The catalytic domain is roughly referring to the same part of the protein as an active site and may be used interchangeably in some circumstances:

See here, where "catalytic domain" redirects to "active site."

There is, however, a difference:

From a free online medical dictionary:

  active site:
  the place on the surface of an enzyme where its catalytic action occurs.

From Wikipedia:

  catalytic domain: structurally conserved (tertiary) structure containing the catalytic function of the protein.

To further clarify: the catalytic domain is the 3D structural independent folding unit of the protein that contains an active site, while the active site (aka "catalytic site) is the area located within the catalytic domain where substrate molecules bind and undergo a chemical reaction.


The whole point of this problem is that for each 100 molecules of annealed oligos, you need to have one molecule of each fragment.

You need to take into account the following:

The MW of each fragment is approximately proportional to the length of the fragment. Thus if you divide the concentration by the length of each fragment, you can get a value that simulates the molarity, meaning that you can use these values to fix to the ratio that you are asked between the different fragments.

For example, if the fragment1 is 100 bp and you have 10ng/µl, fragment2 is 200 bp with the same concentration, then you need to add 1 volume of fragment1 and 2 volumes of fragment2 to get the 1:1 molar ration.

In a similar way, you can calculate the amount of oligos added to have 100x more (of the ratio of concentration to bp length) than the respective fragments.


Are efflux pumps mutations or are they originally present in N. gonorrhoea?

Efflux pumps are common in bacteria, as well as eukaryotes. The mutations included in their model would not include efflux pumps. A mutation could potentially affect the efficiency of a pump in a strain but the mutations in their model are not creating the pumps.


A Brain Implant improves memory--but how?

From what I understand, when we learn we go over things quite a few times, this is so that our brain goes over the memory cells where we store that information with electrical impulses. Thus when an electrical impulse travels over some branches they strengthen the branches, (I don't know the science behind this). This is what helps us memorise data. So if we ran lots of Impulses over the branches it could help strengthen them or fry your brain, just saying try this in a safe environment such as a lab and not in a homemade electric chair. Also like you said it helps them run easier over the brain which makes it a lot easier to remember things.

Hope this helps,

IbnJalal


Can someone help me analyze this article?

I will answer the questions one by one-

Why does this miniaturization necessitates insulation ?
An organism's volume determines the total amount of heat that can be stored. The loss (exchange) of heat between the body and external environment mainly occurs on the skin's surface. Hence, body volume determines how much heat is stored, while body surface determines how fast that heat is dissipated to the environment. Volume increases with a power of three with radius, while surface increases with a power of two. Hence, smaller animals have large surface-to-volume ratios, which decreases rapidly with body size. Hence, small animals will dissipate relatively more heat per unit of time.
Dinosaurs suppose to have tetrachromacy. The article mentions "dinosaurs were endowed with the highly differentiated color vision of birds". Does this mean Dinosaur's "inherited" their tetrachromacy from birds ?
No, birds are the closest living relatives to dinosaurs, and birds can be said to have inherited tetrachromacy from dinosaurs - see the cladogram below.

Why does the article mention reptiles before that ? Are birds reptiles ?
Birds are not reptiles, they are separate classes within the animal kingdom.
What is the direct connection between mammals and the dinosaurs ? ... why bring the mammals into the discussion ?
Here below is another cladogram; there is no obvious, direct (evolutionary) connection between dinosaurs and mammals. The thing is that dinosaurs ruled the world before the last mass extinction, thereafter it were the mammals. That's why the authors discuss them both, I guess. Especially since we are mammals it may make sense to draw parallels.

What is the connection between pennaceous feather and planar feathers
As far as I could track the two down, they are the same (Prum, 2006)

Lastly, in response to your original question, before edits: Here is a link with a plain-English popular-scientific web article published online by the first author.


I did some research and I found this site : https://www.covance.com/content/dam/covance/assetLibrary/posters/StrubleEVER14.pdf

It has the weight for ocular tissues for different kinds of animals ( rabbit , human  etc. ).

I also found that the area of a retina is 1094 mm² and the thickness is 0,12 mm , so if you can find the density you can find the mass.

(found on this site https://faculty.washington.edu/chudler/facts.html#sensory )


Why don't we have vaccination against all diseases caused by microbes?

Mainly cost/benefit analysis. Using vaccines has a cost, both in dollars and in risk. That cost may be very low (cheap safe vaccines, like measles vaccine), or may be relatively high (smallpox vaccine is relatively risky, with around a 1 in 300,000 chance of moderate to severe side effects); but there is always some cost.

Vaccines may not have any significant benefit. I live in the urban USA; it's unlikely that an Ebola vaccine would offer me any benefit (as of the current situation in 2019). Very few people in 2019 have a significant chance of being exposed to smallpox, since it's extinct in the wild; the benefit of universal smallpox vaccine would be small.

So if the risk of a vaccine is greater than the benefit, delivering the vaccine would be more harmful than good. This calculation is done as a routine, and the vaccines people receive are known to be ones that confer more benefit than risk.

In fact, with vaccines, the benefit needs to be much higher than the risk, because with vaccines the benefit is invisible (nothing happens - you don't die of measles) while the risk is something that happens. Typically, vaccine benefit/cost ratios are very high, for that reason.

Monetary cost is also a factor. It may seem harsh to think that saving a child's life with a vaccine is given a price, but at some point the finite supply of money can be used more effectively elsewhere. If it costs a billion dollars to give a particular vaccine, and it ends up saving one life, is that the best use of money? Could it be better spent on nutrition, sanitation, etc?

This applies to quite a few diseases. There are, in academic labs and in the freezers of pharmaceutical companies, vaccines against a lot of pathogens that are not being used, because the cost is too great for the benefit. That's an equation that changes all the time; it applied to the Ebola vaccines at one point, but in the face of an Ebola outbreak those vaccines -- in those areas -- are now cost-effective.

Finally, there are a handful of pathogens for which a reasonably-priced good vaccine would certainly be cost-effective (HIV, malaria, tuberculosis, for example) but for which reasonably-priced good vaccines don't exist, because vaccines are sometimes really hard to make.


In general, alleles don't have to be the same size. Two major examples which come to mind are the Huntingtin gene and FMR1.

Huntingtin is the causative gene of Huntington's disease. In people with Huntington's, a sequence of three nucleotides is repeated. The number of repeats varies, from a low of 9 in unaffected individuals, to more than 60 in severely affected ones. So depending on how many repeats you have, each of your Huntingtin alleles may have a different nucleotide size.

FMR1 is the causitive agent of Fragile X syndrome. Like Huntingtons, the gene varies in the number of trinucleotide repeats, but for FMR1, affected individuals can have over 1000 repeasts, meaning an extra 3 kilobases of genetic material versus the alleles of an unaffected individual.

Other genetic disorders are also related to the difference in allele size. You can have a deletion of a region of DNA (or an insertion) which is normally silent (recessive). The normal-length allele compensates for the defective allele, but the differently-sized disease allele is still present in the population, and counts as an allele of the gene.

It's not just disease-prone alleles which exhibit length polymorphism. A number of other genes will show variation on both the DNA and on the protein level. If the insertion/deletion is a multiple of three nucleotides and occurs in a loop region of the protein or on an intrinsically disordered domain, the insertion has a reasonable chance of minimal structural effect on the expressed protein. For one (completely arbitrary) example, PER3 has two major length variants in the population, with a 54 base pair difference between the two. Different populations have vastly different prevalence for each, with a range of 20-90% for the shorter version.

One thing to keep in mind is that "locus" points are just a human convention to help us map DNA. To the cell, DNA is just a single long molecule. (Or multiple molecules, for different chromosomes.) There isn't any labels for absolute position in the cell, so inserting or deleting a chunk of DNA mainly affects just the local environment. There isn't any sort of long-range indexing that gets messed up by the insertion.


What are the purposes of granulocytes in acute inflammation?

MattDMo's answer

  Essentially, [neutrophilic granulocytes] are the first infiltrating
  cells to arrive at the site of injury at the beginning of acute
  inflammation (bacterial infection, environmental exposure, etc.).

which I agree with.


The experiment is easy to design: Measure the concentration of the pheromones in the test sheep versus the control sheep and see what the outcome is. Further compare the reaction of the male sheep on both, control and treated sheep. Ideally you treat both animals with some kind of treatment to avoid an influence by the application method of the estradiol. Also blind the researchers to avoid their influence on the experiment.
The hypothesis would be: Has estrogen E2 an influence on the pheromones in female sheep and do these pheromones influence the male sheep.


Are insects attracted to near infrared light?

In general, insects are most attracted to UV light. If you switch to a light source without UV-light, the amount of insects attracted will reduce to almost zero.
It has been hypothesized that this sensitivity to UV-light is because direct light sources (sun, moon) contains more UV than objects that reflect light. In this way, it may help insects to distinguish between open spaces and shelter.
It has long been thought that insects are blind to red and IR light. However, there is evidence that some insects do see, and are attracted to, IR light, at least up till 740 nm. However, red or IR light will attract far less insects compared to ypur incandescent light source.


Why do cherries sometimes grow as triplets?

Why do they (cherries from a cherry tree) sometimes grow like that (in triplets) and how often does it happen compared to their regular twin counterparts?

After doing a considerable amount of research, I also wasn't able to find much of any literature that addresses your question, aside from this. From that article it says:

When you think of cherries you imagine them in pairs, don't you? It's also common to find cherries grouped in quadruplets on a single bunch of stems. This happens because of the way cherry flowers bloom -- several pink blossoms grow from a single focal point, and when those flowers wilt and become fruit, the resultant cherries are connected, too. It's smart to keep cherries attached to their stems whenever possible, as they will stay fresh for much longer. And when you're harvesting the fruits, harvest the cherries at the stem (no higher!) or you risk next year's buds snapping off along with them.

The bolded section seemed to be most revealing, and so, I was able to find a time-lapse video that depicts the various stages of the flowering & fruiting process for a cherry tree. The video is only 4 minutes long, and I highly suggest watching it.
From watching the video, it can be confirmed that the statements made by the previously quoted passage are true -- "several (pink) blossoms grow from a single focal point, and when those flowers wilt and become fruit, the resultant cherries are connected, too".
Consider the following series of images, which are screenshots from the time-lapse video. You should view these images in an alternating left to right, right to left fashion, going from top to bottom (so, snake-shaped).

As can be seen, each flower does grow from a shared focal point, and, the cherry fruit does originate out of the exact same location as where the flower was.

What's most interesting to note, and which begins to answer your question, is:
When viewing the third row (left to right), for the first two images, there are multiple cases of three cherries growing from the same stem. However, in each case, one of the three cherries are actually extremely underdeveloped. But then, if you compare the second and third image (still in the 3nd row, left to right), those underdeveloped cherries completely disappear!
It would then seem to me that, since one of the three cherries are severely underdeveloped (most likely due to limited nutrition & resources), the farmer who is tending to the tree will prune these (underdeveloped) cherries, thus leaving only pairs of two. In extreme cases, perhaps, the third (or even fourth) cherry achieves enough development for the farmer to not consider pruning it, but, this appears to be the exception.
Further supporting this idea, consider the next series of screenshots (from the same video).

When harvesting, the farmer deliberitely picks the cherries by pairs of two. There's even a time when he almost pulls off three, but then makes sure to leave the third. This process of pruning underdeveloped cherries, as well as harvesting in pairs or two, is most likely common practice amongst cherry growers.

And when you're harvesting the fruits, harvest the cherries at the stem (no higher!) or you risk next year's buds snapping off along with them.

Given that quote, it could be that picking in pairs of two is the most efficient method of harvesting that also best ensures the safety of next year's buds. So, to restate the reason, it would appear that cherries are rarely seen in groups of three (or more) due to nutritional constraints, and the pruning & harvesting methods of the farmer, or tree owner.


Why don't all bacteria have F-plasmids by now?

Conjugation occurs between cells of the same species too. For this to occur cell have to be close to each other. Now, if you have an isolated population of bacteria that never gets in contact with an F+ bacteria then this population would stay F-. Also not all conjugation events are successful, mechanical perturbations can disrupt the pilus through which genetic material is transferred.
This old article can give you good details:
THE ORIGIN OF BACTERIAL SPECIES - GENETIC RECOMBINATION AND FACTORS LIMITING
IT BETWEEN BACTERIAL POPULATIONS ARNOLD by W.RAVIN

  F+ shares, however, an important property of bacteriophage: after infection
  it behaves as though it were an addition to the bacterial genome. As an addition, it can furthermore exist in one of two forms: in one form, it
  is an unintegrated part of the bacterial genome, and may be  replicated either more or less rapidly than the "chromosomal" or linked genes (being
  infectious or lost through dilution, respectively); in its other form, it
  is integrated in the sense that its replication is coordinated with the
  replication of the host's genes, as though attached to them. In this latter form, found in Hfr bacteria, the F+ factor is incapable of infecting other bacteria (while permitting conjugation with them) and also prevents
  superinfection of its host bacterium by a nonintegrated F+ factor.

Taken from the linked paper. So you can see that are situations where conjugation occurs yet the F- won't become F+.

Also :

  What is particularly interesting about the F+ factor is the fact that there
  seem to be a number of different  kinds. An F+ factor making a bacterium
  fertile with some  F- cultures does not necessarily  make it capable  of conjugating with others (49).

So not every F+ cell can conjugate with another F- cell.


What is these mushrooms in my indoor pot?

They do look a lot like a common mushroom called "shaggy mane" mushroom (Coprinus comatus). This may not be a correct identification though, so do not eat them.  They are widespread around the world, but usually grow outside.

Yes it is amazing how rapidly the fruiting body of many fungi can grow. I am providing an interesting Wikipedia link with more information. You can also search to find other images using Google images online.

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


What happens if a speciation event causes the new species to evolve out its clade's defining trait?

Yes, it would. A clade is defined as an ancestor and all of its descendants regardless of whether they look alike or not. Now, it is of course up to us (humans) to decide what we want to call strepsirrhine. If we decide that the new species that has no rhinarium is not a strepsirrhine, then strepsirrhine will stop being the name of a clade but will be the name for a paraphyletic group (and we would probably need a new name for the current clade of strepsirrhine).

You can get more information about phylogeny in this post and much more info in an intro class to evolutionary biology such as Understanding Evolution for example.


Can translation ever occur without transcription?

I am assuming that the question is whether, in single-standed +ve RNA viruses, translation of plus-strand RNA can occur before transcription.

First, there are many different families of viruses, and there are bound to be counter-examples to whatever I say here. However, with that rider:

We generally refer to replication of RNA viruses by RNA-dependent RNA polymerase, rather than transcription. I am not aware of any RNA virus that has an RNA polymerase recognizing promotors and transcribing specific genes. These viruses tend to replicate in the cytoplasm and therefore do not have access to host RNA polymerase.
There has to be replication, and this tends to be conservative, rather than semi-conservative. By this I mean that when minus-strands are generated they act as templates for many plus-strands, which are needed for the virus particles.
In the case of picornaviruses, such as polio, translation can occur before replication. As is common with small RNA viruses, there is a single initiation site for translation — in the case of polio, a polyprotein is produced, which is subsequently cleaved into individual polypeptides. The diagram below is from the Wikipedia entry for poliovirus and is reproduced here under the Creative Commons license.

[Nidia H De Jesus (image and caption) - De Jesus NH (2007). "Epidemics to eradication: the modern history of poliomyelitis". Virol. J. 4: 70. DOI:10.1186/1743-422X-4-70. PMID 17623069.
The cellular life cycle of poliovirus. It is initiated by binding of a poliovirion to the cell surface macromolecule CD155, which functions as the receptor (1). Uncoating of the viral RNA is mediated by receptor-dependent destabilization of the virus capsid (2). Cleavage of the viral protein VPg is performed by a cellular phosphodiesterase, and translation of the viral RNA occurs by a cap-independent (IRES-mediated) mechanism (3). Proteolytic processing of the viral polyprotein yields mature structural and non-structural proteins (4). The positive-sense RNA serves as template for complementary negative-strand synthesis, thereby producing a double-stranded RNA (replicative form, RF) (5). Initiation of many positive strands from a single negative strand produces the partially single-stranded replicative intermediate (RI) (6). The newly synthesized positive-sense RNA molecules can serve as templates for translation (7) or associate with capsid precursors to undergo encapsidation and induce the maturation cleavage of VP0 (8), which ultimately generates progeny virions. Lysis of the infected cell results in release of infectious progeny virions (9).]


How do macromolecules (large drugs) in the eye reach the bloodstream and what are the relative significances of these pathways?

Antibodies are a unique case.  I recommend reading PubMedID: 26726925 regarding the pharmacokinetics of ranibizumab (Lucentis), a Fab fragment, after intravitreal administration.

"We assume that the principal pathway for the ocular clearance of large molecules is by a first-order transfer process from the vitreous to the aqueous chambers, from which the molecule is absorbed into the circulation via Schlemm’s canal by the physiological process of aqueous humor turnover."

A comprehensive analysis of the pharmacokinetic processes are included in the mechanistic model that they have developed.  I will not copy and paste them here.


Are alleles passed down and shuffled randomly to the offspring during meiosis or fertilization?

Crossing over/synapsis in Prophase I of Meiosis I is when alleles are switched over from one non-sister homologous chromatid to another non-sister homologous chromatid. This happens before fertilization ever happens. Meiosis occurs even before birth in females in order to make gametes in the form of oocytes. In contrast, this frequently occurs in men who continue to produce gametes in the form of spermatocytes throughout their lifetime. Fertilization simply refers to the fusion of two gametes-- a spermatocyte and oocyte combining together-- and does not involve meiosis.

Here's a short and straightforward Youtube video about Meiosis.


classical conditioning paradigm for hippocampal learning

First of all, your first sentence assumes something which may not be true and is still controversial in the literature. Learning and memory are thought to be related to the phenomenon of LTP but it appears you are taking this as a given.

There is a huge swath of literature on hippocampal-dependent behavioural tests like the Morris-water maze etc so I assume you are already aware of these. If you wish to monitor the HPC firing pattern:
1) during training --- you can set-up an in-vivo electrophysiology platform coupled to a virtual navigation interface and record from cells while the animals are performing a spatial navigation task.
2) after training- you can take slices from the animals as is classically done and try to induce LTP and see if your spatial learning task has influenced the amount of LTP you can get. The condidtioned and unconditioned animals will simply be the two groups which you can compare to see if the behavioural readout(spatial memory task) corresponds to changes in what is though as the cellular basis for memory(LTP)

  Whitlock, J.R., Heynen, A.J., Shuler, M.G., and Bear, M.F. (2006). Learning Induces Long-Term Potentiation in the Hippocampus. Science 313, 1093–1097.

  Goh, J.J., and Manahan-Vaughan, D. (2013). Synaptic depression in the CA1 region of freely behaving mice is highly dependent on afferent stimulation parameters. Front Integr Neurosci 7.

  Heynen, A.J., and Bear, M.F. (2001). Long-Term Potentiation of Thalamocortical Transmission in the Adult Visual Cortex In Vivo. J. Neurosci. 21, 9801–9813.


What's the difference between evolution fitness and reproductive success?

The concepts are very similar but there are a few differences.

Firstly, fitness is usually applied to alleles or genotypes, reproductive success to individuals.

Secondly (and partially as a consequence of this), fitness is an average or idealised/expected property across a population; but actual reproductive success per individual is stochastic. Individuals possessing an allele with a relative fitness of "2" will on average have twice as many offpsring as their competitors, all else being equal, but individual reproductive success will vary as a consequence of other factors such as predation, parasitism, starvation etc.

Finally, absolute fitness relates to the proportional representation of a genotype in a population. Reproductive success relates to offspring per individual. For example, in a growing population a genotype could be simultaneously declining in proportion while it is increasing in absolute number, if other genotypes are increasing in number more rapidly.


Will a 0.2g/mL sugar concentration cause vomiting in humans?

Sugar (be it sucrose, glucose, fructose or honey) does not have emetic properties in any concentration, unless there is a personal (and highly individual) psychological adverse reaction to sweet substances.

Sugar is not a local gastric irritant (like dishwashing detergent, or syrup of ipecac, copper sulphate, zinc sulphate; yellow mercuric sulphate, ammonium carbonate, powdered mustard and other local gastric irritants.) Some non-irritating substances (e.g. cod liver oil) may induce emesis because of a repugnant smell, taste, or texture. Few people find the taste of sugar repugnant. Gastric distension to the point of emesis does not occur with 12 or 16 oz. of fluid.

Psychological causes of vomiting include aversions (e.g. some people vomit when they see someone else vomit.) That would involve a cerebral cortex mechanism.

No sugar of any concentration is listed here as an emetic. If it were true, we would have a much less significant incidence of obesity.


The comments and answer so forth are mainly related to the visibility and possible social and evolutionary explanation of the 'red face'.

While not discussing the social or evolutionary factors, I can give an overview of the biochemistry involved.

Anger and associated feelings such as stress are part of the 'fight or flight' response. This response is regulated mainly by the release of epinephrine and norepinephrine (the same as adrenaline and noradrenaline) into the blood stream by the adrenal glands, and from neurons into the synapses.
Wiki:Fight or Flight response
(Hence, the signal is send out both in the whole organism, and locally between neurons).

These hormones/neurotransmitters have a number of physiological effects:

They trigger a combination of vasoconstriction and vasodillation  in different parts of the body, meaning that the blood vessels constricted and widened, respectively, in different tissues.
This allows for a more effective transfer of nutrients to the muscles and brain. Wiki: Epinephrine
They trigger the increase of blood sugar by breakdown of glycogen deposits. Again, the body is in a situation where it needs to use the available energy ressources.
The heart rate is increased. Again, this allows for more effective transportation.

As listed above, the hormones related to anger both trigger the constriction and dilation of blood vessels in different tissues. Thus, the routing of the blood through the system also changes.

However, the routing of the blood seems to differ, depending on the exact feeling, where blood sometimes are routed to the surfaces areas of the skin, and sometimes away from them (by means of vasoconsttriction and vasodillstion, respectively).

Intuitively, this is can be a way of controlling the body temperature, as the body can expose the warm blood to the surroundings to a lesser or greater extent.

I don't think it is entirely understood, what determines this, but a guess could be that in situations of anger, the body has to be able to effectively use the muscles and fight, and thus also needs to be cooled, in order for the systems to work properly.
In situations of fear you might to hide instead for a long time and preserve the body heat and energy (just speculations).

Besides, it also could have a social impact.

But when blood is transferred to the facial areas, including the brain which needs energy to think quickly, and the skin surface for cooling down, it can have an affect on the perceived color of the face.

As noted by others, the degree of visibility is highly personal, as it depends on several factors such as the degree of hormone release, hormone sensitivity, anatomical features of the face such as placement of blood vessels, skin color and so forth.


Do any animals other than humans undergo menopause?

Yes. Menopause is common for long-lived mammals. For instance, in the wild, killer whales go in a sort of menopause as reported in 2009 by Ward et al. Front Zool. 2009 Feb 3;6:4. So it is not due to captivity. According to a Nature review, reproductive cessation has also been documented in non-human primates, rodents, whales, dogs, rabbits, elephants and domestic livestock (Packer et al. Nature. 1998; 392(6678):807-11)


Do goosebumps always appear in the same spots on the skin?

Goosebumps are caused by the contraction of the arrector pili muscles, which are attached to hair follicles. Accordingly, they appear at the same spots on one's body every time.


What forms the base of the coral reef ecosystem?

One role of corals is to provide structure that offers protection from predation to many prey species as well as larvae and hatchlings. Reefs also provide relief from strong currents which, again, afford protection. Many other critters such as sponges, tunicates and other sessile animals use the reef as a substrate for attachment.

Don't be fooled by the apparent inedibility of coral, many fish eat it, notably Parrotfish. To give an idea of the extent of this activity, the bleached white beaches in Palau are carbonate "sand", not silica. They are the product of millenia of Parrotfish activity on the coral. (I don't have a link, this knowledge is courtesy of the Oceanic Society guide on our snorkeling trip.) In addition to Palau, I've snorkeled Indonesia, Honduras, Hawaii and elsewhere. In every venue, multitudes of many species of Parrotfish were to be seen aggressively chomping away at coral.

Also, the reef is also a substrate for many algae which serve as a food for other varietiesw of fish. Many of the coral inhabiting algae wouldn't be recognized as such looking like bubbles, fans and other oddities unlike common kelp.

Other species also feed on coral including welks, fireworms, nudibranchs and some starfish. Here's a link:http://infolific.com/pets/coral-reef-life/eating-the-coral-reef/


Why are turtles classified as reptiles and not amphibians?

Amphibians are not defined for having a moist skin, neither are reptiles defined for having scales on their body.

In biology, organisms (elements) are grouped according to their evolutive history in monophyletic groups, also known as clades. Basicaly, a monophyletic group is

  A group consisting of an ancestral and all its descendants.

"Tetrapoda" is a monophyletic group, formed by vertebrates with four limbs. Inside Tetrapoda, there are two groups: "Amphibia" and "Amniota". Amphibians are non-amniotes tetrapods, and we have some doubt if they are a monophyletic group. Amniotes, on the other hand, are tetrapods having an amniotic egg, including you and me, and they form a monophyletic group.

The amniotes are divided in two monophyletic group: "Mammals", which are amniotes with a synapsid skull, and "Reptiles", which are amniotes with diapsid skulls (I'm using "reptiles" as synonym of Sauropsida).

Reptiles include turtles, lizards, snakes, alligators and dinosaurs (which include the birds: all birds are dinosaurs). It doesn't matter if a animal has or has not scales, or if it lays eggs or if it is viviparous, or if it has 5 fingers or 3 fingers: All the descendants of a given ancestor are included in the monophyletic group that contains that ancestor.

Turtles, despite being strange or somehow different, are descendants from the same most recent commom ancestor of Reptilia... that's why turtles are reptiles (and that's why birds are reptiles as well).

To make this more clear, have a look at this cladogram (from Hickman, Integrated Principles of Zoology):

The apomorphy that defines the tetrapods is "paired limbs". You have Amphibia to the left and Amniota to the right, whose apomorphy is " egg with extraembrionic membranes". Inside them, you have Reptilia, whose apomorphies are "skull with upper and lower fenestra and beta-keratin in epidermis". Turtles came from an ancestor with these characteristics. So, turtles belong to the monophyletic group of "Reptiles".

Post scriptum: You wrote that "turtles (specifically sea turtles) live on both land and water, very much like amphibians". Just a curiosity: the reason why sea turtles leave the water (sea) from time to time shows exactly that they are not amphibians! Amphibians, being non-amniotes, have eggs that survive under water (actually, with few exceptions, they need to be under water). Turtles, on the other hand, are amniotes, and the amniotic egg cannot be laid under water. That's why the turtles have to leave the water to lay eggs: because, contrary to the amphibians, they cannot lay eggs under water.


The short answer is no.  What matters is whether the sequence and folding (if you are talking about binding of A to proteins instead of DNA) of each isoform of your gene still results in the binding of A.

I other words, A may bind to X. Y, an isoform of X may not have the same sequence that A likes to bind to. Or, in the case of proteins and A, Y may fold slightly differently, preventing accessibility of A to Y.


Is it possible to express a mutant gene only in a specific tissue?

It is called conditional mutation.

You flox (put lox sites around) gene of interest and express Cre recombinase driven by tissue-of-interest-specific promoter.

Illustration from here:

Using chemically-activatable variant of Cre recombinase (cre-ER) you can create knock-out in some cells of tissue of interest, not every.

Addition: a bit weird but still useful method is to produce KO by means of CRISPR/Cas9 system. Tissue-specific expression of Cas9 protein together with gene-specific sgRNA will likely produce KO in mosaic fashion. One of positive sides is that such approach requires only one transgenic line, e.g. Tg(promoter:Cas9;sgRNA)

Addition: (via WYSIWYG's suggestion) you can express shRNA or other gene transcription-interfering product from promoter that only active in specific tissue/specific period of time. And beauty of genetic/bioengineering is that you can combine several methods for additional control, robustness, efficiency etc.

Taken from here:

Inducible and sell-specific gene KO with shRNA

For further reading:

http://cre.jax.org/introduction.html

http://link.springer.com/protocol/10.1385/1-59259-065-9:477#page-1

Update

I re-read OP question and, as commented to it, feel some confusion. So I would like to mention as well way to express mutated gene in specific tissue that, when expressed constitutively (all the time, everywhere), is lethal. Imagine some very strong oncogene. Or something like cell-toxic protein, e.g. chemically-activatable nitroreductase or light-activatable Killer-red. Or it might be mutated version of your favourite synaptic protein that, when expressed in all neurons, causes severe lethal phenotype.

What you do, is create transgenic animal with transgene-GFP fusion (nitroreductase, KillerRed, etc) that has floxed stop-codons in front, and cross that animal with transgenic with tissue-specific CreER (for example). What you get is animal that, when injected with tamoxifen, start to express mutated gene/toxic protein in tissue of interest. Then you are sure that only GFP-positive cells express that gene. That is how you "express that mutant gene only in a specific tissue of interest to get a idea of which phenotype it produces".


In this illustration about CRISPR function, what do these objects mean (image provided)?

The arrow direction denote transcription direction and its location denotes the transcription start site. The circle is probably the transcription terminator (I cannot access this article at the moment, but this is what it should mean).

The purple boxes refer to the protospacers which are derived from foreign DNA. These elements help in recognizing and cleaving foreign DNA. These are transcribed as RNA which in turn guide the Cas complex to the target DNA. In a way, these protospacers provide some kind of immunological memory to the bacteria. See the below figure (From Nuñez et al. 2015 ):


Strange Striped Insect identification (Northern Indiana)

This is actually a Painted hickory borer (Megacyllene caryae).

According to the Virginia Cooperative Extension (and here), this species is frequently misidentified as a Locust Borer beetle (Megacyllene robiniae).

Here are their pictures side-by-side (M. robiniae on the left and M. caryae on the right):

Pretty similar, right? There are some differences though:

Appearance:

M. robiniae description (from Virginia Cooperative Extension):

  Both males and females have black bodies with bright yellow markings. These markings are most notable in the "W" on the first pair of wings.  Legs are red and antennae are black. These long antennae place it among the "long-horned" beetles.

The distinction for M. caryae is the white 'W' stripe. From OSU Extension:

  The first marking from front-to-back on the elytra is also a yellow horizontal band; however, the second marking appears as a distinct "W" that is light yellow to cream-colored.

The following image from the Ohio State Extension better demonstrates the white W markings of M. caryae (similar to the OP's picture):

These two insects also differ in Behavior ( this is important).

From OSU Extension:

  Painted hickory borers emerge from cut wood in the spring and locust borers emerge from live trees in late summer to early fall.

Since the OP found this in the spring coming from firewood, it further points to the painted hickory borer.

Finally, they differ in the species they infest:

From the Virginia Cooperative Extension:

  The locust borer is a native insect that attacks black locust (Robinia pseudoacacia L.) and its ornamental cultivars... Unlike locust borer adults, painted hickory borer adults...attack stressed or recently cut hickory and other hardwoods.

M. caryae is named for it's preferred wood, the hickories (Carya spp.).

According to OSU Extension, M. caryae also commonly infests the recently dead wood of ash, black locust, hackberry, honeylocust, oak, Osage orange, walnut, and butternut trees.

M. robiniae, on the other hand, gets it name from the larvae living in and eating their typical host tree, black locust (Robinia pseudoacacia). Adults are also often found eating goldenrod species.

Should you be concerned? Not according to the OSU Extension page:

  Fortunately, painted hickory borers only infest dead wood that has been cut for less than one year. ... The beetles will not infest older dead wood; they will not infest wood that has been dried or processed into home furnishings, or used as structural wood.  So, beetles that emerge from infested firewood in or around a home are only a nuisance pest.

A quick search for M. caryae turns up few other sources, but you can find additional fact sheets for M. robiniae here, here, and here.

For those that don't know trees: here is a link to learn more about the common North America hickory species, and below are some images of common hickory species. More info about black locust (Robinia pseudoacacia) can be found here.


Why are Aardvarks capable of burrowing given their size?

The following paper examines the link between burrowing ability and the stress and strain resistance provided by increased endosteal tissue formation (specifically compacted coarse cancellous bone (CCCB)) in aardvarks:

Physiological constraints associated with digging, however, are known to be strongly influenced by body size, and larger burrowers are likely to exhibit a histological profile more conspicuously influenced by fossorial activity. Here, we describe for the first time the limb bone histology of the aardvark (Orycteropus afer), the largest extant burrowing mammal...
We hypothesize that the unusual histological profile of the aardvark is likely the outcome of physiological constraints due to both extensive digging behavior and strong metabolic restrictions. Adaptations to fossoriality are thus the result of a physiological compromise between limited food availability, an environment with high temperature variability, and the need for biomechanical resistance during digging. These results highlight the difficulties of deciphering all factors potentially involved in bone formation in fossorial mammals. Even though the formation and maintaining of CCCB through ontogeny in the aardvark cannot be unambiguously linked with its fossorial habits, a high amount of CCCB has been observed in the limb bones of other large burrowing mammals.

Digging the compromise: investigating the link between limb bone histology and fossoriality in the aardvark (Orycteropus afer), PeerJ Life & Environment (2018)

Further reading:

Ecosystem engineering through aardvark (Orycteropus afer) burrowing: Mechanisms and effects


Digestion Enzymes in Carbohydrate Metabolism?

1,6-glucosidases are a class of enzymes and not just one enzyme. It does not mean that all the members of this class are the same enzymes. They catalyse the same kind of reactions but their properties and substrate specificities differ. Check BRENDA for details.

BTW, dextrin-1,6-glucosidase is a synonym for amylo-alpha-1,6-glucosidase. Other 1,6-glucosidases are different enzymes with different EC numbers.


Can there be medium height(neither tall nor short) pea plants in Mendel's experiment?

Medium height (like in people) and other traits that seem like a mixture of two extremes are often a result of incomplete dominance. For example, a red and white flower are bred to produce an offspring with pink petals.

Mendelian genetics does not include incomplete dominance (which is classified as, surprisingly, non-Mendelian genetics).

Basically, Mendel got very lucky with his choice of plant. Pea plant height is strictly dominant, meaning one dominant allele results in tall plants, regardless of the identity of the second inherited allele. This is a consequence of the genetic makeup of pea plants. Had he tried a similar experiment with snapdragon flower color, he would be very confused.

(See https://www.ndsu.edu/pubweb/~mcclean/plsc431/mendel/mendel2.htm for snapdragon incomplete dominance example.)


Population where most of the newborns die soon?

Yes, we talk about r/K selection theory:

  In ecology, r/K selection theory relates to the selection of combinations of traits in an organism that trade off between quantity and quality of offspring. The focus upon either increased quantity of offspring at the expense of individual parental investment of r-strategists, or reduced quantity of offspring with a corresponding increased parental investment of K-strategists, varies widely, seemingly to promote success in particular environments.

The type of species you describe are the r type.

Please note the following potential confusions:

A species can vary its strategy through time and space

Species can change from K to r (and vice-versa) depending on the environment and number of individuals. Consider humans as an example.

The expression r/K selection theory can be misleading

The term "selection" in "r/K selection theory" can be a bit misleading as it refers more to a demographic reality (which has come to be due to selection pressures) but not to the selection process behind it.

Alternative meaning of 'r/K selection theory'

The terms r and K are sometimes used to mean whether a species has reached carrying capacity (K) or whether they are growing in number (r) which is not exactly the same as the interpretation of whether there is much parental investment in the species presented in the wikipedia article.

This second interpretation is actually closer to the origin of the terms r and K. The most common (and one of the simplest) equation of population growth through time is the logistic equation (see here for an easy explanation and also wiki > Population ecology )

$$\frac{dN}{dt} = rN \left( 1 - \frac{K}{N}\right) $$

, where $N$ is the population size, $t$ is time in generation, $r$ is the maximal growth rate and $K$ is the carrying capacity. On the graph above, $r$ represent the maximal slope (that is the maximal growth rate).

r selected species are those that have a growth rate as indicated at the center of the graph. K selected species are those that have a growth rate of 1 (no increase in $N$) as the ones that are at carrying capacity $K$.


HIV was identified as an infectious disease through classical epidemiology, and the virus was identified through classical virology.
I won't get into the epidemiology, but briefly it went pretty much as you'd expect -- a cluster of symptoms were identified, patient characteristics were analyzed, the contagious nature of the symptoms were recognized, all through standard approaches of patient tracking and so on.
As for the virus identification, that was long before modern molecular techniques were available.  It was even before PCR was commercially available!  So the techniques that were used were those of classical microbiology.
It seemed most likely that the agent was a virus rather than a bacterium (though every possible angle was covered), and just about every virologist tried looking for their favorite agent, but retroviruses also seemed like logical candidates and several groups tried isolating infectious agents from the blood of AIDS patients.
The two groups who were most successful were those of Luc Montagnier and Robert Gallo.  There turned out to be a lot of politics and personalities involved and I won't get into that.  Here are some comments from Montagnier summarizing the story:

There were only a few patients with this disease in France, but Gallo's idea that a retrovirus was the cause had already crossed the Atlantic. His idea was disseminated by a small group of clinicians and immunologists led by Jacques Leibowitch and Willy Rozenbaum. At the end of 1982, Françoise Brun-Vezinet, a former student of mine and a member of this group, proposed that we collaborate to discover if a retrovirus was the cause of this disease, now called AIDS.
We were ready to start because my laboratory was equipped to hunt for lymphotropic retroviruses in human T cell cultures.  ... On 3 January 1983, Françoise Brun-Vezinet obtained a lymph node biopsy from one of Rozenbaum's patients, ... I minced the lymph node, dissociated the fragments into single cells, and cultured the T lymphocytes with interleukin-2 and antiserum to human interferon. Fifteen days later, Françoise Sinoussi (by then Barré-Sinoussi) found the first traces of RT in the supernatant of the lymphocyte culture, indicating the presence of a retrovirus.  ... A few months later, I received a blood sample from a young hemophiliac (LOI) with full-blown AIDS, and blood and lymph node samples from a young gay man (LAI) with advanced Kaposi's sarcoma. The LAI virus could be isolated from the patient's blood cells and grew very quickly in the patient's cultured T lymphocytes, killing them as well as killing T lymphocytes from blood donors.
New evidence that this strange retrovirus was the cause of AIDS came from our team in the fall of 1983 and the winter of 1984 (7). We observed a high frequency of antibodies against the virus in lymphadenopathy patients, and noted the favored tropism of this virus for CD4+ T lymphocytes. Our results were still controversial, however, and we had difficulty in obtaining the funding needed to better characterize the virus and to develop a blood test. The tide only turned in France when Robert Gallo and his group in the United States made a similar discovery. In the spring of 1984, Gallo published more convincing evidence that HIV causes AIDS ...

--A History of HIV Discovery
Gallo's approach was similar -- focused on isolating replicating virus, more than performing the molecular biology that's become standard in the meantime.


Some animals do like;
Ants prepare their meat not by heating but by marinating it with digestive enzymes to create a glistening protein slurry. With their hourglass figures, adult ants have such tiny waists that solid food can't pass through to their abdomens. Biologists already knew that the blob-shaped larvae predigest meat. Some scientists had suggested that the adults feed meat to the larvae and return later for some regurgitated protein slurry.
some animal chew and regurgitate for their young, monkeys have been observed washing potatoes, and other animals bury and allow food to rot before consumption.
But cooking is certainly unique to humans. There’s no other species that does it. There’s obvious reasons for that because we’re the only ones that can make fire which is a pre-requisite. In a away fire comes first and cooking becomes a process after it. It’s becoming clear that really cooking provides quite a number of advantages. Richard Wrangham from Harvard has been doing a lot of experiments looking at how cooking can change the nutritional value of food. What it seems is that the process of warming food up: in a sense denaturing it has a number of effects. One is that food is much more tender. That we know. If you eat a cooked carrot instead of a raw carrot it’s much easier. We can spend less time chewing, we can swallow it faster and we can digest it faster. It seems that it’s an extension of things we see in other animals. Animals who use techniques often in their stomachs to tenderise food seem to try and make it more easily absorbable. If we turn to the other question of when all this happened the real question is when do we first find evidence of fire? That seems to be about half a million years ago or so. We don’t find direct evidence of cooking then but we do see over the next 100,000 years or so the beginnings of things like burnt stone which suggests that meat is cooked. It’s probably goes quite a long way back in our evolutionary history and some people would argue it’s really a very major change in the way we are able to live and survive.

The second possible advantage for cooking is that it improves digestion. We’ve done a model study here particularly with Zhongquan Sui when she was here – she’s now at the University of Perdue. She found that yes, cooking does to a certain extent improve digestion. You only need cook something for a fraction of the time that you actually do in order for it to be digested properly. The cooking times that people adopt when they normally say this is cooked seem to reflect strong mechanical changes in the food. In other words, these are things that affect you perception of food texture and allow you actually to eat it very much easier, very much shorter eating times than you would do if they’re raw. That I think I would give as the essential answer at the moment.

References:

http://www.sciencenews.org/view/generic/id/6910/title/Ant_Iron_Chefs_Larvae_fix_dinner_but_dont_sneak_snacks
http://www.thenakedscientists.com/


Are there any air-plants with parts that are edible for humans?

Monstera deliciosa seems to fit the bill. From Wikipedia:

  This member of the arum family Araceae is an epiphyte with aerial roots...

  Wild seedlings grow towards the darkest area they can find until they find a tree trunk, then start to grow up towards the light, creeping up the tree.[6][dead reference link]

  Fruit

  The fruit of Monstera deliciosa is up to 25 cm long and 3–4 cm diameter, looking like a green ear of maize covered with hexagonal scales.

  Fruits of plants of the Araceae (Arum family) often contain Raphides and Trichosclereids – needle-like structures of calcium oxalate.

  The fruit may be ripened by cutting it when the first scales begin to lift up and it begins to exude a pungent odor. It is wrapped in a paper bag and set aside until the scales begin popping off. The scales are then brushed off or fall away to reveal the edible flesh underneath. The flesh, which is similar to pineapple in texture, can be cut away from the core and eaten. It has a fruity taste similar to jackfruit and pineapple. The unripe green fruits can irritate the throat and the latex of the leaves and vines can create rashes in the skin, because both contain potassium oxalate: that is the reason why the fruits have to be consumed when the scales lift up.[9]

  Plants grown indoors in temperate regions occasionally produce flowers and fruit.

  In Mexico, a leaf or root infusion is drunk daily to relieve arthritis.[6][dead reference link]

  In Martinique the root is used to make a remedy for snakebite.[6][dead reference link]

Here's a picture of the fruit by Bruno Navez:

Dragonfruit (Hylocereus undatus) is also hemiepiphytic. You may also be interested in this page about epiphytic cactus fruits and this post on Yahoo! Groups where I found M. deliciosa. The author claims:

  I have eaten the fruits off my Acanthostachys strobilacea, an epiphytic bromeliad, and they are reminiscent of the related terrestrial pineapple just slightly more acidic but still very palatable (to me at least). [Hyperlink added.]


What is the relationship between induction of cell differentiation and DNA methylation status?

This is a good question. I'm not as steeped in this literature as I'd like, but here is my understanding of the process:

Methylation is one of the key methods by which cell fate is restricted. The review you're reading is giving specific examples of cell lines that are at least partially restricted into cells that are of an entirely different type. Thus de-methylation is a method for de-differentiation, which then allows differentiation along a different line.

Your three examples that it sounds like you're interpreting as induction of differentiation, are actually examples of that effect -- de-differentiation that then allows for differentiation to a different fate. Constantinides work, for example, showed the conversion of a non-myoblast precursor into functional striated muscle cells. Not only can fibroblasts be turned into muscle cells, myoblast cell lines can be made to look like bone cells or fat cells. None of these things would happen without re-programming the cell fate by de-differentiating the cell lines to form dis-similar differentiation products.

This is consistent with other findings about de-methylation in vivo. An important example is the global de-methylation of primordial germ cells, as demonstrated in this figure from the linked review, summarizing the methylation state of the germ line in mice. Pay particular attention to the blue line. The pronucleus of the highly differentiated spermatazoon (along with its highly methylated DNA and histones) undergoes global de-methylation. Its products include the primordial germ cells of the developing mouse, the most de-differentiated state, which, in the case that it is a male, then become methylated as they become primed to differentiate, and then differentiate.


If I built a concrete pool, would it ever contain fish?

if the pool were just sitting out in open air, on earth and all that good stuff, it certainly would, given enough time.

This thought experiment is in the same vein that inspired Darwin when he reflected on his experiences on his visit to the Galapagos islands.

Think about it - the many islands which are formed by upheaval were lifeless when they first emerged from the ocean.  Over time, the winds or storms eventually populated them all - just about every island has animal life on it.  Not all animal types are found there that are best for the climate; its a matter of accident that some birds or lizards are found on the galapagos islands.  These accidental landings don't happen very often and sometimes a single animal will generate many species which will fill the role that other animals would normally fill on the mainland continents at the same latitude.

This is what happened on the islands- in different islands, Darwin found finches of sizes and shapes would be eating insects from bark or ant hills that might be done by an animal

Eventually, if you wait long enough a frog, then maybe a couple of fish will find their way into the pool from a nearby waterway (yeah that could take a long time I know).  If it takes too long then a new species will show up.  If you build walls around the pool it might not happen.  These accidents of animals showing up by accident can take millions of years.

This experience of Darwins' has inspired an entire field of biology - Island biogeography.  Each island is an experiment and ecological niches can be observed by taking a series of islands and seeing how different animals take up the various ecological roles on each.  A famous experiment EO Wilson and colleagues did was to fumigate some mangrove islands and watching them repopulate.


Here's a good photo of a squirrel eye showing the pupil being round.

Source: https://www.treklens.com/gallery/photo390926.htm

Also, these acrylic squirrel eyes for taxidermy show a round pupil.

Source: https://www.mckenziesp.com/Squirrel-Eyes-Acrylic-C3837.aspx


Does GTP-γS (GTP gamma S) bind all GTP-binding proteins?

This is the figure the question is about. On the right is the control experiment with GTP-γS, on the left without it:

The bands that are visible in both experiments are unspecific binding. If GTP-γS doesn't affect their presence, the mechanism by which they bind to the column can't be specific to the GTPase functionality.

The proteins the authors were after are those that are present in the experiment without GTP-γS, but are not eluted in the experiment with GTP-γS. Those are binding via an GTPase functionality to the GTP on the column. They are marked with arrow heads in the figure.

The general idea behind this control experiment is to distinguish specific binding from unspecific binding to the column. Being able to do that means that the authors had fewer proteins they needed to investigate further, saving them some work.


This is an interesting question and it is rather hard to find reliable information. According to a review which also did a meta analysis of all available articles, pasteurization (and also ultra pasteurization) affects the vitamins to some degree.

According to the analysis, vitamin B1, B2, B6, B12, C, E and folate decreased. The author notes however, that with the exception of vitamin B2, where milk is an important dietary source, the other vitamins are not included in very high concentrations. See the first paper for all details.

These findings are supported by another review (see reference 2), which shows some values in table 4:

This study finds proteins and amino acids not affected to a measurable degree, but data on protein behaviour is missing. My guess is that a part of the proteins are denaturated, but not all of them. There is some research which analyzes the effect of thermal treatment on milk in connection with other processes like the yoghurt or cheese production (have a look at reference 3). I haven't found any data on the proteins in milk which is directed to human consumption.

References:

A systematic review and meta-analysis of the effects of
pasteurization on milk vitamins, and evidence for raw milk
consumption and other health-related outcomes.
Which Milk is Fresh?
The Effect of UHT and VAT Thermal Processing Systems on Whey Protein
Denaturation and Gel Strength of yoghurt


What selective factors drove the evolution of lactose in lactation?

As it happens someone has just published a theory about this. To save you following the link, I reproduce the abstract below.

I must admit that I had never realised that lactose is synthesised within the organelles of the secretory pathway (β4-galactosyltransferase is a Golgi enzyme and α-lactalbumin is, of course, a whey protein, so is in transit through the pathway). This may go part of the way to answering your question: by having a disaccharide that is made within the Golgi, the cells of the mammary gland will effectively partition their glucose metabolism between the cytoplasm and that destined for secretion as lactose (transported into the Golgi lumen).

  Mammalian milk or colostrum contains up to 10% of carbohydrate, of which free lactose usually constitutes more than 80%. Lactose is synthesized within lactating mammary glands from uridine diphosphate galactose (UDP-Gal) and glucose by a transgalactosylation catalysed by a complex of β4-galactosyltransferase and α-lactalbumin (α-LA). α-LA is believed to have evolved from C-type lysozyme. Mammalian milk or colostrum usually contains a variety of oligosaccharides in addition to free lactose. Each oligosaccharide has a lactose unit at its reducing end; this unit acts as a precursor that is essential for its biosynthesis. It is generally believed that milk oligosaccharides act as prebiotics and also as receptor analogues that act as anti-infection factors. We propose the following hypothesis. The proto-lacteal secretions of the primitive mammary glands of the common ancestor of mammals contained fat and protein including lysozyme, but no lactose or oligosaccharides because of the absence of α-LA. When α-LA first appeared as a result of its evolution from lysozyme, its content within the lactating mammary glands was low and lactose was therefore synthesized at a slow rate. Because of the presence of glycosyltransferases, almost all of the nascent lactose was utilized for the biosynthesis of oligosaccharides. The predominant saccharides in the proto-lacteal secretions or primitive milk produced by this common ancestor were therefore oligosaccharides rather than free lactose. Subsequent to this initial period, the oligosaccharides began to serve as anti-infection factors. They were then recruited as a significant energy source for the neonate, which was achieved by an increase in the synthesis of α-LA. This produced a concomitant increase in the concentration of lactose in the milk, and lactose therefore became an important energy source for most eutherians, whereas oligosaccharides continued to serve mainly as anti-microbial agents. Lactose, in addition, began to act as an osmoregulatory molecule, controlling the milk volume. Studies on the chemical structures of the milk oligosaccharides of a variety of mammalian species suggest that human milk or colostrum is unique in that oligosaccharides containing lacto-N-biose I (LNB) (Gal(β1 → 3)GlcNAc, type I) predominate over those containing N-acetyllactosamine (Gal(β1 → 4)GlcNAc, type II), whereas in other species only type II oligosaccharides are found or else they predominate over type I oligosaccharides. It can be hypothesized that this feature may have a selective advantage in that it may promote the growth of beneficial colonic bacteria, Bifidobacteria, in the human infant colon.


By "still work" I assume you are asking if it will still be recognized by an antibody? It might. Internal T7 tag fusions are done, though they may require different antibodies than terminally tagged fusions.

That said, do you have a reason for inserting the the tag after methionine? The T7 tag already starts with methionine and naturally functions to initiate translation of T7 gene10. pET based vectors also contain it for this purpose.

[source]

In this vector, your gene of interest is typically inserted after the tag to create a fusion protein (using BamHI) or immediately after the start codon (using NheI). In either case, the T7 tag start codon is used.


In which order did the cells of the immune system evolve?

As I'm lucky enough to have access to that article, I'm going to extract whatever I can find to answer your question.

To begin with, innate immunity must have evolved first - we can see it at almost all stages of evolution. According to Cooper & Herrin, ever since aerobic respiration gave rise to multicellular organisms which in turn needed protection from invasion by single-cell organisms.

They state that around 500 million years ago, the first adaptive immune systems evolved in vertebrates, but do not explain how although they attempt to. Instead, they explain why we are not able to discern at the moment how this evolution came about. The main reason given is that it is unknown when some key cells evolved (namely natural killer cells and dendritic cells) Additionally, mice and humans evolved two different kinds of natural killer cell receptors relatively recently while sharing a common ancestor only quite a long time ago.

Apparently jawed and jawless vertebrates have also evolved two different kinds of adaptive immune systems. They both seem to rely on the same mechanisms but on a different molecular and genetic basis. Cooper & Herrin conclude that at the current level of research, we are not able to determine the evolution of our immune system.

Source: How did our complex immune system evolve?

Personally, if I'm allowed to give in to the temptation of speculation a bit, I would go by a similar strategy as the evolution of Krebs cycle - look which bits make sense even without the rest. There is of course the major obstacle that the cells of the immune system require an entirely new branch in haemopoiesis: all innate immune cells (aside from natural killer, NK cells) derive from the common myeloid progenitor, whereas all adaptive immune cells (and NK cells) derive from the common lymphoid progenitor.

I think this may even be a first hint: NK cells are innate immune cells but they derive from a different lineage at the highest level - they may have evolved as the first lymphoid cells after the myeloid innate immune cells. The next closest related cell is the cytotoxic T cell (CD8+, aka Tc), which utilises the exact same killing mechanisms (perforin+granzymes and Fas ligand) and attaches to other cells in almost the same way as the NK cell (immune synapse). It is also independent and can kill on its own, as long as it recognises its specific antigen. This is the main difference and also a very large step - the generation of the specific T cell receptor. Once the specific T cells receptor is developed, the step to helper T cells (CD4+, Th) is not far, although these perform a relatively bystander-like role in the immune response, steering the other immune cells from behind the scenes and not directly effecting any killing of the pathogen. Therefore I would guess that before helper T cells, B cells evolved, which are capable of producing antibodies. Antibodies themselves are very similar to the T cell receptor (not in gross structure but in the underlying genetic domains and their processing), so a 'detachable' antigen-specific T cell receptor may have evolved and ultimately caused the development of a new cell type. Once all these components are present, it is necessary (or beneficial) to control which cell types are the most active and in which way they act at the site of infection. This is exactly what helper T cells do, by steering the local immune response either into a Th1 (cytotoxic) or a Th2 ('humoral', anti-parasitic) response direction.


Biology experiment with algae method help

For growth you could measure the mass of algae before and after the experiment. If you have a centrifuge you can pellet the cells or use a filter to remove the culture medium. Alternatively, if you have access to a hemocytometer and a microscope, you could get an accurate cell count that way.

For controlling pH, you'll need a buffer in your culture medium. You should select a buffer with a pKa close to the pH you want to test and then titrate the pH of the medium with a strong acid or base (HCl or NaOH). Make sure to check the pH before and after the experiment to be sure that it didn't change due to growth of the algae.


Relationship between mN and mg in vessel contraction studies?

The difference between above two units is a matter of metric systems used:
The newton (symbol: N) is the International System of Units (SI) derived unit of force. One newton is the force needed to accelerate one kilogram of mass at the rate of one metre per second squared.

Another system:  kilogram (gram, milligram)-force
The kilogram-force (kgf or kgF) is a gravitational metric unit of force. It is equal to the magnitude of the force exerted by one kilogram of mass in a 9.80665 m/s2 gravitational field (standard gravity, a conventional value approximating the average magnitude of gravity on Earth). Therefore one kilogram-force is by definition equal to 9.80665 N. Similarly, a gram-force is 9.80665 mN, and a milligram-force is 9.80665 µN.
Kilogram-force is a non-standard unit and does not comply with the SI Metric System.
See:
http://www.sengpielaudio.com/ConvForce.htm


What is intercalary mitosis in bacteria?

To define, intercalary differentiation or mitosis applies to any cytogenesis through mitosis which arises between different specialised tissues or cells. Spirogyra may undertake either sexual reproduction, should conditions prove to be adverse, or asexual. The latter involves an 'intercalary mitosis'. This entails a fragmentation in the original filament in order to produce additional filaments.

Within bacteria, a good analogy may be the 'Blue-Green algae', a deceptive misnomer for phototrophic cyanobacteria. Thus, in the context of filamentous bacterial colonies, you may consider intercalary binary fission, cell division within the filament.

More information available from: http://bioweb.uwlax.edu/bio203/2010/fenske_megh/reproduction.htm


Separating DNA Fragments by Gel Electrophoresis. Are all the strands for one size the same?

The answer to the part of your question concerned with average lengths of restriction fragments is: if the DNA molecule being digested is of random sequence, and is 50% GC/ 50% AT, then the probability of finding any given short sequence at any position is 1/4N where N is the length of the short sequence. So, for example for a restriction enzyme with a 4-base recognition sequence such as AluI (AGCT) the probability is 1/256 and so the average length of an AluI fragment would be 256 bp. For an enzyme with a 6-base recognition sequence such as HindIII (AAGCTT) the corresponding number is 4096 bp. Please note that this is the average length, and is not an 'expected' length.

The answer to the part of your question about fragments of the same size co-migrating, how would you purify them on a gel for further analysis is trickier. I think the first thing to say is that you wouldn't do this for sequencing, and this is reflected in the various answers you have already received - sequencing no longer requires this sort of approach.

If you were forced into this position for some reason then I can think of two things that could help: the first option would be to run the analysis on an acrylamide gel when you can get much better resolution of different fragments (all 50 bp fragments are not the same molecular weight), but this is really only useful for small fragments (100 bp or less). However the most likely way out of the co-migration problem would be to purify the two comigrating fragments as a mixture and then ligate them into a vector whereupon each recombinant would carry one or other of the two fragments. This is really going back to the original reason why molecular cloning revolutionised things - it allows the 'biological' purification of DNA fragments followed by production of these fragments in large amounts.

You mention "special base pairs that are lacking a hydroxyl group" so clearly you are thinking in terms of Sanger (dideoxy-) sequencing, in which case you could clone directly into an M13 phage vector so that you could make ssDNA for direct sequencing. By sequencing a number of clones you would find two sequences, one for each fragment. You would still have to find a way to decide which one was the fragment that you were actually interested in, however.

Like I say, things just aren't done in this way anymore.


What Software could I use to create Diagrams of Biochemical Processes like these?

By posting to this forum, I presume the question is whether the illustrators of this and other biochemistry books used software specifically designed for the purpose of drawing reaction pathways, or, if not, whether such software exists. From my experience of using such illustrations in my own teaching over the years, I believe that the answer is probably no (although there are a couple of what I would consider ‘almosts’ mentioned below.) The main reason I would not expect this is that it would not seem commercially viable (biochemistry teachers and book illustrators are hardly a huge market) and you can get by with more generic pre-existing applications.

The class of application I consider best for this is termed a vector graphics application (popularly known as a ‘drawing’ application), as opposed to a bitmap or raster graphics application (popularly known as a ‘paint’ application). Although today there are applications that combine both functions, vector graphics applications have the advantage that they are more easily editable and they scale to any print resolution. The professional applications in this area can be very expensive and have a steeper learning curve than bitmap graphics applications (such as Adobe Photoshop). Moreover, they may lack features needed for biochemical use. It is therefore be worth exploring cheaper offerings, or investigating specialist vector graphics applications more focused on engineering or computing diagrams.

For biochemical work I personally would require software to be able to provide the following:

Controllable geometric lines (Bezier curves)
Customizable arrowheads
Text control that at least allows subscripts and
superscripts, and ideally both simultaneously, e.g. for a charged
phosphate species.
Rotatable text (as in the upper example)
Basic graphic primitives (as in the lower example)
Export to vector formats accepted by other applications (PostScript or PDF) to allow output in formats and at resolutions required for print publication.

How do different applications satisfy these criteria? They all support basic graphic primitives, and most allow export at least as PDF, if not the more flexible PostScript.

Surprisingly the creation of a line with an arrowhead is not straightforward as one is dealing with a combination of two separate objects. Although all applications tend to provide straight lines with arrowheads, curved lines with arrowheads tend to be absent from the general applications (even the most sophisticated) because a curved line is not really a line as such, but is generated as an oval segment with a stroke (visualization of its drawn edge) but no fill (the body is transparent). I have tended to use this sort of application (going back to MacDraw II of the Classic Mac) and fudge the arrows on them by combining them with straight lines of the same length as the arrowhead. However they are provided by more specialized diagramming software like OmniGraffle (mentioned in another answer) or the dedicated ChemDraw (which I find too limiting to use other than for export).

Text handling is the other problem. Placing a superscript directly above a subscript is a page layout operation that only dedicated mathematical software (e.g. MathType) is likely to support. Microsoft Word’s equation editor will do this, but export is only as PDF, and import into other applications varies in effectiveness. If you work in a generic application you will have to fudge it yourself with separate text boxes.

What are the choices for generic vector drawing applications? Adobe Illustrator is the most sophisticated, is used by most professional illustrators, but is very expensive (it is now subscription only). Other vector drawing applications that I am aware of but have not used include the commercial Corel Draw (cheaper than Illustrator) and the even cheaper Affinity Designer. As mentioned in a comment, there is also the free application, Inkscape. Free trials are available with most applications, so I would recommend seeing what is the best solution for your personal situation.

Addendum

I have just had a quick look at BioRender, which was mentioned in another answer. It has many different modules, including ones for biochemistry (including a Glycolysis pathway template) and seems quite attractive. However if you want to use the results for publications you need a $35 per month personal academic subscription (or your institution to buy a site license). I guess you tend to get what you pay for.


Just how light-sensitive is ethidium bromide?

Good question.

I found this reference in "Molecular Biology: A Project Approach"

  A phenomenon called photobleaching occurs when ethidium bromide (EtBr) -stained DNA is illuminated by ultraviolet light.... This decreased fluorescence is presumably due to the dissociation of ethidium bromide from the DNA.

Ethidium bromide fluoresces when it is in a hydrophobic environment, such as when its stuck between two base pair stacks in DNA- water quenches its fluorescence.

I also found this article citing the fact that sunlight can break down EtBr but only when a catalyst of iron and titanium dioxide is there to catalyze the reaction.

A lot of the original characterization of EtBr as a stain is very old, so I couldn't access it directly online... It looks like the compound itself is pretty stable, but UV can, somehow interact with it when its bound to DNA to bleach it out.


Did you identify structural domains in the protein using Pfam or some other domain detecting peptide search?

It's pretty useful to cut your constructs at the boundaries of structurally independent domins in the protein if you know where they are.  Hydrophobicity plots might lead you to cut right in the middle of a protein fold, only exascerbating inclusion body formation/protein precipitation.


Why is an excess number of eosinophils consistent with a violent allergic reaction?

The primary function of Eosinophils is to releas digestive enzymes and destroy extracellular parasites, but they also contain pro-inflammatory molecules and cytokines in their granules.

Eosinophils play an important role in late response inflammation. The primary inflammation is caused by degranulation of improper hyperactivation of mast cells when they encounter antigen/allergen (They have IgE bound to their receptors on a membrane). They release cytokines as IL-4 and IL-13 which recruit Th2 lymphocytes. Th2 lymphocytes release i.e. IL-5 which attract eosinophils.

Eosinophils release the content of their granules, which can degrade the tissue on an organism. Their cytokines attract more WBC - eosinophils (macrophages, TH2 lymphocytes and mast cells) and since this process is not controlled, they accumulate in tissues and it can lead to allergic reaction.

Good book contemplating this topic


Production of processed Insulin in bacteria

Insulin is processed from proinsulin by folding the peptide and forming 3 disulfide bonds before cleaving the peptide in 2 positions, leaving 2 peptide chains held in place by the disulfide bonds. This process is summarized in this image:

This only works because the peptide is packaged in a secretory vesicle during synthesis. This protects the peptide against the reductive environment of the cytoplasm, where glutathione is likely to reduce the disulfide bonds that hold insulin together.

When industrial insulin production moved from extracting the hormone from animal pancreases (pancreai?) to bacterial production of human recombinant insulin, glutathione was likely to cause a problem because simple protein production in bacteria just builds the protein in the cytoplasm, where glutathione is present. It is possible to export the protein into the periplasm during synthesis, similar to how proinsulin is moved into the endoplasmic reticulum during synthesis in human cells, but this can complicate protein purification (larger volumes of media, if protein is inside cells you can spin the cells down and work with a smaller volume).

Note that more recent methods use yeast to make insulin, potentially allowing production of actual insulin instead of proinsulin. And modern purification methods can extract insulin from animal sources that is just as good as recombinant sources.

I know from personal experience that it can be very hard to produce proteins with multiple disulfide bonds in bacteria. We attempted to produce mutants of bee venom PLA2 in E. coli, but the protein was misfolded and wound up in inclusion bodies. We purified the inclusion bodies, unfolded the proteins, then slowly refolded them by dialysing the protein in a glutathione solution. We aimed at making a protein with a free thiol for later chemical modification, but that free thiol just picked up a glutathione we couldn't remove without ruining enzyme activity.

Also please note that I am not fully aware of how insulin is made on the industrial scale and I could be wrong. That's why this was originally a comment.


Why is epinephrine not part of the somatic nervous system?

You are confusing different functional systems. Epinephrine released by the adrenal medulla circulates in the blood and indeed dilates the blood vessels in skeletal muscle. This ensures that enough oxygen and nutrients are available for the muscles to perform in a fight/flight response.

The somatic nervous system utilises acetylcholine not as a hormone but as a neurotransmitter. It is not released into the blood but only into the tiny (about 10nm wide) gap (synapse) between the nerve cell's axon terminal and the next nerve cell or muscle cell respectively.

This release by the somatic nerve cells causes an electrical potential in the muscle which makes it contract.

In summary:

The somatic nervous system controls the muscles because it stimulates the contraction which makes e.g. your arm move. Epinephrine released into the blood by the adrenal medulla serves to ensure the muscles have the blood supply they need in a stress response (e.g. a dangerous situation).

Along with muscular blood vessel dilation, epinephrine in the blood for example also stimulates the heart to beat faster and stronger, and dampens down mechanisms involved in digestion - essentially it does everything necessary to allow a quick escape or a strong fight.


Viruses: Adaptation to a new host through repeated host jumps

A friend told me, during a 3 minute discussion, that viruses that are
  endemic in host A and make repeated jumps to host B but can't be
  transmitted between individuals of species B, may slowly adapt
  (through these repeated jumps) to be able to be transmitted between
  individuals of host B and become epidemic.

This is...mostly true. A good example is avian influenza - there are a number of human infections linked to contact with infected poultry, but the virus is not particularly good at sustaining long chains of human-to-human transmission, likely due to differences in the respiratory tract between humans and birds.

  I don't know much about epidemiology. I don't understand how a virus
  population that is endemic to host A may adapt to host B with repeated
  jumps while the viruses that jump to host B are dead end because they
  cannot be transmitted further more. Or Are these viruses able to jump
  back to host A to bring back their newly acquired adaptations to host
  B?

What they mean by repeated jumps, or what they should mean, is not a virus hopping back and forth, but a virus going from A to B many times. This is my problem with your friend's statement, it's not so much a "slow adaptation" as, well, random chance.

Imagine that there's a mutation in Virus A, which lives in chickens, that will make it well adapted to live in human beings. It's an extremely rare mutation, so the dominant strain of Virus A is maladapted for human to human transmission. That means most Virus A infections in humans will be the non-productive kind, that will infect a person, but not go on to infect other people. But, with enough rolls of the dice, a human might get the human-favored Virus A, and since there's now intense selective pressure for that strain of the virus within its new human host, it might establish itself and take off.


Can we use Acetyl Phosphate instead of Acetyl CoA in TCA?

Enzymes are usually specific to a greater or lesser extent for their substrates. In this case we are looking at citrate synthase which catalyses a condensation reaction in which the acetyl group from acetyl-CoA is added to an oxaloacetate molecule to form citrate. This is the entry point for carbon into the TCA cycle for energy production. The condensation reaction follows an ordered pathway: oxalocatetate binds first and this results in a conformational change which increases the enzyme's affinity for acetyl-CoA by a factor of 20.

Citrate synthase is highly specific for acetyl-CoA as a substrate. The cited reference discusses several aspects of this specificity. The enzyme has a well-defined binding site for CoA, with contacts from both the small and large subunits. This includes the recognition of the adenylyl portion of the molecule.

A relevant quotation from the review:

  "Citrate synthase is highly specific towards its substrates. The condensation reaction occurs only with the physiological substrates oxaloacetate and acetyl-CoA."

So, the answer is that citrate synthase cannot use acetyl-phosphate as a substrate because of its specificity for acetyl-CoA.

Wiegand,G and Remington, SJ (1986) Citrate Synthase: Structure, Control, and Mechanism. Ann. Rev. Biophys. 15: 97–117


Your pictures are a bit vague, but I think recognize Euonymus europeus, the spindle tree. So I assume the picture comes from Europe? The fruits are encapsulated in pink capsule, the fruit itself is bright orange.

https://en.m.wikipedia.org/wiki/Euonymus


With a small projectile you will always get some sort of shearing forces: the tissues directly impacted will accelerate faster than adjacent tissues, and so on. This can cause tearing of many tissues, including blood vessels, but other tissues as well.

In the context of the brain, the effects of traumatic brain injury are a constant area of research, for example see here.


How are commercial steroid hormones produced?

In this recent review you can find fascinating information on all aspects of this topic. It's dense in sterol structures and chemical interconversions, but that's what you have to expect. This is my précis.

Direct isolation from primary biological sources This was the heroic phase of research in this area:

  Androsterone was first isolated from the urine of policemen. Quickly, however, it became evident that natural isolation of hormonal steroids would not satisfy the demand, as, for instance, in 1931, 15,000 L of urine yielded only 15 mg of pure androsterone. Similarly, 4 tons of sows' ovaries were needed to isolate 12 mg of estradiol, while extraction from 625 kg of sows’ ovaries produced 20 mg of progesterone.

[edited by removal of citations]

There are still some commercial processes in this class:
Premarin contains estrogens produced from the urine of pregnant mares.

Chemical transformations starting from steroidal sapogenins of Dioscoreae (yam) These processes still make a contribution but there is a limiting availability of the starting plant material. Apparently important in China.

Direct total synthesis
This section describes chemical routes, but there don't seem to be any commercial processes

Chemical synthesis from cholesterol and phytosterols Phytosterols are plant sterols, available from e.g. soy bean oil, rape seed and paper pulp industrial waste. They can be chemically converted to steroid hormones, as described in the review, but there don't seem to be any commercial processes.

Microbial conversion of phytosterols
Bacteria can convert plant sterols into useful products. Mycobacteria seem to be particularly useful.

  Today, more than 1000 tons of steroids are produced annually from phytosterols by microbial transformation, alone.


Why do we need to replicate incomplete DNA fragments by PCR from a crime scene?

This process helps with the signal to noise ratio.  In theory, you could use the fingerprinting techniques to dice up the few billion copies of the DNA and carefully measure them.  However, it is far easier to replicate the DNA to increase the number of molecules of DNA available to the process.

Remember, fingerprinting for crime investigations doesn't involve reading the DNA, but merely uniquely identifying it.


The membrane holding potential is the voltage level set by the experimenter in a voltage-clamp recording.


What's the purpose of colorful mushrooms' caps?

Mushroom is actually the reproductive organ of the actual fungal body beneath the surface. It have a high surface area to disperse or spread the spores.

If the eating predators are low or dispersing is not an option, then it will need other organisms to attract to that they can be spread, so they are not toxic. Analogous to fruits, they uses different colors which are non-toxic to attract.$^1$

Whereas brightly colored mushrooms are less toxic, whereas, most toxic ones are either brown or white.$^2$

Edible Mushrooms

Toxic Mushrooms:

Source:

Why do mushrooms come in so many shapes and colors?
Mushroom poisoning

Image Source:

https://www.etsy.com/listing/93680839/antique-1900-edible-fungi-print


Is the appendix a vestigial structure in all vertebrates?

Smith et al. (2009) provide a survey of the morphology of the cecal appendix. One current hypothesis is that the appendix provides "safe harbor" for symbiotic gut bacteria. Among mammals, there is a vast array of cecal appendices:

In summary:

  A comparative anatomical approach reveals three apparent morphotypes
  of the cecal appendix, as well as appendix-like structures in some
  species that lack a true cecal appendix. Cladistic analyses indicate
  that the appendix has evolved independently at least twice (at least
  once in diprotodont marsupials and at least once in Euarchontoglires),
  shows a highly significant (P < 0.0001) phylogenetic signal in its
  distribution, and has been maintained in mammalian evolution for 80
  million years or longer.


Can we graft a tree with cells from the seed directly?

Tree grafting involves a rootstalk and a scion (part to be grafted onto the rootstalk). Here is a reference on the basics of grafting. Usually, this is done to combine the advantage of a strong or mature root system (from the rootstalk) with desired fruits or buds (produced by the scion). In this case, the roots of the scion plant might be sensitive, disease-prone, or just take a long time to develop (read more here). It is also possible to graft a scion onto the same variety of cultivar. Grafting refers to the joining of vascular cambium of a scion and a rootstock in such a way that they can share resources and continue to grow together (see previous links). As such, adding cells from a seed to a larger plant would not be grafting, because there wouldn't be that pre-established vascular tissue to connect with the vascular cambium of the rootstock. Additionally, a single sprout would not have a good chance of binding well to the vascular system of the rootstock (see link 2).

If you are interested in reading more about different forms of (non-seed) propagation, this resource describes the why/when/and how of grafting and layering (another technique that might help you, if you're trying to propagate only one tree variety as indicated in your question), and there are many great resources on youtube about the basics.


Is ATP Synthase a channel or an enzymatic protein?

ATP synthase is an enzyme, a molecular motor, and an ion channel all wrapped together in one structure (Fig. 1). It is an enzyme, because it generates ATP. It is a molecular motor, because the central rotor part turns about 150 times every second during ATP synthesis (Source: MRC mitochondrial Biology Unit). It is an ion channel, because it funnels protons into the mitochondrion during ATP generation (Source: Davidson College).

ATP synthase. Source: Ace Biochemistry

ATP synthase is composed of two subunits, F0 and F1. The 0 subunit is embedded in the inner membrane, and the other, containing the catalytic parts, protrudes into the matrix.

F0 contains the proton channel and is connected to F1 with a stalk.

F1 consists of five polypeptide chains, alpha (a), beta (b), gamma (g), delta (d), and epsilon (e). The alpha and beta chains make up the bulk of F1 and are arranged in a hexameric ring. Both chains bind nucleotides, but only beta participates in catalysis (Source: ACE Biochemistry).

Another example of complex proteins are G-protein coupled receptors, for example those linked to ion channels (Fig. 2).

G protein coupled receptors. Image source: Wikipedia

Here, a receptor is bound to a G-protein, that becomes activated after receptor binding. The G protein then leaves the receptor and travels to an ion channel and activates it (or inhibits it).


The youngest fathers recorded were 11 years old (see wikipedia >
List of youngest birth fathers).

The youngest mother recorded is L. Medina was 5 years, 7 months and 21 days old when giving birth, which is rather astonishing! Of course, she gave birth by a caesarean section. She had an extremely early puberty; she appears to have had her period when she was 3 years old only. You might want to have a look at wikipedia > List of youngest birth mothers. According to this article, a mother (L. Gryshchenko) became a mother at 6 years old and gave birth "naturally" (not by cesarian section).


How would one track a mineral nutrient in a plant in order to prove that nutrient has been re mobilized?

It is not possible to track individual molecules within a plant. However, one can track the level of radioactivity from place to place. So, in the case you are talking about, one would find that some level of radioactivity persisted for a time at one location, then it is observed to decline while it increases in another. There also might be a delectably increased level of radioactivity along the pathway between those two areas - regardless, one would logically connect decreased activity in one area with increased activity in another.


Alternate genetic codes in newly sequenced organisms

If the organism uses an alternative code, the predicted protein sequences would always include the same type of amino acid substitution errors. This pattern should become apparent when you compare the proteins to other organisms.
In reality, the most common alternative code uses UGA for tryptophan instead of the usual stop. If you make the mistake of using the standard code for these genomes, the predicted genes would become highly fragmented so it is almost impossible not to notice.


Antiparallel DNA Strands - Error Correcting Code?

Double-stranded DNA does have redundancy giving a basis for error-correction, but it has nothing to do with the antiparallel nature of the DNA.

Each strand has an orientation, that is the pieces of the backbone are not symmetric and so chemical reactions have to happen in one of the two possible orientations along the strand.  One end of a strand is called the 5' end and the opposite end of the strand is the 3' end.  The two strands of a DNA molecule run in opposite directions (antiparallel), with the 5' end of one strand being adjacent to the 3' end of its partner strand.  The two strands do not contain the same codes in opposite order like your license-plate coding example.

The redundancy is only pair-by-pair.  A nucleotide in one strand is paired with a unique complement nucleotide on the other strand.  It is thus redundant like bit-for-bit odd parity is redundant.  This redundancy allows errors to be detected from a mismatch in what should be a pair, and a damaged nucleotide can be replaced with the correct nucleotide by using the complement of the nucleotide on the other strand.


Finding specific genotype occurrences given allele frequency

Under Hardy-Weinberg conditions, the frequency of the genotype abcd (in this particular order) is simply $F_a \cdot F_b \cdot F_c \cdot F_d = 0.24\%$.

If we don't consider the order, then we must ultiply the previous probability by 24. There are indeed 24 (=4*3*2*1) ways you can get this particular combination. The probability of abcd in any particular order is therefore $24 \cdot F_a \cdot F_b \cdot F_c \cdot F_d = 5.76\%$.

You might want to have a look at the post Solving Hardy Weinberg problems


Alternative protocol for evaluating RNA integrity, using a bleach gel

I don't think bleach can denature RNA. Bleach is an oxidizing agent and it will damage the RNA. Also, the protocol mentions addition of hypochlorite before heating which I think is illogical because heat will decompose it.

For testing RNA integrity you need not make a denaturing gel. What you can instead do is to heat the RNA with the 2xRNA loading buffer that contains 95% formamide and run it in a normal TBE/TAE agarose gel. Heating with formamide denatures the RNA permanently.

Denaturing gels are only essential for Northern Blots.

You can also run your sample in a bioanalyzer to check for RNA integrity and this is always recommended for RNAseq experiments (even for microarrays but I cannot comment much on that because I have never done it and am not aware of the usual practice).


What is the meaning of dots and dashes in clustalw?

As WYSIWYG touches on in the comments, usually dashes mean that there are gaps in the alignment as the result of an indel event. Dots are used to show specifically point mutations where the biochemical properties are mostly conserved, but the residue has changed.

From original question, not relevant to question as it stands.

You are right in that this isn't a proper alignment, however I'm not sure it is a bug. What you have appears to be the alignment of a nucleotide sequence that has gone horribly, horribly wrong.

As a first guess without any more details I would say it doesn't look like you have installed clustalw correctly or pointed your bioperl to it. From the documentation here are common problems:

  Make sure the clustalw executable is in your path so that
  which clustalw
  returns a clustalw executable on your system.
  Define an environmental variable CLUSTALDIR which is a
  directory which contains the 'clustalw' application:
  In bash:

  export CLUSTALDIR=/home/username/clustalw1.8

  In csh/tcsh:

  setenv CLUSTALDIR /home/username/clustalw1.8
  Include a definition of an environmental variable CLUSTALDIR in
  every script that will use this Clustalw wrapper module, e.g.:

  BEGIN { $ENV{CLUSTALDIR} = '/home/username/clustalw1.8/' }
  use Bio::Tools::Run::Alignment::Clustalw;

Unless you are doing massive amounts of sequence alignment, the clustalW2 webserver is quicker, more sensitive and way easier to use.