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How to calculate extent of Sequence similarity
I had a problem that I was wondering if it could be solved by one of the techniques/algorithms used in bioinformatics to give the extent of similarity.
I have a Problem Statement: we have a sensor (its like a magnetic compass and has a dial with twelve equal zones- 30 degrees each) that every second outputs where its pointing. The typical random output of the sensor may look like (for example):

30 30 30 30 30 30 120 120 120 120 120 120 60 60 60 60 60 60 330 330 330 330 30 30 30 30 210 210 210 210 210 60 60 60 60 60 60 60 60 60 60 60 60 60 ……… etc.

We wanted to see if we can calculate a measure of similarity of two 4-minute sequence samples taken at different times during the day. (It would be great if we could state something like - the sequences are similar and there is a 1 in million (say) chance that we may be wrong.)

very interesting ... the standard methods all work on linear values, and not angles. Is the pattern "30 60 90" similar to "120 150 180"? (I.e. do you only care about relative movement, or also about the actual direction?)

It seems OP asked the question and never returned...

Well. You perhaps need not use the bioinformatic algorithms of string matching. These algorithms were primarily developed because of the extensive search space.
In your problem you just need to compare two recording experiments and you should use mathematical metrics for it. You have a 60x4 i.e 240 dimensional random variable. Moreover this variable is not discrete, it is continuous. For similarity measurements you have to use statistical tests or otherwise define a cutoff either on each element of the vector or the total magnitude defined by any norm.

I tend to agree that bioinformatics has no special general help for matching sequences of numbers.  Most of the specialized algorithms in bioinformatics are string oriented.
If distance metrics, Fourier or wavelet decomposition don't work, you might want to look for motifs in your sequence, then you might try a motif dictionary similar to an alignment algorithm.  They are like NGram algorithms, but then they extend out.

Build dictionary of all sequences of numbers from your reference sequence: say of 5 or 7 length.
Identify identical or better yet linear combinations of those dictionary entries and then expand the comparison by one index in either direction to get the maximal length of comparable identity/similarity.
List all your 'hits' by a score - a length and distance based metric.

is this the sort of thing you were looking for?

The first thing that comes on my mind is to use cross-correlation (CCF).
Essentially you compare one trace with variously shifted version of the other to see if there is a correlation between them.
For example (I am using R but you should be able to adapt this to your software of choice, I have added comments), say A and B are very similar, but shifted of a certain amount in the x axis (10 units in the example) and C is extremely different
# Set the random seed to get a reproducible example
set.seed(12345)
# Number of points per trace
n <- 1000
# All of the possible sensor values
values <- seq(0, 330, 30)
# Sample with replacement to get 100 random values
A <- sample(values, n, replace=TRUE)
# Let B = A shifted by 10 positions and then change one value every 5
B <- c(A[-1:-10], A[1:10])
B[seq(0, n, 5)] <- sample(values, n/5, replace=TRUE)
# C is a completely different trace
C <- sample(values, n, replace=TRUE)
# Plot the traces (I'm offsetting B and C just for visual clarity)
plot(A, t="l", col="red", lwd=2, ylim=c(0, 1200))
points(B + 360, t="l", col="green", lwd=2)
points(C + 720, t="l", col="blue", lwd=2)

# Now calculate the CCF
c.AB <- ccf(A,B, 100)
c.BC <- ccf(B,C, 100)
c.AC <- ccf(A,C, 100)

# Superimpose the CCF plots
plot(c.AB$lag, c.AB$acf, t="o", col="green", ylim=c(-0.5,1), ylab="CCF", xlab="Lag")
points(c.BC$lag, c.BC$acf, t="o", col="red")
points(c.AC$lag, c.AC$acf, t="o", col="blue")
abline(v=10, col="grey", lty=3)
legend("topleft", c("A-B", "B-C", "A-C"), col=c("green", "red", "blue"), lty=1, lwd=2, pch=20)

The CCF graphs look like this:

This graphs means that there is a strong positive correlation (max correlation = 1, here you have 0.8) between A and B and that they are shifted of 10 units. You can see this because the peak is at lag=10, corresponding to the gray dashed line, so the maximum correlation is when you shift trace B by 10 units.
B and C and A and C are instead uncorrelated.

You can try dynamic time warping, or string kernel as a measure of similarity. However, similarity is highly context-dependent, and you may have to invent your own notion of similarity. First you need to ask yourself what do you consider similar. This is a hard problem, and borrowing arbitrary solutions from different fields may not be the best idea.


text:
Is there any advantage of having mitochondria for aerobic respiration?
If we consider the pathway of breakdown of glucose which includes glycolysis, the citric acid cycle and the electron transport chain, all these processes takes place in some  prokaryotes and eukaryotes. In prokaryotes all these processes take place in cytoplasm while in eukaryotes the last two processes take place in mitochondria.
So is there any advantage of performing the last two processes in the mitochondria? Does it yield more energy? If there is no advantage, what is the point of having a mitochondria (at least for this process)?

From the evolutionary point of view, the eukaryotes acquired these metabolisms (except glycolysis) from their prokaryotic endosymbionts. Not all prokaryotes have the ETC. The free living ancestor of mitohondria is supposed to be the alpha-proteobacterium.
Now, glycolysis is a common pathway in lot of lifeforms perhaps because of abundance of glucose. TCA cycle is coupled with ETC at certain steps which makes it essentially a part of aerobic metabolism.
The reason for having a dedicated organelle for respiration
ATP synthesis is a membrane process. Imagine a large prokaryotic cell- as big as an animal cell. Such a cell cannot take care of its energetic demands which primarily consists of protein synthesis with the given area of membrane i.e it needs much more ATP-synthases than it can have to cope up with the energy demands of maintaining such a huge cell (this index is approximated based on surface to volume ratio). Therefore it is wise to harbor multiple efficient organelles i.e. mitochondria which themselves have just a small essential genome and proteome to maintain.
For a better understanding, please read this article. I just loved it.
There is also a book by the same author about mitochondria called Power, Sex, Suicide.

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How do you differentiate between SR protein and SR-like protein?
What are the criteria that the researchers use to choose whether a protein is an SR protein or and SR-like protein?

Im not 100% certain. If something is called an x-like protein, it usually means it is homologous and has some sequence and / or structural similarity to x. However, there may not be enough biochemical evidence to say definitively that it is in family x. I came across this paper where they are speaking about an SR-like protein. They said:

While budding yeast lack alternative splicing, they do have three SR-like proteins: Npl3, Gbp2, and Hrb1. However, these have been best characterized for their roles in mRNA export, leaving their potential roles in splicing largely unexplored.

So in this case the protein has a serine/arginine binding domain and an RNA binding domain (just like SR proteins) but most of the biochemistry points to them being involved RNA export, not splicing (splicing, of course is what SR proteins are known for). So, they get the name SR-like. It will vary though. There is not a unified protein naming system

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Where can I find pdb files for macromolecules like receptors?
I have tried going to the RCSB website and quite frankly it was useless since when I looked up receptors like say the metabotropic glutamate receptor 2 (mGluR2) I got no helpful results.

The RCSB is the primary database for 3D structures of biomacromolecules, if it isn't in there, there is likely no public structure available for that molecule.

As pointed out in the comments, if you look for PDB files and you don't find them in the PDB, there is no solved structure. However, you can look in databases that contain models of proteins. Especially for the receptors the coverage has been increasing in recent years and so you may be lucky.
A good starting place to look for protein information is UniProt, where you find links to the Protein Model Portal and SwissModel. They contain models based on the PDB structure for Metabotropic glutamate receptor 3.

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Why do brain cells use shuttles that pass electrons from NADH to FAD?
Brain cells are cells require one of the highest amount of energy of any cell of body. So why do they use a shuttle which will transfer electrons from NADH produced in glycolysis to FAD(and there by reduce the no of ATP that can be made ) ?

No that doesn't happen. are you sure ?

@WYSIWYG she is correct. Her question refers to the glycerol phosphate shuttle which is more prominent than the malate asparate shuttle in brain and muscle cells.

@SatwikPasani.. Sorry, I didnt know about it so thanks for letting me know. I did a quick check and I could only find this article on G3P shuttle and brain; I couldnt access it right now but the abstract says that G3P shuttle is minimal in neurons and almost zero in astrocytes.

@WYSIWYG Actually, as is already mentioned in the reference abstract you cited, it is not very clear what the distribution of these shuttles is. But the extract refers to pharmaceutical determination studies only. Earlier biochemical studies showed high G3P shuttle prominence in muscles and neuronal tissues but has always been under active controversy. My information was older but Your reference is quite recent and may have solved the issue, but for me it's behind a paywall.

I looked at that WYSIWYG's abstract and it doesn't explain the poster's main concern, namely that moving a hydride via NAD has a different energy yield than moving one via FAD. Won't it be irrelevant if the reducing equivalent enters the mitochondrion via glycerol phosphate shuttle vs malate aspartate shuttle?

In the absence of unanimous consensus and sources regarding the actual distribution of these shuttles,(wikipedia favours G3P shuttle abundance) let me try to explain the cause if the glycerol-phosphate shuttle is assumed to be prominent in brain cells. Several possible reasons might lead to this:-
1) The existing metabolic pathways are all intertwined to form a complex metabolic net. This means that invariably, the intermediates of any pathway are the products or intermediates of several other pathways. Therefore, the G3P shuttles require Glycerol-phosphate and Glycerol-phosphate dehydrogenase (I and II) which might be naturally abundant in brain owing to its use in strict lipid metabolic control in nervous tissue. This means that tapping the already high G3P for use as a shuttle compared to synthesising and operating a distinct metabolic shuttle is more profitable. Furthermore, operating Malate aspartate shuttle migh require intermediates whose high concentrations (required to maintain the shuttle) might negatively interfere with existing metabolic pathways like protein synthesis and regulation.
2) This shuttle has much faster operation time than Malate-Aspartate shuttle and hence is very useful in shuttling reducing equivalents fast in muscles and brain. Compared to the malate aspartate shuttle, it is shorter and hence faster and less prone to cessation due to unavailable intermediates or enzymatic disruption. Due to several enzymes working in Malate-aspartate shuttle, it has a narrower pH and temperature optima than the G3P shuttle which is shorter and depends on lesser intermediates, and hence is less prone to disruption.
3)The last and the most far-fetched (but relevant)reason is that the loss of one ATP may not cause much of a problem because of already high respiratory rate, high Oxygen delivery to brain and ability of the body to quickly transfer available energy sources to brain at the cost of other parts, at times of energy stress. This means that replacing the shuttle with a more energetically conserving one may not have a strong driving force for evolution to operate on, and therefore the presence of G3P may be because of something like phylogenetic inertia, that is, the prevalence of an ancestral character just because it is neutral and does not influence the fitness in a considerable manner. Therefore, the ancestral G3P shuttle would just not have been replaced here but this is very unlikely as G3P shuttle is prominent in 2 very high energy-demanding organs, muscles and brain.
Except the last outrageously far-fetched reason, all other reasons should be enough to explain its prominent presence (if it is true) in brain tissues.

Looking at this question, which has resurfaced after five years, I was not really convinced by any of the possibilities suggested in the answer from @stochastic13, commendable attempt though it is. It happens that I have just been consulting the section on these shuttles in Berg, Tymozcko and Stryer where the following is written:

When cytosolic NADH transported by the glycerol 3-phosphate shuttle is oxidized by the respiratory chain, 1.5 rather than 2.5 ATP are formed. The yield is lower because FAD rather than NAD+ is the electron acceptor in mitochondrial glycerol 3-phosphate dehydrogenase. The use of FAD enables electrons from cytosolic NADH to be transported into mitochondria against an NADH concentration gradient. The price of this transport is one molecule of ATP per two electrons. This glycerol 3-phosphate shuttle is especially prominent in muscle and enables it to sustain a very high rate of oxidative phosphorylation.

I know little about brain metabolism, but if the demand for energy in brain is higher than in other tissues (as stated in the question) then the above would seem to provide the explanation: the greater production of ATP by oxidative phosphorylation possible when NADH entry into the mitochondria is independent of its internal concentration more than offsets the price in ATP of that entry.

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Why in some cells is GTP made in citric acid cycle and in some ATP?
In many  animals GTP is produced in citric acid cycle. While in  plants,bacteria and some animals ATP is produced. Why is this so ? What is the advantage ?

This step is catalyzed by succinyl-CoA synthase which has two different isoforms- one which produces GTP while the other produced ATP.
It seems from this study that predominantly anabolic tissues prefer the GTP-producing form whereas the predominantly catabolic tissues use the ATP-producing from.
In the same paper they discuss that GTP is important for protein synthesis and it is also involved in production of phospho-enolpyruvate by PEP-carboxykinase in mitochondria; therefore playing an important role in anabolic processes.


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Why don't plants get sunburned?
I just saw a video about the biology between sunburn, UVA and UVB and the different things we know about sunburn in humans. ( http://www.youtube.com/watch?v=ZSJITdsTze0 )
I wonder what keeps plants from getting sunburned?
By sunburned I meant that ultraviolet light injures the plant so that it requires some sort of healing process for the plant to be as healthy/strong/resistant to disease as a plant that isn't harmed.

First define what "sunburn" means with respect to plants.

It is seen that cyclic electron flow helps plants growing in high intensity of light.

they kind of do get sunburned. if they dehydrate their leaves become brown and shriveled.  it doesn't resemble animal sunburns.  when they are green they do have a lot of pigment that is the original sunscreen... it absorbs much of the light.

The following study shows evidence that UVB does damage plant DNA.

Rousseaux et al. Ozone depletion and UVB radiation: Impact on plant DNA damage in southern South America. Proc Natl Acad Sci U S A. 1999 December 21; 96(26): 15310–15315.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC24816/

Plants have more leaf surface area which is exposed to Sun and plants do need sunlight for Photosynthesis to produce food and oxygen. But how plants avoid getting sunburned ? (Sunburn for plants might mean like leaf getting dry or premature falling off etc). To explain this first we need to know the leaf structure and its mechanism to absorb light and heat.
Leaf structure:

(Image courtesy Complete Biology)
The major functionality of Waxy Cuticle on upper surface is(Leaf Terminology):

Insulation - Acts as an insulator preventing more heat absorption by the leaf surface. The lower surface of the leaf has 'Stomata' with 'Guard cell' which keeps the leaf temperature moderate by preventing maximum water evaporation. The plants have well adapted to various environment conditions by having various compositions in its waxy cuticle. This has prevented plants from losing water and getting leaf dry.
Light reflection - Surface of plant leaves also has hairy structures which will reflect the light and thus reducing the leaf surface from maximum light fall.
As we know the diffusion and osmosis process in plants to balance the water content in the cell across its body, we can say that depending on environment and temperature plants have mechanism to deliver water to leaves.

To summarize plants have developeb mechanism to prevent heating up of leaf surface which will dry it out. Hence they have evolved and adapted themselves to various environment to avoid getting sunburned. Similar question was answered here Why do plants do not burn
On the other side if there is any change in the environmental condition due to global warming or Ozone hole effect then dangerous rays from the Sun could damage the leaves.


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Can any one reaction in a cell be at equilibrium?
I know that metabolism as a whole can never be at equilibrium (otherwise the cell is dead !) but I wonder whether a few reactions in the cell could be at chemical equilibrium at a  given point of time.
Is it possible theoretically ? Is there any real example ?

@terdon Your link does help but actually I was thinking about chemical equilibrium i.e. when rate of forward reaction is equal to rate of backward reaction.

Accepted but it would be better if someone could give me a typical chemical reaction. For eg.Conversion of A to B by enzyme C is at equilibrium at some particular conditions.

@terdon Ok. I will search it a bit more. I just felt that it would be uncommon because I thought that there is no point in converting a thing into another thing just to convert it back to the same thing . But after the example you gave I think equilibrium is not that pointless, at least in this case .

let us continue this discussion in chat

@terdon. what you are referring to is perhaps treadmilling and that is a steady state not an equilibrium

@terdon: because polymerization and depolymerization are not the same reactions. New G-actin binds to the barbed end with the ATP whereas depolymerization happens because of degradation of ATP on the other end. This is something like protein formation and degradation. If these rates are equal then the entity is said to be in a steady state, not equlibrium

Polymerization is of course the opposite of depolymerization but they are not the same reactions. An equilibrium is a property of a single reaction.

@WYSIWYG fair enough, I'm deleting my comments since they were just plain wrong and only add confusion. Thanks for clearing that up.

Biogirl, sorry about that, I seem to have forgotten my chemistry :(.

I think there are a few principles that we need to consider before answering your question.
(a) When a reaction is at equilibrium, the rate of any elementary reaction is exactly balanced by that of the reverse process.  This is an important one.
The above principle follows from transition-state theory, which holds that the activated state for the reaction in one direction is that same for that in the reverse direction.  It also follows from the principle of microscopic reversibility at equilibrium or, more correctly, the principle of detailed balance at equilibrium, which states that “in a system at equilibrium each collision has its exact counterpart in the reverse direction, and that the rate of every chemical process is exactly balanced by that of the reverse process” (my emphasis) [Laidler, 1987, p 130]. It is important to realise that these two points of view are equivalent.  To again quote Laidler (p130), if one is working within the framework of TST “the principle of microscopic reversibility presents nothing new”.
To put it bluntly: a system where any elementary reaction, either explicitly or implicitly, is not exactly balanced by the reverse process is not at equilibrium. By this criteria, the actin example alluded to above cannot, even loosely, be considered at equilibrium.
This principle has many important consequences, even when a system is not at equilibrium. One is that the product of the ratios of rate constants along any path on a cycle equals the equilibrium constant between the forms (species) connected, and is equal to one around a full cycle (closed loop) (see Cornish-Bowden, 2004, p 104). [see Addendum for an example of where this consequence was not adhered to].
(b) When a species is in a steady-state, the rate of formation equals the rate of breakdown. The steady-state concentration may differ markedly from the equilibrium concentration.
(c) As @WYSIWYG has pointed out, an enzyme (catalyst) does not change the equilibrium constant for the uncatalyzed reaction.
(d) When we are dealing with equilibria, we are usually interested in Gibbs free energy changes.  For example (Silbey & Alberty, 2001, p 277).
ΔGo' = -RT ln K’
(In the above equation K’ is the apparent equilibrium constant, that is the equilibrium constant at specified pH, and ΔGo' is the standard transformed Gibbs free energy of a biochemical reaction.  More on this distinction, if you are interested, in the Silbey and Alberty reference quoted above).
The important point is that there is a relatively simple relationship between Gibbs free energy and the equilibrium constant. The Gibbs free energy, of course, gives a measure of the spontaneity of a reaction and also its capacity to do work.
When the transformed Gibbs free energy is of a reaction (ΔG') is zero, the reaction (at specified pH) is at equilibrium and cannot perform useful work, and reactions with negative ΔG' may be considered ‘spontaneous’.  It is also important to realize that equilibrium is a dynamic state: chemical bonds are continuously being broken and energy is continuously being redistributed (with no loss of energy). [I am dealing here with the transformed free energy, ΔG', that is the free energy change at specified pH, rather than ΔG (the pH independent value), as this is the most useful when considering a biochemical reaction.  However, similar conclusions apply to ΔG].

Having got those out of the way, I can now attempt to answer your question (slightly rephrased). Can a reaction in a metabolic pathway be at equilibrium?
To be extremely pedantic, if there is a flux through the pathway (net conversion of first substrate to end product) then the answer is no (Newsholme & Start, 1973, p 11). That is, if there is a flux through the pathway, ΔG' cannot be exactly zero for any individual reaction.   However, reactions in a metabolic pathway may be very close to equilibrium (Newsholme & Start, 1973, chapter 1).
Let’s (once again) rephrase your question.  Are there any examples of reactions in metabolic pathways that are close to equilibrium, and how can we determine this?
To again quote Newsholme & Start (1973, p11)  “In a series of reactions that constitute a metabolic pathway, a few may be displaced far from equilibrium, whereas the majority of reactions may be close to equilibrium”.
So how can this be determined? One way would be to measure the ratio of products to substrates (or the ratio of product to substrate pairs) in the cell, and compare this with the equilibrium constant.  Note that it is only the ratio of substrate/product pairs we are interested in, not the absolute concentrations. We might be interested in the NAD+/NADH ratio in the cell, for example.
That is, we measure the mass action ratio and compare this with the equilibrium constant.
Such measurements are fraught with difficulties, but let’s agree that they can be made. We could rapidly freeze the tissue sample to -190°C (using liquid nitrogen), for example, and then measure the ratio of metabolites.  Finally, it should be pointed out that comparison of mass-action ratio with the equilibrium constant is not the only way of deducing that a reaction is near equilibrium, and agreement between alternative methods is highly desirable before any firm conclusions are drawn.
Let’s consider glycolysis as an example.  It is generally agreed that the reactions catalyzed by phosphoglucoisomerase, phosphoglycerate mutase and enolase are all close to equilibrium: the mass action ratios and the equilibrium constants are about the same (see Newsholme & Start, 1973, p 98).
It is also generally agreed that the reactions catalyzed by phosphofructokinase and pyruvate kinase are far from equilibrium (see Newsholme & Start, 1973, p 98).
What is the rationale? In general, it is control reactions catalyzed by regulatory enzymes that are displaced from equilibrium. (A key property of a regulatory enzyme is that the activity is controlled by factors other than substrate concentration).
The enzyme phosphofructokinase is a good example.  This enzyme plays a key role in the regulation of glycolysis. Measurement of the mass-action ratio for this enzyme gives a value of 0.029, where the equilibrium constant for the reaction is about 1000 (see Newsholme & Start, 1973, p31). It is clear that physiologically this enzyme catalyzes a reaction that is far from equilibrium.
In conclusion, many reactions in metabolic pathways may be close to equilibrium, but regulatory enzymes almost always catalyze reactions that are displaced from equilibrium.
Finally, if anyone wishes to provide more recent references or to otherwise improve the answer, feel free to edit.
Addendum
For a well-known controversy in the enzyme kinetics field where the requirement that product of the ratios of rate constants around a closed loop equal the equilibrium constant for the cycle was not adhered to, see Selwyn (1993) and Topham & Brocklehurst (1992).  These authors were critizing the work of Varon et al (1992), who made a bit of a hash of things. If you are interested in this area, you may wish to read up on this controversy, which is very informative. (Selwyn’s paper is a great start). [All the above papers are freely available in PubMed Central].
References
Cornish-Bowden, A. (2004) Fundamentals of Enzyme Kinetics. 3rd Edn. Portland Press.
Laidler, K. J. (1987) Chemical Kinetics 3rd Edn. Harper & Row.
Newsholme, E.A. & Start, C (1973) Regulation in Metabolism. John Wiley & Sons.
Silbey, R. J. & Alberty, R.A (2001) Physical Chemistry. 3rd Edn. John Wiley.

Eric Arthur Newsholme (1935–2011) Obituary

Best answer anyone could give to my question :) Thank you so much !

Are you sure about "the product of the ratios of rate constants around a cycle (closed loop) equal the equilibrium constant for the cycle"? What is the equilibrium constant of a cycle? Shouldn't the product of the ratios of rate constants around a cycle be simply equal to one (Equation 1 in Selwyn (1993))?

Ah, I read the reference: it is not for the full cycle, but for parts of the cycle that connects different forms (e.g.: A $\rightarrow$
B $\rightarrow$ C and A $\rightarrow$ D $\rightarrow$ C in relation to the equilibrium constant for A $\leftrightarrow$ C)

Yes, I think you are right. This follows from the principles of microscopic reversibility and detailed balance, very well discussed by Laidler in Chemical Kinetics. But one needs to be very careful! As Laidler points out, there are many misapplications of these principles.

To quote for Laidler (p 286) "For any mechanism, involving any number of elementary and consecutive steps, the overall equilibrium constant is the product of the equilibrium constants for the individual steps, and is the product of the rate constants for the reactions in the forward direction divided by the product of those for the reverse reactions"

Yes, and this, remarkably, is independent of the specific rate law of each reaction, which often makes people forget that not all reaction rate laws obey the law of mass action.

I am assuming that you know the difference between steady state and equilibria. Your definition of equilibrium is correct; fwd rate = bkwd rate.
In a steady state the levels of a component remain constant over time but that may be because of many reactions.
As terdon indicates many protein-protein binding events are in equilibrium (binding and unbinding reactions; which gives rise to terms like association/dissociation constants). Many metabolic reactions are also in equilibrium. Enzymes don't change the equilibria. They just accelerate both the rates and help attain equilibria faster.
So, if a metabolic pathway has slow rate limiting steps then the faster steps go to  equilibrium.


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How significant is RNA degradation with removal of cap/polyA's in eukaryotes, or UTR's in prokaryotes?
Question is rather self-explanatory, but segmented into two parts. I'm attempting to make use of a repression system that employs cleaving RNA at specific areas with ribozymes with the intent of degrading (or just inactivating) them.
This scenario seems more likely in eukaryotes, as they have capped 5' UTRs and a polyA tail at 3' UTRs that lend to RNA stability. How quickly and how much will an uncapped RNA degrade? What about the lack of a polyA tail?
Since prokaryotes lack these structures, I am restricted to the use of UTR regions in my particular instance. Is there any similar mechanism, whether in general or for specific proteins, that will allow me to exploit a UTR region for RNA inactivation in prokaryotes? Please keep in mind adding synthetic sequences to these UTR regions is certainly a possibility.

You can use riboswitches. Small RNAs have been shown to affect RNA stability in prokaryotes too but i think they have a stabilizing role in contrary to that of eukaryotes.

The polyA tail has a different function in bacteria than in eukaryotes, in bacteria the polyA tail seems to trigger RNA degradation, not prevent it. I've never tried to transform bacteria with mRNA, but I've injected lots of mRNA into mice, and the cap and tail are critical for expression, if they are absent the RNA is usually degraded too quickly to detect protein, at least in my bioluminescent imaging assay.

Removal of 5' cap is essential for degradation by 5'→3' exonucleases such as Xrn1/2. Xrn1/2 is constitutive and degradation of uncapped RNAs would be quite fast (don't have a reference for the exact lifetime). Deadenylation generally precedes 3'→5' degradation by exosome but I am not sure if that is a prerequisite. However tailless mRNAs can be stabilized by tethering Pab1p (Poly-A binding protein) to the 3'UTR. See this paper.
Figure 4 of the linked paper.

Tethered Pab1p stabilizes mRNAs that do not receive a tail. (A)
  Strategy. The HDV self-cleaving ribozyme was inserted into the 3′ UTR
  of MFA2/MS2 RNA, yielding an mRNA without a poly(A) tail (A0) in vivo.
  (B) Oligo(dT) cellulose chromatography. RNAs were extracted from cells
  carrying the ribozyme-containing construct depicted inA, or the
  control plasmid used in previous figures. RNAs were fractionated by
  oligo(dT) cellulose chromatography, then analyzed by Northern
  blotting. The ribozyme-containing RNA is not retained by the column,
  whereas the control RNA is retained. (T) Total RNA prior to
  fractionation; (+) retained by the column; (−) not retained by the
  column. The mRNA runs slightly faster in the oligo(dT) retained (+)
  sample than in the total (T) RNA, because less RNA is loaded per lane.
  (C) S1 nuclease analysis. The 3′ end of mRNA prepared from a strain
  carrying the ribozyme-containing RNA was determined by S1 nuclease
  mapping. The position of undigested probe (65 nucleotides) and of the
  protected species (43 nucleotides) are shown. The prominent 3′
  terminus lies at the expected position for ribozyme cleavage. (D)
  Decay of ribozyme-cleaved RNA by a transcriptional pulse-chase
  experiment and Northern blotting. The turnover rate of
  ribozyme-cleaved reporter mRNAs was determined in strains with (left)
  or without (right) MS2/Pab1p. Time (in min) following transcriptional
  repression are given directly at top; half-lives are at bottom. (E)
  Quantitation of results. Amounts of mRNA were normalized to the level
  of 18S rRNA, at bottom of each lane in D. (•) MS2/Pab1p; (○) vector
  alone.

Prokaryotic UTRs do not have any general paradigm. To have a controlled inactivation of a mRNA in a prokaryotic system you can use riboswitches or  cis-repressive RNA (RBS complementary RNAs). RNA-guided RNA degradation is also possible in prokaryotes using the CRISPR-Cas system. See this paper. Proteins Cmr-1,2,3,4 & 6 are required for this activity.


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Genetics: pedigree following a rare trait autosomal recessive

I have two questions pertaining to this pedigree
I believe it to be an  autosomal recessive trait.

The probability that individuals IV-1 and IV-2 would give rise to an affected individual would be:
A. 1/4 b. 1/2 c. 1/8 d. 1/12 e. 1/24
Suppose individual IV-2 was unaffected. The probability of his marriage giving rise to an affected child would be:
A. 1/4 b. 1/2 c. 1/8 d. 1/12 e. 1/24

I worked on this problem for the last hour or so and figured up question 1 to be 1/2 and question two to be 1/4. I don't feel this is correct. I feel like I am missing something. If you don't mind showing the calculations for how you came about an answer that would be greatly appreciated.

Question 1
Okay, so I'll go through my own process for you here step by step, moving down the tree.  Here's an annotated version of your diagram with my own thoughts (it's been a while since I've done this but should hopefully be accurate):

Generation 2:  As you realised, the trait is autosomal recessive so the female (II:2) has the genotype aa.  The male is considered wild type unless informed otherwise, giving him a genotype of AA.  I think you had worked all this out, but they are shown in red on the diagram.
Generation 3: Using the two genotypes of the parents from II (red), we know that all the progeny in generation III are carriers - i.e. Aa genotypes.  This is indicated for III:6 in orangey-brown.  I think you also worked this out successfully.  However in your original chart, III:7 is noted as Aa.  III:7 is from outside of the affected family and would therefore again be considered to have be wild type and therefore instead have the genotype AA - shown in purple.
Generation 4: In order to work out the potential genotypes of IV:1 we have to do a cross between the two parents III:6 and III:7 - which works out as follows:
        |          Male          |
        |     A            a     |
        |------------------------|
F       |                        |
e     A |    AA            Aa    |
m       |                        |
a       |                        |
l     A |    AA            Aa    |
e       |                        |

As you can see, there is a 50% chance of IV:1 being healthy AA and a 50% chance of being a carrier Aa - shown in green.  As IV:2 is affected, we know his genotype is aa (pink).
Generation V:  Now for answer to your first question.  If IV:1 had the AA genotype then the child could never be affected, reducing the odds to 50% immediately. Of this remaining 50%:
        |          Male          |
        |     a            a     |
        |------------------------|
F       |                        |
e     A |    Aa            Aa    |
m       |                        |
a       |                        |
l     a |    aa            aa    |
e       |                        |

50% of the offspring would be affected.
Therefore the probability of V:I being affected is $\frac{1}{2} \times \frac{1}{2} = \frac{1}{4}$

Question 2
The second question seems very odd to me.  If IV:2 was unaffected in the literal sense of the word they would be wild-type AA.  This would make the probability of them having an affected child as 0.
As this isn't one of your options, I assume they mean that IV:2 is a carrier (Aa).  We are this time therefore crossing either AA or Aa (IV:1) with Aa (IV:2).  Again, if IV:1 is heterozygous dominant (AA) none of her children will be affected.  This means the odds are again reduced by a half.  In the case that she is heterozygous Aa then the cross becomes:
        |          Male          |
        |     A            a     |
        |------------------------|
F       |                        |
e     A |    AA            Aa    |
m       |                        |
a       |                        |
l     a |    Aa            aa    |
e       |                        |

Giving 25% healthy, 50% carrier and 25% affected.
As you're looking for affected children: $\frac{1}{2} \times \frac{1}{4} = \frac{1}{8}$

If "affected" means "aa", then "unaffected" should mean "not aa", i.e. "AA or Aa". If neither IV-1 not IV-2 are affected, the offspring could only be affected if both are carriers. The chance of IV-1 being a carrier is 50% whereas the chance of IV-2 being a carrier is 66% (because IV-2 had 1/4 chance to be AA, 1/2 chance Aa and 1/4 chance aa, but we know the genotype isn't aa, thus leaving 1/3 chance AA and 2/3 chance Aa). If they both are Aa, there is a 25% chance of offspring being affected (aa). 1/2 * 2/3 * 1/4 = 1/12 = (D). Edit: Haha excuse my necromancy, was prompted by a flag.

Rory gave a good answer to part 1.  Your main problem is that you have written Aa for III-7, and that's not the right call.  III-7 is not in the family (maybe you missed that detail in the tree), so their odds of carrying a bad allele in the same gene that this family carries a broken gene in is very very small.  So III-7 is AA.
So the III-6,7 mating is AA x Aa.  That means the odds of their kid also being a carrier is 50/50, the odds of the kid passing on the bad allele to her kid is also 50/50, so the odds of V being affected are .25.  (when you have a probability question in the form of "What are the odds of this, then that happening", you multiple the probabilities to get the answer)
In Part 2, if IV-2 is unaffected, then the odds are 2/3 that their genotype is Aa, and 1/3rd that their genotype is AA.  (See the Punnett Square, and notice that you disregard the box that leads to an affected phenotype)
So for V to be affected, we need
1) III-6 to have passed on the bad allele to IV 1(50%)
2) IV-1 to have passed on the bad allele (50%)
3) IV-2 to be heterozygous (66.6%)
4) IV-2 to have passed on the bad allele (50%)
The odds of all of that happening is 1/12

From my own point of view, I think the answer to no. 1 is a 50% chance i.e. 2 out of 4. My reason is because, IV-1 could be a carrier of the trait and since the IV-2 is affected that means 2 will be affected.
No 2. For the second question, the answer is 1 out of 4, because it's obvious both (IV-1 and IV-2) would be carriers of the trait from their family pedigree, and have 1 in a 4 chance of developing an offspring with the trait.

This is rather a comment than an answer. Can you elaborate this?


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How does the enzyme Dicer function in the RISC complex?
I know that the RISC (RNA-induced silencing complex) is one of the primary complexes involved in gene regulation through RNAi.  What I want to know is, what role exactly does Dicer play in this complex?

Dicer is an endo-ribonuclease belonging to the RNAse-III class. Dicer is not a part of the RISC. It however helps in the formation of RISC by cleaving dsRNA or the stem of hairpin RNA on two ends which liberates a small dsRNA product. Then one of the strands is loaded into the RISC.
There are several reviews on this topic and there is a video as well which you can find on youtube.


text:
Is forced cell growth related to apoptosis?
Could an instance of forced cellular growth cause some cells to have their self-destruct mechanisms to malfunction or 'turn off'thus preventing apoptosis?

What do you mean by "forced cell growth"? Cancer? Or something different?

It is trivial to assume that forced growth will overcome apoptosis which is what you see in the immortalized cell lines and in cancer.
But the interesting thing is that there are instances in which forced growth causes apoptosis. The classic example is of the brain in which expression of SV40 t-antigen to make cells proliferative actually caused loss of tissue [1,2].
Knockdown of Aif (apoptosis inducing factor) also causes neurodegeneration and thymic hypoplasia by causing increase in oxidative damage.


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Other than Acetylcarnitine what other orally-bioavailable Acetyl donors exist to assist in the conversion of CoA to acetyl-CoA?
I asked a question on bio stackexchange a few days from which I was hoping to be able to arrive at an answer for this question myself but I have had no such luck so now I am going to just ask outright: other than acetyl-L-carnitine are there any orally-bioavailable compounds (in particular orally-bioavailable to humans)  that exists that can serve as an acetyl group donor for CoA?
My main motivation for asking this question is that I know that acetyl-L-carnitine indirectly promotes the acetylation of histones by serving as an acetyl donor for CoA by serving as a substrate for carnitine O-acetyltransferase and then this resulting acetyl-CoA then donates an acetyl group to histones by means of the enzyme histone acetyltransferase.

You have a good point but it would be just exquisite if you could find some evidence to support the idea that a significant amount of these acetyl-CoA's are used by histone acetyltransferase and thus influence gene expression.

Is there any evidence that acetylcarnitine acts as an "acetyl donor"? I understood that its use as a supplement was to supply carnitine. Could you give a reference for the statements in the second paragraph of the question?

I would assume that acetylcarnitine is not an acetyl donor for CoA. According to this paper, a "typical" ester hydrolysis reaction is less energetically favorable than a "typical" thioester hydrolysis reaction. So hydrolysis of the ester bond in acetyl-L-carnitine will not provide enough free energy for the formation of a thioester bond with CoA. I'm pretty sure @TomD is right about the source of acetyl-CoA. Also, I highly doubt that the acetyl groups used for histone acetylation come from a different source than those used in metabolism.

This is only a guess, maybe acetic acid, ie vinegar?
Acids are effectively hydrogen salts, but the acetyl ion might be alkaline like the hydroxyl ion, making acetic acid less acidic than most? As in water, pH neutral, is a combination of hydrogen and hydroxyl, H and OH, ions?

Hi ! Welcome to Bio Stack Exchange ! I do not know whether your answer is correct or not but I would suggest that if you are unsure of an answer it is better to leave a comment then to write an answer. Also, your answer will be easily accepted if you provide a good source/reference for your answer. Have a great time here !!

Thanks biogirl, I wasn't sure how to just leave a comment.  I found TomD's answer that fatty acids donate acetyl ions interesting.

No worries ! Have fun !

Free acetate is apparently used to acetylate CoA, in an ATP dependent manner, at least according to wikipedia. But I think the question is looking for acetyl donors for which the reaction is favorable on its own (doesn't need to be coupled to ATP hydrolysis to proceed).


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Why can't sodium butyrate be delivered orally in humans and other mammals?
I think I know why -- bioavailability problems but since I have no firm evidence to support this theory I thought I would ask the biology stackexchange community for their input. I'd like some firm bioavailability data of sodium butyrate in mammals, preferably humans.

At least in humans butyrate tastes horrible I think.  that might be way it isn't taken orally.

@shigeta Na, I doubt it seeing how corticosteroids tend to taste terrible (which thing I know from personal experience as an asthmatic) and yet we have methods of getting around this problem such as putting them into capsules or telling the patients to just suck it up.

Apparently it can


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Why is FAD, rather than NAD+, reduced in the succinate dehydrogenase reaction of the Tricarboxylic Acid Cycle?
FADH2 is produced in the conversion of Succinate to Fumarate in the tricarboxylic acid cycle. Why is this so? Why not NADH?

Just a guess: FAD reduction potential is higher than that of NAD; so it should be a better oxidizing agent than NAD. NAD however would be a better reducing agent.
Source

@TalhaIrfan — I have reverted your edit. There is absolutely no reason to place the abbreviations in italics and a different typeface — and every reason not to — which is what your markup did. The poster or who ever edited it previously was quite right in formating with HTML 'sub'. If she hadn't rendered the subscript — OK, but she had. Leave well alone.

@David Latex has been the preferred mode for both Mathematical as well as Chemical equations/formulae on SE; and its italic by default. Just the answer below is an example of its use!

@TalhaIrfan — preferred by whom? This is not a mathematical construct it is a biochemical construct that would be set in a biochemistry text book (e.g. Berg et al.) in the same weight and typeface as other words in the text. Your Latex rendering is further ugly and makes reading difficult. And as I said, is in italic for no good reason. I have not changed the answer below, just as I would regard it rude to change US spelling to UK spelling. Please do not change answers just because you personally prefer a particular style.

@TalhaIrfan — I think that this question should be discussed further on Meta. I'll post a question when I have a moment. That way we can get clarification.

In general, $\ce{NADH}$ and $\ce{FADH2}$ are coenzymes. The structure of the main part of an enzyme determines which coenzyme or which prosthetic group will work with the concerned enzyme. Unlike most other TCA cycle enzymes, Succinic Dehydrogenase involves the participation of $\ce{FAD}$ rather than $\ce{NAD}$ and that is a consequence of its specific structure.
Another possible reason might have to do with the energy gap available. The conversion of succinate to fumarate liberates less free energy as compared to other oxidation reactions. Ususally, the steps which are coupled with NADH reduction have a free energy change of about $\Delta G=-100$ to $-150~ \pu{kcal/mol}$ but the conversion catalysed by succinic dehydrogenase has a free energy change of $ -80~ \pu{kcal/mol}$ (rough figures) and hence releases less energy. It therefore might not be feasible to couple with $\ce{NADH}$ reduction but it would be favourable (thermodynamically) to couple with an easy-to-reduce (since the reduction potential is higher and hence reduction is more favourable) and hence less energetic molecule $\ce{FADH2}$.
Apart from structural and thermodynamic requirement, one last possible reason might be that succinic dehydrogenase is a part of the mitochondrial membrane and involved in the Electron Transport Chain. Here, flavin molecules are excellent electron transporters (in comparison to nicotinamide based reductants) and therefore it might be more profitable to use a flavin based reductant to later facilitate easy electron transport and proton transfer.
Again all these are probable reasons and I dont know for sure.

There is a simple straightforward answer to this question, which I present here because the poster of the accepted answer seems unsure which of his three suggestions is correct, and therefore there is a danger of the reader thinking that an explanation in terms of flexibility or membrane location is correct. It is not.
It’s all to do with thermodynamics — the free energy changes in the different redox reactions. Thus, in their chapter on the tricarboxylic acid cycle Berg et al. write:

Succinate is oxidized to fumarate by succinate dehydrogenase. The hydrogen acceptor is FAD rather than NAD+, which is used in the other three oxidation reactions in the cycle. In succinate dehydrogenase, the isoalloxazine ring of FAD is covalently attached to a histidine side chain of the enzyme (denoted E-FAD).
E-FAD + succinate ⇋ E-FADH2 + fumarate
FAD is the hydrogen acceptor in this reaction because the free-energy change is insufficient to reduce NAD+.
  FAD is nearly always the electron acceptor in oxidations that remove two hydrogen atoms from a substrate.

An internet search brings up any many sets of university lecture notes that provide numbers to back this up. For example notes from Bryant Miles at Texas A & M (slightly reformatted by me):

Why is FAD the electron acceptor rather than NAD+?
The oxidation of an alkane is not sufficiently exergonic to reduce NAD+ — E˚' = –0.315 V
The oxidation of an alkane is sufficiently exergonic to reduce FAD. — E˚' = –0.031 V
Fumarate + 2e- → 2H+ Succinate — E˚' = 0.031 V
∆E˚' = –0.0002 V ∴ ∆G˚' = +0.04 kJ/mol
The change in free energy based on the steady state concentrations of all the reactants and products in mitochondria isolated from pig hearts is approximately zero, a near equilibrium reaction.

I think that flavoproteins are more flexible than NAD. NAD carries exactly 2 electrons, while FAD can carry either 1 or 2 electrons. This is important, as succinate dehydrogenase is at the crossroad between the Krebs cycle and the electron transport chain. Best I can tell, the Krebs cycles is knocking out 2 electrons per enzyme, while the electron transport chains is knocking out 1 electron per complex. So maybe FAD makes the translation between the two systems work?

Please add some references to your answer.

But in the succinate dehydrogenase reaction FAD accepts two electrons to give FADH2, so the fact that FAD is chemically capable of accepting one electron in a different reaction is quite irrelevant. The answer can be found in most biochemical texts, and comes down to the energetics of the reactions involved.


text:
Why are Taurine and Arginine essential components of the feline diet?
Taurine and arginine play a key role in the feline diet but I am unaware as to where exactly they fit in.

From the Taurine Wikipedia article:

The absence of taurine causes a cat's retina to slowly degenerate, causing eye problems and (eventually) irreversible blindness – a condition known as central retinal degeneration (CRD), as well as hair loss and tooth decay. Decreased plasma taurine concentration has been demonstrated to be associated with feline dilated cardiomyopathy.

Arginine is an Essential Amino Acid for cats (and many other mammals - including Humans while we're infants). That is, they cannot synthesize it on their own and must obtain it entirely from their diet. A 10lb. (5kg) cat will require about .86g of Arginine - which is abundant in all meats and can be met with a few ounces of food.
I could not find anything particularly special about Arginine as opposed to other EAA's for cats.

Arginine is not essential for adult humans. Cats and dogs probably (I don't know for certain but I'm guessing) require arginine because of its crucial role in the urea cycle and their high rate of ammonia production as a result of amino acid catabolism for energy production.

Oh and for me to accept your answer regarding Taurine I am going to need something to back that up I saw that article before you mentioned it but I wanted something more scholarly than wikipedia

Depending on who you ask, there are between 8-10 EAA's. Arginine is required during pediatric development, thus it's my habit to include it. Feel free to follow the links from the wikipedia entry (60, 61) at the bottom. The original studies are from the 1980's and I cannot access them as the website is currently taking too long to respond.

arginine is a conditionally essential nutrient in humans - but essential in cats - I will put some effort into this and place an answer


text:
Complementarity of cDNA
Strictly speaking, what is the definition of cDNA?  This confuses me, since usually it is said to refer to DNA that is complementary to mRNA.  Is this correct?  Is it restricted to mature mRNA?
I also find directionality very confusing.  As I understand it, mRNA has a sequence equivalent (less introns, after splicing) to the so-called 'coding strand' of DNA.  Does this mean that cDNA made from mRNA, at least before treated with a DNA polymerase, is also complementary to the original genomic DNA?  Is this the better definition (I have seen this used as well, though the first definition seems far more common).
Lastly, as I understand it each chromosome has a forward and reverse strand, defined by convention, but that the 'coding' strand of a given gene is random.  This seems counter-intuitive... is it just because both strands are equivalent?  Does it introduce complications in terms of the cell 'knowing' which strand is the coding strand for a gene?
The most upvoted reply to this question (http://www.biostars.org/p/3423/) confused me even further.  I feel the same way as 'Onefishtwofish' does, in the replies.  Can anyone clarify?

It's a good question and has confused me as well.
A standard definition of cDNA is that it is a double stranded (ds) product of mature mRNA. I suppose it is possible to get a nascent RNA strand copied into cDNA, but I've never heard of that being done.
Because cDNA is dsDNA, the original strand is made from your mRNA as the complementary strand, but then you dispose of the RNA and make the second strand to get a stable, reproducable molecule. The total dsDNA molecule is what we refer to as cDNA (not a single strand of this material).
consider this simplified DNA molecule:
ATG-INTRON-CTCTAG
TAC-INTRON-GAGATC
this could be transcribed into the following mRNA (corresponding to Met-INTRON-Leu-Stop):
AUG-INTRON-CUCUAG
before nuclear export the intron is removed, making mature mRNA:
AUGCUCUAG
you make cDNA from this:
ATGCTCTAG
TACGAGATC
So, you have both a coding and a complementary strand in your cDNA.
As for directionality on the chromosome, genes can be in either direction (meaning that they can use either strand as the coding strand), but remember that the forces that contribute to transcription are just locally determined (assembly of transcription factors, etc) and pay no heed to what direction they're going or strand they are on relative to any other gene. The strands are labeled as positive and negative, but that's just a reference for orientation. A good place to browse the human (or other species) genome is the NIH's map viewer. Click on a chromosome to see the genes mapped to it. Note the column labeled 'O' is for orientation.


text:
Are there any bacteria that can receive ultrasound signals?
I'm looking for an example of bacteria that could receive ultrasound (at any ultrasound frequency) signal and possibly perform some (re)action afterwards.

... well it can break open the cells and kills them ...

I know but maybe there is some ultrasound frequency that doesn't kill bacteria.

I'm having a hard time thinking of any natural phenomena that produce ultrasound in which the bacteria could then transduce. If the frequency is not immediately lethal, I worry the heat transfer could be.

I'm going to post a quick answer here, really a thought piece.
Usually to detect a sound wave you need a sounding board about the wavelength of the sound.
Bacteria are on the order of a few microns in length.
Ultrasound frequencies range from 2 to 200 MHz (and up I assume).
To have a wavelength on the order of 3 microns, a 100 MHz wave would be needed.
So only on the very high end of the range.  If bacteria make sound though, they probably are on this frequency range.
I wonder if this has been looked at?  Not sure it has.  While in biology you never say never - if a bacterium really needs to pick up a wave it might have a clever adaptation to do so, but in the 100MHz + frequency range seems more likely.


text:
Why can't cell division happen the other way around?
Mitosis in eukaryotes happen in this order: DNA replicates and then the cell divides. Why doesn't it happen in reverse order (i.e., cell divides and then replicates the DNA)?
I am talking about diploid cells.
Why has evolution favoured the first way?

I was thinking about only  cells having even ploidy levels. I know it sounds stupid if we think about odd ploidy levels.

If you are thinking of a process like meiosis but followed by DNA duplication, the problem is that this would create daughter cells that do not have the same genome as the parent cell.
The diploid genome of a sexually reproducing species' cell has different alleles of the same locus. If the cell replicates itself by passing one chromatid to each daughter cell which then duplicate that to make a diploid genome, the resulting cells will not have the same DNA as the original one since each of the daughter cells will have inherited only one of the available alleles. They will then make an exact copy of the DNA they have inherited and become diploid but with a new genome, one that did not exist in their parent. This is not good since the cells of an organism need to have the same genome in order to function in the same way.

Yes.. it would also lead to  homozygosity.

The biggest problem is this: if you have only one copy of the DNA how is it going to divide it between the two cells so that both have a complete copy?


text:
What stops the coagulation process?
Whenever there are minor/major injury to blood vessels, the platelets, fibrin, thrombin, etc. are recruited. They then seal the wound and block bleeding.
What tells them that their job is done?

This paper seems relevant: Dahlbäck. 2005. Blood coagulation and its regulation by anticoagulant pathways: genetic pathogenesis of bleeding and thrombotic diseases.

Exposed collagen at the site of vessel damage simultaneously initiates plates aggregation and the clotting cascade. So, when the wound is sealed and no more collagen is exposed, which is the main factor to activate the cascade, the blood clothing cascade stops.


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Does mitosis include cytokinesis?
I found that some books include cytokinesis within mitosis, but some other books I have referred to include only the dividing of the nucleus as mitosis and do not include cytokinesis.
Can anyone help me out? Please include a source in your answer.

Cytokinesis is separate from mitosis.
What edition are you looking at?  To quote from the Fourth Edition:

The cell cycle culminates in the division of the cytoplasm by cytokinesis. In a typical cell, cytokinesis accompanies every mitosis, although some cells, such as Drosophila embryos (discussed later) and vertebrate osteoclasts (discussed in Chapter 22), undergo mitosis without cytokinesis and become multinucleate. Cytokinesis begins in anaphase and ends in telophase, reaching completion as the next interphase begins.

The mouse-over definition of cytokinesis there is:

Division of the cytoplasm of a plant or animal cell into two, as distinct from the division of its nucleus (which is mitosis)

Oh! I got confused between M phase and mitosis.


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When do kinetochores attach?
I am really confused as to when kinetochores are attached to centromeres. Are they attached soon after replication or after condensation ?

after condensation..

@WYSIWYG Would you like to elaborate and write an answer to this question ?

i will if i find time.. have stuff to do today.. if you found the answer then answer it yourself..

Kinetochore (KT) is a multilayer protein complex. It's main function is to link chromosomes to the positive ends of the spindle microtubules. Also it plays role in the formation of heterogenic region at and around the centromer. The attachment of the KT is not uniform among living species. According to this paper on KT assembly in yeast:

.  ...  KTs  remain attached to the MTs throughout the cell cycle in this organism. However, a temporary detachment of chromosomes  from  MTs  occurs  (for  1–2 min)  at  the  time of CEN DNA replication in S phase in S.cerevisiae (Kitamura et al. , 2007). After completion of CEN replication, a KT reassembles and reestablishes its attachment with  MTs.

source:http://femsle.oxfordjournals.org/content/femsle/338/2/107.full.pdf
(CEN - centromere, MT- (spindle)microtubules)
Thus the exact time of kinetochore attachment depends on the organism, though I must note that S. cerevisiae has somewhat different mitosis than us.


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Where are the gastralia (stomach ribs) attached?
Crocodiles and some dinosaurs have a second set of ribs between the sternum and pelvis called gastralia. Where are the gastralia attached to the rest of the skeleton?


text:
How precise is EEG?
Imagine we want to read impulses within single neurons in the brain. Can we do that now for a single region within the brain? If not, what is the smallest region that can be monitored for an activity in real time? Is there a more advanced method than electroencephalography for scaning brain activity in real time?

EEG is pretty much useless for seeing a single neuorn's activity. With current technology, only invasive technology can see single unit activities.

Okay. But then how "precise" is the EEG right now? Can you monitor 1cm^2 or you only get a "faded" image of an activity for a whole brain due to interference?

Electroencephalography has a good time resolution (milliseconds) but poor spatial resolution (several centimers). The usual estimated figure is that at least 50000 neurons need to fire simultaneously so that the activity can picked up by EEG.
The answer provided by @Jeremy Kemball is not very accurate. The reason why the spatial resolution of EEG is poor is that the signal from even a point-like source on the cortical surface spreads about to every sensor along the scalp due to the conductivity properties of the brain, CSF, skull, and scalp.
This means that in order to get that few centimeter accuracy I mentioned above, one must solve an inverse problem from sensors -> cortex. Inverse problems are mathematically ill-posed, and have infinite number of solutions unless some constraints to the solution are added.
I'll give a practical example. Say that a subject is presented some sounds. You record the EEG. Now, if you look at the sensor-level data, you can find brain activity related to the sounds from almost any sensor, from both sides of the brain (each ear projects to both hemispheres). If you want to know where the signal actually came from, you need to do the source localization using some inverse solver. Some commonly used are for example dSPM, sLORETA, or MNE.
Finally, I want to emphasize that

Brain regions deeper in the brain produce a 'blurred' signal that shows up on several electrodes at once.

that this happens to all activity recorded by EEG. Actually, EEG does not even pick subcortical activity too well.

Is there a more advanced method than electroencephalography for scaning brain activity in real time?

Yes, that is called magnetoencephalography (MEG). MEG records the magnetic fields related to the electric activity. It reaches sub-centimeter localization accuracy, while still having millisecond time resolution. However, this is now strictly only for the cortical activity; MEG does not see subcortical activity almost at all. Google for Elekta Neuromag or CTF to see some MEG systems.
If you would be interested in studying some deep structure, like amygdala, your best choice is then fMRI, which has about ~2 second time-resolution and 1mm^3 spatial resolution.

The smallest area that the EEG can measure is related to the electrode density. Even with research setups with 100s of electrodes, the smallest measurable region is on the order of a square centimeter or so on the skull surface. Brain regions deeper in the brain produce a 'blurred' signal that shows up on several electrodes at once.
fMRI, on the other hand, can measure smaller areas in three dimensions, but not as often.


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Human defenses to toxoplasmosis
Toxoplasmosis modifies the rat's brain to make them love (and be eaten by) cats. It also infects ~30% of humans, and modifies traits in several bad ways (i.e. schizophrenia and increased reaction time). However, humans are thought to be a "dead end" for the parasite. Thus, there is a significant selection pressure for humans to develop resistance but no (or almost no) pressure for toxoplasmosis to counter human resistance. If so, why are so many people infected?

Thus, there is a significant selection pressure for humans to develop resistance but no (or almost no) pressure for toxoplasmosis to counter human resistance.

Well, I think in this case "Significant" isn't qualified. Significant selective pressure can come in many forms, but as you mention about 30% of humans are infected with Toxopolasma, and the vast majority remain capable and functional. Remember that selective pressure applies to the ability to take advantage of resources and reproduce. People with toxoplasmosis are almost always capable of surviving and reproducing, so I doubt the pressure is all that much.
There is also significant incentive for Toxoplasma to develop the ability to adapt to humans, as it would open up a whole new resource for them to take advantage of. How fast the parasite is capable of adapting, or even if it's possible to eventually include humans in their life cycle, is something that would take some studying.
Our immune systems, in turn, try to kill the parasite regardless of whether we're being taken advantage of or not. You might be interested in reading up on the Red Queen Hypothesis - a theory that delineates how the immune system is at constant war with its environment and potential new threats.
As for your last question...

... why are so many people infected?

That's easy. :-)
Cats have become a popular pet, and most of the time the parasite doesn't significantly affect us. If either of those changes, you'll see a change in infection rates.


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Are the byproducts of mammalian digestion simply depleted versions of the food or liquid consumed?
When mammals consume food and digest it or drink fluids that are then filtered by their kidneys, are the waste products generated simply depleted versions of what they consumed?
Are there other byproducts of metabolism and filtration contained in that waste that are generated by the body and are not directly a part of the food or liquid that was consumed that are excreted?

If you are saying if it has modified any food, of course it has. Eg. Urea but if you are saying something totally not derived from food in any way, I think that is impossible. (Except from some microbes in urine/faeces)

The answer really depends on what aspect of the urine and feces one is considering.
On the atomic level, no, urine and feces are composed entirely of atoms taken from our environment. As one would expect, as there is no "Humanium" on the periodic table. In fact, all the atoms in urine and feces were originally created by stars.
On the molecular level, yes. The body produces molecules that we do not ingest, or that we ingest in minute quantities, such as urea and bile.
On the cellular level, yes. The body produces, for instance, red blood cells even if the person eats a vegan diet with no blood intake. The proteins that make up the cells are created by breaking down ingested proteins into their constituent amino acids, which are then used to construct new proteins.
Also at the cellular level are the huge amount of bacterial cells that we support. Estimates of the number of bacterial cells in our body range from ten to 100 times the number of our own cells. The bacterial component in feces is massive - up to 1/3 of feces by weight are bacteria. Urine, being produced from the blood by the kidneys, is relatively sterile.

I totally forgot about the bacteria... of course!


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How does the matter that makes up the fat of your fat cells ultimately leave your body--following weight loss?
I'd like to get some clarification on specifically how the matter from the fat reserves of the Adipocyte physically leaves the body.
In other words, if you were to somehow follow every atom in the fat reserves of the cells of a dieting person, then, via what hole would these atoms ultimately exit the body?
Is the answer to this question merely "exhaling through the mouth"? Or do they come out in feces too?
Note 1: This question is not to be confused with the question: "How does mass leave your body in general?" For there are several ways to accomplish this. (e.g. shedding skin cells, cutting off your arm, cutting your hair, sweating, dehydration, liposuction, bleeding, spitting, blowing your nose, etc...)
Note 2: Please see this other similar StackExchange post here:
https://physics.stackexchange.com/questions/2605/how-does-mass-leave-the-body-when-you-lose-weight

Yes, they are mostly exhaled. The carbon, hydrogen and oxygen that the fats are made of recombine to become $CO_2$ and $H_2 O$ and are exhaled.
It's the same overall chemical reaction as if the fats / carbohydrates were burnt, except it's by a different pathway, and the energy produced goes (mostly) towards driving other chemical reactions rather than becoming light and heat.

Hi thanks. Can you clarify the "mostly" part? Where else would they exit besides the mouth?

@tondog Some of the $H_2 O$ will come out in urine or sweat, for example.


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how to clone a gene fragment in two direction as sense and antisense in vector
I have a sequence ATG GGG CCC TTT AAA TAA and want to use it as antisense RNA in my vector. How should I clone it? I am confused with the direction of my clone. I looking for the direction and sequence of the clones.

Perhaps place a promoter or ori upstream in the antisense direction?

Tour sequence's complementary is TAC CCC GGG AAA TTT ATT. Together they form a DNA strand. Now replicate this and then, after transcription of both the DNA you get the RNA sequence you wanted. Use it as sense or antisense.

Is there something missing from "transcription of both the DNA"?


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evolutionary reason behind sharing the same path for food and air?
What is the evolutionary reason behind sharing the same path for food and air?
For example, we have a nose and lungs, yet they are linked by the pharynx, which is shared with the mouth and oesophagus.
Wouldn't it make more evolutionary sense for the nose + lungs to have their own "path", while the mouth and stomach have a separate system? This would prevent "choking", allow for breathing while eating/drinking, etc.

Note that this does not go for all animals. For instance, the respiratory system in insects is based on a network of "tubes" (tracheae) that penetrate the entire body. This is ventilated through spiracle valves which are distributed over the body of the insect, so in insects the paths of food and oxygen are separated.

While it might make more logical sense to have separate passageways for air and food/water, this did not happen in evolutionary history due to the peculiarities of lung development. Vertebrate lungs develop as an outpouching of the gut tube, which itself has a very long evolutionary history (probably homologous among all deuterostomes).
In the image below, the trachea has budded off the esophagus. Further lung development will involve the differentiation of main, secondary, and tertiary bronchi as well as the alveoli, etc.

Additional images and description at http://www.uoguelph.ca/zoology/devobio/210labs/lung1.html
Air-filled organs like lungs and swim bladders actually have a broad distribution going way down into fishes. Human (and other mammalian) lungs are likely homologous with ancestral air-filled organs of fishes. We can't be certain, but there is no reason to think that mammalian lungs are a de novo evolutionary innovation. So our airway and food-ways are tied together developmentally and are constrained by evolutionary history.
As for breathing and eating (swallowing) at the same time, most mammals can do this, and baby humans can as well.
Like most anatomical systems that seem as though they could have evolved better, this system works most of the time and has worked well enough for hundreds of millions of years.

Incidentally, providing two paths to the lungs could be useful if one is blocked (e.g., from a bad cold) and might allow different specializations to be applied to the different paths to achieve a better balance of trade-offs (e.g., support for panting [higher cross sectional area passage] might conflict with support for smelling [narrower passage]?).


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What's the mechanism for pain-induced swoon?
Is it true that people will pass out when subject to pain too much to bear, or there's no such threshold? What's the reason for passing out under acute pain, even if no physical injuries occur (e.g, loss of blood, etc.)?

Swooning, fainting otherwise termed Syncope or Primary shock (Triggered by pain or any unpleasant stimuli through the vaso vagal effect), is due to generalised vasodilation. The capillaries loose their tone and dilate resulting in an increase in volume capacity of the vascular system. This results in draining of blood to the dependent areas due to gravity thus hindering blood supply to the brain which shuts down and results in collapse (fainting) of the individual. This is a safety mechanism. Once the patient is in the lying down position the blood supply to the brain returns and the patient recovers. An individual who has fainted should not be propped up as this may result in seizures or worse.


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How do muscle relaxants work?
Do they act directly on the muscle and actually relax muscle tissue and ease spasms, or do they just prevent your brain from receiving signals that inform you of tight muscles?
In the latter case, it seems like your brain would sort of become "immune" to the pain even though the muscle is still in a spasm.
I'm obviously not a biologist, just curious about this.
How do muscle relaxants work?

Check out the muscle relaxant article on Wikipedia, it's pretty straight forward.  In short, there are two main types: Neuromuscular blockers, than act at the junction between the neuron and the muscle; and spasmolytics/antispasmodics, which (mainly) act on the central nervous system to reduce excitation or increase inhibition.  Most of the ones I've heard of, such as diazepam, are in the latter category.


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Are there any 6 limbed reptile fossils?
Were any 6 armed "tetrapod" fossils ever found? I've seen some lobe finned fish with two sets of shoulders in an evolutionary bio book... I'm curious because I'd like 4 limbed and 2 winged dragons to have existed :)

I don't know about dragons, but the fossil record does show that some fascinating, tiny vertebrates (including members of the genus homo) existed some 425 million years ago :).

as i understand it cambrian-->orovician-->silurian-->devonian... vertebrate popped up in cambrian... the attached link is talking about silurian... my question (six armed tetrapod) probably localizes to the Devonian...

Sorry, that link is a joke. It is a guy who won an IgNobel for finding what he considers to be fossils of tiny equivalent of various modern life forms,

this research was actually done?!?

Yup :). You should check out the Annals of Improbable Research and the IgNoble prizes, they're great.

I think this is a reasonable approximation. The Genus Draco

I think, you misidentified the unpaired anal fin of coelacanth as an extra pair of limbs.
I personally haven't ever heard of six-legged vertebrates, although the phenomenon of supernumerary legs is well known as an anomaly. Such anomalies can be easily induced in different vertebrates (including mice: Rutledge et al), if you treat their embrya with retinoid acid (which normally defines embryonic polarity) or fibroblast growth factor. In nature, different factors can lead to development of extra legs, and the most well-known and wide-spread cases are limb abnormalities in amphibians, induced by trematodes and pollution (including retinoid acid mimics?) (Blaustein & Johnson).
That said, I would not be surprised by a discovery of a fossil amphibian with extra limbs. But such a find then should be interpreted as an abnormality, if not proved otherwise. It's true that the fore and the hind limbs are serial homologues, but their number seems to have been fixed very early (in contrast to the number of the fingers).

this is the original poster of the question (Jasand)... you're probably right about "unpaired anal fin of coelacanth"... I'm not too knowledgeable about evolutionary biology or zoology... kind of a shame though... I was hoping for another lineage of amphibian/reptile like creatures with six limbs instead of 4... oh well, I guess I'll have to be satisfied with 6 limbed arthropods...
I recall something about retinoic acid affecting the hox genes... the hox genes being responsible for segmentation in insects, but general space planning in vertebrate...

I was looking at a picture of Eusthenopteron, but the picture specifically says "it has paired pectoral and pelic fins with internal bony structure"...  I see more fins than that... probably the extras are cloecanth and whatever... I suppose the number of fingers is variable because it began after the sarcopterygians... but I was looking at these lobe finned fish for the hopes of finding more than 2 sets of paired limbs...

Yes, the unpaired anal fin creates a very strong feeling of another pair of fins. There is great variability in morphology of the fins in "Agnatha" (jawless fishes), such that even a case of paired anal fins was discovered in one fossil. Both paired and unpaired fins seem to have similar origin in terms of being derivatives of body folds, but I don't know, whether they can be considered true serial homologues. (See also this article).

And, please, don't forget to mark the answer as accepted if you find it proper :)

Thanks, sorry I'm new to this site... The picture of the fish I was looking at was in lateral view so paired/unpaired was hard to discern... Also thanks for the follow up info...


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Mechanical cause of loss of consciousness
Consciousness is an electrical and chemical interaction in the brain, caused by neurons firing and chemical interactions. How does a mechanical "force" cause this to stop working?
i.e. How does a mechanical action (such as a punch to the head) cause this electrical/chemical system to stop working (leading to unconsciousness)?

One basic point I can offer is that any proteinaceous structure is force-sensitive. Neurons are soft matter and they're intrinsically sensitive to mechanical forces, right down to the chemical level. So if you picture what an ion channel is, a gate that can be opened or shut through thermal energy, it's easy to see how a density fluctuation (like a sound wave) could flip it between states.

Mechanical force can compress neurons and cause action potentials as you probably experienced in the form of hitting the funny bone. Strong enough acceleration of the brain tissue may be causing massive excitation of neurons as indicated by animal EEG study. It suggests that the loss of consciousness is due to generalized epileptic seizure. However, it is not fully agreed upon: quoting wikipedia entry on Concussion:

It is not known whether the brain in concussion is structurally
  damaged or whether there is mainly a loss of function with only
  physiological changes.[14][needs update] Cellular damage has
  reportedly been found in concussed brains, but it may have been due to
  artifacts from the studies.[15] It is now thought that structural and
  neuropsychiatric factors may both be responsible for the effects of
  concussion.[16]

And following quote is from this

The brief loss of consciousness that characterizes concussion appears
  to be the result of rotational forces exerted at the junction of the
  upper midbrain and thalamus that cause transient disruption of the
  functioning of the reticular neurons that maintain alertness.
  (Allan H. Ropper, M.D., and Kenneth C. Gorson, M.D.; N Engl J Med 2007; 356:166-172 January 11, 2007)

so are you saying that the process is not actually well understood? There seems to be alot of unknown about the process?

@TheShiftExchange Unfortunately, that seems to be the case.

Loss of consciousness, or syncope, can be caused by a number of factors, almost all of which relate to lack of proper blood flow: high G-forces, low blood pressure, low blood sugar, cardiac arrhythmia, and vasovagal responses, such as when I give blood.  These all make sense and are moderately well understood.  The mechanism of loss of consciousness due to mechanical trauma, however, is less well understood, in part because it can be tricky to study.  It almost definitely has to do with lowered blood flow as well, and in particular direct trauma to the brain stem, which regulates consciousness.
Basically, you need to rattle the brain inside its cage, slamming it against the skull.  The easiest way to get knocked out from a punch is usually to the chin; the rotational force is much harder for the brain to cushion against, and is a very sharp force.  The displacement of the brain from such a force can compress blood vessels, cutting off blood flow to the brain.  There's also some evidence that the higher brain and the brain stem can twist around each other, which certainly worsens things.  There's even a theory that consciousness is rooted in the neurological structure, which might support the idea that unconsciousness is caused by parts of the brain inhibiting each other.

ETA This isn't exactly a reliable source, but the guy writing this piece for Deadspin is board-certified in internal medicine, and had this (uncited) to say:

Researchers have examined the brain waves of recently concussed animals and determined that their brains resemble that of an animal suffering an epileptic seizure. This comes as a bit of a surprise, because the brain waves (measured by an electroencephalogram) show hyperactivity, which implies that when a fighter is glassy-eyed and unable to answer the referee's questions appropriately, his neurons might actually be overactive, not underactive.
But a hyperactive brain is not the only problem. When the head is hit at high speed, shearing movements within the skull can cause micro-hemorrhages of the blood vessels within the brain tissue. If the shearing force is large enough, or if the head is it hard enough, a large bleed can occur. This becomes a medical emergency because the skull is fixed, enclosed space. As blood accumulates, usually in the form of a subdural hematoma, it can squish the brain and potentially compromise critical neural functions like breathing; death becomes imminent.

A hit can break blood vessels, produce inflammation and exert pressure in the brain tissue. Pressure in fact can alter the composition and distribution of the cerebrospinal fluid. Since the nervous cells are very sensible to oxygen deficit and the composition of their surroundings, phisical damage can lead to loss of brain function. Moreover, while it's true that cerebral activity is due to chemical reactions, it's also true that this activity must be focused in very specific points (synapses), wich may be damaged by an strong hit.


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Root hair formation in Arabidopsis
In arabidopsis, 2 cell types arise in the root epidermis : root hair cells and hairless epidermal cells.
The immature epidermal cells that are in contact with 2 underlying cells of root cortex differentiate into root hair cells whereas the immature epidermal cells having contact with only one cortical cell do not develop root hair.
What is the advantage of this ?


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Does sympathetic nervous system acts bilaterally for pupil dilation or other two sided organs?
The question might seem weird. Does sympathetic nervous system acts 'bilaterally' meaning if you shout to a person's left ear a loud noise (e.g. by headphones), will it activate sympathetic system just on the left or on the both sides. For example it will only dilate left pupil or dilate both ?

Yes, they do. At least in the case of pupils. In fact, the absense of simultaneous regulation of the diameter of the pupil is used as a medical test for the evaluation of brain damage.


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Does having a total gastrectomy (removal of the stomach) cause individuals to be more prone to infections?
If a patient has a complete removal of his/her stomach (i.e. a total gastrectomy), then does that cause a person to be more prone to infections from eating unsanitary food?
I'm asking this question because the stomach plays a role in sterilizing food and, hence, without a stomach it would follow that one might be more prone to getting intestinal infections.

Yes.I think so as may of the bacteria are killed in our stomach

Yeah I think so too that's why I even asked the question -- to confirm what makes sense.

It would be nice to have empirical/epidemiological evidence to support this hypothesis.

I don't have time for a full right up, but here's a good starting point.


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Extract bacteria from compost?
I'm working on a project where I need to find certain cellulolytic bacteria. I was looking at this list : http://webcache.googleusercontent.com/search?q=cache:CrtQ9T6K7m8J:www.wzw.tum.de/mbiotec/cellmo.htm+&cd=1&hl=nl&ct=clnk&gl=be
How could I selectively separate one of the bacteria types that I had in mind from that list?
So how would I have to extract the bacteria from the compost?

A first (and obvious) approach is the use of cellulose agar in order to isolate all the celluloltic bacteria in the sample. Be careful, however, since the nutrient requirements of some of those microbes may be higher and then they won't grow with only cellulose (they may need some other compounds, like a nitrogen source). Be careful with fungi, too.
If you have the proper equipment, it would be ideal to extract DNA and analyze the environmental rRNA 18s sequences. With this, you should be able to know if your bacteria is present in your sample. If so, proceed with the previous steps.
Once you had a set of suspected colonies, you must proceed with more specific culture media (wich would depend of the exact bacteria you're looking for. For example, if you're looking for Clostridium, you should try to grow your sample in an anaerobic jar and test the ability to reduce sulphur). With this approach, you may reach a point where you can't differenciate similar species. At this point, mollecular characterization is the best option, with the use of rRNA 18s again. Note that the mollecular approach, while relative expensive, can be performed in every step, so you can combine cultures and DNA analyses at will.
Lastly, if you're looking for an specific bacteria, it would be useful to know wich one is, so the community can give you more accurate responses.

Thanks - as for your last question : I'm not sure which species I would like to separate, because I don't know which bacteria are available in my compost heap...

you can also just take some compost and boil it and then use it as a medium for an agar.  if you want to optimize for a particular sort of refuse that might be better..

and - before I forget - Where in the compost heap should I look for bacteria? (the bottom or middle?)

Be careful with the boiling. First, endospores can survive the process if it hasn't done properly. And second, the heat may cause some undesired reactions, changing the composition.


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What is the role of hippo signalling in oral squamous cells
What role do hippo signalling have on squamous cells in oral health & diseases

This is purely my speculation : If hippo signalling gets defective mouth cancer could result.

Mutations in the Hippo signalling pathway cause unusual organ growth in flies.  After a good deal of intensive research, its been shown that Hippo genes are responsible for suppressing organ growth in development, increasing cell death and slowing proliferation.
Given this role, its not surprising that Hippo genes are also important in cancer.  I'm not an expert in cancer, but a quick search turned up an association of cancer with the Yki (YAP in mammals) transcription activator, an oncogene from the Hippo Pathway.  YAP suppression has been linked to cancerous growth.  And its also been shown that YAP is amplified in oral squamous cell carcinoma cells.  This last is circumstantial but consistent with what we know about YAP.

Hippo Signal may affect the turnover rate of oral mucosa

Could you expand on your answer with additional information and/or citations?


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How correlated are proximally related CpG sites in human DNA?
Cytosine residues in DNA that can be methylated (i.e. CpG sites) are likely to be in the same methylation state if they are geographically (proximally) close together.
I can only find one paper that states this empirically (1), that 90% of CpG sites within 50bp of one another are in the same methylation state - see below graph.

However this study is quite dated now (in the fields of epigenetics at least), and is very general.
I would like to know whether CpG's in different regions of the genome are more/less likely to be correlated than in other regions (say, exons vs. promoter regions). It would also be interesting to know whether the correlations change with age, and whether this is related to any disease processes?
Thanks for the input.

Eckhardt, et al, 2006. Nature Genetics. doi: 2010.1038/ng1909

I've got to dash off so I won't be able to give a fully in-depth answer today, but this basically boils down to the concept of CpG islands.  Something like 70-80% of CpGs are methylated in humans, so if they were randomly scattered around the genome there is already a pretty high chance nearby CpGs are in the same state.  However, because of CpG islands, CpGs of similar state are indeed grouped together, depending on promoter activity (to simplify things a bit).
That being said, if you look for articles that cite your article, a plethora of useful references show up.  In particular, this bad boy has a handy figure 1 which displays the overall landscape.  Maybe that's too broad of a view, but in general, like methylation patterns cluster together; otherwise, there'd be no such thing as a methylation pattern!  This paper has a neat figure which sums it all up nicely:

Basically, it's usually high-methylation or low-methylation; rarely is there anything in between.  There's a lot more in there so I'd recommend going through some of them; I'll try to get back to this later.


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Genetics problem-Height of a plant
An inbred strain of plants has a mean height of 24cm. A second strain of the same species also has a mean height of 24cm. When these plants are crossed the F1 are also 24cm in height.However, when the F1 are crossed the F2 plants show a wide range of heights, the greatest number are similar to P1 and F1 but apprx. 4 out of 1000 are only 12cm tall and 4 of 1000 are 40cm tall. What fraction of the F2 plants will be apprx. 28cm in height ?
a)3/4
b)9/16
c)56/256
d)none
The answer given is c).

I know that a and b can not be the answer.

A simple google search will reveal this website where that exact question was asked half a year ago.

Totally unrelated comment: If it is 24 cm high, I doubt it is a tree.

@skymninge done the edit !

From the source that Amory cites :

You know that the number of offspring is shown by Pascal's triangle,
  right?
For two alleles you have 1 : 2 : 1
For three alleles 1 : 3 : 3 : 1
For four 1 : 4 : 6 : 4 : 1 etc.
So, if 4 in 1000 are 12 and 36 cm
  tall, that means that every in 250 plants is tall like that. And on
  which level of Pascal's triangle you have sum of 250? For two alleles:
  1 + 2 + 1 = 4 For threee: 1 + 3 + 3 + 1 = 8 For four: 1 + 4 + 6 + 4 +
  1 = 16 etc. until 1 : 8 : 28 : 56 : 70 : 56 : 28 : 8 : 1 Here you see
  that you have 9 options of height. The difference is 36 cm - 12 cm =
  24 cm. 24 cm /9 = 3 cm, so 1 plant will 12 cm, 8 plants will be 15 cm,
  28 plants will be 18 cm, 56 plants will be 21 cm, 70 plants will be 24
  cm (i.e. "the majority of F2 are like P1 and F1") and 56 plants will
  be 27 cm tall out of 250 plants. Thus C is the closest.


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Free software for measuring parts of an image?
Let's say I have a picture of an insect wing and a ruler on the same image. Is there any computer program that I can use to calibrate with the ruler and then get a measurement on the wing length? Would the software be able to export these data to a spreadsheet?

I'm voting to close this question as off-topic because this question is about software not Biology.

ImageJ is all you need. Particularly see the documentation sections on setting the image scale and measuring.

This is great! Thanks! It even continues to add values from new images into the table. Awesome!

see also Fiji for a distribution of ImageJ with more plug-ins

WebPlotDigitizer is an online application that can also be used to make distance and angle measurements in an image.

Looks interesting. I will try it at the next chance.


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L1 - L5 layers of the brain
I have read in some papers about the layers L1-L5 of the brain (e.g. in this paper). I could not find a definition of these layers. I have found information about the layers V1-V5 in the visual cortex.
Where exactly are L1-L5? And do these definitions vary across mammals?

V1-V5 are different (sub) regions of the visual cortex itself.

via http://www.tecsyn.com
The layers L1-L5 (some regions have a layer 6) refer to the different cellular strata in the depth dimension of the cortical mass.  This stratification occurs to some extent or another in various areas.  Different sections of the cortex, e.g., the primary motor cortex have a predominant level 5 (for the pyramidal tract).  Something like the visual cortex has more cells in layers 4 and 6.

 From http://www.unige.ch/cyberdocuments/theses2003/RivaraC-B/images/fig.2.jpg
Layers 2 and 3 tend to carry interconnections between different areas of the cortex, and the topmost layer is generally less dense.