch of warm days in a row. (The precise temperatures and durations required vary by plant.) When the temperature sum is reached, the blossoms open. Of course, since the National Park Service can’t control the weather, peak blossoming doesn’t always coincide with the Cherry Blossom Festival’s lighting of the stone lantern and the Japanese taiko drummers.
The cherry trees’ habit of marking the start of winter by daylight and the end of winter by temperature is reversed in some other plants. Plant biologists, for example, base much of their genetic research on Arabidopsis thaliana, or mouse-ear cress, a small plant that belongs to the same family as cabbage. (“It’s the laboratory rat of the plant world,” says Nilsson, because its small genome enables researchers to closely observe its genetically based behaviors. ) The plant measures the arrival of winter by a drop in temperatures and decides when to flower in spring by day length.
Click here for the source of this information, hope this helps :)
-Sartoaster

In continental countries winters can be very bright with latent fosts that kill flowers. FT is probably accelerated with high temps.

The University of Saskatchewan Plant Sciences Department builds on Guelph's answer:

In this context, my answer would be that photo-period definitely does
  not play a large role in Malus and Prunus.
Plants in these genera need
  their chilling requirement satisfied followed by temperatures high
  enough to allow growth to occur. Within reasonable limits, the higher
  the temperature, the sooner to bloom.
I have seen apple and plum trees
  that were neglected in a cooler room at 5 degrees Celsius form October
  to April reach anthesis with only enough intermittent/inconsistent
  light to produce barely a trace of anthocyanin and chlorophyll
  pigments.

From The Principles of Fruit-Growing By L. H. Bailey (The Rural Science Series):


text:
Was life less colorful before color vision evolved?
According to Wikipedia, we know that color-vision photopigments appeared in the common ancestors of tetrapods and fish at least 360 MY ago.  Would life have been less colorful before the evolution of color vision?

It's hard to know for certain, but probably. Color is used to signaling to mates, predators, hiding from prey and predators, etcetera. Life would not have been grey or brown, a lot of antioxidant pigments have color to them, but ladybugs/flowers/etc couldn't be as bright as they are now.

It is likely that the world have been less colourful before colour vision evolved, though that is my opinion, I will now back it up a little.
Certainly some of the colour we see in nature serves a function outside of the use of visual stimuli. For example plants have green leaves because of the way that functions with photosynthesis - it absorbs enough energy whilst not so much that the leaves burn. For more on the green leaves in plants see this classic Biology SE question with it's very good answers. Other examples could include functions such as thermal regulation or light contrast for camouflage (if anyone has other valid examples then please comment and I'll add them in).
However, there is likely to have been an increase in the prevalence of colour in nature since the evolution of colour vision. Colour is used as a visual stimulus in numerous ways. My first example is flower colouration. Flowers use coloured petals as a stimulant to attract pollinators. Another example is the use of colour in mate attraction. Peacocks tails, the orange bills of blackbirds, and the brightly coloured cichlid fish. All of these examples take advantage of colour vision, without it they simply wouldn't be as discernible from less colourful variants and given the cost of producing them it is unlikely they would evolve as often as they do. A third example is camouflage, the most striking example I can think of is cuttlefish which match themselves very well to their background.
Although I haven't provided direct evidence that the world was less colourful I have provided a potential theory. Hopefully the examples I've presented have convinced you that my theory of the world being less colourful, even possibly only marginally less so, is not developed without thought.
I will point out it is entirely possible the world was equally or even more colourful before - no colour vision would allow colours to drift around more, selection on colour in the context of camouflage would reduce the variety of colour we see as selection would favour colours matching the surroundings (if camouflage was necessary to survival in a grass environment we would expect most things to look quite green). To this end, I don't think we can currently answer your question firmly but we can put out theories as to how it would have been.


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Why does an electrical shock freeze up muscles?
Why is it when someone comes into contact with an electrical supply that their body freezes up and is unable to move away from the electrical source?
Can someone explain this through a physiological perspective?

Your question is bit incorrect. Person undergoing electrical shock does not get frozen in place. He/she actively grips the wire and holds it with great force. Of course, this only happens if contact occurs with inside of the palm, so the closing fist can actually grab the wire.

Interesting question!
An important factor here is the let-go phenomenon, which is defined as the current level in the arm that will cause the hand to involuntarily grip the current source. When the fingers are wrapped around a large cable, most adults will be able to let go with a current of less than 6 mA. At 22 mA, however, more than 99% of adults will not be able to let go.
Nearly all cases of inability to let go involve alternating current. Alternating current repetitively stimulates nerves and muscles, resulting in a tetanic (sustained) contraction that lasts as long as the contact is continued. If this leads to the subject tightening his or her grip on a conductor, the result is continued electric current flow through the person and lowered contact resistance.
Given that the current flow in the forearm stimulates both the muscles of flexion and extension, it seems surprising that one cannot let go. However, the muscles of flexion are stronger, making the person unable to voluntarily let go (similar to the fact that a crocodile's jaws can be kept shut with your bare hands, but one should better not attempt to keep them open like that...).
Direct currents below 300 mA have no let-go phenomenon, because the hand is not involuntarily clamped.
Several different outcomes may occur when a person grasps a conductor giving 10 kV AC hand-to-hand voltage. Within 10 to 100 milliseconds, muscles in the current path will strongly contract. The person may grasp the conductor more tightly. However, mostly subjects are propelled away from the contact, likely due to generalized muscle contractions.
Reference
- Fish & Geddes, J Plastic Surg (2009); 9: 407-21

When the body comes in contact with an electrical power supply, two things can happen. If the current flow is high enough, the body heats up just like a heating resistor, and opposed to the resistor, the body can't handle the heat, thus severe burns occur after electric shock.
But if the current is low enough not to burn "the conductor" other effects are visible. The nervous system tissue has the best conductor properties from the body. More than that, it works with action potentials, which are small chemical generated currents. When an external current gets to a nervous fiber, the fiber will conduct electricity further to the efector tissue (muscle in this case).

If electric current of sufficient magnitude is conducted through a living creature (human or otherwise), its effect will be to override the tiny electrical impulses normally generated by the neurons, overloading the nervous system and preventing both reflex and volitional signals from being able to actuate muscles. Muscles triggered by an external (shock) current will involuntarily contract, and there's nothing the victim can do about it.

The result is a powerful contraction of the muscle. But the question is what muscular groups contract? Well, all that are under the influence of a nerve under electric shock. And from here comes the freeze effect, because antagonist muscular groups contract simultaneously (for example flexor and extensor, adductor and abductor muscles in the same time). The result of this forced contraction tends to move parts of the body as dictated by the muscles that are more powerful.

The forearm muscles responsible for bending fingers tend to be better developed than those muscles responsible for extending fingers, and so if both sets of muscles try to contract because of an electric current conducted through the person's arm, the "bending" muscles will win, clenching the fingers into a fist.

You can read more on All About Circuits.


text:
Why don't we develop immunity against common cold?
We all suffer from common cold, and that, frequently. Why have we not developed immunity against it till now? By immunity I mean immunity as a species.

The short answer is we do, it's just that there are so many different causes to common cold.  A slightly longer and more complete answer will note that while we know immunodominate epitopes for the 100s of rhinovirus serotypes, we are still researching why viruses like RSV are not immunogenic (my bet is on NS1, possibly NS2 proteins).  If no one has put up a good answer by 2100ish EST, I should be back on then to post one.

What kind of immunity are you talking about? Immunity as a species? Immunizations? Can you clarify?

First, I want to note that ddiez has a good answer, but I thought this was good question to have a more expanded answer on immunology and pathogenesis.
The First thing we need to establish what is a "cold".
The most common cold is rhinovirus (HRV), but the second place holder is a little harder to define.  For example, respiratory syncytial virus (RSV) has been shown to be nearly ubiquitous by age two.  I actually disagree with the Wiki article on the common cold which puts coronaviruses (plural, which is not clear in the article) in second place.  For example, if you take look at sessional reports from hospitals, you can find that RSV and influenza are the more common.  Now this does select for those who were sick enough to seek hospital treatment, but if you look at a recent more in-depth study conducted through health clinics, you will again find coronavirus in much lower showing:

[Editorial note, if someone wants to take the time to MathJax that table in, please go ahead.  It seemed too large to insert the table as text. Here’s the original.]
Thus, a cold is an infection from any of the above viruses, with a common cold likely being HRV or RSV.  But how the body reacts to each of those is different.
Secondly, how do we mount an immune response to a cold?
There are two different kinds of immune responses in humans: innate or adaptive (to not get to technical, you can come up with responses outside of these).  Both responses are excitingly complex, and needed to fight a cold.  The innate immune system is designed to handle the initial reactions to the pathogens, but often the adaptive immune system is what "clears" (viral clearance being the removal of the infection) the infection totally.  In a novel infection, the adaptive immune system takes a few days to ramp up, which is why a cold can last for a few days to two weeks. This is when you get B-cells producing enough antibody to clear the infection.  Then the next time you are infected by something of the same serotype you will have a reservoir of cells already primed to make an immune response, and it will happen quicker.  At least that is what the human body is trying to do.  Viruses are trying to "evade" the immune system and proliferate (acknowledging of course that is a personification of viruses, and that they are not "trying" to do anything).
The key word in the adaptive response is "novel."  If the pathogen is different enough, that is the epitopes are different enough, then the immune system won't recognize it.  This is the principal strategy used by HRV.  Depending on who you ask there are between 96-120 serotypes of HRV, so using a number of about 100 seems reasonable (120 is a much more recent number and the increase has largely correlated with better diagnostic tools).  There don't seem to be additional stereotypes developing/mutating quickly (though conceivably they could), so as opposed to being infected by a mutated version of the cold you had last year, you're getting a different strain/serotype that was already in circulation.  Thus if you got a different HRV infection once a year, you have about 100 years of rihno viruses colds (when you actually get that old you have senescence problems in the immune system).
RSV is a different story.  You don't mount a lasting immune response to the virus in the first place:
 (Table 10.6.  Fields Virology; 6th Edition.  LWW 2013)
In fact, I know a researcher who would infect his lab members with the exact same strain of RSV every 6 months for years (before people would stop such a thing...).  Why RSV doesn't elicit lasting immunity--and in fact notably shorter immunity--is the subject of current research.
As you can see in Table 10.6, mucsal responses are generally not as long lasting as systemic infections.  This can make sense from a macro view—the mucus successfully prevented the pathogen from spreading to the rest of the tissues in the body, so it's not as critical to respond to.  On a more specific level we know that more IgA is produced and the cytokines can be different.  But RSV seems specifically reduced. One leading idea is that two of the proteins produced by the virus, NS1 and NS2, cause an immune response to not be properly mounted.  In other words, the virus is making materials that deliberately interfere with adaptive immune response.  An interesting paper that just came out addresses this idea for a possible vaccine candidate.

This should be the accepted answer.

Long lasting immunity is obtained by means of the adaptive immune system, and mainly involves the development of antibodies that identify specific parts (epitopes) of the pathogen's proteins. Common cold is typically caused by a type of virus called rhinovirus. Viruses have very high mutation rates, which alter the sequence of the virus proteins, modifying their antigenic properties. This consequently alters the ability of antibodies to recognize a particular antigen.
In other words, we do develop long lasting immunity against the virus that causes us a cold today, but the virus that causes us a cold a few months later is somewhat different, and the adaptive immune system has to start from scratch.

Why do viruses have high mutation rates? Because thay divide so fast?

@kinshukkashyap it is because the higher error rate in the genome replicating enzymes. For example, retroviruses use reverse transcriptase that has high error rates (due to lack of proofreading).

@kinshukkashyap, but, it is also connected to faster replication times. If you divide very fast and can produce a large amounts of copies (offspring) then you can accept higher replication errors that may render some of the copies useless, but may lead to some advantage to some other copies (e.g. drug resistance).

@ddiez I'm not sure if mutation rates are the most important factor here, as forward genetic experiments with HRV don't show the virus changing serotypes often.

@AtlLED, could you provide reference for that experiment? Indeed, there are several mechanisms for immune evasion. Serotype changing is one of them. In viruses there is also antigenic drift (caused by mutations) and shift (caused by exchange of sequences between viral strains), Ref Janeway's Immunobiology 5th edition. It has been postulated that HRV uses antigenic drif/shift but cannot find references demonstrating that!

@ddiez sure I'll take a look.  I know from personal experience, but I see what I can find in a lit review.  You certainly can get monoclonal antibody escape variants, but we saw more genetic stability than expected with HRV16 and HRV44 so we never pursued it for a paper.  I know off the top of my head of examples that indicate reinfection is of separate serotypes. I'm not postulating that there isn't genetic drift in HRV.

@AtlLED At any rate, my response to the original question is obviously a very simplified one! I appreciate your comments and insight into this interesting topic. Thank you for the example. I am interested in asthma and other complex respiratory diseases so I will read it with interest.


text:
Can the colour of skin change with age
Can the colour of skin change with age? Can a dark skinned person become fair or vice versa?  Can Melanocyte production vary?

There are all sorts of things that can stimulate melanocytes, most notably UV rays (ie from the Sun).  So yes, melanogenesis can very over age and exposure to the Sun.  Young infants often are lacking build ups of melanin in their skin, eyes, and hair, which is why these things darken with age.
There are other more pathogenic ways to change melanogenesis, including malnutrition, but UV exposure this health common way.

Could you dial back your pigmentation campaign a little? What you are doing is fine but it is generating a hell of a lot of review jobs, and bringing all these old questions to the front page. Please try to only make a few such edits per day.

@terdon I'm done.  Sorry, I didn't think about resurrecting old questions to the front page.  I did find an unanswered one I want to go back and answer.  I won't go through them all at once again.

Hey, no worries, you are actively improving the site, just try and avoid too many consecutive edits like that :). Answering is fine mind you, newly answered questions should be on the front page.

Vitiligo is a loss of skin pigmentation that causes patches of lighter skin as the immune system attacks melanocytes. It can eventually progress to cover the entire body.
Edit:
Ongenae, K., Van Geel, N. and Naeyaert, J.-M. (2003), Evidence for an Autoimmune Pathogenesis of Vitiligo. Pigment Cell Research, 16: 90–100. doi: 10.1034/j.1600-0749.2003.00023.x


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What is the sedimentation coefficient of Mycoplasma?
I have attempted to find the sedimentation coefficient of a number of bacterial species, namely E. coli and a number of Mycoplasma species, but they seemed to be rather elusive in the literature.
If such values cannot be easily found, is there a reason sedimentation coefficients of whole cells are not widely reported, but sedimentation coefficients of proteins are? Mentions of "70S ribosome" and "26S proteasome" are common, but I have never seen any mention of "kilosvedberg" or "megasvedberg" appearing in the literature, and I presume the sedimentation rate of whole cells would fall somewhere in this region.

Alternatively, use regular centrifugation speed to pellete down bacteria for calculation of sedmentation coefficient. Generally its 5000 RPM for 6 min at 4 degree (convert this into terminal velocity). Just find out radius of rotor and angular velocity of your centrifuge then calculate $s = \frac{V}{r*w^2}$


text:
Missing cells from immunopanning
Why do I not have any cells left in my positive panning plate after transferring from the negative panning plate during immunopanning? I am trying to purify retinal ganglion cells from postnatal rats and use a Thy1.1 antibody harvested from a hybridoma cell line supernatant in the positive panning plate.
Following transfer of the cell suspension from the negative to the positive panning plate there are no cells in the pre-trypsinization supernatant, nothing stuck to the panning plate, and no cells in the post-trypsinization supernatant so I have no idea where they could have gone. Checking the negative panning plates however shows that there are many cells stuck to those plates, so could my RGCs have been lost at some point during the transfer and when?
Thanks v much in advance for your help.

Did you check the actual transfer material for cells before you added it to the positive plate? It may be they all stuck to the negative plate...

Or using MACS for sorting?

Immunopanning in my experience takes an awful lot of optimization, but is worth it when it works.  I would plan, if you have the resources, to sac rats just for assay optimization before you even begin to try to get real data out (assuming your planning for a steady stream of primary cells).
That said, there are some real easy checks you can try do first.  Try to get a rough cell count on what you put on your negative plate (depending on your prep steps, that can actually be a bit tricky), and then count the cells again as you transfer the cell suspension to the positive plates.  If you don’t have any cells left, or you have very little cells left, then you might be losing all your population on your negative plate.
If you do have cells in suspension, I would start to question your positive plate.  Are you making them yourself or are you buying them coated? Which rat strain are you using?  Perhaps you need to titer your antibody concentration on the plate.  There are really a whole lot of steps in immunopanning that can be optimized.


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How do animals perform detailed active camouflage?
We often see videos of octopuses and chameleons changing their color to suit their surroundings. If it was a simple color change from white to red, it'd be understandable, but some of these animals can change colors while incorporating a lot of detail.
How do they process so much information and mimic it. Is this a subconscious action, or do they actually draw a picture in their head and then 'print' it on their bodies? Does this ability come from birth or does it get better over time?

Some of it is voluntary and some involuntary and is detailed in this book. Chameleons have chromatophores (pigment containing light reflecting organelles in cells) which help in their colour change and many factors like age, health, etc does affect it. And no, they do not form a picture on their head and print it on their bodies.


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Mutation That Loses Stop Codon
Someone asked this in my class and my instructor wasn't sure in her answer, doesn't anyone know what happens in protein synthesis if a mutation causes mRNA to not possess a stop codon? Would the protein eventually stop? Would it keep coding into the poly-A chain and insert a bunch of phenylalanine?

No, this will not happen. mRNAs are inspected in the nucleus before they are exported into the cytoplasm (at least in eukaryotes), where transcription and translation don't happen at the same place. This ensures that no mRNAs without stop codons or premature stop codons are exported. This phenomenon is called
"mRNA surveillance". mRNAs that do not pass this quality check, are degraded. See the Wiki reference for some basic information and the references below for more.
References:

Process or perish: quality control in mRNA biogenesis.
The exosome and RNA quality control in the nucleus
A faux 3′-UTR promotes aberrant termination and triggers
nonsense-mediated mRNA decay

you can add a note on non-stop mediated decay mechanism

@WYSIWYG You mean how the RNA is removed? I can do that later.

Technically, NMD takes place in the eukaryotic cytoplasm, because that is where the ribosomes are translating mRNAs containing "early" termination codons.  The situation the OP describes, where the wild-type stop codon is mutated to a codon recognized by a charged tRNA will just result in a slightly longer protein with an extra tag on the C-terminus.  A normal 3'-UTR will contain additional stop codons in all frames--on a random basis. This (the extra a.a., residues) also occurs in cells expressing a suppressor tRNA, the activated a.a. will get inserted instead, and the protein will be longer.

@mdperry I am not talking about NMD (nonsense mediated decay). There is another mechanism called nonstop decay. Yes I agree that the protein will be longer in that case. This is detected and the faulty products are cleared off.

Downvote. It obviously does happen, see the answer below.

Yes you are correct. These mRNAs, that lack stop codon will cause translation to continue into the poly-A tail (it will result in addition of lysines not phenylalanine). Since no stop codon is present, the ribosome remains attached to the mRNA. Under these circumstances, a pathway known as non-stop decay is activated.
An important protein in this pathway — Ski7 detects a stalled ribosome and initiates the decay process for both the peptide and the mRNA. The poly-lysine tail of the peptide has been shown to fasten the peptide decay process.

In prokaryotes too, the non-stop mutations cause the ribosome to run through the stop codon and to eventually stall. However, there are no poly-A tails and ribsosome recovery pathway is different from that of eukaryotes. An RNA called tmRNA (a hybrid of tRNA and mRNA) binds to the the A-site using its tRNA-like domain. Then the translation proceeds through the mRNA domain of tmRNA (this is called trans-translation) which causes an addition of a peptide tag (that acts like a degradation signal) to the stalled polypeptide and finally leads to ribosome release when the stop codon is reached.

References:
Non-stop decay:
            Klauer and van Hoof. Degradation of mRNAs that lack a stop codon: A decade of nonstop progress. Wiley Interdiscip Rev RNA. 2012 Sep-Oct; 3(5): 649–660.
tmRNA:              Jannsen and Hayes. The tmRNA ribosome rescue system. Adv Protein Chem Struct Biol. 2012; 86: 151–191.

This is the best answer I think since some mRNA obviously escapes nuclear surveillance (or these pathways wouldn't exist) and the question specifically asks what happens during protein synthesis. Perhaps it's also worth mentioning tmRNA, since we eukaryotes aren't the only organisms out there (it's also an ingenious mechanism of simultaneously targeting the aberrant protein for degradation whilst rescuing the stalled ribosome).

@canadianer thanks for pointing that out. Added :)

In fact, it is rare that stop codon mutation causes translation of polyA sequence in mammalian cells because you will find another in-frame stop codon downstream. And some stop codon mutations still producing the protein stably(1).
However, as WYSIWYG mentions, in the absence of alternative in-frame stop codon, mRNAs would be degraded. It is also called none-stop decay(2). I am not sure that this phrase gets popularity though.


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On which DNA strand is TATA box present?
My book (Snustard and Simmons) mentions that TATA box is present on the non-coding DNA strand but that was for the promoter of mouse thymidine kinase gene.
I have tried to find out more information and stumbled upon these in wikipedia articles which actually said something else:

The TATA box can be an AT-rich sequence "located at a fixed distance upstream of the transcription start site. (from a paper "The RNA Polymerase II Core Promoter'')

Then (from a book: Understanding bioinformatics),

The Transcription start site is the location where transcription starts at the 5'-end of a gene sequence.

So my question is, on which strand is TATA box actually (or generally) present?

TATA box is a feature of organisms that have dsDNA as a genetic material. Like most dsDNA promoter elements, TATA box is basically a section of dsDNA.
However a question like "On which DNA strand is TATA box present?" depends on what you define TATA-box as.
If you go by this definition:

In molecular biology, the TATA box (also called the Goldberg-Hogness
  box)[2] is a DNA sequence (cis-regulatory element) found in the
  promoter region of genes in archaea and eukaryotes

then TATA-box is merely a DNA sequence and is just a representation of a ssDNA region. However, TATA-box is also the binding site for TBP (TATA-binding protein; part of the TFIID complex). While the recognition of DNA elements by the TFs is effectuated by the interaction of amino acid residues with DNA bases and backbone on  one or both the strands, the TF binding and its activity has a stereochemistry.
Likewise, TBP also interacts with bases as well as the sugar-phosphate backbone on both the strands (Juo et al., 1996; PDB:1TGH).

Figure 2. Stereo pair drawings of the human TBP/DNA complex, with TBP at right and the sharply bent C-G-T-A-T-A-T-A-T-A-C-G duplex at left. (a) Molscript skeletal drawing (Kraulis, 1991). TBP residues that interact with the floor of the minor groove are shown in red with one-letter amino acid codes, and residues that interact with the sugar/phosphate backbone are shown in green. The coding strand of DNA is dark blue, and the non-coding strand is light blue. The two yellow-green base-pairs at bottom are the T1-A2 step that is kinked by interstitial phenylalanine residues, while the equivalent kinked step at T7-A8 is marked in orange. (b) Secondary structure diagram, with a-helices as coils and b-sheet strands as flat ribbon arrows pointing along N-to-C chain direction. Color coding as in (a).

Considering this, you can say that TATA-box is essentially a dsDNA region.
However, another twist in the story is that TBP can also activate genes with TATA-less promoters (Kamenova et al., 2014) and this is possibly facilitated by other protein partners of TBP in TFIID complex.

Our results are consistent with the model that sequence-specific
  TBP-DNA contacts are not important at yeast TATA-less genes and
  suggest that other general transcription factors or coactivator
  subunits are responsible for recognition of TATA-less promoters. Our
  results also explain why yeast TBP derivatives defective for TATA
  binding appear defective in activated transcription.

This, still does not contradict with the fact that TATA-promoters need TBP and the binding is on both the strands.
So, my conclusion is that TATA-box is a dsDNA element but has a polarity in its mode of action.

It's probably too late, but that's what I found in a book:
''Also, by convention, the DNA regulatory sequence elements (TATA box, etc) are described in the 5′ to 3′ direction and as being on the coding strand.''
Reference: Harper’s Illustrated Biochemistry, twenty-sixth edition,  Chapter 37 RNA SYNTHESIS, PROCESSING, & MODIFICATION, page 345, Figure 37–5.

Its never too late to answer a question ;)


text:
What do the negative and positive signs mean in the rotation angles of DNA helices?

Does it mean clockwise and anticlockwise?

The signs refer to the direction of rotation. Anticlockwise (right handed helix) is positive whereas clockwise (left handed helix) is negative. The direction of rotation is observed from the side where the helix is ascending towards you (perpendicular to the ascent of helix).
In other words, curl your right hand and extend the thumb out. When viewed from above (thumb points towards you), the fingers curl anticlockwise. This is a right handed (RH) helix. Conversely, you can use your left hand to understand left handed (LH) helices such as that of Z-DNA.

Obtained from http://biomedapps.curtin.edu.au/biochem/tutorials/prottute/helixfigures.htm. Which, in-turn is modified from Lehninger et al (1993) Principles of Biochemistry 2nd Edition Worth Publishers

 This figure depicts a RH helix. Taken from Wikipedia.

These definitions can be defined in a converse sense too and you would find many web sources that do like that. For example, if you look from below your hand such that the thumb points away from you, then the fingers curl clockwise. However, in physics and mathematics, positive angles are conventionally measured anti-clockwise. So my definition here would be suitable with respect to your question.


text:
What is the meaning of -//- sign?

Does $-//-$ sign between trpR and P indicate separation of the trpR gene from the operon? Or could the sign mean that the trpR gene may be present adjacent or far away from the operon, both the possibilities?

I think that means they are omitting a large section of DNA in between the trpR and P sections. You see a similar symbol on plot axes when they skip numbers.

Unlike P and O sequences which are literally joined at their ends, the sequences trpR and P are rather distant. The DNA between them is so long, that the limited space of the page prevents a decent proportional representation. So instead of painting a long line of limited-importance strands, the graphic designer choose to omit the part between slashes.
Note that despite the apparent disconnect possibly suggested by the sign -//-, the intervening DNA is continuous. The sequences trpR and P are still on the same chromosome.


text:
What is heteroduplex?
I fail to understand the what exactly is heteroduplex due to unavailability of a suitable diagram. According to wikipidea:

A heteroduplex is a double-stranded (duplex) molecule of nucleic acid originated through the genetic recombination of single complementary strands derived from different sources, such as from different homologous chromosomes or even from different organisms.

Should the following highlighted structure be called heteroduplex?

Heteroduplex is also frequently used for duplex formed of strands of different kinds of nucleic acid. For example RNA-DNA heteroduplex. As a matter of fact, that's the only reference of heteroduplex that I am aware of.

In 'An Introduction to Genetic Analysis. 7th edition' the DNA structures formed from crossing over between homologous chromosomes have been called heteroduplex through out the text.

Perhaps, but as I said, I was not aware of this usage.

What you've circled is not a heteroduplex. A better name for it would be "crossover" or "junction". Instead, the two duplexes at the bottom of your diagram are what should be labeled heteroduplexes. Your diagram shows one process by which you could generate heteroduplexes starting from homoduplexes.
Here's a better picture from the NCI Dictionary of Genetics Terms that more clearly shows the difference between homo- and heteroduplexes:

The two strands in a heteroduplex still have to have a high degree of sequence identity or they won't be able to form into a duplex in the first place. However, because they come from different sources there's likely to be many short subsequences in which one or more base pair is mismatched, causing a deformation as shown.

So it is a ds DNA molecule in which the two strands are not fully complementary and derived from two different sources?

Yes, with one edit: it is possible for two strands from different sources to be fully complementary. In general it's just extremely unlikely, although exactly how unlikely depends on your sources and your strand length.

What you have shown above should be (and often) called a mismatch instead of a heteroduplex. I have never come across any recent literature that refers to the above kind of arrangement as a heteroduplex. Most modern studies use heteroduplex to mean a duplex formed of different kind of nucleic acids (RNA-DNA, DNA-PNA etc)

@WYSIWYG It's both! (a mismatch and a heteroduplex, I mean) The fact that there's a mismatch is less important than the fact that the two strands come from different sources (which is something we're assuming for the sake of the diagram). Though I too was unaware of the more expansive definition before I started writing this answer, NCI seems to back Wikipedia up on this.

I also was not aware of the definition given in this answer but for the sake of congruence it absolutely makes sense or even has to be that way as two strands of different origin are pairing.

Okay. However, heteroduplex is a term that is technically applicable to a molecule (as it is a molecular property) and not really the genetics behind it. How would the DNA, "know" what is its source? For example, a newly replicated DNA has one of the strands that is brand new while the other is old. Would you call that a heteroduplex too? There is a flaw in this definition.

The Wikipedia entry is (as often) clearly nonsense. Howevear there is no reason why the two strands of a hetero-duplex should not be identical. It may occur in practice, it may be useful for drawing a diagram, but I maintain it is definitely not part of the definition of the word. As it stands, therefore, I suggest your accepted answer is incorrect. You might consider whether you should modify it to make it clear that it is the origin of the strands that makes them hetero, not a lack of perfect complementarity.


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Is induction and derepression the same thing?
Induction
This is a definition that our professor mentioned in class $-$the process of turning on the expression of gene in the response to a substance in the enviornment is called induction.
Derepression
From wikipedia $-$ in genetics and biochemistry the removal of repression, such as of an operon so that gene transcription occurs or is enhanced, with the net result frequently being elevation of the level of a specific enzyme. This effect is called derepression.
In lac operon when Allolactose molecule is present in the medium (in the bacterial cell) it binds to the monomer of repressor and reduces the binding affinity of repressor to the operator site and the RNA polymerase is free to synthesis a polycistronic mRNA. Thus the allolactose molecule turns on the expression of lac operon by removing repression.
So I conclude that in lac operon induction is same as derepression. But does it hold true for all operons or there are operons in which induction is achieved without repressing the repressor?

what is the purpose of the question? Is there a case when you want to use one of the words or it is just curiosity? This will help with answering

@aaaaaa I am both curious and wish to apply the words to my answers during exam.

@SanjuktaGhosh Don't play with words in your exams. Always use the words that the examiner would understand :P

@WYSIWYG :) I usually write which is most appropriate without bothering about the examiner.

I’d prepared this before I saw that @WYSIWYG had answered in the same vein. So the credit to him. But just to clarify:
Technically you are correct. Although having the same end-result, induction can occur by a direct mechanism, not involving de-repression, the example in the lac operon being the catabolite activator protein (CAP). However, it is quite normal to refer to a de-repressor as an inducer.
If we take a simplistic view and regard the key step in bacterial transcription as the binding of RNA polymerase to the promotor then the situations for de-repression and positive induction are:
De-repression
The binding of RNA polymerase to the promotor is prevented by the repressor (e.g. the lac repressor) binding to the DNA (at the operator). The de-repression occurs when the so-called inducer (allolactose here) binds to the repressor, reducing its binding affinity for the operator and hence allowing RNA polymerase access to the promoter.
Positive induction
Here the affinity of the RNA polymerase for the promotor is sub-optimal and is enhanced by the inducer. In fact, this generally occurs by a protein–protein interaction — in the case of cAMP induction of transcription of the lac operon it is the binding of the cAMP to the CAP that causes it to interact with RNA polymerase and increase the binding affinity of the latter.
Another on-line resource on this topic is at LibreTexts, and this has diagrams I should perhaps have included here.
In eukaryotes  direct induction would seem to be more common than de-repression, with inducers such as steroid hormones binding to specific receptor proteins which then bind to the DNA. However the details of the DNA interactions are much more complex.

Induction is an effect of a stimulus on the cell. During an induction of gene expression a gene is expressed in response to a stimulus.
De-repression is a mechanism of gene regulation which may lead to expression of the corresponding gene. The gene can be expressed via direct activation as well. The action of CAP on lac operon would be an example of direct activation. There are several other examples too.


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Infer type of nucleic acid based on number of nucleosides
Let's say we analysed a nucleic acid and found out that it had 20% adenosine, 25% guanosine, 40% thymidine and 15% cytidine. We know that A always pairs with T and G with C.
So, based on these numbers, could we infer that the nucleic acid must've been single-stranded? Or could it be that it was a double-stranded DNA, but just not perfectly matched? Is it even possible for DNA to not perfectly match? Say like a zipper that is shifted?

There's 10% of your nucleic acid that's not A, T, G or C - you may have made a major discovery!

@HarryVervet Haha. Sorry, those were arbitrary numbers. Edited.

Though base pair mismatching is very common and is the basis of evolution, such a big violation of Charagaff's rule (in DNA where just 1% would mean thousands/millions of B.P.s) would only prove that it is ssDNA.

@aayushsrivastav Awesome! Haven't heard of Charagaff's rule before. That would explain the assumption then.

I'd say it depends on how you 'analyzed it'. You can also have a mixture dsDNA and ssDNA, for instance 20% polyT oligos and 10% polyG oligos.


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On what basis is each chromosome given a number?
On what basis is each chromosome given a number? There appears to me to be no visible ordering between each pair. Is there any reason other than differentiation?

Chromosomes are generally ordered by size in terms of number of nucleotides. The first chromosome is the biggest. Note that when there are sexual chromosomes (as it is the case in mammals or birds for example), the pair of sexual chromosomes are typically considered last irrespective of their sizes.
Note that in some species the ordering has been decided and further studies have shown that the actual size order does not perfectly match the ordering. This is for example the case in humans, where chromosome 11 is actually bigger than chromosome 10 (thanks @canadianer).
Numbering is mainly just a simple naming system. It is just handy to be able to refer to a chromosome as chromosome 3 rather than having to somehow describe this chromosome for other to understand what we are talking about.

I think they were ordered by size before the number of nucleotides in each was known. Chromosome 11 is actually bigger than chromosomes 10 and 12.

Well that depends upon the species and when we got interested in their genome. It is true that for humans the ordering does not perfectly match the size order.

Good point, I forgot there were other species out there besides us :)


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Does DNA polymerase always go the same direction?
I read that mutations are more likely to occur on "the strand that DNA polymerase replicates discontinuously". Does DNA polymerase always replicate the same strand discontinuously and, if so, how/why?

Polymerization always occurs 5'->3'. Which strand is replicated discontinuously depends on the location of replication origins, but it doesn't change between replication cycles.

Summary:
In bacteria or organisms with only one well defined replication origin and a circular chromosome, yes for a given DNA region the same strand is replicated discontinuously.
In high order animals, which replicate chromosomes using several origins of replication (ori), this is less clear as the way ori are recognized is still not fully understood but seems to involve DNA structure. Chromatin structure is dynamic which means ori are also likely dynamic which results in defined regions of the DNA not likely to always be replicated discontinuously from a well defined strand (i.e. DNA replication might not always start at the exact same sites).

First off, as you probably know, DNA is always transcribed in a 5' to 3' direction. The why is nicely answered in this post.
DNA replication forks start at replication origins. Replication origins are recognized by origin recognition complexes. The way DNA replication occurs is by having two DNA polymerase complexes traveling in opposite direction (i.e. two bidirectional replication forks) from the origin as shown in the following schema:

This means that given constant origins of replication in an organism (like bacteria which usually only have only a single origin of replication) and given the DNA is replicated in a 5'-3' direction, same strands will be replicated discontinuously from the origin (i.e. in the schema, the bottom one on the left and the top one on the right). A global view of the replication at the chromosome level in bacteria is shown here below:

Now for more complex organisms, the origin of replication is not a single site but rather multiple ones across chromosomes (30'000-50'000 ori in humans). Where does DNA replication starts exactly, this is still not fully understood. DNA sequence is likely to play a role but no highly conserved consensus sequences were found and it is believed that origins of replication are linked to the structure of the DNA instead. In essence the chromatin structure is what seems to dictate where DNA replication starts and as the chromatin structure is dynamic within a cell, it is likely that origins of replication are also dynamic therefore making the identification of the discontinuously replicated strands very difficult (Méchali M, 2010).
Finally if you wonder what happens when two replication forks collide, well the answer is simple, replication stops and the two DNA polymerase complexes leave the DNA.


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What is the scientific name of this plant?
I found this one on a hill here in Palestine. It's about 20 cm in height. Note that it does exist in this regions, but scantily.

The plant is of Lamiaceae family and its common name is Shell Flower or Bells of Ireland.
Its "scientific" aka latin name is Moluccella laevis.


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A state model of sodium channels
I am studying by myself Human Physiology.
I have encountered the following question:
In the following given model of sodium channel with 3 states open closed blocked (which I assume means inactivated), the rates of going from state to stated are given in the picture below.
a. Write matrix $Q$ for the system and find it's eigenvalues.
b. What does these values represent?
If anyone has an idea what is the required matrix I will be grateful.
Thanks!

Interesting question, looks like homework but i won't give you a minus. Can you describe full description, i mean, what  these numbers mean. Suppose it is charge need to be possessed to change the state, if so, i can do that, it looks like simple matrix model if we add some probabilities of generating charge. I also suppose that you need to get eigenvalues just to find stable system state and that's good.

I think Q is supposed to be an adjacency matrix that represents the graph in your diagram. Take a look here: https://en.wikipedia.org/wiki/Adjacency_matrix and here: http://www.cs.elte.hu/~lovasz/eigenvals-x.pdf

This is a homework question. You should at least make some attempt at the answer.

Thank you all. It is from HW I found in the net. So, no other information valid for me. I usually, of course, make a lot of self effort. But, sometimes, like in this case, even though you know you have the right tools, you just don't know where to start, especially, if not all the definitions are given... So, Thanks for your help and comments!

There is no standard notation called Q (matrix).
However in this case I think the matrix that they are referring to is the state transition matrix (similar to the adjacency matrix as mentioned by Justas in the comments, but with rates instead of just the connections). Basically you have three states (lets call them A, B and C) and there is a rate for transition from one state to the other. You can also represent these rates in the form of transition probabilities.
You just represent this as a 3×3 matrix. Put zero where there are no such transitions (for example there is no transition from A to A or A to C):
$$\begin{array}{|l|c|c|c|}
\hline
 & A & B & C \\\hline
A & 0 & 10 & 0 \\\hline
B & 100 & 0 & 50 \\\hline
C & 5 & 0 & 0 \\\hline
\end{array}
$$
You can then calculate the eigenvalue for this matrix. How to calculate eigenvalues and what is their significance is off-topic in this site. You can easily find out how to calculate eigenvalues. Their significance is something that is not that easy to understand but you can read more about that and can perhaps ask a precise question in Mathematics Stack Exchange. Basically, they tell you how the system proceeds in different directions (denoted by eigenvectors).

About the eigen-values, I know that if I view this matrix as a correlation matrix, then the eigenvalues are the variance values in the 3 element basis of eigen-vectors. Can I apply this character here? Anyway, Thank you!!

@user135172 just that this is not the correlation matrix. However, the concept of eigenvalues and eigenvectors is similar. Just like any linear algebra problem. If a matrix is a function applied to a vector (which may denote state of the system), then the eigenvalues somewhat denote the amplification factor of the matrix (along different directions).