text:
What is the beneficial function of IgE antibody?
Dont tell me the "function" of IgE is to cause allergy !
In whatever texts I have seen it is  written that IgE is important to cause allergies but what is the beneficial function of IgE ? Why was it ever created ? Did it have an advantage in the pre historic ages but now causes allergies ?

No, they are of course not there to cause allergies.
It is thought (although not directly proven in human) that IgE is important to fight parasites and worms. They bind to antigens from the parasites, which leads to the secretion of histamines. This causes a local immune reaction (which also is a problem in allergies) which is helpful to fight the parasites.

See these papers for example:

IgE, allergies and helminth parasites: a new perspective on an old
conundrum.
IgE Enhances Parasite Clearance and Regulates Mast Cell Responses in
Mice Infected with Trichinella spiralis
Immunology of Parasitic Helminth Infections

There is also some evidence, that IgE is involved in the immunological response to cancers:

Activity of human monocytes in IgE antibody-dependent surveillance
and killing of ovarian tumor cells.
Animal models for IgE-meditated cancer immunotherapy

I referred to some good texts in immunology and saw the mention of its role in fighting parasitic infections. I feel that IgE might have played an important role in survivorship back in the stone age when parasite infections were so prevalent. Now that the amount of parasitic infections have been drastically reduced, it may exist merely as a genetic quirk which causes allergy. (There are many theories on benefit of allergies but they are inconclusive.)

One obvious thing to determine the function of IgE would be to remove it from body and see what bad effects it causes. There have been several studies on people with lower amount of IgE and they show higher chances and more severe cases of parasitic infections and respiratory tract infections. But these could have been the result of whatever factor caused the reduction of IgE in the first place. It is really important to separate the noise.

authors: Müñîß Fåøøqî


text:
Why are bacteria immune to snake poisons?
In a test I was asked why bacteria are insensitive to snake toxins.
Is it their membrane that provides a barrier to the toxins? Or do snake poisons have specific targets and thus cannot bind to bacteria?

All bacteria definitely aren't immune to snake venom. Infact they're very much susceptible to damage from snake venom eg (P Samy, R., et al. 2012). DO you have a specific bacterial strain in mind?

Short answer
Many snake poisons target specific proteins not present in unicellular organisms.
Background
The question is admittedly broad but the idea behind this question is pretty much what you indicate in your post - many venoms target specific proteins and do not simply destroy their target by, e.g., disrupting gross cellular structure (like alcohol does for example). Instead, they target specific molecules that are essential for the survival of their prey.
Snake toxins can be categorized according to the organ systems they target, namely :

the central nervous system
the cardiovascular system
the muscular system
the vascular system

Central nervous system toxins are carried by elapid snakes like cobras, kraits and the taipan. Typical targets are the nicotinic acetylcholine receptor and the muscarinic acetylcholine receptor. Blockade of these receptors at the neuromuscular junctions resulting in death by asphyxiation. Acetylcholine receptors are not present in bacteria.
Cardiovascular toxins are pretty diverse and include things like angiotensin-converting enzyme inhibitors (leading to a drop in blood pressure) and glycosaminoglycans (the sulphated carbohydrate moieties that occur abundantly in cells of cardiovascular tissues) binding proteins that lead to cardiotoxicity. Again, the targets are specific molecules involved in heart function and hormones, stuff not present in bacteria.
Muscular toxins include those that bind specifically to the sarcoplasmic reticulum of muscles or interfere with specific second messenger systems messing up muscular function. Again, quite specific targets not present in bacteria.
Lastly, typical vascular system toxins include anti-coagulants such as protein C activators and inhibitors of prothrombin complex formation. Again, specific targets.
Reference
Koh et al., Cell. Mol. Life Sci (2006); 63: 3030–3041

Venoms from vipers contain high amount of proteolytic enzymes (serine proteases). Many of them act by cleaving fibrinogen and thereby causing blood clot (ref). There is a likelihood that some of these proteases may affect other proteins also. In a study conducted by Bottrall et al. (2010), it was shown that snake venoms do have a general proteolytic activity. The best among tested was the venom of the viper Bitis arietans. However, its activity was significantly lower than the positive control which consisted mainly of trypsin and proteinase-K.
So the venom may have a little effect on the membrane proteins of bacteria.
But it might require extended treatment by venom to digest these proteins compared to that by stronger proteases like proteinase-K.
However, there are indeed reports on antibacterial activity of snake venoms (Stiles et al., 1991; Perumal Samy et al., 2007; Charvat et al., 2018). But the enzymes responsible for the antibacterial activity are phospholipase A2 and L-amino acid oxidase, and not the proteases.

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text:
What is cross-immunoreactivity, and how does it impact vaccine development?
What I understand about cross-immunoreactivity is that the antibody induced by one specific antigen is also fairly effective against another antigen. How would this be used for vaccine development?
Moreover, cross-immunoreactivity is related to epitopes. And how is how is cross-immunoreactivity defined among epitopes? Are variants of a specific virus hypervariable region some kinds of epitopes? What does antigenic convergence have to do with cross-immunoreactivity? Any comments or directions to further references are greatly appreciated.

Welcome to Biology! I tried to edit your question to clarify. What do you mean with "And how is it defined among epitopes?" - How is what defined (i.e., where does 'it' refer to)?

how is cross-immunoreactivity defined among epitopes? thanks for your help.

Probably this article will help you somewhat. http://www.jimmunol.org/content/189/9/4602.full It is hard to find anything in the topic. Probably with further search... Btw this molecular mimicry is the cause of many autoimmune diseases. http://scholar.google.com/scholar?start=20&q=cross-immunoreactivity&hl=en&as_sdt=0,5&as_ylo=2011

I edited the question again a bit using your comment. Feel free to make further additions or clarifications! Thanks. +1

Cross-immunoreactivity is just as you stated where an antibody that is specific to one antigen may recognize another antigen. I don't think this term is widely used as I see cross-reactive or broadly reactive more often. With regards to vaccines against viruses, cross-reactive immune responses are very important to establish an immune response that is effective against varying strains. Using Influenza as an example, an antibody that recognizes the HA protein of the H3N2 strain and also recognizes the HA protein of the H1N1 strain would be cross-reactive. If we had a vaccine capable of this we would not have seasonal flu.
Epitopes are specific regions on the antigen that are recognized by T cells or antibodies. They are the specific area on the protein structure that is recognized. Thus, for a response to be cross-reactive that specific structure must be present on both antigens. Epitopes could be located in any region of the protein, viruses will often have a region that is highly antigenic and highly variable to trick the immune response into focusing on the highly variable region rather than the more conserved regions.
Antigenic convergence is related to the sequence space available to the virus. Since viruses have limited space  for genes the amount of possible variation is limited as a single point mutation can have a large effect on the virus. Taking this into account some predictions could be made on how the virus might evolve. If the virus is evolving in such a way that there might be conserved epitopes, those epitopes might be important for cross-reactivity. Here is a paper on antigenic convergence in Hepatitis C. http://www.nature.com/articles/srep00267
This is a paper focused on flu, but it outlines the ideas surrounding cross-reactive antibody responses.
http://www.ncbi.nlm.nih.gov/pubmed/26175732

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text:
What is peptide mapping?
After searching online for peptide mapping to my understanding it can be treated as the fingerprint of the protein. It is obtained at the end of several chemical processes and it helps to understand the protein being analyzed.
Does this method operate in "sequence space" then? If so, what exactly is the relation of the two?

I slightly edited the question for clarity. Feel free to roll back.

Shimadzu explains peptide mapping as follows:

Peptide mapping involves selectively cleaving the individual target [proteins] using an appropriate enzyme or chemical and analyzing the peptide fragments obtained using HPLC [high-performance liquid chromatography] or another suitable method. [... I]dentification of the peptide fragments separated by LC [...] [can be done] using amino acid composition analysis, N-terminal amino acid sequence analysis, or mass spectrometry.

As such, it does not provide a sequence of amino acids. Instead, you get a specific set of peptides of different sizes, dependent on the method used, that in turn can be used for protein fingerprinting.


text:
Why "broad" instead of "large" cross-immunoreactivity?
From the articles I read, expressions like "broad cross-immunoreactivity" pops up a lot. So, I was wondering, why "broad" is used here instead of large? Is there a specific reason?

I'm voting to close this because it's about English usage.

@canadianer Stone correctly identified a scientific buzzword by its somewhat awkward placement. This is not about general English usage.

@tel It's a stretch to say that the sentence is referring to broadly neutralizing antibodies, especially without more context. Sometimes broad just means broad.

I vote to re-open, because it fits perfectly under the tag "terminology", which is: "How terms are used or the meaning of words as used in scientific literature".

In this context, "broad" is a buzzword, a piece of scientific jargon. It's a callback to Broadly Neutralizing Antibodies[1], bNAbs. The basic idea with bNAbs is that they target parts of viral proteins that tend not to mutate or change very much between individual strains of some particular virus.
Edit:
To clarify, I am not suggesting that an antibody with "broad cross-immunoreactivity" is the same thing as a bNAb. Immunoreactivity and neutralization are not the same thing (although there is some overlap).

1: Zwick, M. B., Labrijn, A. F., Wang, M., Spenlehauer, C., Saphire, E. O., Binley, J. M., et al. (2001). Broadly Neutralizing Antibodies Targeted to the Membrane-Proximal External Region of Human Immunodeficiency Virus Type 1 Glycoprotein gp41. Journal of Virology, 75(22), 10892–10905. http://doi.org/10.1128/JVI.75.22.10892-10905.2001

Broad means wide as in a wide range. Normally, antibodies have one epitope they recognize, i.e., one specific target; they are said to have a narrow range of targets.
Some antibodies, however, recognize multiple targets, i.e. the number of targets they recognize is larger and their target range is widened. They are said to have a broad cross-immunoreactivity.
A 'large' cross-immunoreactivity, however, is ambiguous, as 'large' can also imply 'large reactivity', and then 'large' becomes synonymous to 'strong'. Wide is unambiguous as it always implies a large range.


text:
What is self-immunoreactivity?
I read something like "some tested variants show self-immunoreactivity". So, what exacly is self-immunoreactivity? Is it something like antibodies induced by a specific variant showing immunoreactivity to this specific variant?

Where did you read this? It would be good to know this to be able to explain the context.

The basic concept of the immune system is that it has to discriminate between self and foreign and that is only allowed to launch an immune reaction against something foreign. This is called immune tolerance which basically makes sure that all immune cells which are directed against the own organism are destroyed.
If these antibodies survive, they can attack the own body (and are hence called self immunoreactive) and cause damage. Self-immunoreativity is a reaction of the body against itself. Problems with the immune tolerance are called autoimmune diseases, examples would be  systemic lupus erythematosus, rheumatoid arthritis or type 1 diabetes.


text:
What is a selectively neutral genotypic change?
I am reading the paper "Neutral evolution of mutational robustness". Because I am new to neutral evolution, I have a few questions.

Firstly, from my understanding, genotypic neutrality means the genotype is not responsible for an increase in fitness. What else can we say about genotypic neutrality? Does it have something to do with the population being randomly selected?
Secondly, how to understand a neutral network exactly? Another article says "by linking every pair of genotypes that are mutually accessible through mutations, genotypes organize themselves into neutral networks", so what means "mutually accessible through mutations"?
Thirdly, the neutral network is like an assumed black box we know nothing about, is it right? That is why in the original article with title "neutral evolution of mutational robustness", the authors mentioned that "one can infer important structural information about neutral networks from data on evolving populations."

Thank you for editing @AliceD. I didn't even tried to read the post the first time!

Can you add a link to the two papers and indicate where the citation come from in the papers? I never heard the term of genotypic neutrality but saying the genotype is not responsible for an increase in fitness sounds like there is some semantic issue in your mind. I don't know either the concept of neutral networks. So the papers would help a lot. You should always restrict your post to only one question.

I'd suggest to divide the current post into two and ask for explanation about the meaning of one particular sentence.

Mutations in DNA or RNA sequences do not necessarily result in significant changes in the functions of the proteins they encode (or in the case of RNA ribozymes, ribozyme function ). This is because, for a variety of reasons, the change in DNA/RNA sequence may not significantly alter the structure and function of the ribozyme/protein (the function that contributes to the fitness of the organism). If two alleles of a gene with different sequence have equivalent function (again with regard to the function of the gene that provides fitness) the differences between them are selectively neutral.
The neutral network consists of every variation in the sequence of the gene that can be reached from another sequence (of equivalent fitness) by a single base pair mutation (these aren't the only type of mutation, possible, but they are common and more likely to be neutral than more drastic changes). So for example (using an unrealistically short sequence), if I had a gene with the sequence  0 AACAATGCTGACTGA, and alleles 1 AACAATGCTGACTAA, 2 AACAATGCTGACAGA, 3 AACAATGCTGACTGG with equivalent function, 1, 2, and 3 would be directly linked to 0 in the neutral network as they all differ from 0 by a single base pair. The sequence 4 GACAATGCTGACTAA if of equivalent function would also be in the network as it differs by one base pair from sequence 1.
Each gene in the network being mutually accessible through mutations means that I could start out with any of the above sequences and reach any of the others through a series of single base pair mutations that traverse the network (i.e. I could mutate 0 into 4 by first mutating to 1, another network member, then to 4).
The genotypic space includes the sequences of all extant alleles of the gene. This paper suggests that there is a tendency for these sequences to form these networks and especially to evolve towards highly interconnected networks. This is the structural information the author refers to. It should be easy to imagine how this might confer robustness to deleterious mutation. Let's think about our sequences from above, imagine if every sequence was only linked to two other selectively neutral sequences forming a long chain. The sequence AACAATGCTGACTGA is 15 base pairs long with 45 possible single mutations, if only two of those are selectively neutral, the chance of mutating to a neutral network member is low, and even if you do hit on a neutral mutation, your chance of hitting another neutral mutation next time (reverting back or moving on down the chain) is still only 2/45. Now imagine that the neutral network is highly interconnected, with sequence 0 linked to sequences 1, 2, 3 and several other neutral 1 base pair changes, imagine those sequences are linked through each other by other neutral intermediates (being 2 base pair mutations away from 0). Not only is the chance of a single mutation being neutral higher, but subsequent mutations (remember that these include reversions from prior mutations) are more likely to stay within the network (you're more likely to come back around to 0.
Would you have more long-term success walking around a fitness plateau or walking across a fitness rope suspended over the abyss?

Oh this is what a neutral network is +1! I never heard of this term before. The concept is closely related to the concepts of adaptive landscape and quasi-species. Can you please add a reference that uses the term neutral network as you defined it? Is this term most often used in the  genetic algorithm literature? You talk about the authors. I am not sure which authors you are talking about.

Ah, the original question before the edit sounded as if it was referencing this paper or related literature: http://www.pnas.org/content/96/17/9716.full.pdf
I don't know the body of the literature well enough to comment on how broadly the term is used. I would

Thnks. I edited the post to add the reference. Feel free to roll back and place the reference elsewhere if you prefer.

Great explanation. Two questions. (1): In the last sentence of the forth paragraph, you said "not only is the chance of a single mutation being neutral higher, but subsequent mutations...", I can not see the reason that the chance of a single mutation being neutral get higher. (2): In your last paragraph, long-term success means being more firness? This is an interesting question.

(1) At any given node in the network (a given genotype) the chance of the next mutational event being neutral is higher if that node is connected to many others (assuming the event is random the chance of a neutral event is (possible neutral mutations)/(all possible mutations)). If the new node also has many connections, the chance of a neutral mutation is likewise higher, and so on. Therefore a network in which most nodes have many connections to other nodes (a highly interconnected network) will be more robust to mutation than a network in which most nodes are not linked to many other nodes.

That makes sense to me now. So, mutational robustness means the insensitivity of the phenotypes to mutations, right? In a highly interconnected neutral network, the phenotypes would be more insensitive to mutations, because the fractions of neutral mutations are higher. --


text:
Terminology regarding cross-immunoreactivity
After reading an article, I saw expressions like "cross-immunoreactivity among epitopes", "cross-immunoreactivity among variants of virus", "immunological reactions among pairs of peptides" and so on.
I wish to verify my following understandings:
An epitope is also called antigenic determinant, and it is part of the antigen that is recognized by the antibody. An epitope, then, is a part of a virus variant. Peptides are short chains of amino acids. Thus, we can talk about the immunological reactions among peptide-pairs, because the virus variant itself is a protein, which is composed of peptides? Did I understand it correctly?
Moreover, I saw a sentence like "this antibody is against a few variants while reacting with all tested peptides", so I guess reacting here includes against? Reacting may include other situations, right?

Everything you state is correct, except that I disagree with your statement that a "[...] virus variant itself is a protein, which is composed of peptides.
A virus is typically composed of a protein capsule with genetic material on the inside. So technically, a virus is not a protein, but its outer shell is composed of proteins. Further, a protein does not necessarily have to be composed of (multiple) peptides - it can be a single amino acid chain.


text:
Homework problem:Introductory genetics
The problem is as following:
Primary Ciliary Dyskinesia (PCD) is caused by an autosomal recessive gene. 50% of patients with PCD also have Kartagener Syndrome. Josh has Kartagener Syndrome. What is the chance his brother or sister also have this syndrome?
A  0%
B  6.3%
C  12.5%
D  25%
E  50%

Is this problem actually solvable without knowing the alleles combination of the parents? The answer states C, but perhaps I´m missing something here.

You must be expected to assume that both parents are heterozygous. Then there is a 25% chance each offspring would have PCD and half of those offspring would also have Kartenger (ie 12.5%).

Why should I expect something like that, is that a rule?

@Jarry if any parent is homozygous dominant then all of the offsprings will not express recessive allele.

I didn't say you should expect it…

You can only solve this problem if you know that 100% of people with Kartengers also have PCD.  The question, at least this portion of it, doesn't say that.  You also have to know that the parents are not affected with PCD; the problem doesn't state that either.

Ok, Josh has PCD. That gives three possible genotypes for parents:- ( let the alleles be P and p)
1) Pp x Pp
2) Pp x pp
3) pp x pp
In (1), the probability for next child to be pp is 25% and to have the disease is 12.5%.
In (2) and (3), the probability of any parent to be pp is rare as the p allele is quite rare (discussions with swbarnes2 in comments). So the real probability will be only slightly higher than that of case 1 i.e. 12.5%

Reduced fertility doesn't mean zero fertility, and they already have a child.

@swbarnes2 that's the point! They have a child. So the mother even can't have the disease.

@swbarnes2 I edited the question. Please see if it satisfies the question. Also in such genetic question, it is always yes or no. If there is a "maybe" then its probability will be given.

In the scenarios with pp parents, the odds of a parent being infertile are 0%.  Because they already have a child.  So the odds for scenarios 1,2 and 3 are 12.5%, 25%, and 50%.  But without knowing the proportion of the p allele in the population, you have no idea how likely each scenario is, so you can't work out the overall percentage.  The problem is only solvable if you assume that both parents are carriers, not affecteds.  It's a poorly written question, because you can't actually solve it from the info given.  You have to make some assumptions.

@swbarnes2 can we say then that lack of information in question would lead to assumption that only case 1 is considered as pp genotype would be rare in population as compared to Pp?

The problem is not solvable unless you assume that 1 is what's happening.  And when you make that assumption, the answer is present.  Realistically, the p allele would be likely be quite rare, so scenarios 2 and 3 would be extremely rare, so the real percentage counting all three would just be a bit higher than 12.5%.

Since the answer is C it means both parents are heterozygous.
There are two possible alternatives:

Both parents are homozygous to the recessive allele
One is homozygous to the recessive allele and the other is heterozygous

In the first case the answer will be 50%, and in the second case it will be 37.5%
So yes, the question is missing crucial information.

No, in the second case, Pp x pp, 50% of the kids have pp, and 50% of the pp offspring have the syndrome, so 25% total.


text:
Can the same target gene be regulated differently by the same transcription factor under different conditions?
I'm very new in biology and doing more computational analysis. I'm confused with the type of interactions between Transcription Factors (TF) and target genes.
Is it possible that the same transcription factor interacts differently with the same target gene under different conditions?
e.g., TF1 up-regulates Gene1 under condition 1 while TF1 down-regulates the same gene Gene1 under condition 2
Does the above example take place in biological systems?
I can only think of different TF complexes which are regulating the gene Gene1 under different conditions with different effect. However, it would be great to know if, in case TF1 does not participate in any TF complexes to regulate Gene1 under certain conditions, it is then possible that "TF1" regulates Gene1 differently under different conditions?

It also depends what you take as "normal expression". Even if you have only an ON and an OFF state for a single interaction, the system can display "upregulation" and "downregulation" of target genes if expression is normally somewhere between completely ON and OFF.

Short answer - yes but probably somewhat rarely.
Transcription factors aren't necessarily limited to being either repressors or activators. In practice they mostly do one a lot more than the other - e.g. if they have an 'activation' domain then they will mostly activate, but they can still do the opposite, directly or indirectly.
A single TF will often regulate different genes in different directions. This can be due to indirect effects - our activator activates a repressor which then switches off a gene. It can however also happen through direct means - for instance a factor might bind a repressing or activating domain at different locations, or displace different factors.
Most of this variation is probably specific to the target gene, so factors are probably more specific in their effect on a given gene. However, since our factors action depends on other genes,and different genes will be active in different conditions, there's no reason a factor couldn't do different things under different conditions while at the same location - perhaps one condition activates a repressor that binds with it, or a stronger activator that it competes with.
It's a matter of ongoing research, but I would expect this kind of thing to be the exception rather than the rule. In general complex interactions between TFs at a given location seem to be rarer than more or less additive effects.


text:
Mutation in pre-mRNA sequence
Has there any mutations been recorded which cause harmful effects due to change in the part of pre-mRNA responsible for proper m-RNA splicing ?

Do you mean mutations in donor and acceptor splice sites?

Adding to Alans question: Mutation of the pre-mRNA only (due to mistakes during transcription) or mutations in the genomic DNA which are then transcribed into the pre-mRNA and which affect splice acceptor sites?

@chris I mean mutations in the genomic dna. By the way, can we call mistakes during transcription as mutations ?

@Alan Yes, any site in the pre - mRNA involved in this.

see http://biology.stackexchange.com/questions/13908/what-type-of-mutation-causes-progeria

Yes, you can find mutations in the genomic DNA which affect splice acceptor sites. Wikipedia lists the following outcome:

Mutation of a splice site resulting in loss of function of that site.
Results in exposure of a premature stop codon, loss of an exon, or
inclusion of an intron.
Mutation of a splice site reducing specificity. May result in
variation in the splice location, causing insertion or deletion of
amino acids, or most likely, a disruption of the reading frame.
Displacement of a splice site, leading to inclusion or exclusion of
more RNA than expected, resulting in longer or shorter exons.

The article lists two interesting papers:
Lim KH, Ferraris L, Filloux ME, Raphael BJ, Fairbrother WG (2011). "Using positional distribution to identify splicing elements and predict pre-mRNA processing defects in human genes". Proc. Natl. Acad. Sci. U.S.A. 108 (27) 11093–11098.
Ward AJ, Cooper TA (2010). "The pathobiology of splicing". J. Pathol. 220 (2) 152–163.
Both papers are open access.


text:
Is AT or GC content important in electrophoresis?
Will it make a difference in running speed if we run samples of same no of bases but different AT - GC content ?

Can we get a little more information on the DNA?   Is it linear, cut, or nicked?  Is it an uncut plasmid or chromosome?  In cut linear DNA I don't think you would see a difference, but you could certainly see differences in the migration of the super-coil.

@AtlLED why? Are you thinking about mechanical things like long stretches of As that will make it bend or something else?

Nucleotide does affect the persistent length of the DNA.. but it is not just the length I guess; it is also affected by the sequence pattern.

@AtlLED It is linear double stranded dna.

It does make a difference on polyacrylamide. A and C are faster while G and T are slower.
Image from publication:

The "standards" are AAA/TTT/GGG/CCC molecules.

nice find - i think that proves the point!

Practically speaking I have never seen a difference, but the agarose gels usually used in the lab do not have the highest resolution. There is one paper showing that the form (A- or B- form) and the GC-content play a role since DNA molecules of higher GC content are less flexible and therefore have more problems getting through the agarose matrix. Interesting paper, but probably not very relevant in the lab (under "related publications" on the right side of the PubMed site you can find more on this topic):

Mechanical Properties of High-G⋅C Content DNA with A-Type
Base-Stacking

There is however a technique, which makes use of the different GC content of DNA samples. It is called "Denaturing Gradient Gel Electrophoresis" and makes use of gradients (either chemical or temperature) to denaturate DNA on the gel. Depending on the GC content, this happens earlier or later, which influences the migration pattern (denaturated DNA is much bigger and slower). See here for more details.

if you run a circular plasmid on an agarose gel you can see more than one band due to different ways the plasmid dna can twist.  In extreme circumstances I could see it making a difference.  Usually it would not.

Ok, I was assuming we compare doublestranded DNA of approximately the same size with different base compositions. In the case of the plasmid the different shapes (coiled, supercoiled, relaxed) make the difference.

hey Chris I was just supporting what you were saying - that if you had an odd collection of bases it might bend up like a supercoiled plasmid and would be visible on a gel.


text:
Association of shorter telomeres with heart disease
From this paper

Those with shorter telomeres in blood DNA had poorer survival,
  attributable in part to a 3.18-fold higher mortality rate from heart
  disease (95% CI 1(.)36-7.45, p=0.0079), and an 8.54-fold higher
  mortality rate from infectious disease (1.52-47.9, p=0.015).

What is the connection between shorter telomeres and heart disease ?

This seems a bit like a hen and egg problem. Telomere length is both associated with age and with heart diseases, but heart disease is also associated with age. The question here is, is one really causing the other here (short telomeres heart problems) or do they occur simultaneously? The other problem with heart disease is that it is a multi-risk disease, with many risks accumulating with age. The figure below sums this up, it is from the first paper:

Have a look on these articles:

Telomere biology in heart failure
Aging, telomeres and heart failure.
Telomeres and Cardiovascular Disease


text:
Definition of species - location of gene
I know that species have been classified on basis of reproduction , DNA similarity , niche, etc.
Has there been a classification based on locus of genes ? What are the drawbacks/shortcomings of classifying this way ?
Isn't it simple to classify on this basis as - a species can have variation at a locus but the position of that locus with respect to a chromosome is fixed in every individual of that species. This fact can eliminate the subjective criteria of DNA similarity.
But I think this isn't valid for bacteria as there is so much recombination going on.

The position of gene is not always fixed within a species. There are Copy Number Variant within species for examples. A great part of the variation within humans is due to CNV. I agree that it is important to consider other genetic variations than only the alleles. CNV, position of genes, regulatory sequences and other stuff are important too. The concept of species is a poor concept which is old as Aristotle and important in the christian culture but we have to accept that this concept is not a natural category. You won't find the perfect objective definition of what is a species.

@Remi.b Yes , but are CNVs genes ? Are there variation in no. of genes in population ?

CNV's are DNA sequences of any length that are present at several different number of copies along individual in a population or along species. THese sequences can contain one or several genes. So the answer to your question is yes! There are variation in number of genes within a species. Here are two references that might interest you: http://adsabs.harvard.edu/abs/2006Natur.444..444R and http://genome.cshlp.org/content/16/8/949. You will as well find some information about CNV on the [wikipedia page] especially under "identification". (http://en.wikipedia.org/wiki/Copy-number_variation)

@Remi.b Hello! I think you have answered my question in the comments. Would you like to write an "answer" ?

The position of a gene is not always fixed neither within nor between species. There are Copy Number Variation for example. A great part of the variation within humans is due to CNV. I agree that it is important to consider other genetic variations than only the alleles though. CNV, position of genes, regulatory sequences and other stuff are important too in the description and the functionality of a lineage.
The concept of species is a poor concept which is old as Aristotle and important in the christian culture but we have to accept that this concept is not a natural category. For french speaker people this podcast(Follow: Biodiversité: Plus qu'une simple histoire de conservation/Pierre-Henry Gouyon) is of interest. You won't find the perfect objective definition of what is a species. Here and here are posts that discuss the definition of species.

I would add:
Most categories in sciencie (species, order, living, planets, moons, stars, organs, fruits, etc.) are not "real". We (humans) create categories and attach objets to them in order to make general assumptions, so we can say things like "Most objects of category X have Y property."
Then, the way we define categories it's mainly the most practical way. And sometimes we addapt definitions, when there are practical motivations.
I think the motivation to define species related to the usual intra reproduction hability (and usual inter reproduction inhability) it's because that mantains certain homogeinity. Maybe a better definition would be something like "two groups of individuals belongs to the same specie if the rate of fertility among their individuals is > x %".


text:
Renin - enzyme or hormone?
Wikipedia says :

The kidneys secrete a variety of hormones, including erythropoietin,
  and the enzyme renin.

Can a substance be both an enzyme and a hormone ? Why is renin both an enzyme and a hormone ?

Yes, something can be both a hormone and an enzyme. There are a group of hormones known as peptide hormones. These are proteins (such as enzymes) that act as hormones indirectly (and maybe directly too?). A hormone is a chemical secreted by a cell that has some effect on another cell elsewhere in the body. In this case, the chemical just happens to be an enzyme. You can read about them on Wikipedia
Renin is secreted by the kidney, but its involved in arterial vasoconstriction (outside of kidney cells), so it is a hormone. And its also a peptide/enzyme, so it is considered both a hormone and an enzyme

Hormone is just a different class of protein and is not usually an enzyme. Peptide hormones have no catalytic potential and serve only as signaling ligands.
There can be secreted enzymes which is common in the digestive tract but these are not called hormones. Hormone is purely a signaling molecule.


text:
Need of Creatinine Phosphate
In muscle cells most of the ATP's phosphate is with creatinine phosphate.
So why is the displacement of the phosphate group done ? Is it because creatinine phosphate would give it's phosphate more easily ? Is it done so that the negative feedback by ATP on mitochondria is not there and more and more ATP can be generated ?

Creatine phosphate is used as a buffer in high energy using cells, such as muscles. In a cell you have a pool of ATP, which is needed for things like muscle contraction, and then you have your pool of creatine phosphate, which can not directly be used as energy for muscle contraction. The cell only stores so much energy as ATP. And during high energy activities it can be depleted quite fast. The problem is that it takes a lot of time to make ATP through oxidative phosphorylation. And while glycolysis is faster, you dont get nearly as much ATP. Creatine phosphate solves this problem by acting as a reserve of ATP, so when ATP is depleted, the creatine phosphate can transfer a phosphate to ADP, and thus restoring ATP without needing to wait for glycolysis or the electron transport chain to complete.


text:
Do people with gout live longer?
Antioxidants reduce damage to tissue (by scavenging the free radicals) and thus may reduce ageing.It is known that Uric acid is a very good antioxidant.
People with gout have excess accumulation of uric acid.
Considering the above information the authors of the book  "Why we get sick?" put up an interesting question : Do people with gout live longer ?
I would like to know if there are any studies done to answer the question.

As far as I'm aware, the suggestion that anti-oxidants increase lifespan doesn't have any real scientific evidence. Even if ageing is largely due to oxidative damage, antioxidants often do not get access to the mitochondria where the majority of oxidative damage is likely to occur. Moreover, there is some evidence that anti-oxidants disrupt oxidative signalling in the cell, and so may actually cause more problems.

It is actually disputed if antioxidants do good, or if they prevent cells from dying which then can develop into cancer cells. There are a few publications out now, which support this hypothesis.

@chris I remember reading about some of the myths of antioxidants in a Scientific American article but the evidence was not conclusive.

I can look up the references later today.

@biogirl Some more popular written text (which has some references in it can be found here, two original papers are here and here.

In men, gout is associated with a higher risk of death from all causes. This would imply that their life expectancy is shorter. From a review by Kim et al. (1):

Among men who did not have pre-existing coronary heart disease, the
  increased mortality risk is due primarily to an elevated risk of
  cardiovascular death, particularly from coronary heart disease. Also,
  an extension study of a large clinical trial among men with
  above-average risk for coronary heart disease found that a diagnosis
  of gout accompanied by an elevated uric acid level is associated with
  increased long-term (approximately 17 years) risk of all-cause
  mortality that arises largely from an increased risk of cardiovascular
  disease (CVD) mortality.

This does not rule out that some subset of people with gout (patients with less severe symptoms?) might benefit in some way from an antioxidant effect, but in general gout is obviously not good for life expectancy.

The reason some gout patients live longer is beacuse they often get treated with xanthine oxidase inhibitors like allopurinol which have beneficial effects regarding vascular oxidative stress:
https://www.youtube.com/watch?v=v7DL24uca_I
Allopurinol has beneficial effects in several regards:
http://pharmrev.aspetjournals.org/content/58/1/87.long
The high level of uric acid in humans in general is due to the defunct gene for urate oxidase. That mutation appears to be a disadvantage for humans.

David, could you add an article citation instead of the youtube video. Even if the video is scientific, there is no guarantee that it is scientifically correct. You may look at  Dr. Rutledge's (one who posted the video) website or mail him to ask for a reference.

I wrote him without any reply. I also did some searching without any precise hit.


text:
Deciding between chi square and t test
I am always so confused whether to do a chi square test or a t test in the sums given by my biostats teacher. Does anyone have a simple rule to decide this?

You can use a t-test for percents IF you use a binomial distribution for estimating variance.

This is a very subtle question and I encourage you to read the Wikipedia articles on these different subjects (t-test, chi-squared test, p-value, etc) because the authors worked hard to combat common misconceptions about these commonly used statistical tests. Here is a rather oversimplified rule-of-thumb for these different tests:

t-test: Used when you are looking at the means of different populations. For example, you might want to determine whether the difference in the mean gene expression level between treated and untreated cells is different, or if the gene expression level of cells in a certain environment differs from what you would expect in a null hypothesis. Assumptions: You are assuming that the populations you are looking at are normally distributed. The variance of the populations is not known (that would be a Z-test), but it is assumed that the variance of each population is the same. Finally, for the t-test to work, the samples of the data from the two populations are assumed to be independent.
$\chi^2$ test: Several possibilities for this. The most common in biology is the Pearson $\chi^2$ test, which is used when you are looking at categorical data, like the number of pea plants with white or purple flowers and round or wrinkled seeds, and trying to see whether the number of individuals in each category is consistent with some null hypothesis (such as the number in each category you'd expect if the genes for flower color and seed shape are not linked). Assumptions: The data points were randomly and independently gathered from the population, and you have a reasonably large number of samples.

I'd hate to have made a huge mistake, so please edit my answer and/or contribute your own if you think I am completely misrepresenting these topics!

This is correct, though I think the core of it is actually simple. Use chi-square if your predictor and your outcome are both categorical variables (e.g., purple vs. white). Use a t-test if your predictor is categorical and your outcome is continuous (e.g., height, weight, etc). Use correlation or regression if both the predictor and the outcome are continuous.

+1. This is a good account. Out of an abundance of caution--never to be deplored!--you have enunciated overly restrictive assumptions, but they are accurately and well stated. And your remarks about subtleties and misconceptions are to the point: the choice of tests is never as simple as suggested by the preceding comment by@octern, because the nature of the data is one of the least important factors in the decision. The purpose of testing is the primary desideratum; next is a choice of statistical model for the experiment or data; and everything follows from those.

Additional Info
T-test
As A.Kennard said t-test is applied when the random variable is normally distributed. How to know what is normally distributed is a relevant question. Regular measures which suffer some random error of measurement are normally distributed. The mean values estimated from different samples (the experiment that generates that sample may have any distribution) follow normal distribution. For e.g mean time interval of a radioactive decay- the interval itself is exponentially distributed but the mean of the mean decay interval will be normally distributed. You can reason that it is again an error of measurement that leads to variation in the mean value calculated in different samples. This is called the central limit theorem.
A normal distribution has two parameters- mean and variance i.e. you need to know these values beforehand to construct a normal distribution. A uniform distribution has no parameters- that doesn't mean that uniformly distributed samples have no mean or variance (in this case mean and variance are sample properties not distribution parameters).
A t-test or z-test is done to see if a sample is a representative of a given normal distribution. That again means that the calculated mean and variance are equivalent to the corresponding distribution parameters. In case of z-test you know the population variance (distribution parameter). You may ask how can anyone possibly know the population variance beforehand. An example is a case in which you already know the error rate of your measuring device (may be provided by the manufacturer or interpreted from its design).
$\chi^2$ test
There are several variants of the $\chi^2$ test. But what is common between them is that they refer to $\chi^2$ distribution. Variances, which are always positive cannot be a normally distributed. These follow $\chi^2$ distribution. The F-test for variances uses the ratio of the $\chi^2$ statistic of the two random variables denoting variances. Even in the Pearson $\chi^2$ test, the test statistic is a sum of squares which makes it always positive.
In fact this $\chi^2$ distribution is also used in t-test. As . Kennard said, one of the assumptions of t-test is that the population variance is unknown but assumed to be equal. Since population variance is unknown it has to be estimated from the sample. Like the case with all estimates you dont have a fixed value but a range of acceptable values falling in some confidence intervals. T-distribution is basically an average of several normal distributions with variance values falling in the allowed confidence interval of a $\chi^2$ distribution.
It is not necessary that categorical data are to be tested by $\chi^2$ test. Coin toss experiment gives rise to a categorical but it can be tested against a binomial distribution. So $\chi^2$ test can be used for categorical data but it is not the only test.
Bottomline: a statistic tested by a $\chi^2$ test has $\chi^2$ distribution as its sampling distribution. That statistic should be a square/sum of squares- something that can never possibly have a negative value. Perhaps that is why it is called $\chi$ squared.

Its true that T-test are used when your dependent variable is Numeric and Chi-Square test is used when you are analysis categrical variable. But how about this:
You have a categorical response (0,1) to a campaign. 1 who bought the product and 0 who did not. If you sum up the responses in your Test group and Control group and devide them by thier respective population size, lets say you get something like this - .23% response rate in Test Group and .01% response rate in Control Group.
Can't you use T-Test to see if these reponse rates are different? If yes, then let me remind that these variables were categorical (0,1) but we still used them as numeric.
All I want to say is that if we are comparing response rates or percentages, then T-Tests can be used irrespective if the dependent variable is character or numeric.
Sachin

No, you can't compare just two numbers (.23 vs. .01) with a t-test.


text:
Why is Thermus aquaticus and Taq Pol stable?
What is the molecular basis of the stability of the bacterium Thermus aquaticus and the enzyme Taq Pol it produces ?
I have tried googling this but did not get a good answer.

By the way, does Thermus aquaticus belong to archea or bacteria ? Wikipedia says bacteria but I have read somewhere else that it is archea


text:
How does Hemocytoblast constantly get formed into so many blood cells and yet remains there in the bone marrow throughout the lifetime?
I mean, Hemocytoblast is a stem cell which is constantly being differentiated into daughter cells and leads to formation of all the blood cells (having short and limited life spans), so how come those stem cells remain there and continue to function, even when we grow up and finally grow old (i.e for 70 years approx)? The no. of those stem cells gotta be limited.

The trick for the stem cells lies in the way the proliferate and differentiate. See the image (from the reference 1):

Stem cells have the problem that they need to differentiate and maintain their population at the same time (subfigure a). This can either be done by asymmetric cell division which leads to one daughter which is still a stem cell and one which has been differentiated (subfigure b). Then it is possible that the cells divide only symmetrical (as shown in subfigure c) so they will either deliver two stem cells or two differentiated cells. And then it is possible (shown in subfigure d) that both possibilities are mixed and that symmetrical and assymetrical division occurs. Either way you get both: Differentiated cells and you still manage to maintain the stem cell pool.
References:

Asymmetric and symmetric stem-cell divisions in development and
cancer
Asymmetric cell division of stem and progenitor cells during
homeostasis and cancer
Asymmetric cell division

your first link is broken

Can this asymmetric cell division be defined as mitosis?

Is this the only way, how these stem cells remain active for so many years? I don't think, that even with your answer taken into account, that's possible if we consider 70 years of average life span.

@MattDMo Thanks for the notification, I fixed this.

@a.aniq yes, it's mitosis. What else would it be? Also, since these cells do remain active for an entire lifetime, your assumptions need to be re-evaluated.

Yes, this happens via mitosis. The cells most likely get additional signalling when they differentiate in this process which is different from the signals they get when they should maintain their stem cell properties.

From where do they get the signals?

They get them from the environment, see here for some basics.

Data shows lipid metabolism is a big factor in determining how the stem cells differentiate.


text:
Is there a graph or ontology that maps diseases to its possible causes or causing diseases?
I am looking for a mapping, list, ontology or graph that shows the connection between a diseases and its (currently known) causes and/or risk factors.
For example a well known risk factor for acute kidney injury is diabetes. There are other diseases whoms risk factor is diabetes. This meanse diabetes is a risk factor for many diseases. Maybe if one traverses trough this dependencies and builds a graph out of it, there will interesting clusters and lineages.
I dont know if this is inherent knowledge or formulated somewhere in a formal and explicit way (e.g. as ontology).
There is http://disease-ontology.org/, but it does not contain any causes, risk factors, etc.
Thanks in advance!

Welcome to Biology.SE! I think it would help if the question is further specified. As of now it is rather broad and at least to me unclear what you are exactly after.

So you are basically looking for an enormous data base that connects diseases with their risk factors and known causes?

@fileunderwater: Yes, could be a database. I think a ontology would model this behaviour very well. In this sense every node would be a disease or a risk factor (because not every risk factor is a disease), between the nodes you have different links of type "has_cause" and "has_risk_factor". Very much in the way http://disease-ontology.org/ is modelled (click on some concept and then "Visualize"). So this is what i had in mind, but if there exists a database or just a massive text-file, it would also help me!


text:
How long is saliva viable?
Does anyone know if saliva can stay viable for about 5 days, before it gets suspended into a DNA genealogy vial for testing?
Background: My brother wants to do a DNA genealogy test at a US testing facility. The country he lives in doesn't allow it, however. For some reason FedEx has no problem with shipping his saliva to me in the U.S. The fastest they can do is 4 days. Will it still be viable to test? Or will it have gone bad somehow? He wants to ship it tomorrow.

Saliva buffer usualy provides stability at RT for month or even years. Genotyping companies like 23&me use collection kits like Norgen's (https://norgenbiotek.com/product/saliva-dna-collection-preservation-and-isolation-kit) which allows to store the sample up to 5 years.
So my advice would be: get the spitting vial at your place, send it as regular mail to your brother, and then ask him to send it back to you once filled with saliva. By doing so you won't have to worry about temperature.
Sending fresh saliva should be ok if your brother sends it refrigerated (4°C). I keep fresh cells up to at least one week in the fridge in proper medium, and saliva is a pretty decent buffer and has some antimicrobial properties.


text:
What were the symptoms of Phineas Gage after suffering his brain injury?
Phineas Gage was a construction worker who suffered a head injury due to an explosion at a construction site. A metal rod was pushed up his cheek and through his head.
I have heard he demonstrated six symptoms after the accident. What were they?
I have researched this for a while but all I can find is that he was very inappropriate in social situations.

He wasn't just inappropriate , he had a complete personality change. Only his frontal lobe was damaged, similar to a lobotomy. It was the section that allows you to be rational and make clear decisions, the part that has our conscious, so I was told. We studied it a bit in Psycology 101. I don't believe he had any physical ailments from this, but I could be wrong.

I don't see  any question here. You are asking for the case study reference. I am afraid questions on such a kind of reference request is off-topic. Moreover, the question itself is not about any biological mechanism but is just about "listing" the observations. An example of an on-topic question on this area would be: "Why does injury in the X-lobe of the brain result in symptom-Y ?" This may be suitable for [hsm.se]. Also have a look at this.

Gage suffered a massive injury to the frontal cortex due to his accident in 1848 (Fig.1). Recent work using computer assisted tomography (CAT) has shown that contrary to popular belief, the injury was probably not bilateral, but confined to the left-lateral frontal lobe (Ratiu et al, 2004).

Fig.1. Original drawing of the wound sustained by Gage (left). Source: Harlow (1869) and the reconstructed injury using modern CAT scanning techniques on the original tamper and Gage's skull (right). Source: Ratiu et al., (2004).
The question of OP is not very particulate about the nature of symptoms (physical or psychological symptoms), or about the time window of interest after the accident (acute or chronic symptoms). I assume that OP is asking about the behavioral changes of the subject after he was physically fully recovered. The following is a formatted quote from the original publication written by his treating physician (Harlow, 1869) describing the subject's behavior approximately 6 months after the incident:

His physical health is good [...], but says [he] has a queer feeling [in the head] which he is not able to describe. [...] His contractors, who regarded
  him as the most efficient and capable foreman in their employ previous
  to his injury, considered the change in his mind so marked that they
  could not give him his place again. The [...] balance [...] between his intellectual faculties and animal propensities, seems to have been destroyed. He is fitful, irreverent, indulging at times in the grossest profanity (which was not previously his custom), manifesting but little deference for his fellows, impatient of restraint or advice when it conflicts with his desires, at times pertinaciously obstinate, yet capricious and vacillating, devising many plans of future operation, which are no sooner arranged than they are abandoned in turn for others appearing more feasible. A child in his intellectual capacity and manifestations, he has the animal passions of a strong man. Previous to his injury, though untrained in the schools, he possessed a well-balanced mind, and was looked upon by those who knew him as a shrewd, smart business man, very energetic and persistent in executing all his plans of operation. In this regard his mind was radically changed, so decidedly that his friends and
  acquaintances said he was "no longer Gage."

The symptoms of Gage indeed match the current understanding of the functions of the frontal lobes. The frontal lobes are thought to be involved in a multitude of cognitive processes, such as executive function, attention, memory, and language, affect, mood, personality, self-awareness, as well as social and moral reasoning (Chayer & Freedman, 2001).
References
- Chayer & Freedman, Curr Neurol Neurosci Reports (2001); 1(6): 547-52
- Harlow, Bulletin of the Massachusetts Medical Society (1869) and see wiki page
- Ratiu et al., J Neurotrauma (2004); 21(5): 637-43

"…it was proven to have been confined to the left-lateral frontal lobe" sounds like the injury occurred on the lateral side of the left frontal lobe. Did it? Because the tamper looks like it's going right through the middle of the lobe.

@canadianer - they reconstructed the injury using the original tamper and Gage's skull using CAT scans. Sounded convincing to me.

@user117852 - my pleasure, thanks for the interesting question. It took me a while because it needed some detective work :)

Phineas Gage actually recovered from his personality change.
A recent study was just published suggesting that most of what we thought we knew about Gage is incorrect, and he recovered from this extreme personality change. An emeritus professor, Richard Griggs, analysed over 23 books on Gage and came to the conclusion that he made a miraculous recovery, which people rarely discuss in textbooks. Griggs states that Gage ended up immigrating to Chile where he "worked as a horse-coach driver, controlling six horses at once and dealing politely with non-English speaking passengers." The importance of understanding and acknowledging this recovery is an important step towards understanding the plasticity of the brain.
Also, as explained in another answer, recent CAT scans suggest that the injury was confined solely to the left frontal lobe. Therefore some un-updated publications on his personality changes will also be incorrect because they will discuss the effects of bilateral frontal damage rather than left frontal damage.
Griggs, R. (2015). Coverage of the Phineas Gage Story in Introductory Psychology Textbooks: Was Gage No Longer Gage? Teaching of Psychology, 42 (3), 195-202 DOI: 10.1177/0098628315587614

+1 for this answer - It would be really interesting to know how much time had passed since he moved to Chile? My answer deals with 6 to 7 months after the accident. When did his full recovery set in?

I think he moved to Chile around 18 months after the accident. It is really unknown what kind of recovery he made, but he did make some kind of recovery. The problem is that all of this happened in the 19th century and only comments from doctors can be used as evidence for his changes in personality and recovery. There is a really good article on the entire story here: http://www.slate.com/articles/health_and_science/science/2014/05/phineas_gage_neuroscience_case_true_story_of_famous_frontal_lobe_patient.html


text:
What is the magnification necessary to see pond life
My daughter is 5 and wants to learn about Biology. I thought a great start is to see life from pond water through a USB microscope. It would be great if she could see organisms like amoebas, flagellates and ciliates with her own eyes. The microscopes I have seen typically have a zoom range of about 40 to 400x.
Would this range be sufficient to see microscopic pond life?

+1 for awesome parenting and an intellectually curious child, as well as the good question.

It's advised not to start using a regular (meaning here transmitted light) microscope with kids under the age of about 10-12. It has to do with their brain being insuffiently developed to relate the two dimensional microscopical image with the three dimensional reality... I wouldn't know. I'm not a psychologist nor a neurologist, but however I am a dad of a 10 years old girl and an avid amateur microscopist with some 45 years of experience in that field. When my kid turned 8, I gave her one of my microscopes: a nice Zeiss Standard. The first time we did some pond dipping together, we found som

@mydaftquestion Mum teaches biology. she often had a pond slurry aquarium, which is  very interesting for children. they often harbor Cyclops, Daphne, Planaria, Cyclops, Snails and various types of algea. You can use a vase. For microscopes you can mix up some sticks and hay in a mug for 2 days. 10-100x is the best range.

2019-05-01 Edited: Updated dead links
From the comment section:
I would go with a cheap one with a magnification of ~40X. According to this source, 10-20X is already sufficient to see large protozoans and algae in a pond. Here some suggestions on what you could look at.

Both links are dead now.

@PiotrChojnacki Thanks for letting me know! The first link should be back soon (website is under maintenance). The second link is now restored (broke due to a change in the address name).

To me, microscopes are like pacemakers for your heart, they only come in two main categories, junk and not junk. The good news is pacemakers are way less complicated.
In short, 400x (on a $100 or so compound microscope) SHOULD certainly get you all the quality high school level bio class stuff a pond has to offer, without a lot technical skill to try to see it. BUT it is about CLARITY not just zoom. For pond watching, you want a compound (or phase) microscope with four main ingredients - a light condenser, a 10x objective piece, a 40x objective piece, and a 10x eyepiece. ?Why:
Most of the time, unless you are going to spend considerably more money on something that claims really high magnification (ie 1000x - 3000x etc) you wont get clarity and detail, which is everything.
to get best results for a beginner - First you have to look at what is called the "objective piece" (which is the nozzle looking piece that actually looks down into the specimen - it is a lens mechanism) your microscope MUST INCLUDE one objective piece with a 10x AND an object piece at 40x (but NOT so much a 100x - 100x is not needed and requires more work, 60x is good, but NOT 100x unless you are already expert level). These objective pieces should also have a minimum - lets say 'quality' - rating of "achromatic 160" or otherwise an "infinity" rating on what is called the "DIN rating" on that "objective piece." Decent quality microscopes usually have this rating printed right on the objective piece and objective pieces are removable and swappable. Usually, your good basic microscope has 3 objective pieces with different magnifications ranging 4x - 100x. The eyepiece (where you actually look into) should have at least a 10x magnification. The two of these together (40x X 10x), will give you an enlargement of 400x which is the benchmark for "good or quality."  This shopping list also gives you the best value for your money. In fact, you can spend 100 bucks or less for these essentials, while others will cost you 100 bucks or more and DO NOT offer these essentials even though they come in brighter, prettier colors. You can also spend $300 and get a microscope with these min standards that will last her until college (and is upgradeable). SECOND - assuming she is not doing anything like virus research yet - the compound or phase microscope should have a light condenser (which  would be a red flag if it did not).
The only other thing I think is important is to make sure it is a plug in - not just battery operated. That tends to go hand in hand with better quality, but doesn't necessarily mean more expensive.
The things that I mentioned are all the minimums that are inherent in microscopes that give a quality CLEAR image from most, if not all, of what you want to look at from a pond (but you can go much deeper). This can be had for $100 in the year 2020 or 2021. However, these very same microscopes that have these standards will typically include many more useful features (same price - all included).


text:
How does a neuron change as you learn?
I am currently taking a course called "Introduction to Machine Learning with ENCOG 3", and I have a question about how well the Artificial Intelligence (AI) algorithm for a "neural network" corresponds with how an actual neuron works.
In the course, they model a neuron like this:
x1, x2, etc. are voltage inputs, the wij are weights.  The inputs are multiplied by these weights and summed up by the neuron.  The neuron then has an "activation function" which then takes the sum of weighted inputs and calculates an output, typically a value between 0 and 1 (or between -1 and 1). You can think of the wij as representing dendrites (a higher weight means a more dense and thus conductive dendrite), and the output of the activation function as the voltage that gets sent down an axon.
The AI neural network algorithm creates a kind of intelligence by modifying the weights (wij shown in the picture).
My first questions is: Is this a good approximation as to how neurons actually work?  That is, do our neurons "learn" by changing the weights (dendrite density, conductivity)?  Or, is there some other mechanism that is more important (e.g. do neurons learn by changing their activation or summation functions?)
My second question is: If neurons really do learn by changing the density of dendrites, then how fast does this happen?  Is this a fast process like DNA replication?  Does the neuron quickly generate (or decrease) dendrite density when it receives some kind of biochemical signal that it needs to learn now?
I understand that much of this might not yet be known, but would like to know how well the AI algorithm corresponds with current theories on biological neural networks.

have you tried googling and if so, what have you found? these questions are textbook/wikipedia level. for example, you might start with https://en.wikipedia.org/wiki/Hebbian_theory

Note that Hebbian model is quite a simplified one. More complex models of learning exist. There are several posts here that have dealt with similar topics: http://biology.stackexchange.com/a/3783/3340, http://biology.stackexchange.com/q/1198/3340, http://biology.stackexchange.com/q/11276/3340, http://biology.stackexchange.com/q/2595/3340, http://biology.stackexchange.com/a/31310/3340, http://biology.stackexchange.com/q/7762/3340.. Is your question about any topic that is not already addressed by these posts?

@WYSIWYG OP asked for a comparison of the above model to biology. Those posts don't address functional modelling at all.

With respect to your first question, that model isn't intended to take time into account, but is based on Hebbian learning with the goal of computability. It's generally used in simple pattern recognition situations where each case has no bearing on the next. The learning portion is performed ahead of time during the training phase. For example, a deterministic perceptron isn't permitted to change after training. In contrast, the Biological Neuron Model is much more complex, and uses a variety of ordinary differential equations to integrate the cumulative behavior of neurons over time. As such, those models are non-deterministic and don't see as much practical use outside of experimentation.
To address your second question, neurons themselves don't "learn." A single neuron is essentially meaningless. Learning is an emergent process created by the interaction of several systems at once. While one influencing factor is connectivity (zero for no connection, non-zero for the inhibitory or excitatory connection which emulates both synaptic and non-synaptic), what you might call short term learning can also be performed by existing clusters of neurons, without any change in connectivity. Biologically, this is what must occur before any of the comparably slow process of tissue remodelling can take place, and the computationally equivalent process is only possible in time-aware models like the aforementioned Biological Neuron Model.
Take, for example, someone who wishes to learn to play guitar. When they begin playing, existing clusters emulate the desired behavior as best as they can. These neurons act as the functional scaffold that initiates and drives the neuroplastic process. Playing becomes easier because this scaffold becomes more efficient as new connections (shortcuts) are created, existing connections are strengthened, and irrelevant connections are inhibited. The improved scaffold in turn allows further improvements. Newborn neurons may also migrate to the area, though the how, why, and when of that process is unclear to me. This "behavior emulation" or "short term learning" process used in practicing the guitar, or whenever a novel situation is encountered, must be primarily governed by excitatory and inhibitory neurons' influence. Otherwise the whole process cannot even begin.
Further reading

Parameter estimation of a spiking silicon neuron.
Synaptic plasticity, memory and the hippocampus: a neural network approach to causality
Signaling mechanisms in cortical axon growth, guidance, and branching

Do you have references for your second claim?

This model was a reasonable approximation when it was formulated. However, as we learn more about synaptic integration, it appears that neurons are best approximated by two-layer neural networks (1). In this way the active properties of individual dendrites are better taken into account. Each dendrite, or at least a group of dendrites, is viewed as capable of performing input summation from individual synapses, independently of the integration at the level of the soma.
Regarding your first specific question, mechanisms of plasticity other than modifying the individual weights have also been described, for example as you suggested, by modifying the intrinsic biophysical properties of neurons that lead to firing (2). These would be equivalent to altering the sigmoid function or all the weights collectively.
Regarding your second question, we do not think that changes in the weights happen through modification of the dendrite as a whole. Rather, they represent changes at the level of single synapses, what are termed 'synaptic weights'. The biological phenomenon underlying synaptic weight change is referred to as synaptic plasticity. It is thought to manifest through a variety of biophysical mechanisms, including incorporation of new receptors at the post-synapse, changes in those receptors' conductivity, increase in the number of pre-synaptic vesicles etc. These events can be quite fast, in the order of seconds to minutes (3). More long-term changes of the weights, referred to as long-term potentiation are thought to depend on protein synthesis which is a slower process.

References
1) Poirazi, P., Brannon, T., & Mel, B. W. (2003). Pyramidal neuron as two-layer neural network. Neuron, 37(6), 989–99. http://www.cell.com/neuron/fulltext/S0896-6273(03)00149-1
2) http://www.scholarpedia.org/article/Intrinsic_plasticity
3) Harvey, C. D., & Svoboda, K. (2007). Locally dynamic synaptic learning rules in pyramidal neuron dendrites. Nature, 450(7173), 1195–1200. https://doi.org/10.1038/nature06416


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Attraction and hormones levels
Why do we ignore all imperfections in people we fall in love with for a couple of months, but after a certain period we start noticing imperfections?
Can hormones - or any chemical - be used to influence someone to fall in love with you?

Related question: http://biology.stackexchange.com/questions/17250/biology-in-romantic-love  @murmansk

@Mesentery I would like to say that dopamine won't cause "romantic" attachment. It would only cause sexual attachment.

@kirill2485 I don't understand why u commented this :)

well thats what the question asks for. the other answer you linked said that dopamine is a love hormone, when it is a reward hormone, and I would like to make sure that flo knows that dopamine is not gonna cause "love" or "bonding"

Yes. The chemical/hormone that causes attraction is called serotonin. That's what causes attraction between two people. Theoretically, chemicals can be used to make people fall in love with you, such as MDMA, which increases serotonin levels. If the "animal" (such as a cat or a monkey), was in the same room as you and you gave the cat MDMA and you were the only one in the room, the cat would bind with you and seratonin would be released.
This is why MDMA and methamphetamine are known to cause homosexuality and fetishism, for the drug tricks the human into thinking that serotonin is formed with a guy who he is hanging out with or what he is doing at the very moment.
Another hormone that is a "love" hormone is called oxytocin, but this chemical will only cause bonding once the love is formed.
In short, serotonin makes someone fall in love with you, while oxytocin will keep someone in love with you.

References? This sounds like a tremendous oversimplification and exaggeration.

I didn't get this from any sources, just personal experience from participating in numerous clinical trials + knowing the science behind it. But if you want a source:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3183515/ . "This was because oxytocin is not unlike the drug ecstasy, which triggers the release of serotonin, dopamine and oxytocin in the brain and heightens users’ feelings of trust and intimacy, even among complete strangers. "

@CharlesE.Grant Alright, I found an article that shows that MDMA is used as a date-rape drug by making the victim fall in love with the offender: https://www.ncbi.nlm.nih.gov/pubmed/16681170

No, the paper doesn't say that at all! It says that prosecutors, police  officers, and toxicologists have made that argument in date rape cases, but that it isn't really supported by the known psychology of the effects of MDMA. From the paper: "MDMA and amphetamines are not usually able to rob a conscious person of their free will. It is for this reason that producing unconsciousness is a likely aim of the person intending to perpetrate a drug-facilitated sexual assault, as distinct from those intending to engage in seduction, in which suggestion may play a significant role."

@CharlesE.Grant "sexual desire linked with methamphetamine use, remove a person's ability to give a reasoned consent, turning the person into "a helpless slave" to their own sexual desires and those of the alleged perpetrator. "

That's a selective quotation. The full quote is: "However, some law enforcement agents and others have recently obtained convictions by arguing that the empathy· generating and sensual effects of MDMA. and an occasional increase in disinhibition and sexual desire linked with methamphetamine use, remove a person's ability to give a reasoned consent. turning the person into "a helpless slave". That is, it is an assertion by law enforcement, not a demonstrated fact, and certainly not one demonstrated by that paper. (emphasis mine).

I've once overdosed on MDMA and all it was was serotonin syndrome and thats it..

If you actually read the paper rather than just the abstract you'd see that that's part of their point. Alcohol and GBH are used as date rape drugs because they render the victim comatose, and completely unable to resist. MDMA doesn't render the victim unconscious, so it's less likely to be useful as a date rape drug. It may disinhibit people, and that may lead some people into activities which they later regret, but that's a pretty far cry from turning them into sex slaves.

@CharlesE.Grant There's also this: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4023138/
but it doesn't say much.

Let us continue this discussion in chat.

For anyone reading comments, we ended the discussion with this link: https://www.hindawi.com/journals/pd/2012/603631/


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What does the end of DNA look like?

EcoR I ........ 5'-GAATCC-3'
  BamH I ....... 5'-GGATCC-3'
  Hind III........ 5'-AAGCTT-3'
The enzyme BamHI recognizes a palindromic sequence and leaves one strand longer than the other. A piece of DNA is cleaved by BahM I. What does the end of the DNA look like?
A. ...GATCC-3'
       ...C-5'
B. ...C-3'
       ...GATCC-5'
C. ...G-3'
  ...C-5'
D. ...G-3'
  ...CCTAG-5'
E. ...CTAGG-3'
  ...GATCC-5'"

I understood that one strand should be longer than the other, that's why I eliminated the "C" and "E" answer choices.
Then, I thought the answer choice is the "A" one. The first strand is similar to that in the data in the task, while the second is palindromic to it.
But this answer choice is incorrect. Then, I chose the "B" one. I thought: if we are given the sequence 5'-GGATCC-3', then the sequence 3'-GGATCC-5' is palindromic to it. (In this case, we have different letters near each number. That probably means they are vise versa versions of one another.)
It turned out the correct answer choice is the "D" one. I found such an explanation:

The end of the DNA cleaved by BamH I is complementary to the
  recognition site sequence shown in the table. One strand must also be
  longer than the other. The sequence CCTAG-5' is complementary to
  GATCC-3'.

But I can't understand this explanation... Please tell me what I do wrong..

Here is a quick drawing of how BamHI cuts the DNA:

As you can see, after cutting, the two ends are actually the same (always read sequences from 5' to 3').


text:
How are reflexes suppressed?
What neurophysiological process keeps reflex arcs in check? For example, the withdrawal reflex causes the hand to jerk back when the fingers touch something painfully hot incidentally. However, that reflex can be voluntarily suppressed when one deliberately touches that same hot object on purpose. What neural process is involved in conscious suppression of reflexes?

Short answer
The pain withdrawal reflex can only be suppressed when touching something painful on purpose. Deliberate, conscious contraction of the extensor muscle before reflex initiation can prevent the contraction of the flexor muscles once the reflex is started.
Background
The pain withdrawal reflex arc (Fig. 1) receives input from sensory neurons that enter the dorsal part of the spinal cord via the dorsal root of the spinal nerve and synapse onto interneurons within the spinal gray matter. The interneurons in turn synapse onto motor neurons, which send axons that exit the cord via the ventral root. They conduct information to the muscles. The resulting withdrawal reflex is initiated by activating motor neurons of the flexor muscles (agonist), and simultaneous inhibition of the motor neurons to the extensor muscles (antagonist). This loosening of the antagonist while the agonist is being contracted is referred to as reciprocal inhibition (Crone, 1993). More important to the question is the fact that the motor response is well under way before the signals responsible for the conscious sensation of pain (which exit the reflex pathway in the spinal cord) ever reach the brain (Cornell University).

Fig. 1. Schematic of the pain withdrawal reflex arc. Source: Washington Uni.
Hence, the reflex pathway is initiated even before we are aware of any pain. The only possible way to suppress a reflex that is faster than perception is to start counteracting the agonist (flexor) before the reflex is initiated, i.e., by contracting the antagonist (extensor) before touching the painful object.
Reference
- Crone, Dan Med Bull (1993); 40(5): 571-81


text:
How does the muscle return to its resting state after muscle contraction?
I know that when ADP binds to the myosin head, it moves along and as it does so, it releases the ADP. The ATP attaches to the myosin head and releases the myosin head from the actin filament. Then the enzyme ATPase hydrolises the ATP to ADP, causing the myosin head to move to the original position.
My question is:

How does the actin filament (troponin) move to its original
position? Does it use a mechanism similar to a spring?
Is there a limit to how much the myosin head can pull the actin filament?

Christiaan has answered your first question, it is external constraints that restore the muscle `rest' shape — this is also the case for nonskeletal muscle as the bladder.
On question 2, I will give a little more details, broadly based on Huxley 1957: imagine the muscle is trying to contract against something infinitely resistive. Full contraction cannot be achieved. Myosin heads still bind to actin, but actin cannot slide wrt myosin filament, and only a local deformation is possible under this tension increment. But myosin heads don't stay bound for ever, and when one detaches, this tension increment is lost locally (there'll be heat produced, dissipating this energy), thus the global muscle tension doesn't increase further. This is a built-in limitation rather than a question of how much energy is available.

ad 1. : In skeletal muscle, contraction of the antagonist stretches the agonist to its original position (Fig. 1).
ad 2. : Yes, ATP generates a fixed amount of energy that limits the force generated.

Fig. 1. Agonist/antagonist pairs in the skeletal musculature have opposing actions. source: wikipedia

Does the (maximum attainable) force saturate when available ATP is above a certain threshold? If so, what would be the new limiting factor?

@fs137 - At the protein scale, each power stroke uses 1 ATP per cycle, so ATP concentration is not the limiting factor

Thanks. So the time scale for each power stroke (and number of 'units') limits the amount of force that can be generated?

@fs137 - afaik, yes


text:
Relation between trigeminal and facial nerve in sympathetic response
In my neuro-anatomy course notes I found that the facial nerve "uses" the trigeminal nerve to reach its targets. However, I have yet to find any diagram or reference that indicates how this is done. How is the trigeminal nerve "used" by the facial nerve?

Certain parts of the facial nerve cooperatively share structure of trigeminal nerve. For example, to reach the sublingual gland, the chorda tympani of the facial nerve joins the mandibular branch of the lingual nerve. Additionally, to reach the lacrimal gland of the eye, the greater petrosal nerve branch of the facial nerve joins the structure of the maximallary branch of the trigeminal nerve.
For a pictorial demonstration of this, please refer to page 1069 of Clinically Oriented Anatomy 7th edition by Moore.


text:
Why is alcohol such a weak drug?
Most day to day drugs such as caffeine and paracetamol require a dosage in milligrams to have the desired effect.
Why then, does it take many tens of grams of alcohol to have a tangible/noticeable physiological impact on the body? What is it about the composition of alcohol that makes it so weak, gram for gram, compared to other recreational and medicinal drugs? Are there any other psychoactive drugs that require similar dosages to alcohol to have an effect?
For clarification, as per the comments
For example, as a 90kg adult I can consume 30g of alcohol (3 UK units) before it has any noticeable impact, whereas a coffee containing just 100mg of caffeine (300 times less than alcohol) produces a noticeable reaction.

It is an interplay between pharmacokinetics and pharmacodynamics. The question is superbly broad; you talk about overdose first and next to "being hammered". You won't get 'hammered' by paracetamol. You can get battered by it, as an overdose mostly ends through internal bleeding. In contrast, heroine OD is characterized by respiratory failure. What exactly is your question and could you focus it? I think I know where you are heading, but I'd rather not make drastic edits on such a vague question, given the risk of missing the point.

Alcohol is easily metabolized to acetyl-CoA.

Plus: a regular paracetamol dose for an adult is a gram. Which is 1000 mg, but I would call it also the gram range. Likely it's just the worst kind of example drug in the light of this question.

Fats or sugar are even "weaker" drugs. In any case, don't forget that The dose makes the poison. As a consequence, water is a very "weak" drug.

Perhaps because alcohol is fairly common in nature (e.g. in overripe fruit), so fruit-eating creatures with a low tolerance to its effects would have been selected against.

@jamesqf One would think drunk monkeys would be more likely to reproduce :)

@jiggunjer: But also more likely to be eaten by leopards &c.

As Christiaan already pointed out, this depends on the pharmacokinetic and pharmacodynamic parameters. The effective drug concentration depends on the drug-receptor association constant and the drug degradation constant (for a highly simplified model). The degradation/removal depends on the abundance of the enzyme catalyzing this reaction.
Ethanol is primarily thought to cause intoxication by activation of GABAA receptors. However, only a very specific subclass of these receptors are activated at the levels of alcohol that one consumes during "social/moderate" drinking. Others require very high alcohol concentrations (Hanchar et al., 2006). Basically alcohol is not a very specific agonist/antagonist of any neurotransmitter or neuromodulator receptors. In other words, it does not have high affinity to any of these receptors. There is no answer to "why". I would guess that since ethanol is a very common molecule (and is also used as energy substrate by some organisms, to a certain extent), high sensitivity to ethanol would have been evolutionarily selected against.

Although many proteins show changes in their function at very high
  alcohol concentrations (>50 mM), the molecular basis for behavioral
  alcohol effects at low to moderately intoxicating doses experienced
  during social alcohol consumption remains elusive (1). GABAA receptors
  (GABAARs) and the inhibitory GABAergic system have long been suspected
  to be targets for acute alcohol effects (2–4). For example, the GABAAR
  agonist muscimol potentiates the sedative actions of alcohol, whereas
  the opposite effect, a reduction of ethanol (EtOH)-produced sedation,
  is detected with the GABAAR blockers picrotoxin and bicuculline (5).
  Although most GABAAR subunit combinations can be activated by high
  (anesthetic) alcohol concentrations (6), only very specific GABAAR
  subunit combinations (containing the δ as well as the β3 subunit)
  exhibit dose dependencies that mirror blood alcohol levels that are
  associated with mild to moderate intoxication in humans (7, 8) (≈3–30
  mM, because the legal drinking limit is 17 mM or 0.08%).

From Hanchar et al., 2006

Other psychoactive drugs are highly specific and have high affinity to their corresponding receptors. For example, caffeine acts on the adenosine receptors at µM concentrations (Daly et al., 1983). This is because of caffeine's high affinity to these receptors.
Moreover, ethanol is readily metabolized to acetyl-CoA by alcohol dehydrogenase and aldehyde dehydrogenase enzymes which are quite abundant in the body. Some people who have mutations in these enzymes leading to their reduced activity, "get drunk" and experience hangovers even with a low level of alcohol consumption.

Good, nicely formulated and concise answer +1


text:
What is the path taken by an oxygen molecule as it passes into the lungs to a muscle cell in the body?
My teacher tried to describe this question to me, but I just don't  get it.

If you have anything specific to ask after looking at my answer below, please refine your question. Note that I voted to close because of the textbook-nature of the question and lack of research effort. See the help center on homework for assistance in asking good homework questions.

See the figure below:

source: Human Anatomy


text:
How are we able to find the specific sites at which DNA binding proteins bind?
We know that some DNA binding proteins are site specific, that is they recognise and bind to a specific nucleotide sequence. My question is how can we precisely tell at which sites they bind? Is it the amino acid sequence of the protein? Or is it the repetitiveness factor in case they bind to multiple locations on the chromosome?

Do you have antibodies agains your DNA binding protein?

If there are no antibodies for ChIP, DNA footprinting + sequencing can work too.

I will try to answer the question in the title: how can we know the sites where DNA binding proteins bind?
I'll explain two experimental methods to identify binding sites on DNA.

DNase footprinting
ChIP-seq (Chromatin Immuno-Precipitation with sequencing)

DNase footprinting
We can locate proteins bound to DNA by their ability to protect DNA from some degradation. DNase I cleaves DNA in an almost-random manner and is inhibited by proteins covering ('protecting') the DNA backbone.
In order to locate a site which is protected from DNase I cleavage, we need to take some genomic DNA and treat it. We need separate, short lengths of DNA to examine - we can obtain these from genomic DNA by PCR amplification of different stretches. We need to label these amplicons at one end only, beta radiation is a good choice of label.
Taking one labelled amplicon, exposing it to DNase I for a short time - not long enough for complete digestion - produces cleaved DNA of all possible lengths, which looks like a 'ladder' after separation by gel electrophoresis. Digestion time must be short, such that many DNA are only cleaved once, to have a complete ladder.
Repeating this digestion with your interesting protein present gives a ladder with a missing segment. This is because your protein protects a length of DNA from cleavage.

Important points: DNA is labelled at one end only. Hence we only see the label-end-piece of DNA after cleavage: if DNA is labelled 5' and cleaved in half, we only see 5' halves. Thanks to this, we can estimate the position of the binding site: if our DNA is 100bp and our ladder has lengths 0 to 70bp, a gap, then more from 85 to 100bp, then our binding site is somewhere inside 70-85bp from the labelled end. We can sequence the piece of DNA and read the sequence of nucleotides 70-85.
ChIP-seq
This is a more recently-developed method, which is more suited to studying where a protein binds all over the genome or all over a chromosome. It requires an antibody which specifically binds your interesting protein.
First, a 'snap-shot' of global protein-DNA binding is taken by irradiating cells with UV light, causing covalent cross-links between DNA and binding proteins. Chromatin (DNA with associated proteins) is isolated from cells and chopped up to smaller fragments; the cross-links preserve our 'snap-shot' of proteins and short lengths of their bound DNA.
This mixture is incubated with an antibody (immobilised on beads) which binds our protein of interest. We can separate the antibody-covered beads and hence our protein along with it.
Finally we can sequence the DNA fragments caught in this way. It's like "fishing for binding sequences". The end result is a distribution of where our protein was bound across the genome at the time of our snap-shot.

Ideally the DNA fragments should be long enough to place them uniquely in the genome. There are advanced PCR and sequencing methods which separate DNA fragments in to 'bubbles' in an emulsion containing one molecule of DNA each. In this way, we can sequence all the variants that are present and by counting the number of sequences ('reads') of each type, we have a measure of the abundance of each sequence. This abundance is interpreted as the occupancy of the protein at different binding sites.

Genome-wide studies of DNA binding have shown us that proteins are distributed around the genome. They have preferred binding sites but also have some affinity for similar sites, and spend some of their time bound to non-functional bits of the genome.
Especially in mammals, a 'true' binding site isn't only (and isn't always) determined by having the highest affinity sequence, but also by being clustered with binding sites for other co-factors. This is because, in mammals, proteins often bind DNA, not solo, but as parts of large complexes which can interact with nucleosomes and which allow regulation of transcription or whatever else.

My question is how can we precisely tell at which sites they bind? Is it the amino acid sequence of the protein? Or is it the repetitiveness factor in case they bind to multiple locations on the chromosome?

So, we can tell at which sequences (and where in the genome, even with what relative occupancy) proteins will bind to DNA by experiment. You could try to guess where they bind from their structure, but the way we precisely tell, is by experiment.
The amino acid sequence of a protein ultimately determines its folded structure, and there are many DNA-binding motifs or domains which appear in many different proteins. Some motifs bind the DNA backbone regardless of the sequence of bases, others bind specific sequences.
Let's take zinc fingers as an example. The best-known class of zinc fingers basically inserts an alpha-helix in to the major groove of the DNA double helix, where certain amino acids on the appropriate side of the alpha-helix make contacts with the nucleotide bases. These contacts can be hydrogen bonds, or van-der-Waals contact. (E.g. Histidine and serine tend to hydrogen bond guanine; phenylalanine 'ring-stacks' between As and Ts; and threonine contacts the methyl group of thymine.)

Zinc fingers are often found in arrays in proteins, as you might have been suggesting by "repetitiveness factor". Meaning, a single finger might recognise a specific 3 or 4bp sequence, which isn't very unique. A protein will usually have 3 or more fingers held with regular spacing, so that this string of motifs: ZFa-ZFa-ZFb might recognise the DNA sequence: GCTAxxxGCTAxxxCCAA which is a much more unique site (this is imaginary.)
So yes protein sequence and (thus) structure determines what sites a protein can bind (you can imagine a distribution of affinity for sequences, there will be a 'peak' sequence) - but again some proteins bind the DNA backbone non-specifically, and in mammals they often don't bind alone but within complexes.
People have studied protein-DNA binding by engineering their own arrays of zinc fingers or TALENs, and also by engineering their own DNA binding sites, through a process of 'artificial evolution': selecting the strongest binders, mutating them, and repeat. These kinds of studies might come up with a sort of optimal 'binding code'.

If you have taken the picture from an article then it is good to cite the reference.