How long does it take for a cricket to die at subzero temperatures?

The actual paper that the linked article cites never mentioned about freezing the crickets:

  We examined CCR (Chill Coma Recovery) in G. pennsylvanicus exposed to 0 °C. The time
  required for crickets to recover movement of the abdomen and legs
  increased exponentially with the duration of exposure to 0 °C; after
  more than 12 h of cold exposure, recovery time reached a plateau at
  ca. 15 min

And this is how CCR is performed

  A total of 60 crickets were placed individually into 14-mL plastic
  tubes and cooled from 25 °C at 0.25 °C⋅min−1 and held at 0 °C for 2–42
  h. At 2-h intervals (first 24 h), and every 6 h thereafter, four
  crickets were placed on their dorsum in a Petri dish at room
  temperature. Times of four indices of chill-coma recovery were
  recorded: (i) first foreleg movement, (ii) first hind leg movement,
  (iii) initiation of abdominal contractions (active ventilation), and
  (iv) righting. Foreleg and hind leg movement were identified as a
  coordinated directional movement of the limbs, distinct from twitches
  of the limbs observed during rewarming. If crickets had not righted
  within 3 h of removal from the cold, they were considered to have
  incurred chilling injury that precluded recovery.

So, the crickets were never actually subjected to subzero temperatures or freezing or even cold shocks.

How long it takes to die depends on the freezer temperature; based on personal experience I can say that they die in ~10min @ -20⁰C.

Didn't find much information on crickets but according to this paper Drosophila will die in less than 2 hours at -5⁰C upon transferring them to the cold temperature directly (cold shock). However, if the larvae are "hardened" by keeping at +5⁰C before cold shock, their survival chance increased — the temperature required for killing them in 2h (Lowest Lethal Temperature) reduced. Now cricket is bigger than Drosophila but the surface area is also higher. I cannot do more than speculate at this moment (you can apply complex heat transfer equations and see how the rate changes with the size).


What is the relationship between UV wavelength and penetration depth into human skin?

Solar UV radiation is broadly classified as UV- A,B and C (Decreasing order of wavelengths). Penetrating ability of UV is a not a direct function of its wavelength; lesser the wavelength lesser is the penetrating ability (But higher is the energy: a direct function of wavelength). Penetration ability is dependent on scattering and absorption. Most biomolecules in the skin, including melanin and proteins absorb at around 220-300nm range. Plus, scattering (esp Rayleigh scattering) is inversely proportional to wavelength.

Since UV B has higher energy compared to UV A, the former is more toxic to the cells. But a little UV B also does some good; conversion 7-dehydrocholesterol to Vitamin D. UV A doesn't have sufficient energy to directly cause DNA damage  but it can give rise to free radicals and cause DNA damage indirectly.

The paper that you mentioned says that the tissue that they studied has more of UV A mediated lesions. This could be because of higher availability of UV A to the cells. Ozone filters out a major chunk of UV B and C and melanin does little more. If these mechanisms didn't exist then high energy UVs would have burnt us.

To summarize, the inherent order of toxicity is C > B > A

References:

http://www.uio.no/studier/emner/matnat/fys/FYS3610/h04/undervisningsmateriale/Moan7.pdf
http://www.nature.com/jid/journal/v77/n1/abs/5615637a.html


What prevents a pregnant woman's immune system from recognizing her fetus as nonself (and attacking)?

Just so that someone answers this question so that the moderators have less work to do:

The fundamental reason why embryos don't get massacred by the maternal immune system is because of the placenta and several of its functions. Three mechanisms are:

1) Secretion of neurokinin B, which is also secreted by parasites to avoid detection of the host.
2) The placenta has developed immunoevasive actions from a virus. It creates a syncytium to limit transaction of mobile immune cells.
3)It only allows specific antibodies,(IgG) to enter and bind infection. (IgG being the only isotype here).

Yay  for biology


Does osmosis occur when we have two different substances?

If A and B are at the same concentration there will be no net movement of water.

Everything is down to diffusion. In your example of solution A/pure water, water molecules on both sides of the membrane are diffusing through the membrane to the other compartment. However the "concentration" of water is less in solution A, so the rate of movement is less from solution A to water than it is from water to solution A. Water will continue to move into the solution until another force, such as hydrostatic pressure, counteracts the "osmotic pressure".

If solution A and solution B have solute at the same concentration then the rate of movement of water will be the same in both directions, so no net movement will occur.

(In a typical experimental set up using dialysis membrane none of this would apply with the solutes that you mention since they would also be able to move through the pores and you would end up with perfect mixing. You would have to use macromolecular solutes.)


Is there an acceptable term for 'male fox' other than 'dog'?

In the scientific arena, stick to male and female.

The word reynard can apparently describe a male fox or foxes in general (either gender).

It is presumably derived from the French word for fox, renard.

I don't know French, but a little research suggests that la renarde describes a female fox (vixen), while le renard can refer to a male fox, or it can describe foxes in general.

I did a little work with foxes in Alaska years ago and never heard them described with any terms other than fox, male and female.


How do platelets produce proteins (if they do)?

it seems that megakaryocytes, while nucleated, create a large dormant reserve of mRNA and ribosomes, which can be used by platelets later, upon their activation. So platelets can synthesize only certain proteins already transcribed by their megakaryocyte predecessors. The reserve of mRNA decline with the platelet age.


Why do so many parasites infect definitive and intermediate hosts rather than just one host?

Several reasons have been proposed.

  We suggest that complex cycles in helminths without penetrative infective stages evolve by two essentially different processes, depending on where in the cycle a new host is inserted. In ‘upward incorporation’, a new definitive host, typically higher up a food web and which preys on the original definitive host, is added. Advantages to the parasite are avoidance of mortality due to the predator, greater body size at maturity and higher fecundity. The original host typically becomes an intermediate host, in which reproduction is suppressed. In ‘downward incorporation’, a new intermediate host is added at a lower trophic level; this reduces mortality and facilitates transmission to the original definitive host.

--Evolution of complex life cycles in helminth parasites

  Despite these advantages to omitting hosts, the majority of digenean trematodes have a life cycle with three hosts, suggesting strong counteracting forces that maintain hosts in the cycle. Such forces have been proposed to be higher growth and fecundity (Parker et al., 2003), an increased probability of finding a mating partner (Brown et al., 2001), and higher transmission rates (Morand et al., 1995; Choisy et al., 2003; Parker et al., 2003). ... we propose here that maintaining a second intermediate host in the life cycle can be advantageous for the individual parasite to increase the intermixture of different clones and therefore decrease the risk of matings between genetically identical individuals in the definitive host.

--How a complex life cycle can improve a parasite's sex life

Also see The evolutionary ecology of complex lifecycle parasites: linking phenomena with mechanisms.


Why do we need to grow plants to make food?

We are part of a biological system, and we evolved to be part of it. Plants are the base of that system, and the main means of capturing energy and inorganic compounds and converting them to nutrients which are bio-available, along with bacteria.  The further we move from the niche we evolved to occupy, and the further we change the environment of the rest of the system, the more likely we are to bring about our own extinction.
Edit: This answer is somewhat opinion based. We haven't finished the experiment that proves this thesis, yet.


What is the response vector in the fMRI GLM model?

Short answer

The units aren't important, and are typically normalized.

Longer answer

The name "BOLD" is actually very instructive: Blood Oxygenation Level Dependent contrast (or signal). BOLD is not directly measuring anything like oxygenated/deoxygenated ratio, or we would probably call it something more similar to that: oxy/deoxy ratio.

Instead, "BOLD" is just the MRI image you get when you set up the scanner properties in a way that happens to be influenced by the oxygenation level of blood. Oxygenation level is far from the only contributor to the BOLD signal, but experimentally you try to factor out any influences that are time-varying but not interesting, and you ignore baseline levels that don't change.

fMRI works because the transverse relaxation time T2 of water in blood depends on oxygenation of the blood. From the original paper showing BOLD contrast in a rat brain Ogawa et al. 1990:

  At the 7-T field strength used in this study, T2 varies from 50 msec at 100% oxygenation to 4 msec at 0% oxygenation. The venous blood signal becomes very weak when the T2 value becomes comparable to or shorter than the echo time of the signal acquisition. At 60% oxygenation level, the estimated T2 value is 18 msec, similar to the echo time used in this report.

In other words, if you produce gradient-echo images with an echo time of 18 ms, the images you get show very different signal levels at 100% vs 60% oxygenation. Depending on the strength of your magnet, you can tune this time to go after the differences you want to see.

There is no straightforward way to compare images recorded in different conditions (i.e., different scanners, different parameters) on any useful scale of measurement. Instead, people typically report relative values, either in time or space. For this reason, you often see BOLD signals expressed as a % change or in terms of standard deviation (i.e., z-scores).

Ultimately, for fitting a general linear model it doesn't matter: you can freely scale a dependent variable without changing the structure of the model fit, all you influence is the interpretation of the magnitudes of the intercept and coefficients.

References

Ogawa, S., Lee, T. M., Kay, A. R., & Tank, D. W. (1990). Brain magnetic resonance imaging with contrast dependent on blood oxygenation. Proceedings of the National Academy of Sciences, 87(24), 9868-9872.


Why are the hormones dopamine, adrenaline, noradrenaline and serotonin so ubiquitous across the animal kingdom?

Evolution.

This is not special to hormones: receptors and ligands of all types are highly conserved across not only the animal kingdom, but also to single-celled organisms. The degree of conservation is typically dependent on the closeness of evolutionary relationship: more related organisms share more homology.

Because species evolve from common ancestors, they tend to share a lot of the same 'tools.' Changing the purpose of a hormone would likely require some sort of selective pressure, some new reason to use that molecule in a different way, and if the old and new roles conflict then there needs to be a replacement. This can happen, but it's complex and requires just the right conditions. More often, minor changes occur: among the steroid hormones, for example, you will find many small biochemical tweaks that make new molecules that have different functions.

Certainly the functions of some hormones are not entirely conserved, and if you look at the nervous systems of, for example, insects versus mammals, you will find some major differences, but the closer in evolutionary time you look the more similarity you will find.


Do human populations differ in core body temperature?

Yes there are different physiological temperatures in different ethnicities. To know which temperature range differences are inherited and which are learnt by living in different climates requires surveys of people who are from the same region.

This study states a 0.35 degrees difference between a japanese and a malaysian, 36.95 and 37.3, it's alot.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3929238/

The following study states states a 0.15 degree difference measured with similar precision,
https://www.ncbi.nlm.nih.gov/pubmed/20824480

This graph shows that the human body temperature is 36.2 at rest, at night/morning and 37.5 in the middle of the day. :
http://millar.bio.ed.ac.uk/andrewM/WE%20book99/Part2-examples.html#tth_sEc8.3.4.2

That may account for the 1 degrees difference in Japanese studies, they measure first thing in the morning/ at rest/at night, and japanese body temperature of 0.15-0.35 lower that some other ethnic groups.

There are geographic differences if you test the homeostasis response of different populations, the inner body temperature responses, the temperature of the extremities, sweating responses, the physiological responses and the blood cell characteristics.

Mitochondria has also been shown to be selected by climate type. Populations living in colder environments have lower mitochondrial diversity and that the genetic differentiation between pairs of populations correlates with difference in temperature, and they have found certain genes mutations in the ND3 and ATP6 that seem to be independantly implicated in similar climate adaptations.

The temperature is measured in lots of zones of the body and of the extremeties and the capillary flow. That doesn't account for habituation and acclimatization to tropical or northern climates.

The tropical population was found to have different thirst and sweating efficiency, and to change temperature at different rates to compensate for the same ambient conditions and exercise.

Some schools in China enforce that children run around in shorts in the snow in the winter and at playtime so that they regualte their body in the cold. Some northern people are apparently able to override the unconcsious response of the physiology that can raise body tempereture very effectively, and be able to hold in cold tanks for surprisingly long times.

Cold and hot weather are a strong force on natural selection, as illustrated by mitochondrial adaptations, because an advantageous in temperature regulation brings about a global performance advantage. The physiology of temperature regulation has been subject to many theories and studies, and they have found physiological conditionings can be honed by genetic adaptations in different populations.

Even chimpanzees have similar temperatures:

The cycles of increasing and decreasing body temperature of chimps
are exponential and symmetrical, with an amplitude of 2.6-2.9?F
(2-3 AM - 2-3 PM) and a 24-hour mean of 99.0?F, or 98.7?F. The S.D. of the 17 daily means was 0.53?F; and
of the values at any single hour, 0.63'F....Thus, in the bulk of the species the temperature ranges daily from
37.5- to 39+?C whereas the ordinary range in man is 36.5 to 37.5?C. Low
values are similarly reported for several primitive primates.

some references: http://rspb.royalsocietypublishing.org/content/276/1672/3447  https://www.jstor.org/stable/1377087

Actually this study states a 0.35 degrees difference between a japanese and a malaysian, 36.95 and 37.3, and study referenced afterwards states states a 0.15 degree difference,

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3929238/

https://www.ncbi.nlm.nih.gov/pubmed/20824480


What evolutionary advantage do viruses have in host specificity?

It is true for any living creature, that it would be great for it if it could thrive in all environments. Any creature would do better if it had a greater ecological niche while remaining as competitive in each of these niches. However, competition, predation and other biotic and abiotic factors lead species to specialize in specific niches. Of course, some species are more generalist and some are more specialist but I won't go into these details.

When it comes to parasites, such as viruses, the story is the same. A host is an environment. Being less specific would be great but the immune system is no easy detail to get around. Viruses are often quite specific to a given species, just because it evolved to be efficient for a given host but tend not to be that efficient in other hosts.

Note that parasites are not only species specific but also often tissue specific and specific to the specifics genetics of the host (e.g. malaria).

Somewhat related posts:

Why do parasites sometimes kill their hosts?
Why aren't all infections immune-system resistant?

Thank you @DeNovo for helpful comment


As hello_there_andy (and also the Wikipedia page) has indicated, genetic markers are DNA sequences that can be used to distinguish individuals (can also be tissues, cells, etc.).

Linkage of a phenotype with genetic markers is used to identify regions of the genome that are likely causative for that phenotype, as hello_there_andy says, but there is nothing inherent to how a marker is chosen that says it has to be linked to any phenotype. Markers are typically chosen for an analysis because they are easy to measure and track, individuals differ at the locus (so you know that if your phenotype of interest segregates perfectly with the marker, it's unlikely to be chance), and they cover the genome (or the region of the genome you already know is linked) appropriately, among other things.


Ecology has two meanings. The popular and the scientific meaning.

Ecology: the popular definition: Here the term ecology is probably quite poorly defined. To my gut feeling, the concept relates to the concept of global change. It encompass many fields such as biology (ecology (in the scientific sense), evolutionary biology and conservation biology especially), ethics and moral, politics, meteorology, public policy, ...

Ecology: the scientific definition: Ecology is a subfield of biology and earth sciences that studies interactions among organisms and their environment. interaction is an important word here.

Biology has a much broader meaning. Biology is the science that studies life. Biology studies the structure, the ecology (impact on their surrounding), the evolution, development biochemical processes, etc.. of living things. Biology is a very big field of science. A researcher in biology will probably not really consider him/herself as a biologist but rather as a molecular geneticist, a neurologist, a epidemiologist, a plant physiologist, a biochemist, a bioinformatician, a system biologist, etc.. For example, I would appreciate to consider myself as a population geneticist rather than as a biologist as there are many fields of biology I know nothing about. For example, I am a pretty bad naturalist.

In short, ecology is to biology what optics is to mechanics is to physics. Some people may not like this comparison as mechanics might take a larger part of physics that what ecology does to biology. Earth scientists may not like this comparison as well, as they are part of ecology without necessarily feeling like being part of biology. But anyway.

From the text you cite

  [..] as an ecologist [..] what gets me excited isn’t just finding out how the amazing plants and animals we find in the ocean work, but how they interact with each other and their environment [..]

It shows that indeed ecologist are interested in the interaction between organisms and between organisms and their abiotic environment. Matthew Fraser says "he's not only interested in how they work". 'How they work' is obviously an extremely inaccurate sentence. A less misleading reformulation would be: I am not interested in everything about the biology of marine animals, "I am especially interested in how animals interact with each other and how they interact with the environment", but obviously that is less exciting for the reader. The goal of Matthew I guess was to create the interest and the excitation of the reader (or audience) on ecology and for this purpose he kinda implied as ecology being more than biology, while ecology is only a subfield of biology.

For more information, wikipedia is your friend!


How is magnet based bead capture used for indexing-first ChIP-seq?

The anti-H3 antibody will precipitate all chromatin. They could have used an antibody against any histone monomer; that they initially used anti-H3 and then later used anti-H3K4me3 is coincidental. The idea behind the first immunoprecipitation is to immobilize the chromatin on the beads to allow easy recovery of pure chromatin after each step of the indexing process. These steps are seen in the supplementary material (4. Chromatin Indexing). For example, after immobilization, they perform end repair using specific buffers and T4 polymerase and polynucleotide kinase. These enzymes must be removed and the buffer exchanged before the subsequent indexing. The beads facilitate this process.


What are some good biological tests you can do to yourself?

One category of tests that are relatively safe to perform on yourself - are reflex tests. Some of them are actually very fun to test, say Babinski reflex.

No body fluids are used; however, I would still qualify those as "biological" enough.


To answer if the equivalent could be done with plants, we have to understand the histological and anatomical differences between plants and animals.

Just as spraying a nutritive solution over an animal (like you and me) doesn't work, spraying a nutritive solution over the leaves doesn't work as well: the nutritive molecules (let's use glucose in our hypothetical example) don't penetrate the leaf's epidermis. The same happens if you put the nutritive solution in the soil: there are several membrane layers between the external medium and the phloem, and glucose will never reach its destination.

Now, let's try to compare with a IV injection of nutrients, which we can do in an animal. The plant's structure that (kind of) can be compared to blood vessels is the phloem (actually, xylem and phloem, but in our case, dealing with nutrients, we're gonna talk only about the phloem). To inject the nutrients we have to reach the phloem, because the periderm in plants with secondary growth ("cork" in the image) is very impermeable:

Now, even if we reach the phloem, using methods like this...

...we still have a problem: in an animal like you and me, a substance injected in a given vein will quickly spread to all the systemic blood vessels. But the same doesn't happen with the phloem. The injected substance can go up or down (depending on the pressure flow), but it doesn't spread to all of the plant's tissues, unless we perforate the phloem in a lot of places.

Thus, so far, this method is used to deliver chemicals (like pesticides) into the tree. Notice that, just like a person in a hospital, the bag with the solution has to he higher than the perforation:

For a chemical treatment like this, the amounts of the substance are small. But for "feeding" a plant using this technique, the amounts of necessary nutrients are way higher...

Finally, answering your question: is it hypothetically possible to feed a plant in the dark with a nutritive solution? yes. Is it practical, or doable? very hardly.

Source: Utah State University


How many transmissions does it normally take for a neuron to reach threshold for action potential?

How many action potential are needed to cause an action potential in the postsynaptic neuron depends on the strength of the synapse(s) involved. It's not possible to answer this question in general.

It is not just the number of action potentials received but also the firing pattern in which they arrive and the location of the synapse(s) on the dendrites/soma (proximal/distal, on a spine or not, on which kind of spine,...) of the postsynaptic neuron.

However, for some neurons it is possible to trigger an action potential in a postsynaptic neuron with a single action potential. But in this case it is very probable that multiple synapses were involved between the two neurons (example paper).

To your second question: the time until polarization wears off is called the time constant tau of a neuron. It is a property that varies from neuron to neuron and is one of the things that can be measured when recording from a neuron. It is one of the many factors that affects how incoming action potentials are translated into a neuron's output firing.


Can humans transdermally absorb minerals from ocean water, and if so how much?

There is not very much transport of ions or water through the upper layer of the skin, mainly responsible for that is the stratum corneum (SC). Through this layer you will get only with small lipids and also substances which are able to penetrate the lipid layer of the cells like chloroform or DMSO. I think therefore that it is pretty unlikely that you can take up noteworthy amounts of ions (which would have to pass through the lipid layer of the cells which is highly hygrophobic) through the skin. Have a look at these publications:

Routes of ionic permeability through mammalian skin
Skin permeabilization for transdermal drug delivery: recent advances
and future prospects.

Interestingly this is different for other animals. The pacific hagfish is able to resorb organic nutients through his skin, see this article or this publication:

Adaptations to in situ feeding: novel nutrient acquisition pathways
in an ancient vertebrate


Since the matter in the brain is recycled every few days how does consciousnesses work?

That was an interesting read, and I saw nothing to support your statement that "brain parts die every few days".

Neural plasticity demands that some synapses degrade as new ones are formed. But there are (an estimated) 100+ trillion synapses (some put it an order of magnitude higher) so, really, a few here and there means little. It's when there is wholesale loss that problems arise.

A strong argument for a materialist theory of consciousness is that as neurons involved with memory die, so does memory. This is evident in the transition that occurs in early childhood allowing for the formation of long term memory as well as the degradation of short-term memory and other brain functions in people with, say, Alzheimers.

Hippocampal Neurogenesis Regulates Forgetting During Adulthood and Infancy Science 9 May 2014


This is due to states of brain activation promoted by the reticular formation, specifically with the ascending reticular activating system that mediates the general activation of the upper areas, for sleep these areas should promote states of relative low activity promoting the cerebral activation profiles during sleep, it is also interesting to study the descending reticular activating system that mediates the general muscular activation that is generally inhibited during sleep (except clinical problems among others) (that is why you can not make muscular efforts when waking up, try an experiment: try to clench your fists strongly when you are awakening).


Exponential growth equation and bacteria

Considering your assumption:

  I'm just looking at the exponential part, where the simple exponential
  equation works. If we assume there's sufficient nutrients for bacteria
  to grow unchecked for a number of hours (more-or-less true in a real
  culture)

In your original model you are using discrete states and fixed time steps. So, if 30 min is one time step then after n-steps you have $2^n$ or $4^{(n/2)}$ cells. You are basically counting double steps, which is fine. For a continuous approximation you should estimate the rate like this.

You have the first-order growth equation:

$$\frac{dN}{dt}=rN$$

When you integrate this equation (definite integral) you'll get:

$$ln\left(\frac{N_f}{N_i}\right)=r\tau$$

Where $N_f$ is final number of cells, $N_i$ is initial number of cells and $\tau$ is the time interval.

When the cell number doubles then $\dfrac{N_f}{N_i}=2$ and $\tau=30\ \text{min}$ (doubling time).

 Then your rate constant would be: $\dfrac{ln(2)}{30}\approx0.023\text{ min}^{-1}$

After 16 hours (16×30min) your number of cells would be: $e^{0.023\times16\times60}\approx 4.27\times10^9$ (approx 4 billion).

So what is basically wrong? You haven't rescaled your rate. Since the exponent is $e$ and you know that $a^x=e^{x.ln(a)}$, all you need to do is scale the rate constant with $ln(a)$ (a=2). Moroever, in a continuous model, you don't have fixed time steps. So you scale the constant with the doubling time as well.


What are the total number of alleles for a single trait?

To fully answer your question it would take an entire course of molecular genetics and quantitative genetics. I will be only very brief and will let you seek for more information on your own.

Basics of molecular genetics

You are confounding gene copy and allele. As we are diploid, we have two copies (I am ignoring here sexual chromosomes and mtDNA) of every locus. This is true for genes too. We have two copies of each genes. Now, we may or may not have the same allele at these two copies. If we have the same allele at both copes, we are homozygous, otherwise we are heterozygous at this locus.

You might want to have a look at the post Do men and women have the same number of genes?

Now, each chromosome is made of two sister chromatids (although this number varies depending upon the stage of life cycle). The sequences at the two sister chromatids are exactly the same, so you can't have different alleles at two sister chromatids.

You might want to have a look at the post What is the relationship between DNA molecules and the chromosomes?

Basics of quantitative genetics

Of course, a single phenotypic trait is not necessarily mapped out by a single locus. There are usually plenty of loci involved (see Quantitative Trait Loci, epistasis and eventually pleiotropy). There is also other source of phenotypic variance than genetic variance such as environmental variance for example.

You might want to have a look at the post Why is a heritability coefficient not an index of how “genetic” something is?

  Ok ,but I can't get your point .As there are two copies of one gene each from father and mother and we have an allele for every gene copy so, combining these we got two genes and four alleles .?Can we?

We receive one copy of every locus (or gene as you seem to get stuck with this term) from each parent. If these two copies differ, then we have two different alleles (heterozygous), otherwise we have only one type of allele (homozygous). In some life stage of the cell cycle, each chromosome is made of two identical chromatids. When this is the case, there are 4 copies of the gene but never more than two different alleles.

You really seem to use the term "allele" when "gene copy" should be used. Think of an allele as a pokemon card. When you ask someone "do you have Pikachu?", you're not asking whether the person has the exact same card that the one that is in your deck of cards. Alleles are the same! So even if you have 2 copies of a given locus (that is two pokemon cards), you might or might not have two different alleles.

You also use the term "gene" where it would be more correct (or more general) to say "locus". You should check out the definition of locus.


Myosin are motor proteins. Microfilaments (AKA actin filaments) are the tracks for Myosin. Filaments of different sizes are the structural components of cells, giving them their shape, rigidity, etc., as well as providing an intracellular network for transport. Myosin walk along these filaments.

In myocytes (muscle cells), myosin pulls actin filaments towards one another.

Picture from here: https://www.ncbi.nlm.nih.gov/books/NBK9961/


How do membrane proteins find their target locations?

This is a great question. A comprehensive answer would be beyond the scope of an answer on a forum like this. I will summarize the best I can here, but if you are really interested in this you should look at some of the work by Randy Schekman and Tom Rapoport, who have done a lot of pioneering work in this field and have papers from more than two decades ago on their lab websites. I'll talk about membrane proteins generally, but I'm not sure what the state of the field is for Na+ channels specifically, so I can't comment too much on that particular case. Many of the details of the processes I will mention are still areas of active research, so I will try to stick mainly to what has been well-characterized (to the best of my knowledge).

To restate the problem, proteins are generally synthesized in the lumen of the endoplasmic reticulum, which is an aqueous environment similar to the cytosol in many (but not all) ways. However, membrane proteins, which are not stable in aqueous environments, must:

1) Find a way from the ER lumen into a membrane.
2) Get from the ER into the correct membrane so they may perform their cellular function.

We will start with step 1, but the key to both is a critical but often underappreciated aspect of protein biology called the signal peptide. The signal peptide is simply an N-terminal sequence of amino acids that precedes what we would normally think of as the beginning of a mature protein. It is relatively short, usually only ~30 amino acids in length. It is cleaved off the mature protein by a protease once the protein is folded and in the membrane. Until that time, the signal peptide serves as a molecular marker that indicates where the nascent protein should be heading and how it should be handled. Not surprisingly, there are many different signal peptides that serve multiple functions, and they are not only used for membrane proteins.

So let's say we are in the ER lumen, and have some mRNA coding for a membrane protein that is destined for the plasma membrane. The first amino acids that will emerge from the ribosome is the signal sequence, in this case a specific signal sequence indicating that this is to be a plasma membrane protein. Once the signal sequence emerges from the ribosome, it is recognized by a ribonucleoprotein complex (that is, a complex of RNA and protein) called the signal recognition particle. Once the SRP binds to the signal peptide, translation is halted, and the whole complex moves to the ER membrane, where it forms a complex with another large protein complex called the translocon. I can't go into the intricacies of these complexes and their functions in this answer alone, but the simple description is that the translocon contains an ATPase that can insert the membrane protein into the ER membrane as it is translated, with the correct orientation. The hydrolysis of ATP provides energy to move the emerging polypeptide chain into the hydrophobic membrane, where chaperones help it fold. This process is in part driven by the recognition of hydrophobic transmembrane regions of the proteins by the translocon. It can also move soluble, cytosolic proteins across the membrane through a similar mechanism.

Now that the protein has been translocated, a peptidase will cleave the signal sequence off the protein. From here, sorting signals will take over. Generally, these are simple sequence motifs in the first transmembrane domain that act similarly to a signal sequence, but they are not cleaved. However, sorting signals can be stretches of peptide throughout the protein too, in some cases.

These sequence motifs will be recognized by cell trafficking machinery. Without going into too much detail, the proteins will be gathered into vesicles, and transported to other organelles. Usually, the first stop for proteins is the golgi apparatus, which is typically where many post-translational modifications, such as glycosylation, take place. I am a biochemist and not a cell biologist, so I am not the most qualified to go into the details of subcellular trafficking. Suffice it to say, once the protein is finished being processed in the golgi, it will be trafficked into other organelles, such as the plasma membrane using vesicle transport as before. From my understanding, the protein will be sorted into the proper vesicles based on its sorting signals, as well as other markers (in some cases, certain post-translational modifications on certain proteins can influence its trafficking). The vesicles recognize the proper destination membrane in part by the lipid composition of that membrane. For example, phosphoinositides have extensive influence on membrane trafficking, and many membranes can be differentiated by their phosphoinositide signature.

Anyway, that is a very broad overview of the answer to your question. I'm sorry I can't comment too much on the intricacies of cellular trafficking, I don't quite have the expertise to go through that literature quickly enough to answer your question in a reasonable time frame. I hope this is helpful in pointing you in the right direction, and good luck!


Somatic Mutations in meristem tissue in plants

You can see the wikipedia article on meristem.

The apical meristem differentiates into floral meristem that gives rise to flowers.
From this the cells specifically expressing APETALA3 (AP3), PISTILLATA (PI), AGAMOUS (AG) and SEPALLATA (SEP) would give rise to the stamen [ref].

CRC gene is essential for female development and plants lacking this will not produce pistils. So cells expressing this gene will give rise to female parts[ref].

Nonetheless mutation happening at any stage of the development of floral meristem can be transmitted to the pollens/ovules if the mutated cells stochastically give rise to that lineage.


What does genetically tractable strain mean?

You've already basically got the idea of "genetically tractable": if we can readily modify an organism's genome using known techniques, then it's genetically tractable.
That's a moving target, of course, because the set of available techniques is constantly expanding, so this is more of a pragmatic definition than a taxonomic definition. It's a notion that's quite important, however, because it's far harder to study an organism or to develop applications if you can't manipulate its genome.  If you can manipulate genetics, then you can make knock-out strains, introduce new functionality, and apply many, many other powerful and useful biological techniques.
So now to the last part of the question: assuming you've now got a tractable strain, why compare it with the reference strain? Well, if you're working on engineered applications, you probably really don't need to (other than from curiosity).  If you want to use the tractable strain to study things about the original, reference form of the organism, however, then you need to know their differences in detail, in order to have some idea of how much your results obtained by manipulation of the tractable strain are likely to inform your understanding of the reference form.


A request for an overview of the cranial nerves

I am not entirely sure what you are after, but I (as have others that commented on this question) interpret your question as "The linked chapter contains too much technical information". Quite frankly, after scanning the book chapter, I have to agree with you. Therefore I have sought for a quick overview image of all the cranial nerves including their sensory and motor targets.

Encyclopedia Britannica has published all the cranial nerves and their sensory and motor innervations in a single comprehensive figure:

Cranial Nerves and their targets. Source: Encyclopedia Britannica

I can highly recommend this online encyclopedia. Their articles are more concise and better accessible than similar topics on wikipedia. Moreover, this encyclopedia is not freely editable by everyone on the planet, and everything I have seen so far on their website is credible.


Fertilized fish eggs are known as Fish seeds. In simple words, they are the baby fishes used for seeding new Ponds in fisheries.

They can be used in 4 stages:

Hatchling : Larvae stage where it have yolk sac hanging below from where it draws its nutrition for 2–3 days. It can't eat from outside as mouth is not formed yet!

Spawn: Stage where mouth is formed.

Fry: About ~2 cm long, now, it can eat small size zooplanktons!

Fingerling: About ~15 cm long. It is now becomes easier to transport these kinds of fishes to Ponds.

Source (Picture Credits) :

Pic 1. https://www.ucdavis.edu (https://www.ucdavis.edu/sites/default/files/images/article/trout_lg.jpg)
Pic 2. Wikimedia (https://upload.wikimedia.org/wikipedia/commons/f/fe/Anemone_Fish_protecting_it's_spawn.jpg)

Pic 3. Fishbio (http://fishbio.com/wp-content/uploads/2011/03/Oncorhynchus-mykiss-fry.jpg)

Pic 4. Deveron (http://www.deveron.org/wb/media/images/parr.jpg)


What is this animal looking like an Axolotl?

Based on the size and location that appears to be a Common mudpuppy (Necturus maculosus). (Photo © Brian Gratwicke — CC BY)

The four toes visible on the front foot are also consistent with this identification.

This species is found throughout eastern North America and you can learn more about them from the Canadian herpetological society and iNaturalist.


Short answer
It has been shown that plants may already suffer from doubling the atmospheric CO2 concentration from 340 to 610 ppm, something that might happen during the next hundred years or so based on current emissions.

Background
A popular science website tells us that an excess of carbon dioxide (CO2) reduces the rate of transpiration of some plants. This is so because the stomata, which are the openings of the leaves (Mansfield & Majernik, 1970) and used for exchanging gases as well as water vapor (transpiration) will close when there is too much CO2 in the air, or other polutants such as SO2. As transpiration drops, the water flow from the soil to the leaves also drops, causing a runoff of water.This in turn stalls nutrient uptake. Indeed, doubling the present-day CO2 concentration to 610 ppm does not necessarily lead to increased growth and may in fact inhibit growth due to excess starch formation in the leaves, indicating it's simply stored as backup energy, nothing else (Coviella & Trumble, 1999). It is believed that plants might be near their saturation point and cannot eliminate CO2 faster than they are doing right now.

Somehow plants also become more susceptible to insect foraging when CO2 concentration increases.

Note however, that CO2 tolerances are species dependent. Most research in this arena has focused on common crops. CO2 tolerance in for example cotton plants is low, and starch buildup has been observed in the entire plant, but especially in the root systems and the stem (Hendrix et al., 1994). Other species, such as wheat and rice are less prone to effects of elevated CO2 (source: Nature).

References
- Coviella & Trumble,  Conservation Biology (1999); 13(4): 700–12
- Hendrix et al., Agricult Forest Meteorol (18994); 70(1–4): 153-62
- Mansfield & Majernik, Environmental Pollution (1970); 1(2): 149-54

Source
- Earth untouched


Is a sequential double transformation acceptable?

If the plasmids you wish to transform are very big (more than 20kb), the co-transformation might not be very efficient (you might not get any colonies). Electroporation should work though, as electrocompetent cells are more efficient than chemically competent cells. Alternatively, as you have read, you could transform your first plasmid and select for it, and then make these cell that harbor it competent and transform the second plasmid. As long as you select for the plasmids (with kan/carb/etc resistance marker), the cells that grow on the selective media will keep both of them. If I were you, I would try the co-transformation and then if it doesn't work I would do the sequential transformation.


And another insect from SE Brazil Oct 2017

I'm having a difficult time pin-pointing the species, however, I'm fairly certain this true bug belongs to the genus Zelurus.
Zelurus sp.

Zelurus sp.

Z. variegatus

Distribution

Interactive version can be found here.

source


The quote as phrased is a bit non-sensical really because it mostly hinges on what you define as 'sleep' or 'rest'. Plants, like most living things, including us, are far from dormant at night.

It's true that diurnal patterns govern the behaviour of most, if not all, living things that are exposed to them (1). Plants are no exception to this.

For example, photosynthesis is a 2-component process. With the so called 'dark' and 'light' reactions of photosynthesis (more correctly "light-dependent" and "light-independent"). Though both happen during the day and night, it is at it's peak during peak sunlight.

In CAM plants, to avoid dessication, there is differential carbon fixation because the stomata are kept shut during the hot daylight hours.

Respiration however, where the produced food is converted to energy, primarily happens at night.

The Khan Academy has a great 'walkthrough' of the steps of photosynthesis:
https://www.khanacademy.org/science/biology/photosynthesis-in-plants/the-light-dependent-reactions-of-photosynthesis/a/light-dependent-reactions

(1). The diurnal course of plant water potential, stomatal conductance and transpiration in a papyrus (Cyperus papyrus L.) canopy
https://link.springer.com/article/10.1007/BF00379885


Why does radiation sickness cause hair to fall out?

Radiation poisoning causes mutations in DNA that affect normal cell function, often causing them to die.  Cells normally have a number of repair mechanisms but if the damage is too great they won't be able to do so.  In particular, cells that are dividing quickly will not have time to repair their DNA before division and so die far quicker than other cells.  Chemotherapy is built on this concept.  By selectively introducing drugs or radiation that target fast-dividing cells, the cancer cells, which are very dividing rapidly and unchecked, are killed off before most normal cells.

However, there are some cells in the body that are very rapidly dividing.  Hair cells are one such type, hence hair will often fall out during chemotherapy or radiation sickness.  Another big cell type are those in the gut, which are constantly dividing.  That's why you often see people in movies who have been exposed to radiation vomiting.  The radiation targets those cells first, hence those are the first symptoms.


What is the biological significance of k-mer counting?

The applications for counting the k-mer occurences in a sequence are: building de Bruijn graphs [1] for de novo assembly from very large number of short reads, produced by next generation sequencing, fast multiple sequence alignment [2], and [3] repeat detection.

  Compeau PE, Pevzner PA, Tesler G: How to apply de Bruijn graphs to genome assembly. Nature Biotechnol. 2011, 29 (11): 987-991.
  10.1038/nbt.2023
  Edgar RC: MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004, 32 (5): 1792-1797.
  10.1093/nar/gkh340
  Kurtz S, Narechania A, Stein J, Ware D: A new method to compute K-mer frequencies and its application to annotate large repetitive
  plant genomes. BMC Genomics. 2008, 9 (1): 517-10.1186/1471-2164-9-517

To be clear, here is the biological significance of each of these applications:

Sequencing any genomes (bacterial, plant, mammalian) has become very cheap and easy recently with the next generation sequencing technologies. As opposed to the Sanger sequencing (the first generation), these produce as a readout very short sequencing reads, which have to be assembled into longer ones, and subsequently, into whole genomes. Counting the k-mers is part of the assembly process and this is its biological importance.
In order to compare whether proteins might have similar function, and thus belong to the same protein family, a multiple sequence alignment is performed. This is crucial step when annotating new protein sequences and studying their biological functions.
There are many repeats in our genome, as well as in plants. Repeated sequences are also involved in neurodegenerative diseases such as Hungtingtons, so being able to identify them is of medicinal importance.


The short answer seems to be that fevers help combat microbes (a term I take herein to include viruses for brevity), which aren't a part of the threat addressed in an allergic reaction. While there's not a full consensus on which benefits, if any, a fever brings to the response to microbes, both humans and other warm-blooded vertebrates fare better with infections when a fever is present.

Fevers appear to mobilise leukocytes and enhance their phagocytosis while suppressing endotoxin effects (see Craven, R and Hirnle, C. (2006). Fundamentals of nursing: Human health and function. Fourth edition. p. 1044) and proliferate T cells (see Lewis, SM, Heitkemper, MM, and Dirksen, SR. (2007). Medical-surgical nursing: Assessment and management of clinical problems. sixth edition. p. 212), rather than mobilising basophils.

Higher temperatures are also more damaging to at least some pathogenic cells than the body's own, as they are typically smaller with higher relative surface area. Note this also explains why fevers wouldn't be as natural a response to such large parasites as helminths. (Even their cells, being eukaryotic, are comparable to human cells.) It is unsurprising that IgE would be a more specialised response, found only in mammals.

On the subject of malarial fever, for which the pathogen is relatively large because it is eukaryotic, there is ongoing research into both the mechanism and function of this fever. It seems to be Plasmodium itself that creates and presumably benefits from the fever, not the host. I'll discuss the evidence in a moment, but note this means the "endogenous fevers follow suspected small pathogens" hypothesis is unthreatened.

According to this 2013 paper, the timing of such ruptures may (I stress may; the paper discusses the uncertainty around a number of ideas about this) serve the function of controlling the time at which the immune response is most active, so the reproductive cycle is unaffected. According to this 2007 paper, the malarial parasite's hemozoin causes the disease's characteristic fever following erythrocyte rupture. The same paper mentions that the timing of the fever has been used as a diagnostic criterion for malaria, and the 1927 Nobel Prize for Medicine was awarded for the now discontinued treatment of syphilis with a malaria-induced fever.


What is the difference between a protein and a factor?

Short Answer

There is no agreed upon naming convention for proteins - there are some rough standards because in language people usually try to convey their ideas in a way others can understand, but that doesn't necessarily mean fixed rules.

Longer Answer

I think it's important to recognize the process for understanding what proteins do is not always straightforward. Most often, a protein's function is first understood by seeing what happens if that protein is absent (and sometimes overexpressed).

The terminology factor implies that a protein is either modulating a process or at least is not by itself sufficient for a process. That is, it is named because when it was omitted, some other measurable process changed. It  maybe implies something that has its main function by binding, rather than catalyzing a chemical reaction, or at least that the actual mechanism of action is not yet known at the time of naming.

You would not expect, for example, an enzyme with a known target to be called a factor: it's most likely to be named according to its target and the type of reaction being catalyzed.

However, it's possible for a name to stick from when there is less complete understanding. Something might be called a factor initially because of how it influences some process, but the actual contribution is only understood later. Just for an example, take Complement factor I. Initially named because it had some role in the complement system, now it's known that it enzymatically cleaves another protein.

Importantly, there isn't any pure terminology here or consistent naming convention: in most cases, it just goes back to however the first person to describe the protein discussed it. Some proteins are named (controversially, I'll add) things like Sonic hedgehog - related to the similarly named Hedgehog signalling pathway which is all named because of one person/group's creative description of a related fruit fly phenotype.

Naming something "protein" just identifies that it's a protein, little more.


It's probably Arbutus unedo, strawberry tree. Native to Mediterranean region and some part of western Ireland.

Edit: I've just spot that you found it in California, so it's probably one of north american Arbutus species, eg. Arbutus menziesii.


Anode reaction,

$\small Glucose + 2NAD^+ (Embden-Meyerhof pathway) \leftrightharpoons 2 Pyruvate + 2NADH$

$\small Pyruvate + Ferredoxin_{(ox)} (Pyruvate-ferredoxin Oxidoreductase) \leftrightharpoons Acetyl-CoA + CO_2 + Ferredoxin_{(red)}$

$\small NADH + Ferredoxin _{(ox)} (NADH-Ferredoxin Oxidoreductase) \leftrightharpoons NAD^+ + Ferredoxin_{(red)}$

$Ferredoxin_{(red)} (Hydrogenase)\leftrightharpoons Ferredoxin_{(ox)} + 2H^+ + 2e^-$

[Last one: http://en.wikipedia.org/wiki/Ferredoxin_hydrogenase]

Cathode reaction,

$4 H^+  + 4e^- + O_2 \leftrightharpoons H_2O$

$C_6H_{12}O_6 + 6O_2 \leftrightharpoons 6 CO_2 + 6 H_2O, DG° = - 2870 kj$

Full paper: http://www.altenergymag.com/emagazine.php?issue_number=07.04.01&article=haldia


Why do cats like enclosed spaces (e.g. boxes) so much?

"Cats like boxes because they are cryptic animals; they like to hide,"And a box gives them a place of safety and security."
While inside a box, cats feel that they cannot be snuck up on from behind or the side — anything that wants to approach them must come directly into their field of vision. In effect, such hiding spaces allow them to watch the world around them without being seen.

And if something interesting passes in front of the cat — be it prey or a toy — it can dash out to get the object, and then quickly return to its safety spot.

Boxes also provide cats with a cozy, safe place to sleep, which is very important given that the felines sleep for up to 20 hours a day.


What is the meaning of the word "Ligandable" in "ligandable proteome"?

In biochemistry, ligand is usually taken to mean a substance which binds to a larger molecule such as an enzyme or other protein, thereby forming a larger complex.  The study of ligand binding has been important for pharmaceuticals, particularly in ligand-based drug design.

The term ligandability (and hence ligandable) seems to have come into significant use with a paper by Edfeldt, Folmer, and Breeze in which they say:

  In recent years, the term druggability has increasingly been adopted to describe the ability of a protein target to bind small molecules with high affinity; however, we believe the term ‘ligandability’ is more appropriate for this purpose. Although ligandability is a requirement for finding drugs for a particular target, it is not a guarantee that such ligands will make good drugs.

So, ligandable usually refers to the capability of a molecular target of drug design to bind small molecules.  A ligandable proteome would then be a set of proteins capable of binding small molecules.


The behavior can be explained evolutionarily just like any other trait. It came about either through adaptation, neutral evolution, or as a by-product of another adaptation.

An intermediate step, like the one you suggested, is not required. But if it did occur, there's no reason to believe that such a trait would cause extinction. Bloody eyes, whether they squirt or not, could be beneficial in some species. We know that blood-squirting eyes appears to be a defensive trait. Take away the ability to squirt and the blood could provide defense in some other unexpected way, or it may have had nothing to do with defense at all. Maybe the blood was just a lubricant before, or maybe the blood somehow enhanced vision during a stressful event. Or maybe it was just there and didn't do anything; nothing good, but nothing bad.

There's nothing special about this lizard. It does have a unique trait, but there's something novel in every species.


What is anorexia nervosa?

Generally, it is an eating disorder which is characterised by a tremendous fear of food as well as an extreme weight loss.
Patients with anorexia nervosa do not necessarily lose their appetite but rather obsessively control and restrict their food intake.

Anorexia Nervosa as an inherited disease/genetic factors

There has been a lot of research proposing that eating disorders are often biologically inherited and tend to run in families.

  Recent research suggests that inherited biological and genetic factors contribute approximately 56% of the risk for developing an eating disorder. Individuals who have a mother or a sister with anorexia nervosa are approximately twelve times more likely to develop anorexia and four times more likely to develop bulimia than other individuals without a family history of these disorders. Studies of twins have shown a higher rate of eating disorders when they are identical (compared to fraternal twins or other siblings).

The hormone serotonin

There has been found that anorexics have an overproduction of serotonin, which can cause a continual state of acute stress and anxiety.

  Researchers are still puzzled as to why, if anorexics already have high levels of serotonin, then SSRIs (medications like Prozac which raise serotonin levels) are successful treatments for some individuals. These scientists speculate that that there may be different subtypes of this disease, and that different groups of anorexics may have different neurochemical characteristics.

  Researchers have also noted that abnormal eating behaviours and the resulting changes in the body can actually cause a disruption in serotonin levels, thus contributing to an already existing problem. Abnormalities in serotonin levels can lead to depression and anxiety. Studies also suggest that there are genetic predispositions to serotonin disruptions that appear to run in some families.

The hormone dopamine

  Research suggests that women who develop anorexia nervosa may have altered levels of dopamine in their brains. Dopamine disturbances can cause hyperactivity, repetition of behaviour (such as food restriction), and anhedonia (a decreased sense of pleasure). This neurotransmitter also affects reward-motivated behaviour.

The hormone cortisol/hydrocortisone

  Numerous other hormones in the brain have also been linked to eating disorders. Stress triggers the production and release of a hormone called cortisol; chronically elevated cortisol levels have been observed in patients with anorexia. Cortisol can inhibit appetite.

The hormone leptin

  Leptin is a protein hormone produced by the body's adipose tissue. Leptin is regarded as a hormone which can regulate fact storage and appetite. If individuals with anorexia nervosa lose extreme amounts of body fat, their levels of leptin drop which is known as hypoleptinaemia. The side effects of hypoleptinaemia can include amenorrhea, impaired metabolism, and bone loss.

Also, if people receive treatment, their leptin levels do not immediately return to normal. Initially during the treatment, leptin levels rise through the sky, which is also the reason why most patients are most susceptible of relapsing back into an eating order, since very high levels of leptin may cause a weight gain.

Sources:

ENGEL, BRIDGET, NATALIE STAATS REISS, and MARK DOMBECK. "Causes Of Eating Disorders - Biological Factors Continued." Mental Help Causes of Eating Disorders Biological Factors Continued Comments. 2 Feb. 2007
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3010958/
http://www.apa.org/monitor/mar02/genetic.aspx


Are there viruses that show definite enzymatic activity?

As some of the comments mention, this question could use some clarification.

First, assuming you're asking in general about enzymatic activity in viruses:

A few classes of "non-autonomous" viruses (particularly endogenous retrotransposons) don't encode any enzymatic functions and sometimes don't even encode their own structural proteins - they rely on the structural proteins and/or enzymatic functions of the "autonomous" viruses.

With the exception of those non-autonomous viruses, all retroviruses encode the reverse transcriptase and integrase functions, while many non-retroviruses (those which don't have a step in their lifecycle where they convert RNA into DNA) also have RNA-dependent RNA polymerase activities.

Now, assuming you meant to limit your question to the viral coat (AKA capsid) proteins of an intact virus-like particle (VLP):

Most do not have any "enzymatic" activity per se - they do not catalyze the formation or breakage of any covalent bonds. However, many viral coat proteins have membrane associated domains which undergo conformational changes essential for uncoating and trafficking of the virus across the membrane:

Gao, D., Lin, X., Zhang, Z., Li, W., Men, D., Zhang, X., & Cui, Z. (2016). Original Article: Intracellular cargo delivery by virus capsid protein-based vehicles: From nano to micro. Nanomedicine: Nanotechnology, Biology, And Medicine, 12365-376. doi:10.1016/j.nano.2015.10.023

This membrane translocating (aka cell penetrating) activity sometimes does depend on the "collective" action of oligomeric complexes of capsid proteins, but it is not an enzymatic activity.

However, the parvoviruses do encode a phospholipase enzymatic activity in their coat proteins which serves to disrupt cellular membranes and allow viral entry:

Kobiler, O., Drayman, N., Butin-Israeli, V., & Oppenheim, A. (n.d). Virus strategies for passing the nuclear envelope barrier. Nucleus-Austin, 3(6), 526-539.

I don't know of any other classes of coat proteins with bona fide enzymatic activity, but I wouldn't be surprised if some exist, and I've only touched on a few of the multitude of enzymatic activities exhibited by other viral components.


What governs the distribution of blood vessels?

The growth of blood vessels is called angiogenesis. This process occures during embrional development, tissue repair, and even tumor formation (in fact this is a crucial step for tumors to survive). This Nature review ("Molecular regulation of angiogenesis and lymphangiogenesis")provides great overview of the process, I'll try and briefly summarize things:

In general large arteries grow circumferential  to keep up with increased blood transfer, while capillaries branch to a more complex network in order to be able to supply blood to every cell. The circulation system starts as a

  primitive
  and uniform vascular structures, known as primary capil-
  lary plexi,

that later develop into a hiearchical system of arteries, capillaries and veins. Main regulator of the morphogenesis of blood-vessels is the

  vascular endothelial growth factor A (VEGFA; also known as vascular
  permeability factor (VPF)).

This needed for the chemotaxis (the movement of an organism in response to a chemical stimulus. from: http://en.wikipedia.org/wiki/Chemotaxis) and differentiation of endothelial precursor cells (EPCs; angioblasts), endothelial cells (ECs) and the assembly of ECs to vascular structures (termed vasculogenesis), as shown in the figure taken from the article I linked. EPCs themselves differentiate from mesodermal cells during early embryo development and aggregate to form blood islands that later form the  vasculogenic formation of honeycomb-shaped primary capillary plexi.

Also it is important to note that :

  alternative splicing of VEGFA can generate several variants of the growth factor, including the so-called b isoforms that differ in the last six C-terminal amino-acid residues and have anti-angiogenic properties. The balance between the different VEGFA isoforms can regulate blood-vessel
  growth and patterning.

Also local composition of extracellular matrix (ECM) and the interaction between ECM and cells can affect angiogenesis. For example release of matrix bound VEGF is important in the regulation of the level of available VEGF. Also:

  Furthermore, the physical contact between ECs and pericytes is thought to induce a quiescent, non-sprouting phenotype.

Sprouting itself carried out by the selection of some ECs in the capillary wall to lead the growth of the new sprout. See next figure also from the linked article:

Notch receptors and Delta-like 4 (DLL4) ligands play key role in this process. In tip cell(s) DLL4 expression is induced (in response to VEGFA), while the Notch signaling in neighboring cells (activated by the DLL4) represses sprouting (by down regulating VEGFR2 - VEGF receptor 2) . This is important, because otherwise excess sprouting would lead to a dense network of capillaries and blood would just spread out too thin and would be unable to supply the organs with oxygen and nutrients.

In order to tip ECs be able to grow new capillaries they ahve to undergo some changes. Mobility is most likely gained by activated secreted or cell-surface bound proteases, to locally degrade the basal membrane. Interaction with other ECs have to be changed, without completely disrputing cell-cell junctions and the integrity of the vessel-wall. Also the apical-basal (apical side - faces the lumen of the vessel) polarity of the cells have to be reversed in order to be able to grow outwards (from the basal side of the endothelium. In order for the new capillary vessel to grow, the elongation of the new sprout has to be polarized and directional. This is achieved by spatial concentration gradient of ECM bound VEGFA isoforms along with prominent expression of VEGFR2 in the tips of sprouts.
For blood functional blood vessels to be formed the tips must cease growing and exploratory phenotype when they find their target, and string EC-EC junctions need to be formed. Also the generation of the lumen of the newly formed vessel is required.

As you can see forming of new blood vessels is a complex process that is controlled by local signals, yet it is part of a bigger process - the development of the embryo and organs that is regulated by many many genes and processes. Since our general architecture is the same it is logical that or circulatory system is similar. As for the abnormal structure of a body I think perfusion of that extra body part depends on the local environment.

The review linked at the beginning of this post has extra info on arterio-venosus differention and many other things.


Examples of seeking behavior by brainless animals

Yes, there are plenty of examples! We refer to this seeking behaviour as taxis.

Taxis

There are many types of taxis such as chemotaxis (attracted to chemical stimulus) or phototaxis (attracted to light). A complete list of taxis can be found on wikipedia > taxis.

For the purpose of this answer I will restrict to chemotaxis only

  Chemotaxis (from chemo- + taxis) is the movement of an organism in response to a chemical stimulus.

Chemotaxis in Bacteria

Chemotaxis is very common in bacteria such as E. coli for example (Macnab and Koshland 1972, Wadhams and Armitag 2004).

Chemotaxis in Plants

Chemotaxis is also observed in plants such as rhibozium spp (Currier and Strobel 1976) for example

Chemotaxis in eukaryotes

Chemotaxis is also found in eukaryotes such as in Amoeba or Tetrahymena (Köhidai 1999,Bagorda and Parent 2008) for examples.

Chemotaxis in animals that have "primitive" brains

Nematodes (Ward 1973) and plathelminthes (Bone 2012) for example show chemotaxis.

Chemotaxis in "brainless" animals

Evidence of chemotaxis also come from Echinodermata (sea stars, sea urchins and others) (Miller 1985).

Echinodermata have quite definitely no brain!


Function of ER in reviewing mutated proteins

Membrane proteins have to go to the ER from where they are transported to the Golgi apparatus. Usually these proteins are translocated into the ER while translation is still going on. There are chaperones (such as calbindin) in ER which help in translocation and also catalyze initial steps of folding. ER is also involved in unfolded protein response. Unless the protein is properly folded it is not transported to Golgi. However, this process is regulated at many steps and I wont add a detailed explanation of the mechanism, in this answer.

To conclude ER is involved in this case because the protein considered is a membrane protein.


If eating 100% fat 2 times more worth the energy I spend during the day, will I store body fat?

There are a couple of reasons why this approach doesn't work quite as well as you might hope.

First, insulin doesn't go away after a high-fat meal. This paper reports changes in serum insulin following pure-sugar and pure-fat meals. Although there is much less of an increase in insulin following the pure-fat versus the pure-sugar meal, you will notice in Figure 1 that the insulin levels following the pure-fat meals (panel A) are higher than the levels during a fast (panel B). So even if high insulin were the only signal for fat storage, your dream of eliminating insulin with a high-fat meal is not realistic.

Second, when a high-fat diet is designed for medical purposes, a good deal of care is required to avoid significant potential adverse effects. Adequate protein intake is still required, and amino acids from the protein can be converted to glucose. Furthermore, ketoacids are produced when fatty acids from ingested fat are in excess. (As noted in comments, humans do not convert fatty acids to glucose.) Although ketoacids can be excreted in the urine (admittedly, heading toward your goal of not storing all the calories you consume), the net metabolic effect on the body when you excrete ketoacids is increased acidification, which in turn can lead to difficulties with potassium regulation and thus, in severe cases, with heart function. In the extreme if this were continued for a long time, you may face a problem of life-threatening ketoacidosis as occurs in type-1 diabetics (low/no insulin) whose disease is not being managed.

That said, your basic idea is similar to the arguments for low-carbohydrate diets. How well they work and, if they do, through what mechanisms are still somewhat controversial, as I understand. Insofar as they work through excreting some of the ingested fat through urinary loss of ketoacids, however, the associated risks need to be considered.


Find Mutations Frequencies by Cancer Type

There is one paper called "Mutational heterogeneity in cancer and the search for new cancer-associated genes" from the "The cancer genome atlas" which should be interesting for you. This project aims to map the mutations occurring in different cancers, one of the results is this figure (from reference 1):

The project itself has numerous data on the different cancers available on the project website, which can be found in reference 2.

References:

Mutational heterogeneity in cancer and the search for new
cancer-associated genes
The cancer genome atlas project website


Forgot to vortex antibody before staining

It depends on how much time elapsed between adding the concentrated antibodies to the diluting solution and adding the diluted antibodies to the slide. If it was just a couple of seconds, then I can abolutely see there being a difference. Even if it was longer - say 30-90 seconds, even - there potentially could be antibody gradients in the solution without vortexing. There are a few reasons why. First, many unconjugated primary antibodies that are not intended just for immunostaining are provided in a glycerol solution, with concentrations ranging from 10% or so up to 50% or more, sometimes in addition to a carrier protein like BSA (I used to work for a well-known antibody company, and theirs are in 50% glycerol with 10 µg - 2 mg BSA per ml, depending on the antibody type). The glycerol prevents the solution from freezing solid at -20°C, eliminating ice crystal formation, protecting the antibody protein from degradation and allowing for longer storage times without loss of activity. As a result, however, the solution takes longer to solubilize in PBS or whatever diluent you're using on its own, with no additional mechanical activity.

On the other hand, even if the primary (or secondary) antibody is simply formulated in PBS, the equal diffusion of the proteins to all parts of the tube can take some time. As an experiment, put 1 ml of PBS in an Eppendorf tube, then add perhaps 10-50 µl of a dark dye, such as methylene blue, bromphenol blue, or Trypan blue. Watch it dissociate into the solution over time against a solid white background like a piece of paper. While none of these have the exact same solubility profile as antibodies, it's good enough to show you what happens over the first 30 seconds or so until you can't distinguish the dye anymore.

So, always vortex, even if it's at a relatively slow speed, for a couple of seconds to ensure everything is evenly distributed.


Is there some genetic variance underlying music appreciation?

In 2013,
Dr. Liisa Ukkola-Vuoti, University of Helsinki, Finland, done a detailed GWCNV(Genome-Wide Copy Number Variation) Analysis of certain group of people for musical creativity and aptitude.

Genome-Wide Copy Number Variation Analysis in Extended Families and Unrelated Individuals Characterized for Musical Aptitude and Creativity in Music

They did a Genome Wide Copy Number Variations (CNVs) in five extended
pedigrees and in 172 unrelated subjects characterized for musical
aptitude and creative functions in music
Muscial Aptitude is taken as Sum of Scores of Auditory structuring ability, Seashores test for pitch and for time. Along with data on creativity in music was surveyed using a web-based questionnaire.
Several CNVRs containing genes that affect neurodevelopment, learning
and memory were detected.
A deletion at 5q31.1 covering the protocadherin-α gene cluster (Pcdha 1-9) was found co-segregating with low music test scores (COMB) in both sample sets. Pcdha is involved in neural migration, differentiation and synaptogenesis.
Creativity in music was found to co-segregate with a duplication covering glucose mutarotase gene (GALM) at 2p22. GALM has influence on serotonin
release and membrane trafficking of the human serotonin transporter.
Genes related to serotonergic systems have been shown to associate not only with psychiatric disorders but also with creativity and music perception.
Both, Pcdha and GALM, are related to the serotonergic systems influencing cognitive and motor functions, important for music perception and practice.
A 1.3 Mb duplication was identified in a subject with low COMB scores in the region previously linked with absolute pitch (AP) at 8q24.
No differences in the CNV burden was detected among the high/low music test scores or creative/non-creative groups.

  In summary, CNVs and genes found in this study are related to
  cognitive functions. Our result suggests new candidate genes for music
  perception related traits and supports the previous results from AP
  study.

Source:

[1] Genome-Wide Copy Number Variation Analysis in Extended Families and Unrelated Individuals Characterized for Musical Aptitude and Creativity in Music

[2] Musical Aptitude Is Associated with AVPR1A-Haplotypes


Why do you need the intrinsic pathway when you have faster extrinsic pathway?

In short: The extrinsic cascade reacts to damages of the blood vessel, the intrinsic pathway reacts to damages of the walls. But as with all things, the long version is ways more complicated:

The extrinsic pathway is activated when you damage tissue and factor VII come in contact with tissue factor (also known as factor III). Tissue factor is located in the membrane of the cells and is only released when the cells are damaged.
Then the cascade starts and delivers a very fast large amounts of active thrombin, which then converts fibrinogen to fibrin to build a block of the damaged blood vessel. The step from the thrombin is common between both pathways.

The intric pathway is also called the "contact pathway", which starts when the factor VII comes in contact with collagen or anionic surfaces.
The main advantage of this pathway is the strong amplification of the initial signal from the intrinsic pathway by a factor of about 1000 fold. The intrinsic pathway is also co-activated by active thrombin (which stands at the end of the cascade) meaning it is also a powerfull feedback loop to make the initial reaction much stronger. This also overcomes weak activation which where the active thrombin will be inactivated by Tissue Factor Pathway Inhibitor.
The coagulation cascade has a pretty nice article in the Wikipedia.

Interestingly it is now believed, that the start of the intrinsic pathway plays no or almost no role in vivo. There are people which "suffer" from a deficiency in factor XII which is necessary to start the intrisic cascade. These people have absolutely no problems with their coagulation, so the first steps are not necessary (any more?). This article presents findings, that it stabilizes a thrombus:"The intrinsic pathway of coagulation is essential for thrombus stability in mice."
Here are some further articles about the intrinsic pathway:

In vivo roles of factor XII.
Factor XII: what does it contribute to our understanding of the
physiology and pathophysiology of hemostasis & thrombosis.


Does an annealing temp higher than primer's Tm contribute to primer dimer?

I don't think primer dimers are your primary concern here. Usually in my experiences, I get primer dimers all the time, even if the reaction works and I get my bands of interest.

Maybe you ought to troubleshoot other aspects of your PCR that might account for why your reaction isn't working. Have you tried using a positive control with your primers? You may try varying the parameters of your PCR as well. Remember, standard Tms are calculated according to a 50mM salt concentration: is that what you're using?

Generally, if the annealing temperature is above the predicted Tms of your primers, this represents a more restrictive and selective amplification of your target. You usually use a high annealing temperature if you're seeing lots of non-specific products. Since you're seeing no products at all, consider lowering the Tm to that of your primers (50º).

If you start seeing non-specific products at that Tm, I'd do what we call a "Touchdown" PCR -- that is, you start the reaction at a higher annealing temperature, and as each cycle progresses, it "touches down" to a lower annealing temperature. The principle behind this is that it starts it off at a restrictive temperature -- so your yield is very low initially, but then by gradually decreasing the "restrictiveness" of the reaction, your yield will improve. This will still prevent non-specific amplification b/c the less restrictive amplification will be on the fragments already amplified from the restrictive condition. Remember, biology is not exact science. Just because something says the Tm is such and such does not mean it's absolute and doesn't give you some margin of error. For example, we exploit that margin of error to optimize our experiments in the example I outlined above.

Anyways, (might have went on a tangent a little bit) you also have to consider how you designed your primers. Primers wil high self-complementarity will self-anneal at higher Tms.


How does a higher channel density increase speed of propagation of an Action Potential?

As @another'Homosapien' mentioned in the comments, the reality is actually the opposite:  action potential speed is inversely proportional to channel density.

In other words: lower channel density increases speed of propagation of an Action Potential.

If you decrease the density of ion channels, you increase membrane resistance. This results in less "leakage" of cations, which allows voltages to spread farther and thus reduces the number of action potentials that need to be generated. This results in increased conduction velocity.

 Long Answer

It's important to note two things about action potential propagation:

Each action potential takes time to occur.
The charge (i.e., voltage) that is created dissipates with $ \uparrow $ distance.

In fact, we have equations to calculate both the time a voltage change takes to occur and how current flow decreases with distance.

You can read more about the mathematics behind this and passive membrane properties in general here and here.

Importantly, these equations rely on two constants: length and time.

The time constant, $\tau$, characterizes how rapidly current flow changes the membrane potential. $\tau$ is calculated as:

$$\tau = r_mc_m$$

where r$_m$ and c$_m$ are the resistance and capacitance, respectively, of the plasma membrane. (See this previous answer for an explanation of resistance and capacitance. )

Importantly, these variables partially rely on membrane structure.

c$_m$ (the capacitance of the membrane) decreases as you separate the positive and negative charges.
r$_m$ (the resistance of the membrane potential) is the inverse of the permeability of the membrane.

The higher the permeability, the lower the resistance.
Lower membrane resistance means you lose ions quicker and therefore signals travel less far

But why? This is where that length constant becomes important. The length constant, $\lambda$, can be simplified to:

$$ \lambda = \sqrt {\frac {r_m}{r_e + r_i} } $$

where, again r$_m$ represents the resistance of the membrane and r$_e$ and r$_i$ are the extracellular and intracellular resistances, respectively. (Note: r$_e$ and r$_i$ are typically very small).

Basically, if the membrane resistance r$_m$ is increased (perhaps due to lower  average "leakage" of current across the membrane) $\lambda$ becomes larger (i.e., the distance ions travel before "leaking" out of the cell increases), and the distance a voltage travels gets longer.

 Why am I telling you all of this??

How are the time constant and the space constant related to propagation velocity of action potentials?

The propagation velocity is directly proportional to the space constant and inversely proportional to the time constant. In summary:

The smaller the time constant, the more rapidly a depolarization will affect the adjacent region. If a depolarization more rapidly affects an adjacent region, it will bring the adjacent region to threshold sooner.

Therefore, the smaller the time constant, the more rapid will be the propagation velocity.

If the space constant is large, a potential change at one point would spread a greater distance along the axon and bring distance regions to threshold sooner.

Therefore, the greater the space constant, the more rapidly distant regions will be brought to threshold and the more rapid will be the propagation velocity.

Sooo....

If you decrease the permeability of the membrane (i.e., if you prevent ion pumps from moving ions in/out of the axon), you increase the resistance of the axon membrane, which allows for the voltage created in the action potential to travel farther before dissipating.

By allowing the voltage to spread farther before necessitating the generation of another action potential, you reduce the time it takes for signal propagation.

In other words, if you decrease the number of ion pumps, you increase  membrane resistance (r$_m$). This causes voltage to spread farther and thus reduces the number of action potentials that need to be generated. The result? increased conduction velocity.


Volterra’s Variations and Fluctuations of the Number of Individuals in Animal Species living together features what is nowadays often called the generalised Lotka–Volterra model.
Thus it captures competition between and with populations.
In particular, Section 2 is titled:

  Biological Association of two Species which contend for the same Food.


How to statistically test the predictability of evolution?

I think Lenski's evolutionary long-term experiment should be a good example, without being familiar with Luria & Delbrück (1943). There they use replicated populations of E-coli to study (among other things) the "repeatability" (historical contingency) of evolutionary changes. Nice overviews of the project are given in Blount et al. (2008) and Philippe et al (2008), where they study to what extent certain mutations are repeated in replicate populations, in relation to citrate metabolism and size/shape.

References:

Blount, Borland & Lenski. 2008. Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli. PNAS vol. 105 no. 23
Philippe et al (2008). Evolution of Penicillin-Binding Protein 2 Concentration and Cell Shape during a Long-Term Experiment with Escherichia coli. Journal of Bacteriology 191(3):909-21


Functions of tracrRNA and crRNA in the CRISPR/Cas9 system

I have also been wondering the same thing for a while now and I think that the best answer that I could find after reading several review papers on CRISPR/Cas9 and online information, points to tracrRNA as serving the role of multiplexing with pre-crRNA which helps pre-crRNA mature to crRNA. This process activates the crRNA. I'm not exactly sure how this multiplexing action "matures" the pre-crRNA or what exactly that even means, but that is as much insight as the literature provides (see e.g. this abstract to a conference talk).

There most likely are some more important functions that have not yet been discovered for tracrRNA yet.


Identifying flying insect from northern Poland / Baltic Sea area

It is possibly a vine weevil (Otiorhynchus sulcatus)

Others of the family:


it seems to mean persistent or long-lived. Is that correct...?

Yes, it's correct, but how persistent the effect is is related to the rate of dissociation or rate of turnover of the receptor. It is relative, so to speak; relative to the effect of non-irreversible receptor binding.

Irreversible inhibition of, say, a cell surface receptor means that a drug (agonist/antagonist) binds permanently to the target receptor, usually by binding covalently; the chemical reaction is not reversible. This isn't synonymous with a permanent effect on a cell or organism; that depends on turnover of the receptor. A "faulty" receptor may be replaced quite quickly or not; it depends of the cell and the receptor.

Pseudo-irreversible means that the drug acts in a manner similar to  irreversibly bound agonists/antagonists, but there is no covalent bond formed; if a drug/molecule which has a sufficiently high affinity for the receptor is introduced (in a sufficiently high quantity), the new molecule will replace that which was strongly bound before (the pseudo-irreversibly bound drug.)

Some of these types of reactions have been studied more than others. One  example of this can be seen with h5-HT7 receptors, which are subject to pseudo-irreversible inactivation by risperidone and 9-OH-risperidone.

Clozapine and other competitive antagonists reactivate risperidone-inactivated h5-HT7 receptors: radioligand binding and functional evidence for GPCR homodimer protomer interactions


Help identify these (two) fishes - Netherlands

The second fish looks like a rock gunnel (or Butterfish; Pholis gunnellus).

This is an eel-like fish found in the intertidal and subtidal zones of the North Atlantic.

Interestingly, the rock gunnel is capable of remaining above the waterline at low tide and breathing air.

According to Campbell (1984):

  Fully grown adults can reach 30 cm in length. A long dorsal fin spans the body from just behind the head, supported by soft spiny rays. Its anal fin begins roughly midway along the body. The head is rather small with its lower jaw protruding and mouth turned upwards. Coloration is highly variable, ranging from hues of yellow-green to brown to crimson. A row of 9-13 dark spots, each surrounded by a pale ring, lines the dorsal fin

Sources:

1 Campbell, A.C. 1984. The Country Life Guide to the Seashore and Shallow Seas of Britain and Europe. Country Life Books. ISBN 0-600-34396-0


MOL2 to PDBQT conversion via OpenBabel and MGLTools removes hydrogen atoms

You saw my last answer of your question? you can do that easily, just use

prepare_ligand4.py -l  my.mol2 -A "hydrogens"


How long can E. coli stocks be stored at -20°C?

I think that cells get damaged at -20°C not because they are stored for a long period of time, but because they undergo cycles of thawing and freezing (the ice crystals that form damage them).

I never keep cells at -20°C. I store them at -80°C in 50% glycerol. The idea behind the glycerol is that it serves as cryoprotecor. It forms hydrogen bonds with the water molecules and thus it disrupts the water-water hydrogen bonds. As a result, it disrupts the crystal formation of ice, and the cells don't freeze. The freezing temperature of glycerol is −37.8 °C (60-70% glycerol in water), which means that at -20°C glycerol does not freeze and thus it cannot protect the cells from damaging from ice crystals formation.


Why is the separation of biochemical synthesis pathways safer and more economical?

False Economies?

Goodness knows what the poster’s teacher meant by saying that the separation of biochemical pathway is “more economical”! This is not a term usually applied to metabolism and, anyway, in life people who are economical do not always get value for the money they do spend, never mind obtain a better quality of life.

Most treatments of the separation of biochemical pathways justifiably emphasize the advantages of being able to regulate forward and reverse reaction sequences independently. However let us have a look at the separation of pathways in terms of energy, as the poster requested.

Some basic thermodynamics

The poster also requested the explanation be clear and simple. The following is simple, as long as you are familiar with the some basic ideas of chemical thermodynamics. If you are not, I suggest you read the three pages in  Section 8.2 of Berg et al. online. (Whether it is clear or not I leave others to judge.)

What determines whether a chemical reaction proceeds is the overall
(Gibbs) free energy change (ΔG). If it is negative, the reaction is
thermodynamically favourable.
The actual free energy change depends on ΔG0, the standard
free energy change (reflecting the chemistry of the reaction(s)),
together with the actual concentrations of reactants and products.
Enzymes are necessary to catalyse reactions in living organisms,
but do not affect the position of their equilibrium.

Argument

For simplicity, let us consider a series of reactions interconverting compounds M and P:

  M ⇄ N ⇄ O ⇄ P

No separation between pathways

Consider a situation in which the forward (M➞P) and reverse biochemical transformations (P➞M) involve the exact same chemical changes catalysed by the exact same enzymes, i.e. no separation between pathways. In order for this to work the overall ΔG0 must be near zero, otherwise reaction in one direction will be very difficult to achieve (require a very high concentration of starting reactant). For a ΔG0 near zero there will be equilibrium (no net reaction) at equal concentrations of M and P. In order to cause a flow of metabolites, say in the forward direction, there must be an increase the concentration of M relative to P.

There are two problems with this.
First, quite a large ratio of M to P, say, would be required to achieve net flow through the pathway, and this would involve having a large pool of unreacted M. (Section 8.2 of Berg et al., cited above, has some calculations that illustrate this.) This may or may be regarded as economical use of thermodynamic energy, but is not particularly economical in the  use of resources. However, a ‘pathway’ in which it is employed is glucose transport in the liver (actually a single transport process).
Second, the direction of overall reaction is controlled solely by the ratio of M to P, a situation that lacks flexibility.

Separation between pathways

If separate pathways are involved, the first problem of a single pathway mentioned above is overcome in the following way. Each overall reaction can have a high negative ΔG0, so that it does not require such a large pool of reactant and is essentially unidirectional. One might ask how this can be, as the value of ΔG0 for the chemical reaction, M ⇄ P is fixed. The answer is that separate pathways will involve  other reactants, so that the overall forward reaction might be
M + X ➞ P + Y
whereas the reverse reaction might be
P + A ➞ M + B
This is considered for glycolysis and gluconeogenesis in Section 16.3.6 of Berg et al. — with actual equations. The ΔG0, for glycolysis is quoted as – 84 kJ/mol, and that for gluconeogenesis as –38 kJ/mol.

Of course, if both reactions have a thermodynamically favourable values of ΔG0, it is necessary for the cell to prevent the uneconomic cycling of P back to M after it has been formed. However the fact that the pathways are different means that different enzymes will be involved, which are the targets of regulatory molecules that can switch them off and on. These regulatory molecules usual reflect supply and demand, but need not be intermediates in the reaction sequences, and they can act as far more sophisticated ‘switches’ for the enzymes. The particular details of this for glycolysis and gluconeogenesis can be found on the first page of Section 16.4 of Berg et al.

…the price of everything, the value of nothing

So are separated biochemical pathways energetically more economical? The large free energy change that drives these reactions is ‘lost’ as heat, so one could argue that the reverse is actually true. Or, then again, one might say that “you get what you pay for”.


Chromosome and chromatid numbers during cell cycle phases

The chromosomes copy at S phase. So S/G2 checkpoint up to early anaphase has 2n. You are on the right track to understanding the cell cycle, important to note the differences between homologous chromosomes (homologous pair) and sister chromatids, while understanding  ploidy.

During S (synthesis) phase which occurs between G1 and G2 , all the somatic DNA replicates. So every chromosome gets copied and thus  has a sister chromatid.

Animals that undergo sexual reproduction have 2 sets of chromosomes, one from mom the other from dad. The chromosomes of each pair represents homologous chromosomes.

Your answer is almost correct. I believe it could be adjusted to:

G1: 6 chromosomes
G2: 6 chromosomes /12 chromatids Prophase: 12 chromatids
Metaphase:  12 chromatids
Anaphase: 12 separating chromatids
Telophase: 12 chromosomes, 6 one each pole of the cell

These very simple figures explain the principles I mentioned earlier


Resource for learning analysis of sequence data via QIIME 2

The QIIME 2 tutorials are the place to get started - see here.


Do skull bones have pain nerves (nociceptors)?

Yes, bones can be innervated. I say "can be" because although I'm not certain that ALL are, I know that most are. "Innervation" is your key word to learning more about the presence or absence of nerves reaching to any body part. Googling "are bones innervated" yields plentiful results, but the short answer is yes.

If you were to chop your leg off with surrounding tissue numbed, you would still feel it for this same reason.


First of all, the $\mu$ is not expected time for a mutation to occur and get fixed; it is the rate at which mutations are fixed in the population. The basic result states that if neutral mutations arise at a locus at rate $\mu$ within individuals, mutations at this locus will be fixed in the population at rate $\mu$ as well.

The expected time for a given neutral mutation to fix after arising, given that it is not lost from the population, is approximately $4N_e$, where $N_e$ is the effective population size. Kimura and Ohta (1969) derive this result using a diffusion approximation; Kingman (1982) develops coalescent theory and in the process obtains what in my opinion is a more elegant derivation of the same approximation.

Now what is the probability that some mutation goes to fixation in the population as a function of time? Even though the fixation rate in the population is $\mu$, this does not mean that with probability 0.5 some mutation fixes within $1/\mu$ time units. That probability will depend on the distribution of fixation events in the population. Here's a good way to think about it. If fixation events were evenly spaced and occurred at rate $\mu$, then with probability 1 you would have a mutation within an interval of length $1/\mu$. If fixation events were highly clumped, then you would have a very low probability of having a fixation event within an interval of length $1/\mu$ -- but if you did have one event, you would probably have many. If fixation events are distributed as a Poisson process--which I suspect they would be in a purely neutral model--the probability of having a fixation event within a time interval $1/\mu$ would be given by a (negative) exponential distribution and thus the probability of having at least one fixation event in a time interval of length $1/\mu$ would be $1-\frac{1}{e}$.


You definitely have a seedling with prominent cotyledons still present.

My initial guess is Acer pseudoplatanus (sycamore maple, or just called "sycamore" or "planetree maple" in parts of Europe)

 Source: Wikimedia

You can see a detailed image of an A. pseudoplatanus seedling here and a time-lapse of a seedling growing to the point of cotyledon release in Neil Bromhall's youTube video.

According to the range map available from Euforgen, A. pseudoplatanus is present (blue) throughout Belgium:

As for confirming nearby adults, you're looking for a tree that looks as follows:

 Source: Blue River Nursery

For more information regarding identifying the adult, please see Virginia Tech Dendrology