Maximilian

Homo sapiens!

Thanks Sir for your solution. Now I am clear. I have added DTT in buffer used for gel filtration that's why protein's molecular weight from SDS-PAGE and gel filtration is approx. 40 kDa and from Native Page it is coming approx. 146 kDa i.e. actually it is homotetramer.

Yup, that seems about what you'd expect under those conditions! I'm glad I could help.

This question is hard to answer because it depends on how you decide to define a living thing, what cellular structures you are looking for, what you mean with genetic material, and what you mean with "basic feature".

In my opinion, the answer to this question will change depending on who asks it. For example, if your professor is of the opinion that Viruses are not alive and you just went over viral genetics, then she might be looking for the answer "Cellular structure because viruses also contain genetic information and are not alive". However, perhaps your professor chose to define life as any entity that carries genetic information, and also talked about the formation of vesicles that might look like microorganisms under the microscope. In this case, he might be looking for "genetic information".

It's a question which can be interpreted in many different ways, and so there is no "correct" answer.

In general, organic molecules with no conjugated double bonds will tend to be "white" because they do not absorb photons with wavelengths in the visible range, they just scatter them. The color depends between the difference in energy between the highest occupied molecular orbital ("HOMO") and the lowest unoccupied molecular orbital ("LUMO"). The HOMO-LUMO gap for the average non-conjugated organic molecule tends to found in the UV range, which is invisible to most of us. In general, as you add more PI bonds into a conjugated system, the energy required for an electron to jump from the bonding HOMO to the antibonding LUMO is reduced. Hence, adding more conjugated PI bonds to system will "red-shift" the compound. Other substituents will affect the electronics and hence the color, as well as the surrounding environment around the chromophore (for example, in fluorescent proteins with the same chromophore but different amino acids surrounding it, and all three human opsins absorb different wavelengths using the same retinal molecule).

For a good treatment on MO's I recommend you Ian Flemming's Molecular Orbitals and Organic Chemical Reactions. The first chapter talks a lot about conjugation.

This applies to organic molecules without metals.

Metals have different electronics and often times the color of their complexes depend on the reduction state of the metal, that is, the number of electrons present in their d-orbitals.

There are more complications when it comes to color, such as "why is solid elemental sulfur yellow?" or how to explain the color of some solid metals and minerals, while many of these can be explained purely with electronics of the molecular orbitals, sometimes other optical phenomenon need to be invoked (especially with more complicated materials).

There's a video on it here:

https://www.youtube.com/watch?v=rt3aR87SFQI

Also, here's a list with the color of elements:

http://www.periodictable.com/Properties/A/Color.html

How are you running your gel filtration? If there are no denaturing agents and the pH is right, it should look the same as native.

In native, you are keeping the proteins in their native form. This means that the quaternary structure should remain conserved. On the SDS-PAGE you use denaturant (SDS to disrupt secondary/tertiary and a reducing agent such as beta-mercaptoethanol to reduce the disulfide bridges) to denature your protein. This will convert multimers into their monomeric form.

When you run gel filtration you can choose your conditions to keep the protein native or you can also denature it. If your conditions are denaturing, the results will likely look like SDS-PAGE. Otherwise they should look like native.

I am thinking your protein is a homotetramer because the small weight is approximately 1/4 of the bigger weight, but this is not necessary.

If you are running the SDS-PAGE and the native after purifying the protein with a his-tag, and there is only one band in the SDS-PAGE, I would think it is a homotetramer. It is hard to know without knowing exactly what the protein has gone through and your gel filtration conditions.

The sad truth is that we currently lack the methodology to study consciousness at that level in a truly scientific manner. It is debatable whether we will ever come up with a way to do so - finger crossed!

The pKa for the imidazole conjugate acid is of around 7. You do not want your pH to go any lower than that, as the imidazole will become protonated and won't bind to the resin (might still get some elution from protonating the his-tag, but it's not very efficient). At pH 9, the imidazole will not be protonated, so it will still elute your protein. However, your protein will remain in the elution buffer, and for many proteins a pH of 9 is not optimal.

I would add HCl until the pH goes down to 7.5. Add a bit, mix, measure pH. Repeat until you get to 7.5.

In general, it would not be necessary to "cancel out some existing genes", unless the specific phenotype requires it.

Yes, it is possible. Simple in theory, but very, very, very complicated in practice.

For example, hair thickness, color, and straightness could be modified by inserting the appropriate gene variants. I don't think the hairline location could be manipulated genetically in an adult because that involves the expression of genes during the development rather than genes being currently expressed. I mean, you could do it, but that is not simple in theory at all. You'd have better luck performing surgery.

Is your protein a tetramer?

If the monomeric unit is 36.5kD that could explain the results.

Methionine racemase

Is there a known genetic mechanism through which a given polypeptide can have its amino acid sequence inverted?

For example:

A DNA sequence is translated into the sequence:

N-MKTSTRFLDGYFPVAANK-C

-Mutation occurs-

Which leads to the production of:

N-MKNAAVPFYGDLFRTSTKM-C


The obvious problem is that an inversion will invert the codon sequences (ex. CUU GGA-> AGG UUC = LG-> RU). Is there any known mechanism in nature through it is possible to change something like "AAU UCU GAC" into "GAC UCU AAU"?

Furthermore, I've been running blast searches using inverted amino acid sequences of arbitrarily chosen proteins to see if I find any interesting matches, but haven't gotten any expect values lower than 1x10^-3. I've been doing this manually because I am not trained in bioinformatics - do any of you know where I could learn enough to make a program that will automatically go through inverted amino acid sequence blast searches and retrieve the matches with low expect values?


Thanks!

the release of endorphins by the spinal cord, happens whenever you pop a joint, its really addictive so don't do it

 

i have a bad habit of occasionally dislocating my shoulder and wrist joints because of this

(lets just say i have bad sleeping habits, and loose joints)

 

 

Interesting, do you know of any books/papers where I can read more about this? I haven't been able to find anything on endorphin release when popping joints.

~Thanks!

Are you sure you added methanol? Try evaporating a pure methanol solution and see what happens.

That would be a positively charged methyl carbocation. CH3+

Are you sure it's not spelled "Raffinose"?

Hello!

I have been trying to find a ribozyme which can cleave peptide bonds but have had no luck. Do any of you know whether one of these has been artificially produced? Is there any reason why it would be impossible to make one? I would like to make some proteases capable of breaking a specific peptide bond, and I was thinking that it could perhaps be easier to evolve one from RNA than from a protein, but I am not familiar enough with the field to know whether this is viable or not.

I think you may be misunderstanding the term. In this context, "acquired trait" refers to a trait that is acquired during the organism's lifetime. So for example; if my muscle mass increases because I do a lot of exercise or I eat a lot of food and become really fat, these would be acquired traits or acquired characteristics. This is because these changes in the phenotype do not come because of changes in the genotype, but because of the interaction genotype's interaction with the environment.

A novel trait that emerges due to a mutation is not an acquired trait.

You can see a simple explanation here: http://utahscience.oremjr.alpine.k12.ut.us/Sciber01/7th/cells/html/inhvsacq.htm

This is an oversimplification, as epigenetic variations can be transmitted from parents to progeny.

Interesting question. That's a change from the question why plants are green. I found this pdf where the abstract gives no hope:

 

I have no idea why plants have not chosen to be black bodies.

I posted this mainly to show you someone read your question...

Thank you Michel, that's a very interesting paper.

On several ocations I've stumbled upon explanations like "Photosystems in plant ancestors evolved in a different environment and now it's sort of "stuck" the way it is, it's too hard to change it", "The plant would become too hot!", and "The plants can't handle so much energy". I am a bit skeptical about these explanations, but if you have any data testing any of these hypothesis I'd love to know about it.

While reading "Photobiology: The Science of Life and Light" (Amazing book) I stumbled upon what looks like an explanation. The problem is that I can't fully understand it, and I would like your help.

You can read it here: http://books.google.com.mx/books?id=bRWd5bGhXM4C&lpg=PA156&vq=Why%20are%20plants%20green%3F&hl=es&pg=PA156#v=onepage&q&f=false

On the third paragraph it says:

"As for the idea that an ideal pigment should absorb everything, we should remember that the better a substance absorbs, the better it emits, and the transformation of radiant energy into other energy forms is just the balance between absorption and re-radiation"

I am trying to understand this and I am unsure about whether I'm on the right path or not. Some of the reactions in photosynthesis are reversible (Example: http://jgp.rupress.org/content/34/6/809.full.pdf), so I guess it means that by increasing the absorption you increase the emission and increases the chances of the reaction going backwards and emitting a photon... If this is correct, that would mean that being able to absorb (and emit) green light would somehow lead to a decrease in net absorption. I am still quite confused, if anyone could enlighten me or point me in the right direction that would be GREAT.

I don't think the results are contradictory. The second study did challenge the assumption that multiple-choice decisions are evenly shared among the decision-makers in the colony, but this doesn't really affect the outcome of the first study.

The first paper "Rationality in collective decision-making by ant colonies" by Pratt et al. focused on one of the principles of rationality that is commonly violated by several animals, including humans.

A = B are perceived as equal. However, when C is added and it is dominated by one of them but not both, the one which dominates C is now preferred. In this case A, B and C were nesting sites. Here is the description of the nests;

"For ternary choices, colonies were given options A and B, as well as a third decoy nest, either D_A or D_B. Decoy D_A was dominated by A, but not by B; it had the same interior illumination as A (40 lux), but a larger, and thus less preferred, entrance size (9.5 mm diameter). It was not dominated by B because D_A had a darker, and thus more preferred, interior light level. Decoy D_B, on the other hand, was dominated by B, but not by A; it had the same entrance size as B (1.6 mm), but a brighter, and thus less preferred, light level (300 lux), achieved by fitting it with a transparent plastic sheet (Grafix Dura-lar) instead of a neutral-density filter. It was not dominated by A because D_B had a smaller, and thus more preferred, entrance size. "

What happens is that humans and other animals see the three options, and thus their judgement is affected by the decoy. But ants are not individuals who perceive the three of them and choose, the ants do a random search, find a nest, and recruit/transport. The better the nest is, the faster and more efficiently they recruit/transport. The first nest which gets to the quorum threshold will serve as the new nest for the colony. Because of this, the decoy can't affect their judgement. Aproximately the same amount of ants will arrive at A, B, and Da or b, however, the recruitment/transport towards A and B will be similar and higher than that of Da and b, so there is no irrational decission making.

In the second study, the researchers put a nest near the nest of the colony, marked the workers, and saw which workers explored the empty nest. This nest became the "familiar nest", because several workers had explored it. They induced emigration by destroying their current nest, and added a new nest which was just as good as the familiar nest but was "unfamiliar" to the workers.. The workers that had never been to the familiar nest explored randomly, and were as likely to find either nest. However, the worker ants with the "private knowlege" of the familiar nest would get to the familiar nest quicker and initiate recruitment/transport quicker. Thus, the worker ants with the private knowledge would contribute disproportionately in the decision making, making it more likely for the quorum threshold to be reached in the familiar nest first.

The findings from the second study did not come into play in the first study because the ants were not allowed to explore the surrounding nests before being induced to emigrate, and thus there were now knowledgable ants, only naïve ones.

Two interesting studies I can think of;

-Repeat the first study but let the ants explore the surrounding nests before inducing emigration.. Will more "knowledgeable" ants prefer whichever nest dominates the decoy?

-Repeat the second experiment but make the "unfamiliar" nest superior to the "familiar" one. Will the superior quality from the unfamiliar be enough to speed up the recruitment/transport to achieve the quorum threshold before the familiar one? For this experiment, different colonies should be exposed to the familiar nest during different amounts of time before inducing emigration.

This is my opinion. But it's late and I'm tired - so I could be very wrong

Anyway, thank you.

Im trying to change ants so they can live in other types of enviroment such as extreme temperatures etc.And by exposing queen to x-rays for short period of time im hoping to increase chances of mutations so that mutated ants can adapt faster/with more efficiency.

Don't expose the queen to the mutagen, expose the eggs.

A strong mutagen will just end up killing all of your ants. You could expose them to UV light, which will increase the mutation rate by a smaller amount, but you will probably end up killing the ants as well to be honest.

As far as I am aware, evolutionary biologists who perform selection experiments on arthropods do not use mutagens. You really don't need them, you just need an organism which is easy to maintain in the lab and has a high reproduction rate, like Drosophila sp. and Gryllus sp. because variation and mutations are always naturally present. Ants are really bad candidates for selection experiments because of the reasons others have stated above.

As far as I understand, you want to expose an ant colony to a new environment and see how their social strategy changes to cope with this changes. You want to increase the mutation rate to increase the chances of obtaining ants capable of thriving in this new environment, thus forming a new colony of ants with a different way of working as a group. This way you can observe how group interactions change as the environment changes, which is why you want a social creature. If the group interactions are not your focus, then I highly recommend you to think about using other organisms.

Now, if the description I just gave describes your intentions accuarately, then I am afraid your methodology won't work. If you wanted to create a colony capable of thriving under different conditions then you would need to focus in the selection of colonies rather than individuals. A hypothetical experiment (not feasable) would be to have a large area with thousands or millions of ant colonies, and then gradualy change the environment. (Ex. increase the temperature by x amount after x generations)... Then, the colony as a whole is the superorganism which receives the selective pressure. This is because, if you have only one colony, and you manage to create an ant which has the set of rules necessary for thriving in the novel environment, this ant will be useless. It won't be able to work with the rest of the ants which still follow the old set of rules.

If you ask me, I don't really think it's feasable. But perhaps you come up with some different way and prove me wrong. Oh, and if I did not describe your intentions accuarately, maybe you could explain with more detail exactly what you want to achieve with this experiment, perhaps we can think about a more fit organism or methodology.

There is a great book called "Experimental Evolutions" by several authors which talks about selection experiments in great detail, I highly recommend it to you. Good luck!

Apparently some Ambystomatids are trying to keep up with the Elysia! http://www.nature.com/news/2010/100730/full/news.2010.384.html

They probably still need a few millennium to figure out the gene transfer though, that is, if we don't kill them off before that.

This sounds like fun! Do you know what "Invisible theater" is? It's when people act in front of an "audience" (Which can be, the people at the mall) without letting them know that it's all an act. The actors usually try to make the audience participate in the play without them knowing, and the audience should learn a lesson from this. I think that your project could also be considered a kind of "invisible theater" as you will be performing without the audience knowing, and they will interact in an indirect way with you through their expressions (And if you are lucky, perhaps someone will stare at you and then ask you if you need help with those cubes, or question your sanity). If you don't know this kind of theater already, I would recommend you to read about it! It could give you some really nice ideas to work with!