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What is this hard shelled insect in my house?
I moved to a new city in west India last year and I've since, on several occasions, seen this insect on walls and it's usually climbing using its head. It has a greyish long shell and moves in a very wobbly way. I've asked people in the locality if they know what that insect is, but no one has a clue. And my curiosity is piqued everytime I see it and I really want to know what it is.
Here are two closeup images:
https://ibb.co/HNDLCMm
https://ibb.co/6JCMH7j
I have a video as well but I don't know how to share it here.
I was suggested that this question is a possible duplicate of: What insect is this? (India)
The insect in my case is probably much smaller and has a plain grey shell (as opposed to building a shell from material lying around, which would most probably be different every time). I don't explicitly see any legs although there may be.
I want a definitive answer as to what moth it is or if it is one or not.

Possible duplicate of What insect is this? (India)

I think if you want a better ID you need a much much better picture.

Your close-up images are not any better than the current one.

Related: Identifying a creature that appears to be a worm wrapped in a cocoon, What is this black and white worm in a white case?,  Help in identifying an unknown arthropod, What insect is this? (India), Identify this smooth-cocoon worm from Southern India, Small worm living in some kind of cocoon......

Related:  What is this animal that hides in dustlike structure?, What in the world is this critter?, What is this hard shelled insect in my house?, What is this insect found commonly in coastal India?, Insect identification - pantry moth vs clothes moth

That's a plaster bagworm [ https://en.m.wikipedia.org/wiki/Phereoeca_uterella ] :)

Doubt if it's the same species. Probably a different one since it's always grey (but could be that the larvae are rising from same source and using the same material). It is a moth larva for sure though right?

For sure it's a moth larva because it's order is Lepidoptera.. and lepidopterans are either butterflies or moths.


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B cell receptor editing
If a B cell contains two mu chains and two lambda chains and is self reactive can it go back and rearrange its kappa light chains? I'm not sure if it can only try to rearrange its lambda light chains or if it can go back and try to rearrange kappa chains as well.
Background info: the light chain is the smaller of the two types of polypeptide chain in an immunoglobulin molecule. There are two classes of light chain known as the kappa and lambda light chains. During B-cell development the light chain genes rearrange. First one kappa gene is rearranged; if this doesn't produce a functional protein then the kappa gene on the second chromosome is rearranged; if a functional protein is still not produced then the lambda gene is rearranged one chromosome at a time until a successful rearrangement is produced.

When I look at Wikipedia I can't find definitions of kappa versus lambda light chain. In the interest of making this question more broadly useful, would you mind adding some more definitions to your post? It might also help someone who is less of an expert do the requisite research to answer your question.

The short answer is no.
Here's a review article with some evidence:

B cell receptor editing in tolerance and autoimmunity
Section: Receptor Editing in Mice with Conventional Autoantibody Transgenes
If multiple κ rearrangements fail to yield a suitable L chain, the κ
locus undergoes rearrangement to a non-coding gene called RS in mice
(RS is referred to as the κ deleting element in humans). RS
rearrangement results in either deletion or inversion of Cκ,
consequently inactivating κ L chain expression on that allele. In cell
lines with λ rearrangements, one or usually both κ alleles are
deleted, whereas in κ-expressing B cells the fraction of RS
rearrangements is approximately 15%.

In summary: After a point with (probably multiple) κ rearrangement failures, both κ loci (usually) get deleted, leaving only λ. So if a B cell expressing a BCR with λ is self-reactive, it won't have the chance to rearrange its κ.
However, there's a lot more involved. For one, it's possible to get a functional and non-self-reactive λ chain BCR without repeated κ rearrangement failures.
Since the quoted passage might be confusing out of context, I'd like to mention briefly that your question's description of light chain recombination is very simplified. In reality, there are many additional mechanisms involved and many different paths to get a functional κ rearrangement, a functional λ rearrangement, neither, or even both. Moreover, there's a lot we don't know, since we learn one experiment at a time, and we can't always directly measure what we'd like to.
First, rearrangement has been observed to occur simultaneously in  κ and λ. This fact might explain why it's possible to get a functional λ chain BCR right away as mentioned above. Second, allelic exclusion (between both κs and both λs) doesn't always work as you and I might expect it to, and a developing B cell can express different BCRs simultaneously (even one with κ and the other with λ). Third, due to receptor editing, a B cell has multiple opportunities for a functional κ chain rearrangement on a single chromosome, meaning that neither λ nor the second κ is needed despite an initially nonfunctional κ rearrangement.
I highly recommend reading the review article!

source: Stack Exchange

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

authors: رنيم محمد صوافطة

sort: votes


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DNA polymerase I exonuclease activity
Does DNA polymerase I in bacteria use forward or reverse exonuclease activity to remove RNA primers? One of my books says it uses 5' to 3', but another says it uses 3' to 5' exonuclease activity.
Update: I know RNase H can remove the primers, but the exonuclease activity of pol I can also remove them.

Googling your question showed that it is RNAse H that removes the RNA primer. DNA Pol I has both 3'-5' as well as 5'-3' exonuclease activity for proofreading and nick repair activities, respectively. See the wiki on Pol I

From wikipedia:

In the replication process, RNAse H removes the RNA primer (created by Primase) from the lagging strand and then Polymerase I fills in the necessary nucleotides between the Okazaki fragments (see DNA replication) in 5' -> 3' direction...

And elsewhere in the same article:

Pol I possesses four enzymatic activities:

A 5' -> 3' (forward) DNA-Dependent DNA polymerase activity, requiring a 3' primer site and a template strand
A 3' -> 5' (reverse) exonuclease activity that mediates proofreading
A 5' -> 3' (forward) exonuclease activity mediating nick translation during DNA repair.
A 5' -> 3' (forward) RNA-Dependent DNA polymerase activity. Pol I operates on RNA templates with considerably lower efficiency (0.1–0.4%) than it does DNA templates, and this activity is probably of only limited biological significance.

So the answer to your question is neither. RNAse H removes the primers, and the exonuclease activity of DNA Pol I is irrelevant to primer removal, although it turns out it can operate in either direction depending on the context.

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PSI-BLAST website algorithm parameters
http://blast.ncbi.nlm.nih.gov/Blast.cgi
In this website, when I want to apply the psi-blast algorithm on a sequence, under the section of algorithm parameters , what does PSI-BLAST threshold mean? The question mark says it means that:

Set the statistical significance threshold to include a sequence in the model used by PSI-BLAST to create the PSSM on the next iteration.

Another parameter is there called pseudocount. Did not understand that too. Could not understand what this means, someone please explain in simple language.

PSI-BLAST is an iterative algorithm. Each cycle it uses a model (the position-specific scoring matrix, or PSSM) to search for sequences matching the model, next updates the model with the sequences found, and then runs the search again with the updated model. That P-value controls which of the sequences found in each iteration should be included in the new model (i.e. only include those sequences satisfying the P-value).
Regarding the pseudocounts, this is a value to be added to each column in the PSSM. The reason is to avoid zero count entries, which may give problems later. But as the help suggests:

Pseduocount parameter. If zero is specified, then the parameter is automatically determined through a minimum length description principle (PMID 19088134). A value of 30 is suggested in order to obtain the approximate behavior before the minimum length principle was implemented.

It is probably OK to leave the default option unless you have some reason to change it.


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HIV and effectiveness of inhibitor cocktail over single inhibitor
I'm looking for clarification on the answer to this question. It's in my biochemistry class but I figured this is more Biology than Chemistry, so I'm asking it here.
The question is:

One of the more effective treatments for HIV-positive individuals has been for them to take
  protease inhibitor cocktails. Certain proteases are required for the virus to mature and these inhibitors prevent them from functioning. A cocktail of inhibits means that numerous inhibitors are used at once. Why would a cocktail be more effective than a single inhibitor?

My answer to this is that there could be more than one mutation of the virus, and with each mutation a variation in specific protease. So, the protease cocktail would defend against a wider range of the mutated virus.
Is this correct? Is there an answer that might involve describing epitopes?

Your answer is correct. HIV-1 encodes a single homodimeric aspartic protease, with each monomer containing the classic Asp-Thr-Gly motif, and the dimer's active site being formed with the two monomeric active sites creating a cleft where the proteolysis takes place. In it, water acts as a nucleophile in conjunction with the aspartic acid residue to hydrolyze the peptide bond in the protein's target.

WikiMedia: Aspartyl protease mechanism.png
A number of HIV-1 proteins are synthesized as polyproteins, and protease is required to cleave them in the appropriate spot(s) so they can assume their mature forms. This is a very big deal, because without these cleavage events HIV-1 cannot complete its replication cycle, and so becomes non-infectious.

WikiMedia: HIV-replication-cycle.svg
Protease inhibitors act by "sticking" in the binding cleft, obscuring the aspartate and preventing binding of the target proteins. However, these small-molecule inhibitors are very specific to HIV-1 and the amino acid residues that compose the binding cleft, otherwise they could potentially inhibit one or more of the many aspartyl proteases our body makes naturally. While it is not very likely that a destructive mutation in the Asp-Thr-Gly motif would result in a replication-competent virus, other more conservative mutations may occur in the binding cleft that still allow the target to bind and be cleaved. However, depending on the exact protease inhibitor being used, a single mutation, even if it's conservative, may still be enough to dramatically decrease the inhibitor's binding efficiency and allow protease to maintain some or all of its functional capacity. This is why cocktails of inhibitors are used: they each depend on different amino acids for their binding, so if mutations arise at some point that do affect the activity of one inhibitor, others may still be unaffected. Evolutionarily-speaking, the inhibitors put a tremendous selection pressure on the virus, which combined with HIV-1's naturally "sloppy" replication process, leads to mutants appearing in relatively short periods of time.
There are two kinds of epitopes in the adaptive immune system: those recognized by antibodies and B cells, and those recognized by T cells when presented in the context of MHC. Antibody epitopes are generally found on the surface of a pathogen or a pathogen-infected cell (when speaking in the context of infectious diseases), as proteins or other compounds capable of raising an immune response that are only located completely inside of the pathogen or infected cell are not available for binding. T cell epitopes, on the other hand, are linear peptide fragments (and sometimes other molecules, like glycolipids) generated by internal processing in the antigen-presenting cell, and are usually pretty representative of the complete contents of the cell, native and foreign. Native epitopes generally don't produce immune responses - when they do, autoimmunity occurs. Foreign epitopes are recognized by circulating T cells, and help prime an immune response against the infected cells. (As a side note, since HIV-1 infects a subset of T cells, it is a way for them to escape immune detection). Mutations in the protease protein may affect some of the epitopes it produces, but those mutations are just as likely to increase visibility to the immune system as decrease it, so overall there's no net gain or loss.

According to wikipedia:

HIV protease inhibitors are peptide-like chemicals that competitively
  inhibit the action of the virus aspartyl protease. These drugs prevent
  proteolytic cleavage of HIV Gag and Pol polyproteins that include
  essential structural and enzymatic components of the virus. This
  prevents the conversion of HIV particles into their mature infectious
  form.

Competitive inhibition means that it just slows down the conversion, but it does not stop it. In the case of building a virus we are talking about a multi step process. By using multiple inhibitors we slow down multiple steps in this process. So it is much more effective than just using a single inhibitor for slowing down only a single step in the process...


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Understanding different genetic terminology - Genotype vs SNP
I recently came across a study that refereed to variations in genes like this:
IGF1 (CA)19/(CA)19, IGF1(CA)19/X, IGF1 X/X
(From this study: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3274549/)
I wanted to know, as a member of 23andme, how I could check these "markers" (?) against the SNP's listed in 23andme.
I would be very grateful for any help.
Thanks.

Here are list of tools that you can use now that you have you DNA raw data: https://www.xcode.life/23andme-raw-data/23andme-raw-data-analysis-interpretation/

The "IGF1" at the front indicates that the genetic variation is in the gene for Insulin-like Growth Factor 1. The notation (CA)n is used to describe n adjacent repetitions of the two-base sequence CA (Cytosine, Adenine) present in a particular IGF1 DNA sequence. Hence IGF1 (CA)19 / (CA)19 is referring to a genome in which both copies of the IGF1 gene have 19 adjacent repetitions of the CA pair of bases, that is, which is homozygous for IGF1 (CA)19.
Such a repeat is usually called a microsatellite or Short Tandem Repeat (STR). They are common sources of variations in genes because the DNA matching process during meiosis sometimes "slips" one or two repeats over.
The type of test performed by 23andMe reports values for selected SNPs (Single Nucleotide Polymorphisms).  SNPs are a different kind of variation from STRs, so the data available from 23andMe does not allow you to determine the kind of IGF1 (CA)n variant present.

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Difference between modules in KEGG Module
The KEGG module M00115 includes a set of reactions while M00542 does not have any; it just shows the list of enzymes. Is the reaction set for M00542 still unknown?

Module means, as defined in the KEGG Module page, a functional unit. So it can be anything, from groups of enzymes to genes to metabolites. About the two that concerns you:

Pathway modules represent groups of functionally related enzymes part of the metabolic network. I think this one is easy to understand because it represents the classical understanding of "module". The modules involve metabolites (compounds with id starting with "C"), enzymes (represented by KEGG ortholog ids starting with "K") and reactions (represented by ids starting with "R"). The reactions integrate compounds and enzymes in a particular step in the chain of reactions included in that module.
Signature modules represent molecules associated with a particular phenotype. In particular, the example listed in the KEGG page points to EHEC pathogenicity signature, Shiga toxin. The two molecules in module M00363 are associated with the phenotype, which is in this case EHEC pathogenicity. But in principle they do not necessarily need to be related to each other (in this case they are, but not in the same meaning as the metabolic module).

In your particular examples, M00115 is again a pathway module including enzymes, compounds and reactions, all connected in an integrated manner. Module M00542 on the other hand shows the proteins part of the T3SS (Type three secretion system) used by Gram-negative bacteria for infection. These are not enzymatic reactions, just proteins associated with the EHEC/EPEC pathogenicity phenotype. They are however related in that they form a protein interaction complex that mediates infection.
Other Module categories include:

Structure complexes related to molecular machineries.
Functional sets seems like a miscellaneous category.

You could argue that the T3SS is a molecular machine and should be classified in the Structural complexes category. Indeed, something important to remember is, as stated in the KEGG module's page:

KEGG MODULE is a collection of manually defined functional units [...]

As anything manually defined, there is some degree of arbitrariness. Use the information in KEGG modules as far as it serves your needs, but it would be better not take it as written in stone.

M00115 is a pathway module (NAD biosynthesis) whereas M00542 is a signature module (EHEC/EPEC pathogenicity signature).
From the KEGG page on modules:

pathway modules – representing tight functional units in KEGG
  metabolic pathway maps, such as M00002 (Glycolysis, core module
  involving three-carbon compounds)
signature modules – as markers of phenotypes, such as M00363 (EHEC
  pathogenicity signature, Shiga toxin)

Can you please explain the difference? The reaction for the M00542 is unknown right?

what is meant by signature module?

@Rishika I have mentioned in the answer what signature module means. It does not have reaction pathways. It just has a set of biomarkers for a phenotype.


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Why is there a compound highlighted in red in a KEGG Module search?
Considering the following module:
http://www.kegg.jp/kegg-bin/show_module?M00115+C00003
why is the compound C00003 marked in red?

It is just a way of highlighting your search term. If you search M00115+C03722, you will see C03722 in red.

where did you search using this syntax?

@Rishika On the browser address bar. You can also do that by going to the KEGG home page and searching.

no data found, did you use this exact syntax " M00115+C03722" ??

@Rishika Just click on the link. If you want to see the actual link just right click and select "copy link location". The syntax is same as the link you posted in the question. I just replaced C00003 with C03722.


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How to calculate the Jaccard index
I want to calculate the Jaccard index between two compounds. What is the algorithm? I have searched for it, it just gives the formula but how to apply it on compounds is not known to me. Can you help?

Exactly how do you want to use it? In ecology, it is usually used to compare how similar communities of species are, but you are referring to only two compounds. What entities do you want to compare? As for coding it, you could probably find much useful information in the currently 345 StackOverflow questions on the Jaccard coefficient/index

I missed the detail about "two compounds". My answer includes a reference for two sets of compounds but it would be good if you clarify what you mean exactly.

How do you denote a compound? just by its composition?? For e.g. C₃H₆O₃ can be lactic acid, glyceraldehyde or trioxane.

Yes, denote a compound by their atoms that consists them..

or by SMILES format

The Jaccard index is a measure of similarity between two sets. Take a look at the Wikipedia article here. It is very easy to compute:
The Jaccard similarity coefficient for sets X and Y is defined as:
J(X,Y) = |intersection(X,Y)| / |union(X,Y)|

Where | | indicates the size (number of elements) of the set. Imagine you have two sets X and Y defined as follows:
X = {A, B, C, D}
Y = {C, D, E, F, G}

Then:
intersection(X,Y) = {C, D} => |intersection(X,Y)| = 2
union(X,Y) = {A,B,C,D,E,F} => |union(X,Y)| = 5

Therefore: J(X,Y) = 2/5
Alternatively, the Jaccard distance would be D(X,Y) = 1 - J(X,Y) = 1 - 2/5 = 3/5
In Biology the Jaccard index has been used to compute the similarity between networks, by comparing the number of edges in common (e.g. Bass, Nature methods 2013)

Regarding applying it to compounds, if you have two sets with different compounds, you can find how similar the two sets are using this index. The elements on the sets, in this case the compounds, correspond to A, B, C, etc. in my example.

chemical compounds would have atoms, so basically for each compound we create a set of atoms and then find the index. Will that do?


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Visualizing GFP in transgenic rice seeds?
I want to express GFP in rice as a method for differentiating transgenic from non transgenic rice seeds. I want to know if I can visualize them using a hand held UV lamp as the GFP I will be using has a excitation maxima at 395nm. If yes, how is to be done? Do I just flash the UV lamp on the seeds in the dark room and I can see the GFP expressing seeds glowing green?

I don't know about GFP in rice, but I've made GFP expressing bacteria, and they glowed ok on a UV tansluminator usually used for DNA gels. The RFP colonies I made were visibly red even without UV, but glowed good too. A simple UV transluminator would probably be fine, and you should have one for working with DNA anyway.

395 nm is not quite UV, so if you're not getting a strong enough signal (depending on the exact wavelength your transluminator emits, and the excitation profile of your protein), you could try using a purple light bulb. You can sometimes find them in big-box home centers like Home Depot, Lowes, etc., and you should also be able to find them at party stores. BTW, are you using GFPuv?

I am using mgfp5, optimized for plant expression which has excitation maxima at 395nm and 473-477nm(blue).What should I do?


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Do I have to use sucrose to induce a lac promoter?
I'd like to optimize the expression of a Fab fragment in Escherichia coli.
For induction of the lac promoter on the pAK400 vector I use IPTG and sucrose. Do I optimize the expression in case I would just add IPTG?

You can induce the lac operon by two things: Lactose (or more precisely Allolactose a metabolite of it) and lactose analogons which are not metabolized by the bacteria.
Lactose induces the expression and is metabolized while IPTG is not a target of the $\beta$-Galactosidase and will give you a strong and permanent induction. Sucrose will not have any effect on the promoter.


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How to estimate a genome's size?
The genome size of human is 3.000.000.000 bp and for Arabidopsis it is 255.000.000 bp. I know these numbers because their genomes have been published. Which methods are used by scientists to estimate the genome size before they sequence that genome?

A rough estimate can be given using gel/electrophoresis on different chromosomes.

Can U explain more or insert a protocol link, please?

More details and links may help you get better answers.

This is rather broad as there are many ways to do it. I'd speculate that reassociation kinetics was one of the first methods used.

this link from NAR is good but I am looking for an up to date review. http://nar.oxfordjournals.org/content/31/10/e56.full

Gel electrophoresis is a basic lab method to get size info about nucleotide fragments, although one might need to chop up larger DNA to be able to apply this method. The wikipedia page covers the topic well, thus I'd suggest reading it. I'll just give a short outline:

Nucleotide fragments are loaded into a gel (agarose or acrylamide).
The gel is put into a static electric field
Nucleotide fragment move to the positive end, because they have negative charge
larger fragments migrate slower than smaller fragments
standardized DNA ladder can be used to get approx size.

UV fluorescent dye is used to stain the fragments.
Another way, is to check closely related species. Among closely related species it is a fair assumption that they have similar genome size. You can also hybridize the unknown DNA to a DNA of such close relative to see how much of them are similar and you can also make estimates based on the size of the hybridized regions.

Thank you. even I think both methods are not sensitive enough

I find this link: http://nar.oxfordjournals.org/content/31/10/e56.full But I think there most be some better and easier ways.

Well, I just gave some examples, there are many methods if you look around :) Without knowing how much knowledge do you already have, I've tried to give the simplest examples and explanation.

General agarose gel electrophoresis for DNA can not tell chromosome length because it is too big to run. It is tough to run DNA having length more than 100kbp, which is too short to estimate the length of chromosomes. Then how can you tell the chromosome length?

Another way is to digest the DNA and measure the total nucleotide content. I think that's how earlier experiments were done.

In the absence of molecular sequencing data the most accurate estimates are based on reassociation kinetics, more commonly known as Cot curves. Here is a classic paper from 1974 that describes the basic approach. While pulsed field electrophoresis can be used to resolve the chromosomes of species with relatively short chromosomes (like baker's yeast), there are really no suitable size markers that you could use to construct a standard curve for size estimation. C. elegans has six chromosomes, but they are all fairly close to each other in length, and the genome size of 100 Mb is the same as a single long human chromosome.

I guess you could estimate the length various ways. Pulse field electrophoresis could show DNA length, but you need a standard.
When you combine Karyogram and FISH, you would could make a map. By genetical approaches, you could estimate distance on the map by centimorgan. Then you could know how many centimorgan chromosomes are. One centimorgan would be 1 million base pairs.
Oh, I forgot the simplest way. For example, take 1 million cells and estimate how many grams of DNA there.

" One centimorgan would be 1 million base pairs." That is false. Centimorgan is based on recombination frequency and can be very very variable between species (your info is only true for humans at best). It is not an actual distance between genes.

@canadianer I know, my last comment became obsolete after the edit...still that is a very rough estimate in my opinion.

I was not able to tell you I edited. About centimorgan, you can not apply human results to others, but you can apply the methods as they do with human chromosome. And DNA amounts would be a very rough estimation , but I do not know how exactly MySky want to estimate. Rough estimations are still estimations.


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Why do human ears have a lower boundary for the lowest energy perceivable signal than eyes?
I am currently hearing a lecture about human machine interaction. The lecturer is not a biologist (neither am I, we are both computer scientists), but he makes some statements about biology which I think are questionable.
One statement was that the energy of the lowest perceivable signal for eyes is  and the energy of the lowest perceivable signal for ears is . He cites those values from the following (German) source:

Schmidtke, H. et al. Handbuch der Ergonomie mit ergonomischen
  Konstruktionsrichtlinien und Methoden. Koblenz: Bundesamt für
  Wehrtechnik und Beschaffung (BWB)
HdE (2002): 2.4.1, Abb. 2
[KIT-Bibliothek: 2007 E 1808-1(2) (Präsenzexemplar)]

It is clear that those values vary from person to person. Assuming they don't vary too much, it is interesting to know why the human ear can detect signals with lower energy than the human eye.
According to my lecturer, the reason is because we can hear in all directions, but see only in one direction. He argues that hearing is much more important for this reason to detect predators, even if they are silent.
However, this argumentation seems very weak to me. I would rather think that there is a range in which "interesting" signals occur. If the interesting signals have lower energy for sound than for visual signals the ear adapted to this range.
I guess if the hypothesis of my lecturer is correct, then animals which can see in all directions would (always / very often) have much worse ears. If my hypothesis is correct, then there would be no significant difference in animals with "panorama-vision" and animals without in terms of lowest perceivable energy for ears and eyes (assuming fair comparisions; unfair would be comparing fish with land animals as the medium might play a big role).
Is there any source (written by somebody from biology, not form computer science) which makes a claim about this question?

Isn't this comparing apples and pears? Electromagnetic stimuli and vibrational stimuli are not in anyway comparable. The first are, arguably,  considered to be energy packets (photons) while the latter are transient air pressure differences.

@ChrisStronks That was another concern I had. I will ask him next week.

@ChrisStronks You could calculate the energy required to make a minimum audible air pressure difference and minimum visible number of photons. Maybe that's what going on here, even though it doesn't make sense to compare them.

@user137- of course both visual and acoustic stimuli at threshold contain a certain amount of energy that can be calculated. But it is comparing apples and pears as they are totally different physical stimuli.

The hypothesis about seeing in all directions is not correct.  Horses, for instance, have a nearly 350 degree field of view, with as good or better visual acuity than humans (though limited depth perception), and much better hearing than humans.  They can also rotate their ears for directional hearing: http://www.extension.umn.edu/agriculture/horse/care/horse-hearing/

Does the citation provide the confidence interval? It may well be the case that even though the average threshold energy for hearing is lower, the mode is higher.

Preamble. There is a lot of misunderstood science here and you are more than right for questioning the lecturers interpretation of these energy values; something the other answers do not discuss. The problem arises from a dodgy reference and a lot of conjecture.
In summary.

Light and sound cannot be compared energetically in a biological context.
Our ears probably don't hear lower energies than our eyes see to avoid prey.

Let us ignore the reference...
The reference is from BWB which is as far as I can tell a non peer reviewed federal technical publisher and that this is a textbook about ergonomics. But given its obscurity, it having never undergone peer review, it being not biologically scientific, it is safe to ignore from the context of a scientific biological topic. The fact it is in German doesn't help either.
If anyone can provide an open link to this reference or correct me on this I would be grateful. Google scholar turned up no hits other than a citation.
Let us give your lecturer the benefit of the doubt. This answer assumes that there are derived energy values for sight and sound as your lecturer suggested and that eyes sense higher energy than ears.
Is hearing omnidirectional to detect predation?
I'm going to use the term sensory setup to describe that our senses use fixed ears that hear omnidirectionally and forward facing directional eyes.

... hearing is much more important for this reason [omnidirectional] to detect predators, even if they are silent.

Let's flesh out this hypothesis so that it makes sense in practical terms.

A small movement is made by the predator. This generates some sound and some change in light. In the case of forward sighted animals, the sound is much more difficult to detect than the light would be as it contains less energy. The ears must compensate by detecting lower energy signals than the eyes would need to in order to detect the predator.

Before we question the physics, this biological hypothesis is very tough to swallow. Without citation I would say it is unreasonable conjecture.
Examples that contradict this hypothesis:

Gorillas have no natural predators or prey but have a very similar sensory setup to ours that helps social bonds.

Meerkats on the other hand rely on sentries that broadcast a series of bleats after spotting prey by sight. Other meerkats immediately hide when hearing this signal (interestingly, this call is mimicked by Drongos who steal the meerkat food that is abandoned in the panic) before checking if a predator is present. Meerkats have a similar sensory setup to ours.

There are other megafauna like deer that are prey for the big predators; predators that would have put ancestral humans on the menu. Deer-like prey animals rely heavily on near-omnidirectional eyesight and can angle their ears to focus on an area to hear stealthy predators. This is the "opposite" sensory setup that has the same conclusion of predator evasion.

Even those non-exhaustive examples makes the hypothesis questionable at best.

...there is a range in which "interesting" signals occur. If the interesting signals have lower energy for sound than for visual signals the ear adapted to this range.

This answer too is based on pure conjecture it seems, however it more aligns with how biology might work.
It is sensible to say evolution selected for animals that could detect noises and lights that, if reacted to, saved the organisms life to continue propagating. This hypothesis bypasses the idea that sound and light are comparable energetic signals too, which is good (discussed below).
This hypothesis also allows for various morphologies to have evolved depending on what an "interesting signal" is to that species.
Light vs Sound.
These aren't the same thing.
The elephant in the room of this question is that light and sound are non-comparable energies. This is due to source, speed, distance, medium, mechanisms for receiving the energy (eyes and ears) and most significantly in a biological context neural interpretation. These values are so abstract that even if an energy value is calculated, it is not in anyway quantitatively comparable in biological organisms. For example a really loud subsonic whale call is not the same as a small change of grass parted by a wolf as it sneaks up on you. One is absolutely essential for survival, the other is undetectable. Both could theoretically have the same "energy".
Note Frequencies are the biologically important part of the "energy" but must be considered as two different methods of acquiring sensory information. The difference between a chimp mating call and a territorial threat are very similar but for their frequency, and eating the delicious red berries compared to the toxic blue berries is also down to the frequency reflected from them!
There is little to no biological literature that uses energy values as sensory input. This would just obscure the actual important physical aspects of the sensory input values.

I hope that helped clear things up and accurately discussed your dis-satisfaction with your lecturers' hypothesis despite being months too late!

I can't check the sources, but I think they must estimate the relative energy of a threshold-sensitivity signal. I don't think the energy of a sound wave can be assigned an arbitrary value the way a photon can...certainly only a photon can propagate in a vacuum...
Both light and sound waves scatter less, as they propagate, if they're higher frequency/energy. So all things being equal blue light scatters less than red light, and ultrasound scatters less than infrasound. So audible sound is less directional than visible light, and any sound receptor provides information that is less directional compared to any light receptor. So of course sound's a good thing to pick up for alert signals, that doesn't really mean it's been prioritized over vision through evolutionary processes.
Since most of vertebrate evolution occurs in the ocean, where sound and light propagation are quite different than in the terrestrial milieu, the lecturer's conjecture is likely irrelevant. Our sense organs are far more influenced by their evolutionary history than considerations of "best possible" (globally optimal) function.

Audible sound is less directional than visible light? This does not make sense. The scattering you mention may add some noise, but sound is highly directional and the auditory system is remarkably well equipped to localize sounds horizontally and vertically. Furthermore, if you refer to hair cells with 'sound receptors' than they not only have little directional sensitivity, they have none. Photoreceptors, due to their retinotopical organization, are directional, but only in the field of view. In contrast, we can localize sounds from behind. Your arguments don't make sense.

Yes, sound is less directional than light, comparing audible sound and visible light. Sorry this doesn't make sense to you. Maybe another commenter can suggest a better way to explain this.


text:
How do antioxidants affect human metabolism?
I'd like to know how antioxidants affect human metabolism and which ones are essential for metabolic processes.

This mainly depends on which kind of antioxidants you're talking about.

Vitamin A and E are antioxidants acquired from the food
Superoxide dismutase, Catalase and the Glutathione system are enzymes produced by the cell.

Antioxidants keep the oxidative balance of the cell and quench free radicals which are generated by the mitochondrial respiratory chain. Very simplified: Antioxidants are thought to be anti-ageing compounds because free radicals destroy cellular compounds, which can be related to the ageing process.
I would be very careful with products claiming to contain antioxidants and be therefore anti-aging. This whole anti-ageing marketing is far from being scientifically proven.

so in answer to the OP, the antioxidants don't affect metabolism per se, but they are required for 'normal' functioning of a cell over a prolonged period of time, otherwise the cell would get damaged by free radicals? Which particular ones will likely be tissue/context specific I guess?

The last question is not so easy to answer and AFAIK unknown. The first question is right, it's more on the cellular level.

@zenbomb is right. The essential exogenous antioxidants are vitamins. How they, and the non-essential ones affect the metabolism is an active area of research. zenbomb is especially right to warn you against commercial products (or particular foods) claimed to have health benefits.

Anti-oxidants affect human metabolism by altering the redox states of the cell and redox-regulated functions and signaling mechanisms.
The following quotes are from The Redox Stress Hypothesis of Aging (Free Radic Biol Med. Feb 2012)

More recently, in a major conceptual shift, ROS have been found to be
  physiologically vital for signal transduction, gene regulation, and
  redox regulation, among others, implying that their complete
  elimination would be harmful. An alternative notion, advocated here,
  termed the "redox stress hypothesis," proposes that aging-associated
  functional losses are primarily caused by a progressive pro-oxidizing
  shift in the redox state of the cells, which leads to the
  overoxidation of redox-sensitive protein thiols and the consequent
  disruption of the redox-regulated signaling mechanisms.

Many proteins contain cysteine residues which can undergo reversible modifications such as S-nitrosylation and S-glutationylation.
The redox state affects the oxidation levels of these redox-sensitive protein thiols and the consequent disruption in protein activity and the redox-regulated signaling mechanisms.
Under normal conditions the usual types of oxidation modifications of these protein thiols are reversible, and is a way to protect the thiol in transient periods of oxidative stress.
When the redox state shifts to a more oxidised point then more irreversiable protein thiol modifications occurs, i.e. damages the protein.

As shown in Figure 6, prolonged exposure of sulfenic acid, formed at
  the active or regulatory sites, to H2O2, sequentially leads to the
  formation of sulfinic- (−SO2H) and sulfonic-acids (−SO3H), which are
  deemed to be largely irreversible reactions. In addition, protein
  disulfides may undergo over-oxidation, leading to the formation of
  thiosulfenate and thiosulfonate, which are also believed to be
  relatively irreversible reactions. The level of oxidation of protein
  cysteinyl thiolates depends upon the strength (concentration) and the
  duration of exposure to H2O2.

Protein activity and enzyme catalytic efficiency which affects metabolism, such as sirtuins, are affected by the these thiol redox modifications.
(eg SIRT1 is a redox-sensitive deacetylase that is post-translationally modified by oxidants and carbonyl stress and A redox-resistant sirtuin-1 mutant protects against hepatic metabolic and oxidant stress.)
The primary arbiter of redox state is glutathione, i.e. the GSH/GSSG couple. The effect of anti-oxidants appears to vary depending on whether it affects the redox state.
The antioxidant activities of SOD and catalase neutralize the ROS species, O2− and H2O2, without having a direct impact on glutathione redox state.  However this frees up glutathione from having to neutralize the ROS species, which it can do so with the glutathione peroxidase enzyme.


text:
Why do neurons have only one axon?
I have just learnt about neurons. I wonder why neurons have only one axon. Can they transmit nerve impulses faster and more rapidly when they have more axons? Does having more axons help in coordination?
Could anyone tell me why neurons have only one axon?

"Technically", not always true...
http://www.psyweb.com/Physiological/Neurons/NImages/Unipolar.gif

are you considering multiple axons that transmits a single (synchronized) action potential? Or multiple action potentials generated at separate axon hillock?

i saw from a website that mentioned that "each neuron has only one axon" but i didn't understand why.

http://www.csuchico.edu/~pmccaffrey/syllabi/CMSD%20320/362unit12.html paragraph 7

Perhaps it's to do with the timing and energy of the ion flow in the Neuron, because the cell hasn't got the flexibility to efficiently manage two axon timing and energy potential with as much precision and power as two cells with one axon. After all, with millions of neurons to coalesce into systems, flexibility is there, added flexibility would be redundant and efficiency of the individual building blocks is necessary.

Neurons generally have one axon, because of the way it sums potentials from its dendrites. Right at the axon hillock (the little area where the axon protrudes from the soma), all the potentials are summed together. Now, you have to consider that what is actually summed here is dependent on the shape of the neuron, potentials lose amplitude as they travel towards the axon hillock. If there were multiple axons protruding from different sites, they would send out different signals and compromise the computational integrity of the neuron.
Instead of having multiple axons, a neuron simply branches its axon with axon collaterals. This way, all post synaptic sites are receiving virtually the same message.

I think during the early evolution of nervous systems it was very important to have long axon cells. For example a worm has 3 giant axons which are almost the same length than the worm itself. So there was selection pressure on the length of the axon. The neuron requires a lot of energy to send signals to other neurons. Neurons use energy on nanowatt scale, average human cells use energy on picowatt scale... By long axons it requires less energy to send the message through a single axon than send it through multiple axons. That's the same why we use limited amount of undersea internet cables - currently about 200. If there is more data than a single cable can handle, only then lay we a parallel cable. So a possible answer is evolution of worm nervous systems combined with energy consumption optimization.
Another answer can be that neurons would be never capable to build multiple action potentials parallel. Maybe they cannot consume enough energy to hold charges separated by multiple axons. I don't intend to look for the details of that. It is technically possible to have neurons with multiple axons, so you can grow things like that, but it is not clear if their axons can work parallel or not, and if they don't work parallel does they interfere the communication of each other.
About single axon neural networks there are existing mathematical models. Until there is no mathematical model how a neural network with multiple axons would work, or there is no evidence of it is not possible to build such a thing, you cannot say for sure that it is because of the mathematics of neural networks.
So I have this 3 theories. I think you can find more about this topic by googling a lot, and making new experiments. For me it was enough. :-)


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Fate of erythrocytes after splenectomy
The spleen is considered a graveyard for red blood cells. So in case of Splenectomy (complete surgical removal of the spleen), what would be the fate of red blood cells? Would this cause Polycythemia?

The spleen is not the only organ which removes "old" erythrocytes, this happens as well in the liver and the lymph nodes. The whole process is termed Eryptosis, the Apoptosis of Erythrocytes. During the aging of erythrocytes sialic acid on their outer membrane surface is removed. This leads to the recognition by macrophages and phagocytosis of this cells by macrophages which are located in liver and spleen. For more information see this article: "Physiology and Pathophysiology of Eryptosis"
Polycythemia is the state when you have an elevated number of red blood cells, characterized by an increased Hematokrit level. This is caused by the over-production of red blood cells, which can be caused by an overproduction of hematopietic cells in the bone marrow (so called myeloproliferative syndrome, which are basically cancers), the exposure to permanently low oxygen-levels (this is what athletes exploit when the do training at high altitudes) or malignancies (usually lymphoma). It is also possible due to the mis-use of Erythropoietin (EPO) which induces the production of red blood cells. Another possibility for having too much red blood cells is the over-transfusion during a blood transfusion. For further information have a look into the Wikipedia. The article there is pretty complete and contains a number of references.

Lymph nodes do not play a role on RBC destruction. There are no red cells in lymph. Nor does your article support it.

When you downvote, could you please make a short comment about your criticism? Only then answers can be improved. Alternatively you could write an own (and better) answer.

So in case of Splenectomy (complete surgical removal of the spleen),
  what would be the fate of red blood cells? Would this cause
  Polycythemia?

According to wikipedia none of the side effects are related to red blood cell count (just the quality of those cells).

As splenectomy causes an increased risk of sepsis due to encapsulated
  organisms (such as S. pneumoniae and Haemophilus influenzae) the
  patient should receive the pneumococcal conjugate vaccine (Prevnar),
  Hib vaccine, and the meningococcal vaccine; see asplenia. These
  bacteria often cause a sore throat under normal circumstances but
  after splenectomy, when infecting bacteria cannot be adequately
  opsonized, the infection becomes more severe.
An increase in blood leukocytes can occur following a
  splenectomy.2 The post-splenectomy platelet count may rise to
  abnormally high levels (thrombocytosis), leading to an increased risk
  of potentially fatal clot formation. There also is some conjecture
  that post-splenectomy patients may be at elevated risk of subsequently
  developing diabetes.4 Splenectomy may also lead to chronic
  neutrophilia. Splenectomy patients typically have Howell-Jolly
  bodies5 and less commonly Heinz bodies in their blood smears.7
  Heinz bodies are usually found in cases of G6PD (Glucose-6-Phosphate
  Dehydrogenase) and chronic liver disease.8

wikipedia - Splenectomy

Splenectomy can be recommended by inherited blood diseases (e.g. hereditary spherocytosis, thalassemia, etc...) which cause anaemia due to the destruction of abnormal red blood cells in the spleen. After surgery the RBC count is around normal in these cases, so removing the spleen does not cause polycythemia. If you check wikipedia - polycythemia, splenectomy or other spleen related diseases do not cause polycythemia, while polycythemia can cause enlarged spleen which may be removed.
Erythropoiesis and so red blood cell count is regulated by EPO which is regulated by blood oxygen level, so spleen does not regulate the production of red blood cells directly. Removing the spleen cannot cause upregulation of EPO and so polycythemia. Mean erythrocyte age is increased, so in long term there can be a slight increase of RBC count because of a function loss by old cells, but that is not significant enough to cause disease.

2010 - Partial splenectomy for hereditary spherocytosis: a multi-institutional review
2014 - The spleen and sickle cell disease: the sick(led) spleen
2013 - Red blood cell vesiculation in hereditary hemolytic anemia
2007 - Erythropoietin after a century of research: younger than ever
1982 - Glycosylated hemoglobins (GHb): an index of red cell survival.

To support the speculation that macrophages might also have a function
  in erythropoiesis in the context of disease and to further
  characterize their importance in erythropoiesis in vivo, Ramos and
  colleagues show that macrophages regulate erythroid development in
  polycythemia vera, β-thalassemia and anemia (Ramos et al., 2013).
  Chemical depletion of macrophages by clodronate liposome
  administration prevents mice from recovering from induced anemia,
  suggesting an essential function of macrophages in promoting stress
  erythropoiesis in vivo. Conversely, macrophage depletion not only
  improves the phenotype of polycythemia vera and reverses the
  pathological aspects of the disease, but also alleviates anemia caused
  by β-thalassemia. These results propose an important dual role of
  macrophages in physiological and pathological erythropoiesis in vivo.
  Both studies suggest that macrophages exert two seemingly
  contradictory actions on erythropoiesis. On one hand, macrophages are
  indispensable for stress erythropoiesis in vivo. In their absence
  erythroid production in the bone marrow and spleen in response to
  bleeding is impaired. However, macrophages can also be deleterious in
  the context of polycythemia vera and β-thalassemia, since depletion of
  macrophages leads to a decreased disease pathology. Moreover, ex vivo
  cultured human macrophages from polycythemia vera patients promote
  proliferation of human erythroblasts and diminish differentiation.
  This suggests a function for macrophages in disease progression since
  polycythemia vera is characterized by an overactive erythron and
  excessive erythropoiesis (Ramos et al., 2013). These findings might
  pave the way to future therapies implementing macrophage depletion in
  the treatment of erythroid disorders like polycythemia vera and
  β-thalassemia.

2014 - Review article of macrophages and red blood cells; a complex love story

Recovery after surgery is about 4-6 weeks. Liver and lymph nodes can take over the functions of the spleen partially. Every blood cell count may be elevated (esp. platelet count). The functions of the spleen are:

storing iron (in the form of ferritin or bilirubin, to protect it from pathogens)
storing blood (for the case of blood loss e.g. injury)
filtering out damaged or old blood cells (by inherited diseases abnormal red blood cells are removed from blood as well)
filtering out phatogens, infected blood cells, etc... (to protect the body from sepsis)

And ofc. a lot of immune cells live there. Therefore in rare cases sepsis can occur after splenectomy immediately, and can cause life threatening conditions.

2001 - Infectious complications in asplenic hosts
1996 - Overwhelming postsplenectomy infection
1975 - Immunological studies in the postsplenectomy syndrome
1995 - Preservation of the spleen improves survival after radical surgery for gastric cancer.
2009 - Effect of splenectomy on antitumor immune system in mice.
2012 - Thrombocytosis in asplenia syndrome with congenital heart disease: a previously unrecognized risk factor for thromboembolism.
2009 - Vascular complications after splenectomy for hematologic disorders
2014 - Review article of macrophages and red blood cells; a complex love story

Asplenic individuals are compromised not only in their ability to
  destroy infectious agents, but are at increased risk for death from
  autoimmune disease, certain tumors, and ischemic heart disease.
  Enhanced mortality is attributed to lack of phagocytes sequestered in
  spleen that efficiently engulf and destroy appropriate targets,
  although related cells are found elsewhere.

2012 - SIRPα/CD172a and FHOD1 Are Unique Markers of Littoral Cells, a Recently Evolved Major Cell Population of Red Pulp of Human Spleen
2011 - Splenectomy Associated Changes in IgM Memory B Cells in an Adult Spleen Registry Cohort

The spleen contains immune cells, from which macrophages phagocytose the senescent red blood cells. They degrade the hemoglobin into amino acids, bilirubin and iron. The iron is sent to the blood with transferrin, which can be captured and stored by the spleen or the liver or can be used to build new red blood cells in the red bone marrow. The amino acids can be used to build new proteins or they can be degraded by the liver or the kidney. The bilirubin is transported to the liver where it is conjugated and excreted into the bile. The other parts of the red blood cells are recycled as well. For the macrophages it is easier to do this kind of work if you have a dedicated organ which can help to filter out the cells for destruction, but it is not impossible without it, because macrophages live in other organs/tissues as well.
Red blood cells can get rid of damaged parts by creating microvesicles so they can elongate their lives. Vesiculation is facilitated by the spleen. These microvesicles can contain hemoglobin as well, and they are captured by the liver.

2004 - The red cell revisited--matters of life and death.
2008 - Microvesicles in haemoglobinopathies offer insights into mechanisms of hypercoagulability, haemolysis and the effects of therapy
2003 - Hemoglobin loss from erythrocytes in vivo results from spleen-facilitated vesiculation
RBC Storage
2008 - RBC-derived vesicles during storage: ultrastructure, protein composition, oxidation, and signaling components.

The macrophages of the spleen have a remarkable function that enables
  them to remove unwanted damage from the RBC membrane, leaving the RBC
  intact (Crosby, 1957; Schnitzer et al., 1972). Removal of these
  intracellular inclusions seems to occur within the open circulation
  where the RBC are also checked for their loss of deformability to
  check for age. To achieve this, RBC must pass through the endothelial
  slits of the sinus to reenter the blood circulation. During this
  course, cells that are non-deformable will be removed from the
  circulation by residential macrophages. In the mean-time all inclusion
  bodies are also being removed. In splenectomized patients or in
  patients with a non-functional spleen, phagocytosis of the inclusion
  bodies fails and results in a retention of a variety of intracellular
  inclusions within the RBC, such as Howell-jolly bodies (inclusions of
  nuclear chromatin remnants) (Wilkins and Wright, 2000), Heinz bodies
  (inclusions of denatured hemoglobin caused by oxidative damage)
  (Wilkins and Wright, 2000) siderocytes (RBC containing granules of
  iron that are not part of the cell's hemoglobin) (Wilkins and Wright,
  2000) and Pappenheimer bodies inclusion bodies formed by phagosomes
  that have been engulfing excessive amounts of iron (Wilkins and
  Wright, 2000).
The molecular mechanism that underlies the removal of inclusion bodies
  is largely unknown. In Willekens et al. (2003) presented an analogy to
  the removal of Heinz bodies when discussing RBC that lose hemoglobin
  through vesiculation. Via the process of RBC vesiculation the RBC
  loses aggregated hemoglobin, which is important to maintain the
  homeostasis of RBC, increases in density and becomes smaller (Piomelli
  and Seaman, 1993). It was suggested that this process is also
  facilitated by the macrophages of the spleen, in which older cells
  vesiculate more than younger ones. Clearly, macrophages play a pivotal
  role in the clearance of damaged content from circulating RBC (Crosby,
  1957; Willekens et al., 2003) and vesiculation is an interesting and
  plausible mechanism to explain the efficient removal of damaged
  content while leaving the RBC intact (Wilson et al., 1987). The
  molecular mechanism by which macrophages in the spleen would be
  facilitating RBC vesiculation is still unknown.

2014 - Review article of macrophages and red blood cells; a complex love story

Aged or abnormal red blood cells with exposed phosphatidylserine
  (PS-RBCs) are cleared from the circulation by splenic macrophages. In
  asplenic patients, other mononuclear phagocytic cells in tissues and
  in circulation may function in this capacity.

2010 - Activation of mononuclear phagocytes and its relationship to asplenia and phosphatidylserine exposing red blood cells in hemoglobin E/β-thalassemia patients

Suicidal death of erythrocytes (eryptosis) is characterized by cell
  shrinkage, membrane blebbing, activation of proteases, and
  phosphatidylserine exposure at the outer membrane leaflet. Exposed
  phosphatidylserine is recognized by macrophages that engulf and
  degrade the affected cells. Eryptosis is triggered by erythrocyte
  injury after several stressors, including oxidative stress.

2006 - Mechanisms and significance of eryptosis.

CD47 on erythrocytes inhibits phagocytosis through interaction with
  the inhibitory immunoreceptor signal regulatory protein alpha (SIRPα)
  expressed by macrophages. Thus, the CD47-SIRPα interaction constitutes
  a negative signal for erythrocyte phagocytosis. However, we recently
  reported that CD47 does not only function as a ‘don't eat me’ signal
  for uptake but can also act as an ‘eat me’ signal. In particular, a
  subset of old erythrocytes present in whole blood was shown to bind
  and to be phagocytosed via CD47- SIRPα interactions.

2013 - CD47 functions as a removal marker on aged erythrocytes
2013 - Mechanisms tagging senescent red blood cells for clearance in healthy humans
2011 - Physiologically aged red blood cells undergo erythrophagocytosis in vivo but not in vitro
2011 - Human red blood cell aging: correlative changes in surface charge and cell properties
2012 - Naturally Occurring Autoantibodies in Mediating Clearance of Senescent Red Blood Cells


text:
Gene duplication and subfunctionalization
I’ve been intrigued by gene duplication and want to learn more about it.
I’ve read the following from here:

several studies suggest that the proportion of duplicated genes
  retained in vertebrate genomes is much higher than is predicted by
  this model [4-6]. This has led to the suggestion of an alternative
  model whereby complementary degenerative mutations in independent
  subfunctions of each gene copy permits their preservation in the
  genome, as both copies of the gene are now required to recapitulate
  the full range of functions present in the single ancestral gene. This
  was formalized in the Duplication-Degeneration-Complementation (DDC)
  model [7] in a process referred to as subfunctionalization.

Can someone explain this?  What is meant by “both copies of the gene are now required to recapitulate the full range of functions present in the single ancestral gene”?
Can you suggest any other good articles on gene duplication?

I would interpret that to be a situation where a gene codes for an enzyme that does some necessary metabolic reaction that needs 2 steps, A -> B -> C. The gene gets duplicated, but in order to preserve both copies each copy needs to mutate. Let's say copy 1 can only do A -> B now, and copy 2 can only do B -> C. This means you need both copies to do A -> B -> C. Alternatively, copy 1 could still do A -> B -> C and copy 2 picks up a gain of function mutation that allows A -> B -> D or something. As long as D increases the odds of reproductive success the second gene copy is selected for.

Suppose a gene performs two distinct functions 1 and 2, both of which are essential. We'll call this gene A, for ancestral gene.
A duplication copies A to another locus. Now there are two genes, A and B, that perform the same two functions. At this point, if either A or B is deleted, the organism is fine.
Over evolutionary time, A and B undergo genetic drift to become A' and B', respectively. Let's say that B' loses function 1, and that A' loses function 2. This isn't a problem for the organism since A' still performs function 1, and B' still performs function 2. In other words, the two genes complement each other.
However, now A' can't be deleted without losing function 1, and, similarly, B' can't be deleted without losing function 2. The result is that both genes are fixed in the genome by evolution.
This means that now, after hundreds of millions of years of relevant evolution and genetic drift, we many duplications like A' and B'. The key to this is that through genetic drift with no selective pressure, it's very easy to lose function but extremely difficult to gain it.
As for your second question, I'll look for a paper on gene duplications that I think would be the most helpful, but there are many.


text:
How do animals handle light refraction in different media?
For a human, when diving underwater, everything is blurry because of the water's different refractive index compared to that of air, which we are accustomed to. How do animals, like turtles, seals or penguins, handle that difference when changing the medium? Are they nearly blind at surface and can focus underwater or the other way around? Can they adapt to different refractive indexes on the fly? How?

I guess that they are optimized for one particular environment. In the other they might have to rely on other senses.

It is more complicated than this, but... I don't think it has as much to do with the refractive index of water but rather the shape of our corneas and the loss of this shape advantage under water, for if the eyes are protected by goggles, one can see quite clearly underwater (much the same as a camera can, as the shape of it's lenses are not affected). Any change in the shape of the cornea changes the way light passes through the eye, and results in a change in vision. The following is from Ch. 9 Optics of the eyes of marine animals, from Light and Life in the Sea:

This is different for penguins (and turtles): the surface of their eyes, the cornea, is not as much vaulted as for humans (it's much flatter), and the lens is much rounder (meaning the shape can change more than our relatively flat lenses can), so the difference between air and water is not so big and the light isn't refracted too strongly. Also, the ciliary muscles (not to be confused with the pupillary muscles) holding the eye's lens (behind the pupil) are stronger, increasing their accommodation, so a penguin has a sharp sight in the water. Or as stated in A Survey of Vertebrate Strategies for Vision in Air and Water

Whereas the cornea is usually the major refractive element of the terrestrial eye, it is of little or no refractive consequence to an aquatic vertebrate.

See the difference in these four vertebrae groups (the first is man, the second is fish, the third is whales (similar to penguins) and the fourth is sirenians - manatees and dugongs)1:

Penguins.info
[1] Comparative anatomy and physiology of vision in aquatic tetrapods

This answer is great and seems feasible. Thank you!!! So in a nutshell: The effect of light refraction in different media is only a problem for beings with very convex corneas an flat lenses. Does this mean that e.g. Penguins have a sharp sight inside and outside of the water because of their ability to bend their lenses much more than humans could do. Thus, making their visual system far superior. Or are there some disadvantages with a flat cornea-design?

No, you have it precisely correct. Their lens does all the work. They can see well in or our of the water because their cornea has little to do with their vision.

Nice answer.. But the refractive index does have a role and the convexity of the lens as you rightly explained corrects for it. I had read about fish's highly convex lens but was not aware of diving animals having a flexible lens.


text:
Number of transcription factor genes in the human genome
What is the number of the transcription factor genes present in the human genome? Does this value differ compared to Mus musculus, Drosophila melanogaster, Arabidopsis thaliana, C. elegans and S. cerevisiae? Additionally, does the proportion change between eukaryotes and prokaryotes?

do you mean the number of genes? Or the proportion of TFs relative to something?

either the proportion of number of TF genes in the entire gene pool, or the number of TF genes and I can make the math myself

I slightly edited the question. It may be advisable to specify your model organisms as the 2nd question is very broad as of now. For example, name a few such as Drosophila, Canis, Arabidopsis or whatever suits your question.

There are some things to be clarified here. For example would you consider enhancer binding proteins such as C/EBPs or epigenetic modulators like HDAC as transcription factor. In any case you can look this up and unless more details are provided this question would be considered homework (It would take me the same effort as you to find out the answer. I would appreciate if you ask - "how to find out the number of TF", instead of the question as it is).

I meant DNA binding elements

I disagree with closing votes but agree the question could be narrowed down a little bit. For example, "DNA binding elements" may be certainly too broad. Also, assume by proportion the OP means the percentage of TF genes relative to total number of genes in each species. Disagree with changing the question to "how to find out the number of TFs"- thats a completely different question (but an interesting one, mind you).

"Also, assume by proportion the OP means the percentage of TF genes relative to total number of genes in each species" correct

Here I will assume we are talking about eukaryotic sequence specific transcription factors (ssTFs) and try to answer your first and part of the second question. There is in any case not definitive answer yet.
An estimate of ssTFs genes in humans is given in the 2009 Nature Reviews Genetics paper by Vaquerizas, JM et al, A census of human transcription factors: function, expression and evolution.
An excerpt from the abstract:

Here, we present an analysis of 1,391 manually curated sequence-specific DNA-binding transcription factors, their functions, genomic organization and evolutionary conservation.

The numbers are somewhat higher now. Wingender et al. have counted 1,558 human genes in their TFClass database 2013 NAR paper. In their 2014 NAR paper they included 1,557 human, 1,147 mouse and 1,105 rat orthologs.
Another way to look for this information is to see the number of entries listed in TF databases, like for example JASPAR. This has the advantage of including other species. However, the coverage here depends on the availability of position weight matrices (PWMs) for the binding specificities. Many uncharacterized TFs may not be found.

To try to answer your third question, that is, what is the proportion of TFs in the different species, a naive approach would be to divide the number of predicted TFs by the number of predicted genes in the target genome. For example, taking the latest estimates above with the predicted number of coding genes from Ensembl database (version 78) will return these percentages:
# Human
100 * 1557 / 20364 = 7.64%
# Mouse
100 * 1147 / 22606 = 5.07%
# Rat
100 * 1105 / 22777 = 4.85%

This suggests humans have a slightly higher proportion of TFs than rodents. However, these differences are not too big and may be dependent on the accuracy of the different estimates on TFs and gene numbers. An in itself, these numbers are not so interesting.
A much more interesting question is whether TF families have expanded more or less in different species (that is, whether the number of  proteins within each family has increased, regardless of the proportion to the total number of genes in the genome). I could find at least one paper where this has been done systematically for several eukaryotic species, covering animals, plants and fungi, and focusing on TFs common to the ones found in plants. The main conclusion of the paper is that some TFs families have expanded more in plants than in other organisms. Quoted from the abstract:

To investigate if differences exist in the expansion patterns of TF gene families between plants and other eukaryotes, we first used Arabidopsis (Arabidopsis thaliana) TFs to identify TF DNA-binding domains. These DNA-binding domains were then used to identify related sequences in 25 other eukaryotic genomes. Interestingly, among 19 families that are shared between animals and plants, more than 14 are larger in plants than in animals. After examining the lineage-specific expansion of TF families in two plants, eight animals, and two fungi, we found that TF families shared among these organisms have undergone much more dramatic expansion in plants than in other eukaryotes. Moreover, this elevated expansion rate of plant TF is not simply due to higher duplication rates of plant genomes but also to a higher degree of expansion compared to other plant genes.


text:
Why is the Krebs cycle considered a part of aerobic metabolism if molecular oxygen is not involved in any of the reactions in the cycle
Why is the Krebs cycle considered a part of aerobic metabolism if molecular oxygen is not involved in any of the reactions in the cycle?
I originally thought that Krebs cycle was aerobic metabolism because it is in the process that oxygen is the final electron acceptor, but my teacher claims that glycolysis is anaerobic so what makes the Krebs cycle aerobic?

Oxygen is actually not needed in the Krebs cycle - it is needed in the electron transport chain that is downstream of the Krebs cycle to regenerate NAD+ from NADH. NAD+ is a co-enzyme and acts as an electron carrier in oxidizing reactions at various positions in the Krebs cycle. However, note that without O2, NADH accumulates and the cycle cannot continue as it needs NAD+ to run.
Krebs cycle - No O2 needed:

Electron transport chain - O2 needed to regenerate NAD+ essential for the Krebs cycle:

Why is it often the case that krebs is considered to be the stage before the electron transport chain, if the krebs can't complete without the Electron transport chain completing?  And another question - since glycolysis requires NAD+ and NAD+ is produced by the electron transport chain, then if glycolysis uses the NAD+ from the electron transport chain, would that make glycolysis aerobic, and if so, then why is it considered anaerobic?

"... needed in the electron transport chain that is upstream of the Krebs cycle..." - "upstream" makes me think of the glycolytic pathway - which is not what the second figure shows, correct? Why isn''t it "downstream"?
Are there two contexts of "aerobic"? A. See answer: O2 is essential for  metabolisum, which is not the case in glycolysis? ATP in glycolysis is not produced by breaking down O2? B. in context of Warburg/cancer "aerobic" means that O2 does exist, is there (but not metabolized by the metabolism referred to by "aerobic" (glycolytic cancer cells).

@PeterBernhard - it should be downstream for sure thanks. Does that answer your question as well?


text:
Why proteinase K doesn't degrade itself?
Can anyone tell me why proteinase K doesn't degrade itself?
If possible please provide me the source.

Are you asking about in vitro or in vivo?

According to invitrogen proteinase K does undergo autolysis, but that some leftover fragments still have protease activity. The solution should be stored at -20C, this low temperature is probably the best way to prevent autolysis. If you're using the enzyme to digest protein at 37C, you'll just have to deal with losing the proteinase k during the reaction and make sure you add enough to destroy the target protein before the proteinase is depleted.

Proteinase K is sensitive for autolysis. The enzyme is stabilized by the presence of calcium ions (which bind to the protein). Absence of calcium promotes autolysis of the enzyme and also reduces the half life of the enzyme activity. The most likely reason why most researchers never notice an substancial effect of autolysis is that this takes around 48h to get noticed, while the most proteinase K digest take only a few hours. For details read the following paper:

The enzymatic activity of proteinase K is controlled by calcium


text:
Synthesis of immunoglobulin Fab fragments: Where can I learn about Fab?
I wanted to know the chemical reaction involved in Fab synthesis. I looked everywhere for it. No luck. I know I will find it here.
All I know for now is:
Fab is a monovalent fragment that is produced from IgG and IgM, consisting of the VH, CH1 and VL, CL regions, linked by an intramolecular disulfide bond.
Molecular basis of Fab will make more sense.

For the generation of Fab-fragments antibodies, (possibly genetically modified) which can be made in large quantities by cells or animals, are used. Antibodies as a whole are not synthesized.
The Fab fragment is obtained from antibodies using the enzyme papain, which cleaves the antibody over the disulfide bonds in the hinge region. This results in two Fab fragments (which contain the antigen binding sites) and one Fc fragment (which contains the constant region of the antibody). See the image (from here):

If you want to go further into the topic, read one of the references below.

Preparation and separation of Fab and Fc fragments from human
immunoglobulin G with papain digestion
Fragmentation of IgG Using Papain

FAbs are genetically engineered and not organically synthesized as such. This PNAS article nicely describes the construction of a phage (virus) library to generate a large amount of different FAbs and screen for FAbs with the wanted epitope (antigen) affinity: http://www.pnas.org/content/95/11/6157.short


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How to conduct PSI-BLAST for a given protein sequence against bacterial protein database only?
I have a list of 100+ proteins and I need to conduct psi-blast for each one of them against "bacterial proteins" only.
I went to NCBI's protein blast tool, but couldn't figure out how to select/limit the targeted database.
Here are the 2 configs I tried:

Database: pdb, Organism: bacteria (taxid:2)
Database: landmark, Organism: bacteria (taxid:2)

Can anyone tell me if either of the approaches is correct? If not, please point the right way.

Edit 1 - add more details
All of my data is from "Supplementary Table 10" of paper "Comparative genomics of the neglected human malaria parasite Plasmodium vivax".
About 5% of all my protein sequences are ISS predicted. Remaining sequences are IEA predicted

pdb only contains IDs with deposited structures. I have not heard of landmark, could you provide a link to it? I agree with @Michael_A that Uniprot is the way to go.

Your approach is correct but it is worth considering which database will work best for you. Questions to consider are;

Does the database provide a large search space for the organism(s) you're interested in?
Do its IDs work well for searching other databases?
How does the host database handle identifiers over time?

For protein sequences I would use;

Database; UniProtKB/Swiss-Prot(swissprot)
Organism bacteria (taxid:2) (or a subset)

The reasons for this are that I am comfortable with how Uniprot handles their ID's, they provide a large search space with includes clear delineation between reliable (reviewed) and other (unreviewed) sequences, and finally UniprotKB IDs map well to genes. The latter can be problematic. I also know that I won't have trouble searching PDB with UniprotKB IDs.
Despite using and liking the Protein data bank (PDB) I wouldn't use them for this kind of search as they are a structural database which reduces your search space. PDB has 8292 structures for E.coli compared to 23 017 reviewed and 1,335,860 unreviewed sequences in Uniprot. If you are only interested in structures then the PDB is an ideal fit.
I haven't used landmark.

I am looking for structural homology in bacterial proteins. Since you pointed out that PDB is a structural database, would that make it a better candidate?

I'd still use Uniprot as the uniprot IDs can be used to search PDB. However, you could do both. The only downside to Uniprot is that it will likely return a large list. Taking time to understand the structure of uniprot's holdings will help you to deal with that. If you can get away with reviewed sequences I'd stick with those.


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Why can't the immune system start at the mating time?
The immune system has a great role in our body. When foreign particles
enter our body, the immune system can recognize and start
defense mechanisms such as the complement system and others. But when sperm enters
into the female organism, why does her immune system not recognize this?
In that time which kind of mechanism is active in the woman's body?

The obvious, if simplistic, answer seems to be one of evolutionary exclusion.  If the female did develop an immune reaction to sperm, the individuals with this quality would not be able to reproduce, and the trait would die out.

These questions are not completely easy to answer, since the immune reaction in this area is not completely understood. There are two different mechanisms  which play a role here:
Semen is immunogenic and can cause the generation of specific antibodies against it in men and women. The main question here is if the presence of semen in the females reproductive tract is the consequence of a suppressed immune reaction or because it is not recognized. There are indications for both possibilities but I think the first is a bit stronger. The mucus from the vagina is immunosuppressive as well as the seminal fluid, which contains prostaglandins which have the same effect. Have a look at this article for some more background:

Sperm survival in the female reproductive tract: presence of
immunosuppression or absence of recognition?

For the situation in the uterus between mother and fetus the situation is better understood. This is the so called immune privilege of some tissues (among them are the uterus, testes and the eye) where immune reactions are suppressed.
The placenta forms an immunologic barrier which seperates mother and fetus. This is done by secreting immunomodulary substances and also by the subpression of some T cell subpopulations. For more details see here. This is a highly developed system to protect the developing fetus (which is foreign) from the mothers immune system.


text:
PDB file SEQRES have different data?
In PDB file, SEQRES represent the aminoacids but some pdb file present the "GLC" and some other.
for example
SEQRES   1 A   26  GLC GLC GLC GLC GLC GLC GLC GLC GLC GLC GLC GLC GLC
SEQRES   2 A   26  GLC GLC GLC GLC GLC GLC GLC GLC GLC GLC GLC GLC GLC
SEQRES   1 B   26  GLC GLC GLC GLC GLC GLC GLC GLC GLC GLC GLC GLC GLC
SEQRES   2 B   26  GLC GLC GLC GLC GLC GLC GLC GLC GLC GLC GLC GLC GLC

In that PDB ID: 1C58
What are this and What are represent the SEQRES?

The pdb file that you mention is entitled:

V-Amylose at atomic resolution: X-ray structure of a cycloamylose with 26 glucose residues (cyclomaltohexaicosaose).

So, it isn't a protein at all, it is a circular oligosaccharide consisting of 26 glucose (GLC) residues. I imagine that the usual fields in the pdb file have been fudged to accommodate this.

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


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In theory, could a woman that has fathers and mothers cromosome identical, be able to live?
What Im getting at is something totally impossible, but im making some mental experiences.

Assuming I have a machine that can produce a living being just from a DNA code (like in the movie  The Fly). If I make a DNA sequnce, that has mothers and fathers cromosomes identical, would such a being be a monstrosity or a human being when it got out of the machine.
For such a person, when DNA recombination between 2 eqal cromosomes is done, it will just be creating clones if itself.
Now we introduce a new monstrosity, a male twin male version of the identical-cromosome woman, that only hase the Y Chromosome altered. His sperm cells too will all be the same.
when theese 2.people mate, it will produce a clone.

EDIT:
To clarify my question number one.. Chromosome pair 1 has 2 chromosomes, one from father, one from mother. If theese two would be identical.

Geneticaly identical organisms are possible.  Lab animals are bred to be genetically identical.  Animals are inbred, with culling of animals that show recessive traits. Eventually there are no recessive traits except any which might arise by chance mutation.    This is also routinely done with livestock - a bull with desirable traits might be mated (via frozen sperm) his daughters, granddaughters, great granddaughters etc, each time with the offspring animal having a greater proportion of the bull's DNA.
If you mate 2 genetically identical organisms, you will not have a clone.  Gametes are scrambled via meiosis.
https://en.wikipedia.org/wiki/Meiosis

No new genetic material is introduced, but the chromosomes are resorted in random ways which result in slight variations gamete to gamete, and in the resulting progeny.

hmm, perhaps i wasnt clear enough with the question.  If X is a chromosome ( and XX is a chromosome pair), ill call it XX=XleftXright. My question is, couldn an organizm that has Xleft=Xright survive?

Typically when you have maternal twins the X chromosomes (and all the others chromosomes) are essentially identical. There is  nothing pathological per se about having an identical pair of chromosomes. It just depends on the presence or absence of recessive alleles.

To further elaborate, since my knowledge is limited in this topic:clarify:   Chromosome pair 1- has 2 chromosomes, one from father, one from mother. If theese two would be identical.

There is no need to invent some fantastic machine to create genetically identical animals. This is done all the time in plant and animal breeding, just not with people. It's accomplished by inbreeding over many generations.. Animals are typically about 98.6% identical after 20 generations of inbreeding.
The danger in inbreeding is the hidden presence of recessive traits in the parents that will be fatal (or at least deleterious) in the offspring, since the offspring will get two copies rather than one. Breeders find parent stock that can withstand such intensive inbreeding by trial and error. Of course mutations continue to occur after a genetically identical strain has been created, so genetic drift is a problem for laboratories using identical strains of plants or animals.


text:
What is the point of DNA sequencing?
This is a very very basic question. I've looked at methods such as chromosome sequencing and shotgun sequencing. Wikipedia says that:
DNA sequencing is the process of determining the precise order of nucleotides within a DNA molecule
For instance, with methods such as shotgun, we already have the original DNA. If we have access to the original DNA itself, don't we ALREADY know the sequence of nucleotides?
Why exactly do we need to 're-build' the DNA with methods such as shotgun and chromosome walking, when we already have the original DNA available? If we have the original DNA, don't we already have the original sequence of nucleotides?
It makes me think that these techniques for 'DNA sequencing' is sort-of pointless. But, obviously I am misunderstanding something.
Thanks in advance, any simple pointers would be great.

In some sense, this is like saying "what is the point of studying a cell, we already have the cell in our hands." We don't know anything about a cell by having a test tube full of them. This goes for DNA, proteins, RNA, etc. as well. You can purify DNA from an organism without knowing the nucleotides.

No, you don't. Having the DNA in your hand means that you have access to a macromolecule, not more.
Think of the DNA as a book (or a library). From holding the book in your hands, you don't know what the content is. You have to actively read the book to get this information.
Sequencing a piece of DNA is basically the same. Your readout is the sequence of the bases which is essential to understand (or do research on it) a certain piece of DNA. With this knowledge you can see where genes start and end, define introns and exons (for eukaroytes) and so on.

From a bioinformatics point of view: We are given a string of DNA characters (e.g. CTCGAT), then use shotgun to re-create the exact same string? I don't quite understand the point of that when we have the original string available.

@lostguy If you're given a DNA sequence, you obviously don't need to sequence it. But what if you're given a DNA molecule where the sequence is unknown? That is where sequencing is useful.

Oh okay, thanks a lot. that makes more sense. I am doing bioinformatics homework and this type of problem came up. I kept asking myself: "What's the point of this"? But now I see.
Out of curiosity, how are methods like shotgun used practically (if we don't have the original DNA string)? Do we physically randomly cut-up DNA? (Hmm, that doesn't seem realistic)

@lostguy Yes, that's exactly what occurs. DNA is physically sheared into random sized fragments, typically through sonication. Appropriately sized fragments are selected by gel electrophoresis and cloned into plasmids for amplification/sequencing. That's a very general overview, actual experimental protocols will differ and modern (next-gen) sequencing uses different methods.


text:
Confusion regarding niches in evolution theory
This is the definition of a niche from Crash Course:

An area of the environment that requires a special set of skills or traits to extract food and reproduce.

Obviously, this version of the definition has been dummed so that it appeals to mass audiences, but after some research, I believe that the general concept remains the same.
Here is what I've learnt about species living in a niche:

The more the competition, the slower the evolutionary process.
Lack of competition provides an ideal environment rapid evolution.

But these points seem non-intuitive to me, because:

Why would a increased competition slow down the evolutionary process? Shouldn't it speed it up, as different species will try to evolve the fastest in order to beat adversaries?
Why does a lack of competition promote rapid evolution? Won't it slow down the evolution, as there is no reason to evolve?

I know that there is a logical reasoning behind this, and I would very much like to understand it.

My source is Crash Course, specifically this  video. I've found it to be extremely reliable over the past, and highly doubt that they are supplying incorrect information. If anything, it is probably my inability to understand the concept.

what is the source for your definitions?

I've updated my question to answer your question.

having watched the video (and developed quite a headache, why don't these presenters stop for breath??) I think the key is in the context they are talking about, mass extinction events have cleared out bunch of niches, suddenly then species which weren't filling a niche before because they were being competively excluded can fill a gap if they evolve rapidly enough, see ~8:40 in the video

I think part of the confusion is that these terms are very loosely defined.  Also this discusses evolution in terms of taxanomic radiation, e.g. macroevolution at large spatial and temporal scales.
Problem 1 is that you haven't been clear about what kind of competition, inter or intraspecific competition?  These will have opposing effects generally which can counter balance each other [1]
[2].  When a species is free from interspecific competition, but under high intraspecific competition, that will promote an adaptive radiation, which concurrent morphological changes.  The most famous example of this would be Darwin's finches as studied by the Grants [3].  With a lack of interspecific competition, the finches exhibited rapid morphological divergence.  Following the logic of this, you'll see that lack of competition will lead the kind of rapid taxanomic radiation the video is discussing, especially over a longer time scale.
However increased interspecific competition will have two effects. It will reduce the number of available niches for an existing species to expand into [4], this generally will drive specialization of a species, which tends to limit genetic diversity which will lead to less "raw material" for evolution to work with. This specialization though is also technically evolution.  However with fewer niches, the new species tend to arise via replacement of existing species in an existing niche, as opposed to an adaptive radiation.
So you can see how actually both conclusions are right depending on the type of evolution and competition being considered.
More interspecific competition -> More specialization (one type of evolution), less adaptive radiation (another type of evolution)
More intraspecific competition -> More adapative radiation, less specialization.
I hope that helps answer your question.


text:
What factors limit a shape and size of an organ
We all know that anatomy deals with structure of human system. I am interested in knowing the factors that determine the shape and size of each organs in the body. For example, we know that kidneys are bean shaped, stomach is a C- shaped organ.
During the developmental stage, like mitosis, and other cellular pathways, what factors sets a boundary for cell division, so that an organ takes its respective size and shape.

Externally applied forces, contact signaling and intracellular checkpoint systems work in concert and underly tissue development, but as far as I know it's very poorly understood! Interesting, related article

To be precise, size and shape of an organ involves mechanobiology. Thanks Kendall for the supportive article.

Every organ is going to be way to broad, each organ has its own pathways.


text:
Linkage disequilibrium D sign
Linkage disequilibrium D equals
$D=x_{11}−p1⋅q1$
where:
Haplotype        Frequency
$A_{1}B_{1}          = x_{11}$
$A_{1}B_{2}          = x_{12}$
$A_{2}B_{1}          = x_{21}$
$A_{2}B_{2}          = x_{22}$
and
Allele    Frequency
$A_{1}=p_{1}=    x_{11}+x_{12}$
$A_{2}       = p_{2}=x_{21}+x_{22}$
$B_{1}       = q_{1}=x_{11}+x_{21}$
$B_{2}       = q_{2}=x_{12}+x_{22}$
Shouldn't:
1) $D = x_{11}-p_{1}q_{1}$ or $x_{11} = p_{1}q_{1}+D $
2) $**D=  x_{12}-p_{1}q_{2}$ or $x_{12} = p_{1}q_{2}+D**$
3) $**D=  x_{21}-p_{2}q_{1}$ or $x_{21} = p_{2}q_{1}+D**$
4) $D=  x_{22}-p_{2}q_{2}$ or $x_{22} = p_{2}q_{2}+D$
Why do all the papers show:
1) $x_{11}=p_{1}q_{1}+D$
2) $**x_{12}=p_{1}q_{2}-D**$
3) $**x_{21}=p_{2}q_{1}-D**$
4) $x_{22}=p_{2}q_{2}+D$
ex: http://en.wikipedia.org/wiki/Linkage_disequilibrium
Question:
why for the relationship between the haplotype frequencies and allele frequencies and D is there a difference in sign. In other words by the formula shouldn't it always be +D rather than -D?

Your question would be more appreciable if you'd use MathJax. For example "x12=p1q2-D" becomes "$X_{12}=p_1q_1-D$" by writing "X_{12}=p_1q_1-D" between dollar signs. More info about MathJax here


text:
force required to do damage to child's leg/feet in collision
I'm currently working on a toy robot for a student project. Part of this robot is the fact that it will be moving around quite fast. As such hitting the child can and most likely will happen. As such we are obviously worried about safety. So what type of forces can a child safely withstand? The robot will most likely not be very tall (45 cm) and be shaped like the top half of a sphere, as such most collisions will happen with the shins or the feet.
I do hope this is in the correct  stack exchange and that this isn't supposed to go into a different stack exchange.

This question appears to be off-topic because it is about not in the scope of biology SE, not likely to be answerable given the current information, not likely to be answerable at all (I doubt any one has been able to get funding to study how much force a child's legs can take before they break...) & there's too many variables. You should be considering other options first such as how to make the robot not damage a child, like padding, shape, or not having it hit the child at all!

You should also take in account that it is a toy. Even if a collision does not damage the child, it might still scare it. Which is reason enough to avoid collisions.

I know that I have to use padding but the main question is: how much padding? In order to find out I would like to know a maximum safe force so that I can calculate how much padding to add. I will of course add in AI that avoids targets but this can never be assumed to work(it only has to go wrong once).


text:
Can we spike with a different enzyme to a SYBR Green Master Mix?
I followed the standard SYBR Green Protocol for doing a qPCR. For which I used

10 uL of 1X SYBR Green Master Mix
Forward Primer and Reverse Primer (each at a final conc. = 8.5 uM)
Template (unknown concentration from an aptamer selection)
Made to 20 uL with water.

Performed the PCR amplification using

95 C Initial denaturation
95, 68, 72 - cycled 35 times.

But, one set of sample from my aptamer selection (probably high GC content) did not amplify at all. I checked on an agarose gel too.
Important Notes:

My primer conc. is intentionally high - I have always amplified with such concentrations and it works perfectly using Vent Polymerase.

My annealing temperature is also high at 68 C because my aptamer sequences tend to be GC Rich.

Using Vent polymerase my amplification is very strong

On reading notes from vendors, I found out that the polymerase in the mastermix to be some variant of Taq Polymerase[1][3] (varies from vendor to vendor) and also it is known to poorly amplify GC Rich Sequences[2].

https://www.thermofisher.com/order/catalog/product/4309155

https://www.thermofisher.com/order/catalog/product/N8080241

https://www.fishersci.co.uk/shop/products/powerup-sybr-green-master-mix/15366158

Hence, I wanted a suggestion from anyone working with aptamers, or if you have experience working with GC rich sequences on how I could amplify my sequences.
Much appreciated if I could have an answer before next week.
Thanks a lot for your help!!!

Can anyone help with this if you work with GC rich sequences?

I know its too late now, but this is a question well suited to ResearchGate.

I found this following answer in a Stack exchange post and seems to be helpful from the point of view of my question. If it helps anyone the following answers my question that I asked initially:
https://biology.stackexchange.com/q/46649/33379


text:
What percentage of DNA do people share?
If you picked two people in the world at random, sequenced each of their entire genome, and compared their DNA, what would the expected percentage match be?

Based on fine scale mapping of human genome structural variation, which is expanded on here, according to this study, the amount of genome structural (nucleotide diversity) ranges from 0.1% to 0.4% (look under section "Fine-scale map of human genome structural variation"). Hence humans have an up to 99.9% nucleotide similarity. And according to this study the average proportion of nucleotide differences between a randomly chosen pair of humans (i.e., average nucleotide diversity, or pi) is consistently estimated to lie between 1 in 1000 and 1 in 1500.