How did the largest/longest dinosaurs hold their head and necks up?

There are lots of papers on this. A good summary article is Why sauropods had long necks; and why giraffes have short necks, by Taylor and Wedel.  They list a number of anatomical features that allowed sauropods to support such long necks:

  Several anatomical features enabled this extreme elongation, including: absolutely large body size and quadrupedal stance providing a stable platform for a long neck; a small, light head that did not orally process food; cervical vertebrae that were both numerous and individually elongate; an efficient air-sac-based respiratory system; and distinctive cervical architecture. Relevant features of sauropod cervical vertebrae include: pneumatic chambers that enabled the bone to be positioned in a mechanically efficient way within the envelope; and muscular attachments of varying importance to the neural spines, epipophyses and cervical ribs.

Let's take these one by one.

A stable platform for a long neck. Large, heavy quadrupedal bodies, so the long neck didn't unbalance the animal when it stretched out.
"A small, light head." Sauropods didn't chew their food, so didn't need large muscles or heavy bones in their head, so they didn't have a heavy weight at the far end of the long neck.
Numerous small, elongate cervical verterbrae. Sauropods had 12-19 vertebrae in their necks. By contrast, giraffes have seven, each of which needs to be large and heavy, limiting how long the neck can be.
Efficient respiratory system. Sauropods, like modern dinosaurs (birds) have a more efficient respiratory system than mammals, so they could tolerate the inefficiency of a long trachea.
Pneumaticity of cervical vertebrae Sauropod vertebrae had air sacs (i.e. hollow pockets of air) in them, making them much lighter than mammalian vertebrae of the same size and strength.

Edit to add Figure 4 from Taylor & Wedel, illustrating how relatively light sauropod necks must have been for their size:

  Figure 4: Extent of soft tissue on ostrich and sauropod necks.
  1, Ostrich neck in cross section from Wedel (2003, figure 2). Bone is white, air-spaces are black, and soft tissue is grey. 2, Hypothetical sauropod neck with similarly proportioned soft-tissue. (Diplodocus vertebra silhouette modified from Paul, 1997, figure 4A). The extent of soft tissue depicted greatly exceeds that shown in any published life restoration of a sauropod, and is unrealistic. 3, More realistic sauropod neck. It is not that the soft-tissue is reduced but that the vertebra within is enlarged, and mass is reduced by extensive pneumaticity in both the bone and the soft-tissue.

Muscular attachments.  This is the aspect that most directly answers the original question, but it's first important to understand that other sauropod features as noted above allowed them to get away with less neck strength than you'd otherwise expect.  In fact sauropod necks were much less (relatively) muscled than, say, ostriches. They got away with this by improving mechanical advantage:

  In effect, sauropods inflated their vertebrae within the muscular envelope of the neck, moving the bone, muscle and ligament away from the centre so that they acted with greater mechanical advantage: higher epaxial tension members, lower hypaxial compression members, and more laterally positioned paraxials.

Taylor and Wedel go into this in much more detail, with many helpful diagrams, and the paper is open-access, so I won't repeat all their points here. They talk about neural spines, epipophyses, cervical ribs, and muscle attachments in various combinations.

The cervical ribs are easily visible on the Patagotitan skeleton image in the question:

There's a long description of cervical rib anatomy and possible functions here:

  My favorite hypothesis is that long tendons allow an animal to shift the bulk of the muscle–and therefore the center of gravity–toward the base of the neck, but that long unossified tendons can be distorted through stretching, which wastes muscular energy. Ossifying those long tendons is like putting bony wheelbarrow handles on each vertebra, allowing the muscles to move the vertebra from a distance without so much wasted energy, and probably with finer positional control.

That's just one aspect of the way sauropod necks were structured.

TL;DR: Sauropod necks could afford to be relatively light, because of the small head; their neck bones tended to be relatively hollow and light for their size; their scale and shapes meant that muscles had good mechanical advantage; and different species had other adaptations including ligaments and stiffening bones that also helped.


What is the significance of the amplitude of brain waves?

Brain waves are a colloquial term for EEG recordings. EEG recordings are gross potential recordings, in other words, they represent the responses of thousands of neurons together. Much of the background is stochastically determined, meaning it represents, basically, random activity. In other words, oftentimes neurons fire stochastically and they cancel out each others contribution to the EEG, resulting in random ('white') noise.

However, certain parts of the brain do exhibit synchronized activity in certain frequency bands (Fig. 1). Oftentimes a time-to-frequency analysis is necessary to visualize these activities, e.g. by FFT. Certain stages of sleep, most notably slow-wave deep sleep, is characterized by gross synchronized, slow-wave activities across the cortex, showing up in the raw EEG. In fact, simply closing ones eyes has marked effects on the cortical synchronization on the raw EEG. This is caused by the fact that certain swaths of the cortex become synchronized, resulting in more clear responses.

In general, to come to your question, gross potential recordings like EEG thus are plagued by background noise. Synchronized activity increases the amplitude of brain waves and hence increases their amplitude. Amplitude is hence directly related to the level of synchronization. This shows up as larger peaks on the FFT.

What synchronization exactly does to the brain boils down to down to is the classic interpretation of EEG frequency bands (Table 1).

Fig. 1. EEG waves. source: Neurosky

Table 1. EEG frequency bands and their associated mental state. source: Liang et al. (2016)

Reference
- Liang et al., J Sensors (2016), 1831742


Open-access medical images:

MedPix (by keyword, organic system, pathology and diagnosis A-Z)
Radiopaedia (by keyword)
PEIR Radiology (by keyword, organ or anatomic region)
Ultrasound Cases (by keyword and organic system)
Open Access Biomedical Image Search Engine (Openi) (by keyword)
Wikimedia Commons (by keyword)
Google image search (using the filter "creative commons," "public domain" or "open access")
Google image search (using filters: black/white, noncommercial, photo)

More:

Gray's Anatomy
Dermatology Atlas


are the spontaneous generation and evolution the same idea but in a different time scale?

You are right in the sense the evolutionary biology doesn't try to explain the origin of life as it is not within its scope. Other fields of biology investigate the question of origin of life (abiogenesis).

Now, there is a very important difference between spontaneous generation and evolution. Life originated at some point and the through repetitive speciation events, created the whole diversity of species existing on earth. You could say that what really happens is that there was one spontaneous creation of life (although there is more a continuum from non-living to living things than a sudden switch from non-living to living) out of non-living things.

The main fallacy of spontaneous generation is that under the spontaneous-generation-conceptualization of life, every species are made de novo and independently which is definitely not the case as in reality species speciate (split in two) causing the existence of to two new species. There are tons of fallacies hidden behind the spontaneous generation conception of life, one of which relates to the concept of species and another one is the origin of within population variation.

So, in short spontaneous generation is definitely something different from a single abiogenesis and evolution and the hypothesis of spontaneous generation has been ruled out a long time ago already.

So I am not so much aware of the grading philosophy in your school but your argumentation was wrong and probably the F was worth. Next time, you will probably want to discuss your opinions with your teacher before the test to make sure you agree.


The relation of a schizophrenia drug side effect and caffeine intake

I used Google Scholar with the search terms of clozapine, caffeine.
I only found small scale studies, but they agree that it is likely that Clozapine levels are affected by caffeine intake.
To really understand the implications of this it would be necessary to research what the range of Clozapine levels actually are in patients and what the effective level is, as well as the levels that give side-effects.
Only then can the changes due to caffeine be seen to be significant or not
Example paper studying 12 volunteers below (full text available)
Hägg, S., Spigset, O., Mjörndal, T. and Dahlqvist, R. (2000), Effect of caffeine on clozapine pharmacokinetics in healthy volunteers. British Journal of Clinical Pharmacology, 49: 59-63.
https://doi.org/10.1046/j.1365-2125.2000.00111.x
Available at:
https://bpspubs.onlinelibrary.wiley.com/doi/full/10.1046/j.1365-2125.2000.00111.x


When collecting cell lysates for a Western blot, how do I induce di-sulfide bonds?

For the introduction of new cystine bonds, you will probably need to maintain an appropriate redox potential when dialyzing your cell-lysate to allow your cystine bonds to reform. To break the current di-sulfide bonds, we have been adding in Disulfide Bond Isomerases (DsBC to be precise) which will allow your lysate to get to an appropriate equilibrium.

As for examining for disulfide bond formation that has already occured between proteins in your lysate, removing reducing equivalents like DTT and beta-mercaptoethanol should do the trick. You can even denature your proteins by incubating them in LDS or Laemmli buffer at 90C as those components will not reduce your cystine bonds. In our experience the bands typically run at the expected molecular weight on a SDS-PAGE.


If it weren't for animals, insects, or people, would plants that produce seeds (nuts, fruit, etc) cease to exist?

No

Not all seeds need to be ingested in order to be spread from one place to the other, in fact some won't grow at all if eaten, some need the fruit to help them germinate and sprout after they hit the ground. Nuts simply will not grow at all if you crack them open.

Most plants rely on the wind to disperse their pollen and seed.

Dandelions are a prime example of a plant with wind carried seeds, their seeds can travel for hundreds of kilometres on parachutes before settling down and germinating in the ground, plenty of other weeds and plants go to seed the same way.

Cotton bearing trees produce their cotton so the wind can carry their seeds, like the Cottonwood and many species of Poplar tree.

One of the fun ones is helicopter seeds. Maples, elders and ash trees are among the species that disperse their seeds this way. The seeds will literally helicopter down, and fly great distances on the wind if it's strong enough. Even as an adult it's still fun to pick these seeds up of the ground and drop them just to watch them fly.

Some trees don't even need to go to seed in order to spread and multiply. Poplars are notorious for sending out suckers underground. Their roots systems spread out from the tree near to the surface and sprout suckers that will pop up out of the ground an grow into another tree. Other bushes and plants do this as well, like raspberry plants.

Not even all fruit is intended to be eaten, The fruit of the chestnut tree is sour, and covered in sharp spines that hurt. We used to spin them around and throw them at each other as kids imaging we were medieval warriors wielding maces. The spikes can get rather long and sharp, I've seen them stick to kids that have been hit by them, and after plucking them off they develop a golfball-sized welt covered in lots of tiny puncture marks.

Worst case scenario for plants that spread their seeds via burrs or by being ingested a pooped out elsewhere if animals were to suddenly cease to exist is that they wouldn't be able to disperse their seeds as far. They'd simply drop their seeds beside them, but they would continue to exist.


How is the fluoride in toothpaste absorbed?

The chemical mechanism by which fluoride protects teeth is the remineralization of hydroxyapatite $\ce{Ca5(PO4)3(OH)}$ in the tooth enamel into fluorapatite $\ce{Ca5(PO4)3F}$:

$$\ce{Ca5(PO4)3(OH) \ (s) + F- \ (aq) -> Ca5(PO4)3F \ (s) + OH- \ (aq)}$$

This reaction occurs at the surface of the enamel, i.e. directly within the mouth.  The fluoride ions participating in the reaction are dissolved in the saliva and other fluids present in the mouth.

Thus, the fluoride does not need to be absorbed into any part of the body (although, as part of the remineralization process, it can be said to be absorbed directly into the tooth enamel), and, in particular, there is no need for it to be swallowed.  Indeed, because of potential adverse effects of high levels of fluoride when absorbed into the body through the digestive tract, swallowing strongly fluoridated dental care products like toothpaste or mouthwash should be avoided.

That said, any fluoride that is swallowed and absorbed into the body, e.g. through fluoridated (or naturally fluoride-rich) drinking water, can still contribute to the remineralization of teeth, simply because some of it will be secreted back into the mouth as part of saliva.

While the fluoride levels in saliva (assuming a safe level of fluoride intake) are much lower than those in, say, toothpaste, your teeth will be constantly exposed to the fluoride in saliva, whereas they will only be exposed to toothpaste for a few minutes each day.  Thus, while the rate of remineralization due to systemic fluoride may be much slower than that due to e.g. fluoridated toothpaste, the total amount of remineralization per day may well be of a comparable magnitude.


Those are two mating "love bugs". Flies (Diptera) in the family Bibionidae. https://en.wikipedia.org/wiki/Lovebug


Insulin and monoclonal antibody production

I recommend that you take a look at this:

  Jeong KJ, Jang SH, Velmurugan N. (2011) Recombinant antibodies: engineering and production in yeast and bacterial hosts. Biotechnol J. 6:16-27.

This fairly recent view discusses the progress and prospects for producing functional antibodies in yeast and bacteria. As pointed out by @Nick in the comment to the OP, the main stumbling block in both cases is the engineering that would be necessary to ensure correct glycosylation in the heterologous expression systems. This quotation from the cited review sums up the situation:

  The N-linked glycan structure in the Fc region of antibodies is indispensible for binding to receptors (FcγRs), but glycosylation has been one of the major limitations in choosing possible production hosts. Eukaryotic yeast as well as bacteria, including E. coli, have not been used as the main hosts for the production of recombinant antibodies (full-length IgG format) for use in humans because of glycosylation problems.

They do however go on to discuss some interesting developments such as the expression of a Campylobacter N-glycosylation pathway in E.coli, as well as strategies for the production of functional antibody fragments.


It is correct that O- and B+ parents cannot produce biological children with A+ and AB+ blood groups, with the exception of a few rare edge cases.

Firstly, as noted in the other answer, your grandmother may have the Bombay phenotype. However, this is unlikely, due to the fact that she has been previously hospitalised and it was not noted.

Another unlikely possibility is that your grandmother is a genetic chimera. This means she would have two sets of genes, and her bone marrow hematopoietic cells had the O- genotype and phenotype, while her reproductive cells had an A allele.

If we exclude the rare edge cases, then it is strong evidence that your mother and aunt are not the biological children of your grandparents, and you should consider performing genetic testing to verify this if you wish.


How to understand influenza strain designations?

The sub-type is named for the broad classes of the hemagglutinin (HA) or neuraminidase (NA) surface proteins sticking through the viral envelope. There are 16 HA sub-types (designated H1 - H16) and 9 NA sub-types (designated N1 - N9). All of the possible combinations of these influenza A subtypes infect birds, but only those containing the H1, H2, H3, H5, H7 and H9 and the N1, N2 and N7 surface proteins infect humans, and of these, so far, only H1, H2, H3 and N1 and N2 do so to any extent.

Read more: http://www.fluwiki.info/pmwiki.php?n=Science.NamingInfluenzaViruses


When using a primer to replicate DNA in a plasmid, does it replicate the whole plasmid?

PCR produces linear DNA, not circular. You can replicate whole plasmids using PCR, but the DNA will still be linear, as if you cut the plasmid with a blunt-end restriction enzyme.

So why doesn't the whole plasmid get copied when using PCR? Let's assume the primers are designed to bind 1000 bases apart from each other. The first round of PCR will probably produce longer pieces of DNA, because the oligos can only bind to the plasmid and the Polymerase can keep going. But the polymerase will fall off at some point, either randomly or when the temperature is pushed up for the next round of PCR. But in round 2, there should be equal numbers of circular plasmid and linear copy. The proportion of linear copy will increase every round. As the linear copies increase, the oligos are more and more likely to bind to linear copies than to circular plasmid.

Binding to linear copies is why the PCR product size is controlled. Let's assume that a linear copy is 1500 bases, because the polymerase ran an extra 500 bases past the other oligo site on the plasmid. But when the reverse oligo binds that site on the linear copy, the polymerase will run 1000 bases and fall off the end of the linear copy. This new copy will have the forward and reverse oligo sites at the ends, so it's the right size. Any copies produced from this strand will also be the right size. As the reaction proceeds, the proportion of correct-sized strands increases, and create more correct-sized strands.


Do all transmembrane proteins contain channels or tunnels?

Transmembrane proteins don't all have tunnels.

  Do all the transmembrane proteins have to have channel or tunnel for transport of materials?

Calling transmembrane proteins tunnel proteins is very misleading. There are a wide range of functions carried out by transmembrane proteins. I'd say the most famous example that don't include a tunnel are the GPCRs that have 7 transmembrane segments. These are used for passing information across a membrane by acting as a receptor to a molecule on one side causing a conformational change which causes an action on the other side of the membrane.

How many transmembrane proteins do have tunnels?

Here is a link to all the GO annotation held by UniProt on transmembrane proteins. There are 10s of millions of results including, but certainly not limited to tunnels and channels.

In the human proteome, there are 831 transmembrane proteins tagged with G-PCR (7TM proteins without a tunnel).
The "Transport" keyword, which probably has some sort of tunnel, is present in 1106 transmembrane proteins.
In total there are around 5200 human transmembrane proteins in the human proteome.


Is there a difference between ISH and ISHH? (In Situ Hybridization, In Situ Hybridization Histochemistry)

The term appears to be in use as a synonym.  PLOS ONE is a good journal, and in it Okubo, 2016 write "The protocol for ISHH was described in detail previously [22]."  Where [22] is Yamanaka, 2007, describing a classic ISH protocol.
Note that both papers use good old fashioned nuclear tract emulsion for S-35 labelled probes.  The ISHH protocol is in its own section separate from IHC.  It seems a bit odd because no literal "chemistry" is involved in recognizing the target - the RNA probe binds non-covalently and emits radiation.  However, as noted in the question discussion, IHC is formally defined (OED) as "the branch of science concerned with the identification and distribution of the chemical constituents of tissues by means of stains, indicators, and microscopy".  For example, though I have seen immunofluorescence and immunohistochemistry used to describe mutually exclusive visualization options, noncovalent binding of fluorophore-labelled antibodies is described as "fluorescent IHC".


Sure it is!

When we say that an allele is dominant on another what we really mean is that the phenotype obtained from that specific mutation of the gene somehow "masks" the phenotype of the other.

The easiest example would be that of pigment. A gene X could code for an enzyme which produces a red pigment. A mutation in X could result in a allelic variant x coding for a non-functional enzyme that does not produce pigment. In this case X will be dominant on x, as in the presence of both the pigment will still be produced (because you will have half functional and half non-functional enzyme molecules).

Things can, however be slightly complicated.

For instance, if the allele R codes gives a red pigment and r gives a white pigment Rr could give pink. This is called incomplete dominance.

On the other hand you could have co-dominance, where WW is white, ww is black and Ww is black and white.

The example you are asking for is called serial dominance and the "classical" example given is that of the rabbit coat color where you have for alleles with a dominance hierarchy like:

c+ > cch > ch > c

c+ gives a fully functional enzyme, called tyrosinase
c gives a non-functional enzyme, resulting in an albino phenotype
cch (chincilla phenotype) and ch (hymalayan phenotype) give partly functional enzyme (interestingly, the latter gives a temperature sensitive fur color).

In reality the rabbit coat genetics is even more complex, see this documents (PDF) for a more complete list of all the various loci and possible alleles involved.


How was the diversity between ethanol fermentation and lactic acid fermentation evolved?

First, it is not clear from the physiology or biochemical information alone to determine what evolved from what. The intermediate pyruvate is always there, so lactose dehydrogenase (LDH) and pyruvate decarboxylase (PDC) could have each evolved anytime, and there are good reasons for both:

LDH: the reaction pyruvate + NADH/H+ = lactate + NAD+ + 25 kJ/mol is highly exergonic, i.e. produces heat
PDC: the reaction pyruvate = acetaldehyde + CO2 (and with ALD present) acetaldehyde + NADH/H+ = ethanol + NAD+ where ethanol is poisonous to other species

Add to it that there are organisms like Sch. pombe that have both enzymes, so can do both reactions, your questions should be rather:

How has the enzyme LDH evolved?

The enzyme is similar to malate dehydrogenase, both form a family. They belong to a group of enzymes that all have a NAD(P) binding domain, so it's not too far-fetched to state that LDH and MDH evolved from another enzyme with NAD(P) binding domain.

http://www.ebi.ac.uk/interpro/IEntry?ac=IPR016040

How has the enzyme PDC evolved?

  Protein sequences of pyruvate decarboxylase (PDC) derived from cloned
  yeast (Saccharomyces cerevisiae) and bacterial (Zymomonas mobilis)
  genes were compared with each other and with sequence databases.
  Extensive sequence similarities were found between them and with two
  others: cytochrome-linked pyruvate oxidase from Escherichia coli and
  acetolactate synthase (ilvI in E. coli; ILV2 gene in S. cerevisiae).
  All catalyse decarboxylation of pyruvate using thiamine pyrophosphate
  (TPP) as cofactor. General overall similarity suggests common ancestry
  for these enzymes.

cited from abstract of

Green, Jeremy. "Pyruvate decarboxylase is like acetolactate synthase (< i> ILV2) and not like the pyruvate dehydrogenase E1 subunit." FEBS letters 246.1 (1989): 1-5. http://www.ncbi.nlm.nih.gov/pubmed/2651151?dopt=Abstract


If only dicots have pith, what is the foam in the middle of cornstalks?

Monocots do have pith in their stems. The link even has an image of a maize stem:


How to find PDB id of an amino acid sequence

One way of doing this is to run a protein BLAST search at NCBI in which you specify the Protein Data Bank as your database, as in the example shown below:

The results will be all for proteins in the PDB.


How do I view the simulated protein structure along with ligand in VMD?

After you load the molecule in VMD, from the menu bar select Graphics->Representations... In the box labeled Selected Atoms, type "hetero" and hit enter. You should now see only your ligand (and whatever other non-protein/DNA atoms that happen to be in your PDB file). Hit the Create Rep button, enter "protein" in the Selected Atoms box and hit enter (you can see a list of all the possible selection words in the Selections tab). You will now have a separate representation for your protein and your heteroatoms, and you can modify them with the other settings in the Graphical Representations dialog in order to make them visually distinct from one another.

If this doesn't fix your problem, open up your PDB file in a text editor and check to make sure that there are lines that start with ATOM or HETATM that correspond to the atoms in your ligand. If they aren't there, your problem isn't with VMD but with one of your prior manipulations.


Is there anything that is completely non-toxic to humans at any dose?

I’ll answer this theoretically, since that’s how it has been posed. And if we’re ignoring practicalities, we may as well posit that the substance in question will be introduced directly into the bloodstream (This is, of course, simple to do in reality, but not how most people consume their non-toxic substances.) The easiest way to show that any unspecified substance can be toxic at an unlimited volume is to invoke the human body’s mechanisms for volume homeostasis.

As mentioned in this answer, the human kidneys functioning optimally can produce up to ~ 25 L/day of urine.1 This would require complete suppression of ADH (anti-diuretic hormone, a.k.a. arginine vasopressin), which would occur only if the “toxin” load were markedly hypotonic (think water).2  There is therefore a theoretical maximum volume of any substance that can be dealt with by the body, which is something less than 25 L per day. (For any substance other than water, the maximum will be lower because ADH will not be as fully suppressed by a less hypotonic load.)

A volume of any substance introduced into the bloodstream (including a product precisely mimicking the constituents of the bloodstream itself!) will overwhelm the body’s homeostatic mechanism. This will result in edema which is unpleasant and, in the case of pulmonary edema, certainly pathologic - a “toxidrome” in your scenario. In the case of hypotonic fluids, serum osmolality will also fall causing hyponatremia with all of its consequences.

Summary: No, the human body can not tolerate an unlimited volume of anything, therefore there is no substance that is non-toxic "at any dose."

1. Christopher Lote. (2012). Principles of Renal Physiology. Springer New York.

2. No, you may not drink 25 liters of water per day. For one thing, urine can not be made with a tonicity of 0 to balance this (more like 60 mOsm/kg minimum). Additionally, ADH can rarely be completely suppressed, yielding a somewhat more concentrated urine and therefore lower tolerance for hypotonic intake before serum osmolality is compromised.


Reading and Understanding profile bands in DNA Fingerprinting

How you would determine the plasmid map from just the restriction digest data

The thought process behind doing this is a bit involved.

From the question you are told that the Gene is 8kb and does not contain an EcoRI site inside of the gene

I say not inside because the ends of the gene were made with EcoRI cuts, but digesting in EcoRI will only produce the 8kb fragment of the gene

The vector is 6kb and you know that they have EcoRI sites at either end, but you are not told what other cut sites there are.
When you digest the plasmid in BamHI you get 3 fragments, meaning that your plasmid has 3 BamHI sites somewhere in it.
You know that your total plasmid size is 14kb (easiest way to know is just look and see that they tell you that there is an 8kb gene and a 6kb vector). Looking at the Double Restriction Digest, you can see that the five fragments add up to 14kb, which implies that there are only one of each fragment in the plasmid, and they are produced by 5 separate cuts.

This is an important piece of information because this tells you that you do not have 2 fragments of the same size making up different parts of the plasmid.
Remember that when you do a restriction digest on a circular piece of DNA, the number of fragment you get equals the number of cuts (restriction sites) in the plasmid. So because there were 5 fragments, you have 5 separate restriction sites
From the Double Digest data, you also know that the smallest fragment of DNA that you have is 1kb and the largest is 4kb.

Since the 4kb site is common to both the BamHI only and the the Double Digest, as since you do not have a 0.5kb or 1.5kb fragment (the remainders if the Double Digest 4kb fragment had been produced from the 4.5kb or 5.5kb fragments in the BamHI digest) in the Double Digest, you know that the 4kb fragment is the same in both the BamHI digest and the Double Digest, and is produced by 2 BamHI cuts.

You can now work on roughly placing where the 4kb fragment should be in the map.
If you try to place that 4kb fragment in the vector, then you would either generate a 2kb fragment, or something less than 2kb and a very small fragment.
Since you do not have a 2kb fragment or fragments smaller than 1kb, you know that it cannot be in the vector region. Also in order to get a 2kb fragment from the 6kb vector the 4kb fragment would have needed to be cut once with EcoRI and from the description, above, we worked out that the 4kb fragment is produced by two BamHI cuts
It could have been that the vector was 1kb + 4kb + 1kb, however from point 4 you determined that you only had one of each fragment, so you can't have two 1kb fragments.

All of that tells you that it has to be in the 8kb gene portion, though you need some more information to determine exactly where.

Remember that you do know that the 4kb fragment was produced by 2 BamHI cuts, which means that it cannot be at the very end of the gene region, as that would require it to be cut once with EcoRI
This also tells you that you have at least two BamHI cut sights in the gene.

What I would do here is draw two circles, the first having an 8kb arc and a 6kb arc, then draw second circle and make three cuts in it.

From 6 we worked out that the 4kb piece will overlap somewhere in the 8kb area, that it cannot be at an end and that there need to be 2 BamHI restriction sites within the gene.
You also have to consider the 4.5kb and 5.5kb parts from the BamHI digest. Since 4kb plus either of those two are greater than 8kb, then you know that the cut that separates 4.5kb from 5.5kb will be somewhere in the 6kb vector. This is how you know that the third BamHI site is in the vector.

Now that you have determine that the 4kb fragment is in the gene you can start to work out the other pieces.
You had 2 fragments from the BamHI digest that were 5.5kb and 4.5kb and in the double digest you have fragments that are 1.0kb, 2.5kb, 3.0kb, and 3.5kb.

Since you have already determine that that 4kb piece is the same for both digests, then at this point you can tell yourself that the 1.0kb and 3.5kb fragments made up the 4.5kb fragments and the 2.5kb and 3.0kb fragments made up the 5.5kb fragment.

Since you know that there has to be two EcoRI cuts that make the 6kb fragment, you are going to need two fragments that add up to 6kb.

The only way to get this with the four fragments that you have from the double digest is with the 2.5kb piece and the 3.5 kb piece.
So you have now determined the exact position of one of the BamHI cut sites. It is in the Vector, 2.5kb from one of the EcoRI sites and 3.5kb from the other EcoRI sites.

Now that you determined where one of the sites is, you know that the 2.5kb fragment was paired with the 3.0kb fragment, so this tells you that there is a BamHI site 3kb away from the EcoRI site in the Gene.
From there you can connect the 4.0kb piece to the end of the 3.0kb piece because you know that the 3.5kb piece has to be attached to the 1kb piece and cannot be attached to the 3kb piece.
All that is left is to close the circle. You know that you have 1.0kb more of the gene that needs to be place and this will connect the 7.0kb that you determine of the gene in step 11 to the 3.5kb fragment in the vector. You have that 1.0kb fragment, and that is the one.

So that is how you determine how to construct the plasmid map from the restriction digests.

What the distances between the cut sites tell you

The cut sites are determined by the sequence of the DNA that the Restriction Enzyme recognizes.

EcoRI recognizes GAATTC
BamHI recognizes GGATCC

You will notice that these are palindromic sequences, so 5'-GAATTC-3' is 3'-CTTAAG-5' on the complimentary strand.

All that the distances are telling you is that in the areas in between the cut sites, the sequences GAATTC and GGATCC do not appear. If they did, then the Restriction Endonuclease would recognize that position and cut the DNA, and you would have an additional cut site at that location.

Assuming that you were given the plasmid map, this should be the answer.

The answer should be C. The 1kb and 3kb fragments are the DNA fragments from the gene that are generated from the EcoRI / BamHI digest. So one end of the fragment was produced with EcoRI and the other end of the fragment was produced with BamHI

The 4kb fragment is the result of BamHI restriction alone. So both ends of the fragment were produced by BamHI so it cannot be the answer to a fragment produced by EcoRI / BamHI restriction.

If they are saying that they also want answer A as well, then their question is very poorly worded, in my opinion.


How do adult differentiated somatic cells divide?

There is no known alternative mechanism of proper cell division apart from mitosis and meiosis in animals. I think this is an unfortunate phrasing where the author is trying to introduce the term "postmitotic". The reason for saying "most  adult differentiated cells" is because some cells in adults are considered differentiated but they still proliferate under certain conditions, like for example the cells of the adaptive immune system.

It could also be that the author is trying to be overly cautious because there are cells that split parts of themselves off and release them. These mechanisms could be considered cell division in some sense but are neither mitosis nor meiosis. Examples of this are the release of platelets by megakaryocytes and the release of extracellular vesicles by cells undergoing apoptosis.


Why aren't plants' roots as diverse as leaves?

To answer this type of question, we should start by defining 2 concepts: the functions of the root and the external condition that brought to a specific evolution.
Evolution is a necessary process to all organisms, which evolve to optimize a specific function and to better adapt to the external conditions.

There are 3 main and common functions between all land plant's roots: fix plants to the soil; absorb water and minerals; establish specific relationships with other organisms, principally fungi and bacteria. The external conditions of roots (soil) are quite stable, even though, the different "physical" composition of soil, that is the quantity of sand, clay and rocks, change the physical appearance of size and proportion between the main and the lateral roots.Therefore it is plausible to say that it is not necessary to have a great variety in root's structure; since all roots must carry out same functions, all plant's root underwent a similar evolution.

For the leaves it is a bit different. Leaves must also carry out specific and common functions, as: exchange gas (CO2 and O2); contain photoreceptors to "absorb" light for photosynthesis. However, the external conditions of leaves are shortly and continuously changing and highly different (consider the vary regions of the world, as desert and rainforest) with reference to roots. Therefore each plants underwent evolution depending on these types of external conditions, so as to, of course, optimize their functions but at the same time protect themselves as much as possible. Consider, for example, the intensity of sun's radiation, which, if too strong, can destroy cellular structures, the quantity of CO2 in the air, or the high biodiversity of insects, which can carry diseases, ecc...

Interesting book about evolution is: J.C. Harmon, S. Freeman, "Evolutionary analysis", where it is given an idea of the type of evolution, different species, could undergo.
(hope my english is not too bad)


What makes learning more difficult as we age?

The answer(s) to this question can fill libraries. But I can give a few pointers here, as the question is relevant and timely, giving the tendency to an ever increasing life expectancy of the general populace in developed countries (notable exception: US).

I think your question can broadly be answered by the fact that degenerative processes in the brain slowly, but steadily, impairs all of its functions. Possible reasons for the specific decreased capability of the brain to adapt itself to new situations are:

The hippocampus plays a critical role in forming memory representations that are important for flexible cognition and social behavior (Rubin et al., 2014). Decreasing hippocampal neurogenesis during aging may impair the functioning of the hippocampus (Couillard-Despres et al., 2011)
Degenerative processes in the striatum impairs implicit learning that is necessary for mastering new tasks (Rieckmann & Bäckman, 2009);
Deficits in serotonin and dopamine neuromodulation in various brain structures due to degenerative processes during aging results in decreased learning and decision making (Eppinger et al., 2013);
Age-related altered neurosteroid levels may impair cognitive abilities (Vallée et al., 2011).

And the list goes on.

References
- Couillard-Despres et al., Gerontol (2011); 57: 559–64
- Eppinger et al., Ann N Y Acad Sci (2011); 1235: 1–17
- Rieckmann & Bäckman, Neuropsychol Rev (2009); 19(4): 490–503
- Rubin et al., Front Hum Neurosci (2014); 8: 742
- Vallée et al., Brain Res Rev (2001); 37(1–3): 301-312


It is possibly a milky ribbon worm (Cerebratulus lacteus).

source:  intertidal-novascotia.blogspot.com

They can be found anywhere and everywhere along the Atlantic coastline in healthy abundance - http://intertidal-novascotia.blogspot.com/2012/05/cerebratulus-lacteus-milky-ribbon-worm.html


Viruses affecting transmission capability of mosquitoes

There have been some studies looking at this, but not many. One is this study which reported an interaction between Aedes densovirus (AeDNV) and dengue virus (DENV) in Aedes albopictus: mosquitoes already infected with AeDNV were more resistant to infection with DENV, although DENV infection appeared to accelerate the replication of the existing AeDNV infection. A similar interaction was not seen with chikungunya virus (CHIKV).

In addition there are indirect interactions between pathogens of all kinds - viruses such as AeDNV which kill a high proportion of the mosquitoes they infect reduce the average survival and population density of the vector and therefore the ability of the local population to transmit disease (ref).


Can CRISPR be used in editing primary cells? How is the transfection efficiency?

The most efficient CRISPR-based editing of primary cells that I've read about used a technology called prime editing, developed in 2019.

Search-and-replace genome editing without double-strand breaks or donor DNA (PDF download)

Normal CRISPR-Cas9 protocols involve generating double-strand breaks (DSBs), and then either introducing a template for homologous repair or allowing the cell to repair the break without a template, leading to insertions or deletions at the lesion site.  Off-target cutting is common, so normal CRISPR-Cas9 produces undesirable or lethal mutations in a majority of transfected cells.

Prime-editing uses a catalytically impaired Cas9 (generates nicks instead of DSBs) fused to a reverse transcriptase.  The fusion protein is guided to its target by a prime-editor gRNA ("pegRNA") that contains a normal targeting domain at its 5' end and a template for reverse transcription at its 3' end. A nick is generated by the Cas9 on the exposed strand (i.e. the strand not bound by the gRNA), and the 3' portion of the pegRNA partially hybridizes to the the 5' side of the nick, providing a free 5' end and a stretch of ssRNA for DNA polymerization.  Resolution of the resulting "flap" by endogenous nick-repair mechanisms results in editing at the target site without DSBs or exogenous DNA template.

This method was assessed for its efficiency in several cell types, including primary mouse cortical neurons, which are post-mitotic and terminally-differentiated.  The authors observed the desired edit of DNMT1 in 7.1% of cells, with 0.58% indels on average.  Cas9 nuclease editing of the same cell type with the same lentivirus transfection system resulted in 31% indels, on average, an error rate more than 50 times that of prime-editing.


What does it take to start producing(cultivating) probiotics?

I did a master's thesis involving enzymes from a probiotic bacteria. Many of the known probiotics were cultivated from faeces but others have also been isolated from breastmilk. Many of the probiotic bacteria are strict anaerobes and can only be succesfully cultivated in modified atmosphere. You may need to use selective plating with various prebiotic compounds such as Galactooligosaccharides or similar compounds in order to control bacterial growth. I recommend incubating at 37°C or slightly below depending on how well controlled your incubator is.


Can different proteins be produced during translation of a single mRNA in eukaryotes?

There are multiple mechanisms that are known to lead to translation of substantially (or entirely) different proteins from a single mRNA. While these mechanisms are more typically seen in viruses, I'm focusing on examples documented within the endogenous transcriptome of eukaryotes.

Alternative translation initiation

One process that can lead to different proteins being translated from the same mRNA in eukaryotes is the use of alternative translation initiation sites.1,2 Translation typically starts with a pre-initiation complex recognizing the 5' cap and loading onto the mRNA. This complex scans until it finds an appropriate start site. The choice of start site depends on the how well the ribonucleotide sequence matches the Kozak consensus sequence.3 If the region around the first AUG is not a good match for that consensus then a process known as leaky scanning occurs and the pre-initiation complex can continue along the mRNA until a "good" start site is found.

While this can result in proteins with different functions, they will typically still have large regions of amino acid sequence in common. One example of this is in a kinase known as MK2, which is "a key regulator of transcription, migration, death signaling and post-transcriptional gene regulation".4

Polycistronic mRNAs

While more common in prokaryotes, in some cases eukaryotes also have polycistronic transcripts5,6.  These transcripts encode multiple separate proteins (i.e. from independent open reading frames). The examples that I have found for mammals are all bicistronic (operons with two genes): LASS1-GDF1, SNRPN-SNURF, MTPN-LUZP6 and MFRP-C1QTNF5. You can search for those gene pairs, but there doesn't seem to be a huge amount of information available and in many cases one of the genes is almost completely uncharacterized. Eukaryotic operons (aka polycistronic mRNAs) are ubiquitous in trypanosomes, appear to be very common in nematodes (round worms), and are also frequently seen in Drosophila (a fly).6

Translational read-through

Translational readthrough aka. stop codon suppression occurs when an in frame stop codon is ignored either stochastically or under specific conditions and translation continues beyond that point. This leads to a C-terminal extension of the protein which in some cases has been shown to have functional implications7,8. An example of this is the [PSI+] prion in yeast, which promotes translational readthrough throughout the yeast transcriptome by inactivating a factor involved in translation termination.7

Translational frameshifts

This is well covered in the answer by @Dirigible.

References:
1: Kochetov, A. V. (2008). Alternative translation start sites and hidden coding potential of eukaryotic mRNAs. Bioessays, 30(7), 683-691.
2: Wan, J., & Qian, S. B. (2013). TISdb: a database for alternative translation initiation in mammalian cells. Nucleic acids research, 42(D1), D845-D850.
3: Acevedo, J. M., Hoermann, B., Schlimbach, T., & Teleman, A. A. (2018). Changes in global translation elongation or initiation rates shape the proteome via the Kozak sequence. Scientific reports, 8(1), 4018.
4: Trulley, P., Snieckute, G., Bekker-Jensen, D., Menon, M. B., Freund, R., Kotlyarov, A., ... & Gaestel, M. (2019). Alternative Translation Initiation Generates a Functionally Distinct Isoform of the Stress-Activated Protein Kinase MK2. Cell reports, 27(10), 2859-2870.
5: Tautz, D. (2008). Polycistronic peptide coding genes in eukaryotes—how widespread are they?. Briefings in Functional Genomics and Proteomics, 8(1), 68-74.
6: Blumenthal, T. (2004). Operons in eukaryotes. Briefings in Functional Genomics, 3(3), 199-211.
7: Schueren, F., & Thoms, S. (2016). Functional translational readthrough: a systems biology perspective. PLoS genetics, 12(8), e1006196.
8: Loughran, G., Jungreis, I., Tzani, I., Power, M., Dmitriev, R. I., Ivanov, I. P., ... & Atkins, J. F. (2018). Stop codon readthrough generates a C-terminally extended variant of the human vitamin D receptor with reduced calcitriol response. Journal of Biological Chemistry, 293(12), 4434-4444.


how can a recessive allele become represented in a significant number of individuals in a population

A recessive allele is one whose phenotype can be masked by a dominant allele. A recessive allele is not necessarily deleterious, and the dominant allele does not necessarily have higher fitness than the recessive allele. Fitness and dominance are often confused, but they are not the same thing.

In some scenarios, the recessive allele indeed confers a fitness benefit, and when it does, it is predicted to increase in frequency rapidly because homozygous recessive individuals have higher fitness than both homozygous dominant genotypes and heterozygotes.

A recessive allele can also persist in a population if it is deleterious in homozygotes but confers a heterozygote advantage. The most famous example of this phenomenon is in Africa, where individuals heterozygous at the sickle cell locus have a fitness advantage because they are resistant to malaria. A higher prevalence of sickle cell phenotypes occur because selection for heterozygotes maintains a high frequency of recessive alleles in the population. For more, see Templeton (1982, http://www.indiana.edu/~curtweb/L567/readings/Templeton.pdf) and Allison (1954, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2093356/).


Is it correct to use the terms multinucleate and syncitia interchangeably?

No, the terms multinucleate and syncytium are not synonymous in this context.  Most cardiomyocytes are not multinuclear. To be clear, syncytium is used to refer to multinuclear cells that originate from fusion of uninuclear cells, including the skeletal muscle, but that isn't what is referred to in the context of cardiac muscle.

The Wikipedia page on syncytium summarizes this nicely:

  Cardiac tissue is therefore described as a functional syncytium, as opposed to the true syncytium of skeletal muscle.

The "intercalated disks" of cardiac muscle are filled with gap junctions and desmosomes. The desmosomes hold the cells together physically, while gap junctions allow ions (and small molecules) to pass directly between cells, forming "electrical synapses". This allows electrical signals to propagate between the myocytes to coordinate contraction.

Gap junctions are formed by proteins, rather than fusions of the plasma membrane, so they are relatively small. This means that not everything in the cytoplasm can pass through them, mostly just ions and some small molecules. Proteins, for example, would not pass through gap junctions. Therefore, cells that are connected via gap junctions, like cardiomyocytes, are still somewhat independent, unlike fully multinuclear cells.

There are also types of neurons, including some in the CNS, that also form gap junctions and act at least somewhat in concert in this way.


Does vitamin D form crystals in the blood with calcium and magnesium?

Vitamin D does not bind to Calcium. It is a pre-hormone which is converted to calcitriol. Calcitriol has an intracellular receptor (VDR) that, as a heterodimer with Retinoid-X receptor, regulates gene expression.

I guess the "should not be had together" is because of possible over-absorption of Calcium. There are commercially available supplements (e.g. 1, 2) that have Vit-D + Ca + Mg.


Non-ribosomal peptide synthesis: why Glutathione cannot be produced by the ribosome?

It's definitely not the length. Although ribosomes can't make really really small peptides because they need something to hold onto and in any case proteins start with methionine(usually), there are workarounds. There's no reason why a tripeptide couldn't be coded for by a gene directly.

The 'traditional' method of producing very short peptides is producing a longer protein and cleaving off a chunk of it, which works great for signal peptides and a number of other systems. Very small peptides are more efficiently made by enzymes like this but in principle there's no reason to besides efficiency and complexity. (You need a special protease for each small peptide etc etc etc)

However, this gamma bond is a different beast entirely, and no ribosome could ever produce it, even in the middle of a longer protein. Amino acids 'snap' together in a very specific way. The amino group bonds to the carboxyl group of the previous amino acid, making a chain. The side groups of an amino acid aren't involved. Like Legos that snap together only one way and can be any color or have any designs on the side. The difference here is glutamate has a carboxyl group as part of its side chain. It's like a Lego with holes on two sides. The NRPS here connects the cysteine to the side chain of the glutamate instead of the 'bottom' where it would go if a ribosome-synthesized glutamate-cysteine bond.

This gamma bond also explains the increased longevity of the product. Proteases aren't designed for things that look like this. The gamma bond doesn't 'fit right' in the protease active sites and therefore activity is slower.


Where can you find the quantities of each amino acid of a particular protein or food?

There's a fantastic database available from the United States Department of Agriculture that includes almost 9,000 common foods, including their nutritional information. This database is searchable and available from the USDA Agricultural Research Service. Here is a link for the online searchable database.

Within the database you are able to search for a number of parameters; including, food composition, water content, individual amino acid content, fatty acid and total fat content, vitamins, minerals, phytonutrients, and more! One of the nice things is that you can ask it to rank the foods in order of nutrient composition. For example, ranking all the foods in the database in order of protein content or a specific amino acid (or whatever else you're interested in).

It's a great database, especially for researchers that need a database of trusted nutrient data.

Within the database you can search by nutrient or by food, whichever you are curious about. For example, as you mention in the question, I entered potato and in the second screen shot below you can see the listing of all the nutrients in the potato. These are listed as % weight per 100g of potatoes - with or without the skin.

To get to the amino acid content breakdown, click on Full Report (All Nutrients) at the top.


How does the light-independent stage of photosynthesis get H+ ions?

Summary
The question shows confusion about the purpose of the splitting of water in photosynthesis. Quoting from Berg et al., in the light reactions of photosynthesis

“Light is absorbed and the energy is used to drive electrons from
water to generate NADPH and to drive protons across a membrane. These
protons return through ATP synthase to make ATP.”

The useful product of splitting water is energy.
There is no problem in the provision of hydrogen ions for biochemical reactions as such — they are available from the dissociation of water.
Explanation

The diagram above, summarizing the light reactions may be helpful, although it conceals detail and introduces the complexity of energy generation. It shows the (thalkaloid) membrane separating the location of the reduction of NADP+ (outside) from where water is split (inside).

The important product of the reaction of light photons with water is excited electrons. The chemical products are relatively unimportant — certainly for oxygen, and the only importance of the hydrogen ions produced is their location within the thalkaloid, lowering the pH.

The initial fate of the hydrogen atom is complex, and there a many intermediates to which the excited electron is transferred before, ultimately to NADP+:

NADP+ + H+ + 2e– → NADPH

It is important to realize that the energy is used to reduce NAD to NADPH, that NADPH can be regarded as a special type of ‘high-energy compound’ — not a general one like ATP, but one that can specifically drive the reduction of carbon backbones needed in synthesis.
The misapprehension is that there the hydrogen ions for the above reaction are those produced in the splitting of water, or that there is in general any problem in obtaining hydrogen ions for biochemical reactions. Biology exists in an aqueous environment, and water dissociates into hydrogen and hydroxyl ions.

H2O ⇌ H+ + OH–

So hydrogen ions are irrelevant to the reduction reactions involved in the conversion of carbon dioxide to carbohydrates in the light-independent reactions of photosynthesis (they are actually produced in NADPH reductions.). It is NADPH that is supplying the hydrogen component of the carbohydrates.
ATP
The diagram also brings in a complexity that needs a book chapter to explain: the hydrogen ion gradient generated between the inside and outside of the thalkaloid space provides the energy to phosphorylate ADP to ATP. The ATP is relevant to the light-independent reactions of photosynthesis in that it ultimately provides the energy for formation of the carbon–carbon bonds.


This is explained in the linked article.

  We found several recurrent translocations of likely pathogenic significance, including an intra-chromosomal translocation on chromosome 4 involving FGFR3 and TACC3 (n=3). The breakpoints were in intron 16 (2 cases) or exon 17 (1 case) of FGFR3 and intron 10 of TACC3 (confirmed by DNA sequencing and RNA-seq). All three lead to fusion mRNA products whose predicted proteins include the N-terminal 758 amino acids of FGFR3 fused with the C-terminal 191 amino acids of TACC3 (Fig. 2a). Based on the structure of the FGFR3-TACC3 fusion protein, we predict that it can auto-dimerize, leading to constitutive activation of the kinase domain of FGFR3. FGFR3-TACC3 fusion, which was recently described in both glioblastoma21 and bladder cancer7,8, represents a promising therapeutic target.

FGFR3 is a member of the fibroblast growth factor receptor family. It is a transmembrane kinase that is normally activated upon ligand binding which triggers dimerisation. TACC3 is a protein that can dimerise through a coiled-coil domain.

The FGFR3-TACC3 gene fusion that is generated by the reported intra-chromosomal translocations thus generates a version of the receptor that is predicted to be constitutively active because it can dimerise in the absence of the growth factor.

Recurrent means occurring frequently.


Does sociality evolved before or after the ability of motility?

I'm going to hazard that primordial sociality by this definition and this question proceeded primordal motility in cells.

Algae started to form physically attached groups like these filaments, giving them some of the advantages of higher organization.

Its easy to see how this is a relatively simple adaptation - just have proteins or carbohydrates on the cell surface that stick together.  This might also have evolved from large cells compartmentalizing since we're talking about very ancient stages of life on earth.


What's so special about Chassaignac tubercle?

The reason massaging the carotid artery can relieve symptoms of supraventricular tachycardia is because by massaging the artery, as you point our yourself, you artificially increase BP within the carotid artery, this activates a reflex (via the glossopharyngeal nerve) that lowers bloodpressure by reducing the heart rate via the vagus nerve, by increasing the refractory period of the AV-node, so the heart rate drops.
It should be noted though, that it can be a bit dangerous to play with these reflexes in some patients, especially because massaging the carotid arteries can lead to an embolism in older individuals with atherosclerosis, or in some patients, it can lead to asystole or ventricular fibrillation (i.e. cardiac arrest).
It's not really about which vertebra is at the level you are massaging, rather it's about being near the carotid sinus, which is where the baroreceptors are located, and that might vary between individuals and how you position the head etc.


Why do ion concentrations change with different secretion rates in pancreatic juice?

An interesting question!

I am attaching the picture from Boron & Boulpaep, Medical Physiology, 2nd Ed, p921 here to clarify the details left out in the hand drawn picture.

The flow of the digestive pancreatic enzymes increase mainly during food consumption. This is brought about by a number of redundant systems. The fasting secretion of pancreatic enzymes depends on the MMC (migrating motor complex).

Bicarbonate ions are exchanged with chlorine ions in the apical membrane of the acinar cells through a Chloride Bicarbonate Exchanger. This process is driven by:

Secretin - most important humoral factor - Increases secretion
ACh through muscarinic receptors - Increases secretion
GRP (Gastrin Releasing Peptide) - Increases secretion
Substance P - Decreases secretion

Mechanism of action of secretin seems to be through activation of cAMP. However even small amounts of secretin which do not raise the cAMP levels measurably can stimulate bicarbonate secretion. This suggests secretin response may be by

Unmeasurably small amount of increase in cAMP
Raise in cAMP levels in localised compartments
Activation of alternative second messenger pathways

In case of GRP the second messenger is not known.

The answer to your question is that when secretin is secreted, the Bicarbonate-Chloride transporter is accelerated to achieve the result displayed. This mainly happens when food enters the small intestine so as to neutralize the acid permitting the digestive enzymes to function at the optimal pH.

The Chloride-Bicarobonate Transporter is an exchange transporter which explains why there is a sharp fall in the chloride levels.


How does the hypothalamus get the information out of the blood?

First of all, there is not such a thing as "the" hypothalamic membrane. The hypothalamus consists of multiple nuclei, and each nucleus contains numerous cells (neurons and glia cells).

The mechanisms by which the hypothalamus senses hormone concentrations in the peripheral blood are rather complex. In recent years, considerable research has been done to elucidate the central mechanisms underlying thyroid homeostasis [6], which involve the regulation of TRH release from the hypothalamic paraventricular nucleus [1, 2]. Therefore, my following explanations are focussed on the control of TRH secretion, but similar considerations apply to other hormonal systems [7-9].

First, hormones have to be conveyed by special transport proteins across the blood brain barrier (BBB). In case of thyroid hormones, this is accomplished by tanycytes in the circumventricular organs [3]. They control the transition of hormones from the blood to the cerebrospinal fluid (CSF), and partly directly to glia cells via the transport protein OATP1C1. In glia cells thyroxine (T4) is deiodinated to form the more active hormone triiodothyronine (T3). T3 is then transferred to neuronal target cells via the transporter MCT8 [4, 5], where it exerts its homeostatic effects by inhibiting TRH release. Hypothalamic TRH secreting cells have, however, multiple afferent signals. In addition to thyroid hormones they include clucocorticoids, leptin, alpha-MSH, norepinephrine, cocaine and amphetamine-related transcript (CART), endocannabinoids, agouti-related peptide, neuropeptide Y (NPY), GABA, galanin and probably multiple additional signalling substances. This enables the TRH neuron to act as an integrator of energy homeostasis [1, 2, 6].

Of course, the TRH-secreting cells in the respective hypothalamic nuclei have receptors for all afferent hormones and neurotransmitters. Some of them (e.g. for catecholamines) are located on the cell membrane, others (e.g. for thyroid hormones or steroids) in the nucleus.

As mentioned, similar considerations apply to other hormonal systems [7-9]. Recent research suggested e.g. the existence of a receptor-mediated transport system, which conveys insulin trough the blood-brain barrier [9].

1: Joseph-Bravo P. Hypophysiotropic thyrotropin-releasing hormone neurons as transducers of energy homeostasis. Endocrinology. 2004 Nov;145(11):4813-5. PMID: 15489313. http://www.ncbi.nlm.nih.gov/pubmed/15489313

2: Joseph-Bravo P, Jaimes-Hoy L, Charli JL. Regulation of TRH neurons and energy homeostasis-related signals under stress. J Endocrinol. 2015 Dec;227(3):X1. doi: 10.1530/JOE-14-0593e. PMID 26527565. http://www.ncbi.nlm.nih.gov/pubmed/26527565

3: Rodríguez EM, Blázquez JL, Pastor FE, Peláez B, Peña P, Peruzzo B, Amat P. Hypothalamic tanycytes: a key component of brain-endocrine interaction. Int Rev Cytol. 2005;247:89-164. Review. PMID 16344112.
https://www.ncbi.nlm.nih.gov/pubmed/16344112

4: Kersseboom S, Visser TJ. Tissue-specific effects of mutations in the thyroid hormone transporter MCT8. Arq Bras Endocrinol Metabol. 2011 Feb;55(1):1-5. PMID 21468514.
http://www.ncbi.nlm.nih.gov/pubmed/21468514

5: Bernal J, Guadaño-Ferraz A, Morte B. Thyroid hormone transporters—functions and clinical implications. Nat Rev Endocrinol. 2015 Jul;11(7):406-17. doi: 10.1038/nrendo.2015.66. Nat Rev Endocrinol. 2015 Sep;11(9):506. PMID 25942657.
http://www.ncbi.nlm.nih.gov/pubmed/25942657

6: Hoermann R, Midgley JE, Larisch R, Dietrich JW. Homeostatic Control of the Thyroid-Pituitary Axis: Perspectives for Diagnosis and Treatment. Front Endocrinol (Lausanne). 2015 Nov 20;6:177. doi: 10.3389/fendo.2015.00177.  PMID 26635726.
http://www.ncbi.nlm.nih.gov/pubmed/26635726

7: Thon M, Hosoi T, Ozawa K. Possible Integrative Actions of Leptin and Insulin Signaling in the Hypothalamus Targeting Energy Homeostasis. Front Endocrinol (Lausanne). 2016 Oct 20;7:138. PMID 27812350.
http://www.ncbi.nlm.nih.gov/pubmed/27812350

8: Herman JP, Tasker JG. Paraventricular Hypothalamic Mechanisms of Chronic Stress Adaptation. Front Endocrinol (Lausanne). 2016 Oct 31;7:137. PMID 27843437.
http://www.ncbi.nlm.nih.gov/pubmed/27843437

9: Blázquez E, Velázquez E, Hurtado-Carneiro V, Ruiz-Albusac JM. Insulin in the
brain: its pathophysiological implications for States related with central
insulin resistance, type 2 diabetes and Alzheimer's disease. Front Endocrinol
(Lausanne). 2014 Oct 9;5:161. doi: 10.3389/fendo.2014.00161. PMID
25346723,
http://www.ncbi.nlm.nih.gov/pubmed/25346723/


Can we use cancer cells to generate blood vessels?

Using cancer cells in this manner would be far too dangerous, as there is nothing to prevent the cells from implanting and forming new tumors. Fortunately, we already know a great deal about angiogenesis, which is the process by which new blood vessels are formed or grown out of existing ones. If you want more details on how the process works, the article I linked to goes into a good amount of detail regarding the key players and how they interact.

It would be much easier (and safer) to use our knowledge of the cytokines and growth factors responsible for blood vessel formation to develop biological therapies that could potentially be used to treat varicose veins. However, current therapies can be quite successful, and there may not be a large enough market to justify the quite large expense required to develop angiogenesis-based therapies.

Unless a patient has some sort of genetic or other issue, angiogenesis is already involved in wound healing. As new tissue grows back, capillaries and perhaps slightly larger blood vessels expand out from the nearest sufficient vein/artery pair to vascularize the new cells. There may be issues with patients who are taking angiogenesis inhibitors as part of a therapy plan for cancer, for example, in which case compromises would have to be made if necessary.


The best way for scaling up these kinds of reactions is to set up many reactions. Prepare a mastermix for lets say 20 reactions. You can pool them together, precipitate the RNA and dissolve to appropriate concentration in nuclease free water. Also, use gene specific primer instead of oligo-dT and don't add poly-A tails (poly-A does not affect the in-vitro stability of RNA).

As Mad Scientist already indicated, you would not need to make DNA again from RNA. Simply take 1:2 molar ratio of your IVT template dsDNA (restriction digested) and the RNA (post IVT). Heat and anneal slowly. DNA-RNA hybrids are stronger then DNA-DNA hybrids and the former is more likely to form after annealing. You can digest the unpaired strands using enzymes like mung bean nuclease.


Monomer in this context means the protein has only one polypeptide chain. In some  proteins, after the individual chains have folded into their 3D or tertiary structure, they associate (generally non-covalently) into a higher order or quaternary structure. A protein with a quaternary structure containing  two copies of the same chain would be called a homo-dimer. One with one copy of each of two different chains is a hetero-dimer.

Haemoglobin is a well-known example of a protein with quaternary structure — it has two copies of the alpha- and two of the beta- chain. Further elementary treatment can be found in Berg et al. and explanation of the nomenclature in this Wikipedia page.

Monomeric polypeptide is somewhat misleading in the sentence quoted. Monomeric protein would have probably been better as you wouldn't be likely to say ‘dimeric polypeptide’, given that polypeptide implies a single chain.


Does a phenotype include the presence of a recessive gene

I agree with one of Alan's comments when he says:

"I think this comes down to whether you include being a carrier of a genetic "condition" a part of your phenotype. It's almost a question of semantics"

To expand on this, I would say there are two major definitions of phenotype, and both are employed by geneticists depending on the context.  Definition one is a bit more naive, and I tend to use it when teaching or trying to explain phenotype to a layman: anything you can observe is a phenotype.  Under this definition, having red hair is a phenotype, not having red hair (or, more directly, having black, brown, blonde, etc. hair) is a phenotype, but carrying the recessive gene for red hair is not a phenotype.  I can observe without checking your genome that you do or don't have red hair, I cannot tell without checking your genome that you have one copy of the recessive gene for red hair.

Definition two is more complete, and I tend to use it more in a lab research setting: anything that is the OUTCOME of a genotype can be defined as a phenotype.  Again, red hair and not red hair (meaning brown, black, blonde, etc) are outcomes defined by the genotype.  However, depending on the context (let's say I'm interested in understanding heritable potential and not the color of hair) I'd say that the phenotypes would be 1) the ability to pass on red hair to progeny (outcomes of genotypes RR, RN, RN in your example), and 2) lack of ability to pass on red hair to progeny (outcome of genotype NN in your example).  In both cases, the phenotype is the outcome of the underlying genes, I just have to make sure I frame my scientific context appropriately.


reason for "not for diagnostic use" advice in protocols

the FDA has to approve diagnostics - a rigorous and expensive process.  Its a legal distinction, but also one which conveys a significant level of usefulness and reliability.


Why won't birds move an inch in total darkness?

Most birds are diurnal and have vision adapted for daylight. Vision is among the most important senses for most birds, so much so their eyes have evolved to be quite large -- much larger than human eyes, proportionally to body size. In order to have excellent daytime vision, many birds also sacrifice some of the cells in the retina that allow for dim lighting conditions. (These photoreceptor cells are called rods and cones; cones are responsible for color perception while rods are more sensitive in dim lighting. Diurnal birds can have a lower percentage of rods than other animals adapted for nocturnal activity.)

Falconers have been exploiting this trait for millennia, by using a hood, diurnal birds of prey calm down in darkness.

Owls are a great example of a bird that can see in very dim lighting conditions, though they can't necessarily see in total darkness. They also rely on acute asymmetrical hearing in order to pinpoint prey in extremely dark conditions.

Your avian visitor likely can't see in dim conditions in which you can still see. To avoid injury, birds will hold still and wait for light.


Assembling small DNA parts using Golden Gate

Purely going off experience here having used golden gate assembly methods for 5+ years now, there is a definite lack of literature regarding small part assemblies. In my current lab, we use CIDAR MoClo (a golden gate method) and have assembled 100's of constructs successfully with parts as small as ~ 70 bp. However, when we assemble smaller parts we tend to increase the amount of this part compared to bigger parts. For example, we dilute each part to 10 fmol ready for assembly as a basis for all assemblies, this then allows us to play with the ratios and quickly optimise reactions. So as a standard, when the part is small we automatically start with at least a 3:1 instead of 1:1, where we put 3x the volume of the small part compared to others in the assembly. This usually helps, but on top of that we try to increase transformation efficiency by using SOC media and generally avoid building parts < 100 bp. e.g. we don't tend to use promoters and RBS separately we make larger combined parts containing both.


What is the transmembrane 'Positive-Inside Rule' nowadays? Has the definition changed over time?

I think you have misunderstood the "inside" part of the "positive-inside rule". Perhaps because "inside" is indeed an imprecise term (but now it is history and cannot be changed ;) ). In order to understand it a bit better it helps to think about the topology of the membrane. During synthesis most membrane proteins (ignoring peroxisomal and mitochondrial proteins, which are a whole other topic) are inserted into the ER membrane by the Sec translocon. The parts of the membrane protein that are exposed to the lumen are matured by the ER and Golgi apparatus to be presented on the extracellular surface. Secretory proteins (those that will ultimately be exported from the cell) are made in similar way except they pass entirely through the translocon and end up in the ER lumen. Therefore, the lumen of the ER (and consequently the lumen of other endomembrane compartments) are topologically consistent with the extracellular space, "outside", and not the "inside" of the cell. Perhaps is is easiest to see in a picture (borrowed from here: http://www.bioon.com/book/biology/mboc/chapter12/figure12-4.gif)
Coloured in pink are compartments whose topology is consistent with the "outside" and coloured grey are compartments whose topology is consistent with the "inside". So, for membrane proteins found in the endosome, for example, amino acid residues in the lumen are actually "outside" not "inside". It is true that this may not be immediately clear to those not steeped deeply in the field. As the initial studies used bacteria, which do not have membrane-enclosed subcellular compartments, "inside" was simple and made sense. Perhaps "positive-in-the-cytoplasm rule" would have been more accurate. Hope this helps!


What characteristics do living organisms (like humans or plants) have that viruses don't?

Linving organisms have intricate metabolic pathways that viruses donot have viruses stay in equilibrium till they infect host meaning that they they donot exachange matter and energy with surronding when they are outside the body but is a property shown by humans and living organisms.


CB1 and CB2 are indeed particular genes which are present in neurons, but also liver and other tissues.  The HGNC website is a good resource for questions like this - HGNC is the international organization that tries to unify and track gene names.

The official gene names are CNR1 and CNR2 respectively.  Gene names are a bit of a mess, since many genes have been found by different experiments and so have many names.

CNR1 has other aliases, I see:
CANN6, CB-R, CB1, CB1A, and CB1K5.

CNR2 has only the one alias: CB2.

I also searched the HGNC website for those alternate gene symbols and they appear to be different genes, although CB1 and CB2 are GPCR class receptors, humans have hundreds of these genes.  Most cell scientists would not be surprised if cannabinols bound other receptors - the fact is probably only that CB1 and CB2 bind strongest and were found first.  Often weak binding is important to specific pharma/neuro responses.

That is to say there shouldn't be any single Cannabinoid receptor in the animal repetoire.  CB1 and CB2 almost certainly have a primary function other than cannibinol binding.  Primates evolved in the old world and cannabis is thought to have originated in the Himalayan regions.  From an evolutionary standpoint, the activity of cannabinoids is as much coincidence as anything, so you would expect that a single receptor gene is unlikely.


What is a set of chromosome and what is a pair of chromosome

Yes those two expressions refer to different things.

Set of chromosome

The term "set of chromosome" refers to ploidy number. A haploid has one set of chromosome, a diploid has two sets of chromosomes, an hexaploid has six sets of chromosomes.

In humans, each set of chromosome is made of 23 chromosomes (22 autosomes and 1 sex chromosome).

Pair of chromosome

A pair of chromosome refers to the two homologous chromosomes in a diploid individual (one chromosome from each set for a given chromosome number).

Source of information

If the above is unclear, then you should have a look at any intro course to genetic such as these courses by Khan Academy for example.


Are there foods which not only prevent but help fighting cancer?

The short answer is, no.  There really isn't any good evidence that a person can eat enough of any chemical to have a clinically detectable effect on cancer.

Note that any study that shows an effect on cancer cells in a petri dish doesn't count as demonstrating that it would do anything in a person with cancer.  It might be that the chemical would not work the same in the body, or would not work the same on real cancer cells growing in a person (not cells cultivated to grow in a petri dish for 30 years).  And even if they did kill cancers like in a petri dish, that doesn't mean that you can actually eat enough of the chemical to get a high enough concentration to have that effect.

That link is pretty much click-bait, and nothing more.


General undergraduate zoology textbook recommendation?

I used Zoology by Miller and Harley in my undergraduate years and I found it to be an engaging, informative text book.


Detecting nuclear DNA in suspension of mitochondria

Centrifuge the suspension in Cesium Chloride solution at a particular g value which causes the mitochondria to settle to the bottom of the centrifuge tube but leaves nuclear DNA forming a layer near the top of the centrifuge tube. This is since the nuclear DNA is less dense than the mitochondria. Using a needle syringe, extract a small part of the centrifuged suspension from the very bottom of the centrifuge tube. This extract is most likely to contain no nuclear DNA. Hope this helps :).


Looking for good reference book in molecular biology

These always have a place at my library

HF Lodish, Berk, Arnold, and S. Lawrence Zipursky. Molecular cell biology. Vol. 4. New York: WH Freeman, 2000.

Alberts, Bruce, et al. "Molecular biology of the cell." Garland Science, New York 4 (2002)(the first few editions had James Watson himself as the editor)

Brown, Terence A. Genomes. Garland science, 2006.

For basics. I would recommend staring with Brown, and going on to Bruce Alberts and then Lodish. That's the way I learnt it.

For a really nice book with pictures (yes, we all like those) you might want to look into Lippincotts illustrated reviews (biochemistry, cell and molecular biology and the like). They are also quite good.

For a specific emphasis on techniques, I'd  recommend this:

Sambrook, Joseph, Edward F. Fritsch, and Tom Maniatis. Molecular cloning. Vol. 1. No. 7.58. New York: Cold spring harbor laboratory press, 1989.
(You can read the contents here http://www.molecularcloning.com/)


Microsatellites and Minisatellites: Which of these form the basis of DNA fingerprinting?

1) I'm told that VNTRs are used in DNA profiling. Does this refer to both minisatellites and microsatellites...or just minisatellites?

Actually, it refers mostly to STRs. I worked a bit in forensic genetics and we always published works using STRs markers (one example here, there are plenty in the literature).

In addition, I would not be surprised if current forensic identification used SNPs instead, e.g. as proposed in this paper

2) If only one of them is used, why disregard the other? They're both (technically) VNTRs aren't they? So shouldn't either of them work just fine?

I really don't know, but I am sure that it has to do with one of a) level of variation, i.e. if minisatellites have lower mutation rates and are less variable, then they also are less useful, b) ease of genotyping.

Browsing in the web I found this website from which I understand that the minisatellites were the first to be used to perform DNA profiling (using a method different from sequencing) and that "modern" DNA profiling is performed using STRs. However, I insist that modern DNA profiling should be better performed using SNPs.


Stability of the chromosomes of thermophilic bacteria

The stability and replication of the DNA of thermophiles is an interesting problem, for which there does not appear to be a single unequivocal answer. However the way you express this question is unfortunate: the hydrogen bonds in the DNA of thermophiles (which include some eubacteria as well as archea) are the same as those in any other genomic DNA. The question is, rather, why the strands of the DNA do not dissociate. This is not really my area, but as there have been no other answers I shall summarize what I have learned from the literature.

A review that was the starting point for this information is:

D.W. Grogan, Hyperthermophiles and the problem of DNA instability Molecular Microbiology (1998) 28(6), 1043–1049.

One obvious possibility would be that the genomes of thermophiles have a high percentage of GC, as GC base-pairs have three hydrogen bonds, whereas AT base-pairs have only two. However, this is NOT the general case.
It has long been known that the melting temperature (the temperature at which 50% strand-separation has occurred) is increased by increased concentration of cations. It has been suggested that this could be a factor, especially in those thermophiles that are also extreme halophiles.
In eukaryotes genomic DNA is condensed into chromatin by the interaction of the basic histone proteins. These proteins are not found in prokaryotes, but different basic molecules, polyamines, have been observed that are more abundant in thermophilic than mesophilic bacteria. As they have been observed to protect DNA from thermal denaturation in vitro, it has been proposed that they may also perform this function in vivo.
Type I topoisomerases that introduce positive supercoils into DNA (‘reverse gyrases’), occur in hyperthermophiles examined but not in mesophiles, and it was suggested that this could stabilize the DNA. However, the Grogan review presents a body of evidence that casts doubt on whether this is, in fact the case.
In addition to strand-separation, the genomes of thermophiles face the problem of increased damage to their DNA. Although, again, the situation is complex, it appears that they have evolved more extensive and active systems of DNA repair to deal with this.


Apparently I asked too soon. Summarizing my recent findings, I conclude that adrenaline is the better term.

To be more explicit, here is why:

The US National Library of Medicine recommends “epinephrine”, this is however mainly due to historical reasons (adrenaline used to be a trademark name in the USA).
This quite comprehensive paper on the issue presents a series of arguments for the use of “adrenaline”. These include: Better compatibility with other languages (where epinephrine is not at all in use); Better integration with other biological terms (adrenergic receptors, adrenal gland, adrenectomy, etc.); Better historical accuracy (epinephrine used to be the name for a neurochemically inactive crude extract from the adrenal glands).

I find the arguments of the referenced publication convincing, though I would recomend you read them in full.


Per Wikipedia, typically when one needs a lot of virus, it is grown in a controlled cell environment. This used to be eggs, but is moving toward cell cultures instead.  So basically yes, factories full of virus (though more like in nice discrete bioreactors than big Joker-friendly vats).
Synthetic vaccines, such as the mRNA vaccines for COVID, do not need this step at all, since they do not actually use the virus, but can be done through cell-free biochemical reactions that replicate the mRNA directly.


How do prodrugs exactly work? Are there multiple varieties of prodrugs?

Prodrugs are extremely common; we often don't even think of some of them as prodrugs unless we're also familiar with the metabolite. Psilocybin, for example, is a prodrug; the active molecule is psilocin. Aspirin is a prodrug of salicylic acid (though there are also other active metabolites).
Prodrugs can be categorized according to where they are converted to active forms: intracellularly in target tissue or other organs like the liver, or extracellularly like in the gut or in the bloodstream. The Wikipedia link at the beginning of this answer includes a table with some examples.
Prodrugs may be converted to active forms by enzymes or by environmental conditions in the body, like pH. I'd argue they are diverse enough that it doesn't make all that much sense to study them as a category, rather that in any pharmacological class of drugs you should be aware that they may be administered in a modified form, often to improve bioavailability or storage stability.


Is it possible to correctly identify presence of Y chromosome with external physical test only?

No, an external physical examination would be inconclusive. The reason is the TDF
gene. To be more specific, if a person has XY and the gene is not active then the subject
would have a female appearance. Also we cannot conclude that a person has a Y
chromosome even if it has penis because that gene could be transferred on the X chromosome.

Here is a reference: http://en.wikipedia.org/wiki/Testis_determining_factor.


How do porcupines keep from pricking each other while mating?

The female stood with the tail held sharply to one side, and the quills on
  the back lying very flat.  The male stood on his hind legs, while the
  front legs grasped the sides of the female. There was no repetition  of the act.

The male's urethra is 115-120 mm long, and his penis is 75 mm, so the he doesn't need to be as close to the female as one might think.  The retractor muscles are attached to the lower portion of the pelvis, which is likely well below the level at which the male's quills end.

Apparently, a dozen or so porcupines will den up in close quarters for the winter, so one can probably guess they have a good sense of whether their spines are hurting another, but that's only conjecture.

I suppose the take-home message is, nature will find a way.

Struthers, P.H. (1928) Breeding Habits of the Canadian Porcupine (Erethizon dorsatum).  Journal of Mammalogy, 9(4), 300-308. http://www.jstor.org/pss/1374084

Mirand,E.A., Shadle,A.R.(1953).  Gross anatomy of the male reproductive system of the porcupine
Journal of Mammalogy, 34(2), 210-220. http://www.jstor.org/pss/1375622


Who was the first to coin the terms of soft and hard selection?

I believe it's Wallace, B. 1968 "Polymorphism, population size,and genetic load" In R. C. Lewontin Population Biology and Evolution. Wallace also discusses his distinction between soft and hard selection in his 1975 paper "Hard and Soft Selection Revisited" (JSTOR link).


Hypothetically, what is the smallest functional form of human?

This question is for Doctor Frankenstein!

The answer would depend on what you would accept to consider being a human.

Does it still need to be able to make simple calculation in order to be a human?
Yes, because otherwise we would have lost some functions. But then you may ask…
Does it need to have big enough hands in order to fulfill the social function of hand shaking.
Does it has to be attractive to the other sex?
Does it need a heart or is it fine if oxygen diffusion through tissue only is enough for this creature to live?

I guess that if you change the number of cells you will necessarily change the functionality. I am not saying that small guys are not as functional as big guys. For example, big guys are better runner, while small guys are better climber.

Are we allowed to shrink the cells to have minimal sized cells?
Are we allowed to shorten the DNA in order to shrink the cells?

Notes:

There are approximatively 200 different cell types in a human

My reference is not a peer-reviewed article (ref). Wikipedia lists cell types and it doesn't seem to go over 200. However, it is important to realize that it probably very much depend on how you define cell types.

Terminologica Anatomica lists over 7,500 names parts of the human body
There are 13 or 14 (depending on the gender) gland types
This article provides an estimation of the number of cells in the human body
Here (wikipedia) is a discussion on the concept of the minimal cell
Here and here (biology.SE) are discussions on the minimum number of genes/amino acid to sustain life
Here (biology.SE) is a discussion on which species has been found to have the smallest genome


Where does Taq polymerase migrate during electrophoresis?

Unlike in an SDS-PAGE, where the SDS adds negative charges to all proteins, in a standard agarose gel for nucleic acids all proteins should move according to their own charge.

You can get a rough idea in which direction Taq would move by getting the amino acid sequence and calculating the isoelectric point at the pH you are running your get at. It might be that the protein isn't even negatively charged at this pH, then it would move in the opposite direction of the DNA out of the gel.

An exact prediction is rather hard, as it depends on the shape and size of the protein, the pore size in the agarose gel and the exact charge. It is not as simple as for DNA. You would have to just try it out to get an accurate value.

You can use any common method of staining proteins like Coomassie.

I think reusing the Taq is very unrealistic. It is still pretty stable at higher temperatures, so it will probably survive the temperatures the gel is running at. I would guess that you lose so much during PCR, gel and purification that it would not be worth the effort. And you would need to purify it extremely well, unless you want to amplify the same DNA in all your future PCR reactions. Any DNA contamination left from your gel might interfere with your later reactions.

If you require a very large amount of Taq and want to cut costs, I'd rather try and produce and purify the enzyme yourself. That should save you a lot of money if you really use a lot of it, but it is likely not worth it on a small scale.


How do normal cell division chance into a tumor forming cell division?

In a word: mutation.

If you step back and think about it, multicellular organisms are really, really complex systems. Different cells have to do different kinds of things and interact with each other, they form organized tissues and organs and so on. That much is obvious.

For all of this to work in concert, cells have to grow and divide (to replace dying cells) in a nice orderly fashion/at a nice orderly pace. Since that's a complicated process, lots of the genes in any given cell play a role in managing how long that cell lives/how fast it divides (i.e., cell cycle regulation).

So now, if DNA in a given cell gets mutated, there's a chance that mutation will hit one or more of these genes that are involved in cell cycle regulation. And you can imagine there are two extremes of what might happen: On one extreme, the mutation could mess up the cell cycle in such a way that it's broken (the cell can't grow/divide, things get screwed up, and it dies off); on the other extreme, the mutation could instead destabilize the cell cycle in such a way that it's "kicked into overdrive."

In the first example, we wouldn't observe the effect; the mutated cell would just die off, no big deal. But in the second example, with the cell cycle in overdrive, that cell would barrel ahead, growing fast and dividing faster than the cells around it. And since each of its child cells would have the same DNA and thus have the same "kicked into overdrive" mutation, they'd divide too quickly as well, and so would their children…and eventually you'd have a crazy mass of out-of-control cells. That's a tumor.

p53 is a tumor suppressor because it effectively "sounds the alarm" when it notices DNA damage (mutation)—meaning, when it finds DNA damage, it initiates several processes to try and control/fix/stop it. This is important because if that DNA damage is like the second example above, it could lead to a cancer that harms or kills the whole organism.

If the p53 gene itself is mutated, then the cell has lost one of its major defenses against damaged DNA, and thus there's a much greater chance that a cancer-causing mutation in some other gene could go unchecked. That's why damaged p53 is found in lots of cancers: because the cell lost a big defense mechanism against cancer, and then cancer happened.


Alcohol consumption and central nervous system

After alcohol intake, the cerebrum related functions like vision and speech is affected first and later on there's problem with the cerebellar functions like balancing and hand-eye coordination. My question is- why is it so? Why do they appear in that order?

It is and it isn't complicated. When you include what each does, it's an interesting question.

We know from experience (and even research, though the ethics of carrying out such research is questionable) that of the noticeable effects on the brain, the first part of the brain (that we can see the effects of) are on the cerebrum. At relatively low doses, the drinker feels more relaxed, more talkative, less inhibited. (there is also a measurable decrease in information processing and reaction time, as well as other less obvious effects.) All these are under the control of the cerebrum.

At this stage, the cerebellum is affected as well, but not grossly (in a manner that we can observe as change in behavior.) The cerebrum is critical to functioning; the cerebellum is critical to survival. Although it's presented as a teleological argument, the simple fact is that effects of alcohol and other sedatives on various parts of the brain are dose-dependent.

  First, dose-dependent functional magnetic resonance imaging (fMRI) changes were revealed in orbitofrontal (OF) and motor (but not cerebellar) regions; visual and medial frontal regions were unaffected. Second, cerebellar regions were significantly associated with driving behavior in a dose-dependent manner. Finally, a global disruptive effect of alcohol on the ICA time courses was observed with highly significant differences in OF and motor regions. Alcohol thus demonstrated some behavioral effects and unique, disruptive, dose-dependent effects on fMRI signal within several brain circuits. The fMRI data also suggest that the deficits observed in alcohol intoxication may be modulated primarily through OF/anterior cingulate, motor and cerebellar regions as opposed to attentional areas in frontoparietal cortex.

If you want to know why different parts of the brain require higher doses to become impaired, that is easy in theory but very complicated in reality. In theory, the brain is no different than any other complex organ in the body: it's made up of different cells. Sure, they're all neurons (excluding glial/etc cells), but not every neuron is the same, just like not every cardiac myocyte is the same. In reality, the answer is unknown.

  Neuronal mechanisms underlying alcohol intoxication are unclear. We find that alcohol impairs motor coordination by enhancing tonic inhibition mediated by a specific subtype of extrasynaptic GABAA receptor (GABAR), α6β3δ, expressed exclusively in cerebellar granule cells. In recombinant studies, we characterize a naturally occurring single-nucleotide polymorphism that causes a single amino acid change (R100Q) in α6 (encoded in rats by the Gabra6 gene). We show that this change selectively increases alcohol sensitivity of α6β3δ GABARs. Behavioral and electrophysiological comparisons of Gabra6100R/100R and Gabra6100Q/100Q rats strongly suggest that alcohol impairs motor coordination by enhancing granule cell tonic inhibition. These findings identify extrasynaptic GABARs as critical targets underlying low-dose alcohol intoxication and demonstrate that subtle changes in tonic inhibition in one class of neurons can alter behavior.

The above sounds like a reason, but it is debated still. I think it's safe to say that like so many cellular reactions, the answer will come down to receptors and their activation or inhibition, be it for GABA/NMDA, combinations or others.

Alcohol impairment of behavior in men and women
Differential effects of ethanol on motor coordination in adolescent and adult rats
Alcohol Intoxication Effects on Simulated Driving: Exploring Alcohol-Dose Effects on Brain Activation Using Functional MRI
Modulation of GABA A receptors in cerebellar granule neurons by ethanol: a review of genetic and electrophysiological studies
Ethanol affects NMDA receptor signaling at climbing fiber-Purkinje cell synapses in mice and impairs cerebellar LTD


Just to add a little more on the interface between optics and dentistry:

Whilst teeth do not phosphoresce, they do in fact autofluoresce.

The differential auto fluorescence of healthy tooth and carious tooth has been used for the early diagnosis of caries. (Gugnani N, Pandit IK, Srivastava N, Gupta M, Gugnani S. Light induced fluorescence evaluation: A novel concept for caries diagnosis and excavation. J Conserv Dent 2011;14:418-22 and http://www.opticsinfobase.org/boe/abstract.cfm?uri=boe-2-1-149)

To see teeth glow, or rather, fluoresce, they should be illuminated with short wavelength light, like blue light (wavelength 450 nm) and the teeth will glow green, which will be visible if the the blue light is filtered out.

Also see http://www.inspektor.nl/dental/qlfmain.htm#QLF%99%20Basic%20Principle


Are there any known microbes capable of living in almost pure carbon dioxide?

These aren't technically extremophiles, but one paper identified twenty species of bacteria that grow under a low pressure, mostly CO₂ atmosphere1.

One relatively well studied species is Serratia liquefaciens (a Proteobacterium) that has been shown to grow under

  low temperature (0 °C), low pressure (0.7 kPa), and anoxic, CO2-dominated atmosphere-conditions intended to simulate the near-subsurface environment of Mars2.

References:

1: Schuerger, A. C., & Nicholson, W. L. (2016). Twenty species of hypobarophilic bacteria recovered from diverse soils exhibit growth under simulated martian conditions at 0.7 kPa. Astrobiology, 16(12), 964-976.

2: Fajardo-Cavazos, P., Morrison, M. D., Miller, K. M., Schuerger, A. C., & Nicholson, W. L. (2018). Transcriptomic responses of Serratia liquefaciens cells grown under simulated Martian conditions of low temperature, low pressure, and CO 2-enriched anoxic atmosphere. Scientific reports, 8(1), 1-10.