text:
Does Spinning dancer has anything to do with your eyesight
I came across the spinning dancer as part of the brain test to determine left brain vs right brain dominance.

I saw the dancer is turning clockwise. The other people around me saw it turning clockwise for the first time, but soon they got confused and said they saw it turning it in both direction.
I know the tips of how to see it anti clockwise, but no matter what I do I always see it clockwise. I have shown it to a number of people and all of them could see it spinning in both direction after looking at it for longer time.
I am the only person who has never see the dancer turning in both direction.
My question is does this has anything to do with my eyesight? I have very limited(almost blind) eyesight in my left eyes. This is from birth.
Does my visual impairment has anything to do with this or does this mean anything else?

It's very frustrating to me that I can only see her spin one way…

@canadianer Check the answer to see her spin the other way.. We'll just cheat.. No thanks necessary.. :P

Okay actually now my life is complete because she's going the other way. It really helps if you just focus on her lower foot. I actually scrolled the page up so I couldn't see the rest of the image.

When I first saw this it quickly started switching back and forth on me, then for me. However after reading your predicament I too found my perception stuck. Looking at image, I closed my eyes and imagined it spinning the other way. When I opened them what I saw matched my new perception. Hope this helps anyone else.

For a bit of background, this test was devised by Nobuyuki Kayahara and it was originally thought that it shows the dominance of one part of the brain to the other. This was later on discarded as a misconception (reference). It is now widely believed that the clockwise - counter-clockwise rotation is a phenomenon called Bistable perception (Reference 1 and reference 2).

Multistable perceptual phenomena are a form of perceptual phenomena in
  which there are unpredictable sequences of spontaneous subjective
  changes. While usually associated with visual perception, such
  phenomena can be found for auditory and olfactory percepts. Famous
  examples include the Necker cube, structure from motion, monocular
  rivalry and binocular rivalry, but many more visually ambiguous
  patterns are known. Since most of these images lead to an alternation
  between two mutually exclusive perceptual states, they are sometimes
  also referred to as bistable perception(reference 1 and
  reference 2).

No, the fact that you can only see her turn clockwise has not got anything to with your vision (for the record, I have never been able to see the girl go counter- clockwise myself).

Sometimes, a person will stare at an image and it will never reverse.
  Dr. Toppino advises staring at one part of the image, such as the
  foot, and most of the time it will eventually flip. In people who
  can’t see the reversal, it may be that one underlying neural structure
  is more dominant, but once someone finally manages to see the flip, it
  will start to happen more often (reference).

This image would help you watch her rotate counter-clockwise.

Here she is spinning clockwise.

That blew up my mind. Now I can see her rotate in both direction!!! Thanks for the references.


text:
Among xerophyte plants, which one grow faster and consume water the least?
In an effort to select for the most suitable plants to possibly colonise desert and stop its expansion,
what would be the xerophyte plants that grow the faster and expand on surface, while using the less water and produce a maximum of biomass?

I don't think that there has been a comparison done among xerophytes as to which one grows fastest and which one the slowest. A list of fast growing trees can be found here and here.

Allan Savory recommends carefully managing grazing animals to promote grass growth. While his methods have been criticized, it hasn't seemed to damage our farm, where we raise cattle through intensively managed grazing, but our land isn't subject to desertification. I doubt you could solve desertification with a monoculture of xerophytes though.

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text:
Why do different pain killers have different effects on people?
I've noticed some pain killers working great for me, while others have no effect.
Works for me

Aspirin
APC †
Naproxen

Doesn't work for me

Paracetamol
Diclofenac
Tramadol

I doubt there is much of a placebo effect at work, since most of these either did or did not work when I first took them, without having expectations either way.
Whenever I have a head ache, I take an APC. I suspect it's actually the aspirin in there that does the job, since when I take just paracetamol, it doesn't do squat. As a kid I got children's aspirin, which worked.
I once had a severe back ache. I was prescribed diclofenac (a heavier variant than the over the counter one), which didn't work. I was then prescribed tramadol — same results. I then tried naproxen, which worked rightaway.
Why do some pain killers work while others don't?
Is there an underlying mechanism, that explains why some of these work while others don't? Does that predict if pain killers that I haven't used yet will work?
Please note that I'm not looking for medical advice on which pain killers to take; I'm just curious about how my body interacts with the various ones.

†: the one consisting of aspirin, paracetamol, and caffeine, not the one containing phenaticin. Think Excedrin.

Related: http://biology.stackexchange.com/questions/2922/how-do-the-pharmacodynamics-of-the-nsaids-differ-and-are-there-resistant-cox-p

@jonsca That's interesting. The weird thing is that diclofenac is an NSAID as well, but doesn't work for me. So it's not just a case of NSAID vs non-NSAID.

NSAIDs are a pretty diverse group of drugs. You might find http://en.wikipedia.org/wiki/Diclofenac#Mechanism_of_action interesting.

I've read that, and more, but I still don't have a clue. I don't even have a clue where to look.

Even if you're not looking for medical advice, I can't help but see this as a personal medical question.  If you wanted to re-write it as a general question, I would be more inclined to answer. Right now I'm questioning why it shouldn't be voted to close.

@AtlLED I understand your concerns, but other than writing in the third person about myself, I don't know how to make it more general, without losing any significance for me.

Well here are some pointers, and info that will give you insight. Not all pain is the same.  It can be from verious tissue (pain from muscle injury isn't the same as bone), with verious stemilius. If you think of a headache and back ache, there might be some drugs that are better for one of the other.  The effectiveness of verious pain relief mechanisms are well studied, so you might look at some to see how you can break down your types of pain, types of medication, and their applied efficacy for different types of pain. Don't forget stress and neuropathic pain when considering headaches.

Also, that comment solidfies my opnion that as written this is a personal medical question.  If you can not imagine how to extraplote it generally, the chances are it is personal.

NSAID is a very broad chemical category and the only similarity between different NSAIDs is that they are not steroids and act on Cycloxygenase-2 (?).
Mechanism of action for almost all of them is poorly understood. Even structures- paracetamol and aspirin are somewhat similar. Naproxen  is very different. When you say some drug acts/doesn't act you have to note that both are delivered to the body in equal doses. Properties like solubility can also affect the pharmacokinetics of a drug.

Bounty will be auto-awarded. My question hasn't been answered fully, although I have learned some valuable insights.

X-posted: https://medicalsciences.stackexchange.com/q/1696/12704

I don't know of any interesting mechanism that is specific to pain killers, so I will instead answer for drugs in general.
Drug action is a complex process consisting of many steps. Let's take a simple example: A systemic direct inhibitor of a kinase. This drug would need to*:

Be absorbed into your bloodstream
Remain in your bloodstream for sufficient time
Be absorbed into the tissue
Be able to bind the target protein

1 can fail due to interaction with other concurrently taken drugs or food, or simply genetic factors affecting the particular functioning of the gut mucosa. 2 can fail because the kidneys are too good at eliminating it, or the liver is metabolizing it too agressively (both also subject to modulation by other drugs, foods and genetic factors). 3 can fail because the transports in the cells aren't working as rapidly, or represent an allele less likely to take in the drug, or are modulated by other drugs/foods. The tissue can also have efflux pumps or enzymes that break down the drug. 4 can fail because the drug was designed for a specific allele of that kinase, but you happen to have a different allele, which has a slightly different structure that is no longer targeted by this drug.
Then you have a host of physiological variables, and addiction/tolerance.
Apparently the most common genetic reason by far for variable drug sensitivity is the specific set of CYP genes you have. CYP enzymes are abundant in the liver and chemically process various molecules (including drugs).
Besides this, an interesting set of specific examples used to be available from 23andme. I'm not sure if they still provide this after the FDA ban on health information.

Clopidogrel sensitivity - CYP2C19 variation
Proton Pump Inhibitor (stomach acid reduction) - CYP2C19 variation
Abacavir (HIV drug) - HLA-B*5701 SNP
Acetaldehyde (alcohol flush) - ALDH2 mutation
5-fluorouracil (chemotherapy) - DPYD mutation
PEG-IFN-alpha/RBV combination (Hepatitis C medicine) - IL28B SNP
Phenytoin (epilepsy drug) - CYP2C9 variants
Choline esters (class of muscle relaxants) - BCHE (CE degrader) variants
Sulfonylurea (used for type 2 diabetes) - CYP2C9 variants
Thiopurine (immune suppressant) -  TPMT (enzyme that degrades thiopurine) variation
Warfarin (anticoagulant) - CYP2C9 variants
Caffeine - CYP1A2 SNP
Metformin (diabetes drug) - SNP rs11212617, near the ATM gene
Antidepressant - SNPs in ABCB1 affect likelihood of sexual dysfunction (common side effect)
Beta-Blocker (heart disease) - Mutations in ADRB1 which is normally blocked by the drug
Floxacillin (drug for staphylococcal infections) - SNPs in the MHC region affect liver toxicity of this drug
Heroin - OPRM1 receptor (target of heroin) SNPs affect efficacy
Lumiracoxib (used to treat pain and symptoms of osteoarthritis) - SNPs in the MHC region affect liver toxicity
Naltrexone (alcohol and narcotic addiction drug) - SNPs in OPRM1 affect how much it can reduce pleasurable feeling from narcotics
Statins (cardiovascular disease) - SNPs in COQ2 (mitochondrial component) affect risk of myopathy

As you can see, our friends the CYP family enzymes come up frequently, and some are even repeat offenders like CYP2C9. Besides that, there is a fair number of cases where variation in the specific target of the drug are relevant.
Note that this list is not comprehensive: Many drugs have not been studied in sufficient detail, and some may have complicated mechanisms instead of just "bind and inhibit protein X".
I have omitted many details and links to literature, I am sure you can easily find them by searching on Google Scholar with the keywords I already gave. Let me know if that doesn't work, though.

*: Note that these aren't necessarily required for all drugs. For example, some drugs can be applied directly to the skin and hence do not need to pass through blood.

Drugs, even for the direct inhibition of a kinase, don't have to enter the blood.  Many do, but one could also, just as a quick example, apply a drug in a cream/skin permeable solution (to a skin tumor for the sake of argument for a kinase inhibitor). This is what defines a "local" treatment.

Out of curiosity: Are there any cancer treatments which are not systemic? Besides the tumor cells at the actual tumor site you always want to hit metastatic cells as well. At least for melanoma all kinase inhibitors (like vemurafenib) are given systemically as far as I know.

@Chris off the top of my head imiquimod, but when discussing pain management, there are far more. I find the phrasing "must: ..." to be incorect/misleading in this awnser.

Also, if you open yourself up to treatment and not drug, you had better hope your radiation treatment isn't systemic.

@AtlLED You definitely have a point with local treatment, but I can't figure out how to work it into my answer. To be sure, I was only giving an example of an inhibitor which happens to be delivered by blood, in order to illustrate how there may be several distinct families of factors at play.

@Superbest I don't think you have to work in local treatments, just adjust the phrase "Even in a very simple case, direct inhibition of a kinase, the drug must:" by noting items 1 and 2 are not actual requirements ("must"), given that a kinase inhibitor can be administered locally.  I get the point you were trying to make, I just think it's a little misleading as written.  You can probably just add the word systemic, and maybe add some info on step 3 related to targeting.

Short answer: different people have different amount of active receptors.
In treatment, combination scores of Pharmacodynamics and Pharmacokinetics determine the final effect of the drug.
Receptors determine many effects of the drug in many pathways.
Different people also sense pains differently (Psychology).
Review answer
The purpose of treatment is to relieve pain and maintain function.
Your question is biased.
You cannot only concentrate on painkilling in maintaining health.
These both are the reasons for the complains of the patient, not only the pain.
For instance, in rheumatoid arthritis, response to therapy can be quantitated using many measures including American College of Rheumatology system values ACR20, ACR50 and ACR70, which denotes the percentage of patients showing an improvement of 20%, 50% or 70% in a global assessment of signs (maintaining function) and symptoms (pains).
Each patient has own health, different from one another.
Our body adapts to the environment and individual conditions of the body to maintain homeostasis.
Receptors adapt for instance.
They can be active or inactive - in short-run and long-run - again depending on the conditions at hand.
Painkillers i.e. analgesics have different properties:

anti-inflammatory effect - acute and chronic conditions (inflammation is the major mechanism under many pathologies) e.g. nonsteiroidal anti-inflammatory drugs (NSAIDs, please, see this answer about the particular mechanisms and how different people have different effects from NSAID painkillers) and glucocorticoids (most)
symptoms relieving specific drugs e.g. disease-modifying antirheumatic drugs (DMARDs)
anti-platelet effect - e.g. the older you get, the more platelets stick together.
anti-pyretic effect
...

which all can be toxic.
Note that many drugs alone or/and as combination can work as painkillers i.e. pain relievers.
Aspirin for instance has both anti-inflammatory and anti-platelet properties.
However, it is rarely anymore used as anti-inflammatory.
The anti-platelet property is dependent on the exact dosage of the administration.
Aspirin's mechanism of action is to inhibit platelet COX which antiplatelet effect lasts 8-10 days (life of the platelet).
In other tissues, synthesis of new COX replaces the inactivated enzyme so that ordinary doses have a duration of 6-12 hours.
Please, review any Pharmacology -textbook for more info about aspirin.
Each these drug has own Pharmacodynamics and Pharmacokinetics

Pharmacodynamics answers to the question What drug does to the body? It stimulates some receptors, activates some pathways, ...
Pharmacokinetics - What does body do to the drug? It metabolises it (enzymes, receptors). It distributes it. It excretes it (kidneys, feaces).

In treatment, you consider what is the target organ.
You need to think what is causing the dysfunction and the pain.
You try to restore the function and relieve pain.
The component of drug needs to reach the target tissue e.g. your pancreas' beta cells do no produce insulin so your blood glucose is high.
Complications of this are polyuria and eventually exodus if untreated.
Insulin is injected into the fatty tissue.
We do not have long-term acting insulin administered orally - our metabolism start to break the drug so it does not have wanted treatment.
If insulin administered to the muscle, the time of action is too times less, again because muscle is metabolising the insulin i.e. a chain of peptides (protein).
No all symptoms and diseases have painkillers.
For instance, prehemorrhoid and some types of itching related to  posthemorrhoids.
However, for both, there are some special salvas for proplylaxis but they are not complete.
Now, you can start to read something in SuperBest's answer about host's physiological variables and addiction/tolerance which alters the mechanisms (receptors) of pathways in Pharmacodynamics and Pharmacokinetics.
Sources

Basic and Clinical Pharmacology, 11th edition, 2009, Bertram Katzung.
My notes in Pharmacology classes during 2014.

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text:
What is this microscopic image from Peter Gabriel's New Blood album cover?
This image appears on the cover of Peter Gabriel's album New Blood.  It appears to be a photograph of some microscopic biological cell.  But it doesn't look like a blood cell to me.   What kind of cell is it?

I would say it is a cell at the tip of a micropipette.

This is an embryonic stem cell on the tip of a needle photographed on a scanning electron microscope (SEM). The image was taken by Steve Gschmeissner, see here for the original.

you can't be "Here's the source" for the best answer.  I did a Google search for the image, and all I found were album covers.   Thanks to the others who provided answers.

@DavidDubois I will improve the answer if you can tell me what you find missing here. I don't like to have this short answer, but what else can you write?

@Chris The way I read it, David made a typo and was actually praising your answer: “you can't beat "Here's the source" for the best answer.”

@svick Good point. :-)

@svick is right.  Sorry.  I meant to say that your answer can't be BEAT.  :)  I can't imagine any answer better than "Here's the source"

@DavidDubois Everything is fine, I didn't get it first :-)

This looks like a macrophage to me, which is a white blood cell. Try Googling "macrophage sem" to see similar images (SEM  = scanning electron microscopy/micrograph).
The clue is the nature of the cell surface - those ruffles reflect the macrophage's role in engulfing foreign material. Indeed it is possible that some of the particles on the surface are bacteria which have been opsonised and are bound by the macrophage cell surface.

In addition to Alan Boyd's answer of a macrophage, it could also be a T cell or B cell. Try doing an image search for lymphocyte SEM and browsing through the different cell types. While the traditional image of T and B cells has been of a smooth round blast cell, they actually have numerous projections, folds, etc. to aid in forming the immunological synapse.


text:
Are there anatomical differences between male and female mammal brains before action of hormones?
is there any evidences of these differences during development stages prior to hormone driven sexual differentiation? mice studies ?

Yes. Dewing et al. (20030 found that gene expression in mouse brains differs between male and female mice about 10.5 days after the mice had sex. This occurs before hormonal contributions to brain development. They identified about 35 genes that were appeared to show preferential expression in the female brain and another 16 that appeared to be show preferential expression in the male brain. Most of the genes identified were transcriptional regulators, signaling molecules, or involved with cellular differentiation. Of these 51, three were verified as showing female bias, and two of these were located on the X chromosome. Four genes were verified showing male bias, and two of these were located on the Y chromosome.
Similar results were found by Xu et al. (2002). They identified several of the same genes as Dewing et al., plus others that were linked to the sex chromosomes. They identified a total of six genes on the X chromosome that showed strong female expression bias during brain development. At least three of the genes were homologous between the X and Y chromosomes but showed different expression patterns between male and female brains at different stages of development.
The differences in genetic expression may cause some microscopic anatomical differences during brain development that is not explained by hormones (Bocklandt and Vilain 2007). They reviewed several studies that found differences in neuron growth, and density of vasopressin fibers in the lateral septum were more likely to be due to genetic expression than to hormonal expression. Bocklandt and Vilain did not identify the specific ages of the mice that showed these apparently gene-regulated differences but it is reasonable to speculate that these differences begin to appear in association with the differential gene expression.  Bocklandt and Vilain did not identify macroscopic differences between male and female brains prior to hormonal expression.

Citations
Bockland, S. and E. Vilain. 2007. Sex differences in brain and behavior: Hormones versus genes. pgs 245-266. In: Genetics of sexual differentiation and sexually dimorphic behaviors (D. Yamamoto, ed.). Academic Press.
Dewing, P. et al. 2003. Sexually dimorphic gene expression in mouse brain precedes gonadal differentiation. Molecular Brain Research 118: 82-90.
Xu, J. et al. 2002. Sex differences in sex chromosome gene expression in mouse brain. Human Molecular Genetics 11: 1409-1419.

interesting ! differences in gene expression but anatomical?

@Matoeil I've updated my answer to include what info I could find.


text:
Modeling intracellular interactions between sender and receiver bacteria
I am involved in a modelling task of a biological process described as follows:
--
"Objective: to model behavior of a sender receiver type system
The process goes as follows

Pre-signal [PS] is in media
Pre-signal diffuses into bacteria
Pre-signal binds to activator as a co-activator
Co-activator activator complex binds to DNA and starts transcription of enzyme mRNA
Enzyme mRNA is transcribed then translated into enzyme
Enzyme begins converting Pre-signal to signal [S]
Signal diffuses out of the cell into media
Signal diffuses into receiver cell from media
Signal binds to repressor inducing activation of reporter gene

Questions for model:
What concentrations of signal will be required to get a response from receiver cell?"
--
My questions are: what kind of mathematical/computational model or simulation tool is more suitable for this task? is it neccesary to model every step, or can some of these be ignored? I know the basics of ODEs, so I wonder if these are enough or something else would be required. Any other advice about how to go through the modelling is welcome.

You can start with deterministic model using ODEs for reaction rates.
However, if you are considering diffusion then you would have to use Partial differential equations for Fick's diffusion law.
You can, however, assume that there is no "diffusion" but just transport of the signal molecule from a well mixed system (medium) to another well mixed system (cytosol). In this case you can use an ODE for "conversion" of extracellular signal to intracellular signal.
The model becomes simple and easy to analyze if you reduce the number of steps. Certain steps can be removed by making certain assumptions such as Equilibrium approximation (EA) or Quasi-Steady-State approximation (QSSA). If a reversible reaction is extremely fast compared to all other reactions (such as binding-unbinding of the activator to DNA), you can assume that reaction to be in equilibrium and represent the concentration of some species using equilibrium constants.
In Quasi-Steady-State approximation, you assume that certain species are in steady state with respect to others i.e their concentrations do not change over time. In the model you just set $\frac{d[X]}{dt}=0$ for that species. Then obtain the concentration relationships as a function of reaction rate parameters. I'll explain QSSA and EA using the Michaelis-Menten (MM) kinetics.
MM considers following steps:

Enzyme-Substrate binding (Reversible): $ E + S \rightleftharpoons ES $ with forward rate constant k1 and reverse rate constant k2
Enzyme-Substate complex converting to Product and Enzyme (Irreversible): $ ES \to P + E$ with rate constant k3

EA (The actual MM model):
Assuming step 1 is in equilibrium. $k_1[E][S]=k_2[ES]$
 Get [ES] in terms of [E] and [S]
QSSA (The revised MM mddel):
Assuming [ES] is in steady state. ${\Large \frac{d[ES]}{dt}}=k_1[E][S]-k_2[ES]-k_3[ES] = 0$  which means $[ES] = \Large \frac{k_1[E][S]}{k_2+k_3}$
This way you have removed certain reactions from the model.
You can do stochastic modeling as well.
For simulations you can use Matlab or Fortran.


text:
Mechanism of Muscle Growth
According to this video (sorry for the poor reference but it represents my level of understanding in physiology), muscle grow as a consequence of repairing micro-lesions.
How are these micro-lesions sensed in order to activate protein synthesis? What are the key molecules that trigger myosin synthesis and muscle growth?

It's not so much due to muscle damage, but due to certain proteins being released from the Z-disks of the sarcomeres which initiate certain signaling cascades involved in muscle proteins. Moreover, during exercise  there is a certain amount of metabolic stress which activates other pathways also involved in muscle protein synthesis. I suggest you read up on the STARS pathway (http://link.springer.com/article/10.1007/s00424-014-1475-5) and mTORC1 regulation.

During exercise muscles are put under stress which eventually causes micro tears in the muscle fibres.
These micro tears put pressure on the nerve endings which causes the pain.
The body will then repair the tears during rest and recovery using proteins and sufficient fuel. The muscle will then become slightly bigger and stronger.
Energy systems used to repair these lesions are the following
There are three different types of energy systems:

Phosphocreatine
Lactic Acid
-Aerobic
1.Phosphocreatine Energy System

The ATP-PC system lasts for 8-10 seconds.
During the ATP-PC system a phosphate breaks off of the ATP to form ADP and a lot of energy.
ADP will then bind with another free phosphate to form ATP.
The ATP-PC system is an anaerobic energy system as it dose not use oxygen.

Lactic Acid Energy System

Glucose is broken down sustain performance for a longer amount of time than the ATP-PC system.However this system does not use oxygen so is not suited for events over 90 seconds.
When the ATP-PC system starts to fade the process of anaerobic glycolysis begins.
Glycogen is stored in the liver and is broken down without the presence of oxygen.
This produces lactic acid which limits energy production.

Aerobic Energy system

The aerobic energy system is constantly being used in your body to supply the muscles with energy.
In sport the aerobic energy system is used for events that last anything over 90 seconds.
The aerobic system can be used constantly but only if there is a constant supply of glycogen and fatty acids.
The aerobic system uses oxygen, glucose and fatty acids to yield large amounts of ATP.
The system takes place within the mitochondria and produces two bi-products, carbon dioxide and water.

These are some generalizations, I beleive the aa which is responsible for protein synthesis is BCAA leucine.

Thank you. I am no so interested in "where does the energy allowing muscle work come from?" but I am interested in  "the key molecules that directly trigger the synthesis of new myosin proteins?" Sorry if my question was a bit unclear.

You summarized the three main energy systems (why?) and gave no explanation of the actual mechanism. This does not answer the question at all.


text:
Mechanisms of bone growth
The length of a bone is caused by growth of hyaline cartilage which is then replaced by bone tissue. How do cells know whether they should grow the hyaline cartilage? What are the key molecules that trigger the synthesis of hyaline cartilage?

How do cells know whether they should grow the hyaline cartilage?

Both growth factors and cytokines are involved but the trigger mechanism is unclear [1].
Bones grow in length at the level of epiphyseal plate where chondrocytes produce hyaline cartilage which by addition of calcium and phosphorus ions turns into hard bone [2].
It is believed that the growth process is under the regulation of local mediators like cytokines and growth factors:

In recent years, a large number of cytokines have been discovered and their molecular structures and biological activities described. A surprisingly large number of cytokines have been shown to affect skeletal tissues, at least experimentally, making this a complex topic, but one which is furthering knowledge of how the cellular events of bone growth may be so precisely regulated [3].

References

Ossification. (2014, July 3). In Wikipedia, The Free Encyclopedia. Retrieved 15:47, September 30, 2014, from http://en.wikipedia.org/w/index.php?title=Ossification&oldid=615387908
http://www.personal.psu.edu/staff/m/b/mbt102/bisci4online/bone/bone5.htm
J.S. Price, B.O. Oyajobi and R.G.G. Russell. The cell biology of bone growth. Available from http://archive.unu.edu/unupress/food2/UID06E/UID06E0U.HTM


text:
What do you call a virus when it's cured?
When a cure has been found for a virus, can it be called such anymore?
Virus implies it's something you've contracted that you just have to live with until (hopefully) your body can overwhelm and destroy it.
But say someone found a cure for the Common Cold tomorrow, would we still call it the cold virus or would it just be known as the "cold infection" or something to that effect?
Is "Virus" just a nomenclature we've adopted for a bug that has no cure, or is it used to describe a certain type of organism?

It is indeed "a certain type of organism". I think that you might find the Wikipedia page http://en.wikipedia.org/wiki/Virus useful. It certainly answers your question.

Lets start with the definition of a virus (from the Wikipedia page on viruses):

A virus is a small infectious agent that replicates only inside the
  living cells of other organisms. Viruses can infect all types of life
  forms, from animals and plants to bacteria and archaea.

So basically speaking you have a piece of genetic information (DNA or RNA) which encodes proteins which are important for the function of the virus and a hull (not always, but mostly). These invade a cell type, take over the cell (litarally, after an infection the cell will mostly only make viral proteins and DNA/RNA). Finally new viruses are built inside the cell and released to infect more cells. In principle this works like in the figure below (from here):

There are two possibilities for cures: The first one are vaccinations. Here you either use dead or attenuated viruses (or parts of viruses) to train the immune system. When this has happened, the immune system "knows" this specific agent and can rise a fast and highly specific immune answer against it, before the virus can replicate in high numbers and infect a lot of cells. This happened for example for the small pox virus which could be eradicated from the human population.
The other would be drugs which either target a virus (or some of it functions) specifically or prevent them from spreading. The immune system usually does the final cleanup here.
Both methods only work for people which either take the drug or are vaccinated, so they have no influence on the virus in people which are not protected. For further information have a look on the Wikipedia page on Viruses.


text:
Receptors for red and far-red light in plants: Shade avoidance
Franklin (2009) describes how plants use the ratio of the red wavelength (660-670nm) over the far-red wavelength (725-735nm) (R:FR) in order to avoid shading.
My question is: which receptor is stimulated by the red and which receptor is stimulated by the far-red?
In his paragraph on Phytochromes (3rd page, right column), K. Franklin seems to say that PhyB is responsible for measuring this ratio but I am not sure.

The articles Canopy Light Signals and Crop Yield in Sickness and in Health and Phytochrome B Enhances Photosynthesis at the Expense of Water-Use Efficiency in Arabidopsis may be of interest.

As far as I know there are 5 receptors for far-red and red light which are the phytochroms(phyA-phyE) Its all about the ratio between red and far-red light.
Each phytochrom has an inactive(PR) and an active(PFr) conformation. phyA is the only phytochrom which is activated by far-red light, so its active state is PR. (Only if the ratio between red and far-red light is low.) The other phytochroms, are activated by red light (high ratio between red and far-red).
An active phytochrom blocks the COP1/SPA complex. This complex is a E3 ubiquitin ligase which ubiquinates transcription factors for the light answer like HY5 or HFR1.
Example:
Under normal light conditions, phyB-phyE is active. They block the COP1/SPA complex so the transcription factors for the light answer are not getting ubiquinated. The plant can get a light phenotyp.
In the case that a plant grows under another plant, it gets less red light because the higher growing plant uses it for its photosynthesis. phyB-phyE become inactive. COP1/SPA can ubiquinate the transcriptions factors. The plant gets an low light phenotyp by trying to grow out of the shadow.
The function of phyA is to produce a light phenotyp if there is a lot of far-red light but almost no red light. Than it is getting activated and blocks the COP1/SPA complex. Under red light phyA is not only inactivated it also gets degraded.
I just found a paper for further reading: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2828699/

So the mechanism seems much simpler than what I expected. The ratio is directly "computed" by the phytochrome and the ratio is not "calculated" from the interaction between the molecular pathways activated by the phytochromes. Thanks a lot. I will clearly have a look to the paper your attached.


text:
What is a catalytic domain of an enzyme?
Is this another name for the active site of an enzyme? What does the structure of the catalytic domain of an enzyme look like?

Quick answers: yes, and it varies tremendously. Enzymes catalyze a huge variety of reactions, from cutting DNA to adding amino acids to a growing polypeptide chain, to breaking down complex sugars, and many more besides. Catalytic domains vary from enzyme family to family, and even between enzymes in a single family. There really is no generalization you can make about structure or function, as it is so different from one to another.

AFAIK MattDMo is correct. The catalytic site is the active site where the reaction takes place that triggers the conformation change. He is also correct about there being nearly infinite potential catalytic site designs.

I would say that catalytic domains are a little different from active sites. The active site is the location where the substrates bind and the reaction occurs, the catalytic domain is the portion of the enzyme that contains the active site. Many proteins have multiple domains.

I agree with @user137. The catalytic domain is a subdomain of active site (which also contains binding domains).

Both parts overlap. Proteins are a chain of linked amino acids. This chain can be grouped into functional units which are called protein domains. Usually all parts of a domain are closely located in the protein and they form functional domains in the 3D structure of the protein. Proteins usually contain more than one domain (these are manifold but for example can be dimerization, activation or binding domains).
The catalytic domain is the part of the protein chain which contains the region where the catalyzed chemical reaction takes place. The 3D structure of the catalytic domain forms the active site, so the enzyme requires proper folding to be active. If you denature the enzyme, the catalytic domain will still be present (as this is a function of the protein sequence) but the active site will be gone.
As there are really many enzymes for all kinds of reactions it is hard to define a general form for the active site. A motif which is present in a lot of enzymes is the the form of a catalytic pocket or groove to which only the correct substrate of the enzyme has access. Additionally the binding of the substrate to the enzyme often induces a conformational change in the protein which closes this pocket. When the reaction is finished and the substrate is not bound anymore by the enzyme, the conformation changes again and releases the products of the reaction. See the image for a schematically drawing of this principle (image from here):


text:
What is the difference between a DPY-10, DPY-11, and DPY-13?
My TA mentioned these three mutations of C. elegans since we started working with the worms but seems to skip over what the differences are...

Dpy is a class of genes. Usually they're written in lowercase when referring to a mutant allele. The name Dpy itself stands for dumpy and comes from the morphological change that occurs when one or more of the genes are mutated: the worms appear short and fat, or dumpy.
Another big class is Unc. Mutations in those genes cause uncoordinated movement.
For a description of the genes, see http://www.wormbase.org


text:
What is the meaning of this poor sequencing result?
What is the meaning of this poor sequencing result? What is the problem?
Can anyone guide me, please. Thank you.

It means that your srquencing failed. In my sequencing experience there is nothing so to save here, you simply have to repeat the reaction. What have you exactly done? Are you sure that your primer works on your template?

Was your template a PCR product or a plasmid ? Have you seen your template DNA on electrophoresis before sequencing ? If yes, was it just one band, or many ?


text:
genomatix software linux install
I have installed the genomatix software which is a jar file the name is InstallChipInspector21.jar.But now I really don;t know how do I start it ,can any one suggest me a method??

This question appears to be off-topic because it is about a computer package installation. Refer to the readme associated with the package for details on this or contact the developer.

well it's not about installation I have installed it I need to run the program,that is what I'm asking for

I don't know what else to say as an answer but here is a link to the user manual. If you are looking for more specific usage instructions, I would suggest that you try Biostars though I can't guarantee that you receive an answer.

I have seen the pdf it doesn't talk about how to start the program...

@krushna Try the command java -jar InstallChipInspector21.jar ?

yeah I have installed the software using the command but I need to run it how do I do that??


text:
Warm water bath
Why is it advised to take bath in warm water when we are sick?I know that as homeotherms we need to generate metabolic heat to adapt to the environment temperature.But what is the mechanism by which it makes people feel better(except those who are allergic to it)?

Why someone likes bathing in water at some particular temperature is just based on personal choice. Some people like cold water. Some people are also allergic to bathing in warm water.

1) A hot bath, or soak in hot water raises our body temperature. Several benefits of this rise include:  Improved blood circulation, Improved lymph circulation, increased metabolism and calmer nervous system.
2) During this increased temperature your body releases endogenous opioid peptides, which are primarily endorphins.That’s why you might feel like a new person after a hot bath!(reference)
It apparently also takes your feeling of loneliness away (reference)

It is a myth that sweating detoxifies you. See for example, http://www.uamshealth.com/?id=12247&sid=1

@ChrisInEdmonton thx for pointing that out

@TheLastWord Can you edit your answer then, please? It is a good answer, except for the detox stuff. I promise to upvote it if you fix that ;-)

@JohnEye I edited it


text:
Do humans have the hyaloid canal, after all?
Most Google Images results for "eye anatomy" are pictures of eyes that don't have the hyaloid canal while some do (proof). Do humans have it, after all, or not? :)

Yes, humans do have the hyaloid canal.

Schematic diagram of the human eye (reference)
For function and other information, please refer to this journal article.

What, in your opinion, justifies that it is missing in the vast majority of eye anatomy images? I don't even remember seeing it in my high school biology textbook.

@user132181 Can you send me links to a few such images?

Look at the mentioned Google Images search.

@user132181 I would have to say that most of them are showing you the full eye while you get to see the Hyaloid canal if you go for a cross-section view. In full eye images, the hyaloid canal would not be marked.


text:
Why are hard boiled eggs so homogeneous?
A eukaryotic animal cell is a complicated piece of biological machinery.  Some major structures inside of the cell (see the image below) include: the nucleus, mitochondria, Golgi vesicles, and various tubular structures.  Why then is the single-celled, unfertilized chicken egg so homogeneous when it is cooked (or before)?  The only major structure I can recognize is the cell nucleus.

*Image Credit: "Animal cell structure en" by LadyofHats (Mariana Ruiz) - Own work using Adobe Illustrator. Image renamed from Image:Animal cell structure.svg. Licensed under Public domain via Wikimedia Commons - http://commons.wikimedia.org/wiki/File:Animal_cell_structure_en.svg#mediaviewer/File:Animal_cell_structure_en.svg

From what I understand, the yolk is part of the cytoplasm of the egg cell, but all cell structures are located in the germinal disc (a small whitish disc on the yolk). The yolk is stored food (mainly protein) for the embryo.

@anongoodnurse I'm just repeating what I've heard from memory - there is a reason I'm not posting an answer.

Also, what I wrote should only hold for unfertilized eggs.

@anongoodnurse Can you support that claim?  Everything I can find says that they are single cells.  This article, on the NCBI website claims that "the eggs of most animals are giant single cells, containing stockpiles of all the materials needed for initial development of the embryo through to the stage at which the new individual can begin feeding."

When looking around it seems to be a matter of definitions as well. However, the egg white (albumen) is secreted from the oviduct and cannot be seen as part of the egg cell (oocyte).

@fileunderwater - I've read more about eggs in the past hour than I care to, but I owe you an apology. An unfertilized egg consists of genetic material and cell structures (organelles, etc) in the germinal disc (or whatever the precursor to the germinal disc is) and the cell is it plus the yolk (by some definitions). Since man makes the definitions of structures, not nature, we find that science has made the egg or ovum of three or more types by definition. It so happens that with or without the yolk and albumen, the poultry ovum is the largest living cell.

If you investigate the details, one of the egg (ovum) definitions does make the Ostrich Egg a one cell unit. I'm sure that like so many other definitions in science, there is not a complete universally accepted agreement. Whatever, there is only one cell in the unfertilized chicken egg when it is laid.

@anongoodnurse That's ok, and I was only making a suggestion. However, it is easier to have an understandable conversation, if people don't remove their comments all the time (not only you - I saw another comment pop-up and disappear as well). As for egg definitions, it seems more reasonable to me to view the finished (unfertilized) egg as an egg cell (oocyte) surrounded by supporting structures (egg white, shell etc).

@fileunderwater - I agree. I was surprised to find that the membranes were acellular. I took my comments down as I realized my error(s).

Disclaimer: This is my understanding of the egg anatomy as a general biologist. There is most certainly better references and sources out there to explain this (please add better references if you know of any).

If I understand you correctly, your question is why we do not see cell organelles in a cracked or boiled egg. If so, your question seems to stem from a misunderstanding of what the egg white and egg yolk represents. A chicken egg is not simply an enlarged cell, and the egg yolk is not the cell nucleus.
When an oocyte matures in the chicken ovary, it stores yolk inside the cell and therefore enlarges. The yolk is therefore part of the oocyte cytoplasm. However, as it enlarges, the yolk is separated from the germinal disc, which holds all the other cell organelles (including the nucleus). The germinal disc is seen as a small white area on the egg yolk. Eventually, when the oocyte has accumulated enought yolk, it disattaches from the ovary (ovulation) and goes into the hens oviduct. This process is happening continuously, and oocytes of different stages of maturation are present on the ovary, which can be seen in this image:

(image from Chickscope: Formation of the Egg. University of Illinios)
When the oocyte passes through the oviduct it builds up layers of egg white (albumen) and other supporting structures. The shell is formed last in the shell gland, which is located at the end of the oviduct. Therefore, the egg white and the shell is formed externally of the oocyte and the egg yolk.
So the reason why we do not see more structures in a boiled egg is that the majority of the egg is yolk and egg white, which are both structures to store energy ment for a growing embryo (mainly protein and fat). It should also be noted that oocytes in most (all?) animals contain yolk granules, but the storage of yolk is most extreme in birds (see this webpage on animal development from State university of New York for a short comparison).
It should also be noted that an egg that is fertilized will naturally contain more than one cell, since the embryo will have started growing.
References:

Chickscope: Formation of the Egg. University of Illinios (webpage)
Chickscope: The yolk. University of Illinios (webpage)
Chapter "Eggs" in Johnson et al. 2002. Molecular Biology of the Cell. 4th ed. Garland Science, New York
Wikipedia: Egg
Animal development. State university of New York (webpage)

+1. Good answer. Clearly we were looking at some of the same pages, because that picture was one I studied as well! (Well, close).


text:
Some sort of Lymantriidae caterpillar?
I found this larva in Sweden in July. It was about 15 mm long. It reminded me of Orgyia antiqua that I've seen before, but smaller and with a somewhat different colouration.

http://en.wikipedia.org/wiki/Lymantria_dispar_dispar

I think it's indeed a young, and possibly worn, specimen of Orgyia antiqua (also Rusty Tussock Moth or Vapourer, see also UKmoths). This species is relatively common in large parts of Sweden. However, the tufts and "tail" are usually more pronounced, but there is probably intra-species variation, and old, worn individuals can have sparser tufts. As you say, they are usually longer than 1.5cm but there is large variation, sexual dimorphism and younger larvae (early instars) are natually smaller.

(picture from wikipedia)
Swedish specimen:

( from http://krypinaturen.se/fjarilar-lepidoptera/nattfjarilar/tofsspinnare-lymantriidae/orgyia_antiqua_1878_20130626/)
Lymantria dispar is rather rare in Sweden and is only found in certain localities in the south (Blekinge, Småland coast) along with Öland and Gotland.

It's so hard when they don't look like perfect representatives of their species! But this sounds convincing enough. Thanks!

This caterpillar is known as Lymantria dispar dispar. Not to be confused with the Lymantria dispar, as the Lymantria dispar dispar is the classified as it's subspecies for the sake of further taxonomy. The Lymantria dispar dispar, is locale to Europe and North America (via migration), the latter being sourced in Asia. They only possess a minor (however it's deemed as rather significant in the animalia kingdom) difference - the female Asian Gypsy moth can fly!
In the contrary, The U. S. Department of Agriculture, defines the Asian Gypsy moth by means of flight capability partially ignoring location; "any biotype of Lymantria dispar possessing female flight capability". Which demonstrates the evident flair in confusion on this topic.
The difference in the moths visual appearance in comparison to the pictures of species you'd more commonly see (i.e. the color of its head), is possibly due to the stage of maturation of the Caterpillar or the present season. That's just my hypothesis though, i am unaware of any evidence to back that up.
Here are some further images:
http://www.papillon-poitou-charentes.org/Lymantria-dispar-Linnaeus-1758,4446.html
Reference to the facts:
https://en.wikipedia.org/wiki/Lymantria_dispar_dispar
(Edit: I was proved incorrect! However, this information would be useful for others who seek the answer!)

Are you sure? They don't look alike to me. :-/

I'm fairly certain... not all from the species look identical just like, zebras don't all have the same distribution of stripes. It's difficult to say with 100% certainty since, nothing looks exactly  same!  Sorry, if this sounds sloppy - I'm very tired :P

I think that's incorrect. The OP's caterpillar has dorsal tussocks on segments 4, 5, 6 and 12 (or abdominal segments 1, 2, 3, and 9.) Yours has none. That's a big mismatch. Note, I didn't find a match yet, either.

Also, do you have any idea why my answer on another health post is being classed as 'spam'? I followed the advice posted on getting past this issue but to no prevail?

I have absolutely no idea then... However, I'm 100% certain that it's from  the genus 'lymantria' - feel free to check through the 220 other species of that genus ;) I apologise for my mistake.

No apology necessary; this one is clearly out of my league as well. Regarding your "spam" answer, I can't see it (I'm not a mod on this site.) You can ask about it in meta, though.

So it was a harder question than I thought! Thanks for the input, anyway, I'll keep looking...


text:
How well understood are the long-term effects of nuclear radiation?
Sometimes, when people are concerned about radiation, it is not because it is precisely quantified how dangerous it is, but because we don't know how dangerous it is.
How well understood are the long-term effects of nuclear radiation, for example on cancer? (As opposed to short-term effects such as acute radiation sickness, which is easy to quantify)
I assume this can be researched from an epidemiological approach (Wikipedia mentions an epidemiological study on the atomic bombing of Hiroshima and Nagasaki, for example), and also from an experimental approach.
Also, is the effects of radiation easy to understand, or difficult? My assumption is that something physical, like radioactivity, would be easier to understand than the effects of more complicated things, like complicated organic chemicals or obesity.

Related question, but not quite what I'm asking: http://biology.stackexchange.com/questions/14377/radiation-and-safe-dose

Great question - and a question I was asked in my local bakery this morning!

The three major nuclear incidents I can think of are the Japanese atomic bomb attacks, the Chernobyl disaster, and Fukushima disaster. Of course other nuclear incidents have occurred, but usually give much higher doses to far fewer people.
Many studies have been done on the survivors from the atomic bomb attacks, and increased rates of cancer have been the strongest conclusion. This review article looks at those studies for both cancer and non-cancer effects. Leukemia is the most well known cancer to be caused by radiation, and excess leukemia was discovered in bomb survivors within 5 years of the attacks. Rates of most solid tumors had increased by 10 years after the attacks. However "Even 55 years after the
bombings over 40% of the Life Span Study cohort remain alive", indicating that the amount of radiation most people were exposed to wasn't enough to kill them. Here is another article on atomic bomb survivors.
The Chernobyl accident was a very different type of exposure, but many people were exposed to radioactive materials. Immediately after the disaster, the "liquidators" received high doses of radiation while cleaning up the site and building the containment structures, but very few have died from radiation exposure. While the environment around the power plant did suffer in the years after the accident, after the humans moved away the environment has greatly improved. Thyroid cancer rates increased due to Iodine-131 exposure, especially among those exposed as children, but rates were still low.
 Yellow = adults Blue = Adolescents Red = Children.
It is too soon to draw many conclusions about the Fukushima accident, but some studies (7, 8) have tried to predict the number of cancer cases that will be caused by it. In general the rates are expected to be low, with far fewer deaths than were caused by the earthquake and tsunami that caused the accident.
A few instances exposed small numbers of people to very high doses, and are interesting from a radiation safety veiwpoint. The infamous "Demon Core" killed 2 scientists in separate accidents while handling the core. The Goiania incident involved men breaking into an old hospital and stealing a radiation source without realizing what it was. They broke the source open and passed the radioactive material around because it looked cool, resulting in several deaths due to acute radiation sickness.
While radiation can be dangerous, with proper precautions we can avoid accidents and disasters. Remember that Chernobyl was a poorly designed Soviet reactor, and that Fukushima was a 50 year old plant that needed both a magnitude 9 earthquake and a 30 foot wave to disable it. Modern nuclear plants can be built safely and provide clean electricity for many decades, and if they are breeder reactors can recycle the used fuel to reduce both the amount and half-life of the material, making storage easier.


text:
At what rate do chromosomal rearrangements occur?
How often do chromosomal rearrangements occur?

I am interested about these kind of chromosomal rearrangements that are passed on to the descendants, i.e. germ line chromosomal rearrangements. The value I am looking for is similar to the mutation rate but only take into account major mutations such as chromosomal rearrangements.
Supposing there might have some important variance in this rate among species, then I am interested in eukaryotes and particularly in plants. If needed, the answer can be split into the different types of chromosomal rearrangements (robertsonian translocation, other translocations, inversions, ...)

You can have a look at these papers: 1, 2. Gotta go now. will post an answer when I get time.

Just to clarify; you are asking only about larger chromosomal rearrangements (as in translocations, inversions, deletions etc), and not the frequency of also "normal" chromosome crossovers between homologous chronosomes?

Yes, indeed, I am interested in major chromosomal rearrangements and not about normal standard cross-overs.

Do you care particularly about the difference between somatic and germline rearrangements?

I was thinking about germ line rearrangements only. I would necessarily refuse insights about somatic rearrangements though! I edited my question to clarify this point. Thanks for your comment

@WYSIWYG must be really busy...

@RenaissanceProgrammer I was free for quite some time between Sep 2014 and now but nobody reminded me then. I am busy again now :/

Obviously, there won't be a single number for this.
The phenomenon is fairly well understood in yeast. Unfortunately, most studies tend to focus on the rate of formation of specific well-understood rearrangements, and then use that as a baseline. I am having trouble finding a measurement of overall rearrangement rate, although the system is ideal for this.
There has been some work on characterizing rates of rearrangement (and its evolution) across evolutionary history, I don't know if that is directly relevant.
This paper has a decent breakdown of the incidences in humans across different kinds of translocations. For example:

Additional studies (5, 6) followed and the incidence of balanced translocations was ultimately determined to be 1 in 500 in the general population.

Studies using cleavage stage biopsy for reciprocal translocation PGD have reported proportions of unbalanced embryos as high as 82% (57).

There is good reason to expect that it varies significantly across species and across chromosomes. For example, the Drosophila Y is a hotspot.
And (first paper):

Rearrangements involving chromosomes 13 and 14 (der(13;14)(q10;q10)) account for 75% of Robertsonian translocations (12).

For an early paper looking at a large population, you can see here.
Note that most of these human numbers are indicative of population incidence rather than rate of occurrence. Others have attempted to study effects on the translocation rate directly.
The best citation that I found for directly measuring translocation rate is here. However, the data are apparently for somatic translocations and are rather unevenly sampled so I am unsure of how generalizable it is. I looked at WYSIWYG's papers and they might provide some specific examples but they don't seem to address translocation rate directly either.
Take-home, it's hard to directly measure rearrangement rate in humans due to inviability of many/most aneuploidies early after fertilization. Somatic is easier to estimate but may not be representative of rearrangements in the gametes.

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


text:
How are arms different from legs?
How are arms and legs defined physiologically? For example, we say humans have two arms and two legs, while cats have four legs, and some monkeys (appear) to have four arms (although I guess they could be legs too). It's really unclear to me how we make these distinctions.
What is the physiological definition of both "arm" and "leg"? How are they different?

perhaps to do with whether or not they are walked on?

Why do they have to be defined physiologically? It is a matter of common everyday language, and human language is generally inconsistent and full of "because we've always called it this way" and "because they look similar" reasons. Do you have any example of any scientific research which divides appendages in "arms" and "legs" and proves results which are true for the one and not for the other? Maybe if you got to stuff which is about gripping, or bearing weight, but then you are back at the informal language level.

I don't think "arm" or "leg" is a matter of everyday language, and it just seems really silly that I don't know a) why my cat has four legs instead of two arms or b) how many legs/arms a monkey has.

I think that's more of a matter of linguistics rather than any scientific/physiological reason. For instance, in Portuguese, you wouldn't call legs to a cat or a dog's limbs. You would say they have 4 "patas" (roughly translated as "paws"). And calling them legs, in Portuguese at least, would be weird.
When veterinary doctors refer to animal limbs, they usually use anterior and posterior limbs. In fact, anatomically speaking, anterior limbs in cats and dogs (and probably in other animals too) have more in common with human arms (upper limbs) that with their own posterior limbs.

Also, as rg255 commented, maybe the reason behind the colloquial nomenclature is quite simple...
To (miss)quote Nancy Sinatra:

These "legs" are made for walking
And that's just what they'll do

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


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Bowtie: cannot read fasta file?
I am trying to use bowtie2 to analyze my data in FASTA format, but it seems that this version can't read properly my data. My command line is as follows:
bowtie2 -x $REFERENCE -f $TARGET -S $TARGET.sam

The version 2 of bowtie complains with the following:
Warning: skipping read 'ORIGINAL: GACACTGTTCATGCTGGTGTCGCTGTCGGGCATTAT' because length (0) <= # seed mismatches (0)
Warning: skipping read 'ORIGINAL: GACACTGTTCATGCTGGTGTCGCTGTCGGGCATTAT' because it was < 2 characters long
Warning: skipping read 'ORIGINAL: GGCTATCTTGAAGCCAATGAGTTGTTAACTGGCAAG' because length (0) <= # seed mismatches (0)

Note that bowtie (version 1) is pleased by my FASTA! Here's a snippet and what bowtie says:
>ORIGINAL: GCTACGGAATAAAACCAGGAACAACAGACCCAGCAC
GCTACGGAATAAAACCAGGAACAACAGACCCAGCAC
>ORIGINAL: ATTAACAACAAAGGGTAAAAGGCATCATGGCTTCAG
ATTAACAACAAAGGGTAAAAGGCATCATGGCTTCAG
>ORIGINAL: GCAGAAAATGGGAGTGAAAATCTCCGATGAGCAGCT
AATGGGAGTGAAAATCTCCGATGAGCAGC

# reads processed: 471409
# reads with at least one reported alignment: 464583 (98.55%)
# reads that failed to align: 6826 (1.45%)

Now I'm at loss. Can anyone see what I'm doing wrong here? Can I trust anyway bowtie2 when it finishes and outputs how many sequences are aligned?
Thanks!

Since I apparently don't have enough reputation to comment, I'll post this as an answer and let someone move it.
Firstly, try to ensure that the order of the arguments are correct. You should be typing bowtie2 -f -x $TARGET -U $TARGET -S $TARGET.sam, since bowtie2 (as with many other programs) can be a bit picky about the argument order.
Secondly, it's usually advisable for the example input to include lines that are causing the problem (since it's apparently not complaining about the lines you posted, we can only assume that it's aligning them).
Thirdly, you'll typically only get those warnings if they're true. For example, if you were to grep -A 1 -w GACACTGTTCATGCTGGTGTCGCTGTCGGGCATTAT $target then my guess is that you'd find it to have no remaining sequence. Presumably these are the result of you trimming adapters or something like that, so just have your trimmer discard really short results (they won't align meaningfully anyway).

it makes a fine answer @DevonRyan

Yeah even bowtie-1 doesn't take the argument bowtie -f $target.fa ..<other options>

Apparently, bowtie2 when reading headers will try to understand if the string is a DNA sequence: it does not ignore the content. However, it processes fine. Why it complains about headers, remains to me unknown.


text:
How were the synaptic areas identified in the somatic sensation pathways?
I'm studying the somatic sensation pathways in neuro-anatomy and I was wondering what was the experimental procedure for identifying the number and location of the synapses in these pathways? Additionally, how were they known to not branch anywhere? Did they use dyes or green fluorescent protein? These are the only visualization techniques I know.

Check out the work of Denny-Brown in humans.  I suspect this work that you describe was done much earlier, but you may be able to follow some of the references backwards from him.


text:
Safety of cobalt-chromium and nickel-chromium dental implants
How safe are cobalt-chromium and nickel-chromium alloys used in dental implants (porcelain fused metal)? IARC groups nickel and cobalt metals in group 2B and chromium in group 3 (hexavalent chromium is group 1!). But what is the likelihood of these metals leaching from implants and affecting the body? Aren't some of these metals already used for kitchenware (stainless steel vessels for instance contain chromium) and in industrial containers used for food processing? Is the risk much higher when these metals (not their more toxic compounds/salts though) are present in mouth when compared to their being used for food storage or cooking?

I would guess these are steel-alloys, right?

@MattDMo you can convert this comment to an answer.

Alloys have completely different chemical properties than their component elements. Elemental mercury is liquid, and is toxic, but when alloyed into amalgam with silver, tin, and some other elements it is perfectly safe, and has been used in dental fillings for a very long time with no negative effects. The same is true of cobalt and chromium alloys - they are chemically bonded to the other elements in the alloy, making a new molecule, and cannot "leach out" without the chemical bonds being broken, which cannot happen in the mouth or at standard cooking temperatures. Hence, they are safe for food prep and for fillings/implants.

But I have read reports in health columns warning that amalgams with some heavy metals can be dangerous in the long term since some tiny amounts of these elements will inevitably enter bloodstream occasionally, accumulate in some vital organs and hereby have the potential to cause chronic illnesses. I even saw a somewhat similar thing mentioned in a health awareness book written by a neurologist - that certain tooth fillings are suspected to be the cause of some degenerative neurological conditions. Are these studies flawed?

@so2 Please give some references to these "health columns" and the "health awareness book". Anyone can write anything they want, that doesn't mean it's true, or supported by peer-reviewed research.

Here is one of the many websites that mention amalgams can be dangerous: http://www.curezone.org/diseases/cancer/cancer_dental_risk.asp. Many of these websites mention names of doctors and medical institutions. I agree that the internet has a lot of misleading information and I also find an increase in the amount of health news that we cannot use, but was concerned about dental implants thing because I have also read articles in reputed newspapers that mention health hazards of heavy metal contamination in general, though they were not in the context of dental implants.

@so2 that page is full of random quotes from dentists, unsourced claims, and links to other unverified websites, without a single citation to reputable peer-reviewed literature or actual evidence - it's scare-mongering. Just because a doctor associated with a medical institution says something, doesn't mean it's true - you need evidence. Yes, heavy metals on their own can be highly toxic. However, as I described in my answer, amalgam is an alloy of different elements, and its chemical properties are entirely separate from the properties of the individual components that make it up.

Here is another one that cautions against using aluminum foils to store food while clearly stating that there is no strong scientific evidence showing these practices to be harmful to health: http://www.whfoods.com/genpage.php?tname=newtip&dbid=8. It also cites some studies. Atleast it provides a more balanced view & is not bent of creating a scare.
Would you mind updating your answer to state that no scientific study has given a conclusive evidence of long-term harmful effects of metallic dental implants, or if a study has proven they are perfectly safe, provide a link? Thanks!

Made the request to update your answer since I feel that at least when it comes to health, we have a much bigger moral obligation towards the society and hence must exercise more caution when we state something is perfectly safe. I want to accept your answer but would like to ensure that we either substantiate the claim of safety with some references or caution that the claim is based on studies done so far and leave room for future studies that may find some health effects.

@so2 I understand. I'll update the answer as soon as I can (I'm at work now, and a bit busy).

Thanks and no problem. Will wait for you to update whenever you get time


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Regarding cancer cells and telomeres
If cancer cells have telomeres are they different than the telomeres in non-cancerous cells? Would cancer cell telomeres be somehow 'set-up' to function almost indefinitely; in other words are 'they' very 'robust' or 'durable'? If these cancer cell telomeres are 'durable could their functioning cause any apoptosis mechanisms to 'shut down'?

In a normal cell, during each replication the telomere is shortened slightly due to the end replication problem, as you probably know. As mutations occur and a normal cell begins to exhibit cancerous characteristics, it needs a way to stop the self-destruction which happens when the telomeres become too short. In fact it is the cancer cells themselves which 'short-circuit' the shortening process and cause the telomeres to stay long enough.
90% of tumors do this by activating telomerase, an enzyme complex which elongates telomeres and keeps them from getting too short, so that the cell is effectively immortal from this sort of destruction. Usually telomerase is not active in most cells, except for stem, germ, and hair follicle cells, but cancer cells use this to their advantage and activate it to stay immortal. The other 10% or so employ a method called ALT, or Alternative Telomere Lengthening, a not yet thoroughly understood process which involves the recombination of tandem repeats between sister chromatids.
This page explains how cancer cells bypass the telomere shortening process well, and also provides a series of further reading on telomeres and telomere shortening.

Is there a process in cancer cells that causes the formation of telomerase? How does it get 'activated'? How do shortened telomeres cause the apoptosis mechanisms to be activated? Could telomerase prevent the apoptosis mechanisms from turning off?

Can the apoptosis mechanisms be 'turned off' in a stem cell?

In cancer cells, the telomerase is not "formed" but activated, mainly due to an amplification and a gain of copy of the 5p chromosome arm, containing the gene coding for TERT. For example, a very common way to immortalize primary cells to establish a cell line is to stably express TERT.
Shortened telomeres initiates DNA damage response pathways, resulting in the activation of ATM and ATR, and downstream kinases CHK1 and CHK2, and phosphorylation of p53. Once activated, p53 upregulates genes that mediate cellular senescence and/or apoptosis.

Telomerase is activated in a cancer cell, it is not formed. In a 'regular' non-cancerous cell is telomerase 'formed' and if so is the 'activated' telomerase in a cancer cell different than the 'formed' telomerase in a non-cancerous cell. Different maybe in chemical make-up or 'amounts used' ?

If telomerase is not formed but activated is it 'within' a cancer cell but 'dormant'? Does telomerase promote the formation and/or repair of telomeres?

Are there any natural substances that can be injested that promote the formation or activation of telomerase?


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Does a pregnant female body treat the fetus based on gender?
I have seen on a youtube video that the female body produces antigenes and antibodies when she is pregnant with a boy. But this behaviour is not produced when she is pregnant with a girl. These means that the more antigenes she produces, the more femminin the next child will be. More antigenes are produced when she is pregnant with a boy.

Is this correct? if yes, then why does the female body produce antibodies and antigenes when the fetus is a boy and not a girl?
What other pregnancy actions or behaviours are gender based?

Can you link your source? Otherwise I would consider higly unlikely.

http://youtu.be/5Tg_3OVizrA?t=2m15s

Hmm, I always have my problems with the "scientists have found out" phrase when not linking to the actual publication, but I will have a look into it.

I haven't found any articles besides the formation of antibodies against the "Rhesus"-antigen which happens when the mother is Rh- and the baby is Rh+. This is not restricted to male babies but happens against both sexes. Besides this, it doesn't really make sense for the body to react in this way. The mechanism of immunologic tolerance prevents the mother from launching an immune reaction against the fetus.

@user2360 If you don't get an answer here you may then want to ask your question on skeptics.SE. It is a SE website that deals with questions of the kind "is this claim (source) true?" question.


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How does myopia develop, exactly?
Recently I was reading about myopia and I understood a few basic facts about it:

Its initial cause is a constant spasm in the ciliary muscle.
To do less work, the eyeball elongates a tiny bit.
During adolescence, because of the growth of the body, the eyeball elongates accordingly even more (i.e. the myopia is progressing).

I don't really understand the exact mechanism responsible for the transition from 1 to 2. Is the ciliary muscle capable of elongating the eyeball on its own, or is there some other relationship to another part of the eye?
It's weird how myopia is so common these days and I wasn't able to find the precise mechanism behind it.

What is myopia?
Myopia, a.k.a. near-sightedness, is a refractory error. Refraction is the process by which the optical system focuses images of objects on the retina, which are then transmitted to the visual cortex of the brain to be interpreted as vision. The major components of refraction are the cornea, lens, and axial eye length (distance from the front to the back of the eye). The problem in myopia is that images are focused anterior to the retina, like this:

Causes of myopia
You ask

I don't really understand the exact mechanism responsible for the transition from 1 [ciliary muscle spasm] to 2 [elongation of the eye].

Swelling or spasm of the ciliary body (the circumferential tissue inside the eye composed of the ciliary muscle and ciliary processes) can be seen after trauma or in inflammatory conditions. Contraction of the ciliary muscles causes decreased tension in the suspensory ligaments that connect the ciliary body to the lens. The results in the lens becoming more rounded and/or moving anteriorly. Both processes also bring the focal point more anterior, i.e. further in front of the retina, resulting in a configuration as in the picture above. You could call this "elongation of the eye" if you wanted. This 25 second video explains the process succinctly with pretty pictures.
Although interesting to think on, this is not the most common cause of myopia. Myopia is an extremely common condition, occurring in ~25% of the US population. Myopia can be classified as axial or refractive.

Axial myopia: The refracting power of the eye is normal but the length of the eye is too long.
Refractive myopia: The length of the eye is normal, but the lens refracts too much for a given axial length.

Both axial and refractive myopia are usually caused by failure of emmetropization, the process by which a normal eye has coordinated growth of its refractive components. This process takes place mostly during the childhood and adolescent years, which is why myopia most commonly develops during that time. There are certain disease conditions that increase lens power (e.g. osmotic effects in diabetes) or axial length (e.g. posterior staphyloma) that may also cause myopia at other points in life, but these are less common.

References:

1. Neil J. Friedman and Peter K. Kaiser. Essentials of Ophthalmology. © 2007, Elsevier Inc.

2. Albert, Daniel M., MD MS.Albert & Jakobiec's Principles & Practice of Ophthalmology, Third Edition. © 2000, 1994 by W.B Saunders Company, © 2008, Elsevier Inc.

Image from:
http://en.wikipedia.org/wiki/Myopia


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

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


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How come degraded eyesight still holds with a mirror?
When you use a mirror to look at something, you can position it at an angle arbitrary to your face and still look at an object far away. My question is, for degraded eyesight, how come the picture is still degraded in the mirror? Is it because of an imperfect mirror? Is it theoretically possible to have a mirror that when looked at an angle with perfect scattering to give you better vision than without the mirror, just looking regularly with degraded vision? I am just wondering, it seems like a photonic process, but i don't know enough about the eyes to turn them into any sort of functional system

No, if your eyes are defective, the quality of an image cannot be upgraded with a mirror.

You need to clarify the question - it would help to be a little more concise and say why you think it should help to use a mirror

I asked this same question to my high school physics teacher when we were going over optics. I'm nearsighted, and wondered why I could see clearly from 6 inches away, but if I looked at a mirror from 6 inches away things were still blurred. The answer has to do with the angles of light entering the eye instead of distance.

It's been too long since physics to have a good answer, but I know that if you look at an object in a flat mirror, the light coming off the mirror would be identical to light coming a real object in the same position. The angles of the light rays are the same. Therefore, no matter how close the mirror is to your face, your eyes treat the image as if it's coming from 10 feet away, or however far the object in the mirror is away from the mirror. Bent mirrors will change this, that's why you get the "OBJECTS IN MIRROR ARE CLOSER THAN THEY APPEAR" warning.
I made a diagram to to try and explain it better.
The eye is looking at a mirror, the light from the arrow on the left of the mirror reflects off the mirror and toward the eye. The eye sees an image that appears as if it were behind the mirror, on the right.

The working of a mirror is not what the OP is asking about. The question is whether a defective eye can see a clear image reflected off a mirror (i think).

If the mirror is shaped to correct the image, then yes, just like how lenses can adjust the light so that it enters the defective eye in such a way the eye focuses it into a good image, a mirror could be made to do the same thing. However, getting the focal length right will be very hard and you'd have to put your eye in the exact same position relative to the mirror every time you use it. Flat mirrors will not fix the image and defective eyes will still see the images poorly.

Degraded eyesight can mean two basic processes:
1)  Degradation of the imaging optics in your eye that focus light onto the retina such that light is not focused correctly, or
2)  Damage to the retina itself so that light is focused, but signals to your brain are not generated in response to light.
What these two processes have in common is that they are problems with your eyes ability to process and interpret light.  Placing a mirror close to your eye (but outside of it) does not directly compensate for either of these problems because, other than transforming the coordinate system, it doesn't actually do anything to the light or to your eye.
Possibly what you are thinking of by "degraded" eye sight is simply being near or far sighted, which is the specific case where your vision still works normally, but your eye does not under some conditions (nearby for farsighted, etc) due to a loss of accommodation (the physical flexing the lens of your eye that adjusts its focusing).  In this case, a curved mirror can be chosen that operates just like eye glasses.


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Why would yeast grow but not produce alcohol?
I'm studying for my intro to microbiology test and I have a question asking why a culture of yeast responsible for producing alcohol would be growing, but not producing alcohol?
The multiple choice answers are:
a) the maltose is toxic
b) O2 is in the medium
c) Not enough protein is available in the agar
d) The temperature is too low
e) The temperature is too high
EDIT: There is not much more context that what I gave here. The question simply asks me to assume the position of a scientist at a wine production company, and then asks the question I posed above - nothing too specific.
I think it is (b) because the presence of O2 would cause the yeast to respire aerobically, but I can't eliminate (d) and (e)
I figure it probably isn't (a) because a toxic chemical would inhibit the growth of the yeast. I don't believe protein is relevant so I don't think it is (c).

I think we generally ask people with homework questions to explain their work and reasoning as much as they can first. Look up some stuff about yeast fermentation and you might answer this yourself. And please clarify how the yeast is making bacteria?

Changing the temperature would tend to cause the rate of metabolism to increase/decrease, but it would not tend to cause the actual metabolic products to change significantly.

I think only b.) is true.

a. I cannot find evidence that maltose is toxic to yeasts (and I would hardly believe it, because it is a glucose dimer), however I found evidence, that yeasts might need the presence of oxygen to process maltose.

1977 - The Requirement of Oxygen for the Utilization of Maltose, Cellobiose and D-Galactose by Certain Anaerobically Fermenting Yeasts (Kluyver Effect)
1994 - Effects of oxygen limitation on sugar metabolism in yeasts: a continuous-culture study of the Kluyver effect.

b. Alcoholic fermentation is an anaerob process, so it won't work in the presence of oxygen.
c. Alcoholic fermentation is for creating energy. Proteins are normally not involved as substrate (maybe by gluconeogenesis, but that's another story). If the yeast grows, then there is enough protein available to build fermentation enzymes as well.
d. I found some articles about the temperature dependency of alcoholic fermentation:

Juices fermented at 10°C exhibited ethanol concentrations between 7.4
  and 13.4% and populations of K. apiculata, C. stellata and C. krusei
  in the range 106-108 cells/ml.

1988 - The effects of temperature and pH on the growth of yeast species during the fermentation of grape juice

At low temperatures, alcohol yield was higher. Secondary metabolites
  to alcoholic fermentation increased as the temperature increased.
  Glycerol levels were directly affected by temperature.

2003 - Effects of fermentation temperature on the strain population of Saccharomyces cerevisiae

The immobilized yeast showed an important operational stability
  without any decrease of its activity even at low temperatures (1−12
  °C). Specifically, at 6 °C the biocatalyst favored wine production
  within 8 days, which is less time than is required for the natural
  fermentation of grape must.

2001 - Wine Production Using Yeast Immobilized on Apple Pieces at Low and Room Temperatures

It seems like low temperature does not necessary have an adverse effect, but this could depend on strain.
e. Just the same as the previous answer. I think the main fermentation products will be always ethanol in the yeasts chosen for alcoholic fermentation (if the other conditions are right), so it is not temperature dependent in this case. A growing yeast will produce alcohol on both low and high temperatures. The ratio of ethanol and the byproducts can depend on the temperature, but not the presence of the ethanol itself. By too low or too high temperature the yeast will die or will stop to grow. (My experience that CO2 production is faster by high temperature, so it is because everything is faster or because the ethanol/CO2 ratio is lower.) An example of temperature dependence by wine making:

Temperature control is vital in the production of fine table wines as:

High temperatures encourage the loss of alcohol and aroma and flavour compounds due to volatilisation. If the temperature goes above
  30 -35ºC, the yeast becomes sluggish and fermentation may stop.
Low temperatures will lead to a poor extraction of colour and tannins in red wines and can also cause sluggish fermentations and the
  production of high levels of ethyl acetate.

Managing the alcoholic fermentation

I think "sluggish" means stop growing in this case, and ofc. stop fermenting due to the death of the yeast cells.

I think you put in way more effort than this question required. Not that that's a bad thing.

@canadianer Maybe. Btw. your answer is perfectly valid too, and you solved it with pure logic, +1 :-) Ohh I have not known that this is an old question.

Depends on the yeast but some (most notably S. Cerevisiae) readily ferment in the presence of oxygen. So this question is a little ambigious. Although not surprising for biology, Im surprised the microbio prof did not clarify the question.

You're right, the answer is b since the presence of oxygen would lead to aerobic respiration and not fermentation.
If maltose was toxic, the yeast wouldn't grow.
Proteins are required for growth, but the yeast is growing.
Any temperature that is extreme enough to prevent fermentation would also prevent other cellular processes and the yeast wouldn't grow.

IMO, the answer to this one is (b). The reason is the (often overlooked) Pasteur effect: oxygen inhibits fermentation.
The Pasteur effect occurs in many cell types, including skeletal muscle, brain, heart, liver, bacteria and yeast (Tejwani,1978) .
The mechanism of the Pasteur Effect has been much studied and debated and it it probably true to say that it has still not been fully explained. However, in abstract terms, it  be explained to a good approximation in terms of the allosteric regulation of the the enzyme phosphofructokinase, a key regulatory enzyme of glycolysis, where ATP, inorganic phosphate, and citrate (among other allosteric effectors) play critical roles. (Krebs, 1972, Tejwani, 1978).
Refs
Krebs, Hans (1972). The Pasteur effect and the relations between respiration and fermentation. Essays in Biochemistry 8, 1–34.
Tejwani, G. A (1978)  The role of phosphofructokinase in the Pasteur effect.  Trends in Biochemical Sciences, Volume 3, pages 30-33


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About excessive cellular growth
When there is 'excessive' cell growth 'ordered' by the human body in some specific part of the body that is not part of the usual repairing mechanisms, does this cause extra telomere 'shortening' or damage even though a lot of cell growth and repair is 'required'. If a lot of cell growth is 'activated' with problematic telomeres does this cause telomerase to be formed which then might shut down the apoptosis mechanisms and keep the cell 'going' indefinately. Note; I read some acid reflux problem causes parts of the throat to scar or be damaged causing excessive cellular repairs on those parts of the throat where tumors have later developed. When someone gets sunburned on the shoulders say, and this damages the skin there, then does every future time the persons shoulders get in the sun ,do those same areas get further damage causing excessive growth and repair of skin cells on the shoulder. With a lot of excessive repair tumors might develop. SO could excessive cell growth (that might be caused by many different factors ) help to cause cancer??

Long story short: Absolutely.
Short story long:
While your intuition that growing a lot of cells can increase the risk of damage that might cause cancer is spot on, your specifics are a little off. It's not the telomeres themselves that are the problem, but broad spectrum DNA damage and transcriptional changes. The condition of the telomeres doesn't directly affect the likelihood of a cell growth becoming more cancer-like. A cell with perfect telomeres fresh from a telomerase-expressing stem cell and cell with shortened telomeres have an equal chance of becoming cancerous. Cell populations with longer telomeres have 'more time' or more chances to develop mutations and cell expression damage, however. You're more likely to get in a car crash if you go to the store across town  than the neighborhood convenience store, even though it's not intrinsically more dangerous per mile driven.
The sunburn example can be a little misleading. It's not cell regrowth that's the key carcinogenic factor, but instead the direct DNA damage UV radiation can cause. In a particularly bad sunburn your skin cells may be killed or commit suicide(apoptosis) because of the DNA damage they've sustained. If the cells are damaged but do not die, they're likely to recover. Over time and repeated sun exposure, the skin cells that are most resistant to orders from the body to stop growing or die stick around and may grow and divide. Freckles are when this happens to a population of skin cells that ignore orders about how much brown pigment to be, but still listen to the orders that instruct them on how to be skin. When they stop listening to the skin orders, they officially become precancerous.
The acid reflux example is excellent. There are populations of stem cells throughout the adult body that produce skin cells and hair follicles and blood cells and all the other kinds of cells that are more or less expendable. Generally speaking these stem cells don't have do very much work replenishing esophagus cells, so when they are taxed by something killing off the esophagus lining regularly, they can 'break down' and lose control of their own replication.
It seems like you're both pretty interested in cellular mechanisms of cancer and a little shaky on current theories of cancer formation(there are a few), so if there's a section of this answer that needs to be more detailed or followup questions please let me know.

Are there ways to retard or slow down excessive cellular growth? Can telomere damage cause the apoptosis mechanisms to malfunction? I'm fascinated with Biology but am shaky on a lot of theories..

Depends on the kind of growth. In the case of acid reflux, no. You need to replenish that lining once it is damaged. Telomeres are rarely 'damaged', as they're very long highly repetitive sequences. Think of them as 'margins'. When the margin is missing, you start to lose words off the page, and indeed telomere shortening is used as a trigger for apoptosis. If damaged or short telomeres interfered with apoptosis, very little apoptosis would every happen.