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When does identical twinning happen?
What is the window during which division into twins is possible (for instance can it still happen after implantation in the uterus)?
Is one twin the "original" and the other its clone?

In the case of two healthy, viable identical twins, the separation generally occurs at the first division from one zygote to two cells. So they are equal partners in the split, not an original and a clone. During the first several cell divisions in the morula and blastula, there is no significant growth. So these divisions produce smaller and smaller cells. If one of these smaller cells is separated, it is very unlikely to be substantial enough to survive and implant in the uterus.

That answer is partly wrong so I gave another one. Twinning isn't about a single cell breaking off from the rest but about the whole structure (or relevant parts of it) splitting in two, so it isn't limited to the first division.

This page describes what happens pretty well:
http://discovery.lifemapsc.com/library/review-of-medical-embryology/chapter-30-multiple-pregnancies
Division into twins can apparently happen at several stages up to and including implantation, but not much after that. The later the division the worse the prognosis because the more the twins share. The article mentions three stages in particular: division at the 2-blastomere stage (i.e. when the original zygote is cleaving), which leads to two completely separate embryos that implant separately, division at the embryoblast stage which leads to the embryos sharing a chorionic cavity (i.e. placenta), and division at the embryonic disk stage, which happens after implantation and involves the fetuses sharing everything - apparently to the point that they rarely survive until birth because they get tangled in each other's umbilical cords. Later divisions, after the primitive streak starts forming (i.e. about two weeks after fertilization), can lead to conjoined twins, because the division happened when the cells have already started to differentiate into which part of the body they'll be.
In no case can one twin be considered "the original" and the other not. Twinning involves whatever stage we're at dividing into two; we can't talk about one being an offshoot of the other, anymore than if you pour cake batter into two molds instead of one you don't end up with an original cake and a copy, you just end up with two cakes. Whose batter happened to be in the same bowl until some point in the baking process.
Moreover the twinning events usually involve a symmetrical division, meaning we can't even talk of one twin having a claim to a higher percentage of the original embryonic material or whatever. An exception may be parasitic twins and other examples of asymmetrical twins, but I haven't been able to find a good source on what causes those - it's unclear whether it involves twins resulting from an unequal division, or whether later development made them unequal.


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When do chimeras happen?
If one developing twin absorbs another, when does that happen?
Is it possible for an appendage or organ to develop and be the only remaining vestige of an absorbed twin, such as a hand or a mouth, or a heart?

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Is there a limit to twinning?
Can developing twins further divide and subdivide and become identical quadruplets or octuplets or...?
Can twinning be induced, either in utero or in vitro?
Might it be possible to just keep harvesting a few cells off the original clump indefinitely and making an unending stream of identical embryos for implantation in a surrogate uterus?

Sequentially:
Yes. Up to the limit of what the mother's body can tolerate.  Of course, if the cells never aggregate, that suggests some sort of fundamental problem with the embryo's developmental process, and you will probably not get a viable organism.
Sort of and yes.  In utero, fertility drugs can cause multiple eggs to be released per cycle, which can cause fraternal twins when each egg is fertilized.  IVF can do the same thing, but you can also manually subdivide a single embryo into two (smaller) viable embryos, provided you perform the division before any cell differentiation occurs.
Yes, but good luck getting an ethics review board to approve that :D

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What does dominant generation mean
In my texbook it is written that for non- vascular seedless plants the dominant generation  is the gametophyte as the gametophyte generation is larger and longer lived.
Is the criteria for dominant generation?-( Which generation the plant spends most of its life in?)

According to "Wile, Dr. Jay L. Exploring Creation With Biology. Apologia Educational Ministries, Inc. 1998" and reported here,

In alternation of generations, the dominant generation is the generation that occupies the largest portion of the life cycle

I guess that it has to be understood in terms of "time". I am not quite sure though if it has to be understood in terms of generation time of life span. Intuitively, I would say that generation time would make much more sense. Therefore, I'd say that, the dominant generation is the generation which have the longest mean generation time (=mean time from the birth to reproduction).
As @Shigeta said in the comments: For example, in Homo sapiens, the dominant generation is the diploid phase (sporophyte, you and me) and the non-dominant generation is the haploid phase  (gametophyte, sperm/ovule).

an example is the human animal, which is dominant over the gamete (sperm/egg) generation.

The wikipedia page Alternation of Generations actually has a pretty sophisticated discussion of this issue, and discusses the fact that plants can and do fall at a lot of different places on a gradient of one generation being dominant over another.
I think the root of this complexity is that this is an issue of terminology, and is connected to your concept of "what is an organism", which is a complex issue in and of itself (see this answer).
Despite this, I think that you can still usefully discuss use a number of criteria which argue for a generation being more or less dominant, including generation time, but also:
1) size (as you say in your question)
2) morphological complexity
3) ability to independently undergo "life" processes like photosynthesis and mitosis
4) conspicuousness/salience to humans (as we're the ones making up these categories)

I should also link to @Remi.b's answer to OPs other question, which is very similar: http://biology.stackexchange.com/questions/14186/sporophyte-and-gametophyte


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When happens when pollen grains land on the a part other than the stigma of a flower of the same species?
When happens when pollen grains land on the a part other than the stigma of a flower of the same species? Would the pollen be transported to the stigma or would it just sit where it landed and nothing would happen?

Sometimes, the morphology and the topology of the flower structure is such that the pollen grains falling on certain parts are gravitationally (or hydrostatically) drawn towards the stigma.
I remember having read that the waxy streamlined stigma of submerged hydrophytes (Vallisneria, Hydrilla)  creates mini vortices around it during steady water flow. These vortices then pull nearby pollen, (which may be sitting on nearby flower parts) towards itself. Certain hydrophyte morphologies also maximise the water flow towards stigma, which in turn gathers pollen incident elsewhere on the plant and bringing in towards the stigma.(For example, the streamlined and bladder shaped hydrophyte flowers have stigmas at their centre)
Another way to do this is via the common sloping surface of the petals or the perianth, which on gathering pollen, gravitationally push them to the centre of the flower where the stigma usually resides. The entire inflorescence stalk might be modified into specific shapes to do this. The common pyramidal arrangement of the inflorescence (broad at the base, tapering towards the apex) helps in gathering the pollen incident on non-stigma parts of the apex region at the bottom.
Apart from this, pollen falling elsewhere, may again be taken up by the agents of pollination. But I believe the formation of pollen tube never occurs at any place other than stigma. Nor does any re-absorption take place.
It is also worth mentioning that just because pollen falls on the correct stigma does not ensure fertilization. Absence of stigma maturity/receptivity, synergid abnormality, inviable pollen etc could still hinder fertilization.
[I am not perfectly aware about studies on whether any chemical reaction occurs if pollen lands on places other than stigma. But I doubt it, since the chemical specificity required to begin the pollen tube formation is very high in most species.]


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Breathing in and out
I was reading my textbook and it says that breathing involves inhaling and exhaling but it doesn't say whether they happen simultaneously or sequentially.
Also is my overall understanding of breathing competent?  When you breathe in air, air ends up in the lungs passing through the nasal passages (heated, moistened, cleaned) through the pharynx, through the glottis through the larynx, through the trachea and into the bronchi and then into the bronchioles. Once air gets to the lungs, Is their already carbon dioxide in the lungs waiting to be expelled or will carbon dioxide diffuse into the alveoli and into the lungs when oxygen diffuses into the blood. And after this the carbon dioxide will be expelled?

My understanding is that gas exchange is a simple diffusion process in the alveoli level. When there's a concentration difference, it happens. It happens for every molecule simultaneously.

I think you should: 1) change the title to reflect your question and 2) edit the body and decide whether you are asking about inhaling & exhaling (which are sequential) or gas exchange in alveoli (which is simultaneous).

Inhalation and exhalation happen sequentially as Herman stated in the comments.
Yes, your general understanding of inhalation is correct. After the air gets into the lungs, the oxygen is diffused into the capillaries covering the alveoli. The now oxygenated blood travels back to the heart to be circulated throughout the body. As this blood enters capillaries in other regions in the body, the oxygen diffuses out of them and into the surrounding cells. Carbon dioxide (CO2) produced by the cells as a waste product then diffuses into the blood vessels. The CO2-rich blood is then circulated back to the heart to be pumped back to the lungs. This blood flows into the capillaries surrounding the alveoli, and diffuses out. The exchange of carbon dioxide and oxygen occurs simultaneously. So, as oxygen is diffused from the lungs into the bloodstream, CO2 in the bloodstream is diffused out into the lungs.
Here are diagrams to depict what is described above.


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RNA interference
If dsRNA is produced through a mutation (such as forming of a hairpin structure) in a particular gene and RNAi has become possible because of that, will an organism which is a heterozygote to this gene (whereby one of his alleles has the mutation and one doesn't) have his healthy allele be partially unaffected by the dominantly mutated allele when the siRNA doesn't fully bind to the healthy allele?

Josh - try editing your question... you have written one extremely long run-on-sentence that is difficult to follow (if you break it down and edit it will make it better)


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Do saltwater fish need to drink?
In my biology class we got the question if saltwater fish need to drink. We need to use the term osmosis, but I cannot think of a valid answer and we were allowed to ask help.

Short answer, yes. The fresh water concentration inside saltwater fish is higher than the surrounding sea water, and the salt concentration inside the fish is lower.  This means that fresh water continuously flows out of the fish through their gills via osmosis.  To combat this loss of fresh water, fish must constantly be drinking sea water to replenish the lost fresh water. This also requires that they pump out the excess salt in the sea water they drink using their kidneys and specialized chloride cells in their gills.

Some more information can be found here, or you can watch a short video on the subject here.

Perfect, me and my classmates loved it. Our teacher gave us an apple pie for the good answer :D i'd bring a piece over if I could!


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How does low cysteine conditions affect pheomelanin production?
So we were studying this amino acid called cysteine. Specifically we were studying it's effect on melanin genesis.
Our teacher told us how excess of cysteine affects the melanin synthesis  by generating more pheomelanin. Low amount of cysteine promotes formation of eumelanin.
 He told us that if the concentration of cysteine is increased in cells then the above reaction starts producing pheomelanin in brown/black skinned people. I searched it on net and it seems to be true.
The question is that if someone who has fair skin (produces more pheomelanin) is forced to live in low cysteine condition, then what happens? Eumelanin production should increase. His complexion must change. But it doesn't occur anywhere. Fair skinned people affected by malnutrition remain fairskinned. How is this possible? The pheomelanin production must stop since they aren't getting enough cysteine. Then how...?
He also told us that onions contain large amount of cysteine yet it can't be used since it is destroyed by stomach acids.

First: Your teacher is right with the statement that a low cysteine concentration affects the synthesis of pheomelanin. To understand this, you need to take a look at the biosynthesis pathway of melanin (from here):

The first steps for both melanin forms are the oxidation of the amino acid Tyrosine to DOPA (L-3,4-Dihydroxyphenylalanine) and the to DOPA quinone by the enzyme Tyrosinase (abbreviated Tyr). In the following step the branches divert, if there is enough cysteine present in the cells, then Cysteinyl-DOPA and subsequently Pheomelanin are synthesized.
If the cysteine concentration in the cell falls below the threshold of 0,13µM (this is taken from this paper), then the switch to eumelanin production occurs.
In the case of you second question, there is a different setting. The overall rate of the melanin production (no matter which flavor) depends on the amount of active Tyrosinase (for the production of the first steps in the synthesis cascade). The production of this enzyme is regulated by receptors in the cellular membrane (and different other factors).
In fair skinned people (classically red-haired and with freckles) these receptors are not fully functional, resulting much less Tyrosinase enzyme in the cells. This results in fewer available precursors for the melanin production and in turn in less need for cysteine. The reason is that the cysteine pool of the cell is not getting exhausted.

Sorry. But I couldn't understand the last paragraph.Tyrosinase affects melanin production. If fair skinned people have less tyrosinase ,wouldn't it mean that the production of melanin itself decreases ,regardless of its type. Also would cysteine deprivation affect the color of fair skinned people? Also would cysteine deprivation affect the skin color? Is the cysteine in onions unusable since it is destroyed by stomach acids? How can this be true? I mean ,shouldn't all amino acids be destroyed since they have to pass through stomach. Once again thx for ur help

@AScientist Yes, they also produce less pigment in total, that's why these people have a much lighter skin type. But it also affects the type of melanin produced. Without enough cysteine the pathway would be shifted to eumelanin.

This is the UPDATED information on L-Cysteine production for Pheomelanogenesis, which says nothing about L-Cystenine levels falling and creating Eumelanin as this "guess" (not even a theory) makes no sense published May-Jun 2008
Chemistry of mixed melanogenesis--pivotal roles of dopaquinone.
Ito S1, Wakamatsu K.
Author information
Abstract
Melanins can be classified into two major groups-insoluble brown to black pigments termed eumelanin and alkali-soluble yellow to reddish-brown pigments termed pheomelanin. Both types of pigment derive from the common precursor dopaquinone (ortho-quinone of 3,4-dihydroxyphenylalanine) which is formed via the oxidation of l-tyrosine by the melanogenic enzyme tyrosinase. Dopaquinone is a highly reactive ortho-quinone that plays pivotal roles in the chemical control of melanogenesis. In the absence of sulfhydryl compounds, dopaquinone undergoes intramolecular cyclization to form cyclodopa, which is then rapidly oxidized by a redox reaction with dopaquinone to give dopachrome (and dopa). Dopachrome then gradually and spontaneously rearranges to form 5,6-dihydroxyindole and to a lesser extent 5,6-dihydroxyindole-2-carboxylic acid, the ratio of which is determined by a distinct melanogenic enzyme termed dopachrome tautomerase (tyrosinase-related protein-2). Oxidation and subsequent polymerization of these dihydroxyindoles leads to the production of eumelanin. However, when cysteine is present, this process gives rise preferentially to the production of cysteinyldopa isomers. Cysteinyldopas are subsequently oxidized through redox reaction with dopaquinone to form cysteinyldopaquinones that eventually lead to the production of pheomelanin. Pulse radiolysis studies of early stages of melanogenesis (involving dopaquinone and cysteine) indicate that mixed melanogenesis proceeds in three distinct stages-the initial production of cysteinyldopas, followed by their oxidation to produce pheomelanin, followed finally by the production of eumelanin. Based on these data, a casing model of mixed melanogenesis is proposed in which a preformed pheomelanic core is covered by a eumelanic surface. Source: https://www.ncbi.nlm.nih.gov/pubmed/18435614
As stated above Eumelanin and Pheomelanin are two chemically different compounds. So even if Pheomelanin levels dropped one would not attain Eumelanin through the depletion of sulfhydryl compounds, because they follow completely different pathways of synthesis. This is determined by Genetics, one would have to turn on the SLC24A5 and SLC45A2 genes as a start.
α-MSH/MC1R plays a major role in the production of Eumelanin. MC1R Variants
"Melanocortin 1 receptor is a highly polymorphic protein, and in humans many of the loss-of-function variants are associated with the “red hair color” (RHC) phenotype. Individuals with a dysfunctional MC1R may have decreased eumelanin synthesis leading to fair skin and an increased sensitivity to UV exposure."
MC1R and Pigmentation
"There are two major types of pigment present in the skin, the darkly pigmented eumelanin and the red/yellow sulfated pheomelanin. Eumelanin is chemically inert and is highly photoprotective by absorbing UV radiation and oxidants. In contrast, pheomelanin is much less efficient at blocking penetration of UV radiation into the skin and can promote UV-induced cellular damage by contributing to free radical and oxidative injury. MC1R signaling is a major determinant for the amount and type of melanin pigments synthesized by melanocytes, regulating both basal pigmentation and the UV induced tanning response. **MC1R signaling increases **eumelanin synthesis****, the ratio of eumelanin-to-pheomelanin, and enhances melanosome transfer to enhance melanin deposition in keratinocytes.
Both eumelanin and pheomelanin derive from the sequential cyclization and oxidation of the amino acid tyrosine (Figure Figure33) (Ito, 2003). The first two biosynthetic steps are shared between the two pathways: the conversion of tyrosine to DOPA and then to DOPAquinone by the enzyme tyrosinase. Eumelanogenesis and pheomelanogenesis diverge after formation of DOPAquinone. Other enzymes beside tyrosinase are needed for melanin synthesis including dopachrome tautomerase and tyrosinase-related protein 1. Defects in many pigment enzymes yield hypomelanotic phenotypes such as albinism. Pheomelanin production is dependent upon the incorporation of a cysteine and retention of sulfur after the synthesis of DOPAquinone, which may explain why mature pheomelanin pigments are reddish/yellow rather than dark brown/black as eumelanin is. Although the control of the pigment switch between eumelanin and pheomelanin is regulated by multiple factors including the pH of the cellular milieu and the levels of tyrosinase (Burchill and Thody, 1986; Ancans et al., 2001), the presence of a functional MC1R is required for effective synthesis of eumelanin. Since eumelanin absorbs UV radiation, the more eumelanin the skin has, the more protected it is from UV damage." Source: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4885833/

I know this paper - and it says it itself: "Regarding the production of pheomelanin, the intervention of sulfhydryl compounds (such as cysteine) gives rise exclusively to thiol adducts of dopa (cysteinyldopas) among which
5-S-cysteinyldopa (5-S-CD) is the major isomer (38). Further
oxidation of the thiol adducts leads to the formation of
pheomelanin via benzothiazine intermediates." Without cysteine the formation of cysteinyl-DOPA and subsequently pheomelanin is not possible. Also: Read the paper of Land from 2003 which explains the mechanism. If you don't have access, let me know.

You can down my comment because you do not agree with it but you are interpreting the information incorrectly. A fall in L-Cysteine levels will not change to  Eumelanin because you want it to, thats not how genetics works.

This is not genetics, is regulation of enzymes. Genetics is the layer above this step. And here a lot of other factors come into play. So your comment is pointless and your answer doesn't really answer the question.

The question is that if someone who has fair skin (produces more pheomelanin) is forced to live in low cysteine condition, then what happens? He is not asking about MIXED melanin which is something altogether different than the figures you or I have posted.

The melanocortin 1 receptor controls which type of melanin is produced by melanocytes. (NOT CYSTEINE) When the receptor is activated, it triggers a series of chemical reactions inside melanocytes that stimulate these cells to make eumelanin. If the receptor is not activated or is blocked, melanocytes make pheomelanin instead of eumelanin. https://ghr.nlm.nih.gov/gene/MC1R

Nope. The receptor regulates the major transcription factor important for pigmentation: MITF. This one regulates the transcription of genes involved in pigmentation, for example the tyrosinase (which is the first enzyme in both cascades). If tyrosinase is missing or inactive you would be an albino. Little MC1R signalling (as in red haired people) due to mutations leads to little production of tyrosinase and subsequently little DOPAquinone. Therefore the cysteine levels are not depleted below the critical threshold and only the red pheomelanin is made.

"Pheomelanogenesis may have evolved as an excretory mechanism to remove excess cysteine, and in humans this might potentially confer a greater ability to avoid disease such as Parkinson's and Alzheimer's disease, in which excess cysteine is a contributory cause." Source:https://onlinelibrary.wiley.com/doi/full/10.1002/bies.201200017
In this instance your teacher has his information incorrect. L-Cysteine has nothing to do with the production of Eumelanin. "Melanocortin 1 receptor (MC1R) is a key signaling molecule on melanocytes that responds to α-MSH by inducing expression of enzymes responsible for eumelanin synthesis. Some forms of Pheomelanin production lack the MC1R receptor to form eumelanin entirely; others have a weak signal if they have mixed Pheo/Eumelanin. Eumelanin has a strong MC1R receptor connected to the (Melanin Stimulating Hormone) α-MSH. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4299862/
Pheomelanin and Eumelanin have completely different pathways of formation. "Pheomelanin, consists mainly of sulfur-containing benzothiazine and benzothiazole derivatives (Figure 1a). L-cysteine is the chief source of sulfur and is, therefore, essential for the pheomelanin synthesis (12). Eumelanin, on the other hand is an extremely heterogeneous polymer comprising of 5,6-dihydroxyindole (DHI) and or 5,6-dihydroxyindole-2-carboxylic acid (DHICA) units (Figure 1b)."https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4299862/
Individuals with Eumelanin maybe less able to synthesis Sulfur based Amino Acids like: Methionine, Cysteine, Homocysteine, Taurine, and Glutathion. :)

First: Both pathways have the common starting point of tyrosine and its oxidation. Then: As I said in my answer (and referenced there as well) availability of cysteine does influence which of the melanins is produced. If there is excess cysteine available, no eumelanin is produced. So your answer is wrong in the way it is written. Please correct it. Also: Please stop giving unreferenced health advices, these are off-topic here.

Pheomelanin and Eumelanin have completely different pathways of formation. "Pheomelanin, consists mainly of sulfur-containing benzothiazine and benzothiazole derivatives (Figure 1a). L-cysteine is the chief source of sulfur and is, therefore, essential for the pheomelanin synthesis (12). Eumelanin, on the other hand is an extremely heterogeneous polymer comprising of 5,6-dihydroxyindole (DHI) and or 5,6-dihydroxyindole-2-carboxylic acid (DHICA) units (Figure 1b)."https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4299862/

Have you taken at least a short look at the diagram in the answer above? It shows the schematical pathway (not in all details, but still enough).

So you contend that if one born with only Pheomelanin "falls below the threshold of 0,76µM in L-Cysteine" one would gain Eumelanin? Even though L-Cysteine has nothing to do with Eumelanin production. Even in the figure you posted that theory makes no sense.

Read the paper of Land. BTW: Ito and Wakamatsu (the authors of the 2008 paper you copied above) are co-authors of this study. The concentration of cysteine is the decision point which melanin is made from the common precursor dopa-quinone. Both ways have a common starting point.

I did I actually posted it and it says nothing about L-Cysteine levels dropping and turning into Eumelanin.

Once more: You go from DOPA-quinone either in the direction of cysteinyl-DOPA (and then Pheomelanin) or DOPAchrome (and then to Eumelanin). The decision which way you go is influenced by the Cysteine concentration. And exactly this is described in the Land paper on page 4. Is this so hard to understand?

Another thing: The Nasti review (where you took the images from this answer from, also contains what I am saying: "Melanogenesis produces mixtures of eumelanin and pheomelanin at different mixed ratios. The ratio is determined by tyrosinase activity and the substrate concentrations of tyrosine and cysteine (27)." Reference 27 is this one: https://www.ncbi.nlm.nih.gov/pubmed/19627559/ Which also gives this explanation.

Basically you are saying that a white person can turn black if their sulfur levels drop. Now tell me if that makes sense to you.

No, this is not what I am saying. I say (and the papers back this) that low cysteine concentrations affect the synthesis of Pheomelanin. Regulation of pigmentation also happens on other levels as well, which play an important role,  too. And please, don't start to tell this is all MC1R. There are more factors (transcriptional) involved here.

I will read the Land paper give me one moment...

That study is nearly a decade old and new information has been attained on the subject. The information I posted is current information from 2016 on melanin. I can show you more.

Then show me the paper which proofs this connection wrong. BTW: That a paper is old doesn't necessarily mean it is wrong. The Nasti paper itself shows this connection (in the text and also via reference 27).

I don't think you a factoring into account that Genes play the top role in this as stated above. Next there are 3 different types of melanogenesis. Eumelanogenesis, Pheomelanogenesis and MIXEDmelanogenesis; all three do not occur in the same fashion. The synthesis is different for each. Yes in mixed melanin a lower amount of the Sulfur amino acid L-Cysteine would produce a person with darker skin however, you cannot take a person with only Pheomelanin put them in an environment with no Cysteine and think that Eumelanin will spontaneously occur due to a "drop in sulfhydryl compounds."

The melanocortin 1 receptor controls which type of melanin is produced by melanocytes. When the receptor is activated, (by the MSH) it triggers a series of chemical reactions inside melanocytes that stimulate these cells to make eumelanin. If the receptor is not activated or is blocked, melanocytes make pheomelanin instead of eumelanin. https://ghr.nlm.nih.gov/gene/MC1R

This is nice statement, but an overall simplified as well.

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Is the Malaria vaccine the first vaccine against a Eukaryote?
RTS,S or Mosquirix was recently released to the public, offering the first Malaria vaccine. This struck me as particularly important because I don't know of any other vaccine that protects against organisms that aren't prokaryotes or viruses.
Is that accurate? Have there been any other vaccines developed for Eukaryotic organisms? I'm defining vaccine by the CDC definition: "A preparation that is used to stimulate the body’s immune response against diseases. Vaccines are usually administered through needle injections, but some can be administered by mouth or sprayed into the nose."
I'm interested in any developed vaccine that offered immunity regardless of relative effectiveness or side effects. Even if it wasn't released to the public.
Alternatively, if anyone has a definitive source indicating that the vaccine is the first of it's kind, that would also answer the question.

According to Wikipedia, in the entry for Giardiasis, there is a commercially available vaccine against Giardiasis that veterinarians can give to cats and dogs.  Giardia is a eukaryote.  https://en.wikipedia.org/wiki/Giardiasis

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C to T Transition Mechanism
I am seeing C to T transitions in my sequencing data, but also some strange signatures that follow along with that. I am trying to understand the biology of what is occurring. In the data I see more C to T changes than G to A changes, when it would be expected that these numbers would be relatively the same.
So, in vivo when a C to T transition occurs, does the complementary base get changed to ensure watson and crick binding, or will you end up with a T-G pair? This would explain the phenomenon that I am seeing but I don't know if this happens. (Andy references would also be super helpful. Thanks.)

Depending on how your sequencing data is being presented to you, this may not be an issue. Are you looking at FASTQs, BAMs, VCFs? In my experience (human resequencing), variants are generally reported from one strand instead of both -- that is, a variant, which really causes two paired bases to change in tandem, is represented in the results by just a single letter change. When a C to T transition occurs, I would assume it's a C-G pair transitioning to a T-A pair, unless your biological or sequencing situation is unusual somehow. Give us a bit more detail about your file format and sequencer.

You have not told us what kind of sequencing data you are using, for example in bisulfite sequencing you change non-methylated C to U which are read as T. The context is very important here.

@KoustavPal This is deep genome sequencing from an Illumina 4000.


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Evolution- Variations, adaptations and selective advantages
I am trying to understand Variations, adaptations and selective advantages  and how they are all related.
Feel free to add or correct me if I'm wrong- Variations are structural, functional, or physiological differences between individual's within a species that result from mutations.  If the variation provides a selective advantage (genetic advantage) the organism's chances of survival in terms of both survival in a changing environment and reproduction increases. The variation is then considered an adaptation. So basically adaptations are variations which provide a genetic advantage and give some organisms within a species a better chance of survival than those without the adaptations. This survival advantage allows those organisms to reproduce and pass on their adaptation more frequently than those who do not possess these adaptations.

I think you should think about/define the terms more clearly - from what you write I would label your "Variations" as traits (or rather differences in traits between individuals). "Variation" is close to the techical term variance (as in phenotypic trait variance and additive genetic variance), so you risk misunderstandings.

I would define variation as something a little less specific. When talking about evolution I would consider it to mean any phenotypic variation that exists. I say phenotype because that is what selection "sees" but there can be genetic variation without phenotypic variation (see synonymous mutations). The trait could be physiological, morphological, behavioral or a life history trait (a trait which, all else remaining constant, affects fitness e.g. Lifespan or development time). This is also not necessarily just within species too, comparing homologous trait between two species could reveal between-species variation. For example, in one species every individual might day at exactly 100 days old, in another it may be 102 days, there is no variance within species but there is variance between. The phenotypic variation can be a result of genotype, environment, or a genotype-environment interaction.
If a trait positively affects fitness it is an adaptation, it is a trait that offers some kind of benefit over other current or previous incarnations of the trait. The variance for that trait can be zero - a highly adaptive trait is likely to spread rapidly and variation for that trait would zero if it was entirely genetically defined and fixed in the population but that trait would still be considered an adaptation. I would define fitness as the lifetime reproductive success of your evolutionary unit, commonly thought to be the gene. If a variant of a trait increases relative fitness it provides a selective advantage, and any genes (alleles) causing that trait should spread through the population at the expense of other alleles.
It is important to remember that not every biologist will define these in the same way, there is some debate about definitions in biology.


text:
Reconstituting genomes of archaic tribes of humans
Will it be logically possible for genome studies to reconstitute the genomes of our local human populations as they were 2000 and 4000 years ago? What is the mathematical precision and science for that kind of thing?
I am fascinated by human facial features and i wonder what our archaic tribes looked like regionally when they were isolated, a few thousand years ago, before mixing into the melting pot that they are today.
If we can one day image facial construction from DNA using some thousands of facial genes, it will be cool if we can also find what local dna pools were like precisely a few hundred generations ago. Is it possible?

Thrilling thought. May already possible. 4000 year old specimen can still be fine for sequencing.  https://en.m.wikipedia.org/wiki/Ancient_DNA   and faces can already be partially reconstructed from DNA sequences https://www.newscientist.com/article/mg22129613-600-genetic-mugshot-recreates-faces-from-nothing-but-dna/

Are you asking about genomes from individual people 2000-4000 years ago, or population structures? Full genomes have been sequenced from a number of individuals in that time range, but understanding population-level genomic information is a very different task

You should not believe that many human populations lived in isolation for long times. Almost all human populations had massive gene flow with many other human populations. Human history basically is a history of migration after migration after migration. Humans have always been genetically heterogeneous (rather than previously homogeneous and then faced a 'melting pot' that caused heterogeneity).

You should not believe that many human populations lived in isolation for long times An Aboriginal Australian Genome Reveals Separate Human Dispersals into Asia says "We show that Aboriginal Australians are descendants of an early human dispersal into eastern Asia, possibly 62,000 to 75,000 years ago.  ... Our findings support the hypothesis that present-day Aboriginal Australians descend from the earliest humans to occupy Australia, likely representing one of the oldest continuous populations outside Africa."

The answer is basically 'No.'.
Too much mixing has happened since then. Fortunately, in most of the world we had scientists 2000 years ago describing facial features, and in part of the world (i.e. China) we had scientists describing facial features 4000 years ago.
We do occasionally recover viable DNA samples from both 2000 and 4000 year old corpses, also actual corpses that still retain significant vestiges of their facial features, but expecting to recover even general facial features over hundreds of generations from present DNA is quite frankly unrealistic.
The good news is that human facial features aren't actually super variable; humans are just super good at spotting small differences (which comes with the territory as social animals). The bad news is that as a modern reader of latin or chinese texts on phylogeny (if you can find them, which I won't guarantee) the subtle differences in what they mean when they describe a nose as, let's say hooked, will probably be lost on you, or me, or any of us.
Your best chance is probably sequencing corpses from the relevant era and matching them up with phylogenisists' descriptions to form an idea of what they were talking about; and you might end up with a general sense of what people looked like.
I expect it will lead to severely underwhelming results, but I suppose it's worth a shot.


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Atomic Force Microscopy Imaging of Proteins
I was reading about various imaging techniques, and I came across Atomic Force Microscopy (AFM).  It sounds very interesting, and it also sounds like it is capable of imaging proteins (Page 4)
http://www.cma.fcen.uba.ar/files/prepmuestras.pdf
If that's the case, and since AFM can be done with relatively low expense, why haven't more proteins been imaged?  Apparently around 6500 protein structures have been solved via imaging.
If AFM is a viable technique for protein imaging, what would the consequences of using it on a large scale be?


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Can Thraustochytrids such as Schizochytrium do photosynthesis?
I know they belong to the phylum of heterokonts and that they are being heterotrophically grown on an industrial scale but I can't seem to find any reference to them being grown photoautotrophically. People call them marine algae yet there is no mention of photosynthesis.
I did find this paper which says they have several carotenoids so I assume they have those because of their LHC's and photoprotection. It would be great if anyone had some more detailed information (papers) regarding their properties.

I think not.
from Kingdoms and Domains: An Illustrated Guide to the Phyla of Life on Earth By Lynn Margulis, Michael J Chapman. as found on google books
You will see there are no chloroplasts depicted.  These are eukaryotes and so to do photosynthesis they would need chloroplasts which should be evident.

I was hoping for a more definitive answer since photosynthesis jumps in and out of the heterokont lineage but your information is a lot better than what I found. Thanks!


text:
What Goes on in Photosystems at the Molecular/Atomic Level?
In light-harvesting complexes, how is the energy of a photon transferred from one pigment molecule to another? And in reaction-center complexes, how does the primary electron acceptor capture an electron from the chlorophyll a? It’d be best if any of you could explain this to me in terms of what’s happening at the molecular or atomic level, say with electrons.

The energy transfer is achieved by a process called "resonance energy transfer". It needs the positioning of the donor and the acceptor in very close proximity to each other - the light harvesting complexes are optimized for this. This allows the collection of small amounts of light energy and still enables photosynthesis. The figure shows how this works schematically:

The figure is from this webpage, which gives a good introduction.


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Statistics: How are protein species distributed over cell types?
There are roughly 10,000 to 20,000 protein species in the human proteome (while I've seen also numbers of 500,000 to 1,000,000). Furthermore, there are roughly 200 different cell types in the human body. My question is:
How are the protein species distributed over the cell types?
This means specifically:
How many proteins are expressed by n cell types?
How many cell types express n proteins?
Probably these numbers are not known exactly because not all the proteins may be known that a given cell type expresses.
But there might be evidence which general form the two distribution curves do have. Are they Poisson distributions and do look more like this?

Or this?

Or that?

Or some other kind of distribution, e.g. Gauss or even multi-modal?

You can refer to this website - https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4889822/ This website gives a wide view of protein species distribution. So you can correlate it with the statistics.

You may be able to find some relevant data at this site: https://bionumbers.hms.harvard.edu

@Dirigible gives an excellent answer with some good literature-  you may also find this recent paper to be of interest "Analytical distributions for detailed models of stochastic gene expression in eukaryotic cells" - includes proteins (Fig 5): https://www.pnas.org/content/117/9/4682

From my searches, there is no single resource that includes an atlas of all human proteins produced across all human cell types.  However, there are several recent mass spectrometry studies that look at cell-type-resolved proteomes for specific human and mouse tissues that provide some insight into the distribution of proteins across different cells.
A Cell-type-resolved Liver Proteome
This study identified between 6200 and 8500 mouse gene products in each of four cell types -- hepatocytes, hepatic stellate cells, Kupffer cells, and liver sinusoidal endothelial cells -- and a total of 10,075 gene products across all four cell types.  Figure 1D shows that there is significant overlap between the proteomes; 5,246 proteins (52.1%) are shared by all four cell types, and only 1,451 proteins (14.4%) are cell-type exclusive in this set.  Besides cell-resident proteins, the authors also report secreted proteins unique to hepatocytes and Kupffer cells.  These results by-and-large corroborate an earlier publication, Cell-Type-Resolved Quantitative Proteomics of Murine Liver, where the authors reported 8,338 of 11,520 (72.4%) proteins were common to the five hepatic cell types tested.
Cell type- and brain region-resolved mouse brain proteome
This study looked at four types of isolated neurons from specific regions of the mouse brain as well as five types of primary cultured neurons.  Of 13,061 total proteins, 10,529 (80.6%) are common to the five cultured cell types tested, and only 194 (1.4%) are unique to a single cell type.  Figure 2D makes clear that protein abundance across cell types - not just binary presence/absence - is important to cell identity.  (More on that below...)
Region and cell-type resolved quantitative proteomic map of the human heart
Getting to the human proteins mentioned in your question, this publication analyzed three cardiac cell types and adipose fibroblasts across 16 anatomical regions, giving both spatial and functional perspectives on protein type distribution in the human heart.  Figure 5A, like Figure 1D for the mouse liver proteome paper, shows a great amount of overlap of proteins between cell types:  of 11,163 total proteins, 7,965 (71.4%) are common to all cell types (including adipose fibroblasts), and 617 (5.5%) are unique to one type of cell.  Interestingly, and perhaps not surprisingly, the subsets of proteins unique to specific cells are enriched for cell surface markers. (Related:The in silico human surfaceome)
Social network architecture of human immune cells unveiled by quantitative proteomics
These authors identified more than 10,000 different proteins across 28 primary human hematopoietic cell populations, with three or four biological replicates per cell type, including 17 distinct types of immune cells.  They identified an average of 9,500 proteins per cell type, and, for the immune cells, generated both "steady state" and "activated" proteomes, giving insight into how the proteome changes both across cell types and within each type between states.
To directly answer your question,

How are the protein species distributed over the cell types?

I took the data from Supplementary Table 6, averaged the replicates, converted protein copy-number values to a binary presence/absence matrix, and computed the number of immune cell types (1 - 17) represented by each unique protein ID.  The inset graph combines cell type and activation state labels to ask whether the effect of activation dominates over cell-type differences in proteome divergence.

Presence/Absence, no threshold -- Unique protein distribution across 17 primary immune cells types.  A protein is considered "present" in a cell type if average copy-number value is greater than zero.  Data from Rieckmann et al. Nat Immunol. 2017.

Because the inferred protein copy-numbers from the mass spectrometry data cover a high dynamic range, I also looked at the distribution of proteins that had average copy-number values at least double the zero-depleted cell-type-specific median copy-number value.

Highly abundant proteins -- Unique protein distribution across 17 primary immune cells types.  Protein-cell pairs are only counted if the average protein copy-number is at least double the median protein copy-number for each cell type.  Data from Rieckmann et al. Nat Immunol. 2017.

Taken together, these distributions suggest a few things:

for this diverse set of immune cells, a majority of proteins are present in all cell types when looking at strict presence/absence data
after subsetting for highly abundant proteins, a bimodal distribution appears, suggesting that protein abundance is a better metric for functional comparison of proteomes than a simple binary metric
the proteomes of one cell type between different activation states are more similar than the proteomes of different cell types in the same state

For anyone interested, I've made the cleaned-up data available on Dropbox.
A more complete answer might combine the data from the immune cell and heart cell publications to get a sense of proteome concordance across tissues, but, just from a cursory analysis, differences in protein labels between the datasets would make comparison tedious, so I'll leave that to someone else!


text:
How to calculate the occurrence of a stretch of nucleotides in a genome?
I have seen that the formula to calculate the number of times a given sequence of nucleotides occur in a target genome is derived from that to calculate the expected frequency of restriction sites:
a = (g/2)^G+C × ((1-g)/2)^A+T,

where:
a = probability
g = G+C content of the target genome
C+G = number of G and C in the stretch
A+T = number of A and T in the stretch.

An example was given for the mitochondrial genome and the restriction site for EcoRI (GAATTC). I calculated, based on the example:
a = (0.44/2)^2 × (1-0.44)^4 = 0.0005

given that the length m of the mitochndrial genome is 16 000 bp, the number of occurrences is:
n = am = 0.0005 × 16 000 = 4.92 (against 4.80 reported in the paper).

I then tried to calculate the occurrence of a primer based targeting E. coli: GTGTCCATTTATACGGACATCCATG.
The GC content of E. coli is 50.8%, thus:
a = (0.58/2)^11 × (0.42)^14 = 1.22×10^-6 * 3.24×10^-10 = 3.95×10^-16

and the number of occurrences is:
n = 3.95×10^-16 × 16*10^6 = 6.32×10-9

Looks to me, that the primer should not occur at all in the E. coli genome.
Are the formula and its application correct? Also, I don't like the fact that one needs to know the CG content beforehand (although, one can assume 50% content) and an exponent at the 11th power; is there an alternative formula?
Thank you.

Strictly speaking the question is from the realm of probability theory. If the probability of a nucleotide $X$ in the genome is $p_X$ ($\sum_x p_X=1$), then the probability to encounter a particular sequence, where nucleotide $X$ occurs $n_X$ times, is
$$
\prod_X p_X^{n_X} = p_A^{n_A}p_C^{n_C}p_G^{n_G}p_T^{n_T}.
$$
The formula given in the question is a particular case for $p_C=p_G=g/2$, $p_A=p_T=(1-g)/2$,
$$
\left(\frac{g}{2}\right)^{n_C+n_G}\left(\frac{1-g}{2}\right)^{n_A + n_T}
$$
which is obviously always the case for DNA, where the numbers of Cs and Gs (or As and Ts) are always the same, but the more general formula could serve for RNA or proteins.
What one should keep in mind is that the formula above is for a sequence with a particular order of the nucleotides! If the order is immaterial, and only the content of the sequence matters, the formula has to be multiplied by a binomial factor, which is effectively summing over all the possible arrangements of the nucleotides. Thus, for the case of DNA we obtain
$$
{n_A + n_C + n_G + n_T \choose n_C + n_G}
\left(\frac{g}{2}\right)^{n_C+n_G}\left(\frac{1-g}{2}\right)^{n_A + n_T}
$$
You can check yourself that the difference due to the binomial factor is striking!

Thank you. Would you have a reference paper for this formula?

@Gigiux I can't give a reference for specific use in biology. Generally this is known as the binomial distribution: https://en.wikipedia.org/wiki/Binomial_distribution

Are the formula and its application correct?

Your formula is correct, and Vadim gives a good discussion of the underlying theory.  However, concerning your application...

Looks to me, that the primer should not occur at all in the E. coli genome.

This is the point of primers -- because of their length, they are unlikely to occur at random in a given DNA sequence.  So, starting with a known DNA sequence, you can create a primer that matches that sequence and have good confidence that you are not getting off-target priming, which may give you false-positive amplification in PCR.  This is precisely what the authors do in your linked paper.1  Using the known sequences for Rfb and SLT-1 genes in E. coli O157:H7, the authors make primers for the specific detection of those genes in drinking water, and, by extension, the presence of the organism that harbors those genes.

Bonetta S, Borelli E, Bonetta S, Conio O, Palumbo F, Carraro E. Development of a PCR protocol for the detection of Escherichia coli O157:H7 and Salmonella spp. in surface water. Environ Monit Assess. 2011 Jun;177(1-4):493-503.

I tried to calculate the values given your binomial formula. The number of EcoRI sites in E. coli should be:
a = (0.44/2)^1 * (0.44/2)^1 * ((1-.44)/2)^2 * (0.56/2)^2 =
= 0.22^2 * 0.28^2 = 0.0484 * 0.0784
= 0.0038
which is ten times the value given in the paper.

The expected number of restriction sites is:
n = 0.0038 * 1.6*10^7 = 60 712.96.
This is hundredfold more than the expected value of 645 reported by this paper (https://mmbr.asm.org/content/mmbr/62/3/985.full.pdf). In the paper, they calculated the number of expected 6-mer in a genome as long as that of E. coli (1113) but they did nor provide the calculation.

As for the primer, the probability of findig it in the E. coli genome is:
a = 0.25^5 * 0.25^6 * 0.25^8 * 0.25^6 =
= 8.810^-16
n = 8.810^-16 * 1.610^7 =
= 1.410^-08.
Again, there should be -- as acvill pointed out -- unique.

I did not understand how the binomial factor is defined. It should be:
B = n! / x! (n-x)!
where n is the number of trials and x the number of success. Thus it should look something like:
B  = 16 000! / (6!15 994!)
B' = 1.610^7! / (25!1.610^7!)
which are very big numbers. I understood this calculation was an easy one. Where am I getting it wrong? Thank you


text:
Was it a mucus or a spider's web? How can a mucus look like a spider's web?
Today I found a small slug, 35-40 mm dangling on a shiny thread from a branch 175 cm above me. I thought that the slug had slid on a spider's web, so I touched it and it instantly snapped and the slug fell on the floor. I think it was wet and was mucus. How can a slug mucus, in 5-12'C, become 2 meters long, 50 microns wide and hold a slug from a branch?

Fascinating, I do not understand why down voting has become more prevalent in this community. Nonetheless, this question pertains to biophysics, materials science and biochemistry. I am by no means an expert in any of these fields. I assume the phenomenon you observed was due to the unique physical and chemical properties of the mucus, as well as the temperature experienced (5-12°C is quite cool) which would have altered the properties of the mucus.

Using Google Scholar, I was able to yield these results: 'The Physical Properties of the Pedal Mucus of the Terrestrial Slug, Ariolimax Columbianus', 'The role of mucus in the locomotion and adhesion of the pulmonate slug, Ariolimax Columbianus', 'Mechanical Properties of Pedal Mucus and Their Consequences for Gastropod Structure and Performance' and 'The role of gastropod pedal mucus in locomotion', which may provide interesting information to your question, but not answer it, such is the nature of science, we can not 'know' something.

Lastly, if you do not have a background in these fields, it can be extremely frustrating trying to read and comprehend scientific articles. This is by convention and in my opinion by mistake, since articles narrow their audience significantly, by lacking explanations of prerequisite concepts and critical background information, and context.  For example, in science often people will tell you that something is, not how we figured out or have reason to believe that it is. Meaning readers can not formulate an idea on the level of human understanding of a specific subject.

This is a separate matter, hopefully someone answer your question by using logic and outlining the limitations of our knowledge on the subject.

Hey thanks a lot for the comments, I will look into it. I just had an idea that the slug gelatin became some kind of organized cylinder of organized organic chemistry called mucins and when I touched it with my hand the dryness and oil of my hand instantly disrupted the organic chemistry and it just exploded like when glass that is under pressure erupts. I was stupid not to examine if the mucus was had conpletely sprung up or if was a web cos I was just confused.


text:
What constitutes FDA's First in Class designation for New Molecular Entities?
What constitutes a First in Class designation for new molecular entities? I've seen this term on FDA documents, as well as in databases (Chembl for example), but I was curious if there are any set criteria for First in Class drugs? The easy definition, in my mind, would be a drug that hits a novel target given its indication. However, if you look at antifungal drugs, you see that drugs with the same target for the same general indication (anti-fungal) treat completely different fungal infections because of their pharmacokinetics.
Are there discrete criteria for the FDA's first-in-class designation for New Molecular Entities?

This page on the FDA website gives a rather terse definition: "Drugs with a new and unique mechanism for treating a medical condition". I'm not sure how that's applied in practice, though.

What is FDA? What is the biological problem regarding this molecule?

@David the FDA is the Food and Drug Administration in the US. Among other things, they are charged with regulating and approving pharmaceuticals.

@MattDMo — So the question is about public health policy in one particular country, and not about a problem in biology of the type defined in the [Tour].

"First-in-class drugs are ones that use a new and unique mechanism of action for treating a medical condition. These products are often referred to as innovative and cited as offering new treatment options for patients."
Lanthier, M. et al. (2013) "An improved approach to measuring drug innovation finds steady rates of first-in-class pharmaceuticals, 1987-2011." J.Health Aff. (Millwood) 32:1433-9;
Pharmaceutical Research and Manufacturers of America. 2015b. Innovative Oncology Medicines Have Led to Impressive Gains in Patient Survivorship. Retrieved August 26, 2015. <www.phrma.org/innovative-oncology-medicines-have-led-to-impressive-gains-in-survivorship>."
From: Lexchin, J. (2016) "How Safe and Innovative Are First-in-Class Drugs Approved by Health Canada: A Cohort Study" Healthc. Policy 12:65-7.


text:
Can coding DNA be used for DNA fingerprinting?
I am confused if coding DNA can be used for DNA fingerprinting because I have read that non-coding segments of DNA are used to identify and analyze DNA. I want to know if coding DNA segments are of equal length in all individuals?

It's not non-coding regions in general, it's specific repeat sequences - microsatellites - that are highly variable. In principle you could use a full genome sequence to identify individuals.

When selecting sequences to use for DNA fingerprinting, you have to use sequences that are highly variable within the population.  Coding sequences mostly aren't, and they aren't going to vary much in size, the way tandem repeat sections do.

You are correct, but even so you need to provide a reference to document your answer and to allow the reader to find out more details.


text:
Do we as humans develop tolerance to deodorants or antiperspirants?
Do we as humans develop tolerance to deodorants or antiperspirants? In particular when they contain isobutane, isopropyl, palmitate, isododecane, dimethicone, coconut oil, magnesium oxide, allantoin, dimethiconol, disteardimonium hectorite, propylene carbonate.

What do you mean by tolerance? This implies that by default we should have some reaction to these agents. What makes you think that?

I thought that these agents might modify the behaviour of sweat glands, which is itself some reaction.

deodorants don't modify sweat glands they just act to mask or absorb scents. some anti antiperspirants act to plug sweat glands.

Thanks for your comment John. Can you please restrict to the effects of the substances that I've listed? What about long term effects then? In other words, if I stop using deodorants/anti perspirants, does my body revert back to when I hadn't started using them yet? The answer to this is not obvious, in particular given your comment "some anti antiperspirants act to plug sweat glands."


text:
Tryptophan side-chain structure, how should it be orientated?
I would like some clarification on whether it matters where the NH and double bond are placed in these two structures of tryptophan (W) that I drew. I marked the right side as correct and the left side as the incorrect one, but suddenly I am thinking that where you place the double bond and NH don't matter as long its placed in either orientation of the structure it should be tryptophan right?
Simply put, I took my chemistry classes a few years ago and don't remember if this changes the structure if I changed the position of the NH and double bonds, that is all, and would some clarification on it.

EDIT / UPDATE:
I noticed a mistake and re-drew the structure, but am still not clear about the so called "trivial" rotation mentioned. Does the new picture reflect whether or orientation not mattering? I am still confused if I drew it correct.

Care to explain why that is the case?? Don't really understand why this question is so poorly received I am genuinely trying to learn about amino acids.

Some suggestions about why this is being poorly received. 1) This qualifies as a "homework" question since it "addresses a basic biology concept that may seem trivial to biology professionals". For such questions, you are required to use the "homework" tag. 2) It is actually a (trivial) chemistry question in disguise, since you are just asking whether a chemical compound is still the same after rotating a bond. ——— Have another look at a correct structure for tryptophan — you have the placement of the aromatic ring and the nitrogen wrong.

But its not a homework question, how do you want me to prove this? I'm not taking any classes and am studying for the MCAT exam, I wanted to memorize the amino acids, but am confused if switching or rotating the orientation of the NH and double bond would make it a different molecule other than tryptophan

I have looked at the structure beside what I drew at least 100 times over and I cannot spot the difference between what I drew (incorrectly) and the correct structure. If I were asking a homework question, how come I did not reference a problem or something, I'm not trying to pick this molecule out of a list or anything like that, it is for my own personal understanding, not a homework related question, not sure how you would like me to prove this.

Did you read the page I linked to that describes what "homework" means on this site? I quoted the part that is relevant to this question. ——— You appear to have forgotten that sigma bonds freely rotate and thus that the two structures you drew are just different representations of the same molecule. Consequently, I encourage you to refresh your understanding of basic chemistry before taking the MCAT. ...

I have found that starting with a relatively accessible and reliable source like Khan Academy can be very helpful, however they aren't perfect for chemistry. Online platforms called MOOCs offer free (or very low cost) courses on a wide variety of subjects — two I am familiar with are Coursera and edX. Finally, textbooks with a good level of detail are also freely available online e.g. from NCBI.

Hi Tylersome,
Thanks for attempting to put on the right pathway. And no I did not see "homework", and have since read that in your new posts. I guess a follow-up question I have is how would I be able to discern what is a "trivial" question is for one person and not for another? Questions I ask whether they are trivial or not, are intended for my own personal understanding, not for homework purposes as I have already graduated from university and am currently trying my best to refresh my knowledge. However, I would still like somebody feedback on the second image I uploaded of the structures

since I still don't know if I drew them correctly (in the second image). I even tried inputting my drawing into chemspider and it comes out either as zero results.

Just to clarify are you referring to my 2nd picture or the first? And yes, the NH is supposed to be part of the 5 member ring, sorry if my drawing isn't clear enough for this indication. I think I now see the bond rotation, especially in the 2nd picture I drew.

I dont think this is a trivial question, it is rather a core biochemistry question regarding the positioning of amino acids side chain in proteins. The various positions are called rotamers, and it is important to understand this in structural-biology and enzyme catalysis

Good question, this regards rotamers!
Basically, the side chain of amino acids can rotate as shown in the figure below for glutamate (Glu; E). The various option for side-chain rotation is called rotamers! Some amino-acids side chains have the potential of many rotamers (such as glutamate) while some can only adopt a few (such as tryptophan) due to steric restraints. You can read about it here on FolditWiki or in the article 'Rotamers: To be or not to be?: An Analysis of Amino Acid Side-chain Conformations in Globular Proteins'.

The set of amino acid side-chain conformations in globular proteins
cannot be considered as normally distributed around some rotamer
points. Outliers occur systematically. The rotamericity of an amino
acid depends essentially on the different environments the amino acid
meets in real protein structures. Factors such as the backbone torsion
angles of the residue itself, the secondary structure and tertiary
contacts influence the rotamericity. (...)

When solving a protein structure, scientists spend a lot of time on placing the amino-acid side chains into their correct rotamer position. Which rotamer a particular side chain should adapt, depend on the surrounding environments. Some amino acids side-chain are also very flexible and will move around the various rotamer position that they can adopt. In the example of glutamate (figure above), it would most likely adapt a rotamer position pointing either out towards solvents (if the the side chain is on the surface of the protein), or perhaps towards a positively charged amino acids side chain such as Arginine (R) or Lysine (K) to form salt-bridges or H-bonds.
In the case of Tryptophan (W), it is often involved in pi-stacking and would therefore be found in a rotamer position that stacks with other aromatic amino acids side chains. It is also a very bulky amino acid, and might therefore only have space in one particular conformation. Note that tryptophan (W) only has two rotamers, which are similar to the two that you drew in the updated figure, and again shown below. Note that both of these are correct, and that my hand-drawn bond angles are a bit off. These two rotamer options for tryptophan are even found in enzymes catalytic site, where the 'flipping' from one confirmation to the other is the key-mechanisms the allows substrates into or out of the active site!

These structural arrangements are a lot easier to understand in three-dimensions, if you are still struggling then it could be a good idea to use a visualisation program (e.g. PyMol or Coot) and take a look at tryptophane's and other amino acids side chains by downloading some protein structure from the PDB database.
Here are also some related questions

Protein Structure Parameters
How to convert PDB file of Amino Acids to rotamer tuples list of all AAs instances


text:
How can viruses spread so fast in a plaque assay?
I understand the basic idea of viral plaque assay, but I don't understand how the virus spreads so quickly in the culture.
For example, at 1:30 in an educational video about the subject, you can see various viral plaques all growing from single infection points and then multiplying to cover a circular area as the new virions spread outwards.
However, if you think about it, we know the virus cannot move, so when the new virions bud they can only infect adjacent cells (or bacteria). So the spread is limited to whatever cells are immediately adjacent to the infected cell(s).
So, let's say a virus is 100nm in diameter and replicates every 8 hours. In 4 weeks there would be 30 days or 90 replication cycles. Let's imagine that a virus can "reach" things 5 times its body diameter when it buds, so that is things 5 x 100nm = 500nm away. If we have 90 replication cycles then the total radius of the viral plaque could be at most 500nm * 90 = 45,000nm or 45 micrometers, which is a speck invisible to the naked eye.
However, when we look at the plaques in the video we can see they are 5-7mm in diameter and are very visible to the naked eye. So, how could the virus be traveling this far?

As Bryan pointed out in the comments, viruses infect cells, where they replicate and then spread from those cells. They do not bud off from existing virions. Cultured human cells might be roughly 200 to 500x larger in diameter (20 - 50µm) than your hypothetical virus. The virus does spread only to adjacent cells, but it does so in all directions, increasing plaque diameter by roughly 2x the cell diameter with each replication cycle.
So, to estimate plaque diameter D from cell diameter d and number of replication cycles r, in a perfecly confluent monolayer, a more accurate equation might be something like: D = d + 2dr
If you plug in your theoretical 90 replication cycles and a cell diameter of 25µm, you'd get 25 + (2 x 25 x 90) = 4,525µm or 4.5mm.
In case it's not already understood, cells in a monolayer will vary in both size and shape, and replication times will vary between different viruses, environmental conditions, and cell types. So, it's not a perfect calculation, more of a back of the envelope to show that plaques can reach visible sizes in a reasonable number of replication cycles.


text:
Will all bacteria become resistant against all antibiotics in the long term?
(I asked the same at medicalsciences beta, but I expect a quite different perspective on it here)
This is about bacteria that can infect humans, and their multi-resistance.
The evolution of bacteria to be resistant against antibiotics is certainly a trait that is helpful for the bacteria, and there is not much evolutionary pressure to loose it.
We will always hope that the next best antibiotic will help against a given infection, giving the bacteria a chance to get immune against the next as soon as we lost the battle for the previous one.
Does that deterministically add up to all bacteria being resistent against all antibiotics in some point in time?
Or is there reason to assume that we can find new antibiotics fast enough to outrun bacteria evolution? I assume it's not, because evolution will not stop, and there is a finite number of antibiotics, I would expect.
(Or is there reason to believe that we become extinct before all bacteria become resistant, so we do not need to worry about bacteria?)

The problem about finding new antibiotics is primarily cost not time. Namely, a new antibiotic will not generate much revenue as it is a reserve drug, so is mostly reserved to academic endeavors. Also, resistance comes at a cost. E. coli resistant to streptomycin is adapted to it and grows poorly without it (dependent). So a bug resistant to dozens upon dozens of drugs will be less fit. Also, for some topical compounds resistance is highly improbable (chlorhexidine (stuff in corsodyl), iodine etc.)

@MatteoFerla That looks like a pretty solid answer!

Regarding the close vote as opinion based: I do not think it is, the answer in the comment above is evidence for it. (That answer may be controversial, but it is about facts, not opinions.)

and there is not much evolutionary pressure to loose it

The energetic cost of replicating antibiotic resistance genes in the absence of antibiotic selection is not trivial, and varies depending on the environment and genetic background of the strain.1  Beyond simple metabolic costs, there is some recent research that suggests that carriage of resistance genes in the absence of antibiotic selection leads to more frequent DNA breaks, adding a mutational burden to resistant strains.2
It may also be the case that expression of a resistance gene by one cell affords a protective phenotype to neighboring cells.  Consider β-lactams, the most common class of antibiotics.  Resistance to β-lactams is often achieved by secretion of β-lactamases, so genetic heterogeneity of a bacterial population can be maintained with respect to β-lactamase gene carriage as long as the cells with the gene are producing sufficient enzyme to protect their susceptible neighbors.

Or is there reason to assume that we can find new antibiotics fast enough to outrun bacteria evolution? I assume it's not, because evolution will not stop, and there is a finite number of antibiotics, I would expect.

Then why not use evolution to our advantage?  Phage therapy is a field that has been around for decades, but there has been a resurgence of interest as the frequency of infections by multidrug-resistant pathogens increases.  Because phages parasitize bacteria, the effective sequence space for phage evolution is as large as the sequence space for bacterial evolution, and equally fast.  Phage therapy has been highlighted recently for its ability to eliminate infections that are recalcitrant to antibiotic treatment.3  Interestingly, phage selection can be used in conjunction with antibiotic treatment to re-sensitize resistant bacteria to antibiotics.4

Durão P, Balbontín R, Gordo I. Evolutionary Mechanisms Shaping the Maintenance of Antibiotic Resistance. Trends Microbiol. 2018 Aug;26(8):677-691.
Balbontín R, Frazão N, Gordo I. DNA breaks-mediated cost reveals RNase HI as a new target for selectively eliminating antibiotic resistance. bioRxiv. 2020.
Dedrick RM, Guerrero-Bustamante CA, Garlena RA, Russell DA, Ford K, Harris K, Gilmour KC, Soothill J, Jacobs-Sera D, Schooley RT, Hatfull GF, Spencer H. Engineered bacteriophages for treatment of a patient with a disseminated drug-resistant Mycobacterium abscessus. Nat Med. 2019 May;25(5):730-733.
Chan BK, Sistrom M, Wertz JE, Kortright KE, Narayan D, Turner PE. Phage selection restores antibiotic sensitivity in MDR Pseudomonas aeruginosa. Sci Rep. 2016;6:26717.

As mentioned, antibiotic resistance is actually quite expensive. Bacteria that fail to discard it when antibiotics are not present will be wiped out by competition from other bacteria that devote more resources to reproduction.
One major source of antibiotic resistance is the 'multidrug efflux pump' which transports harmful chemicals outside the cell. You can imagine how it costs energy to run a pump. These pumps also protect the cell from other harmful molecules such as heavy metals and organic pollutants, so making them more specialized for antibiotics will increase vulnerability to other toxins.
Looking at the question more broadly, if bacteria could become universally resistant, it would have happened already. Remember that the most famous antibiotic, penicillin, was discovered because a fungus invaded and killed bacteria being cultured in a petri dish. The microbiological world is a brutal war that has raged constantly for billions of years between bacteria, phage, fungi, other bacteria, etc. Antibiotics and the resistance to them have been around much longer than humans, let alone modern medicine. If we don't take that into account, it seems like medically important pathogens have developed new defences in a very short time, so we overestimate their ability to adapt to new threats.


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Remove RNAse from pipettes?
Our lab uses old Gilson Pipetman pipettes. I've been using some for making mRNA by in vitro transcription and started running into RNAse issues. I'm trying to clean everything up, including the pipettes. I'm not sure these old pipettes can be autoclaved, at least not in one piece, I think I can take them apart and autoclave the parts that might touch the solutions. Is there some way to wash the pipettes out effectively and remove any RNAses?
I use boxes of RNAse free barrier tips, do all my work on new pieces of aluminum foil, use commercial RNAse free water, gloves, labcoat, facemask, etc. However yields from the in vitro transcription kit have been reduced, and yields from the tailing kit are even worse, sometimes losing 90% of the RNA. There's only so much I can do, our building is old and full of dust and the damn pipes above my work bench leak ( all the pipes leak, had 2 major pipe bursts in the last 6 months ).
I'll probably have to get new kits. Just have to prove to my advisor that the kits are contaminated.

I'd disassemble the pipettes and put the appropriate parts in DEPC solution. I would also consider other issues aside from RNAses, reduced yield can have many different causes.

I took apart the pipettes and sonicated the lower parts in RNAse Away, rinsed in ddH2O, then 70% ethanol followed by autoclave. Reassembled with new seals and o-rings and checked the calibration. They seem ok so far. Been using this same kit for about 3-4 months, so it's had a lot of freeze thaws. Will have to replace soon anyway. Running denaturing gels shows smears instead of bands, suggesting degradation.

I'd also switch out all ingredients for your in vitro transcription if you have any RNAse problem. You might also want to aliquot the stocks further, to limit the damage contamination causes, and to protect the more sensitive stocks. Some stuff just gets bad quicker, DTT should be reasonably fresh, and NTPs also get noticeably worse if they're older. But we also don't use kits but prepare all the stuff in our lab.

wipe the pipette's neck with RNAseZap/RNAseAway and use filter tips for your experiment. Degradation is not essentially because of contamination by pipette- check your plasticware- tubes, tips, gel tanks etc. Also check the buffer that you use for your gels (was it autoclaved. is the pH fine). And if your building is dusty, you can perform the experiments in a laminar hood.

According to the Gilson Pipettman User Guide you can autoclave the following parts: Tip ejector, Tip holder and the connecting nut (have a look into the PDF linked above if you are not sure about the parts). All other parts can not be autoclaved. Gilson says the following conditions can be used (page 17 in the user guide): Autoclave for 20 minutes at 121°C, 0.1 MPa.
However, when you really have a DNAse contamination, you will not get rid of it with autoclaving, since RNAses are too stable. You can either try the various solutions on the market which made for killing RNAses or simply get a new set of pipettes used only for RNA work (on a different bench in a different lab with a completely different and fresh set of chemicals and plastic ware). And I would recommend filter tips for this work. They are more expensive but in the long run it will save money since you don't have to repeat experiments.
Regarding your leaking pipettes: The pipettes contain rubber rings and teflon seals in the inside which have to be replaced from time to time. The image below shows how (parts C and D), the ring can be purchased from Gilson. If you don't know how to do this work (and have no technician who does) you can also send in the pipettes for service. This costs a bit of money, but is ways better than to use unreliable, leaky pipettes.

And don't worry, Gilson pipettes are pretty good. I have used now more or less all brands on the market and I still prefer them. They only need some service from time to time.

The pipettes aren't leaking, the pipes are leaking. It's a plumbing problem. I'm cleaning the pipettes right now and I have replacement seals and o-rings, so hopefully this problem will be solved. Can't fix the pipes without a plumber.

Pipes. I somehow made this into pipettes here. Probably I had too much leaky ones as well :-)


text:
Can a bacteriophage be used to treat bacterial diseases?
Some bacteriophages reproduce using the lytic cycle which ends with the destruction of the host bacterial cell. I was wondering if theoretically this could be used therapeutically to treat bacterial diseases.

Yes: http://en.wikipedia.org/wiki/Phage_therapy

Yes, this is possible and is researched as an alternative to antibiotics. It has been used experimentally before antibiotics became widely available. Research was abandoned when antibiotics became widely available. See for example here and here for reports on this.
Today bacteriophages are researched for the treatment of bacteria which have a lot of resistances against antibiotics like Mycobacterium tuberculosis, Enterococcus faecalis, Staphylococcus aureus, Acinetobacter baumannii and Pseudomonas aeruginosa. See the references for more details (the first article also contains a nice historic overview of the field):

Bacteriophage Therapy
Bacteriophages: an appraisal of their role in the treatment of
bacterial infections
New ways to treat bacterial infections


text:
Is there a risk that genetically modified organisms displace genes of other species via horizontal gene transfer?
It is known that species can rely on certain genes to survive. See for example this publication.
An argument often made by environmental groups is that genes introduced by genetically modified organisms can spread via horizontal gene transfer and could potentially displace native genes and thus lead to extinction of organisms. Are there any publications which support that assertion?

[converted from a comment that got unwieldy]
Why necessarily HGT and not simple breeding? There is a term genetic pollution for this, looks like it's somewhat controversial as an environmental issue but it seems a more readily available means (and undoubtedly happens at some rate).
HGT of e.g. microbial antibiotic resistance is well-founded, but there's not much evidence that lab antibiotic resistance genes are anywhere near as good as "natural" resistance genes. We tend to just use stuff that's already in nature.
One might look at glyphosate resistance in weeds, given the very high rate of glyphosate usage and glyphosate-resistant agricultural varieties. However that linked 2005 USDA report doesn't even bother to mention introgression from ag varieties, instead focusing on the much more numerous weeds that are naturally resistant, or have evolved resistance in response to glyphosate pressure in the field. Here is a more recent pop science article arguing that weed evolution is by far the most acute problem in this case.
So it's formally possible that genes escape from GMOs to the wild, but I'm not sure that there are any reports of genetic pollution actually being a "problem" from an environmental point of view (at least relative to the much more prevalent naturally occurring resistance).
There are of course still plenty of good reasons not to use glyphosate resistant varieties or antibiotics more broadly! There is some evidence of a glyphosate-cancer association, and more generally relying on these tools to support industrial monocultures has tons of environmental problems. Glyphosate application is almost certainly contributing to extinctions. It's more that this particular objection to biotechnology (GMOs escaping and outcompeting non-GMOs) isn't too convincing.

Horizontal gene transfer is a poor argument against green gene-technology. Like most arguments, it boils down to "The method in general is totally fine, it's just Monsanto that's evil, since as a monopoly, they do/did whatever the f*** they want".
The problem of horizontal gene transfer would be solved by transforming not the nuclear genome, but chloroplasts (Ruf et al.2021). By doing so, plants that reproduce in the wild "dilute" the transgene with each subsequent generation. However, this technique isn't seen in the industry.
I know that my botanics professor mentioned chloroplast transformation in a one-hour rant about the unfairness/stupidity towards green gene-tech. He also stated that restrictive laws allowed Monsanto to become a monopoly, which freezed any progress in this kind of industry. RoundUp everywhere.
Chloroplast transformation seems really promising though (Siddiqui et al 2020).


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Why don't phage vectors lyse mammalian cells?
I have read many articles on bacteriophages (like the lambda phage1) being used for transferring genes into mammalian cells, but none of them mention any sort of lysis of the cells even though in bacteria, lysis would occur. Of course, killing the cell would beat the purpose of the gene transfer, but why doesn't the bacteriophage kill the mammalian cells? Has there been any research on lysis of the mammalian cells with phages?

Lambda phage undergoes lysogenic cycle where host cell is not lysed immediately, it becomes a prophage and divides along the host cell. It causes lysis when exposed to UV or some other chemicals.

@JM97 are there any bacteriophages that do lyse immediately?

why doesn't the bacteriophage kill the mammalian cells?

Phage are molecularly equipped to infect only their bacterial hosts. Consider the barriers that a phage needs to overcome in order to replicate and lyse a eukaryotic cell:

The phage needs to get its genetic material into the cell, whose membrane has a vastly different lipid and protein composition compared to a bacterial cell.
The phage genetic material (assuming DNA) needs to translocate to the nucleus. There's no cytoplasmic RNA polymerase to carry out transcription.
The phage DNA needs to be bound by nuclear RNA polymerase. Bacterial/phage promoters have different motifs than eukaryotic promoters and will likely not be bound the eukaryotic transcription initiation complex.
The phage transcripts need to be translated, and the viral proteins need to self-assemble to produce new viral particles.

Under normal conditions, phage λ can carry out none of these steps in mammalian cells, save instances of cytosolic import via energy-independent endocytic mechanisms which may incidentally overcome barrier #1.1
In the linked paper,2 highly modified versions of phage λ are used to deliver a construct encoding firefly luciferase (luc) into mouse cells in vivo and human K562-αvβ3 cells in vitro. These λ variants contain recombinant components from mammalian viruses that help them to perform the desired functions in mammalian cells:

A high-affinity αvβ3 integrin binding protein (3JCLI4), engineered from human FNfn10 for enhanced binding and endocytosis into αvβ3-positive cells.3 This addresses barrier #1.
A domain from the HIV-1 Tat protein fused to λ capsid protein gpD enhances mammalian cell entry 4 and permits nuclear translocation.5 This addresses barriers #1 and #2.
A reporter gene cassette for luc expression driven by a human cytomegalovirus
promoter (CMV) that can serve as a site of transcription initiation by mammalian RNA polymerase II. This addresses barrier #3. Further, this construct is made such that only genes directly regulated by the CMV promoter are transcribed when "infecting" the mammalian host,4 so only luc is expressed and not the full repertoire of phage genes.
It's not entirely clear from the text of the linked study whether this is true of their λ variants, but the original paper describing the λ lysogen they utilize 4 includes gpD constructs fused with integrin-binding peptide RDG, the heparin-binding domain of vitronectin, and the nuclear localization signal of simian virus 40 T antigen, each of which serve to enhance λ entry into mammalian cells and/or nuclear translocation.

Moreover, WT λ produces holins and endolysins to permeabilize the host cell wall in the final stage of lytic infection.6 Even if they were expressed in mammalian cells, these proteins are evolved to degrade bacterial cell walls, not eukaryotic cell membranes.
All of this to say that bacteriophage lack the molecular machinery to infect and replicate in mammalian cells, and that even phage that have been engineered to enter mammalian cells lack the components to engage in productive infection.

References

Huh H, Wong S, St Jean J, Slavcev R. Bacteriophage interactions with mammalian tissue: Therapeutic applications. Adv Drug Deliv Rev. 2019 May;145:4-17.
Lankes HA, Zanghi CN, Santos K, Capella C, Duke CM, Dewhurst S. In vivo gene delivery and expression by bacteriophage lambda vectors. J Appl Microbiol. 2007 May;102(5):1337-49.
Richards J, Miller M, Abend J, Koide A, Koide S, Dewhurst S. Engineered fibronectin type III domain with a RGDWXE sequence binds with enhanced affinity and specificity to human alphavbeta3 integrin. J Mol Biol. 2003 Mar 7;326(5):1475-88.
Eguchi A, Akuta T, Okuyama H, Senda T, Yokoi H, Inokuchi H, Fujita S, Hayakawa T, Takeda K, Hasegawa M, Nakanishi M. Protein transduction domain of HIV-1 Tat protein promotes efficient delivery of DNA into mammalian cells. J Biol Chem. 2001 Jul 13;276(28):26204-10.
Vivès E, Brodin P, Lebleu B. A truncated HIV-1 Tat protein basic domain rapidly translocates through the plasma membrane and accumulates in the cell nucleus. J Biol Chem. 1997 Jun 20;272(25):16010-7.
Young I, Wang I, Roof WD. Phages will out: strategies of host cell lysis. Trends Microbiol. 2000 Mar;8(3):120-8.


text:
What is "irrational" drug/molecule design?
Both the papers "Directed evolution: the 'rational' basis for 'irrational' design" by Tobin et al. and "Rational and 'Irrational' Design of Proteins and Their Use in Biotechnology" by Nixon et al. reference the concept of "irrational" drug design, but never formally define it in their text.
Is there a formal definition of what makes a drug design process "irrational"? What is the meaning of the term "irrational" in this context?

Nixon AE, Firestine SM. Rational and "irrational" design of proteins and their use in biotechnology. IUBMB Life. 2000;49(3):181-187.
Tobin MB, Gustafsson C, Huisman GW. Directed evolution: the 'rational' basis for 'irrational' design. Curr Opin Struct Biol. 2000;10(4):421-427.

"Irrational" design in these papers refers to combinatorial mutagenesis, which is put forward as the alternative to "rational" protein design.
Rational design involves using existing information about a protein to choose residues to mutate.
From Nixon et al.:

Alteration of function by rational approaches can be achieved through single-point mutation, exchange of elements of secondary structure, exchange of whole domains, or generation of fusion proteins

Whereas irrational design uses random mutations to gain insight into the functional capacity of specific residues or domains, which may then be further manipulated by rational approaches.
From Tobin et al.:

‘Irrational’ protein design using directed evolution methods relying on entirely random mutagenesis techniques has also had its successes, particularly in cases in which sequential rounds of mutagenesis have been pursued.

According to "Drugs: From Discovery to Approval" by Rick Ng. The "rationality" of drug design refers to whether structure is used to inform the design.
The Irrational approach:

involves empirical observations of the pharmacological effects from
  screening of many chemical compounds, mainly those from natural
  products. The active component that gives rise to the observed effects
  is isolated. The chemical formula is determined, and modifications are
  made to improve its properties.

Whereas the Rational approach:

Requires three-dimensional knowledge of the target structure
  involved in the disease. Drugs are designed to interact with this
  target structure to create a beneficial response.


text:
Time required for DNA replication in E. coli
In a particular strain of E. coli, it was observed that DNA polymerase could add nucleotides to a growing chain of DNA at the rate of 600 per second. If the genome of this organism is 1.1mm long wherein a base pair occupies 0.34 nm, then how much time (in minutes) would be required for the complete replication of the chromosomal DNA molecule?
(Report the closest integer value.) {Source}
I solved this question using this method.
No. of base pairs: $ \frac{1.1  \times 10^{-3} \space m}{0.34 \times 10^{-9} \space m/bp} = 3.23 \times 10^{6} \space bp$
Time required for replication (in minutes by the DNA Polymerase) = $ \frac{ 3.23 \times 10^{6} \space bp}{(600 \space bp/s)\times (60 \space s/minute)} =89.86 ≈ 90 \space minutes$
The answer, however, is 45 minutes. What am I getting wrong?

Remember that E. coli has a single circular chromosome, and that chromosome is replicated bidirectionally. Hence, your calculated value (90 minutes) is exactly twice that of the correct answer.


text:
What type of Caterpillar is this?
What type of Caterpillar is this?

My hand brushed against this last night and it burned and itched immediately. Today it's starting to blister, is red, and itches all around the bumps. I was camping at the John Knox Ranch in Fischer, Texas. It was dark and I reached to grab the chair when I suddenly felt pain. It was about two inches long. This is the reaction I initially got. I didn't even feel when i brushed against it until i started feeling pain.
These were the best pictures I could get.
Any help is appreciated!!

Picture is not very good, but I think this might be an Eastern Buckmoth Hemileuca maia caterpillar.

 Photo credit: Gary L. Spicer ; Source: butterfliesandmoths.org
Description: From the University of Kentucky:

The two-inch long Buck Moth caterpillar is brown to purplish-black with numerous yellow spots. The body is protected with branched reddish spines that may have red or black tips....
Common...from spring to mid-summer.

Reaction: Your wound/reaction would not be an unexpected reaction from touching this caterpillar species. From UFL IAFS:

The spines in the buck moth occur on raised, sclerotized (hardened) portions of the larva's cuticle that are known as tubercles and scoli. The spines found on these structures are associated with venom glands that occur within the caterpillar's body... The sting produces pain immediately, which then spreads to nearby lymphatic nodes. The caterpillar's sting then causes swelling and redness to occur. These symptoms can last for as little as a day to over a week. Wagner (2005) reported that the stings he received from a buck moth caterpillar were still present after ten days and the venom of the caterpillar caused a small hemorrhage where each spine had stung him. According to Diaz (2005), severe reactions to the venom of the buck moth (such as anaphylaxis) are rare.

Treatment: The video here suggests running your hand under cold water, air dry, use tape to get out remaining spines, and then apply some ice. UFL IAFS corroborates this approach as well.

Range: According to the incidence map on butterfliesandmoths.org, H. maia is found in Texas:

Wikipedia corroborates the range of this species to include Texas.

it was spiney/spikey. Thank you for your response.


text:
Pharmacological inhibition of Ras
I was reading this review and came by this:

Direct pharmacologic inhibition of RAS has been a major challenge.
  Interference with the nucleotide-binding pocket of the protein seems
  to be far more difficult than interfering with the analogous
  ATP-binding pocket in kinases. This is presumably due to the much
  higher (picomolar) affinity of RAS for GTP.

What is meant by affinity? How do inhibitors work (in this context)?
Kindly help me as to what does this mean, I am new to biochemistry.

It is a paid subscription, but still here is the link http://www.nature.com/nrd/journal/v13/n12/full/nrd4281.html

There is a section with a non-mathematical description of Receptor/ligand binding affinity in the Wikipedia entry for Ligand, and a numerical approach in Alberts et al. — especially Fig.3-44. The treatment of protein inhibitors in textbooks is usually done in relation to enzymes, which are more complex than other binding proteins. However the section on competitive inhibitors in Wikipedia, for example, is relevant to other proteins.

I have edited your title to make it appropriate to the specific question you have asked about inhibition of Ras (note conventional capitalization). This makes for better indexing, should others have a similar question later.

Protein binding interactions are usually referred to by how easily the binding partner can be displaced by something other than the preferred substrate. Usually, this is in reference to the concentration of the binding partner required such that the average occupancy of the protein (in this case RAS) to the binding partner is ~ 50%.
If the affinity protein for a given binding partner is in the picomolar range, that means that it binds so tightly that very very little substrate is needed to achieve 50% occupancy. In order to interfere with RAS's preference for GTP, you would have to design something that RAS likes to bind to with even greater preference that would be able to displace GTP. This has proven quite challenging.
Other kinases, whose affinity for their substrate is not nearly as high, have been easier to design molecules that displace their endogenous ligands and hence interfere with their function.
I know it is Wiki, but the activation/deactivation section of this Page provides some insight into how RAS binds GTP and turned on, how GAP functions to help RAS hydrolyze GTP->GDP, resulting in turning off RAS downstream signalling. RAS signalling is actually a balance between Guanine nucleotide exchange factors causing RAS to drop GDP for GTP (turning RAS on) and GTPase activating proteins mentioned above (GAP).
Mutated RAS in cancer often involves a coding change such that the ability to hydrolyze GTP->GDP is mitigated, thus leaving RAS in the ON state.
For your initial question of inhibitors (and more general). Cellular signalling involves the interaction of proteins with other proteins and/or signalling molecules and/or DNA/RNA. Very generically, inhibitors interfere with this interaction.
Example: Kinases add a phosphate group to another protein, that can among other things change the affinity of that protein for its binding partners, and thus set off a downstream signalling cascade. If kinase A phosphorylates protein 1, and you inhibit kinase A from doing this, you have inhibited downstream effects from protein 1's signalling cascade.
Take a look at this picture:  The two drugs in red interfere with downstream signalling cascades in B-cell receptor signalling by preventing endogenous binding/signalling events.