text:
Do animals other than humans have different blood types?
Humans have the ABO and Rhesus blood typing systems. I have two questions about it:

Why have we evolved these blood types?
Do other animals have different blood types as well?

The answer to this question can be found by searching the Internet.

For some blood types, evolution and environmental selective pressures
  are clearly important for their persistence. For example, the Duffy
  blood type includes a receptor that allows certain types of malarial
  parasites to enter the red cell. Thus, in some malarial areas of
  Africa, populations with Duffy-negative blood types have a distinct
  survival advantage because absence of the Duffy antigen provides a
  measure of protection against malaria. The percentage of people
  lacking the Duffy antigen is much higher in these locations than in
  areas not endemic for malaria.

more here http://www.scientificamerican.com/article/why-do-people-have-differ/

Animals and bacteria have cell surface antigens referred to as a blood
  type. Antigens from the human ABO blood group system are also found in
  apes and old world monkeys, which have inherited the same system.
  Other animal blood sometimes agglutinates (to varying levels of
  intensity) with human blood group reagents, but the structure of the
  blood group antigens in animals is not always identical to those
  typically found in humans. The classification of most animal blood
  groups therefore uses different blood typing systems to those used for
  classification of human blood.

more here  http://en.wikipedia.org/wiki/Blood_type_%28non-human%29

So somebody really did write on Wikipedia that "…bacteria have cell surface antigens referred to as a blood type". But that's nonsense. I'll go and edit it now.

Blood group systems occur where there are multiple alleles of a gene which produces polymorphism in a surface component of the erythrocyte such that the different forms of the component display different antigenicities. This can cause haemolysis of transfused blood that has a different antigenicity to that of the erythrocytes of the recipient, whose immune system consequently regards it as foreign.
The major ABO blood group system of humans involves the gene for a glycosyltransferase which catalyses the addition of particular sugars to glycocoproteins or glycolipids. In addition to inactivation of the gene (giving blood group O in homozygotes) there are two forms of the active gene, encoding enzymes  transfering either N-acetyl galactosamine or galactose (1):

The ABO system is found in non-human primates, although with AO, BO and AB as variants in different species (2). Various other animals have polymorphism in this system — pigs, for example, are AO (3). Most animals possess the ABO gene (4), although it may or may not be expressed, and, if it is, may or may not give rise to polymorphism.
Blood group systems exist in other animals that involve different genes. The confusingly-named AB system of cats, for example, involves the gene for an acetylneuraminic acid hydroxylase, which catalyses the formation of the activated precursor for addition of N-glycolylneuraminic acid to cell-surface glycans (5).  This gene is inactive in humans (6).

Not all such blood group systems involve changes in the sugars of glycoproteins or glycolipids, but those involving mutations in proteins (e.g. in dogs (7)) tend to be less well characterized at a molecular level.
A common answer to the question “Why have we evolved these [ABO] blood types?” is that the ability to change the sugars on the erythrocyte membrane provides resistance to pathogenic organisms (parasites, bacteria and viruses). This could be because the pathogens bind the sugars to gain entry into the cells, or because they have similar sugars on their own cell surface and so do not provoke an immune response from the host. However the counter-argument of non-functional genetic drift (@CactusWoman) is difficult to exclude if one focuses solely on the ABO system.
The functional argument becomes more convincing if one considers that the ABO blood types are just one example of the ability of animals to vary the sugars on their cell by selecting from a large repertoire of genes with the potential to specify different glycosylating enzymes (8). This is shown by the fact that different animals exhibit different sugar antigens on the surface of their erythrocytes (whether or not they display polymorphism). There are over 100 genes for glycosylating enzymes, but one example of this diversity is instructive. The ABO gene has undergone duplication and, of perhaps seven members of this family (9), the products of three are well characterized (10,11,12), although their genes are either inactive in humans or not expressed in erythrocytes (i.e. in their precursors). Like the ABO gene product, the enzymes are α-1,3-glycosyltransferases, but differ in the acceptor carbohydrate:

I know this is coming late to the party, but I became interested in the topic from a molecular and genetic viewpoint following a more recent post that was marked as a duplicate. Happy to be told of typos or errors. I'll reference the piece shortly.

One of your references (https://www.pnas.org/doi/10.1073/pnas.1210603109) in points towards selection acting on multiallelic balanced polymorphism as an explanation to the existence of the ABO system in primates, what's your take on that hypothesis?

@Ponce — Six years since I posted, and it's not my area. I certainly am not competent to criticize the hypothesis. What you can do if you are interested is find papers that have quoted this one and see what those in the field think.

To answer your first question; it is not necessary that every trait have an evolutionary advantage. Neutral traits can persist in the population without having any adaptive value, or they can persist as a byproduct of another trait that does have adaptive value. Even a slightly detrimental trait can become fixed due to genetic drift. Take a look at this rather famous paper critiquing the "adaptionist programme" if you're interested.
That being said, I personally don't know for sure whether or not different blood groups have an adaptive advantage. Someone else can probably provide a better answer to this portion of your question.
However, to answer your second question: yes, yes they do. Indeed the Rhesus blood typing system was named after the rhesus monkey.


text:
Reason for different color perception in left/right eyes?
What could be the reason for a difference in color perception between the two eyes of an adult individual without any known eye conditions? In particular, a difference in the perceived color temperature in each individual eye and an average of the two when looking through both eyes.

It may be advisable to remove any reference to self. At Biology SE we explicitly discourage self-help questions, as we support seeking professional advise. However, we are happy to share information on general scientific questions :)

This is not a personal health advice question even though the OP has used a personal example. Therefore I suggest that personal references may be removed to avoid that confusion.

Edited accordingly, first time posting outside of code/math questions.

Most likely, tumor. Also, there is asymmetry between left/right hemispheres, so why not eyes, which are also central nervous system

@aandreev Why is tumor most likely? Folks can reproduce this phenomenon by lying down, and there's some variability in normal people (title: "Inter-eye comparison on the 100 hue test" if unavailable).

Good question. I've noticed this difference since my childhood.

source: Stack Exchange

license: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/3.0/

sort: votes


text:
Genotype to phenotype map and the G-matrix
Suppose I have a genotype-phenotype map defined by the matrix $\mathbf{Z}$:

The scalars $G,P$ represent the number of genotypes and traits, respectively. The map assigns a set of phenotypic traits (the columns) to a set of genotypes (the rows), where $z_{ij}$ is the quantitative measure of an individual of genotype $i$ with respect to a trait $j$. I want to know how the average value of each of the phenotypic traits changes over time, suggesting I should use quantitative genetics theory and formulate the equation
$\Delta \bar{\boldsymbol{z}} = \mathbf{G}\mathbf{P}^{-1}\mathbf{s}$,
where, $\mathbf{G}$ is the additive genetic variance covariance matrix, $\mathbf{P}$ is the phenotypic variance covariance matrix, and $\mathbf{s}$ is a vector of covariances of each trait with fitness. Assume that I know the frequencies of the different genotypes in the population.
Question 1 Can I formulate the additive genetic variance-covariance matrix from the genotype-phenotype map alone (and pop freq)? Note, I don't know anything about the underlying genetic model - number of loci representing each genotype, dominance structure, epistatic interactions, etc.
Question 2 If I assume the genotypes represent haploid individuals, does this change things? Is the additive genetic variance always equal to the phenotypic variance (assuming no environmental effects) in a haploid model? In other words does $\mathbf{G}\mathbf{P}^{-1} = \mathbf{I}$? What I'm thinking is that epistatic variance might affect things, but it shouldn't affect heritability in a haploid model, which is what $\mathbf{G}\mathbf{P}^{-1}$ is a measure of.

From the pheno-geno map and the genotypes frequencies, you have the whole distribution of phenotypes in your population. The mean of the phenoype $n$, $P_n$ is the
$$\bar P_n = \sum f_{G_i} P_{G_i}$$
, where $f_{G_i}$ is the proportions of individuals having genotype $G_i$ and $P_{G_i}$ is the phenotype of the individuals with genotype $G_i$. Therefore, the variance of $P_n$ is
$$var(P_n) = \sum f_{G_i} (P_{G_i} - \bar P_n)^2$$.
The covariance between the phenotypic traits $n$ and $m$ is
$$cov(P_n,P_m) = \sum f_{G_i} (P_{G_i} - \bar P_n)(P_{G_i} - \bar P_m)$$
The only assumptions you need is that there is no environmental variance. I don't think the above calculations required any other assumption. $G$ can be defined at the haploid or diploid stage, it doesn't change anything.
The above calculations however give you the genetic variance and covariance but not the additive genetic variance covariance. I think (but I might be mistaken) that the additive genetic variance would be equal to
$$\sigma_D^2 = \sum_i f_i^2(1-f_i)^2(2 \cdot P_{n,i,12} - P_{n,i,11} - P_{n,i,22})^2$$
$$\sigma_A^2 = \sum_i 2f_i(1-f_i)(f_iP_{n,i,11}+(1-2f_i)P_{n,i,12} - (1-f_i)P_{n,i,22})^2$$
, where $f_i$ is the frequency of the allele $A$ at the locus $i$ (you should get those data by reformatting your geno-pheno map matrix) and $P_{n,i,11}$, $P_{n,i,12}$ and
$$P_{n,i,22} =\frac{1}{l-1} \sum_j P_{n,i,j,22}$$
is the $n^{th}$ phenotypic trait for the genotype $22$ and locus $i$ averaged over all other genotypes. There are $l$ genotypes in total. Of course, this works only for biallelic loci. I don't know what it would look like for more alleles.

all_licenses: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/3.0/


text:
Why do restriction-modification systems work?
Some RM systems (restriction-modification systems) are plasmid-borne and are transferred through bacterial conjugation. As you all know, there are two genes in an RM system, the gene that codes for the restriction enzyme that restricts a certain nucleotide sequence and the other that codes for the methyltransferase that methylate the sequence to protect the cell from its own restriction enzymes. If these genes are both being expressed at the same rate after the bacteria receives this plasmid, how is the bacteria's DNA protected from the restriction enzymes for the first few hours of expression if the methyltransferase have not yet methylated the entire host genome yet?
Thank you,
CDB

About which systems are you talking? CrispR? LoxP?

Is it different from one system to another? My main focus would probably be type II, but beyond that it doesn't really matter, any system you choose to answer for would be fine.

So you're asking about what happens when bacteria are simultaneously transformed with a gene for a restriction enzyme that cuts at unmethylated site X, AND an enzyme that methylates site X?

In essence yes. I'm wondering how the cell protects its own DNA from the restriction enzymes until the methyltransferase methylate the DNA.

I don't really know, but I assume it comes down to how quickly each protein is expressed, how quickly each enzyme catalyzes its reaction, and how well a cell repairs it genome. With a large population of transformed cells, I assume some will be methylated before they are cut, and survive. If methylation can be passed down from generation to generation, those will be selected. But again, I barely know anything about DNA methylation.

You have a good point there. My original assumption for why this happens was that one methyltransferase can methylate almost an unlimited number of sequences, whereas restriction enzymes can only restrict one sequence, I'm actually not sure if this is true though, thus why I asked the question. Thanks for your answer.


text:
Why do insects avoid being on their back?
I have noticed that when insects are placed on their backs, they tend to turn themselves over quickly or else appear to be in distress. Is there a physiologic, anatomic, or adaptive reason why supine positioning might be unfavorable in insects?

Because they can't get back to their legs and they therefore get stuck somewhere where they can gently wait for death to come.

Do you wish to know what the adverse stimulus is to them? Subjective perceptions, let alone feelings in bugs is mere speculation.

I'm voting to close this question as off-topic because it seems a question on  emotions in insects. Question holds potential when made objective.

@Remi.b Can you post that as an answer.

@AliceD : Is it behavioral rather than emotional ?

@AliceD The OP can roll back that edit if I'm mistaken, but it seemed likely to me that "like" was being used more loosely, intending to describe an observation about a behavioral pattern rather than emotions.

@Susan - looks OK now! Will retract close vote later (I am mobile)

Welcome to Biology.SE
Insects don't "like" being on their back because they can't get back on their legs and they therefore get stuck somewhere where they can gently wait for death to come.
Not all insects are unable to switch back on their legs but some can't do that (or can hardly do that). The reasons for which many insects are not able to get back on their legs (while mammals for example usually can do that) is that they have a exoskeleton. Their exoskeleton limits drastically their movements.

I'd guess that this varies quite a lot among different insects; in some, lying on their backs was a sign of their impending death, while others will flip over onto their backs to play dead. This isn't really surprising --- there's over a million described insect species, so some amount of variety is to be expected! Here's a video of a bunch of insects exhibiting different strategies for turning themselves over.


text:
Why do some bacteria have most genes on the leading strand of the genome?
Genes in the (+) strand are black and genes in the (-)strand are red.
The gene distribution in E. coli genome is somewhat expected: transcribed regions would tend to alternate with non transcribed regions, as a consequence of (random) evolutionary process. Also, genes don't overlap (it would be highly  unlikely that two complementary strands both carried useful information).
In B. subtilis, on the other hand, there seems to be a preference for one of the strands in each side of the chromosome. What sort of evolutionary pressure could give raise to such a pattern?
I have a guess, but I'm not sure, that this may be related to bacterial transformation.

The pattern we see in B. subtilis is quite common in prokaryotes. The origin of replication is shown at the top of the genome diagram. DNA replication proceeds bidirectionally from this point. In the B. subtilis diagram, most genes are located along the leading strand in each direction. Even in E. coli, by the way, important genes, including all rRNAs, tend to appear on the leading strand.
Why is that? Rapidly growing bacteria are replicating their genomes most or all of the time, so you've got replication and transcription happening at the same time.  If genes are on the lagging strand, RNA transcription proceeds in the opposite direction from DNA replication, and the DNA polymerase will often collide with the RNA polymerase. If the genes are on the leading strand, however, RNA transcription proceeds in the same direction as replication and collisions are minimized. Hence the selective advantage to positioning most genes along the leading strand.
Some genes may also be on the lagging strand in order to target them for mutagenesis (Paul et al. 2013, Million-Weaver et al 2015). This goes back to the concept of transcription-replication collisions where the head-on collisions are worse than co-directional collisions. Head-on genes actually have a higher mutation rate and incidence of convergent mutations which suggests that they are mutated and evolve faster than leading strand genes. This is a controlled process in that it only occurs in lagging strand genes, and only when the gene is transcribed (i.e. when it is needed). It was argued that this is a way bacteria can control and ratchet up or down the rate of evolution in a controlled way. This was argued against by Chen and Zhang based upon computer based modelling. It is an interesting concept that has been hotly debated.
EDIT for additional clarification and references:
This diagram from Chen and Zhang (2013) helps show what is going on:

Caption: "Schematic drawing of a collision between a working DNA polymerase and a working RNA polymerase in bacteria. (a) Codirectional collision when a gene is encoded on the leading strand. (b) Head-on collision when a gene is encoded on the lagging strand. Arrows show the directions of movement." (Chen and Zhang 2013)
A few references

The original idea goes back almost 40 years to Nomura M. and Morgan,E.A. (1977) Genetics of bacterial ribosomes. Annu. Rev. Genet., 11, 297–347.
An early paper about highly transcribed rRNA on the leading strand: Ellwood M. and Nomura,M. (1982) Chromosomal locations of the genes for rRNA in Escherichia coli K-12. J. Bacteriol., 149, 458–468.
A recent overview: Rocha, E. P. (2004). The replication-related organization of bacterial genomes. Microbiology, 150(6), 1609-1627.
Why some genes remain on the lagging strand: Chen, X., & Zhang, J. (2013). Why are genes encoded on the lagging strand of the bacterial genome?. Genome biology and evolution, 5(12), 2436-2439.
Paul, S., Million-Weaver, S., Chattopadhyay, S., Sokurenko, E., and Merrikh, H. (2013). Accelerated gene evolution through replication-transcription conflicts. Nature 495, 512-515.
Million-Weaver, S., Samadpour, A.N., Moreno-Habel, D.A., Nugent, P., Brittnacher, M.J., Weiss, E., Hayden, H.S., Miller, S.I., Liachko, I., and Merrikh, H. (2015b). An underlying mechanism for the increased mutagenesis of lagging-strand genes in Bacillus subtilis. Proc Natl Acad Sci U S A 112, E1096-1105.

It's an interesting idea; do you have any references for it? Transcription and replication always occur in the same direction (3'->5') relative to a strand.

@canadianer I've added a few references and a diagram -- I hope this clarifies. Yes, both DNA and RNA polymerase move 3' to 5' on the template strand but the 3' to 5' direction of the RNA polymerase can move toward or away from the replication fork, depending on whether you're on the lagging or leading strand.


text:
Is it possible to isolate and analyse intermediates of protein folding?
I would like to know if there is an assay which could allow us to analyse a protein before it has assumed its 3D functional form.
While studying structural biology, I only came to know the forces that stabilize the structure, but not the gap between the original random coil and the protein in its native form.

http://en.m.wikipedia.org/wiki/Protein_folding#Experimental_techniques_for_studying_protein_folding

Sometimes multiple techniques are combined, such as in intrinsically disordered proteins, like so.

Theoretically by molecular modeling -- see the works by Harold Scheraga:
https://www.ncbi.nlm.nih.gov/pubmed/?term=Harold+Scheraga%5BAuthor%5D

Note: An unfolded protein is not a random coil.
Fitzkee & Rose (2004) PNAS 101:12497-12502; emphasis mine:

denatured proteins are biased toward specific conformations, in
  ... conflict with the random-coil model

https://www.ncbi.nlm.nih.gov/pubmed/15314216

This is difficult. You need to use stopped flow methods(CD, fluorescence, NMR) or single molecule methods. What exactly do you want to know about the protein? I mean, it would be hard to get the complete accurate 3d structure, as you can't crystallize an intermediate. Apart from that, if you have an accurate folding simulation for that protein, you can of course see what the common intermediates are. I am sure that if you have the Rosetta protein folding algorithms, you know the final structure, you can calculate likely intermediates with some accuracy. Then you may be able to use stopped flow methods to try to refuse those findings. If that fails, you may be able to make a convincing case that you found those intermediates.

Can you add sources or references to your answer?


text:
What is the minimum functional biological light sensor?
As a follow up to this question regarding the evolution of the eye, it was suggested that primitive eyes only needed to evolve a light sensor and could perhaps use the existing biochemical cascade infrastructure.
What is the minimum of this biological light sensor? Please provide a detailed biochemical description of how many proteins are involved and their interactions which can be "hooked up" to the existing biochemical cascade infrastructure. (to the best of our knowledge)

What do you mean by minimum?

minimum would be molecule of retinol, i suppose. 11-cis-retinal will switch to trans isoform when exposed to light. Some enzymes sense that and launch signal transduction which gives rise to vision

The minimum biological light sensor is just an existing signaling molecule that, by chance, also has some change in its activity due to light.  There are several ways this could happen.
One extremely simple example would be based on a G-protein coupled receptor (GPCR).  GPCRs are a family of related signal transduction proteins (the largest family) that sit on the surface of a cell's membrane.   Each one is sensitive to a molecule or small group of related molecules.  When exposed to the molecule it is sensitive to, the GPCR sets of a series of chemical cascades that trigger some activity in the cell.  For example, it can serve as a signal for the cell to move towards the place where the chemical was detected, or move away.
Now, imagine that, just by chance, the molecule the GPCR is sensitive to has some sensitivity to light, in that when exposed to light the molecule either has a larger or smaller chance (even slightly) of binding to the GPCR.  This is not improbable, a ton of biological molecules have this characteristic, in fact many have substantial responses to light even though they are not involved in light-sensing pathways.  A good example is called "photoisomerization", where the same molecule can have more than one shape, and switches between two shapes when exposed to light.
This would be a biological light sensor.  Not necessarily a very sensitive one, but once you have such a basic light sensor, natural selection would take over and lead to stronger and stronger effects.
In fact, this is pretty much how our eyes work today.  It uses a GPCR whose target is a molecule that changes its shape when exposed to light, which makes it no longer able to bind to the receptor, shutting of the signaling cascade.  What is more, this molecule is not only used in sensing light, it is a precursor to a molecule needed for gene transcription and signaling.
In fact, you can splice light-sensitive GPCRs from bacteria (which are different than those in animals) into non-light-sensitive animal cells, and those molecules will automatically integrate with existing GPCR signaling cascades, rendering the cell light sensitive.

interesting. i wonder how you would explain the emergence of say the pit viper's infrared camera which started off in a full blown animal (according to wikipedia it evolved independently in boas,pythons, and vipers). maybe i will post that as a new question.

The pit organ is just a more sensitive version of the standard heat-sensitive cell.  It doesn't require anything new at all.

my point is that it's not just a cell. it's a whole system see http://en.wikipedia.org/wiki/Infrared_sensing_in_snakes

Yes, it is a system, but it is not a new system, it is a modification of the normal temperature-sensing system.

ok and how about the platypus bill or the elephantnose fish's probe etc.

I am not familiar enough with those to say.

Yes, I am familiar with the pit organs. This is getting very off-topic, though.

Let us continue this discussion in chat.


text:
Monochromator in fluorescence microscopy
I'd like to ask why are there no fluorescence microscopes that use a monochromator instead of filters?
If there are any, then I should change my question as, which ones use it and why are they so rare?

Add Little bit of more data.

Well, according to Cold Spring Harbor Protocols, xenon arc lamp/monochromator-based fluorescence microscopes are economical, performant, and rather common.

It is a very clear question about use of a specific piece in a laboratory equipment. It doesn't mean that a question is unclear, whenever you don't have the necessary background to answer it.
I don't think each question should be asked by providing background information in such a way that, anybody related to biology should understand what is going on. Biology is a wide field and it is very unpractical, if this is what you are suggesting. And if not, I really can't see the point of putting this question on hold.

Zeiss LSM780 uses essentially monochromator to spread all fluorescence across 34 detectors for multi-spectral acquisition. It is used to detect autofluorescence, unmix closely positioned emission spectra (unmix GFP and YFP for example) and to measure precise spectral peaks with ~1nm resolution.
Monochromator is useful when you need to transform frequency domain information into spatial domain. In fluorescence microscopy we usually collect light from wide bands of well-separated GFP-like proteins, so that filters make more sense. We usually don't detect 1-nm wide lines or plot spectra. LSM780 does allow all that, if you need to.
You can use spectral imaging, but for that you will have to either scan for very long time, or spread signal onto array of detectors.

I'll add that signal is usually limiting in biological fluorescence microscopy, so it can be impractical or impossible to get good data in narrow wavelength bands. As a result most people use filters. And in turn this creates strong market pressure to design new fluorescent probes to match the spectra of existing probes and filters.

@TSwayne I think it is funnier: GFP and other proteins and dyes are/were designed to match laser lines (e.g. 488nm argon line).


text:
Are gene variants at different loci also called alleles?
I think the title says it. I always read that alleles are gene variants at a given locus, which confuses me. Thanks!

I really hate that term "allele" and avoid its usage as much as possible :P I feel it is a prehistoric term which I don't know for what reason is still in use. I generally use "allele" only to differentiate maternal and paternal copies; I call gene variants as paralogs. Many people call paralogs as alleles too if they are quite identical.

@WYSIWYG Are you referring to e.g. "functional" alleles (alleles defined by functional differences) vs. alleles as DNA-sequence variations?

@fileunderwater As I said, the term confuses me a lot. So I restrict my usage to paternal/maternal copies.

EDIT:
Short answer : Yes: "allele" is a synonym for "gene variant", irrespective of location (locus).
Background
Original answer: From About Education I found this definition for an allele:

An allele is an alternative form of a gene (one member of a pair) that is located at a specific position on a specific chromosome.

EDIT:
Hence, two alleles are located at the same locus, but are situated on a different chromosome.
ADDITION EDIT: Given the many high-quality comments (and the downvote) I erased the concluding sentence of my first attempt and I will elaborate below:
Feero et al. (2010) gives the following more elaborate definition of "allele" (text relevant to the question is bolded out):

Specific locations in the human genome where differences between individual people
  are found are generally referred to as variations, and the term “normal” or “wild type” is often used to refer to the most common variant at a location in a given population group. In its simplest form, the variation has two different spellings, referred to as “alleles.” If the frequency of the minor allele is greater than 1%, such variants are called polymorphisms. The word “mutation” is generally reserved for changes in DNA that are believed or known to be pathologic [...] or for changes that are [very] recent (e.g., not inherited DNA changes).

Hence, from my understanding, the original quoted definition from About Education still stands.
As to the critical comments placed by the PO, @fileunderwater and @WYSIWYG:
(1) [...] what is a copy or a variant of a gene at a different locus on the same chromosome? - That is a very interesting question, and I think Feero et al. (2010) deals with that simply by saying

In its simplest form, the variation has two different spellings, referred to as “alleles.”

In other words - perhaps the gene duplication is a step too far for this terminology. And in fact, although I regret having to cite wikipedia here, it does provide a very enlightening sentence:

[...] [A]t the gene locus for the ABO blood type [...] classical genetics recognizes three alleles, IA, IB, and i, that determine compatibility of blood transfusions. Any individual has one of six possible genotypes (IAIA, IAi, IBIB, IBi, IAIB, and ii) that produce one of four possible phenotypes [...].

Hence, what this implicitly tells us is that an allele is, as Feero et al. (2010) also says, simply a gene variation.
This means that it basically boils down to what is a "chromosome locus"?
An article by Proulx & Phillips, 2006 entitled "ALLELIC DIVERGENCE PRECEDES AND PROMOTES GENE DUPLICATION" mentions:

[...] [H]eterozygotes at a single locus are broken up by segregation, whereas for duplicate loci an individual can carry copies of alternative alleles at separate
  loci.

Hence, what the authors implicitly say is that an allele is a gene variation and that a locus is a fixed position on a chromosome. Hence, a gene duplication means 2 loci that can carry the same or a different allele. This should answer
(2) Are the alleles at the two duplicated loci then named differently, even if their DNA sequences are identical (as well as the protein they might be coding for), namely no, an allele has a name (e.g. IA) that remains unchanged when duplicated. The locus is then different for the duplicate, but the name of the allele stays the same (as an allele is, by definition, simply a gene variant wherever on the chromosome).
(3a) [...] two versions of a gene at two different loci are alleles (not paralogs)?: yes
(3b) What about the same identical version at two different loci: same allele or not? yes, same allele, allele has nothing to do with locus. Just a gene variant. Where ever.

Reference
Feero et al. N Engl J Med 2010;362:2001-11
Proulx & Phillips. Evolution 2006;60:881-892

Ok, but what is a copy or a variant of a gene at a different locus on the same chromosome?

Is this really the case when you have recent gene duplications, so that a species e.g. has two loci with the same gene (paralogs), and still only two versions of this gene irrespective of loci (so two alleles at one loci duplicated to two original alleles found at two loci)? Are the alleles at the two duplicated loci then named differently, even if their DNA sequences are identical (as well as the protein they might be coding for)? Mostly a question on naming convensions I guess, but I'm curious.

@user14860 If they are the result of duplication they are called paralogs.

@WYSIWYG Ok, so saying that two versions of a gene at two different loci are alleles (not paralogs)? What about the same identical version at two different loci: same allele or not?

@fileunderwater Can be called. But it is confusing; there should be a term that explicitly means homologs at the same locus in the homologous chromosomes.


text:
Is Norway spruce (Picea abies (L.) Karst.) isohydric or anisohydric species?
Question from a thesis defense list ask me this. But I can't find the exact answer on the internet or in books. In my thesis, I described isohydric plants, for example maize, lupin, pea, poplar. This plants response to a decrease in soil water in same way. How Norway spruce response to decrease in soil water? As a isohydric plant or anisohydric?
Thank you for your time and help.

Welcome to Biology SE. Please Edit your question and re-post it, with little more details.

What do you think and why?

According to this report, maize, lupin, pea, and poplar are all anisohydric.

@augurar According this study:

For this reason, in these species leaf water potential is a better indicator of soil moisture than gs. Isohydric species (e.g. maize, lupin, pea, poplar), on the other hand, close their stomata in response to a decrease in soil water and/or an increase in VPD, controlling plant water potential.

@Hawk81 I think you are right and that was a mistake in the report I linked -- one of the papers they cite lists maize and poplar as isohydric.

This review paper states that spruce is isohydric, citing Physiologie und Ökologie der Gehölze by Lyr, Fiedler, & Tranquillini:

Spruce appears to reﬂect an isohydric strategy (Lyr et al. 1992), reducing stomatal conductance at early stages of soil drought.

It's important to note that this is not a binary distinction, isohydric and anisohydric are two extremes in a spectrum of how plants respond to drought.


text:
Do all organisms have to die?
I understand (a little) that there are biological clocks and reason that after a certain amount of time organisms die. I'm wondering if that is something inherent in our DNA or in biology/chemistry in general. EG, is it possible that there could be a complex organism that would not die and would just regenerate it's cells In Perpetuam? I'm specifically interested in mammals and even more specifically interested in humans. But, I would be interested in hearing about other organisms like bugs, fish, plant, algae, etc.
I'm not asking if this practical, do we know how to do this, etc.. I just want to know theoretically if living forever is biologically possible, as far as we know. If not, is there an estimated upper limit?

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

It's definitely not practical. Lets assume an organism had evolved past disease and aging. It would still eventually die because with infinite time, the odds of it eventually falling into a situation where it runs out of food, or gets eaten, or dies in an accident go to 100%. So even an immortal species would still need to reproduce. If birth rates remain normal, but death rates are much slower, the population would explode, leading to many problems with food supplies and space and environmental issues.

@user137 - I'm not considering about practicalities.

Given current world state (lifestyles, climates, environment, food and water resources) and health tech I'd suggest it's in the region of 130-140 years, not sure anyone has lived longer and with billions of people on the planet that's a pretty good sampling effort but then again I'm guessing no one has yet stumbled across the perfect combination of genes and lifestyle so maybe a little longer

This interesting post is very much related

@user137 Might not be practical for the species, but evolution doesn't really care about species survival.

Are you also interested in bacteria and fungi that reproduce clonally? The situation is a bit different compared to higher animals.

@fileunderwater - no - I'm interested in the possible immortality of a single organism.  There may be similarities in how they deal with the Hayflick limit, but I'm not sure.

@Yehosef "single organism" isn't that easy to define though. Do you consider aspen clones a single organism or not? They are considered as one of the oldest living organisms, and should be relevant to your question, even though they are in one sense a multicellular plant analog to bacterial clonal growth.

@fileunderwater - fair enough.. I'm more interested in animals, but it's interesting to see other examples like you mention.

According to Agent Smith (The Matrix series): Everything that has a beginning has an end, Neo...

@user137 This argument makes no sense. There is no reason why if an animal only died through accidents, its birth rate couldn't adapt to reflect this. All animals' birth rates are tuned in a feedback loop which reflects death rates at different life stages, whether by accident, disease or old age, fertility rates and the size of breeding populations, and the potential consequences of overpopulation.

@jwg assuming the organism developed immortality over a long time the birth rates would have time to adjust as well. But as human life spans have increased over the last century and infant mortality has been greatly reduced, birth rates tended to remain high for several years, leading to a large increase in the number of humans. This is relevant because there are some researchers who think they can develop immortality for humans. Which, if possible, would happen over a short time scale, and birth rates wouldn't adjust.

possible duplicate of http://biology.stackexchange.com/questions/8176/do-immortal-organisms-exist?rq=1

related http://biology.stackexchange.com/questions/7010/is-there-any-kind-of-immortality-in-plants?lq=1, http://biology.stackexchange.com/questions/6884/why-is-the-hydra-biologically-immortal

The immortal jellyfish can revert back to its immature polyp stage after reaching maturity, then mature again, over and over. You can read more on the wikipedia page, but this ability means it can potentially avoid senescence altogether.

It too will die when the sun becomes a red giant.

@Joshua Technically, it will be boiled. But I can say this with certainty that it will surely die when you will disintegrate it into atomic particles. :P

@Joshua naturally, but it will fry, not senesce, and that's what the question is asking about ;)

The cited wiki page cites one iffy reference, but the other is good, and available online: http://www.biolbull.org/content/190/3/302.full.pdf+html  The authers of this article indeed claim that Turritopsis may be immortal (!!). Thanks for this great answer.

@Joshua It is considered Biologically immortal, meaning that it will not die as a result of cellular processes... That does not mean that an external agent can't kill it.

@Joshua Well, if someone took such Jellyfish into an aquarium in a spaceship and took it to another solar system, then it could go on living. But of course, any such activity would probably eventually fail.

Won't most bacteria be biologically immortal as well? If food wasn't a limitation.

You have a very interesting question there!
In order to answer, however, we must examine the most widely accepted "reason" for why we age and eventually die. Most scientists agree that it is because of mass cell death. Normally you and I would be able to deal quite well with mass cell death (such as a very large injury), the problem comes in when we are older because we cannot replenish them because we have physically exhausted our own supply of something called stem cells.
Most cells in our bodies actually cannot divide, so they rely on these stem cells (which can divide into any cell; think of them as a wild card) to replenish whatever cells die.
Sounds perfect, right? Not quite, each of us only have a given number of stem cells in our body (even though stem cells can divide into more stem cells, they usually don't). So the reason we age and die is because we "run out", if you will, of these stem cells and our supply of cellular replenishment is slowly cut off.
Back to your question, is it possible to stop this? Well you've probably already come to this conclusion by now, but theoretically if you could somehow supply the body with a constant number of stem cells, theoretically, you could live forever (or at least a really long time). This is evident, as you are aware, in flatworms, who have stem cells constantly circulating their bodies and are practically immortal.

Why do you call "running out of stem cells" the reason we die? It can just as easily be a side effect.

Sorry? Side effect of what?

Death process..

That's what I have found to be the reason for aging in the time that I have studied it.

Oh, I see. I'm only saying that it is one reason for death, not all. Death can be caused by many things.

I know we study a lot of things that are not proven yet. I can remember things from my first biology books that we can laugh about now. That's when I try to bring as much logic in the game as I can. The fact is, we are not born with a fixed amount of stem cells. They grow and multiply rapidly at young age. And then at some point, you can observe a change of direction, instead of increasing, the amount of stem cells starts to decrease. Something causes this.

And I do not profess to know the answer to that, thus why I said it was theoretical. Of all the studies I have done this would most likely be the most mysterious, we know that we stop producing the chemicals needed to stimulate stem cell division as we get older, but beyond that we really don't know. It almost appears to be programmed into us, as if on purpose. I don't know how much Yehosef is wondering about the reason for aging though, and I was just presenting an idea on how to stop it (with a bit of needed scientific background for him to understand the idea of course).

Running out of stem cells seems more like an answer to "how" than to "why".

His question was regarding how immortalization could occur, therefore only a "how" answer was required, therefore that's all I gave.

Interesting - I thought that most cells can divide, its just that https://en.wikipedia.org/wiki/Hayflick_limit that limits how often before the DNA becomes too damaged (see also https://en.wikipedia.org/wiki/Senescence).  Meaning, it seems that the cells stop dividing after a while but new stem cells can take their place and make new cells.  So if you can either stop the DNA damage via expression of telomerase (see lobster longevity) or by generating adult stem cells to regenerate cells that can no longer divide.  Either of these might work.

With many cells that is the case, however the cells I was speaking of are generally those that don't divide, such as nerve cells, brain cells, heart (muscle) cells and blood cells and those cells that rarely divide, such as liver and kidney cells. I suppose that stem cells would replenish those cells that are nearing or have reached the Hayflick limit merely by slowly replacing them with cells that have fresh DNA.


text:
Is it possible to train allergic resistance by exposing yourself to allergens?
My hypothesis is that one can decrease the allergic reactions over time by continuously exposing yourself to slowly increasing doses of allergens.
Is there any scientific evidence pointing this right or wrong?

This is exactly the point of allergy shots. The continuous exposure to an allergen causes tolerization. Maybe instead of me writing a bunch of stuff up check out this simple Wikipedia article:
http://en.wikipedia.org/wiki/Immune_tolerance

Then if you have specific questions you can ask them here.
Hope that helps.

Can you add a few-word summary?

Yeah I can do that.

The phenomenon called oral tolerance is quite a common way to reduce allergic reactions. Basically patients have to eat a lot of the antigen with their daily diet under the supervision of doctors, so in time allergic reactions can be alleviated. The idea behind this is that our immune system is much more tolerant to things that get in our digestive system (in most cases). Here is a good article on oral tolerance from Nature.
Citation: Pabst, O; Mowat, A M - Oral tolerance to food protein Mucosal Immunology 2012 https://doi.org/10.1038/mi.2012.4

all_licenses: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/4.0/


text:
Why are there no known photosynthetic archaea?
I'm taking a microbial physiology course and we noted that, while some archaea are phototrophic, there are no known photosynethetic archaea.  Are there any physiological characteristics that make archaea less suited for photosynthesis?  Or is it simply a matter of there likely being photosynthetic archaea, but they have not yet been found (which seems like it could easily be the case, given that there are many extremophilic archaea)?

There are photosynthetic archaea (such as Halobacterium) but the mechanism is different. They use rhodopsin-like ion pumps (bacteriorhodopsin and halorhodopsin) to move ions against the gradient and produce ATP via chemiosmosis (like mitochondria).

I was under the impression that this was distinct from photosynthesis.  At the very least, my professor emphasized that this was not the case, as rhodopsins do not utilize an electron transport chain in order to make a proton gradient, but photosynthesis does.

@Squirrel: Isn't this just a matter of definition?  That is, one could define photosynthesis in very general terms as using light to synthesize energy-bearing chemicals, or specifically as the clorophyll-based synthesis used by plants.  As for why no archaea use clorophyll, I don't know for sure, but would guess it's because plants evolved it after they split from archaea, and the identical process is unlikely to evolve twice.  But I'd certainly be interested in a more authoritative answer.

@Squirrel rhodopsins work just like electron transport chains and produce ATP with the help of F₀F₁ ATP-synthases.

@Squirrel If your professor said haloarchaea don't count, then (s)he probably wanted to ask for photoautotrophs instead. Both plants and haloarchaea are phototrophs, but haloarchaea are photoheterotrophs since they cannot fix carbon. Knocking out PSII in plants will also convert them into photoheterotrophs.


text:
Enzyme\Protein amounts in cancer
I am searching for source, that providing information about enzymes\proteins, in different types of cancers, that their amount in cell is significantly higher - comparing to normal, healthy cell.
Some pathways that exist in cancer in much more higher amounts.
For example - Telomerase.
Is there some sort of database for this information?

You could try expression atlas: http://www.ebi.ac.uk/gxa/home

Yes. The dbDEPC 2.0 database for example.
If you want to extend your search to pathways the best database I know of is the KEGG.
There are multiple databases out there. You might want to look at this wikipedia page.
By the way what you are looking for is called a cancer proteomic signature.


text:
Can anyone identify this mystery caterpillar?
I found this caterpillar in in El Cerrito, CA and was wondering what kind it is?

Best assumption, Gulf Fritillary Caterpillar (Agraulis vanillae). I could be wrong though.

The larva is a caterpillar which grows to approximately 4 cm (1.6 in) in length. It is bright orange in color and covered in rows of black spines. The spines are soft to the touch and do not sting, but the larva is poisonous if eaten. Source: Wikipedia.

Thanks! The caterpillar looks like a close match and the adult butterflies do too!


text:
What, if any, diseases do larder beetles carry?
I found one of these beetles on my bed as I was attempting to get in. I'm 80% sure my cat carried it in (I found it in the exact same space he had been sitting ten minutes previously).
My question is what, if any, diseases do these bugs carry? It did not bite me, though it may have bitten my cat. I'm more worried about bacteria etc that it may have carried around my bed/room. Can they transmit salmonella? Should I break out the disinfectant, or is it no big deal?
I have researched them as best I can, and I found someone noting that they can spread bacteria, but found nothing on how severe it is. For example, my cat obviously spreads bacteria, but I let him on my bed without worry. I have never see one of these beetles before.
I have a secondary question, if that's allowed - what are the chances it laid eggs on my bed? It was there for possibly 4-5 hours if my cat indeed carried it in. I have rodents (pets) in my room and am peripherally worried about an infestation happening.
For context, I live in the center of the UK.

Looks like you planned to put up a pic but it is missing

I have never heard of larder beetles carrying any serious diseases and chances are slim that it could have laid any eggs, so you probably have nothing to worry about. If you want you can spray the area down with a cleaner, but as I said earlier, it's probably fine.


text:
Introducing novel genes to an adult multicellular organism?
Is it possible to introduce a novel gene into the genome of every cell (or at least most cells) of an adult multicellular organism? How would this be done?
Thanks,
CDB

How multicellular? Are you referring to sponges or mammals? What is "most"? Does the gene need to be expressed as well? You need to give more detail.

Short answer, in theory yes, in reality, at the current state of the art, no.
I guess you are speaking about higher organisms (such as mice or humans), if you are referring to small non-complex multicellular organisms then the answer is yes as far as you can transfect every cells with the system described hereafter.
The most promising technique is using the CRISPR/Cas9 system which has already been used to create all types of modified organisms but starting from the embryo. Here a good Nature reference http://www.nature.com/nbt/journal/v32/n4/full/nbt.2842.html.
There are no ways, at the moment, to transfect an entire organism with the full system. The most recent attempts I heard off is to target specific cells using an encapsulation techniques that only merges with the membrane of specific cells therefore delivering the CRISPR/Cas9 system in a targeted manner. This was in an attempt to knock-out a defined genomic regions in those specific cells, not to introduce a new gene.
I believe in the near future that this will be possible. Not necessarily every cells of an organism but at least some specific cell types.


text:
Nomenclature of genes and proteins
With respect to this paper:
Identification of Host Proteins Required
for HIV Infection Through a Functional
Genomic Screen
In the abstract, I found names such as Rab6 and Vps35 and TNPO3. So Rab6 and Vps35 are proteins and TNPO3 is a gene? So the strings written in full caps are the genes and those strings whose just first letter is capital and the rest of the letters are small is a protein?

Thats a really tough one due to the scope of things.. here's a resource as to gene nomenclature, and here's another one for proteins.

Genes, conventionally, are always written in italic (e.g. SHH) which is not the case for proteins (in the former example SHH). That should allow you to tell apart gene and protein symbols (SHH vs SHH).
The capitalization of gene/protein names is a bit more in the grey area. Usually one will use capitalized gene and protein symbols for human and primates (e.g. SHH and SHH) and use non-capitalized symbols for mice and rat genes (e.g. Shh but still SHH for the protein). This is dependent on the organism and journals usually have specific guidelines on how to exactly write gene and protein symbols.
In your case the article refers to Rab6, Vps53 (not 35) and TNPO3 as proteins, if not clearly stated differently, such as the Rab6 siRNA, not only in the abstract alone but over the entire article. They use italic names for genes as shown in one of the sentence:

... and 48 hours later staining for p24, produced from the HIV gag gene...

Just as a footnote, full gene names (e.g. the sonic hedgehog gene) are not italicized.


text:
Relationship between leaf structure and Photosynthesis rate
We can see numerous leaf structures in plant kingdom. As the leaves are designed for photosynthesis, their structure must be a factor for any optimization in photosynthesis or chlorophyll distribution.
This link describes many leaf structures but I cannot find what I am looking for in anywhere.

I think taxonomy of plants deals with the flower structure but is their any relationship among plant species that we can describe with leaf structure ?
Do the leaf structure is optimized for maximum photosynthesis rate if so then why these different structures ?
Any other advantage for these diverse leaf structures ?

Two comments: 1) plant taxonomy takes multiple types of morphological traits into account + molecular information. Linneus original sexual system for plants was however based on flower morphology.
2) Leaf morphology is based on tradeoffs between many different functions, and besides the efficiency of photosynthesis you also need to take e.g. water loss (desiccation), nutrient/water transport and stability into account. Hence the diversity of structures.

1) Your understanding of taxonomy is outdated by a few hundred years. Linneaus' original system was based on flower morphology, but we since realized that the most effective taxonomy takes into account many different traits. In today's times, we mainly use DNA sequencing to determine relationships between organisms.
2) The leaf structure is not necessarily only optimized for maximum photosynthesis rate. For instance, the leaves of cacti are spines: thin and pointy to minimize water loss and defend the plant. In fact in cacti the stem is the photosynthetic part of the plant, not the leaves. More generally, leaves may be thicker or thinner to cope with drought. You can check out the wikipedia page for Specific Leaf Area for more information.
Long story short: different plants grow in different environmental conditions, so the optimal leaf shape for any one plant depends on conditions like drought and shade.
3) There are many advantages that can be conferred by leaf shape. One example is how leaf shape can affect what is known as the boundary layer of the leaf. The boundary layer is thicker in larger, uniformly-shaped leaves and thinner in dissected or compound leaves. The intro on this webpage seems like a good resource
Overall, good question. You have to keep in mind that any trait is going to be the product of many different factors; no one factor can entirely determine a trait's morphology. For leaves, it's many different factors including photosynthetic rate, drought, shade tolerance, defense against predators, etc. that determine the shape of the leaf.


text:
What are the roles of cadherins in epithelial mesenchymal transitions?
I know that cadherins control the expression of cancer cells involved in the epithelial-mesenchymal transitions, but I was wondering exactly how the process worked.

It's kind of a broad question, can you narrow it down? Simply, loss of cadherins is necessary for breaking cell-cell junctions.

Cadherins have a relatively well-characterized role in EMT, answer is straightforward and actually rather specific.

@Kendall The figure on signalling that you posted shows just how broad this question is; asking "how the process works" is in no way specific. Your answer, while good, is in no way exhaustive and therefore does not answer the question (note I'm not trying to diminish your contribution, only trying to explain why I think the question is too broad). Furthermore, the exact role of EMT in carcinoma metastasis is still under investigation and, while there are clear parallels with the developmental program, their are also differences. The question could easily be narrowed with effort from the author

So let's just quickly define what cadherins are, using general information from wikipedia,

Source: Wikipedia
Cells express E-cadherin (epithelial), N-cadherin (neuronal, or P-cadherin (placental). These generally interact with ß-catenins to modulate cell adhesion. There are pathways intrinsic to cancer which downregulate the expression of cadherins,

Source: Epithelial–mesenchymal transition in development and cancer: role of phosphatidylinositol 3' kinase/AKT pathways
We see in the above pathway described in a study of PI3K/Akt signaling in cancer, some of the ways E-cadherin (encoded by CDH1) becomes downregulated. We also see that ß-catenin may be sequestered by E-cadherin at the plasma membrane, and cytosolic ß-catenin actually interacts within the nucleus as a transcription factor for SLUG (or snail2) where Snail2 is an essential mediator of Twist1-induced epithelial mesenchymal transition and metastasis. In the above figure this modulates reduced cell-cell adhesion, but we also see there's a number of other pathways which modulate the entirety of the EMT process.
What I found interesting, maybe unrelated
An interesting concept currently being investigated involves many of the shown membrane receptors, most of which are involved in some sort of crosstalk in aggressive cancer types. ROR1 was identified as a critical component for modulating EMT, and was shown to participate in Wnt signaling through it's frizzled domain, as well as crosstalk with Met tyrosine kinase, EGFR, and TGFß in some way. These interactions were able to increase expression of snail1/2, vimentin, etc. i.e. characteristics of EMT in breast adenocarcinoma (The linked article provides most of this background, but some may be missing, I'm unsure), and decrease expression of epithelial biomarkers like E-cadherin. When they used a ROR1 Ab to target ROR1, they found cadherin levels could be rescued, and morphological components returned to a more epithelial phenotype. Other articles showed this targeting could induce apoptosis in CLL and this occurs through interaction with PI3K/Akt.


text:
What's a protein pulldown assay?
I'm reading a paper and the authors mention a "protein pulldown" assay.
I've never done this before, and googling doesn't bring up much. Could I get a rundown of the basic theory behind it?
Also does % coverage have anything to do with this assay?

Pull down mostly refers to immunoprecipitation, however pulling down can be done using other interactions such as streptavidin-biotin or His-tag-Nickel.
In a protein pull-down a protein is enriched along with the molecules bound to it. When the DNA that is bound to a protein is studied, the experiment is called ChIP (Chromatin ImmunoPrecipitation). When other proteins that are bound to a given protein are studied then the experiment is called Co-IP.
Similarly RNA bound to protein can also be studied.
It is also possible to pull-down an RNA or a DNA fragment using complementary oligonucleotide, streptavidin, antibodies etc and study their interacting partners.
In the linked paper, they have immunoprecipitated a HA (haemagglutinin) tagged protein using an anti-HA-tag antibody (Note that this is just a small tag of 9-10 amino acids and not the entire HA protein. Such tags are useful when you don't have the antibody for a given protein).
They have done both co-IP and ChIP:

HA-tagged, full-length PfSET10 protein and interacting proteins from
  3D7/PfSET10HA and control line 3D7 were purified using anti-HA beads

Chromatin Immunoprecipitation (ChIP) and Transcriptional Profiling
ChIP analysis was performed as described (Flueck et al., 2009).

Coverage is a term used in sequencing experiments which usually refers to average number of reads that map to any locus; this is also called depth. This is commonly used in RNA/DNA sequencing studies (See this post too). In this paper, as mentioned in the other answer, the term coverage is used for peptide reads (analyzed by mass spectrometry) and it is the horizontal coverage not a vertical coverage. Horizontal coverage refers to the fraction of actual molecule (DNA/RNA/protein) covered by the assembly of reads.
Coverage has got nothing to do with the pull-down assay; it is used in the context of the downstream experiment.

From Life Technologies

The pull-down assay is an in vitro method used to determine a physical interaction between two or more proteins. Pull-down assays are useful for both confirming the existence of a protein-protein interaction predicted by other research techniques (e.g., co-immunoprecipitation) and as an initial screening assay for identifying previously unknown protein-protein interactions.

It is essentially the same as an immunoprecipitation experiment but using proteins instead of antibodies.
Coverage comes into play for identifying the pulled-down proteins as they used an LC-MS/MS analysis. You essentially have to map back the short peptide reads you get from the MS to the actual pulled-down proteins which gives you a coverage score, i.e. how much of the full protein sequence you covered with short peptides.


text:
RNA-Polymerase III transcribed genes
I have a list of differentially regulated genes from a high-throughput experiment of the human genome. I would like to find out which of these genes are transcribed by a RNA polymerase III and which of them (probably most) are transcribed by the RNA polymerase II.
I have downloaded some Chip-Seq tracks for polymerase II and III and some GO categories which apply for the RNA polymerase III transcription.
I have also tried the biomaRt repository to search for these mentioned GO categories, but I can't really find substantial results.
For example I have the gene RN7SL1 which according to the literature is transcribed by PolIII, but I'm not able to find any repository which also says so.
Is there any (better) way to search for this kind of data/annotations?
thanks a lot
Assa
PS.
I am not sure, if I have found the correct GO categories (e.g. GO:0006383 - transcription from RNA polymerase III promoter). So are there any better one?

GO is based on experimental evidences; biomart is quite good. GO:0006383 seems to be the right tag.
If you want to use the ChIPseq data then you can do this:

Map the ChIPseq reads to the genome. If you already have the tracks
then you need not do the mapping. You would have the position of the
reads in the genome.
Now count the number of reads mapping to each geneic region. The gene boundaries can be obtained from a GTF file.
Optional: Normalize the reads with the length of the gene.
Find the difference between the number of Pol-II and Pol-III reads for each gene.

By doing this you still won't be able to say that "gene-x is transcribed by pol-III". All you can say is that "pol-III binds to that geneic region". If there is an even distribution of the ChIPseq reads along the gene then you can assume that there is an active transcription and the polymerase is not merely stalled. You can also do a CLIP (Crosslink-Immunoprecipitation) of Pol-III followed by a RNAseq. This will enable you to find RNAs transcribed by pol-III (this is a better way than ChIPseq but I don't think anyone has done it yet; so no ready data).


text:
What are microRNA, siRNA and antisense RNA?
From what I understand, microRNA binds to proteins which can cut certain mRNA strands do that this protein is not synthesised. This seems like gene silencing to me, however I have also come across the term siRNA and antisense RNA...
Would be grateful if someone could explain what these are and how they work, and perhaps how they can be applied to treating diseases... Thank you in advance :)

Can you please clarify your question? At the moment it is hard to understand.

@Chris I am looking for a description of the functions of microRNA, siRNA and antisense RNA and how they carry out these functions. Also, if possible, how they can be applied to treating diseases. I have heard, for example, of microRNA being used to treat cancer, but I don't understand how...

I have edited your question slightly to replace "bones" with "binds". If this was not what you meant, please revert the edit.

Is this from homework or for a class?

There is an entire review on this. Your question is too broad as of now.

@WYSIWYG Neither for homework or class- i'm just really interested!

MicroRNA (miRNA) are gene-regulatory RNAs that are loaded onto the RNA-induced silencing complex (RISC) and interact with partially-complementary targets on mRNA to suppress protein expression.  The miRNA is originally double-stranded and composed of strands about 21 nucleotides long; on loading onto RISC, one strand is degraded and the other, the "guide" strand, is held on the surface of RISC where it can interact with mRNA. The targets recognized by the guide strand are most commonly on the 3'-untranslated region (UTR) of an RNA.  Binding can suppress assembly of an initiation complex on the 5' cap of an mRNA because the mRNA is bound into a circular shape at the initiation of translation, bringing the 3'-UTR and 5'-UTR close together.
If the RISC loads an RNA than then finds a perfectly complementary target, RISC cleaves the target RNA using the activity of one of the protein components of RISC called Argonaute.  This property is exploited experimentally by manufacturing small interfering RNAs (siRNA) intentionally targeted to particular target sequences.  Once loaded into RISC these siRNA might recognize and cleave their perfectly complementary target sequence within an mRNA (though there is a significant failure rate, so several sequences are often tried).  The siRNA will also have miRNA-like effects on some partially-complementary targets on various mRNAs, leading to the observation that a single siRNA sequence can modulate expression of hundreds of off-target genes.
Antisense is a nucleic acid strand (or nucleic acid analog) that is complementary to an mRNA sequence.  Antisense occurs naturally and can trigger RNA degradation by the action of the enzyme RNase H.  Originally natural antisense RNA was tried as a method for silencing a gene, but the poor stability of RNA in cells led to development of nucleic acid analogs that are more nuclease resistant and still activate RNase H (such as phosphorothioate RNA) and other nucleic acid analogs that bind to RNA and sterically inhibit processes without activating RNase H (such as 2'-O-methyl phosphorothioate RNA, Morpholino oligos, locked nucleic acids, or peptide nucleic acids).  These latter RNase-H independent oligos do not trigger degradation of mRNA but they can be used like molecular masking tape to block translation, alter splicing of pre-mRNA, inhibit activity of miRNA, block ribozyme activity, and interfere with various other processes that require some other factor to bind to a particular sequence on an RNA molecule.

Thank you for your reply! So it seems to me like the siRNA is just like microRNA, but we make it ourselves rather than it being a natural cell process like how microRNA is used? And also, is the microRNA code on an intron?

I have looked up more about siRNA and see that mmicroRNA does not have to be 100% specific, but siRNA does. Therefore siRNA only leads to cleavage of the mRNA strand from which it came (so it is complementary to this). Dooes this mean that siRNA is likely to be coded for on an intron in a gene? Also, I have read that microRNA 'inhibits translation of mRNA' and siRNA 'cleaves mRNA', so it seems like they work in two different ways (this is from a website comparing miRNA and siRNA). Could you elaborate on how exactly each works?

In some cases, miRNAs are clipped out of introns.  These miRNAs are sometimes called miRtrons. https://en.wikipedia.org/wiki/Mirtron  The mRNA cleavage and the translational inhibition are both mediated by the RISC, using the miRNA as its target-recognition moiety.  The cleavage activity is catalyzed by Argonaute, one of the protein components of RISC.  https://en.wikipedia.org/wiki/Argonaute


text:
How does alternative splicing work?
I am trying to find out what controls what exons are spliced out, and I keep coming across the term cis regulator, but I cannot seem to find a clear explanation of what happens...
Thank you in advance :)
EDIT: to clarify, I have tried to read the Wikipedia article on alternative splicing and I get the main idea (some exons being cut out of the mRNA with the introns to produce the mature mRNA, I think...) but I don't understand the 'mechanism' section, I.e. What controls which exons will be cut out? And what enzymes 'splice' the mRNA- how do they do it in the right place, and stick the mRNA together again?

Just to be clear, do you want to know how alternative splicing works? Have you tried reading the Wikipedia article on it? Can you tell us, what you don't understand more specifically? Actually this is pretty broad...

@Chris thank you for your reply! I have tried reading the Wikipedia article- I get the main idea of alternative splicing (some exons being cut out of the mRNA with the introns to produce the mature mRNA, I think...) but I don't understand the 'mechanism' section, I.e. What controls which exons will be cut out? And what enzymes 'splice' the mRNA- how do they do it in the right place, and stick the mRNA together again?

Can you add  this comment into your question? It would make it much clearer.

21joanna12, look into snRNPs.  These are parts of the splicosomal apparatus and some of them (the U1 and U2, U11 and U12 snRNPs) are also the guideposts that bind near the splice junctions at the end of introns.  These help guide the splicing apparatus to the splice sites. There are also proteins that bind RNA and interact with the splicing apparatus to switch alternative splicing, such as SP proteins.
https://en.wikipedia.org/wiki/SnRNP
https://en.wikipedia.org/wiki/SR_protein
https://en.wikipedia.org/wiki/Exonic_splicing_enhancer
Here's a recent review that might serve as an entry into the literature: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4232567/

I'm a little familiar with U1 - U6 because I just read a paper on splice switching oligos to control splicing of a defective dystrophin gene to skip a frame shift mutation. But I haven't heard of U11 or U12. I still don't understand how cells select specific alternative splicing patterns to produce a specific protein. Could the pool of miRNAs produced by a cell affect alternative splicing in a manner similar to splice switching oligos just by binding to certain splice sites and forcing the spliceosome to find a different site?

There are two sorts of spliceosomes.  The major spliceosome uses the U1 and U2 snRNPs and the minor splicosome uses the U11 and U12 snRNPs.  It is binding of the splice-regulatory proteins that influence where the splices occur.  I have not heard of RNA directly influencing splicing patterns.  I'm very aware of the DMD splice switching using Morpholino oligos - it has great potential as therapeutics for genetic diseases.

The oligo-based methods of altering splicing can take two different approaches.  The most common strategy is to use an oligo to block the binding site of a guidepost snRNP (U1 or U2, U11 or U12).  The other approach is to block the binding site of a regulatory protein, preventing that protein from docking with the pre-mRNA.  It is the latter approach that is interfering with the mechanics of alternative splicing.  The former method, blocking snRNP binding, can cause skipping of an exon that is never skipped by "normal" alternative splicing mechanisms.

And if that exon contains a frameshift or bad stop codon, skipping it can create a protein that retains enough function to still work. Now if we can just get some good delivery methods for getting the oligos into cells.

user137, the arginine-rich peptides, such as (RXR)4, are pretty good.  Moulton HM, Moulton JD. Morpholinos and Their Peptide Conjugates: Therapeutic Promise and Challenge for Duchenne Muscular Dystrophy. Biochim Biophys Acta. 2010 Feb 16. [Epub ahead of print]. http://www.sciencedirect.com/science/article/pii/S0005273610000520

Along the same lines, this published yesterday.  Betts CA, Saleh AF, Carr CA, Hammond SM, Coenen-Stass AM, Godfrey C, McClorey G, Varela MA, Roberts TC, Clarke K, Gait MJ, Wood MJ. Prevention of exercised induced cardiomyopathy following Pip-PMO treatment in dystrophic mdx mice. Sci Rep. 2015 Mar 11;5:8986. doi: 10.1038/srep08986.    http://www.nature.com/srep/2015/150311/srep08986/full/srep08986.html

A review by Penalva and Sánchez explains one example of how alternate splicing is regulated at the molecular level.  There are other possible mechanisms that I am only vaguely aware of.
https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/12966139/
Sex determination in Drosophila melanogaster is largely controlled by a cascade of alternate splicing events.
In a brief (and admittedly incomplete) summary, the product(s) of one gene (RNA binding protein) recognize a particular splice site in a downstream transcript.  On binding, that site is no longer available as a splice acceptor site and the splicing mechanism is "forced" to work with the next available acceptor site.  This leads to the excision of the former exon, which has now become an intron.
This process is represented graphically in the above cited review in Fig 3A where female/functional Sxl product (when present) blocks another RNA-binding protein (U2AF) which is involved in default splicing, and tells it to move on to the next available acceptor site.  (I would like to include Fig 3A here but don't know how.  Perhaps this will help: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC193869/figure/f3/)
Sex-lethal gene product exists in male- and female-specific forms, produced by (who would have guessed?) alternate splicing of the Sxl transcript.  The male-specific transcript has an early stop codon and yields a non-functional protein. The female form modifies splicing of the transformer gene product to produce a female-specific (functional) version of the transformer mRNA.  The unmodified (male) version again produces a non-functional protein.  The female-specific version of the tra gene product (wait for it!) modifies the splicing of the doublesex transcript to produce a female-specific doublesex protein.  The unmodified/default splice dsx transcript produces a male-specific protein.  These male- and female-specific proteins lead to male- and female-specific expression of an array of genes further downstream.  By the way, the Sxl gene product not only affects the tra transcript but it also modifies the splicing OF ITS OWN TRANSCRIPT to keep Sxl expression going after its initial onset.  It also plays a role in setting the overall level of X-chromosome transcription to achieve "dosage compensation".
Hope this helps.

the product(s) of one gene recognize a particular splice site in a downstream transcript. On binding, that site is no longer available as a splice acceptor site and the splicing mechanism is "forced" to work with the next available acceptor site.
But what determines which splice site is chosen? Suppose pre-mRNA has exons 1,2,3,4. What determines that in one scenario exon 2 will be skipped, whereas in another scenario exon 3? Do we need a different RNA binding protein for each exon of each pre-mRNA molecule? Or can the same RNA binding protein interact with multiple exons, if yes, how?


text:
Can human mRNA be translated in vitro by prokaryotes?
As the genetic code is universal, can mRNA from a human cell be correctly translated by a prokaryote in a in vitro translation system?

Short answer: Yes, you can.
Usually these are coupled systems for transcription and translation. For these you clone the gene of interest into a vector which contains a prokaryotic promoter which is then used to generate the mRNA in the tube. This mRNA is then translated in the second step into a protein. This works very well, but the protein is missing the typical post-translational modifications of eukaryotic cells like glycosylations, as these are not existant in the bacteria.
These kits can be purchased of the shelf from the usual biotech companies. Mostly these are based on E.coli cell lysates. They work like shown in the figure (from here):


text:
DNA sequencing problem
First off, let me start by outlining the problem:
Your laboratory has established a technique for examining DNA replication in a cellular extract. To the cellular protein extract, you add nucleotides, a small amount of radiolabeled 32P-dGTP to aid visualization of the synthesized DNA, and a 4000-base-pair linear double-stranded DNA molecule that contains an origin of replication in the middle. After allowing the reaction to proceed for 30 minutes at 30°C, you boil the mixture to denature the proteins and the DNA strands, separate the components on an acrylamide gel, and detect the radiolabeled DNA products. This complete reaction is shown in lane 2 on the gel in the Figure below.

Problem A:
You perform the assay by yourself for the first time with no one else is in lab. The tube labeled “nucleotide mixture” has only enough for a single reaction, but you find a tube with a label that reads “dATP, dTTP, dGTP, dCTP” and you use this in a second reaction. You find the first reaction looks like lane 2 and the second reaction looks like lane 3. Why was no DNA synthesized in the second reaction?
My answer:
Because deoxyribose triphosphates do not have a –OH group to attach. You essentially can’t build with them.
Problem B:
Your lab partner has recently isolated a mutant strain that can replicate its DNA normally at 30°C but exhibit no DNA replication at 40°C. He calls the mutant tsr1, for Temperature Sensitive Replication. The wild-type strain replicates efficiently at both temperatures. You believe that you can use the biochemical assay of cell extracts to identify which genes are defective in the mutant. You grow wild-type cells and tsr1 cells at 40°C, make the extracts, incubate the DNA replication reaction at 40°C, and detect the products on a gel. You observe the pattern shown in lanes 4 and 5. You are so excited by the results that you run to your lab partner and tell him that you know what enzyme is defective. He is delighted by your results but says that there are three different enzymes that can account for your results. What are they?
I am 100% lost on this one.
I understand from the figure that the wild-type at 40 degrees has 4000 nucleotides so it's not being cut off. The mutant, trs1 is being cut off one into two slices of 2000 and one of these slices has been cut off into slices of 500? Am I understanding this correctly?
I also don't understand why the 500 line is so thick compared to the others?
Anyhow I feel really confused on this. I've been learning about Sanger sequencing and it makes 100% sense with ddXTP added into the mix to view the length of each sequence and therefore be able to read the sequence, but I'm not even sure if that's what's happening here.

The title of the question is a bit misleading as the problem/ question you have detailed is not really a sequencing problem

Even though you - or the problem did not clarify, I assume in my answer that you work with eukaryote system, even though the principle of the replication is the same.
dNTPs do have an OH group on their 3rd carbon atom (for eg. check this wiki-page for dCTP) so I don't think that's the issue here. My guess is that the first tube contains the radio labeled GTP and the second does not, so even the DNA is there, you cannot see it - even though the question specifically asked why DNA was not synthesized, my opinion is that it's a tricky question to confuse you.
For the second problem we need to dig into the replication process a little bit:
In the replication fork the two strands are synthesized differently. The so called leading strand is made continuously, without interruptions, however the other strand - the so called lagging strand is synthesized by ligating small fragments - aka Okazaki fragments. These small fragments require their own RNA primers that need to be removed after synthesis is done.
Now since the origin of replication is in the middle and replication can proceed both ways, on a linear fragment such as yours you can get two 2000bp fragment from the two leading strands. Would it be a circular DNA, then you could still get 4kbp fragments since the replication could go around the DNA circle.
The smaller 500bp fragments that are quite abundant in the tsr1 lane, are the fragments that cannot be ligated. That being said I must admit that 500bp Okazaki-fragments would by atypical for eukaryotes (usual is around 100-200bp). So the enzymes responsible for this could be:
DNA Ligase - the one responsible for ligating (joining ) the lagging strand's fragments.
Polymerase delta (Pol δ): That is responsible for lagging strand synthesis and primer removal - in this case the primer removal function might be defective, this causes that the primers stay on the DNA and complete synthesis and ligation cannot occur.
The last protein although it is not quite an enzyme is the DNA clamp complex (PCNA). This complex stabilizes the polymerase to DNA, but when reaching a previous fragment the polymerase should dissociate. But if the clamp is dysfunctional than the polymerase gets stuck on the end of the fragment thus no primer removal and ligation can occur.
If need more info read this wiki-page.

You need not assume a eukaryotic system. The principle is same for prokaryotes also (the Okazaki fragments are longer in prokaryotes though ~2000nt).

yes it is. It stated it only to indicate my logic in the answer. That being said the 2kb fragments could easily be Okazaki fragments of a prokaryotic system, but then what about the 500bp fragments? Plus if explicit enzymes are required for the answer that you must know which system does the assay use. I am going to edit my answer to indicate that the principle is the same for both eukaryotes and prokaryotes.


text:
Doubt on genomic code for nucleosome positioning?
I was reading "A genomic code for nucleosome positioning" (by Eran Segal et al). And I am having 2 doubts.

The figure(b) in this image from the paper shows the graph of fraction (3-bp moving average) of AA/TA/TT dinucleotides of nucleosome dna sequence they analysed statistically as far as I understand.
What is 3-bp moving average here?
I also don't understand how they chose 0th position (the so called dyad).
Also what does it mean to have oscillations (correlation?) in this graph?

UPDATE : I am adding some supplementary information related to finding the dinucleotide fractions. Still I don't understand why is the fraction found so?

Your image is a little blurry. Can you upload a higher resolution image?

@WYSIWYG : done

Okay I edited the answer. Let me know if that is clear.

Dyad is the centre of the DNA that is wrapped around the nucleosome core (It basically is the centre of symmetry of the nucleosome). It is a common practice to set it at 0 thereby making incoming DNA half, negative and outgoing DNA half, positive.
By oscillations the authors mean that there is a periodic repeat of A/T dinucleotide. IMO it is actually not correct to call it oscillation which is mostly used in a time course dynamical sense.
I guess this is what is meant by the 3-nt moving average:
You have conditional dinucleotide probabilities for each position (As shown in the figure). Now you calculate the A/T dinucleotide probability which is:  P[A/T] = PAA + PAT + PTT + PTA
Now you find the moving average for 3 steps:
MA(n) = (1/3)×(P[A/T](n) + P[A/T](n-1) + P[A/T](n-2))

where n is the nth position of the DNA

The term "oscillations" is my word, not authors'.

I did not understood the 3-bp moving average filter argument, but now I have access to ~70 page supplementary data of the paper. I am updating my question.

In the graph (b) of first image but "AT" is not mentioned? only AA/TA/TT is mentioned.

@dexterdev I think TA and AT are grouped together as TA (combination of T and A); there is no rationale for not including AT.

AT and TA in this paper are different. AT is T after A and TA is A after T. The supplementary data shows a different separate plot for this. Should I update the question with those plots. I am still in confusion?

@dexterdev Unless I read the entire paper I wont know what they have done. I know that AT is different from TA but all I am saying is that when TA is counted then it makes no sense to exclude AT. You need not modify your question because this doubt is just about what have they counted and for that you just need to look at the paper. The answer will still remain the same.

Any way thanks for the effort, but they are counting both the AT and TA differently.

@dexterdev they must have mentioned why they are doing so. You just need to read the paper carefully. You must exempt me from that effort :)

I agree to that. :)


text:
Is it possible to insert DNA without cutting the recognition site with CRISPR/Cas9?
We are looking for a way to insert DNA into a genome, but we would like to do it in a way that the recognition site stay intact to be able to add again DNA at the same location. Do you know if it is possible or if it is already the way CRISPR/Cas9 does it? Apparently multiple systems were already engineered but the few papers we read weren't about our problem.
Sincerely,
Emilie

Inserting into the genome of what organism?

Why not just make sure your inserted DNA segment contains the same CRISPR/Cas recognition site, so you can just cut it again?

@MarchHo I had the same thought initially, but then Cas would cut your target DNA as well. Furthermore, the target DNA would also have a region of homology which doesn't contain your desired insert and repair could occur which doesn't result in insertion of your desired sequence.

We would like to use it on E.coli genome.

@canadianer And Cas9 ignores methylation too. Perhaps try another nuclease (eg ZFN or TALEN) which is affected by methylation?

@EmilieCuillery Is there any reason you cannot just use a plasmid?

The nice thing about CRISPR/Cas is that target recognition is done by RNA, which is relatively easy/cheap to obtain. Could you just get another gRNA which recognizes the new sequence after insertion?

@MarchHo we could do that but then we would have little sequences coming from the former recognition sites "polluting" our added DNA. Our question would be more then: Do you know if Cas9 cuts in the middle of the recognition site or if a special engineered protein Cas that cuts after the recognition site (Whatever the sequence to cut is) exists?

What we want to do is to insert again and again the same sequence at the same location using only one recognition site. Does it seem crazy? we've been searching, looking for few days now but still have problems understanding real mechanism of CRISPR/CAS9... @MarchHo we'll use a plasmid for sure to get the protein we want be then we want our protein to act over and over by adding DNA again and again each time increasing the genome (with notion of order)

I'm not sure about an engineered Cas, but I think nucleases like TALEN don't cleave the recognition sequence. The problem I think you'll face is that your insert must also contain the recognition sequence to be homologous and would thus also get cleaved. You might consider using a mutated recognition sequence in the insert so that it isn't cleaved but still has sufficient homology to be used for repair. Even then, I would expect the target sequence in the gDNA to be replaced by the mutated version in the insert as nucleotides are resected from the double strand break.

@canadianer "Cas would cut your target DNA as well" - what about protecting the target DNA somehow?

I think the best option would be to add protecting groups which can be removed later after Cas9 is cleared. If it is cleared ever. I have low skills by genetic engineering. :D

Look into site-specific recombination.  You can use a site-specific recombinase, specifically an integrase, that can insert a sequence of DNA at a certain attachment site.  You can add an identical attachment site into the DNA sequence to insert, allowing for the reintegration of a new attachment site.  Note however that you might get SSR onto the insertion plasmid itself, so don't do this if you need a specific amount of integration.

Look at the bottom subfigure of A for an example of integration.  Recombinases can also do other things, such as excision and inversion, based on the orientation of the attachment sites.

Doesn't use CRISPR though. Right?

It seems that this also suffers from the same issues as pointed out in the comments. If your insert has the recombination site, it may recombine with copies of itself.

Our projects is basically based onto recombinase. And work...published 2 months ago ... but not by us :( So we are looking for a better efficiency (10^-4 with recombinase) allowing a faster system. As i understand CRISPR/Cas9 doesn't allow insertion of several piece of DNA at the same place butCas9 is a very powerful tool do you think we could engineer it to cut not the homologous sequence but just after of before? (We really have problems understanding where the DNA we want to insert is coming from and the exact mechanism of it. Are you thinking of another way faster than recombinase?

Anyway thank you all for your help but i think we will abandon the idea for now as we learned in our researches that the Cas9 rate and efficiency is much too low to do what we want... i'm sorry ! But thank you again for your help :)


text:
Why is knowledge of bacterial pathogenesis important?
Why is knowledge of pathogenesis increased more and more for common bacterial pathogens? Most of these studies lack a near application in disease control such as vaccines or antibiotics.
Examples:

Studies on the interactions of Haemophilus parasuis with porcine
epithelial tracheal cells: Limited role of LOS in apoptosis and
pro-inflammatory cytokine release
Sialic acid in the lipopolysaccharide of Haemophilus influenzae:
strain distribution, influence on serum resistance and structural
characterization

Because it is also important to do basic research. It has no goal besides solving questions and is the basis for applied research.

@Chris You should convert that to an answer :) Also it is important to note that these small contributions make it possible to improve the applied part of science.

Because it is first important to understand a mechanism before you can think about using it for drugs. Take melanoma for example: A large subset of melanoma has a mutated and constitutive active BRAF kinase which permanently signals towards the nucleus and thus deregulates gene expression. Once this mutation was found it was possible to design inhibitors which only work on this specific mutation, which are available in the clinic today.
The same is true for example for activity of antibiotic on bacteria and the fight against resistance. Once it was known that the enzyme beta lactamase inhibits beta lactam antibiotice (penicillin or ampicillin for example) it was possible to find an inhibitor of the enzyme. The clavulanic acid works as a specific inhibitor and has been added to beta lactam antibiotics subsequently to overcome resistance. The same is true for changing antibiotic molecules chemically so they evade the established resistance mechanisms.
The contributions of basic research is the basis for applied research and drug design. Without them, this wouldn't work. Besides that it is also the curiosity of humans which drives science - without having any particular application in mind. These often come much later.


text:
RNA migrating slower than DNA on Formaldehyde Gel?
So I ran into an interesting problem.  I'm getting a linear DNA band that is twice as long (4x bases, but as denatured probably only 2x) as an RNA band running at the same size in a formaldehyde gel.
Both sequences have been isolated an 100% confirmed.  The gel was run in MOPS buffer.  My experience, and all the publications I've found, show that if anything RNA should run faster.  Can anyone think of a reason why the DNA band and RNA band would be running the distance despite the DNA being twice as long?
I've read a lot of fun papers on drag factors in gel matrices now, but none of it leads to this confusing and repeated result.
Edit: Gel and Conditions
Gel was 1M formaldehyde, 1% agarose.  Run at 100V for 1.5h.  RNA was mixed in a RNA loading dye which contained 15.3% v/v formaldehyde, 41.3% v/v di formamide, 4.6mM EDTA, MOPS, and bromophenol blue.  We believe our RNA loading dye to be denaturing, and it ran at expected size with RNA ladder.
................(1)........................(2)............................(3)

Lane 1 is a DNA template plasmid, cut 1 location.
Lane 2 is the Template + DNase from in vitro transcription reaction w/o polymerase.
Lane 3 is the RNA + DNase from in vitro transcription reaction.
There are no other bands in the DNA lane, and it looks like if anything, the DNA is migrating much faster than expected, despite being sequence confirmed (both before the process, and gel purified out and confirmed again).

I've deleted my answer as it was useless. In the comments you said that you're running a denaturing gel. Have you considered polyacrylamide/ polyacrylamide-urea gel?

Interesting. Do you have a picture of the gel?

I'm trying to get an OK from the tech office to post an image now.

Maybe this is stupid but could it be that in the RNA (which I suppose is single stranded) there is only one phosphate backbone therefore less negative charges per length so that it migrates slower ?

Maybe your RNA does secondary structures...

@Pao I'm assuming that might be true for the RNA, but in a formaldehyde gel, how does that happen?

What's your agarose percentage, solution pH, voltage and running time?

Well, did you add denaturing agents such as SDS or urea?

@Kendall Gel was 1M formaldehyde, 1% agarose. Run at 100V for 1.5h; updated question

@Pao 15.3% v/v formaldehyde, 41.3% v/v di formamide; updated question.  Think that should be denaturing, and does SDS actually help denature RNA? That's probably off topic though.

Since RNA and DNA of equal sizes and equally denatured would have pretty much the same charge and almost the same mass, why wouldn't they run at the same rate? Never run both DNA and RNA on the same gel, so I don't know what's supposed to happen.

They are not of equal size, that's the question.  The RNA is 1/2 the length of the DNA.

Then off the top of my head, maybe the RNA isn't being fully denatured for some reason. That lane also looks very overloaded, could that alter the migration rate?

Some sources note that old formamide or formaldehyde may cause issues in the gel. pH may also cause mobility issues if it's too acidic.. as for optimizing the gel, I see some resources using a 1% agarose gel with 2M formaldehyde.. i believe here and they also suggest running the gel in a 1x MOPS buffer for 10 minutes during prep. It's still confusing, though. You could try a different denaturing method, and see if you can repeat the result.

+1 for the "overloaded" explanation. At least for SDS PAGE gels, overloading a well results in the lane "blobbing" and travelling slower than expected.

@Kendall That's a good idea.  We're giving it another go.  Oddly enough the RNA seems to be running the right size, it's the DNA that's migrating to far.

Do you see the correct size bands for the integrity of RNA?  28S, 18S and 5S bands?

The inclusion of formaldehyde in the gel and buffer is to keep the RNA denatured (ie after heating the sample to melt the double-stranded stem-loops, just prior to loading the gel), in the hope that the RNA will migrate through the gel with an Rf proportional to its molecular weight (approximated here by its length). Therefore the correct size markers would also be made of RNA (and prepared the same way, by heating).
It is difficult to predict, a priori, how a double-stranded DNA fragment would migrate under similar conditions, without also including a lane of ds DNA size markers.
In other words I would only use DNA markers for DNA and RNA markers for RNA. By repeating this experiment (1 lane of DNA MW vs 1 lane of RNA MW) at different voltage gradients and different concentrations of agarose, you might be able to plot two standard curves that would let you predict where your DNA fragment is expected to migrate relative to the RNA transcript, but without that data I would not assume that a larger DNA fragment would run slower than its RNA transcript.
Even if the dsDNA was exactly the same length as the ssRNA (and pretending that the MW of the dNTPs and NTPs are identical), the DNA's MW would be twice as much as the RNA, but the negative charge on the DNA would also be twice as much.

Instead of a standard curve, why not just run two ladders on your gel? 1 DNA and 1 RNA.

@user137 Exactly, that is the immediate practical solution.

While I agree with everything you mentioned, it doesn't really address the issue.  I've been working on a standard curve. It is odd that the DNA is migrating much quicker than expected, as you point out it should be slower for the same length, doubly so for twice the length.  And yet under multiple conditions I am seeing the same thing.  Might be  the long poly-A tracks in the DNA, I don't know.  At this point it's not as import for the project as it is a curiosity.