Why does hexokinase bond phosphate to the hydroxyl group on carbon-6 of glucose in glycolysis?

First of all some nitpicking, but the actual phosphorylation happens not to the Carbon-6 but to the hydroxyl group bound to this carbon atom. The mechanism is a nucleophilic attack of the hydroxyl group on the terminal phosphoryl group of ATP. Schematically, this looks like this (image from here):

The main question, why the reaction happens on this carbon atom can be answered rather simple (although the explanation is a bit longer): Because only this is openly available for a chemical reaction and the others are inside the hexokinase and thus shielded.

Hexokinase exists in two forms: One relaxed, open when no substrate is bound and one closed with a changed morphology when the enzyme has bound its substrate. This mechanism is called "induced fit" and a quite common motif in enzyme catalyzed reactions and brings together the active center of the enzyme, possible co-factors and the substrate and excludes interfering other actions.

In the example of the hexokinase, glucose is brought into close proximity to the terminal phosphoryl group of enzyme-bound ATP to enable the chemical reaction. Because all other potential hydroxy groups are shielded by the enzyme, only the group at the carbon-6 can be chemically active. For more details, see the references.

Schematically, this looks like this, with the open form to the left (the arrow indicates the binding site for glucose) and the closed form right (image from here):

References

The Structure and Mechanism of Hexokinase
Mechanism of liver glucokinase.


What do red ants secrete while marching in a line, one after the other?

The simple answer is that ants secrete a substance called trail pheromone as they forage for food and each ant follows the trail of trail pheromone that is laid down by the preceding ant.

The term 'trail pheromone' can be a bit indistinct, however. Rather than consisting of a single chemical, trail pheromone is composed of many different chemicals, the exact compositions of which appear to be used deliberately to deliver complex information about the details of a given foraging site.

In the linked paper, the authors suggest that the

  use of several trail pheromones that differ in their persistence
  provides memory over differing time scales. In particular, a
  non-volatile pheromone can provide a longer-term memory, while a
  volatile pheromone can allow rapid choice among potential feeding
  locations by quickly ‘forgetting’ depleted locations.

This means that ants may be able to use pheromones to assemble a sort of "collective memory" for the colony, concerning the locations of food and the quantity of food found at each location.


First, your description is accurate. The only pedantic critique I would make is that the technical term for nucleotides in DNA is deoxyribonucleotide.

Second, I don't want to say that non-helical DNA never occurs since the structure of any macromolecule is dynamic, but I am specifically avoiding exceptions to the rule to avoid confusing the issue.

The helical structure of DNA is a low energy form which makes its formation thermodynamically favourable. Chemical bonds in DNA (and every molecule) have conformational flexibility which means that the molecule as a whole can adopt different structures. If you picture two DNA strands joined by hydrogen bonds but in a non-helical, straight form, you can simply twist the strands about their central axis to form a helical structure. This twisting is allowed because of the conformational flexibility of the chemical bonds. The helical structure is more stable than the "straight" form (because of base stacking interactions), and so it forms spontaneously. I struggled in vain to find a good animation of this, but came up short. You can skim through this video to see an example of what I'm talking about. It's subtle, but you may be able to see, or conceptualize, that as the two strands are twisted around each other, the adjacent bases in a strand come closer together. This permits stabilizing interactions between the adjacent bases which favours spontaneous helix formation (I briefly discuss this at the end of another answer).

As for how frequently the "rungs occur", this is dependent on the specific helix geometry. In B-form DNA, the geometry thought to occur predominantly in vivo, the helix completes one full turn approximately every 10.5 bases and the spacing between adjacent bases is ~3.4 Å, as shown below:


The previous answer isn't quite correct, because, well, blood flow is complicated and the body has autoregulatory mechanisms. As Alex mentioned, vasoconstriction doesn't occur in capillaries because they lack a muscle layer. It does occur in the small arterioles before and after the glomerulus (the afferent and efferent arterioles, respectively).

Bernoulli's principle mainly applies to larger arteries and arterioles, and not capillaries. Capillaries are so tiny that the red blood cell is a significant portion of the diameter, so the assumption of no viscosity is no longer valid. See this discussion for an explanation.

To address your question, here's a basic picture of the glomerulus, from Gray's Anatomy.

The afferent arteriole is in red, and the efferent arteriole in blue. The glomerular filtration rate (GFR) depends on the pressure difference between the two, which affects the hydrostatic pressure at the glomerulus. Also, note that vasodilation has the opposite effect of vasoconstriction on GFR.  (For a nice image and explanation, look at Figure 6 here) So:

Constriction of the afferent arteriole decreases the blood flow into the glomerulus and thus the glomerular hydrostatic pressure, which leads to a decrease in GFR.
In contrast, constriction of the efferent arteriole decreases blood flow out of the glomerulus, and this increases the glomerular hydrostatic pressure and leads to an increase in GFR.

Both the afferent and efferent arterioles are regulated through hormones (and drugs that inhibit the hormones). Prostaglandins dilate the afferent arterioles, and NSAIDs inhibit this action. Angiotensin II preferentially constricts the efferent arteriole, and this action is restricted by an ACE inhibitor. (Source: First Aid for the USMLE Step 1)


The body shape does seem to indicate it's some kind of heron/egret (12 species, of which, have been previously found in Michigan [according to Wikipedia]).

The seemingly large size from your picture (please edit with actual or best approximation of size), the tufted feathers on the head, white face, and the start of a black line on the anterior edge of the eye all suggest that this could be a great blue heron.

Great blue herons are typically grey (not the dark almost black of your specimen), but I did find some photos with nestlings /fledglings with darker plumage, including below:

 Source: Wikipedia


How do proteins get into the blood stream?

Found the answer - the lymph capillaries. I've not researched them too in depth but from what I've read thus far, their job is to essentially pick up fluids not picked up by the blood capillaries. They have walls that allow proteins to enter but make it very hard for fluid to flow out.

Wiki states that an average of 20 litres of blood gets processed each day by the blood, with roughly 17 litres through the blood capillaries/system (1), with the remaining 3 litres through the lymphatic system.

These are also prevalent around skin. 70% of lymph capillaries are found near the skin (2).

1) http://en.wikipedia.org/wiki/Lymphatic_system
2) http://www.lymphnotes.com/article.php/id/151/


Gluconeogenesis is not the reversal of the glycolysis, but the generation of glucose from non-carbohydrate precursors (like odd chain fatty acids and proteins). The reason why we have this process is because some organs and tissues can only use glucose as their energy source. These include the brain (although ketone bodies can be used here as well), erythrocytes, testes and the kidney medulla.

Usually the glucose for the supply of these tissues comes directly from carbohydrates in food or storage carbohydrates as glycogen or starch, but when these are not available, the body has another way to get around this problem and to avoid the starvation of these tissues. See for example here and here.


Transcription factor binding site located in intron

Even in a quiescent state, DNA is bound to a lot of proteins. It is not a lone double-helix of DNA with an occasional protein attaching here or there. Rather, it is tightly wrapped around histones, which themselves have other proteins attaching and detaching constantly. Repair enzymes are always whizzing about and fixing the random damage that occurs in DNA naturally, and transcription factors may be sitting on the DNA for a while and then diffusing away again without doing anything. There are probably more proteins around that I've forgotten.

As you can see, the nucleus, DNA and in general the cell interior are extremely crowded spaces, and for transcription to happen it takes more than just removing some TFs attached to intronic sequences. Histones need to be modified to repel each other and make space. Ultimately, all proteins will need to detach for a short time when RNA polymerase comes through. If they don't, polymerase will stall until they move away, or it may simply fall off, producing an incomplete RNA fragment which will be degraded quickly. Another polymerase will come along soon enough and produce a new transcript if the promotor is still in a permissive state.


How does a virus reach its host, it is always passive?

There are a number of different ways to spread a viral infection. Some viruses sit on surfaces (or infected persons) "waiting" for someone to touch and take them up, this is called smear infection. Other viruses are airborn inside of small droplets distributed by coughing or sneezing. These are inhaled and can then cause a new infection. Other viruses are transmitted through our body fluids (blood, semen) and either need a wound or can be transmitted sexually (for example Herpes or HIV). Other viruses are transmitted by animals which bite humans (Dengue and rabies would be examples here). Have a look into the Wikipedia for more details and examples.

Additionally viruses are produced in vast numbers by their hosts with most viral particles never reaching a new host. This strategy helps a lot to transmit further.s

For entering the nucleus (which is an obstacle) the viruses use the nuclear pore complex (NPC). Depending on what virus tries to enter the nucleus, different strategies are used. Some viruses are too big and release their DNA through the NPC into the nucleus, while others can pass through and some get stuck inside and release their DNA/RNA at this point. A last group uses the time during mitosis when there is no nucleus. See this figure (from here)
and also the references below:

References:

Virus strategies for passing the nuclear envelope barrier.
How viruses access the nucleus.
Viruses challenge selectivity barrier of nuclear pores.


Primary function of the enzyme lipoprotein lipase

Fat uptake means cells eating fat.

I'll try to keep it simple, so forget the many approximations. You need first to consider that most fat circulates in the blood under the form of triglycerides (TG). TG are not soluble in water, so how do they circulate? They are hidden inside cargo vehicles called lipoproteins. When a circulating lipoprotein touches a cell, if the cell expresses lipoprotein lipase (LPL), first LPL would trap the lipoprotein cargo, and then will start to catabolize the TG.

Importantly, there are no efficient TG cargoes inside the cell, so the function of lipoprotein lipase is to make fat easy to move inside the cell. TG are a chemical assembly of one glycerol and three fatty acids. Of note, there are good fatty acid cargoes inside the cell, so LPL will break TG into glycerol and fatty acids so that they can be further metabolized depending on the cell type.

Heart and muscle cells will bring fatty acids to mitochondria where they will be oxidized to produce energy. With reference to your question, adipocyte cells will bring fatty acids to other cellular compartments where they will be converted back to triglycerides and stored as fat. That's why you read that LPL facilitates fat uptake and storage in adipose tissue.


Can PCR tubes be made of different materials than plastic?

The key property would seem to be, at first glance, thermal conductivity. According to this table copper wins. But then, what about chemical reactivity? Maybe gold is a better choice. And that brings us to cost and disposability. These factors make the choice of a metal problematic. That leaves plastic and glass. Glass has better thermal conductivity, but clearly it has other drawbacks.


Until now, it looks good. When you are looking at basic mendelian gene linkage problems like these and you find out that the chi square analysis rejects your hypothesis, it means that there is linkage. In that case, you should have a case where your two recombinant genotypes have an approximately equal number of progeny and your two parental genotypes also have an approximately equal number of progeny. In your case, 220 is about 230, and 270 is about 280.

(source: k12.ny.us)
This image is just like your problem. I want you to imagine that b+ and b represent A and a in your problem and that vg+ and vg represent B and b in your problem, respectively. You start out with an AaBb crossed with an aabb. On the gametes line, it lists all of the possible gametes of this cross. On the line where it describes testcross offspring, we see a situation very similar to yours. In this case, AaBb = 965, aabb = 944, Aabb = 206, and aaBb = 185. We have our two pairs: AaBb/aabb and Aabb/aaBb. Sound familiar?
The recombinant offspring are defined as the offspring that do not have a genotype of either parents. The reason this is important is because you need a crossover to get a recombinant. The closer two alleles are together on the same chromosome, the harder it is to get one of the alleles to cross over without the other one crossing over with it.
Let's clarify. This means that if the alleles are closer, you get less crossovers. All recombinant exist because of a crossover. Therefore, the closer two alleles are, the less recombinants you get.
Quick note: the formula for the distance two alleles are from each other is expressed by this formula:
100(recombinant frequency) / (total offspring) = distance apart.
This is consistant with everything we have said, because as recombinant frequency decreases, distance apart decreases as well.
Another way to explain it: on the gametes, AB and ab really like to stay together, as they are LINKED. It is very difficult to separate them. That is why there are more AaBb and aabb; they only require the gametes AB and ab.
Apply the formula to find out how far they are apart. I think you can figure out the rest from here. I want you to try and answer the question.
Hope this helped! :)


Is there any difference between hydrogen acceptor and hydrogen carrier?

Actually, both NAD and FAD accept a hydride ion, H$^-$ (a proton with two electrons), not a hydrogen atom (a proton with one electron). For this reason, I would not refer to NAD or FAD as "hydrogen acceptors" or "hydrogen carriers" at all. It just gets confusing. (I guess you could call them "hydride acceptors" if you want, but it's not common terminology.)

"Electron acceptor" is the right name for NAD and FAD when discussing a redox reaction where they in fact accept electrons, in the form of an H$^-$ ion. Pyruvate dehydrogenase which you mentioned is one such example. This is not unique to biology, it's standard chemistry terminology: any molecule that accepts electrons in a redox reaction is (cleverly ;-) called an electron acceptor. For example, oxygen is an electron acceptor in combustion reactions. So "electron acceptor" is just a name for the role that the molecule plays in a redox reaction.

"Electron carrier" refers to the fact that NAD (and also NADP, and quinones, and some cytochromes ...) can carry electrons between reactions that occur at different places. For example, after NAD picks up an H$^-$ ion in the pyruvate dehydrogenase reaction to form NADH, it can carry the two electrons over to complex I where it donates them to ubiquinone. (And here, NADH acts as an electron donor, while the ubiquinone is the electron acceptor.) So the term "carrier" emphasizes the transporting role of the molecule. FAD is actually a bit different in this respect, because it is not soluble; it's a prosthetic group bound to certain enzymes like Complex II, and therefore it cannot really carry anything anywhere, or at least not very far. So to be precise, I personally would rather not call FAD a carrier. But maybe that's just me.


The activators are proteins that bind to specific DNA sequences in the enhancer region. These activators also bind to the RNA polymerase and other associated members of the transcription complex, which makes it more likely for an RNA polymerase to hang around the promoter sequence of the region it enhances.

This in turn increases the chance of the gene being transcribed.

It's basically a little magnet that sucks in the RNA polymerase and then nudges it towards the promoter.


Concentration gradients across membranes with different ions

I try to answer your two questions briefly:

Ion gradients are dependent on charge, but there exist independent transport mechanisms, extending diffusion. Trans-membrane transport proteins can specifically move only one sort of ions. Also symport or antiport exists, that can depend on gradients of other (e.g. non-charged molecules). In addition, the mentioned inorganic ions can form chemical bonding to organic ions for example, which neutralizes the electrical charge.
Beside an electrical potential, also chemical (concentration) potential can act as force on ios. In addition active transport, inactivation as mentioned above and other factors have an influence on the molecule flow.


I am not sure if I can answer the question of why the primary oocyte gets arrested during meiosis (and finishes after fertilization), but the stage of growth the egg is arrested at does vary widely between species; it's not always primary oocyte. This might suggest that the reason is species-dependent.

In sea urchins, it's the fully mature ovum that gets fertilized.
In humans, it's the secondary oocyte (arrested during this stage of meiosis) that gets fertilized.
In the majority of mammals (dogs, etc.), it's the primary oocyte that gets fertilized. In both of these last two, the oocyte finishes meiosis after fertilization & the entry of the sperm nucleus into the egg.

The translational arrest of the egg you mentioned is because the egg is in a "dormant" state until it is fertilized, and it is "activated" by fertilization. Until fertilization, the mRNA's are present in the cytoplasm, but cannot be translated because they are missing poly-A tails (translational arrest); free levels of calcium in the cytoplasm are low; and respiration and oxygen levels are low. This is because the egg is "primed" for the explosion of activity necessary during early development (taking place after fertilization); the mRNA's code for proteins that are used at that time, but they are not translated until fertilization.

Source: http://www.ncbi.nlm.nih.gov/books/NBK10029/ (see the second paragraph under "Late Responses")


Which came first in hominid evolution: language or bipedalism?

This article by Philip Lieberman On the subcortical bases of the evolution of language, page 22, he asserts the neurons associated with language may have developed based on the demands of bipedal posture. While there's no concrete data to support when we see the first languages, here we see evidence of arches (and presumably bipedal posture) in Australopithecus afarensis. So there are still some dots that need connecting.


How are the helices of MscL gating "attached"?

It is the combination of intra- and inter-molecular interactions that determines the conformation of the protein.

There are two types of interactions: bonded and non-bonded. There are two types of non-bonded interactions: electrostatic and non-electrostatic. Electrostatic (also known as 'polar') interactions are usually modeled using Coulombic potential energy equation; non-electrostatic (also known as 'non-polar' or 'van der Waals') interactions are usually modeled using Lennard-Jones potential energy equation.


Understanding intra and extracelullar concentrations (membrane potential)

Afaik you can describe the potentials between the two sides of the cell membrane using the Nernst-equation. Yepp wikipedia writes the same here.

Membrane potential is a very important thing, because human cells require stable internal concentrations of Na+, K+, Ca2+, etc... in order to work properly. These concentration can depend on species, for example plants cells work completely different than animal cells, they have higher Na+ than K+ in their cytoplasm. So every human cell has to maintain a membrane potential if they don't want to die. It requires a lot of ATP (energy) to do so... Human cells typically maintain this potential against the blood plasma. Cytoplasm has around 120mM K+ and 15mM Na+, while the blood plasma has about 5mM K+ and 140mM Na+. You can count the membrane potential from these concentrations using the Nernst equation (a short presentation about how). I don't remember the exact mV value, does not matter. So human cells are working hardly on keeping the Na+ outside and K+ inside, and they can possibly die because of membrane potential changes (e.g. when they require too much energy to maintain the internal concentrations and/or osmolarity).

Excitable cells, e.g. nerve cells or muscle cells are very special because they can change their membrane potential rapidly by sending out K+, Ca+ or sending in Na+. This can create small electric discharges, which can be used to send electric signals or contract muscles, etc... Different cells have different discharge diagrams, e.g. axons have something like this:

Figure 1 - axon electric discharge diagram - source

and muscles have something like this:

Figure 2 - muscle electric discharge diagrams - source

Summa summarum it can depend on the cell type what happens, but basicly you can count the new potential using the Nernst equation by the concentration changes you mentioned...


Your pictures are quite blurry, but I think this is an Osmia, ie a Mason bee (and not a bumble bee). I think you can see a tendency of the “horns” that female Osmia bicornis (red mason bee) have on their heads on your pictures, so this is my guess. Females are much larger and generally darker than males on the thorax and head, and often quite black there while overall red on the abdomen.
Another option is O. bicolour, where females lack the “horns”of bicornis.
See eg this picture:

Head picture of female O. bicornis, to see the “horns” clearly (if it is indeed this species):

(Pictures from artportalen.se)
Another possible species in the same genus is Osmia bicolor (two-coloured mason-bee), which is more clearly divided in black-orange, see e.g.:

This species has an interesting biology, in that it is specialized on using snail shells for egglaying and preparing larval cells stored with food.


Do organisms use detergents to fight off viruses?

To answer your question, consider why soap is effective against bacteria and viruses.  The chemistry of detergents allows them to interrupt the lipid layer that surrounds cells and some viruses.  Viral envelopes, in particular, tend to be composed of host-derived phospholipids and proteins.  So, if an organism were to synthesize a detergent to fight off a pathogen, that detergent would pose a threat to the producing organism, as well.

Edit - most air-breathing animals produce a pulmonary surfactant in their alveolar cells, though the purpose of these molecules is lung function and cell size regulation, not immunity.


Can it be said that proteins determine phenotypic traits?

Yep, that is correct in general. However, sometimes proteins indirectly determine phenotype. For example, the skin colour is dependent on melanin (not a protein) but the melanin producing cells work because of proteins. Further, melanin production is also controlled by proteins. Thus, skin colour is not DIRECTLY determined by proteins but because proteins produce the pigment melanin, proteins are ultimately the reason behind our skin colour phenotype.


How much of your stock solution should you take to make the 1000 cells/mL mixture?

Oh, come on, thats simple math.
First calculate how many cells you have per ml: 50$\mu$l are $\frac{1}{20}$ of 1 ml. So multiply 125 with 20 to get the concentration per ml: $125 \times 20 = 2500 \frac{cells}{ml}$

If you want to know how many cells you have in total, multiply by 8 (for the 8ml you have) and you come to 20.000 cells in your 8ml solution.

When you want to know, how much of your solution you need, you calculate: $\frac{2500 \frac{cells}{ml}}{1000 cells} = \frac{1 ml}{x}$.

This can be transformed into $x = \frac{1}{2,5} ml = 400 \mu l$.

So you need 400 $\mu$l for each ml of your final cell solution. So if you want to have 5ml with 1000 cells/ml you need $5 \times 400 \mu l = 2000 \mu l = 2 ml$ of your cell solution. To reach 5 ml add 3 ml of your solvent/media.


Could fingerprints potentially be changed using a gene gun?

Chimpanzees have fingerprints.  Next all you have to do is find the homologue of SMARCAD1 and let the animal testing begin!  But actually I doubt it will work.  This website goes into some depth and links some additional sources that show fingerprints are developed in the womb and are fully set by 6 months of gestation.

It seems likely that SMARCAD1 may have to do with having fingerprints or not, but not likely that it has anything to do with their composition.  It would be difficult for one gene to have enough variation to provide 6 billion variations in output.  You could hypothesize that it's a combinatorial output from other genes as well, but the studies linked above focus more on environmental interaction as the cause of variation.

I would guess that the patterns are set and no amount of gene therapy is going to change your fingerprints.  The simplest experiment would be to knockout the above gene in an adult for some period of time and see if the fingerprints fade.


How did butterflies evolve to have eyes on their wings?

You're correct with the genetic mutation bit. A basic explanation would be:

Some gene or genes became mutated that lead to the coloration you see, and the end result was that the butterfly or butterflies with the mutated gene were able to produce more offspring or offspring which survived better than the eyeless versions.

There are ways of dating genetic mutations by comparing one organism's genes to another, but accuracy can be an issue without some significant genomic study to confirm mutation rates and other aspects.

However, the butterfly wouldn't be purposefully imitating another creature's eye. It may be by chance and/or predator behaviors that the eyespots look like the eyes of another creature, but the adaptation wasn't a willful act. It was a random genetic mutation or mutations that lead to beneficial coloring, and the eyespots may have improved over time as more mutations occurred.


GenBank includes human proteins and provides APIs for constructing HTTP requests to make searches. Examples are given in Perl, but if you prefer another programming or scripting language you are expected to write your own:

  Equivalent HTTP requests can be constructed in many modern programming languages; all that is required is the ability to create and post an HTTP request.

This approach has always served me well.

Uniprot seems similar in this respect.

SwissProt provides a package for BioPython which may be of interest. I don’t know if this is the library you are referring to — you don’t say, and I don’t use Python.


Gibco has an anti-clumping agent verified for CHO cells, as does Lonza, but I like Gibco reagents more. Cells tend to clump for a number of reasons, including extracellular DNA from lysed cells and the presence of Ca and Mg ions (important ions for cell adhesion and aggregation).

You could try these:

1) Wash and resuspend in balanced salt solution without magnesium or calcium. Like Hank's balanced salt solution.

or

2) Treat with DNase I. I think you could go as low as 1 IU/mL for 30min-1hr to bust up a fair amount of DNA clumping. You can do this in a basal medium (like RPMI, DMEM, etc.), or the balanced salt solution. Your medium can contain serum only if the serum has been heat-inactivated as proteases in the serum with inactivate your DNase. Incubate with DNase under gentle agitation at 37°C (I always had a tube rotator in an incubator for this purpose, just put your cells in a 50mL conical and set them to agitate for 1hr. You could also use a heated shaker unit). If you don't have this setup, you can agitate at room temp, but for a little longer perhaps.

and maybe

3) Once of the other obvious choices is to avoid passaging your clumping cells and collect the rest. You can do this by putting all your cells into a flask incl. the clumps, agitate for a moment, and let it sit so that the chunks quickly fall to the bottom, and collect everything but the stuff that fell to the bottom.


Insect Identification (even the family name would do)

You've found a specimen of Coridius janus or cucurbit stink bug or red pumpkin bug (don't mix up with the red pumpkin beetle). They betong to the suborder Heteroptera (True bugs).

(picturefrom Wikipedia)

Also see:
projectnoah.org: red pumpkin bug

nbair.res.in: Coridius janus

indiabiodiversity.org: Coridius janus


How Incomplete dominance can be explained at molecular level?

Molecular mechanisms of incomplete dominance (a.k.a. partial- or semi-dominance) vary.  As an example, let's look at snapdragons and morning glories, two flowering plants that both exhibit incomplete dominance relative to flower pigmentation.
Snapdragons (Antirrhinum majus) have multiple alleles at the nivea locus.  The wild-type nivea transcript (niv+) encodes a chalcone synthase involved in pigment biosynthesis, and a single copy of the niv+ allele is sufficient for wild-type pigmentation.  However, niv+ is semi-dominant with the mutant niv-525 allele, leading to reduced pigmentation in the heterozygote.  The original publication by Coen and Carpenter 1 describing this effect offers some possible molecular explanations:

Transcription factor sequestration.  The niv-525 allele could encode a defective enzyme.  This allele also contains an inverted duplication of a transcription factor binding domain required for enzyme expression.  The defective niv-525 allele therefore titrates away transcription factor from niv+, leading to less enzyme and therefore less pigment.

Transvection.  There is some physical interaction between alleles on homologous chromosomes, such that transcription of one or both alleles is activated or repressed in trans.  This could be realized as binding of the enhancer associated with the wild-type allele to the promoter of the defective allele.  Figure 9 of Gohl et al. 2 has a good explanatory graphic.

Anti-sense hybridization.  The inverted duplication on the niv-525 allele contains a TATA box.  Transcription initiated at this site would result in a transcript anti-sense to the wild-type mRNA.  Hybridization of the sense and anti-sense
RNAs creates dsRNA that is selectively degraded and/or inefficiently transported out of the nucleus, ultimately leading to less enzyme product.

Morning glories (Ipomoea purpurea) show similar genetics at the A locus, which also encodes a chalcone synthase.  However, unlike the snapdragon niv+ allele, a single copy of the wild-type a allele is not sufficient to produce wild-type pigmentation.  Therefore, incomplete dominance in morning glory results from a simple dosage-dependent mechanism, as described in Johzuka-Hisatomi et al. 3
Citations

Coen ES, Carpenter R. A semi-dominant allele, niv-525, acts in trans to inhibit expression of its wild-type homologue in Antirrhinum majus. EMBO J. 1988;7(4):877-883.
Gohl D, Müller M, Pirrotta V, Affolter M, Schedl P. Enhancer blocking and transvection at the Drosophila apterous locus. Genetics. 2008;178(1):127-143.
Johzuka-Hisatomi Y, Noguchi H, Iida S. The molecular basis of incomplete dominance at the A locus of CHS-D in the common morning glory, Ipomoea purpurea. J Plant Res. 2011;124(2):299-304.


Biology LibreText

Khan Academy

MIT OpenCourse Wave


Ways to identify that proteins are regulating different genes experimentally

Chromatin immunoprecipitation (ChIP) or ChIP-Seq are the first methods that pop into my mind. Essentially, DNA is cross-linked to bound proteins (transcription factors, histones, etc.) by various methods, then broken into pieces by either sonication or digestion with micrococcal nuclease. An immunoprecipitation is then performed by adding antibodies targeting your protein of interest (HIF-1α and HIF-2α in this case), allowing them to bind to their targets, enriching them using bead-conjugated Protein G (or Protein A), then reversing the cross-linking. The enriched DNA can then either be subjected to PCR for known genes (ChIP), or it can be sequenced and aligned with a reference genome to determine all bound sequences (ChIP-Seq).


If a woman was fertilized with her own DNA, would it be her clone?

1)
In principle yes, you could in theory use micro injection to inject haploid DNA into the egg. I don't think this has been used in practice though. However Dolly the sheep was created by exchanging haploid nucleus of a sheep egg with a diploid nucleus from a mammary gland cell.

2)
Not necessarily, DNA is packaged into chromosomes and diploid cells have two copies of the same chromosome (with the exception being the sex chromosomes MALE:XY FEMALE:XX). Remember that gametes are haploid (single copy of each chromosome) and that homologous recombination occurs during gamete formation, therefore the chance of obtaining two identical sets of haploid DNA that also match the females is extremely low, unless all chromosome pairs are completely identical.

3)
In principle yes. I could imagine that DNA extraction from eggs could be used for artificial fertilization and the result of that would be a race of all females.


How does heat shock transformation work?

Heat shock transformation alters membrane fluidity creating pores:

  A sudden increase in temperature creates pores in the plasma membrane of the bacteria and allows for plasmid DNA to enter the bacterial cell.

Reference: Journal of Visualized Experiments. Bacterial Transformation: The Heat Shock Method. 2014. http://www.jove.com/science-education/5059/bacterial-transformation-the-heat-shock-method

  The change in temperature alters the fluidity of the semi-crystalline membrane state achieved at 0oC thus allowing the DNA molecule to enter the cell through the zone of adhesion.

Reference: Anh-Hue T. Tu. Transformation of Escherichia coli Made Competent by Calcium Chloride Protocol. 2008-2013. American Society for Microbiology

  ... heat-pulse (0 degrees C42 degrees C) step of the standard transformation procedure had lowered considerably outer membrane fluidity of cells. The decrease in fluidity was caused by release of lipids from cell surface to extra-cellular medium. A subsequent cold-shock (42 degrees C0 degrees C) to the cells raised the fluidity further to its original value and this was caused by release of membrane proteins to extra-cellular medium.

Reference: Panja S, Aich P, Jana B, Basu T. How does plasmid DNA penetrate cell membranes in artificial transformation process of Escherichia coli? Mol. Membr. Biol. 2008 Aug;25(5):411-22. doi: 10.1080/09687680802187765. PubMed PMID: 18651316.


Inheriting Modified DNA after CRISPR editing

First off, CRISPR can't be used to cure diseases in an adult human or, more generally, for any adult vertebrate at present.

As you can see in this paper, a major problem with CRISPR is it has to target specific cell types in tissues. As long as the targets are somatic and not germline, the edits made by CRISPR will not be heritable.


Do eukaryote cells contain DNA that isn't part of a chromosome or located in the mitochondria?

In plants, chloroplasts and other plastids contain DNA, but I suppose you are more interested in humans. Quoting from wikipedia,

  In many cells cytoplasmic DNA is also found, which is different from
  nuclear DNA, both in methylation levels (cytoplasmic has less), and in
  sequence. EccDNA or extrachromosomal circular DNA is present in all
  eukaryotic cells, derived from genomic DNA and consists of repetitive
  sequences of DNA found in both coding and non-coding regions of
  chromosomes. EccDNA can vary in size from less than 2000 more than
  20,000 base pairs. In animals, eccDNA molecules have been shown to
  contain repetitive sequences that are seen in satellite DNA, 5S
  ribosomal DNA and telomere DNA. The function of eccDNA has not been widely studied, but it has been proposed that the production of elements of eccDNA from genomic DNA sequences adds to the plasticity of the eukaryotic genome and can influence genome stability, cell aging and the evolution of chromosomes


Voltage sensitive dyes technique: What is the underlying measure?

Since these are fluorescent dyes, the most likely method of use is with some sort of fluorescent (likely confocal) microscope. The various types of dyes have different hydrophobic tails, so they target different types of membranes (plasma membrane, mitochondrial membranes, etc.). An excitatory light source (typically a laser, with a single wavelength) is applied to the sample, and the $F_0$ or baseline fluorescence intensity at time zero is measured. When an event happens, such as the contraction of a muscle, the $\Delta F$ or change in fluorescence intensity is measured. This difference is then divided by the baseline, and called the fractional fluorescence (${\Delta F}/{F_0}$). It is plotted like so:

Bu G et al. Biophys J. 2009 Mar 18;96(6):2532-46.


What is this species of asphodel from Morocco?

It appears to be Asphodelus aestivus, but there is similarity with Asphodelus ramosus, both of which have strap like leaves and highly branched stems. They have some overlapping ranges as well in southern Mediterranean/north Africa.

https://en.wikipedia.org/wiki/Asphodelus_aestivus

https://en.wikipedia.org/wiki/Asphodelus#Systematics


Human body power consumption in still state

You're basically correct.  I don't know if you've found the Wikipedia article on Basal Metabolic Rate but it's got everything you need, including a bunch of formulas you can use to figure out an average value for a given body type.  There are also many online calculators, such as this one.  You can easily figure out averages, which I think is what you want, but between two individuals the number can change quite a bit.

Why does 80 watts sound so low?  This is more of a physics.se answer, but Watts are a unit of power which mean they measure energy use over time; W=J/s, or Joules per second.  Every second.  Have you ever touched a 75 watt lightbulb?  They're hot as hell.  If your human does nothing all day, s/he will be like an inefficient incandescent lightbulb on for a full 24 hours.  Maybe that seems low but electricity is relatively cheap these days.  To use another classic physics experiment, 1700kcal=7000kJ=a lot of ice turned into steam.

No wonder my father always made me turn the light off in the bathroom...


What nutrients are best suited for growing E.Coli

Optimal is a funny thing; it depends upon what you want. The purpose of the bacteria, is probably the most important aspect when considering the nutrients. There are many recipes capable of growing E. coli. What does optimal or best mean to you and why? Is selectivity or differentiation a factor? How important is cost? Are you aiming for industrial level production or just testing. Do you have a bioreactor? Or are you looking for something low tech... maybe from food-mart?

For what it's worth, you might find minimal salts media and solid state fermentation interesting.

Different strains like different nutrients, of course. So, phenotypical tests are sometimes helpful when figuring what an undescribed strain likes (and doesn't like).

That being said... I can offer a little insight here.

"+" for growth/utilization;  "-" for weak or no growth/utilization:

                 E. coli    E. coli inactive**  E. coli 0157:H7

Pectin                 -            -                   -
Dextrin                ++           ++                  -
Sucrose                -            -                   +++
Glycerol               +++          +++                 +++
Stachyose              -            -                   -
D-Fructose             ++           ++                  ++
D-Maltose              +            ++                  ++
D-Raffinose            +            -                   +++
α-D-Glucose            +            +                   +
α-D-Lactose            +            -                   ++
D-Trehalose            ++           +++                 +++
D-Galactose            ++           +++                 +++
L-Fucose               +++          +++                 +++
L-Rhamnose             +++          -                   ++
D-Sorbitol             +++          +                   -
D-Mannitol             +            ++                  ++
Methyl Pyruvate        +++          +++                 +++
Tween 40               -            -                   -

Gelatin                -            -                   -
L-Alanine              +++          +++                 +++
L-Arginine             +            -                   -
L-Histidine            -            -                   -
D-Serine               +++          +++                 -
L-Serine               +++          +++                 +++
D-Aspartic Acid        -            -                   -
L-Aspartic Acid        +++          +++                 +++

D-Glucoronic Acid      +++          +++                 +++

Citric Acid            -            -                   -
L-Malic Acid           +++          +++                 +++
Acetic Acid            +++          +++                 +++
Acetoacetic Acid       +            +                   -
L-Lactic Acid          +            -                   -
Mucic Acid             ++           -                   +++
D-Malic Acid           +            +++                 +++
Propionic Acid         ++           ++                  +++
Formic Acid            +            -                   +

D-Salicin              -            -                   -
Lithium Cloride        +++          ++                  ++
Na Butyrate            +++          +++                 +++
pH 5                   +++          +++                 +++
8% NaCl                ++           +                   -
D-Serine (high)        ++           +                   -
Potassium Tellurate    +            +                   +++
Na Bromate            +/-           -                   ++

E. coli inactive** is lactose-negative, non-motile- often misidentified as Shigella


Having a dominant side is advantageous. Instead of seeing it as the brain influences our fine motor skill, think of it the other way round. The way we use our hands or any other part of our body sends feedback to the brain to increase the portion of the brain devoted to that region of the body and of course with disuse the reverse occurs. The more you do a certain task the more that portion of the brain gets better and coordinating the movement. The portion I talk about is the primary and supplementary motor cortices. So basically we are specialising. In the same way a heart doctor is better with treating conditions of the heart than a foot doctor. So we can either devote our experience to the one hand, or both or the other hand. If we use both hands equally our brain adapts so that we are ambidextrous, if instead we use just the one hand our brain develops just that side. But if you do focus on both you are using your dominant hand less so overall same amount of development just over both sides of the brain rather than just one side. You can probably see the benefit of having this plasticity of improving only what is used because why improve what we don't use and waste resources? And you may also see the benefits of higher specialising of one hand rather than having two slightly specialised hands. There are few tasks that require both hands to be very specialised, but if that were the case then the body would go ahead and do that but in spending time training your hands you are probably training your legs or something else less.

///

Why not have a switch between the two hemispheres to give the hand currently being used the fine motor skill located in the other hemisphere? (from comment)

I see. In my answer I only talked about one aspect. The brain doesn't have to learn skills for each hand completely independently. For example imagine if you learn to play a musical piece with your right hand only. If you try it with your left you won't be amazing but you'll definitely be better than a complete novice. Our brain can learn how to do by seeing which is vital for development. But there's a limit to that, your hands aren't completely identical so there's still a portion that needs fine tuning. Your muscles have different stregth, fatigue, resistance, recruitment patterns, places they innervate. Your hands are mirror images. The weight of your hand is different. And not only that but these variables aren't fixed, there's lots of them and they are different for different tasks. So to use your analogy, the more expensive remote can be used but it wasn't bought for use with the black plane. It'll give more control to the black plane but it still won't be the best ever until it learns what the muscle strength is etc. then it will be just as great.


The motion of the eyelid is driven by the levator palpebrae superioris, i.e. elevating muscle of upper eyelid, and it can be positioned to the intermediate, half-closed positions. At least I can do it.

Yes, this muscle tends to shake or oscillate simply because it's a very weak muscle. It's similar with the muscles controlling the motion of the little finger (or ring finger). Vibration and "noise" is present in all muscles but the stronger muscle you have, the more accurately the random motion is averaged out.

If you connected $N$ eyelid muscles so that they move in unison, the noisy vibrations would be reduced by the factor of $\frac{1}{\sqrt{N}}$. This is the well-known scaling of the statistical errors in physics etc.

I would think that this question was totally appropriate at the Physics Stack Exchange.


Can any one identify this insect from Lokhandwala, Mumbai India?

It's looks like a Leaf-Footed Bug (Homoeocerus Sp., Coreidae).

Source: https://www.flickr.com/photos/itchydogimages/17774939209

Source: https://www.flickr.com/photos/itchydogimages/6211603956/


If ants have an antibiotic gland, how can they spread hospital infections?

I have worked in hospitals (US) most of my life, treating both community-acquired, and more pertinently to this question, nosocomial (hospital acquired) infections, and have read many articles on the subject.

I have never, ever seen ants mentioned anywhere.

People, flies, cockroaches and rats, yes.

Ants, no.

However, ants are vectors in a few foreign studies. The key word in these studies is potential.

As you stated,

  From the bulla, ants can groom the secretion onto the surface of their exoskeleton. This helps to prevent the growth of bacteria and fungal spores on the ants and inside their nest.

No antibiotic covers all organisms. Also, the secretions are to protect the ants against infection, not against the carrier state.

Pathogenic bacteria is cultured from ants themselves. The ant can be thought of as similar to a human: humans make antibodies to pathogens but are vectors of many diseases. Ants protect themselves via secretions, but are hosts to potential pathogens.

Part I: Review of Scientific Data Regarding Transmission of Infectious Agents in Healthcare Settings
Hospital hygiene and infection control
Ants associated with pathogenic microorganisms in brazilian
hospitals: attention to a silent vector
Ants in a hospital environment and their potential as mechanical bacterial vectors
Insect/Bacteria Association
and Nosocomial Infection


What is this animal that hides in dustlike structure?

This is likely a case-bearing clothes moth (Tinea pellionella).
Though more information and a better image would aid in confirming that to be the case.

Here are some pictures:


What mechanisms exist for the excision of specific sequences from DNA?

Genome editing techniques like CRISPR-Cas and TALEN use non-specific recombinases coupled to a DNA-recognizing part that can be designed to be specific for any stretch of sequence, as it is constructed out of single zinc-finger 'modules' that each specifically bind a couple of nucleotides (one nucleotide each in the case of TALEN).


why does the bacteria produce H2O2 in the first place?

It is produced by all organisms as a byproduct of respiration. See this wikipedia article:

  All living cells produce reactive oxygen species (ROS) as a byproduct of metabolism. ROS are reduced oxygen intermediates that include the superoxide radical ($O_2^•$) and the hydroxyl radical ($OH^•$), as well as the non-radical species hydrogen peroxide ($H_2O_2$)....The superoxide anion is formed directly from the one-electron reduction of molecular oxygen. Hydrogen peroxide is then formed from the disproportionation of the superoxide anion. This reaction occurs very quickly in seawater. Next, the reduction of hydrogen peroxide yields the hydroxyl radical, $H_2O_2 \xrightleftharpoons 2OH^•$, which can then get reduced to the hydroxyl ion and water.

 Source

But, it has some useful functions too! One of those, as you mention, is in immunity through NADPH oxidase, but there are some more! From the same above wikipedia article:

  These ROS are important in the normal functioning of cells, playing a role in signal transduction and the expression of transcription factors.

For this line, wikipedia cites 3-4 articles, one of which is this:

  The OxyR transcription factor is sensitive to oxidation and activates the expression of antioxidant genes in response to hydrogen peroxide in Escherichia coli. Genetic and biochemical studies revealed that OxyR is activated through the formation of a disulfide bond and is deactivated by enzymatic reduction with glutaredoxin 1 (Grx1). The gene encoding Grx1 is regulated by OxyR, thus providing a mechanism for autoregulation.

It is not produced by obligate anaerobic bacteria and that is why they are very sensitive to oxygen. See this article:

  Obligate anaerobes are microorganisms killed by normal atmospheric concentrations of oxygen (20.95% $O_2$)...Because molecular oxygen contains two unpaired electrons in its outer orbital, it is readily reduced to superoxide ($O_2^−$) and hydrogen peroxide ($H_2O_2$) within cells. Aerobic organisms produce superoxide dismutase and catalase to detoxify these products, but obligate anaerobes produce these enzymes in very small quantities, or not at all.

If so, why would there be organisms that produce H2O2 and still not have a catalase (when the bacteria is outside, not in the phagosome)?

Logically, no. Producing $H_2O_2$ but not being able to handle it would be like suicide for any organism. Also, I could not find any example of bacteria which lack catalase but still produce hydrogen peroxide. However, if you talk about spontaneous formation of $H_2O_2$ from $O_2$ or spontaneous conversion of $H_2O_2$ to $OH^-$ or $H_2O$, then there could be many examples.

Isn't H2O2 is harmful even in the absence of free radical producing enzymes since the fenton reaction is a non-enzymatic reaction?

I think you have used some inappropriate words here; you probably mean free radical metabolizing enzymes (like catalase or superoxide dismutase) instead of free radical producing enzymes. And you probably want to say that $H_2O_2$ can also affect bacteria through fenton's reaction even in the presence of such enzymes (correct me if I'm wrong here).

You are partially correct. It should damage the bacteria, but, as you know, bacteria are ever-evolving and have already found a way to counteract this. First, lets see how fenton's reaction works. See this:

  After addition of the iron and the hydrogen peroxide, they are going to react together to generate some hydroxyl radicals as it shows in the following equations:

  $Fe^{2+} + H_2O_2 \rightarrow Fe^{3+} + OH^• + OH^-$

  $Fe^{3+} + H_2O_2 \rightarrow Fe^{2+} + OOH^• + H^+$

  The typical range for the iron dose is 1 part of Fe per 5-25 parts of H2O2.

  After that the hydroxyl radicals are going to react with the pollutants to oxidize its. Actually the hydroxyl radicals can react according 4 kinds of reactions with the pollutants:

  Addition: $OH^• + C_6H_6 \rightarrow (OH)C_6H_6$

  Hydrogen Abstraction: $OH^• + CH_3OH \rightarrow CH_2OH^• + H_2O$

  Electron Transfer: $OH^• + [Fe(CN)_6]^{4-} \rightarrow [Fe(CN)_6]^{3-} + OH^-$

  Radical Interaction: $OH^• + OH^• \rightarrow H_2O_2$

  During the Fenton's reaction all the parameters are adjusted to promote the two first kind of reaction between the pollutant and the hydroxyl radicals.

Now, lets see how the bacteria tackles this. See this:

  While E. coli Dps can store iron, it prefers to use $H_2O_2$ rather than $O_2$ as an oxidant (Zhao et al., 2002). This suggests that the primary role of Dps in E. coli is to protect DNA against the potential damage of hydroxyl radical produced by the Fenton reaction, rather than an iron storage function. Although an iron storage Dps-like ferritin was found in the gram-negative bacterium Listeria innocua (Bozzi et al., 1997), recent studies have shown that it is indeed a Dps protein, which attenuates the production of hydroxyl radical by Fenton chemistry: DNA cleavage assays showed that the protein, while not binding to DNA itself, protects it against the deleterious combination of $Fe^{2+}$ and $H_2O_2$ (Su et al., 2005). It seems likely that the principle role of this family of proteins is a DNA protecting anti-redox agent (Chiancone et al., 2004).

EDIT: Now, as you asked in comments:

how catalase negative organisms manage with the H2o2 they produce

read the following paragraph from this article (emphasis mine):

  Under different growth conditions we found that both L. plantarum ATCC 8014 and a catalase-positive strain, T-1403-5, were capable of utilizing $0_2$, particularly during the late stages of growth. This suggested the need for enzymes which would protect the lactobacilli
  from $H_20_2$ and $0_2$ which might be formed. Superoxide dismutase was present at low but constant levels in both catalase-positive and catalase-negative strains. NADH peroxidase was present in strain 8014 and this enzyme increased in specific activity as the cells aged and entered the period of increased $0_2$ uptake. The presence of this enzyme should protect the organism against toxic effects of $H_20_2$ in the absence of catalase production. In strain T-1403-5 this role can be performed by the very active atypical catalase, although this strain may also possess the peroxidase. When growth rates of the catalase-negative and catalase-positive strains were compared, the rates of the catalase-negative strains were greater than that of the catalase-positive strain. Therefore, it did not appear that the possession of catalase conferred any advantage on strain T-1403-5.

Or see another article on Streptococcus pneumoniae:

  Aerobic growth of Streptococcus pneumoniae results in production of amounts of hydrogen peroxide ($H_20_2$) that may exceed 1 mM in the surrounding media...The mechanisms allowing S. pneumoniae, a catalase-deficient species, to survive endogenously generated concentrations of $H_20_2$ that are sufficient to kill other bacterial species is unknown. In the present study, pyruvate oxidase (SpxB), the enzyme responsible for endogenous $H_20_2$ production, was required for survival during exposure to high levels (20 mM) of exogenously added $H_20_2$...Thus, SpxB is required for resistance to the toxic by-product of its own activity. Although $H_20_2$-dependent hydroxyl radical production and the intracellular concentration of free iron were similar to that of Escherichia coli, killing by $H_20_2$ was unaffected by iron chelators, suggesting that S. pneumoniae has a novel mechanism to avoid the toxic effects of the Fenton reaction.

From the same article's Discussion heading (there are actually many points, so I recommend you read them yourself too, I'll add main points here):

  The role of SpxB expression in resistance to killing by $H_20_2$ was confirmed by the demonstration that spxB mutants, which produces no detectable $H_20_2$, had a significant decrease in $H_20_2$ resistance and by demonstrating that complementation of the spxB gene fully restored both $H_20_2$ production both $H_20_2$ resistance. These results showed that SpxB expression is required for wild-type levels of resistance to $H_20_2$ rather than merely correlating with it.
  when cultures of both strains were shifted from anaerobic to aerobic conditions with or without chloramphenicol, a protein synthesis inhibitor, $H_20_2$ resistance was not affected. This confirmed that de novo protein synthesis is not involved in the increase of $H_20_2$ resistance observed during aerobic growth, suggesting that an inducible response is not involved.
  Furthermore, the addition of pyruvate to either mutant or wild-type cultures slightly decreased $H_20_2$-mediated killing, arguing that increased killing of spxB mutants is not due to toxic by-products resulting from the reaction of excess pyruvate and $H_20_2$. Together, this suggested that a product of SpxB activity other than $H_20_2$ acts to increase resistance
  Furthermore, the ability of DF to eliminate the EPR signal caused by $OH^·$ in S. pneumoniae suggests that the inability of this iron chelator to increase $H_20_2$ resistance in S. pneumoniae is not merely due to a lack of permeability.

In the end, what I'd conclude is that different bacteria adopt different mechanisms to tackle this problem, and many of those mechanisms aren't known yet. So, there's no definite or exact answer to this question.

References:

ROS production in marine microalgae
NADPH oxidase
Activation of the OxyR Transcription factor by Reversible Disulfide Bond formation
Obligate Anaerobe
Catalase
Superoxide Dismutase
Iron Metabolism: From Molecular Mechanisms to Clinical Consequences - Robert Crichton
Oxygen metabolism of catalase-negative and catalase-positive strains of Lactobacillus plantarum.
Factors Contributing to Hydrogen Peroxide Resistance in Streptococcus pneumoniae Include Pyruvate Oxidase (SpxB) and Avoidance of the Toxic Effects of the Fenton Reaction


Can someone identify the species of this angiosperm?

This is a difficult one to identify down to the species from the photos. It very much looks like a member of the genus Ononis in the pea family. The leaves, flowers, and seed pods are all characteristic of Ononis. It might be Ononis spinosa, but that is a guess.  The bright sunlight make it difficult to discern many morphological details. I can't see any visible spines on the plant to be certain. Links provided:

https://en.wikipedia.org/wiki/Ononis

https://en.wikipedia.org/wiki/Ononis_spinosa


I found out the picture that I posted belongs to  Furcraea foetida 'Mediopicta'. It belongs to "Agave" family like L.Diago suggested in comments.


On which amino-acids residue is the SDS acting on?

If your talking about Sodium Dodecyl Sulfate(a detergent) it has a two main functions:

(1) It disrupts all non-covalents bonds in proteins i.e hydrogen bonds from the main chain, or hydrogen bonds between residues which are dependent on protein shape.

(2) It coats the proteins with a negative charge which is useful for laboratory techniques such as gel electrophoresis.

Your question states "what amino acid residues does it act on?". You can be safe to assume that the SDS will coat the entire protein. About 0.1% SDS solution is enough to sature the polypetide chains of protein molcules with about one SDS molecule per two amino acid residues.


How to identify a coiled coil from the amino acid sequence?

The heptad repeat, denoted [abcdefg]n, typically has hydrophobic residues at a and d, and polar/charged residues at e and g.

From here.

There is a prediction tool with useful images here.


Is Mutation Theory still "valid" for complex organisms?

Change in genetic variance

  From what I have been taught, Natural Selection (or even Artificial Selection) is great for panning favorable genes from a species and bringing them to the fore, however, it does not introduce new genetic changes.

Yes, you are pretty much right. In a given population, directional selection will ultimately reduce genetic variance (Natural Selection selects for a few variants letting the other variants disappear and therefore diminishing the genetic variance) while mutations bring variance back to the population on which further selection can occur.

To go slightly further (but without developing this part too much): Genetic drift decrease genetic variance (on average). Balancing selection (such as negative frequency-dependent selection or spatially heterogeneous selection for examples) help to retain variation (but never create more variation) in comparison to what genetic drift alone would do. Different kind of spatial population structure also affect patterns of genetic variation. The important point to understand is that in an isolated population, mutation is the only process that can create new variants.

Mutations in multicellular organisms - Somatic vs. Germaline mutations

You seem to call complex organism what we usually call multicellular organisms. You are very right that some mutations might be passed on while others won't.

As you said, a mutation occurring in the left leg will never be found in your gametes. We call such mutations that can't be passed on somatic mutations. On the other hand, mutations that can be passed on are called germline mutations. Of course, in unicellular individuals, all mutations are germline mutations.

  [..] aren't those already rare mutations only passed onto offspring if they occur in the short-lived sperm or egg cells of one of the parents

Germline mutations are not only mutations that occur in the eggs or the spermatozoids (egg and spermatozoids are called gametes). Germline mutations are any mutation within the lineage of the gametes. For example, a mutation that occurs during mitosis during the morula phase on the right cell is also a germline mutation. A mutation that occurs in the testis during the division of a cell type Ad spermatogomium to give rise to another type Ad spermatogomium and a type Ap spermatogomium is also a germline mutation (see figure at the bottom of this answer and see the Age-specific mutation rate section). There are therefore tons of divisions during which germline mutations can occur in big multicellular organisms, while (germline) mutations can occur during only the single cellular division in unicellular organisms.

How many new mutations do humans passed on to their offsprings?

Generally speaking, the germline mutation rate per nucleotide is around $10^{-8} \text{or } 10^{-9}$ but don't consider this value too much as the per nucleotide mutation rate varies a lot between species and especially between different genomic regions. FYI, the haploid human genome (just to consider an example) consists of about 3 billion ($3\cdot 10^9$) base pairs.

The number of new mutations per offspring in humans is a Poisson distribution with mean and variance of about 100 mutations (this estimate might be quite inaccurate). This is maybe more mutations that you may have expected.

Age-specific mutation rate

There are typically a lot of cellular divisions happening in the testes in order to produce the very important number of spermatozoids a male produces in his lifetime (See figure at the bottom of this answer and see spermatogonium). Mutations also occur during those divisions and therefore we observe a correlation between the age of the father and the number of new mutations transmitted to the offspring. Hong et al. (2012) suggest using the following formula. The number of new mutations transmitted to the offspring by the father in humans is equal to $25 + 2(g-20)$, where $g$ is the age of the father. Of course, this is just a formula that matches quite well the observations but has no theoretical meaning. This formula applies only to males that are older than 20 years old.

Drake's rule

Empirical observations show that the higher is the number of base pairs $n$, the lower is the per-base-pair mutation rate $\mu$. This correlation between $n$ and $\mu$ is roughly linear with a slope of about 1. In other words, the genome-wide mutation rate $U = \mu \cdot n$ is more or less constant in all species. This correlation is referred to as Drake's rule and again, it is a rough approximation of a more complex reality.

Sexual reproduction vs Asexual reproduction

I am not exactly sure why you are talking about sexual reproduction in your post. Note that the mutation rate during meiosis (a process that occurs during sexual reproduction) is much higher than the mutation during mitosis.

Mutational effects

The mutation effect is the effect of a given new germline mutation. Of course, not all mutations have the same effect and there is, therefore, a distribution of mutational effects. Most recent studies (often mutation accumulation experiments) tend to show that a highly skewed gamma distribution (the negative exponential distribution is a special case of the gamma distribution) is a good fit to model the distribution of mutational effects of either beneficial or deleterious mutations. So the whole distribution of mutational effects is estimated to be best modeled by a gamma distribution for the beneficial mutations and a reversed gamma distribution for the deleterious mutations put side by side (where the density probability of having a perfectly neutral mutation is at the intersection of the two gamma distributions). The exact parameters for those distributions are likely to vary depending on the species but most likely depending on the exact stretch of DNA under consideration. Different papers offer different estimates (the work of P. Keightley on the subject is particularly influential). You might want to have a look at this answer for a summary of empirical data on mutational effects... The two gamma distributions need to be rescaled to make sure that the whole thing sums up to one and I don't know of any paper that suggest actual parameters for this rescaling.

Probability of fixation

Fixation is the event of a given allele (=variant of a gene) to reach a frequency of 1 in the population. In other, one allele is fixed, whenever at the locus (=genomic region of arbitrary size) under consideration is not polymorphic anymore in the population. The probability of fixation of a given mutation is a very important statistic. Let's call $s$ the mutation effect (if $s>0$, the mutation is beneficial). The probability of fixation of a neutral mutation given the population size is $P(s=0 | N) = \frac{1}{2N}$ (assuming a diplontic life-cycle) as it can be demonstrated from Coalescent theory, Wright-Fisher model of genetic drift or Moran (birth-death) model. The probability of fixation of a beneficial mutation is higher, while the probability of fixation of a deleterious mutation is lower. Those probabilities can be estimated with different techniques that use different assumptions: Haldane's technic (assuming that the number of offspring follows a Poisson distribution), Kimura's technic (using diffusion equations), Birth-death models, etc... Some methods assume small values of $s$, some others assume that $2Ns >> 1$, etc..

Number of new mutations in the population and rate of neutral substitution

If the genome-wide mutation rate for neutral mutations is $U_n$ and the population size is $N$, then there is a Poisson distribution of the number of new mutations at each generation with mean and variance $2 \cdot U_n \cdot N$ (assuming a diplontic life-cycle). Because each one of these mutations has a probability $\frac{1}{2N}$ to get fixed, the rate of neutral substitution in this population is $\frac{1}{2N}\cdot 2 U_n N = U_n$. Therefore, the rate of neutral substitution is a function of the genome-wide neutral mutation rate only. This classic result is used in estimating time since the last divergence between sister lineages (molecular clock)

Did you say Mutation Theory?

I have never heard of Mutation Theory. I am pretty sure Mutation Theory is NOT an existing concept (but the question is clear).

Spermatogonium figure


Immunogenicity is

  the ability of a particular substance, such as an antigen or epitope, to provoke an immune response in the body of a human or animal. In other words, immunogenecity is the ability to induce a humoral or/and cell mediated immune response.

If a protein is highly conserved between species it means that its epitopes will be recognised as self by most species, hence the organism will avoid producing antibodies against them to prevent autoimmunity.

You may want to read about central tolerance to see how T cells and B cells are rendered non-reactive to self.


Are there known minimal marine ecosystems that are stable?

This is the one I've heard of - Its a sealed acrylic globe that contains algae and brine shrimp.  There are quite a few references in the bibliography here to previous systems.
Of course, it needs sunlight, but all the elements are recycled.  Its really closed and has reasonable endurance.

The basic commercial version of his closed world -- sold under the label of "Ecosphere" -- is a glass globe about the size of a large grapefruit. My world #58262 was one of these. Completely sealed inside the transparent ball were four tiny brine shrimp, a feathery mass of meadowgreen algae draped on a twig of coral, and microbes in the invisible millions. A bit of sand sat on the bottom. No air, water, or any other material entered or exited the globe. The thing ate only sunlight.
The oldest living Hanson-world so far is ten years old; that's as long as they have been manufactured. That's surprising since the average life-span of the shrimp swimming inside was thought to be about five years. Getting them to reproduce in their closed world has been problematic, although researchers know of no reason why they could not go on replicating forever. Individual shrimp and algae cells die, of course. What "lives forever" is the collective life, the aggregate life of a community.

All of this is a real subject of research for those interested in creating entirely useful ecosystems.

It turns out that ecospheres scale up well. A huge commercial Ecosphere can weigh in at 200 liters. That's about the volume of a large garbage can -- so big you can't reach your arms around it. Inside a stunning 30-inch-diameter glass globe, shrimp paddle between fronds of algae. But instead of the usual three or four spore-eating shrimp, the giant Ecosphere holds 3,000. It's a tiny moon with its own inhabitants. Here, the law of large numbers takes hold; more is different. More individual lives make the ecosystem more resilient. The larger an Ecosphere is, the longer it takes to stabilize, and the harder it is to kill it. But once in gear, the collective give and take of a vivisystem takes root and persists.

Unfortunately larger systems that can support people have not been made yet.

Algae and man lasted a whole day. For about 24 hours, man breathed into algae and algae breathed into man. Then the staleness of the air drove Shepelev out. The oxygen content initially produced by the algae plummeted rapidly by the close of the first day. In the final hour when Shepelev cracked open the sealed door to clamber out, his colleagues were bowled over by the revolting stench in his cabin. Carbon dioxide and oxygen had traded harmoniously, but other gases, such as methane, hydrogen sulfide, and ammonia, given off by algae and Shepelev himself, had gradually fouled the air. Like the mythological happy frog in slowly boiling water, Shepelev had not noticed the stink.

Here is an academic reference you can use to start looking around if you like...


How do chemists calculate the existence of billions of organisms?

It says a "a billion viable cells". The viable is important because it tells you that they employ a method that determines whether the cells are alive or dead. Most likely they did a simple colony count.

The approach is simple, you take bacteria in suspension, serially dilute them in order to reduce the concentration to numbers that can be counted, and then spread onto a solid media plate (usually containing agar) and leave for 1-3 days (depending on organism) and count the number of colonies produced. You can then multiply up this number by the amount you diluted by to get the number of viable cells present in the original.

A billion is not a lot of bacteria. You can expect 100-1000 billion cells per ml in an overnight culture of these bacteria.

Looking at the product description, it specifically mentions CFUs (colony forming units) so I think we can be pretty sure that this is the approach they are using.

(Note that this is standard microbiological technique rather than something chemists would be doing)


Based on fine scale mapping of human genome structural variation, which is expanded on here, according to this study, the amount of genome structural (nucleotide diversity) ranges from 0.1% to 0.4% (look under section "Fine-scale map of human genome structural variation"). Hence humans have an up to 99.9% nucleotide similarity. And according to this study the average proportion of nucleotide differences between a randomly chosen pair of humans (i.e., average nucleotide diversity, or pi) is consistently estimated to lie between 1 in 1000 and 1 in 1500.


Because the "Y chromosome" has nothing to do with sex determination in bees.  Instead, the number of X chromosomes determines the sex.  With only one X chromosome, the egg will develop into a male.  This is called a haplodiploid system of sex determination (the male bees are haploid, having only half the number of chromosomes).

EDIT: I should add that there are many systems of sex determination, not just XY or the haplodiploid system.  See the Z-W system (males are ZZ and females are ZW), the X0 system (the males are diploid for all but the sex chromosome), and temperature-dependent system of sex determination.


Ribosomal RNA (rRNA) genes are shared among all living organisms, including lineages that have diverged from one-another well before a billion years. Bacteria, Archaea, and Eukaryotes diverged over 3 billion years ago, and their rRNAs are virtually identical to one-another. http://www.biologyreference.com/Ar-Bi/Archaea.html
Any genes that are shared between plants, animals and fungi would also be over a billion years old.


The brain and also the erythrocytes need glucose to survive.
Gluconeogenesis is one of the possibilities of the body to keep the glucose levels stable and to avoid hypoglycemia. The precursors needed come from amino acid and lipid metabolism, and is turned on, when the body has no energy sources available which can release glucose, like carbohydrates in the food or the degradation of glycogen.

As you said, it comes at a price, making glucose itself costs a lot of energy. This process is available to maintain the level of glucose, which shows the importance of it.


Chance should always be high on our list of explanations of why the history of life turned out in some specific way. As James A. Coffman has described, there are a couple of different notions of chance. Evolutionary biochemistry is quite difficult because today's diversity of biochemical genotypes and phenotypes are a biased representation of the ancient past.

However, I think a case can be made that it was not 'pure' chance.

As your question itself suggests, the chemistry requires alcohols for the esterification with fatty acids to form acyl glycerols. I think that is 'sufficient' to say it is not 'pure' chance that among molecules that it was glycerol, but since you're also questioning "why glycerol?" over other alcohols, let's look at what glycerol has going for it compared to other alcohols.

Glycerol is relatively small. All else being equal, fulfilling a biological function with a smaller molecule requires less energy than larger ones. Compared to polyphenols, for example, this is a no-brainer because (1) building polyphenol would be expensive energetically, and (2) would be difficult to transport.
Glycerol is flexible. The two outer alcohols have the ability to move with respect to the central carbon so that as we go from glycerol to mono-acylglycerol, di-acylglycerol, and finally triacylglycerol, the outer groups' motion can reduce steric hinderance.
Glycerol can be converted into a lot of other things that form a part of metabolism. While it is conceivable that an extremely different metabolism without glycerol could have come to be, the fact that glycerol is directly and indirectly convertable into a large number of molecules with structural and energetic functions does give it better candidacy than molecules that are relatively unreactive or require large numbers of reactions to build anything useful biologically.
While glycerol doesn't have the greatest number of alcohol groups for its size (size in terms of carbon backbone, not necessarily molecular weight), it doesn't have the least number either. Steric hinderance or difficulty to synthesize of alcohols with the same size would make glycerol a better choice.

Hopefully that convinces you that glycerol was not completely random with respect to all other molecules or even all other alcohols. That is, not all the possibilities in those sets are equally good for the biochemical role that we now see glycerol fulfilling, and glycerol is defintely not the worst. However, there may have been other subsets of alcohols/molecules in existence at that time for which we don't have specific reasons for glycerol being better.

In conclusion, no, not 'purely' random.

UPDATE

Reading my answer above, I can see why someone reading my list of glycerol traits may think I am making a just so story on why it is specifically glycerol that we have today fulfilling a biochemical role of joining together fatty acids via acylation. To be clear, I am not addressing 'why' glycerol is the molecule fulfilling this role but rather whether it is purely random that glycerol is the molecule fulfilling this role. In my vernacular, 'purely random' implies a uniform probability distribution, which is to say that in this context each molecule was as likely as any other to fulfill the role that we see glycerol fulfilling in biochemical systems today. By citing reasons why some molecules are better suited in their properties, we show that the distribution cannot be uniform. We don't need to even place where glycerol sits on this distribution to determine that it is not purely random. We only need non-uniformity. The fact that glycerol has traits that make it more likely than others is an additional suggestion that among the molecules under consideration, glycerol was not the least likely.


Non-coding DNA as a protection to deleterious mutations

You seem to be under the impression that there are a set number mutations per cell, which is not true.  The number of mutations is roughly proportional to the number of bases  — this is because mutations typically happen as a result of errors during DNA replication .1  Consequently, more DNA will not protect the coding portions of the genome from mutation.

The reason why mutations appear to be suppressed in coding regions is due to selection.2

References:
1: Lodish, H., Berk, A., Zipursky, S. L., Matsudaira, P., Baltimore, D., & Darnell, J. (2000). Molecular cell biology 4th edition. National Center for Biotechnology Information, Bookshelf.

2: Griffiths, A.J.F., Gelbart, W.M., Miller, J.H. and Lewontin, R.C. (1990) The Molecular Basis of Mutation. In: Modern Genetic Analysis. W.H. Freeman and Company, New York.


What is the fibre axis in the Watson and Crick paper?

Short answer:
The term fiber axis is not in reference to the DNA model, it comes from the experiments that Watson and Crick referenced to guess their model (performed by Rosalind Franklin).   The fiber axis is the direction along the DNA strand.

Longer:

Watson and Crick created their model of DNA based on the esoteric experiment called X-ray fiber diffraction.  To collect fiber diffraction data ( gathered by Rosalind Franklin actually) DNA is pulled out of a cell lysate and washed with buffer.  It looks like a clear, liquid, string of snot (a technical term that is).  Its stringy though because the long DNA molecules pull out and create viscous fluid where the DNA is pulled along the length of the snot fiber.  Because the DNA is ordered in this one dimension, if you shoot a beam of X-rays through it, it creates a pattern on film that looks like this:

As you can see its got a nice X-shaped pattern.  The DNA in the fiber is mostly aligned along the fiber, in the up and down direction.  Because this is so, the spacings between the different layers is due to the spacings between the DNA bases and the x-pattern comes from the fact that DNA forms a double helix.

Some misc details - you have to use X-rays because their wavelength is about the size of an atomic bond and this is the scale of model Watson and Crick and Franklin and Wilkinson were trying to find.

The fiber axis is along the y axis (top to bottom) because the trail of DNA snot hangs down - it will sag if you hold it an angle.

Rosalind Franklin was a great experimentalist and she realized that the DNA snot trail dries out over time as the experiment would go on for days.  She set up a moist stream of hydrogen gas blowing over the DNA strand during the X-ray experiment and so was the only experimentalist who obtained what we now know to be the true result - double helical DNA.  As it dries out, DNA interconverts to the Z-DNA form I believe, which does not have the x-pattern and also confuses things because the result is a smear of the DNA helix converting from one form to another.

Francis Crick had actually predicted the X-pattern for helices.  The structure actually required these two to come together to get the answer while the American genius Linus Pauling was working hard in California on the structure as well and would have won too if he understood how to keep his snot properly damp.

The reference for nearly all of this is Watson's somewhat self-centered but historically accurate book "The Double Helix".

After some surprisingly difficult Googling, I can't found a picture of DNA fiber... picture below. You can make some yourself from the protocol listed here and some saliva, soap and other common household items.


Please allow me to start by saying I know nothing about LEDs, so my answer isn't going to address your analogy. I'm also going to keep it more simple.

  Can the retina emit light?

Yes. The retina is able to give off light in the form of fluorescence. Since fluorescence is the emission of light by a substance (granted that substance must first absorbed light or other electromagnetic radiation of a different wavelength.)

  “We can use autofluorescence emission to image the retina and see certain features of it,” said Dr. Sparrow, the Anthony Donn Professor of Ophthalmic Science in the departments of Ophthalmology, and Pathology & Cell Biology. ...Most objects in the environment are visible because they reflect, as opposed to emit, light. However, the retina—which exists within the eye’s back wall, known as the fundus—can generate its own fluorescence.

The cells of the deepest layer of the retina, called the retinal pigment epithelium (RPE), contain fluorescent compounds, which when excited by blue light emit a yellow fluorescence.

This ability changes with age, disease, etc.

  Excessive accumulation of lipofuscin granules in the lysosomal compartment of retinal pigment epithelium cells represents a common downstream pathogenetic pathway in various hereditary and complex retinal diseases, including age-related macular degeneration.

Lipofuscin is one of several fluorophores in the RPE. Different fluorophores may be related to different damage to the eye.

  A major hydrophobic component of RPE lipofuscin is the fluorophore A2E... Given that A2E strongly absorbs in the blue region of the spectrum, together with the known susceptibility of RPE to blue light damage, we undertook to investigate A2E as a fluorophore involved in blue light toxicity.

Science Insight: Using the Retina’s Natural Fluorescent Light to Measure and Treat Disease
FUNDUS AUTOFLUORESCENCE IMAGING: Review and Perspectives
The Lipofuscin Fluorophore A2E Mediates Blue Light–Induced Damage to Retinal Pigmented Epithelial Cells


Determination of a chemical compound in a non-homogeneous sample

You should not actually homogenize samples because histamine works locally. If you know which region is releasing histamine then you can just study those regions. You can actually create a transgenic fish with GFP that is a target of histamine receptor signaling.

Using mathematical models or statistical correlations you can obtain the level of histamine based on fluorescence.

Activated histamine receptor H1 causes production of inositol triphosphate (IP3) which in turn causes release of calcium form ER. You can use Cameleon-GFP to sense the change in calcium levels. However, there are many events that may result in calcium release; you should carefully design your experiment.

This is another possibility (just a guess)- a FRET based study using GFP-YFP FRET Pairs (or other variants). Since histamine receptors are G-protein coupled receptors you may fuse the GFP to alpha subunit and YFP to beta subunit. When upon signaling, the subunits dissociate, you would see a decrease in FRET.


I would suggest looking more into karyotype nomenclature; it is admittedly a bit odd. Here is one related question/answer that puts it in context.
I haven't looked at the paper in detail but generally what it means is that there is some cytologically relevant big chunk of chromosome that is missing that roughly overlaps with the chunk of chromosome that we find at band 21 of chromosome 21 (not position 21). Note that these cytobands/karyotype/G bands visible in a chromosome spread under a microscope, so these are quite large deletions.
Looking at the paper methods, it is clear that in 2/3 cases they confirmed the deletions by looking at karyotype data (FISH/chromosome spreads):

For Case 2, CNV confirmation and parental studies were performed by metaphasic and interphasic FISH on leucocytes using BAC RP11-43A6 (chr21:18,414,905e18,567,253, hg19 build). For Case 3, CNV confirmation was performed by G-banded karyotype. Parental studies were not available.

The terminology is quite outdated now as usually we are looking at sequence data these days, which has much higher resolution, but a lot of the stereotypical chromosomal abnormalities still carry these confusing names. And seeing it on a chromosome under a microscope is still the gold standard for these large chromosomal events.


293T safety, transfections with plasmid DNA

293T cells do incorporate partial virus genomes, consisting of about 4000 bases (about 11%, if I remember right) of the adenovirus type 5 genome (Cloning and Sequencing of the Cellular–Viral Junctions from the Human Adenovirus Type 5 Transformed 293 Cell Line).

This amount of DNA is not enough to make a viable virus; it lacks all the structural components of the capsid, for example.

293T cells also include the SV40 Large T antigen, another viral gene. Again, this is not enough to make a replicating virus.

Therefore these cells don't pose any human health hazard aside from the normal almost entirely theoretical risk associated with any transformed human cell line (actually considerably less, since these were never tumor cells but were transformed in the lab, so they have no intrinsic adaptations to replication in humans, unlike say HeLa cells -- which are also demonstrably safe).

293 cells have been continuously cultured in thousands or tens of thousands of labs for over 40 years, and I'm not aware of any safety incidents associated with them.  Of course, you should always handle cultured cells with appropriate precautions and protective wear, but these are not a specific concern.


Yes, the parietal pleura is on the wall of the thorax. That picture isn't great.  Each lung has its own pleural cavity, ie its own visceral+parietal.  Another important thing is the folding over.  Imagine the parietal pleura running along the inside of the ribcage...when it gets to the middle of the chest (the mediastinum), it folds over, or "turns the corner", and is now the visceral pleural running along the surface of the lungs.  The pericardium functions similarly, and so does the peritoneum/mesentery.  Here's another diagram that could help:


Actually, the animal is not a caterpillar but larva.

The species is Abia lonicerae Sawfly, discovered by Linnaeus 1758.

(Another picture)


This is an interesting question with good comments. I did medical school, and I am here on unix.se, so let me give some thoughts:

The central nervous system consists of "gray" and "white" matter. In the spinal chord you have this gray butterfly shape, in the neocortex it is "gray matter" (neuron's cell body) and "white matter" (neuron's myelinated axons).

There is no room for a "pool of glia cells" - from tip to tail all the neurons and their axons are highly organised.

Now the brain is already complicated. It is divided into 5 segments, and the Thalamus is quite in the center of everything. Some other nuclei (e.g. the ones connected with the 12 head nerves) have a well defined function, but the Thalamus is hard to define.

The famous "limbic system" is close by, and is also complex.

A high resolution MRI should give a good estimate of neuron/myelin distribution, to the millimeter.  But I am afraid it is not an easy gray-or-white question, but some complicated arrangement, with e.g. short unmyelinated axons.

(The MRIs can look very different)

It is even worse than I thought: this histologic picture shows how hard you have to look to even define a nucleus.

Thalamus Nissl stained

"thalamus histology" give very nice results in google. In the MRIs you can mostly just see that it is something a bit in between gray and white.

First I checked Nissl stain: this really colors neurons (body and dendrites), but not axons.

The stain is labeled "myelin-nissl", and it is blue and magenta, so this must be a combination. But -- I can't even tell which is which!

Well it must be pink is neurons, and thus blue is myelin. This makes sense with the Cn A = cornu ammonis = hippocampus region bottom right, the pink-white spiral, and with the outlining of nuclei. But very counter-intuitive...I trust them it is the appropriate stain.

Keep in mind this is a section to show the nuclei (at their max?), so other parts/sections will look quite different.


How deep in the soil can a seed be placed and still develop into a plant/tree?

The general mathematical relationship requires an allometric equation. There are not as many for seedlings as there are for mature trees (but see the answer by @Richard-smith for a specific example). But lets start with a basic assumption that the emerging seedling will be a very tall cone (tall = high h to r ratio).

The volume of a cone is:

  $V = \frac{1}{3} \pi r^2h$

Then we need to know the density of the seedling to figure out how much carbon a seedling of height h would require. Lets say that the density is 1.5 g/cc (excluding water).

Then, assume that the biomass is 1/2 carbon (a fairly reasonable assumption).

To figure out how tall a seed could grow given carbon reserves, it would be necessary to determine the amount of carbon in storage in the seed. Say there were 5 grams. There will be a carbon cost of reallocating this to growth, say 50%. So, for a seed that has 5g of carbon, its total volume might be calculated as:

 (5g * 50% growth respiration)/(50% C content of biomass) * 1.5 g/cc = 7.5 cc

assuming that the seedling will have a radius of 0.2 cm, the height could be calculated as:

  $h = \frac{V}{(3 \pi * 0.2^2)}
    = \frac{V}{0.38}$
          = 20 cm (for V = 7.5)

Note: this is just a very quick "back of the envelope" calculation with many assumptions. C is 50% of plant biomass is pretty close (the actually number is closer to 48%). The growth respiration cost is a very rough estimate, and will vary with nitrogen content of the tissue, soil temperature, and etc.. The plant will likely need carbon left to build a leaf, and another resource may be limiting.


What exothermic reaction distinguishes warm blooded animals?

Brown adipose tissue or brown fat is one of the primary ways of generating body heat, and it is only found in warm-blooded animals. It is brown due to the high numbers of mitochondria, and heat is generated by uncoupling the electron transport chain from ATP synthesis by oxidative phosphorylation.

In the typical (ATP-producing) mitochondria, an energy gradient is formed by storing protons within the inter-membrane space, and these then flow through the ATP synthase to power the generation of ATP from ADP and phosphate. In brown fat mitochondria, Uncoupling Protein 1 (UCP1 or thermogenin) forms a pore in the inner membrane, allowing the proton/electron ratio to reach equilibrium and robbing ATP synthase of its motive power. This is what generates the heat.

From Wikipedia


What specific sensory nerves act as receptors for "pins and needles" (neuropathy)?

Pins-and-needles (PAN) sensation and pain stem from the same nerves. The pathophysiologic process is different, though. PAN is characteristic of nerve lesion, and is therefore a pathologic reaction. Pain is a physiologic reaction to a stimulus perceived as ominous.
Pathophysiologically speaking, the PAN sensation is a distortion in somatosensory stimulus processing due to injury to peripheral nerves.
Of course, the PAN sensation will stem from somatosensory nerves. Pure motor nerves will not cause such a sensation.


How do signal transduction pathways utilize transcription factors to express a specific gene?

This is a combination of multiple regulatory systems. Most genes are not regulated by a single factor, but by many. Moreover in eukaryotic organisms there is also epigenetic, which "inactivates" permanently certain areas of the genome by compacting these zones forming heterochromatin.

Moreover, even when we are interested in a single function a TF might have, that does not mean that it only has this function in the cell. We view it as humans, and maybe for us it is logical that a response to a high metabolite in the environment simply leads to expressing the protein that metabolizes it. However, probably it is interesting for the cell to also activate other pathways and gene networks (i.e. anabolic pathways that feed off this metabolite, compensatory pathways to mantain homeostasis...). Because that normally TFs affect more than one gene naturally.

The mechanisms of action of the TFs are multiple, but they tend to simply allow or deny the access to the adequate RNA polymerase. For more information about this check the wikipedia article on TF structure

In this image we see a typical mechanism of action, DNA bending

Different domains interact in activating a gene, enhancers which are usually long distance, promoters which tend to be in the upstream region, though they can be downstream or in the gene sequence, and epigenetic factors that change the compaction of DNA, making it inaccessible to proteins.

Just as a last thing to point out, you should acknowledge that the biological systems are far from exact and yes, a single TF might activate 200 genes, even when its main objective in that moment is to activate one, but it won't really matter as long as the those 199 activated genes express at a very low rate (for example by not having the right RNA polymerase subunit accessible, being marked as inactive by epigenetic systems or having their own inhibitors).


There is this "Controlled vocabulary for /mol_type qualifier" page created by the International Nucleotide Sequence Database Collaboration in 2013.  It says the allowed values are:

  "genomic DNA", "genomic RNA", "mRNA", "tRNA", "rRNA", "other RNA", "other DNA", "transcribed RNA", "viral cRNA", "unassigned DNA", "unassigned RNA"

I found this as the second result of a Google search on moltype vocabulary.


Can a mathematical function be assigned to ECG diagram?


It is a species of Carpobrotus, probably Carpobrotus edulis. However, after looking online, several of the Carpobrotus species look very similar. It is an invasive species in the Mediterranean region. See the Wikipedia link.

https://en.wikipedia.org/wiki/Carpobrotus#Species


Why does the mixture of infant formula with saliva provide an ideal breeding ground for disease-causing micro-organisms?

Doesn't Saliva contain anti-bacterial properties?

Yes, in particular some IgA antibodies and lysozyme, but there are also plenty, and I mean plenty of bacteria in your mouth at any given point; we do, after all, still have to brush our teeth!  In fact, animal (including human) bites should be treated lest they lead to sepsis.  Those bacteria would love all the magnificent nutrients in infant formula.  Contact with an infant's mouth will introduce bacteria to the formula, as will exposure to air, contact with your hand, and anything else it experiences.  As an example, in the past few years, there have been some cases (from China, I believe, someone correct me if I'm wrong) of formula contaminated with bacteria, which were more than happy to stick around.


What species is this blue and white bird?

The bird in the photo appears to be a white faced "variety" of Lovebird - Genus Agapornis - mainly identified by beak and nares not being visible (cere skin and nostrils not visible). The exact species is uncertain due to ease of hybridization between species and the availability of many color varieties.  The links below may be of further help.

https://en.wikipedia.org/wiki/Lovebird#Species

https://www.agapornidenclub.be/eng/?page_id=2