What dictates which protein to synthesize at a given time?

Your asking how a cell or organism regulates protein synthesis. This is a complex question, with many different parts. It is well presented in Alberts Molecular Biology of the Cell, Chapter 7, on genetic switches. Here's an online section from that chapter in the 2002 edition.

There is a lot involved in regulating protein synthesis. As a general rule if you can imagine regulating it, it's regulated. Here's a figure from Alberts to get you started thinking about this:

There are some things that are required for all genes. General transcription factors, for example, and the Pribnow, or TATAAT box. The presence, absence, location, and accessibility of these things can regulate the levels of protein synthesis by the cell. Other things are going to discriminate between different genes. Under certain conditions, certain gene regulatory proteins will be produced, not destroyed as quickly, activated, allowed entry into the nucleus, etc, regulatory sequences will be exposed or not exposed, methylated or unmethylated... and transcription rates will change accordingly (increasing if those protein gene interactions stabilize assembly, binding, and transcription by the polymerase, decrease if they destabilize assembly, binding, and transcription by the polymerase).

This is just a taste of the wonderful world of gene regulation in the eukaryotic cell. As it says in Alberts, of the roughly 30,000 human genes, an estimated 5–10% encode gene regulatory proteins. And these are just the proteins that directly regulate transcription.


Does this mean that if one (or both) parents have something major missing (like a limb), the kid will come out without a limb?

Unless there is a genetic basis to the missing limb, no. Even for people born with missing limbs, this is usually not caused by genetics, but by a problem during limb formation in the womb (for example, through medication taken by the mother). A genetic condition associated with missing limbs is tetra-amelia, which is indeed heritable; however, it is very rare, a recessive trait and people actually showing it rarely have children.

  If someone got melanoma from laying in the sun A LOT, would their kid have a higher risk of getting it?

No, at least not in the way you seem to think from the way you phrased this. There are people who are more susceptible to melanoma due to genetics. For these people, their offspring can also be more susceptible to skin cancer. However, this is passed to the next generation whether or not the parent has melanoma.

  DNA can change over time

Yes, it can. DNA even in adults can change over time, but either this is your germline cells, so it will be passed to the next generation, but won't bother you, or it's in the rest of your cells and may or may not have an effect on you, but won't be passed to the next generation.


Nomenclature of enzymes involved in synthesis of glutamine

Probably a mistake in your notes, or in the lecture notes for the class, but not a very important error in either case aside from the confusion it has caused you.

See the wikipedia article on Synthase and on wikipedia article on Ligase for a note on the terminology: historically synthetases use ATP, synthases do not, but this terminology is not adhered to strictly, and the current standard is that the terms are essentially synonymous; in my experience, however, a particular nomenclature dominates the literature even if the synonym is technically correct.


Can methylation from DNA get copied to RNA during transcription?

I don't believe anything should change in the majority of DNA->RNA transcription. DNA methylation typically occurs on the non-watson crick side of Cytosine so it shouldn't affect the base-pairing.

However, there are a few hypothetical situations that would result in alterations of the transcribed RNA. The sponatneous deamination of the 4' amine would convert the base into uracil. If there is an additional 5' methyl, the 5-methyluracil would be recognized as Thymine.

(edit) I've talked with several genomics folks about this topic and it turns out that M5Cytosine is very resistant to deamination due to the presence of the Methyl group. As a result, the instance that I have just described is actually very rare.

5mCytosine to Thymine deamination

The other situation would be to errors in DNA proofreading. Does the 5mCytosine affect the fidelity of RNA polymerase? I honestly don't know but it would be worth examining.


What is the cause that angina pectoris is felt in your left arm?

It has mainly to do with the embryonic origin of organs, with the heart being a typically left sided organ, it develops sharing some nerves with the left thorax and left arm.

There is however high variability, typically among patients but also among coronary vessels. For instance, right coronary stenosis may lead to abdominal pain, whereas left circumflex artery stenosis may lead to no pain at all.

References:

Essentials of Medical Physiology

Cardiac Pain. Anatomic Pathways and Physiologic Mechanisms

Changing Features of Anginal Pain After PTCA Suggest a Stenosis on a Different Artery Rather Than Restenosis


Using formulas to explain why contraction of blood vessels leads to increased blood pressure

There is an important missing assumption in your statement, I've added it in italics:

  Contraction of blood vessels leads to increased blood pressure if total flow stays constant.

All you need is your first equation:

Flow = Pressure/Resistance

Decreasing the radius increases the resistance. If flow is constant, then pressure has to increase to get the same flow through the smaller vessel.


Evolutionary elimination of recessive gene

Simply put, there may not be enough selective pressure to force those alleles out of the population. For example, take a hypothetical gene for eye color. The dominant allele gives brown eyes, the recessive blue, due to the lack of expression of a certain pigment-processing enzyme. So, two heterozygous (brown-eyed) organisms are crossed:

   |  A |  a |
--------------
 A | AA | Aa |
--------------
 a | Aa | aa |
--------------

which results in 75% brown-eyed offspring, and 25% blue-eyed offspring. Unless there is some very strong factor in the environment that has a negative selective pressure on blue eyes, the recessive allele will remain in the population.

OK, that's for an allele with no negative pressure acting on it. What about a disease allele, for example one that has a point or other mutation inactivating an essential enzyme, such as iduronate-2-sulfatase (I2S), a key enzyme involved in the breakdown of waste in the lysosome. It is part of a group of diseases known as lysosomal storage disorders, and is the causative agent of Hunter Syndrome.

People who have the so-called "wild-type" allele(s) of I2S have normal function, even if they are heterozygous. However, if two heterozygotes produce offspring (or if a heterozygote produces offspring with a homozygous recessive individual), then there is a chance of a child with two recessive or defective forms of the enzyme, and they are much more likely to develop Hunter Syndrome (almost no genetic disease is 100% penetrant). If untreated, this disease can have many quite horrible effects (especially given that it usually appears in childhood). The disease is also progressive (it gets worse the older you get), and while it in itself does not typically cause death, patients have (sometimes severely) limited lifetimes.

So why haven't the mutant, disease-causing forms of I2S been "weeded out" by natural selection? In a single word: heterozygosity. Studies (I don't have a reference, unfortunately) have shown that supplying a Hunter patient with as little as 10% of the typical amount of active enzyme in an unaffected person is enough to resolve the acute symptoms of the disease, and begin reversing many of the long-term effects. All things being equal, one would expect that a heterozygote carrying one functioning allele of I2S and one mutant allele would express about 50% of the amount of enzyme that a completely unaffected individual does, and this is more than enough to prevent the onset of disease. There are likely other molecular mechanisms involved to express the functional version even more, so their levels may be even higher than 50%.

So, while there is certainly a strong negative selection pressure on people carrying two copies of a mutated allele (or two different mutations, there are actually many of them) that prevent most or all expression of active protein, that same selection pressure does not apply to heterozygotes, and so the mutant alleles remain present in the population.

I strongly recommend reading through the fairly short but definitely thorough course Understanding Evolution from the University of California, Berkeley. It may explain some of the concepts I've mentioned more clearly.

Note: I once worked for Shire, which, among other things, specializes in rare diseases including lysosomal storage disorders. I specifically worked with their Hunter Syndrome therapeutic, known as Elaprase. Other companies are also working on various therapeutics.

This is in no way an endorsement of the company or its products, it's just where I learned all of this stuff.


How can inbreeding be used for selecting mutations?

Consider a sibling-sibling mating system, the simplest inbreeding situation, with a simple Mendelian trait.

Step 0:
Let's start with heterozygotes, Aa x Aa.

Step 1:
Their offspring will be a collection of AA, Aa, Aa, aa, in roughly those ratios assuming equal survival.

Step 2:
Now we breed siblings. If we happen to breed Aa x Aa, we are back to the original starting point. Return to Step 1.

If we happen to breed AA x AA or aa x aa, and then continue to breed those offspring with their siblings, all of the following generations will be homozygous unless there is a mutation. Stop here, you have homozygotes.

If we happen to breed AA x Aa or Aa x aa, the next offspring will match those parents: AA, Aa or Aa, aa. If we breed Aa x Aa, return to Step 1. If we breed AA x AA or aa x aa, stop here, you have homozygotes.

Of course, theoretically you could end up with heterozygotes doing this forever, but the odds get lower and lower the more generations you breed.

For selecting a particular mutation, it is often simpler to genotype for presence of an allele rather than zygosity (i.e., just use simple RT-PCR). For example, if you want to eventually produce aa, you can test for the 'a' allele, and not breed any offspring that do not have any 'a', therefore they are AA. If you do this, you will always eventually end in a path with aa homozygotes.

If you have an easily produced model organism, you can also do this simply by phenotype (depending on the trait): once a strain settles into a consistent phenotype, you know you have a homozygote of one type or the other. If your model organism is easy to produce, it's okay if some don't end up carrying the mutation.

For selecting a random mutation, the same is true, except you have many genes instead of just gene "A". Any random mutation in just one individual early in the breeding could potentially be fixed in the inbred population somewhere down the line, following the steps above. If you breed BB x Bb, where Bb has a random mutation, you have a chance to breed a Bb x Bb pair in the next generation, which starts you at Step 0 for that particular random mutation.


Why are Ramachandran angles of first and the last amino acid not necessary to define the full 3D structure of a protein chain?

Think about the case of a chain of N=3 points in space. There are only angles associated with the middle point, the two endpoints don't have angles associated with them because they only have one incident segment rather than two.


What is the difference between polar and charged amino acids?

All amino acids with side chains that are charged at physiological pH are, by definition, also amino acids with polar side chains (e.g., lysine or glutamic acid). The converse is not true; in other words not all amino acids with polar side chains are necessarily amino acids with side chains that are charged at physiological pH (e.g., threonine or asparagine). The pKa of the nitrogen in histidine's imidazole ring is quite close to physiological pH, and in some situations would be charged and in other environments would be uncharged. In either case it would be considered polar (or largely hydrophilic in nature).


What is Oncogene, and how do you get it?

An oncogene is a gene that has the potential to cause cancer. If an oncogene is activated, it will contribute towards cancer, though there are typically many other factors necessary before cancer becomes noticeable and potentially lethal.

In short, your family member presumably died of cancer, though writing the cause of death as "oncogene" is highly abnormal.

Many normal and healthy genes can cause cancer when they are overly active. For example, PDGF produces a growth factor required for normal health, but if too much growth factor is produced it can cancer like breast cancer.


I think this is a fantastic question.

As far as the Parkinson's application, it's definitely within the realm of possible. Taken form a recent review:

  Preclinical research in animal models of several movement disorders
  have shown variable evidence for symptomatic benefits but more
  consistently suggest potential neuroprotective effects in several
  animal models of Parkinson’s (PD) and Huntington’s disease (HD).
  Clinical observations and clinical trials of cannabinoid-based
  therapies suggests a possible benefit of cannabinoids for tics and
  probably no benefit for tremor in multiple sclerosis or dyskinesias or
  motor symptoms in PD.

Kluger et al. in Movement Disorder, 2015 (The Therapeutic Potential of Cannabinoids for Movement
Disorders)

As far as every-day hand steadiness, I haven't been able to find any good sources yet. I'll keep reading, and update this if I find anything interesting.


As with most things in the natural world, there isn't really a single straightforward answer to this question! It depends largely on the ecological contect and the population dynamics.

Basically, in organisms with high mutations rates (such as RNA viruses), Muller's Ratchet suggests that the mean fitness in a population will always decrease. In small populations, mutation-free individuals are rare, and they will be lost through genetic drift. In 1990, Chao showed that deleterious mutations are generated at a sufficiently high rate to advance Muller's ratchet in an RNA virus.

However, in general, Muller's ratchet can be argued to be ineffective in viral populations because populations are never 'small', and drift is usually very weak (or selection is strong, in other words). Chao also notes that the effective population size in nature, 8x10^9 is often irrelevant to whether or not Muller's Ratchet is active, because Viruses often pass through the bottleneck of a single individual. Additionally, frequently recombining viruses such as HIV can also be subject to Muller's Ratchet Yuste et al (1999). The results of Chao have been generalised to many other viruses.

However, these studies are lab-based and don't pertain to your question about what might happen to SARS-CoV-2 'in the wild'. RNA viruses show the highest mutations rates in nature (Sanjuan et al 2010). This can lead to Muller's Ratchet in small populations where selection is weak and drift is prominent, but can lead to high levels of adaptation in large populations. It is not just the census population size which is important, but the effective population size, which can be thought of as a proxy for the amount of genetic diversity within a population. If a population rapidly expands from a single origin, as is expected to have happened with the SARS-CoV-2 outbreak, then the census population size would be larger than the expected diversity. Novella (1995/1996) showed that there is an interplay with the size of the bottleneck and the fitness of the surviving clones; when a more fit viruses passes through the bottleneck, they are more likely to avoid Muller's Ratchet. So in the case of SARS-CoV-2, whether or not the virus would be subject to Muller's Ratchet would depend on both the variation and fitness of mutation of the viruses who jumped from the intermediate animal to humans.

At the risk of overcomplicating things, population/deme structure also plays a role. If the virus evolves in different demes within a structure population, viruses within a deme can evolve population specific mutations. If there is then gene-flow between the demes, there can exist selection between the different mutations, driving up the average fitness across demes (Mirales et al 2009) and avoiding the Ratchet.


Why are there two mature sequences of microRNAs in miRBase entries?

I am not sure whether it is made clear in the Wikipedia article on microRNAs, but, yes, there are two possible mature mir species that can be generated from the stem-loop precursor — one from each side of the stem — although most often one greatly predominates.

The diagram in Wikipedia shows the generation of a single miRNA:

However, the entry mentioned in the question (hsa-mir-15a) shows that although the 5′-stem component (UAGCA…) is most abundant in this case, there is a small amount of the 3′-stem component (CAGGC…).

In Drosophila melanogaster a single stem component (more often from the 3′-stem, but also from the 3′-stem) most frequently predominates, but I have personally found microRNAs in which both components occur in similar amounts (unpublished).


Is telomere length a reliable measure of health/lifespan?

I disagree with Ctina.  So many factors go into determining loss rate, activity of telomerase, gene conversion or unequal exchange at chromosome ends, etc to ever say that length is a function of age.  There is far more variation between individuals and between cells within an individual than aging ever shows.  Here is one study:

Das B, Saini D, Seshadri M. Telomere length in human adults and high level natural background radiation. PLoS One. 2009 Dec 23;4(12):e8440.

however I've seen similar studies published elsewhere.  Telomere length as diagnostic for age is very poor at best.  Here's an article that gives a formula, but acknowledges the R2 is 0.04, which is useless: http://preview.ncbi.nlm.nih.gov/pubmed/18378481


Does preservation in ethanol alter leaf litter mass?

It's very likely that you should have at least minor changes in mass.

The reason is because ethanol can extract a number of substances from leaves (e.g. tannins, pigments, etc.).

However, you could still easily double check on your own.

You could still figure out the mass of the CPOM even without knowing the answer to this answer directly.

Drain and collect the EtOH.
Determine mass of separated CPOM.
Determine the excess mass present due to any leaching/dissolving from the CPOM by using density = mass / volume (or ρ=M/V) with your collected volume of ethanol.

EtOH has a density of 0.789 g/mL  at 20°C. 70% EtOH has a density of 0.885 g/ml at 20°C.
Determine the volume of the collected EtOH.
Determine the mass you'd expect of "pure" 70% EtOH given your volume (m = ρV )
Determine the mass of the collected EtOH
Subtract the expected mass from your calculated measured mass. The difference (if any) would represent mass leached/dissolved from the CPOM.


Effect of pH on life? Use buffer or HCl? How about lactic acid?

That is a variable that you have the pleasure defining yourself. Just know that using a buffer will introduce other atoms that could affect the "living things". Conversely, if you don't use a buffer, it is likely that the pH of your "living things" will be easily altered by the metabolism of your living things (IMHO, this is worse).

I don't know the details of your project, but recommend:

-use a buffer like.. Tris, phosphate...
-use 10 mM Tris-Cl without any extra electrolyte (aside of the HCl or NaOH that you use to modulate the pH of your buffer to different pH's that you want to test)
-e.g. Tris-Cl pH 7, 8, 9.. or Phosphate pH 2,3,4,5,6,7,8,9..


Does ATP hydrolysis reaction have a high or low activation energy?

High and low are not very descriptive since they are relative. ATP hydrolysis may have a high activation energy compared to some reactions and low when compared to others.  The important point is that the activation energy is sufficiently high enough such that ATP is not rapidly hydrolysed under physiological conditions before it can do useful work. In other words ATP hydrolysis is kinetically unfavourable but thermodynamically favourable. The reaction rate is increased by enzymes (by lowering the activation energy), which couple ATP hydrolysis to other processes to do useful work.

Also, a note on reaction spontaneity: it has nothing to do with activation energy but rather depends on the change in free energy; ATP hydrolysis is spontaneous because it is exergonic.


I believe this is called Nephila pilipes.

You can refer to Wikipedia for more information


is there a limit to how much humans can taste?

Yes, there is a threshold of taste.
According to this article

The taste system encodes information about the quantity as well as the identity of stimuli. In general, the higher the stimulus concentration, the greater the perceived intensity of taste. Threshold concentrations for most ingested tastants are quite high, however. For example, the threshold concentration for citric acid is about 2 mM; for salt (NaCl), 10 mM; and for sucrose, 20 mM. Since the body requires substantial concentrations of salts and carbohydrates, taste cells may respond only to relatively high concentrations of these essential substances to promote an adequate intake. Clearly, it is advantageous for the taste system to detect potentially dangerous substances (e.g., bitter-tasting plant compounds) at much lower concentrations. Thus, the threshold concentration for quinine is 0.008 mM, and for strychnine 0.0001 mM. As in olfaction, gustatory sensitivity declines with age. Adults tend to add more salt and spices to food than children. The decreased sensitivity to salt can be problematic for older people with electrolyte and/or fluid balance problems.

Interestingly,

In fact, all of these tastes can be detected over the full surface the tongue. However, different regions of the tongue do have different thresholds. Because the tip of the tongue is most responsive to sweet-tasting compounds, and because these compounds produce pleasurable sensations, information from this region activates feeding behaviors such as mouth movements, salivary secretion, insulin release, and swallowing. In contrast, responses to bitter compounds are indeed greatest on the back of the tongue. Activation of this region by bitter-tasting substances elicits protrusion of the tongue and other protective reactions that prevent ingestion

And in most of the individuals, this threshold is same for both right and lefts parts of the tongue.
Reference
Now as stated by the first article, taste threshold depends on the age of the individual.
More interestingly, it also depends on the individual's state of mind, i.e. whether depressed or anxious.

Circumstances in which serotonin (5-HT) and noradrenaline (NA) are altered, such as in anxiety or depression, are associated with taste disturbances, indicating the importance of these transmitters in the determination of taste thresholds in health and disease.

Measurement of taste function in healthy humans before and after a 5-HT reuptake inhibitor, NA reuptake inhibitor, or placebo showed that enhancing 5-HT significantly reduced the sucrose taste threshold by 27% and the quinine taste threshold by 53%. In contrast, enhancing NA significantly reduced bitter taste threshold by 39% and sour threshold by 22%.
Reference

Hence threshold value varies from substance to substance as well as from individual to individual.
Here is a good article giving threshold values of different chemicals in various food items.
Hope all your questions are solved :)


Why Is The Toughness Of Skin Different On Different Parts Of The Body?

As dd3 said the density of mechanoreceptors dictates skin sensitivity to touch (also look at penfield map. It is a nice illustration of how different senses are mapped to the brain and to what extent each region is sensitive to stimulus). Skin thickness is also different in different regions. This article says that Dikkopf1 (a Wnt pathway antagonist) controls skin thickness.


If you are 30 degrees, and touch something that is 50 degrees, do you only feel 20?

Your sensation of heat is dependent on the change in temperature of your skin, which is roughly proportional to the difference in temperature between skin and material.

However, temperature difference is much less important than the transfer of heat between your skin and an object, which is heavily dependent on the type of material you are touching.

Why does a cold piece of steel feel so much colder than the surrounding air, despite them being in thermal equilibrium? The answer is that steel is a much better conductor of heat, and can therefore draw heat from your hand at a much faster rate than air, which is a poor conductor of heat.

A very interesting study by Lele, Weddell and Williams (1954) [1] demonstrates that the rise in skin temperature is proportional to the rate of heat transfer. The same paper suggests that the sensation of heat is roughly proportional to the rate of heat transfer.

Now for some physics.

Heat transfer along an object of length L and cross-sectional area A is given by:

Q = kAt$\Delta$T / L

where Q is the heat content, t is time, and k is the thermal conductivity.

As you can see, the transfer of heat is proportional to the difference in temperature between the two ends of the object. So a simple interpretation would suggest that your body senses the rate of heat transfer, which is directly proportional to the difference in temperature between your skin and the object you are touching.

However, this neglects the ability of your body to draw heat away from an area (via blood circulation, passive heat conduction etc). Given that your body maintains a core temperature of around 37 degrees Celsius, this complicates matters somewhat, and probably comes into play when you touch a hot/cold object for an extended period of time (e.g. your example of washing your hands to warm up).

So in summary, you are essentially correct, in that your body feels the difference in temperature between your skin and the surroundings, taking into account the thermal conductivity of the surroundings.

[1] Lele PP, Weddell G, Williams CM. The relationship between heat transfer, skin temperature and cutaneous sensibility. J Physiol. 1954;126: 206–234.


Where is DNA during the process of RNA extraction using Trisure?

Expectedly, they don’t really want to tell you what TRIsure is. What they do say is that DNA is found in the organic or interphase after extraction whereas RNA partitions to the aqueous phase. This is almost certainly some variant of acid phenol extraction. As confirmation, the MSDS lists phenol, ammonium thiocyanate, guanidinium thiocyanate, glycerol and citric acid as its components.


Like size and colour constancy, why does the brain not maintain focus constancy?

Interesting question. I concur with @Chris. Color constancy and size constancy are neural mechanisms and can therefore be imposed on visual input from the retina. In contrast, a blurry input cannot be neurally improved. As an analogy: Visual perceptions are processed and rendered by the brain and therefore represent "photoshopped" perceptions. In other words, perceptions are subjective representations manufactured by higher-level visual processing. However, focus is determined by optics. An out-of-focus picture, to push the analogy, cannot be fixed by fotoshop, nor the brain.


I think that "career in synthetic biology" and "involved in planning" both express very vague ideas. There are significant differences in what you will be able to do with a Bachelor's, Master's or PhD, depending on what exactly you end up doing.

I entered a PhD program in biology for no better reason than that I felt awed and fascinated with science and had done really well in science subjects as an undergrad. Grad school seemed like a natural extension of that effort.

In retrospect, my motivations for pursuing a PhD were horribly naïve and easily the greatest challenge that I faced as a grad student was that of defining why I was there and where I wanted to go with my degree. So, to address the issue of vagueness in your question, my first piece of advice is to have a firmer idea of what you want to do. Plans will change, but simply having a plan (a real plan) might provide an anchor when you need one.

As to what you can do with the various degrees, I can't precisely answer your question, the way you've phrased it, but I can give you a general idea.

A bachelor's degree in biology will not get you far in a lab setting. Among the lab techs I've worked with, even most of them have master's degrees. From what I've seen, this holds just as true for academia as for industry.

It's a little unclear what you mean by "planning", but most of the admin that I work with, who are involved in planning our various projects also hold advanced degrees, typically in science, business or public health. I see a strong representation among the management at my institution (Columbia University) of PhD scientists, who left the bench for something less life-consuming, while still wanting to have a hand in research. These people are frequently grants managers or program directors.

As I mentioned earlier, the lab techs around me generally hold master's degrees. When I was considering quitting my PhD program after the master's component, a friend in industry advised me against it, if I ever thought that I might seek work in industry. The picture that he painted was that in industry, a master's degree makes you overqualified for many of the tasks that you can expect to be hired for, but underqualified for significant future career advancement.

Obviously, you shouldn't feel limited to academic vs industrial research tracks. There are plenty of other options out there. Maybe look up people's blogs that involve synthetic biology or whatever other topics of interest you might have to get a wider view of what people who have expertise in the subject are doing.

Good luck!


Was Earth's atmosphere more buoyant in the prehistoric era then today?

While it seems difficult to me to imagine any mechanisms that would allow significant changes to the total amount of atmosphere (and therefore density) in geologically recent times (< 100M year), it's quite difficult to find direct evidence about it.

In 2012 Nature published a paper that calculated the air pressure (and therefore the air density) by noting the distribution of sizes of puddles formed by raindrops in 2.7 billion year old ash. The conclusion was that the air was no more than twice as great as it is today.  This amount would be quite a bit for flying creatures, but would be almost completely insignificant for  supporting the weight of large creatures.

As an example, a large elephant has a volume of slightly more than $10m^3$, and a mass of over $5000kg$.  The buoyancy of the air only takes off the equivalent of about $12kg$ of that mass.  Even an atmosphere 10 times the modern density would be little help in supporting its weight.


Can you "spam" bird sounds so that birds no longer interpret them right?

This is at least doing some confusion, probably also harm. A lot of wildlife conservationists warn about using smartphone apps which replay bird songs, as they are confusing the animals. An example is the Dorset Wildlifetrust.

This phenomenon has even be analyzed scientifically, and the results show that birds are irritated. Territorial birds seem to be affected more and it has been shown that, when a fake call was replayed to them, they sang more often and longer. In the first paper they speculate that this will drain too much energy and prevent the birds from doing other important things.

The second paper looks at zebra finches, which are not territorial. Here they find that birds pay less attention, the more often the song is replayed.
The articles:

Simulated Birdwatchers’ Playback Affects the Behavior of Two Tropical
Birds
Habituation in songbirds.


What really is color and how do we perceive it?

Despite its simplicity, this question demands a so complex answer that we can start by saying:

We still don't know.

Because you are talking about the colour as a sensation, as something that I feel and that I (literally) see. And here is the problem: as such, the "colour" is not a physical reality.

Some people may disagree here, but colour is not a physical property of any material. Light is a physical property. The wavelength, the energy, the frequency of light are all physical properties. Even the crazy quantum nature of the photon with its restless existence is a physical property. But not colour. Colours are creations of my mind, my nervous system, my idiosyncratic consciousness.

For instance, It's simply impossible to know if the red that I see in my mind is the same red that you see in your mind. The fact that we both call it "red" or the fact that we both agree that the colour of the blood is the same colour of the wine doesn't help at all: this is a problem of qualia:

http://plato.stanford.edu/entries/qualia/

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

And the same goes for all other conscious experiences derived from the exteroceptors, such as "taste" and "sound". What I feel is particular and nothing can guarantee that another person feels the same, even if the stimuli are the same and the nervous impulse to the CNS are the same.

To finish, I'd like to propose a thought experiment, for you to understand the subjective nature of the colour:

We tend to imagine that the world is the way we see it (as primates, we value the vision very much). But we have only 3 different cones, giving us roughly 1 million (100$^3$) different colours. Reptiles, as the birds, have 4 different cones, and some of those reptiles, as pigeons, have 5 different cones, giving them the ability to "see" 10 billion colours (100$^5$). This is hypothetical, of course, to really perceive all these colours the animal needs a huge brain cortex, but let's suppose that they see (perceive) all these 10 billion colours.

Now try to imagine these 10 billion colours, you, who are an organism that only perceives 1 million colours. It's impossible. And it's impossible for a talking pigeon to explain to you how he/she sees the world, how all these 10 billion colours are, the same way that it's impossible for you to explain to an animal with achromatic vision what is green, purple, orange, cyan, magenta etc...

This is what we call qualia.

But, as someone that loves cognitive ethology and science in general, I don't think that this is something beyond the realm of sciences, something impossible to know... this is a problem that can be scientifically addressed and, with the ingenuity of the neuroscientists and other biologists, we can someday understand the "redness" nature of the red we see.


Red flower with yellow star in center with fig-like leaves

They are common hollyhocks, they come in many colors. As a little kid from Chicago , I was impressed by flowers taller than me when visiting rural Wisconsin . Then the standard for hiding/decoration outhouses.


Why are chromatophore in phaeyophycae chloroplasts integrated within the endoplasmic reticulum?

Before explaining it, you need to know 2 things.

Fact 1:  a cell of an Eukaryotic organism; such as a higher-plant, an animal, or a fungus, is actually not a single cell, but mixture of cells from different distant taxa.

taxon-1. The main, host cell (probably came from an archaebacteria (archaea) ), whose 'own' genetic material is in its nucleus.

taxon-2. mitochondria (probably derived from an eubacteria (only 'bacteria' of modern use) allied to proteobacteria)
(found normally in all eukaryote, except a few )

taxon-3. Plastid (whose most-important form is chloroplast) (probably derived from an eubacteria, allied to cyanobacteria , i.e. blue green algae) (Found in higher plants, and so-called 'algae' ).

It is now very well-established that mitochondria and plastids are 'cell'-s, with their own genetic machinery (including DNA, whose sequence match not-with host-nucleus, but match to bacteria!! However, some of DNA was probably got mixed with host-DNA, via DNA-transfer). They are partially autonomous because they can synthesize some proteins (metabolic-machines) from their own genes. And such an organelle can arise from pre-existing such-organelle, and can-Not appear de-novo from host cell.

Plausibly, many-many-million-years ago,  the precursor of eukaryote , certain organism allied to archaebacteria, 'ate' (phagocyzed) these eubacteria , and instead digesting them, they involved in a mutually beneficial symbiosis. Gradually they get converted into some 'organelles' through millions of years.

This concept is known as 'Endosymbiotic theory of origin of eukaryotes' .

 Image from Gerald Karp.

(Initially it was unknown,and it was thought that chloroplast and mitochondria evolved by gradual complication of the main cell.  when Harry Margulis gave this as hypothesis, it was rejected because it was unbelievable. Later-on it was established as true)

However, this-type of endosymbiosis is also called 'Primary endosymbiosis', where a purely-single cell engulf another purely-single cell.

Fact 2: The group 'algae', named in a very early-stage of science, was a horribly 'hotchpotch' group (extremely polyphyletic or artificial). This group is a set of organisms which can perform oxygenic photosynthesis. But some of them are similar to plants (green algae), some are highly similar to some protozoan ('primitive animals'), for say, some euglenoid and dinoflagellate algae. There are lots of such close-related protozoans that can't photosynthesize and don't contain any chloroplast. Whereas, Blue-green algae (cyanophytes) (with a highly similar photosynthetic mechanism), is a bacteria.

It was an enigma for the scientists. How  a few members from separate groups can contain plastid? Could they separately evolved the same structure? Is it possible to coincide so-much convergent evolution? or if the common-ancestor of all of them, contained the plastid, then why that structure disappeared in so-many members?

This enigma was quite drastically cleared up after discovery of this past endosymbiotic mechanism.

It was then found-out that, the finest classification (excluding the chloroplast), which was showing the different groups under algae are highly unrelated; is true. Actually members from far-distant taxonomic groups, 'ate' some unrelated photosynthetic primary-endosymbiotic associations, and formed another association. Thus they all got the very-similar photosynthetic apparatus; though the hosts were unrelated. This was something very new-to science.

these 'another-association's, i.e symbiosis between impure cells, is known as secondary endosymbiosis.

It is assumed that, the trace of these secondary endosymbioses; left some remains as the plastid-coves' structure.

Here is a classification of algae, taken from Robert Edward Lee, Phycology, 4th edition, in a simplified diagram. 4 basic types of photosynthetic structure is found in algae, according-which the classification has been done.

 .classification of algae, by Lee.
(Representation concept courtesy- a note shared to  me by a college- friend several-years ago).

Now, How these structures exactly developed?

Each cell contains so-many membranes, that , practically we have poor way to determine from which-of the membrane of which symbiont; certain ultimate membrane came. There are controversies. Such as according to Lee (already mentioned book) and diagram used by Hans Walter Heldt, Plant biochemistry, (3rd edition, Academic press- Elsevier), the outer membrane of chloroplast came from the cell-membrane of host-cell (phagocytic vesicle's boundary). like
 (redrawn from Heldt)

Whereas some other source tells that, the outer cover of chloroplast came from "outer membrane" of cyanobacteria , (Since it is  a gram-negative eubacteria, so carries 2 membrane). (Wikipedia tells "The two innermost lipid-bilayer membranes that surround all chloroplasts correspond to the outer and inner membranes of the ancestral cyanobacterium's gram negative cell wall, and not the phagosomal membrane from the host, which was probably lost." https://en.wikipedia.org/w/index.php?title=Chloroplast&oldid=737014760#Primary_endosymbiosis).

However in my answer I've followed Lee (4th edn).

Answer:

step 1 : Origin of chloroplast, the primary endosymbiosis.

 Diagram from Lee.

(already discussed).

This step's product found in group 2 algae. (Glaucophyta, Rhodophyta, Chlorophyta) Higher-plants probably evolved from Chlorophyta (green algae) and they also contains this-sort of chloroplast.

Step 2:

Probable sequence of evolutionary events that led to a chloroplast being surrounded by a single membrane of chloroplast endoplasmic reticulum. Initially an isolated chloroplast was taken up by a phagocytotic protozoan into a food
vesicle, with the food vesicle membrane eventually evolving into the single membrane of chloroplast endoplasmic reticulum surrounding the chloroplast.
Diagram from Lee.

Products of this step found in Group-3 algae.

Step 3. Another event of secondary endosymbiosis.

The sequence of events that led to the evolution of algae with two membranes of   chloroplast endoplasmic reticulum.

Products of this-step found in group-4.

Diagram from Lee.

by the way, all these steps are assumptions by scientists.

There is another concept called tertiary endosymbiosis. When in certain step of  secondary endosymbiosis, a chloroplast (from certain-one cell out of 2) lost, it is called tertiary endosymbiosis.

  Reference:

  Phycology/ Robert Edward Lee/ 4th edition/ Cambridge University Press.
  Plant Biochemistry/ 3rd Edition, English translation/ Hans Walter Heldt/ Academic Press - Elsevier.
  Cell and molecular biology - concepts and experiments / 6 th Edition / Gerald Karp / Wiley.


The total numbers of mutations on different branches of gene tree are independent or not?

Here is a simple answer to my question. The reason two numbers of total mutations accumulated in two divergent branches are not independent of each other is because they experience the same amount of coalescent time.

While the stationary Poisson mutation processes are independent from each other as long as they happen in different branches of a genealogy, they are likely to produce a similar number of mutations if two such processes happen together for a same amount of time. Thus, the non-zero part of the covariance between $k_{BC}$ and $k_{BD}$ is not from mutation processes themselves, but from the shared coalescent time $T$.


According to the Israeli Scorpions Field Guide, deathstalkers can have also pale metasomal segment V, so a black one isn't a sure identification sign although it is very common among deathstalkers. The characteristic of the Israeli deathstalker are 5 ridges along its back. The species of deathstalker in the Negev (and Israel) is Leiurus hebraeus.


How to prove that pork meat has parasites

Short answer
T. solium infection can be identified in pork meat by visual inspection.

Background
The stage of the life cycle of the tape worm T. solium in pigs is characterized by cysticerci, which is the larval stage consisting of a protoscolex (head) of the tapeworm. Humans are the definitive host, which means they are the species in which the parasite completes its life cycle, reaches adulthood and is able to produce eggs.

The larvae are observable in pork meat, and cysticercosis is generally identified during slaughter when cysts can be seen in muscle or organs (Fig. 1).

Fig. 1. T. solium cysticerci. (A): as seen in infected pork. (B): excised into a Petri dish. The white dot in each cyst corresponds to the scolex. Source: Garcia et al. (2011)

It is not until these cysticerci are ingested by humans that the tape worm starts to develop fully into a meters-long tape worm, as it enters the next and final stage of its life cycle (Fig. 2).

Fig. 2. Taenia life cycle. Source: CDC

Hence, leaving the meat in the fridge will not induce growth, as a human is needed to induce outgrowth of the protoscolex into the mature tape worm.

Reference
Garcia et al., Lancet (2011): 362 (9383): 547–56


How many times is a single strand of mRNA translated into a protein?

I'm answering my own question for the benefit of anyone else who might be wondering about this. (Please note that I'm just a programmer, not a biologist, but thanks to David's comment, I was able to come to what I think are some correct conclusions.)
A single mRNA strand can be translated more than once, even more than once at the same time. The polysome that David references is a group of two or more ribosomes all attached to the same mRNA strand, all working on translating it simultaneously.
I believe that it may be possible for a single mRNA strand to be translated hundreds or even thousands of times. My reasoning for this is that a virus injects one copy of its RNA into a cell, and from this one copy, new viruses are replicated until the cell bursts. This "burst size" varies by host cell and virus, but it can range from hundreds to tens of thousands or more. While there are still a lot of things I don't understand about the specific steps the RNA goes through (are there intermediary copies made from which multiple mRNA strands are produced?, etc.), it still seems to suggest that a single strand of mRNA can be translated a lot.


Why is the quality range of fastq format so broad?

Initially, there were several quality encodings that used to follow different ranges of ASCII characters to denote the quality of read. The range that you mention is a union of all those encoding formats. Nowadays, the most common encoding is Phred+33 (used by Illumina, Sanger, Ion Torrent and other popular sequencers) which uses these characters:

!"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHI

Character I denotes a phred score of 40. Aligners, when they read fasta files, by default assign a score of 40 (I) to all positions. This might be one why reason you are seeing a lot of I.

Anyways, if your fastq follows the phred+33 format then 40 (I) is a pretty good score which denotes a good quality read. Or you could be aligning fasta files. It would be a bad score if your encoding is phred+64 which I guess, is not the case.

ADDITION

The file that you linked is a fastq file. This sequencing experiment has been done on 454 GS FLX Titanium machine. 454 machines use a different way of calculating quality scores compared to the traditional basecalling phred scores. From the manual:

  6.6 Phred-equivalent Base Quality Scores

  Quality scores for individual called bases are determined by a method developed in
  collaboration with the Broad Institute (Genome Research,18(5): 763-70,
  2008), whereby the methodology described by Ewing and Green (Genome
  Research, 8: 186-194, 1998) for the creation of quality scores as part
  of the Phred basecalling algorithm is applied to generating quality
  scores for 454 Sequencing reads. The quality scores computed for each
  called base are written to the CWF and SFF files (and optionally to a file paralleling the basecall FASTA file). Briefly, the method
  compares the properties of each base’s flowgram signals against
  properties that have been found to correlate with accurate and/or
  error-prone signal information, using training sets of read data. A
  multivariate analysis of those properties determines the sets of
  property values that best describe “bins” of basecalls, then assigns
  the training set accuracy rates of the basecalls in each bin as a
  quality score using the following scale:

  $$Q = -10\ \text{log}_{10}(\text{error rate})$$

Usually, you'll have two files for 454 experiments — one that holds the sequence and the other that holds the quality at each position. These files can be combined to generate a fastq. This file is encoded in the phred+33 (also called Sanger/Illumina 1.9) format which I mentioned above. Phred+33, I guess, is also the standard encoding format adopted by NCBI/ENA/DDBJ and all new sequencing runs are encoded in this format. If you do not know the encoding you can run fastqc on your fastq file and it reports the type of encoding.

In your case, I would denote a score of 40 (ASCII value - 33) which means an error rate of 10-4 i.e. the read is of good quality.

The below graph is obtained by a fastqc run on your file. The bars denote quality statistics at each position. Note that the mean quality drops towards the end of the read.

A fasta file does not indicate quality but when you map them to your target, the aligner (I know of Bowtie based ones) assigns a default score of 40 at each position, during the alignment (and in the output).


How fast do stomata respond to environmental changes?

Stomatal speed varies depending on a lot of factors, especially anatomy even within species, but especially between species.

  Evidence from several studies has also suggested that smaller stomata respond faster than larger stomata

The paper I just cited from (first link below) includes is a long review of the what is currently known and also original research into the process. It includes a really detailed, lengthy chapter on the stomatal speed, but which is mostly lacking in easily citable numbers except for closing times:

  Stomatal aperture responds more slowly, typically with half-times of 10 to 20 min, reaching a new stable, (near) closed state after 45 to 60 min

A few more clear numbers come from the second paper I link to below, however this is in response to changes in light, not humidity.

It includes a table (table 1) on mean stomatal closing and opening time delays in four plant groups and plants adapted to two climate conditions. In most groups, closing happens slower, taking about 50 percent longer, with mean times varying between 6 and 18 minutes. Opening is faster in every group but one and takes between 4 and 30 minutes. In plants adapted to dry climate conditions stomata respond faster.

Sources:

Stomatal Size, Speed, and Responsiveness Impact on Photosynthesis and Water Use Efficiency

Effects of stomatal delays on the economics of leaf gas exchange under intermittent light regimes


Is there is difference between "homozygosity" and "homozygosis"?

Homozygosis and homozygosity are NOT synonymous. The two terms refer to the same concept though.

Homozygote

An indivdidual or a cell is said to be homozygote for a particular gene (or any DNA sequence) when identical alleles of the gene are present on both homologous chromosomes. (Wikipedia > Zygosity).

Homozygosis

Homozygosis is the state of being homozygote (Wright 1933) for a particular gene (or any DNA sequence). According to freedictionary.com, homozygosis may also refer to the process of formation of a homozygote. I have never encountered this sense in the literature though. As you found out by yourself, Homozygosis is a term that is rarely used in the literature (in comparison to homozygote and homozygosity)

Expected Homozygosity

Expected Homozygosity is the probability of two randomly sampled alleles (in a population and at a given locus) to be identical by descent.

Expected homozygosity and Expected heterozygosity

As shown in Nei 1973, the mathematical expression of expected homozygosity $Ho$ is

$$Ho = \sum_{a=1}^{n} x_a^2$$

where $n$ is the number of alleles and $x_a$ is the frequency of the allele $a$.

It is more common to use the concept of expected heterozygosity $He$ (a.k.a. gene diversity) rather than the one of expected homozygosity $Ho$. By definition, $He=1-Ho$, that is

$$He =1- \sum_{a=1}^{n} x_a^2$$

In the special case of a bi-allelic locus, and replacing the two allele frequencies $x=1$ and $x=2$ by $p$ and $q=1-p$, the above formulations becomes

$$Ho = p^2 + q^2$$
$$He = 1 - (p^2 + q^2) = 2pq$$

Hardy-Weinberg equilibrium

Under the Hardy-Weinberg assumptions, the observed frequency of heterozygote (a.k.a. observed heterozygosity) is equal to the expected heterozygosity and observed frequency of homozygotes (a.k.a. observed homozygosity) is equal to the expected homozygosity.


How is the rate of gluconeogenesis controlled in the cell?

In mammals gluconeogenesis occurs primarily in the liver (together with the kidney to a much smaller extent). When the blood glucose concentration falls, it is the role of the liver to generate glucose for other tissues that are dependent upon it.

Hormones play a key role in this. If one considers the decrease in blood glucose concentration during starvation, this is signalled by a decrease in the concentration of insulin and an increases in the concentration of glucagon. These have differentials effect on the uptake of glucose by different tissues, depending on whether they have receptors for the hormones and the consequences within the tissues, and mass action effects of metabolites will certainly influence whether glycolysis or gluconeogenesis occurs in liver.

However, you are correct in your concern that there must be a way to prevent the futile cycling of intermediates through the different reactions of the three steps that differ between glycolysis and gluconeogenesis. The short answer to how this is accomplished is that the concentrations of various metabolic intermediates change during starvation/feeding, and that these intermediates are allosteric regulators of the reactions, switching one off and the other on. This is described in the section on Regulation of Gluconeogenesis, in Berg et al. (available on-line), from which I reproduce the  diagram below (Fig. 16.30).

Although this diagram illustrates the principle, a few words of caution about the detail are in order. First, the edition of the book this comes from is 15 years old. Second, it is not clear that all the regulatory molecules are effective in liver — some of the work may relate to bacteria. Third, much of the evidence is from studies with purified enzymes. Although it can be shown that an enzyme can be regulated by a particular effector in these conditions, it is different matter to establish that this occurs in a particular physiological condition. Thus, you will need to consult more recent and specialized sources if you are interested in particular details.


What is a good miniprep protocol for the class room?

The protocol I used in my genetics lab course was alkaline lysis followed by ethanol precipitation similar to this one.  Nothing terribly toxic or requiring a fume hood (at least at the small volumes used).

The more practical, reliable method is to use a miniprep kit (usually spin columns) from one of several suppliers (Qiagen, Promega, Bio-Rad, etc.) which are fairly affordable at $1-2 per prep.


Enzyme with long tube leading to active site?

First of all, as you mentioned, there are a lot of membrane / transport proteins with very nice, well defined tunnels. But you're looking for a soluble / cytosolic enzyme.

Some oxygen-dependent enzymes have quite long tunnels that oxygen is using. For example this one: http://www.jbc.org/content/283/36/24738.short or this one: http://europepmc.org/articles/PMC2698890

Then there are some enzyme with just deep active sites, I think the p450 BM3 is quite known for that, but any enzyme with a reasonable specificity (and especially those that have very reactive cofactors) will have a "tunnel".

You can also find long "tunnels" in enzymes that accept long substrates. I like this example of squalene synthase: http://science.sciencemag.org/content/277/5333/1811.full. The substrate first has to go deep into the enzyme to find the proton it needs to start a quite interesting reaction.

If you want to find new tunnels in your enzyme there are also tools available, such as CAVER: http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1002708 If you look at the papers citing this tool you might also find some cavities.


How might one determine if bacteria are nitrogen fixing or not?

Never mind found the answer myself you can use the acetylene reduction assay.


This actually looks like a Gaudy Sphinx caterpillar (Eumorpha labruscae). It only mimics the appearance of a snake!

You can find more information about this species here.

Range: Argentina north through Central America, Mexico, and the West Indies to Florida, Mississippi, South Texas, and Arizona. Strays to Missouri, southern Michigan, Pennsylvania, Maine, and southern Saskatchewan.

You can find more pictures here or videos here and here. Also the below gif (see whole video here) demonstrates the ability of this caterpillar to vibrate its tail end to -- as far as I can tell -- imitate a snake's rattle:

Below is a picture of an adult moth from UC Berkeley:


With reference to your gel photo, the genomic DNA (in the three Pyura sample lanes) does not look badly degraded.  If the size marker is 1 Kb ladder, then the majority of the DNA is of high molecular size. During extraction it is common for high molecular weight DNA to become "sheared" to some degree (mechanically broken into smaller fragments). This can appear as the faint downward smear. The lanes may be somewhat over loaded as well. You can try to use more gentle extraction technique and see if it helps to your satisfaction. Any of those you mention will work.

Badly degraded genomic DNA would appear as a more intense "smear" near the lower portion of the 1 Kb size standard.


What is the magnification necessary to see pond life

2019-05-01 Edited: Updated dead links

From the comment section:

I would go with a cheap one with a magnification of ~40X. According to this source, 10-20X is already sufficient to see large protozoans and algae in a pond. Here some suggestions on what you could look at.


Why would yeast grow but not produce alcohol?

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.


There is a large population of birds that look like crows or ravens,
  yet fatter. They seem to be quite social and move around in large
  groups.

First of all, this seems like a crow. Crows are very social birds, they live in flocks or murder.

  Theory: It may be a Mating Ritual?

No! The have a very spectacular mating ritual!.

  Theory: It's Making a nest

Obviously No! Crows nests are always way hidden at 18-60 feet above ground(mostly) in the tree trunk.

My Theory

Crows are very curious birds. What you saw, might be a new play the young crows found. It's common that crows will do unusual thing when spectated by the elders and siblings.


Ways to monitor enzyme kinetics with very fast time resolution?

Some ATPases can work with MANT-ATP or similar fluorescent ATP analogs that change their fluorescence properties upon protein binding as well as hydrolysis of their phosphate group. This has been used frequently (see here or here) to study enzyme kinetics on fast timescales.


What does it mean to "cure" microscope slides?

In this context, "cure" is a chemical term. Definition from Wikipedia :

Curing is a chemical process employed in polymer chemistry and process engineering that produces the toughening or hardening of a polymer material by cross-linking of polymer chains. Even if it is strongly associated with the production of thermosetting polymers, the term curing can be used for all the processes where starting from a liquid solution, a solid product is obtained.

So here it means that the slides were incubated at room temperature for 24 hours to let the mounting media harden. Of note, not all mounting media harden, some may require specific conditions to cure like UV light (example), and the curing step changes the properties of the mounting media like the refraction index. From the ThermoFisher website :

Formulations of mounting media that can add favorable properties such as optimizing the refractive index to match that of glass, preventing photobleaching, or preserving samples for long-term storage are widely available. Keep in mind that some require time to “cure” or harden. For mounting media that need time to cure, it’s important to let the sample fully harden before imaging so that you don’t inadvertently damage or destroy your sample by moving it around on the slide or cause photobleaching of your stained cells. Typically, the refractive index of the mounting medium will not reach its specified value until after it has fully cured, and its photoprotective properties will increase during the curing process. The degree of hardness after the mounting medium has fully cured will also vary; some will set like jelly while others will set like hard plastic


Is there a metabolic pathway that generates methanol?

This is an old question by now, but I found it interesting, so here's my two cents :)

Methanol has long been known to normally occur in humans; one study from 1963 demonstrates its presence in breath.

One major source for methanol in humans is breakdown of pectin by bacteria in the gut. Pectin is a complex carbohydrate found in many fruits and other non-woody parts of plants. Pectin is not well metabolized by humans, and so has low nutritional value and counts as dietary fiber. Still, some species of bacteria in the gut are able to degrade pectin, and this process produces methanol.

This article reports measurements of methanol levels in the breath of subjects consuming pectin. Here, 10--15 grams of pectin (equivalent to ~1 kg of apples) was estimate to yield about 0.4--1.4 grams of methanol. The authors also state that there is a basal production of methanol in humans as well, of about 0.3 grams per day; the origin of this methanol seems unclear.

There are also pathways in human cells capable of forming methanol. This study demonstrates this fact by showing that infusion of ethanol (bypassing the gut) leads to a rise in methanol levels.

A recent review of metanol metabolism in humans can be found here.


This is a leaf vegetable called Cichorium, Endive in English. There are several closely related species, Cichorium endivia (also called endive), Cichorium pumilum (also called wild endive), and Cichorium intybus (also called common chicory). I think it looks most like common chicory, but if it comes from your seeds, Cichorium endivia is more likely.

Flower from Cichorium intybus

Flower and leaves of Ch. pumilium

https://en.m.wikipedia.org/wiki/File:Cichorium_pumilum.jpg
(source pictures:wikipedia)


Does the DNA of a tadpole change after it becomes a frog?

Your germline DNA remains the same no matter what you do in the growth process (The DNA of a child is the same as the DNA of the adult). What does change is the expression of the DNA (transcriptomic profile), other regulatory factors (Epigenetic modifications), alternative forms of the same DNA expressed differently (splice site variations and alternative promoters) things like that.

Your somatic DNA does undergo small changes, caused by (retro) transposons, and in a few cells, like the mature B and T cells, they contain only a small subset of a few essential genes (that give them their specificity to an antigen), and other small changes like that (credit: mdperry, see comments).


Can specific B-cells be created in a lab?

We aren't there yet.

There is a complex interplay between antigen recognition, presentation, and activation that would have to be worked out. You would also need to engineer the corresponding T-Cell which could recognize the antigen, become activated, which means you also need to develop a dendritic cell that can present to the T-cells, so that they could then go on to activate the B-Cells. Doing this in vitro would be a challenge.

You are actually asking to design highly specific receptors, and protein engineering then sequencing back to a genome would be difficult to do.

If you tried taking a known antibody, you would need to track down the actual B-Cell that produces it, due to somatic hypermutation creating a unique DNA sequence, which leads to the specificity that increases the affinity of antibodies for their ligands. I guess if you did it with germ free mice, you might have a shot at isolating their B-Cells and then finding out the gene sequence. Not impossible, in my opinion, but very difficult at this point.

The closest thing I have heard of so far is the work that is being done in Dr. Carl June's lab. They are working on taking cytotoxic T-Cells, and recombining their receptor DNA so that they can then recognize a patient's tumor and kill the cancer cells, but that is a bit different than what you are asking.


Is it possible to elicit transient gene silencing by using virus induced gene silencing (VIGS) in plants?

Virus induced gene silencing (VIGS) is definitely an option.

The ease of using VIGS depends on a lot of factors. Current VIGS vectors have limited host ranges. Depending on the species of plant that you are working with, there may or may not be suitable, pre-made VIGS vectors available and published techniques for using them. Many of the VIGS vectors that are available may be limited in terms of which tissues they can infect. Working with the vectors themselves requires that you have some way to propagate them and some way of getting them into your target plants (for example Biolistics, Agrobacterium or direct application of infectious virus).

There have been a number of VIGS vectors developed over the years, capable of infecting a diversity of plant species. Modified Tobacco mosaic virus (TMV) and Tobacco rattle virus (TRV) are two common VIGS vectors used for silencing in a variety of plants. TRV in particular is known to have a very wide host range. If your species doesn't fall within or even near the documented host range of available vectors it may be worth just trying a few different ones. Or, you could always isolate a virus specific to your target plant and build you're own. What fun!

The length of time that silencing will last is difficult to predict. In my experience, it will typically last a few weeks. But this may vary depending on a number of host factors and the VIGS vector used.

One potential alternative would be to just use Agrobacterium. It could be combined with a recombinase system to satisfy your condition of transience. To build such a system you could insert you're silencing construct into a binary vector. By including an inducible recombinase sequence adjacent to your silencing construct sequence and by flanking both of these with the recombinases recognition sequences, you would be able to remove inserted DNA at some point down the road after transforming the plant.

Again, depending on which species and variety of plant you're working on, this could require some trial and error as there may not be published techniques for Agro mediated transformation of you're target plant.

While Agro mediated transformation may not quite be what you're looking for in terms of transient silencing, it may be sufficient for a proof of concept.


Aquatic animals brethe the water around them and this equalizes their body pressure with that of the surrounding environment.

This is how you can still find say a piece of pottery or a watch from a shipwreck... They are filled with water and don't experience the pressure.

Such pressures do affect humans because we breathe air and so we can't adapt to pressures underwater and we need a shell that allows the ship environment to be tolerable for humans beyond a couple of hundred feet or so.

I think the change of pressure would also affect fish or other animals If they dropped in depth too quickly.


For humans, why is red the color of distinction rather than green?

The reason is more historical than biological.

Our own eyes are more sensitive to green light, and ambient light is mostly green (we are a diurnal being). If you start doing real botany, you will notice that you can distinguish a lot of species just from the shade of green (and for trees, this also from far away).

Red is a difficult colour to produce, and often not very stable over time, and in nature is not so frequent. But it was used because it was also not very common in constructed environments. For example, for the Romans it was a symbol of power (and richness) because it was very expensive to produce red dyes. So red is visible because of the contrast with other colours.

The most visible colour is yellow: the "red" cones are really centred on yellow, and the "green" cones are still very sensitive to yellow. A good yellow appears brighter than any other colours because it stimulates both  the medium-wavelength cones and the long-wavelength cones in the human eye. Now emergency services tend to use yellow.

Note: red is not so special (but having a third type of eye cone is very special). Blood is red, but one rarely sees it as red: it quickly turns dark. Fruit? I think blue, green, yellow, orangeish, and dark brown were more common than red (and I recognize a tree by its leaves, from far away, so I'll know what fruit there are).

Traffic light: lights were already very yellowish, and blue, purple, and violets are not that visible, so green, orange, yellow, red, and also white are the most logical colours. I think yellow and white were too similar (especially in cities), because they were the colour of illumination and headlights. Note: in maritime traffic, red, green, yellow, and white are used (not orange).


Yes; the first division starts at around 45min post fertilization in zebrafish. This picture is stuck in every zebrafish lab.


How can sodium and potassium from burned organic matter (ashes) reenter the ecosystem?

Wood ash is commonly used as a fertilizer. It acts this way in natural burning ecosystems also, where the ash from burned plants fertilizes the growth of new plants and those that survive the wildfires.

The primary constituents of wood ash are calcium and potassium salts. Lye is extracted from these salts by extracting them in water; the hydroxide salts are more soluble so the other salts are left in lower concentration than the original ash.

However, when in solution, KOH isn't really a thing anymore: you just have potassium and hydroxide ions floating around separately. Nothing special needs to be done to separate the potassium from the hydroxide ion except dissolving in water. Neutralizing the solution is then just a matter of adding an acid. There are plenty of sources of acid in soil, and rain itself tends to bring acidity. One of the sources of acidity in rain is, in fact, from fires. It is not as strong as the 'acid rain' caused by industrial sources, but there is no magic in fire that causes basic chemicals to be left behind without producing acid ones elsewhere.

The main damaging effects of wood ash are if it is applied in high concentrations where it can directly enter water sources (see for example UGA extension). In this case, it can raise pH enough to be damaging to life. Large quantities from large fires can also raise pH substantially in streams and such (see for example Burton, C. A., Hoefen, T. M., Plumlee, G. S., Baumberger, K. L., Backlin, A. R., Gallegos, E., & Fisher, R. N. (2016). Trace elements in stormflow, ash, and burned soil following the 2009 Station Fire in Southern California. PloS one, 11(5), e0153372.).

Eventually, however, there are enough sources of acid in the environment that there is no way the salts are permanently alkaline from the perspective of the whole environment.


Why not produce protein based on condensation reaction?

It is important to first remember that to do anything useful, the sequence of the amino acids in the protein must be exact. For example, sickle-cell anaemia is caused because one amino acid in a haemoglobin protein is incorrect. Because of this, peptide synthesis involves rather complex chemistry in order to ensure that amino acids are added in the correct order and number, and is only effect up to a chain of a few dozen amino acids.

Now it is possible to produce peptides of various lengths in a cell-free extract, which basically involves taking the cytosol out of cells (with all the ribosomes, tRNA's, and other factors therein) and adding the mRNA template to be translated and an ATP source. This way, a peptide can be prepared by using the cell's own machinery for protein synthesis without actually needing a viable cell.

Remember also that even if it were possible to chemically synthesize a correct peptide sequence, the protein would still need to fold into a correct 3-dimensional structure to work properly, which in some cases is impossible for any artificial method currently available.


Why do these earthworms stay between the road lines?

The first question: what the worms do on the ground during the flood? One of the answers to this question is -

"It gives them an opportunity to move greater distances across the soil surface than they could do through soil," said Dr. Lowe. "They cannot do this when it is dry because of their moisture requirements."

The second question: why they form ball after moving to the ground. There are two answers to this question:

First, as a part of surviving mechanism to prevent drying. As you can see, they cannot come back to the soil across the asphalt, thus they form balls and wait the weather to improve.

Second reason to form the balls - communication:

"The earthworms use touch to communicate and influence each other's behaviour, according to research published in the journal Ethology.
By doing so the worms collectively decide to travel in the same direction as part of a single herd."


Can difference in the expression potential of alleles lead to dominance?

Dominance is not commonly known to occur because of higher expression level, per se of one of the alleles. It can certainly be a factor but usually dominance is mostly known to arise because of a slight difference in function (or in other words activity) of the gene product (which may be a protein or an RNA).

Note that a change of function doesn't mean the alleles would have a totally different function. It just means that the alleles can be different in the way they function. For example two variants of an enzyme may have slightly different kinetic properties (such as Vmax Km and kcat). While change of activity may generally refer to Vmax (maximum enzyme activity), mutations can also change the other constants. Some mutations can make the enzyme sensitive to temperature by affecting the stability of the overall structure. The extreme would be a functional allele and a non-functional allele.

While concentration of the product does affect its activity, it does not change its specific activity, which may change in the presence of a mutation.

Moreover, even if one allele is actually has a higher expression than the other, the resultant trait can be differentiated from that of the aa homozygote only if the two alleles have slightly different functions or if the difference in expression level between of the gene product in Aa and aa is great enough to elicit different biological effects. In the second case there would be no change in the gene function and the effect of dominance is purely based on gene dosage. This review by Veitia and Birchler (2010) explores the possibility of stoichiometric alterations of macromolecular complexes or cellular networks being responsible for dominant phenotypes*.

Now, how can a mutation lead to a difference in expression level without changing the activity of the product?

There are three cases here:

The mutation is in the expressed region (exonic) but doesn't lead to change in activity (for e.g. synonymous mutations)
The mutation is in the transcribed region but in the intron.
The mutation is in the non-transcribed DNA regions such as promoter/enhancer etc. Exceptions: certain downstream promoter elements are actually transcribed.

Only mutations in the promoters/enhancers can affect transcription by affecting the recruitment of RNA-polymerase. However, you should note that mutations in the non-transcribed regions, especially in the distal regulatory elements are not considered a part of the gene in consideration. Since, such complex modes of regulation were unknown during the time of Mendel, the classical genetics does not explain these effects. Hence, these mutants would not be called alleles of the considered gene.

Mutations in the transcribed regions may affect the elongation rate of polymerase (especially if it leads to formation of stable DNA secondary structures). This is just a theoretical possibility and I have not come across any study that has reported something like this.

However, mutations in the untranslated regions of the mRNA can change the expression of the protein. These mutations may affect post-transcriptional regulation of the protein expression or even the RNA localization.

Synonymous mutations in the coding region can affect the rate of translation and hence the protein concentration.

*(quoted verbatim)


Enzyme inhibitor leads to higher turnover rate?

While it's difficult to know just what is going wrong in somebody else's laboratory, apparently paradoxical effects like these are unfortunately common in laboratory work.  Assuming that these are indeed well-established inhibitors that really should be working, let's consider why they might not be in your hands.
The mechanisms of molecular interaction are complex enough that there are many cases where a substance that acts as an activator in one condition can act as an inhibitor in another condition. Another way that you could see such an effect is if your purified system is not actually as good as you think and the problem is being partially relieved by one of the inhibitors, e.g., imperfectly purified and addition of the inhibitor neutralizes some of the imperfections.
Not knowing the details of the compounds you are working with, it is not possible to guess which of the possibilities might be at work. I would suggest, however, that you begin by:

Comparing your quantitative turnover rate with the purified enzyme to the predicted rate from the literature to see if your baseline system is actually working correctly.
Make sure your system is also (not) processing substrate at the appropriate low rate when the enzyme is absent.
Checking for potential differences between your method and the method that you are trying to adapt from the literature, which might give clues to the condition differences that may be impacting your results.


Can iGEM distribution parts be directly PCR'd?

You probably could do PCR on that amount of DNA, but if you screw something up you don't get a second chance. Transforming bacteria and doing a miniprep turns your 3ng into a few micrograms, which is enough to tolerate a few mistakes.


What determines the spiral direction of plants?

First of all, you assumption seems to be incorrect. Plants in same part of the world can twine in opposite directions.

Little seems to be known exactly. Gravity has nothing to do with plant's chirality (or "handedness") or spiraling:

  How plants do this is still unknown. Darwin proposed that it was "autonomously induced." This came to be known as the internal oscillator theory. In the 1960's the gravitropic overshoot theory explained mathematically how circumnutation could spontaneously occur as a result of forces related to gravity and growth. Recent experiments on the Space Shuttle have demonstrated that gravity is not necessary for circumnutation.

Here is another link to a blog, but it does contain reference to original paper on observation of chirality. Main conclusion, taken from the abstract, is:

  The predominance of right-handed helical growth in climbing plants cannot be explained by hypotheses attempting to link plant growth behaviour and global location. One alternative hypothesis for our findings is that the widespread phenomenon of anticlockwise twining arises as a function of microtubule orientation operating at a subcellular level.

To elaborate a little on that, remember that actin filaments as well as microtubules are all chiral polymers. That is, they form spiral structures with defined orientation. Even more, microtubules all start roughly from the nucleus away to membrane, so this might suggest cellular mechanism for preference toward twining chirality. However, this does not address your observation that given plant changes direction of growth twice.


Do invasive species survive in the long run?

This potentially depends on what species you are referring to.

In the case of plants, photosynthesis is used to as their source of energy, so will never run out of food as such. Assuming the conditions are favourable in terms of water and temperature (likely, otherwise the species wouldn't have flourished in the first place) and they stay that way, the only limiting factor is going to be nutrients in the soil. These are returned to the soil when the plant dies, so this is fairly self-limiting, when there's not enough then plants will die and the nutrients will return to the soil.

Animals face a slightly different situation, in that they need to eat to survive. As such, if the population that was introduced was large enough to eat all the prey (whether plants or other animals) in the area and carnivorous animals didn't partake in cannibalism even when times were tough, then the animal may die out.

In general however, predator and prey regulate fairly effectively, a decrease in prey causes a decrease in food availability which leads to a decline in predators. This allows an increase in prey, which gives a higher availability of food to predators so their numbers increase. This causes a decrease in prey numbers and so on. In general once an invasive species has been established, it will require intervention for it to be removed and it will not die out naturally.


How to measure the total number of cells in an average human body?

This is a classic Fermi estimation problem. The usual approach is to estimate the volume of a body, estimate the volume of a cell, and divide one by the other, remembering of course to have both volumes in the same units.

My quick attempt gave 1013 to the nearest order of magnitude.


What is the lifecycle of hanging woody vines?

There are no epiphytic vines in the US. Most likely, if it's sturdy  enough that you can swing from it, it's the vine of a wild grape. (The vine in the video is classic wild grape.)

They grow like most other flowering plants: they start innocently enough with a seed that takes root in the ground. They are initially tender and small stemmed.

From there, they grow along the ground, sending out tendrils. If they find something growing vertically, they cling to it (a shrub, tree trunk, or a low hanging branch) and grow upwards towards the light. If they have enough light (they are shade intolerant), they continue to grow, branch, and elongate. because they can become quite heavy, they break canopy branches of their supporting tree and fall in long loops toward the ground.

If the loop breaks for some reason, you have one swinging vine. But if you diligently follow it back, you'll find either the continuation of the vine near the canopy (the part after the break) or the trunk growing from the ground alongside of a nearby tree.

Though cool-looking, they are very destructive, bringing down not only branches but often entire trees (plural. They intertwine different tree branches, and if they bring down one tree, others fall in a domino-effect.)

Imagine that SOB hanging onto your upper arms for support (not the guy, the grapevine).

Smaller vines (which can also be destructive) that climb up the sides of trees are Oriental Bittersweet, Poison Ivy, Virginia Creeper, etc. (Probably Kudzu as well, but we don't have that here yet.) But these aren't likely to become large or sturdy enough to swing from if they come loose from the tree.

This is a photo of two common offenders: a wild grape (dark shreddy bark, about 2.5 inches in diameter) being slowly strangled by an oriental bittersweet (lighter bark), both climbing this large oak. If you look carefully, the base (roots) of both these vines are behind the tree (about five feet), one on either side. (You might have to take my word for it...)

Wild Grape


How does the telomere repeat sequence vary in Eukaryotes?

A database that answers the question, charting telomere repeat sequences for all known species, is: http://telomerase.asu.edu/sequences_telomere.html

For example in Yeast:


Why is there a compound highlighted in red in a KEGG Module search?

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


How to find the enhancer region of a specific gene?

There are several ways to identify enhancers:

(1) Chip seq / chip-chip recognize transcription factor binding sites,

(2) Enhancer specific factors can also be used to identify enhancers, such as EP300, the binding sites of EP300 are often used to predict enhancers;

(3) RNA polymerase II can bind thousands of enhancers, so POLR2A2a, the largest subunit of RNA polymerase II, can also be used to search for enhancer sites;

(4) The high sensitive site of deoxyribonuclease I (DHS) represents the open chromatin region, many of which are covered with enhancers;

(5) A large number of active regulatory elements, including enhancers, can be identified by formaldehyde assisted separation regulatory elements (face) combined with sequencing;

(6) Some histone modification patterns reflect different chromatin states, such as the binding of h3k4me1 and h3k27ac, which are widely used for enhancer labeling;

(7) Enhancer sequence can be transcribed, and the transcriptional enhancer RNA (enrna) is also a marker of enhancer activation;

(8) The method of chromosome 3D conformation (e.g. 5C and Chia pet, capture-c) can also provide the information of enhancer promoter interaction.


Does photosynthesis occur on cloudy days or does it require direct sunlight?

Yes, photosynthesis does occur on cloudy days where the light exposure is diffuse - but the overall picture is not as simple as your solar cell analogy.

Consider one of the findings of the following article: "Impact of clear and cloudy sky conditions on the vertical distribution of photosynthetic CO₂ uptake within a spruce canopy" (Urban et al. 2011), where one of the findings is that

  that shoots from deep within the canopy contribute substantially to the overall carbon balance during cloudy days. But, although shade-adapted shoots had a markedly positive carbon balance over a 24-h period on cloudy days, their performance was impaired on sunny days contributing only a marginal or even negative carbon balance from the middle and shaded parts of the canopy.

So, while leaves at the top of the canopy have a reduced rate of photosynthesis on cloudy days, leaves within the canopy and those that are shade-adapted, still photosynthesised.

I hope this helps a bit.


Can anyone tell what kind of berry/currant this is?

I am pretty sure this is a species of Ribes (Grossulariaceae, vernacular Finnish: herukat), and that it is not native to Finland.

I would guess that it might be a variety of R. rubrum L., but it also might be a species unrecorded in Finland so far. You might consider sending the photo to someone at Helsinki Botanical Garden, or at the Natural History Museum. (If you got a twitter account, you might just sent the link to this page to @Raino_Lampinen and ask on his opinion.)


How to filter out the antibody light chains into kappa and lambda types on the PDB website?

The instructions are as follows.

Go to the RCSB PDB Webite.
Under the search bar, click Browse by Annotations.
Click the blue tab labeled SCOP.
Click the white arrow next to the folder titled All Beta Protiens.
Click the white arrow next to the folder titled Immunoglobulin-like beta-sandwich (...).
Click the white arrow next to the folder titled Immunoglobulins (Superfamily).

This is where it splits, based on your specific search.

For Light Chain, Constant Domain:

Click the white arrow next to the folder titled C1 set domains (antibody constant domain-like).
For Kappa Type, Click the folder (not the arrow) titled Immunoglobulin light chain kappa constant domain, CL-kappa.
For Lambda Type, Click the folder (not the arrow) titled Immunoglobulin light chain lambda constant domain, CL-lambda.

For Light Chain, Variable Domain:

Click the white arrow next to the folder titled V set domains (antibody variable domain-like).
For Kappa Type, Click the folder (not the arrow) titled Immunoglobulin light chain kappa variable domain, VL-kappa (...).
For Lambda Type, Click the folder (not the arrow) titled Immunoglobulin light chain lambda variable domain, VL-lambda (...).

This should get you to the list of proteins that you are looking for.


Hydra are just one of the many organisms which are immortal.  That is to say all their cells divide forever - there is no senescence (planned cell death) in any of their cells. Interestingly Hydrae that reproduce sexually age and die, but asexual reproduction appear to be immortal.  Animals that are immortal more often reproduce asexually... this may only be because immortality became unpopular in evolution early on and may have not developed senescence in the way other animals have, or lost it when it was not so integral to life.

  Although immortal Hydra also appears to share the (TTAGGG)n telomere repeat, there is as yet no data on how or whether they avoid chromosome end depletion. These data suggest the possibility that senescence or death of asexual individuals and colonies may in part result from a failure to maintain chromosome ends that are restored by going through a sexually reproductive cycle .

So its not clear if the telomeres are protected in hydrae and other immortal animals.  I would guess they probably don't have active telomerase if they are truly immortal, though its possible the telomeres are shortened and are repaired.

There are other factors which are supposed to be important for immortality.  Yeast and single eukaryotes are not individually immortal; an individual mother cell can only divide a limited number of times. While hydrae are not a popular focus of research, there has been a concerted effort in trying to understand yeast mortality and there are more than one mechanism being pointed to.

Since there is no germline in single celled organisms, (they only have one copy of their genome to reproduce from) telomeric shortening would not be a useful mechanism for aging; Calorie restriction has been shown to prolong fission and budding yeast by activating pathways which slow aging by protecting against stress, and slowing down reproduction.  All of these findings have strong parallels in work in aging in animals which is a hot topic now.

Finding these pathways is encouraging strong thought that aging and senescence are an evolutionary adaptation rather than a biological necessity.

  Our current knowledge suggests that an apoptotic program has evolved in microorganisms as a survival strategy beneficial to the group. This program is dependent on cellular pathways like the Sch9, Tor1, and Ras/PKA pathways and its activation reduces cell protection and maintenance and raises the level of superoxide production, which in turn contributes to cell damage and death. Superoxide also elevates DNA damage and mutation frequency in the aging cultures ... Aging and apoptosis are intrinsically related in yeast and the mechanisms that cause them have just begun to be elucidated. ...  will provide important information to understand the fundamental biology of aging in other species and investigate the controversial hypothesis that an “aging program” might be conserved in higher eukaryotes.

There is an open question as to whether an immortal yeast could be engineered to be immortal.  A team at Max Planck Institute did a lot of foot work and found a strain which they claim does not seem to experience individual mortality either.

So this does indicates that immortality might not be a necessity for any cell or maybe even for animals.  Occasionally, even animal and human cells can be coaxed to revert to an immortalized state, though usually it is the result of cancerous rearrangements of the genome.

This is a rich field and there are lots of telomerase focused ideas too.  Maybe someone can post something along those lines.


Processing of speech/non-speech sounds in the human brain

"I'm wondering whether speech and generic non-speech sound processing in the human brain are somehow related and whether one of the two is used as a "basis" mathematically speaking or a reference to understand the other."
They both have in common acoustic energy - whose rate of change is information in itself. The mathematical basis of choice to compare each against the other, I think, is in how each relate that energy to the brain response - aka the forward model of the stimulus-response relationship.
In auditory studies you often get the (spectro)temporal response function (S/TRF) to estimate an approximate "summary" of this relationship. Note that traditionally, this is done independently, that is, either energy from speech or from other types of sound are separately investigated.
"is there any research that studies the difference in brain activity when speech / other sounds are heard"
There is a history of work contrasting the differential encoding of natural versus artificial sound classes (check out foundational work by Theunissen and colleagues). At these scales (neurons or neuron groups), the differences can be rather stark and happen in birds and mammals alike.
If you are more interested in these coding rules regarding "brain activity" at a larger scale, there are local-field-potential studies (e.g. Gaucher et al. 2012 J Physiol-Paris) that also relate mathematically to the S/TRF. However they are most likely invasive animal studies. Also I don't recall if they contrast speech S/TRFs versus other sound's. If you want something closer to human cognition, probably you might want to look at EEG or MEG studies also.
It turns out that finding similarities can be a bit harder than finding out the differences, maybe because the sounds are so different themselves. The mathematical relationship cannot escape this fact, and may then give distinct S/TRF patterns in return.
In a pre-print that seeks out similarities across stimulus types it is reported that certain information about the acoustic energy changes, in particular temporal onset edges, can be coded by the human auditory cortex, be it from speech, or music, or something else, in a more or less generalizable format across classes, at least qualitatively.  https://www.biorxiv.org/content/early/2017/07/27/168997