Does human organism consume water or is it only used as solvent?

Humans and all other animals actually are net producers of water ("metabolic water") by oxidizing sources of energy including fats, proteins, and carbohydrates - effectively the opposite of the chemical reactions that photosynthetic plants use to turn water and atmospheric CO$_2$ into biological materials and oxygen gas. There are also many metabolic reactions in humans that consume water (in particular hydrolysis reactions), but it is less than the amount produced.

However, water is indeed important as a solvent, and there are non-negligible losses through evaporation (especially when sweating) and an important role of water in the kidneys to assist in flushing waste.

If one was able to reclaim all evaporative losses and excretion losses, no additional water would be necessary. However, the energy requirements to do so go up exponentially the closer you get to 100% reclaimation.

The International Space Station has several water recovery systems to reduce the incredibly expensive cost of supplying enough water for humans on long missions in space. These systems include both urine purification and atmospheric reclamation but they do not approach 100% capture.


Feedback affecting myocyte metabolism in humans

Well, ATP is replenished from three energy sources, namely:
1. phosphagen system (very fast, but quickly deprived)
2. glycolysis (fast, but slower deprived)
3. oxidative system (slow, 'impossible' to deprive)

When ATP is used, for example for muscle contraction, ADP is formed. The formed ADP can be rephosphorylated to ATP by the enzym creatine kinase, which also requires creatinephosphate (the phosphate attached to the creatine provides the phosphate group for ADP to form ATP). Additionally, ATP can be formed out of 2 ADP molecules by adenylate kinase. The phosphagen system is largely driven by the law of mass action, i.e. the direction of the enzymatic reaction is controlled by the concentration of the products and substrates. In other words; when ATP is low, and ADP is high, the generation of ATP is favored and vice versa. The energy from the phosphagen system is depleted rather quickly tho.

The second system, glycolysis, simply refers to the breakdown of carbohydrates (e.g. glucose) to resynthesize ATP from the energy stored in those carbohydrates. Your muscles contain a buffer of glycogen, approx. 300~ gr for the average Joe (give or take). The glycogen can be broken down to glucose-6-phosphate, which can then enter glycolysis. The glucose-6-phosphate is broken down to 2 pyruvate and yields 3 ATP netto (2 when derived from glucose, rather than glycogen, due to a first enzymatic step which requires 1 ATP). The enzymatic steps of glycolysis are controlled by ATP, AMP, ADP and other factors, factually integrating the energy status of the muscle (primarly through allosteric regulation of enzymes, especially phosphofructokinase).

The third system, the oxidative system, refers to the breakdown of carbohydrates and fatty acids, requiring oxygen to 'burn' them (citric acid cycle). The yield of this is much higher than for glycolysis, but the process is way slower.

In essence, all are regulated by the concentration of substrates and products, as well as through allosteric regulation (binding of a molecule at a different site, inhibiting or activating the enzyme, often by intermediates of the pathways themselves). Additionally, there is some long-term regulation through gene expression (e.g. up- or down-regulating expression of genes involved in these pathways), mostly by hormones.

Edit:
Well, I guess this is described in any basic biochemistry book (I'm very fund of the book 'Fundamentals of Biochemistry: Life at the Molecular Level'). If you want to see a description of these energy systems in a more exercise related context (since you were aiming at myocytes) I suggest reading Strength and Condition: Biological Principles and Practical Applications from Marco Cardinale et al., and the NSCA book Essentials of Strength and Conditioning.


Do the bacterial species X, Y, Z code for proteins A, B, C?

First of all, don't reinvent the wheel, search for annotated homologs first. Assuming you don't find them, the next step is:

Collect the sequences of your query proteins (not genes) from one species in a multifasta file.
Run a tBLASTn with those sequences against the genomes of all the other species of interest.
Analyze. Look for HSPs with a certain level of sequence identity. The details of what threshold you choose will depend on your data, I can't help you  there.

While the tBLASTn approach is going to be more sensitive, an easier method that can find gene structures and not just HSPs is to use exonerate:

exonerate -m p2g proteins.fa genome.fa

Finally, for a more sensitive search than either of the above, useful for finding more distant homologs, run a Psi-tBLASTn of your proteins against the genomes of interest.

In all of these approaches, the tricky bit is to choose the right threshold. Unfortunately, there is no golden rule here. It all depends on how closely related your species are and how similar the homologs. You will have to try a few different ones before you can choose the right one.


meaning of "initial gene constructions" vs. "under the control of plant promoters" in an article on GM plants

So basically, most plasmids that you buy have an antibiotic resistance marker, I think it's relatively standard, because you want to know which bacteria were transformed, right? Ergo, the initial cloning vectors being used. These markers are under control of a plasmid promoter like T7, for example, not a plant promoter (unless you contsructed it de novo to do this). But your plasmid is going to have a cloning site where you can make a cut, insert more DNA, and ligate it back together.

At least pursuant to the patent by Monsanto here, my assumption is that if you're looking to modify plants, your insert for the cloning site is probably a plant promoter, followed by a structural gene, and then a UTR sequence. I think what the authors are saying is that some groups put an antibiotic resistance gene into the insert as the structural part, and when you use something like an A. tumefaciens system to integrate that vector into the plant genome, you end up with an antibiotic structural gene under the control of a plant promoter. You should keep in mind that the whole plasmid gets integrated, but not all of it is transcribed by the plant, only that within the transcribed region controlled by a promoter the plant can utilize!!*

*I'll add, what they're worrying about in the linked OP article, is that whether or not the plant is actively producing antibiotic proteins, that the sequence for the antibiotic resistance has been introduced at any point in the plant's genome carries the risk that some bacteria will randomly obtain it through horizontal gene transfer.


The problem is partly the definition of Antigen that you quote. It refers to “the body” leading you to assume it’s a specific body — yours. I'm sure there are better definitions, but just taking this one, I would modify to: “A substance that can be recognised as foreign and evoke an immune response in an organism.”

With this definition, which is actually how antigens are thought of, a particular antigen need not be antigenic in every organism to which it is presented. Those organisms or individuals for which the antigen appears as ‘self’ will not recognize it as foreign as they are ‘tolerant’ to it (e.g. by mechanisms which eliminate the cells capable of producing antibodies against the self antigen). But it is still referred to as an antigen.

So your understanding of the situation is correct, but that of the use of the terminology is not. Even if you belong to blood group A and therefore will not mount an immune response to the pink blobs in the picture when transfused with blood of group A, they are still referred to as antigens as they stimulate an immune response when transfused into a person of blood group B.

If you wished to talk about the fact that the A antigen on blood of type A does not provoke an immune response when transfused to persons with blood group A you could say “The A antigen on red cells is not immunogenic (or even antigenic) when transfused into persons of blood group A”.

Footnote on terminology

Scientific terminology allows us to describe things precisely. As our understanding increases, the terminology may need to evolve to allow us to make distinctions of which we were previously unaware. The word ‘antigen’ was coined in the late 19th century, before anything was known of the structure of antibodies, and was defined in terms of the immune response as that was what was observed. The definition evolved in some quarters to include the idea of binding to an antibody or T-cell (see e.g. Merriam-Webster definition).

However this extended definition raises the problem of the terminology to use if something binds to an antibody but does not provoke an immune response. Thus, the Glossary of the textbook Immunobiology (Janeway et al.) defines antigen as “Any molecule that can bind specifically to an antibody” and uses a different term, ‘immunogen’, for “Any molecule that can elicit an adaptive immune response on injection into a person or animal”. (Which explains my mention of ‘immunogenic’, as opposed to ‘antigenic’, above.)


Infecting tumor cells with viruses to provoke an immune response used to be  termed (tumor / immune ) 'xenogenization'.  The approach may now fall under the general headings of tumor immunology, immune modifiers or tumor vaccines.   Xenogenization been explored for decades (with only moderate success).  Some modern approaches include adding immune stimulating genes to the viral 'vector' (e.g GM-CSF) to try and improve an immune response.  Xenogenization is usually intended for use with the patients own (autologous) tumor cells.   Other approaches that use viruses include delivering genes that preferentially act in tumor cells or "tumor antigens".  Some of these modified viruses may have been engineered to have low, or no, ability to replicate in the body.   Note that some viruses, such as influenza or rhinoviruses are not (generally) able to circulate in the bloodstream (viremia) to infect distant tumor cells.  Instead, the goal of using such viruses is to provoke an immune response against tumor antigens expressed on the 'original infected' cells at the site of injection and hope that the immune system goes on to attack distant masses/metastases.


You hit upon several ideas in your post.  First, you are absolutely correct that body fat is composed both of lipids and water, so a 10kg weight loss does not correspond to 90,000 kcals.  The most commonly accepted figure is 7700 kcals per kg of body fat lost (Hall, 2008), but this is a rule of thumb at best.

The translation from caloric deficit to body fat loss is fairly complex, and is the result of feedbacks between metabolism, weight, and other responses.  The National Institutes of Health researchers built a fairly intricate model estimating the actual responses as a differential equation (simulation and references available here), which would probably be a good place to start.

If you're inquiring not from general curiosity but with an interest in developing your own nutritional plan, keep in mind that nutrition is a lot more than merely calories.  It is critical to get macro and micro nutrients, of course, but other factors such as dietary fiber play an important role in the health outcomes.


Is a large tumor is more likely to develop hypoxic regions?

The prescence of hypoxia is independent of size, grade, or histology. It occurs due to a cut off in blood supply to the tumour. Or insufficient vasculature systems, meaning the oxygen cannot diffuse all the way into the tumour. Aberrant growth of tumours can increase the likelyhood of tumours developing hypoxic regions.


If so many different hormones/molecules work by activating adenylyl cyclase, how do they have different effects?

How can hormones/molecules have different effects if they all work through cAMP? The short answer is that receptor expression on cell types is highly specific, and only if a cell has a particular receptor will it respond to a particular hormone. Thus two different hormones can have different biologic effects because the cells that contain those receptors are highly specific. Overall it is the presence of specific cellular receptors that determines the specificity of hormones and their effects.

A little more in depth of an answer... This is a classic concept from graduate physiology and was a real step forward in our understanding of hormone action in the 1950s/1960s. Earl Sutherland, who received the Nobel Prize in 1971 in Physiology or Medicine for this work, was on the faculty at Case Western Reserve University (and later at Vanderbilt University). Dr. Sutherland was studying the actions of hormones that were involved in glycogen metabolism (i.e. glycogen synthesis and glycogen breakdown). These classic studies identified a substance, now recognized as cyclic AMP (cAMP), whose intracellular concentration was increased in liver cells that were treated with hormones that stimulated glycogen breakdown. Conversely, cAMP was decreased by hormones or other conditions that were associated with glycogen synthesis. Most interestingly, it was identified that different hormones that either increased or decreased glycogen synthesis/breakdown had similar effects on the intracellular concentrations of cAMP (e.g. epinephrine, glucagon). This suggested that somehow cAMP was a common signaling molecule (or "second messenger") that transmitted the extracellular hormonal signal to the inside of the cell to have a biochemical effect (in this case stimulating glycogen breakdown).

In the case of Sutherland's studies, the increased concentration of cAMP stimulated the activity of Protein Kinase A (PKA), and the lack thereof decreased PKA activity and allowed the actions of protein phosphatases to predominate. For example, when glucagon binds its receptor on hepatocytes (liver cells), that receptor is coupled to an intracellular enzyme ($G_S$) that is activated and then can activate an enzyme called adenylyl cyclase, which increases synthesis of cAMP from ATP. The increase in cAMP then binds to PKA and phosphorylates the glycogen synthesis enzymes and breakdown enzymes. When the glycogen synthetic enzymes are phosphorylated by PKA they are inactive and, conversely, when the breakdown enzymes are phosphorylated they are active. Thus, glycogen receptor activation leads to activation of the glycogen breakdown machinery and inhibition of the glycogen synthetic machinery. This makes sense physiologically if you think about it - glycogen acts to increase hepatic glycogen breakdown and increase hepatic release of glucose into the circulation.

In brief, once Sutherland's group demonstrated the importance of cAMP as a second messenger protein within the cell, other groups began realizing that many other hormones led to changes in intracellular cAMP but each had there own effects. The differences in these effects were determined by the cell type that the hormone was acting on and whether or not that receptor was coupled to a particular second messenger system. Thus, you could have any number of receptors on the cell surface that are available to bind extracellular ligands (e.g. hormones, nutrients, drugs). However, each of these different hormones can be "coupled" or linked to different types of intracellular "second messenger" processes to transmit a signal. There are many types of second messengers that help transmit extracellular signals to the inside of the cell.

As you mention in the question, cAMP is a common second messenger system for a variety of different cell types. However, those different cell types have different receptors that are coupled to cAMP. Thus, hormones can have different effects depending on the tissues that express the receptors. For example, the glucagon receptor is expressed on hepatocytes which increases $G_S$ activity and thus cAMP, leading to glycogen breakdown and increased hepatic glucose production. Similarly, the $\beta_2$ adrenergic receptor that binds epinephrine/norepinephrine on smooth muscle is also coupled to $G_S$ which increases cAMP and leads to smooth muscle relaxation. These very different hormones have different biologic effects in different tissues, even though the effects are both driven by cAMP-dependent mechanisms. Briefly stated, it is the receptors that are present on a cell, that determine the response of a particular cell to that hormone.

This is graphically shown in the image below from this medical biochemistry link in adipose tissue - though the same concept is true for liver cells. Glucagon signals through its receptor to increase adenylyl cyclase, cAMP and then PKA activity, while insulin inhibits that activation by increasing the activity of PDE (a phosphodiesterase) that works on breaking down cAMP and subsequently keeping PKA in its inactive form.


I'd say that unihemispheric sleep and adaptations like it really are sleep - the brain activity on one side of the brain gives a characteristic sleep pattern.  It certainly must satisfy the needs of an aquatic mammal like a dolphin or a whale since they have to be partially conscious to breathe by surfacing regularly.

It does seem to affect the brain physiology, but is there a reason you would not call it sleep?


What happens between making a DNA library and screening by nucleic acid hybridization?

The library is 'created' during a ligation reaction: plasmid vector + insert (e.g. cDNA). That DNA is used to transform E. coli, and, after plating out the transformation mixture, single bacterial colonies are obtained. Each colony contains, to a first approximation, a single plasmid species (i.e with a single insert). So each colony represents a clone, in the terms that you use.

I don't know if anyone really does things like this any more, but originally each plate would be transferred to nitrocellulose, for probing, and to a fresh plate for archiving. This way, any colony identified as positive after nucleic acid hybridisation could be picked from the archive plate for further characterisation.

This screening can be done on large format Petri dishes to reduce the number of plates needed. I know of one lab which in the 1980s used to screen λ libraries after plating out for plaques on cafeteria trays. That was the heroic era of molecular biology.


Why has malaria only now started to develop resistance against artemisinin?

Selection pressure (1, 2). One way or the other, there were few enough people taking the drug that it didn't really "matter" to P. falciparum (the deadliest of the malaria-causing parasites) on a population level until recently.

According to the 2014 paper
Spread of Artemisinin Resistance in Plasmodium falciparum Malaria (3), the driver of Artemisinin resistance is a single point mutation (ie a change of a single DNA base pair) in a single gene. The thing to keep in mind is that these single nucleotide mutations happen all the time. You yourself most likely have 3 or 4 of them relative to your parent's genomes. Thus, this particular Artemisinin resistance mutation probably has occurred in the past.

However, as with most drug resistance mutations there is likely some fitness cost paid by the individual in which this mutation occurs. In environments without the drug, wild-type (ie non-mutant) parasites will outcompete the mutants, and the mutation will quickly disappear from the parasite population. It is only when the drug becomes commonplace that the mutant parasites gain the upper hand and the mutation spreads.


Human bone density and Brown Bear bone density?

The word density in the medical term bone density is used to quantify only the mineral content of the bone (bone mineral). It's not intended to describe the total mass density of the bone like we are used to from physics.
This is all on wikipedia: http://en.wikipedia.org/wiki/Bone_density
Thus, when one say that a Grizzly bear have 10 times the bone density, it implies that its bones have 10 times the mineral content compared to humans, and this is indeed seen as a proxy indicator for bone strength. However, this claim does seem unsupported and unrealistic as kmm points out.


How to determine whether the energy of a stem-loop fold is significant or not?

You can convert the $\Delta G$ values into equilibrium constants $K$ using the formula

$$ \Delta G = R T \ln K $$

This might help you understand what those energies roughly mean.

But the more important and also more difficult part is judging how good your predicted free energies actually are. I assume you used a secondary structure prediction program like Mfold to calculate this. They typically have a several parameters you can adjust like ion concentrations and temperature, you should make sure that you have some appropriate values here.

Without knowing anything more about your system or data I'd ignore the -0.3 kcal/mole result, the -4.9 kcal/mole structure could be formed, but I wouldn't regard this as certain.

Now, in the in vivo situation the whole thing gets far more complicated. The presence of RNA binding proteins, helicases and the generally rather complex environment in the cell makes it much harder to predict which secondary structures will actually form.

If you wanted to know for sure you could e.g. do SHAPE experiments on your RNA. This is a technique that also works in vivo.


What structural features make a molecule a potent opioid receptor agonist?

Specific parts — moieties — of an agonist molecule bind to the receptor protein, causing the receptor to change shape, which in turn initiates a signaling pathway inside the cell.

Some agonists are better at causing the receptor to change to its "optimal shape" for relaying signal. These are called "full agonists".

Other agonists cause a partial change in receptor shape and reduced signal. These are called "partial agonists". The strength of the resulting signal is called "efficacy".

In addition to differences in efficacy between agonists, the parts of the agonist that bind to receptors can have a different chemical makeup and so create a different environment of electrostatic attractions and van der Waals forces between atoms in the agonist and in the atoms in the binding site in the receptor. Agonists that bind more strongly will stay bound to the receptor longer. These are said to have higher "affinity". Agonists that bind more weakly have lower affinity.

It is affinity and efficacy together that determine potency, or how well an agonist works.

In a biological environment, as well, these agonists swim in a pool with other agonist and antagonist molecules. For example, your agonist of interest might do a good job of changing a receptor's shape, but if it binds weakly, it will "pop off" the receptor quickly — perhaps too quickly to trigger the necessary signal. Another, different agonist molecule comes in and binds more tightly, but it doesn't create as strong a signal. Or perhaps a passing antagonist molecule floats around and pops onto the receptor, stopping any signal from that receptor and also keeping any agonist molecules from binding again for a while.

The population of agonists, antagonists, and receptors all change the number and kinds of binding events that take place, which determines whether you get the signal you want, as strong as you want it.

While the opioid molecules you are looking at have different numbers and varieties of atoms, it is the molecule's shape and electrochemistry that matter. Most specifically, it will be the part of the agonist molecule that actually binds to the receptor that matters most: how well it causes a conformal change in the receptor, and how strongly it binds.

These molecules could look very different from one another, but ultimately it is the part of the molecule that binds to the receptor, and how well it binds, that matters.

I don't know about the receptor-ligand kinetics of how different opioids bind to pain receptors, specifically, but hopefully there is some terminology in this answer that helps with further research.


In our solar system which other planet could have been in the "habitable zone" in the past?

This answer is also speculative, but according to the planetary habitable zone models proposed by "Habitable zone for Earth-like planets in the solar system" (Franck et al. 2000), a key finding was that:

  an Earth-like planet at Martian distance
  would have been habitable up to about 500 Ma ago while the position of Venus was always outside the habitable zone.

So, Mars could have been habitable, but as it is much smaller than Earth, it has a smaller gravitational field presumably a major factor in how it lost much of its atmosphere.


Does the body have a gate control for pain

Pain receptors, more precisely pain signal propagation, can be inhibited in several ways. One is, for example, fine touch receptors (mechanoreceptor in illustration) inhibit propagation of pain signal in spinal cord (a lot of pain processing happens in spinal cord):

That is why humans often rub skin around or nearby injury, whether it is in joints or something more superficial. You should find more information about such control in any textbook on pain. See this page for short primer.

Next, pain propagation is modulated -- still in spinal cord -- by descending pathway from brain and brain stem. See this page for more, or address Kandel's textbook.

Now, I don't know whether or not it is identified how/where brain "selects" to what pain pay attention. My hypothesis is that it happens by competition, e.g. several signals compete by inhibiting each other via some mechanism, probably, related to stress-induced analgesia.


How does an axon "know" it's not connecting to its own neuron?

I think I can partially answer you question. As far as I'm aware, there are many surface receptor molecules such as ephrins that are responsible for axonal guidance and dendritic repulsion in developing organisms such as flies (Drosophila). As you can tell this is extremely crucial since its important for neurons to spread their dendrites and axons as far as possible, evenly spaced out with axons bifurcating (separating) correctly and not sticking together. This is for example important in the Drosophila brain for axonal projections into different lobes.

One such surface receptor, which helps achieving the above is Dscam (Down syndrome cell adhesion molecule) (schmucker et al 2000 Cell). Dscam gene is expressed in over 38000 isoforms (through complex alternative splicing of Dscam mRNA) in flies. It is the homophilic binding and subsequent repulsion of Dscam protein isoforms that enables an intrinsic self-recognition for repulsion of same-cell axon. As far as I understand it, if a number of similar Dscam isoforms are present on axons or dendrites of a neuron, this is self recognised and the dendrites and axons get repelled from one another. This is the molecular pathway that ensures sister dendrites are not adhered together or become concentrated in one area.

In the absence of Dscam or when Dscam protein isoform diversity is removed flies die during larval stages and the early embryonic axonal patterning of the fly nervous system is clearly disrupted. In the absence of Dscam protein, Bolwig's axons exhibit frequent axon pathfinding errors at a specific intermediate target. Most of these processes are conserved in mammals.

For further information please look at Schmucker & chen, 2009 Genes and Dev


The Brassicaceae family (of which cabbage and mustard are members) has a characteristic pattern of flowers - each flower has four equal sized petals, arranged in a cross-shape hence their other name - crucifers.

[h/t wikimedia commons]

It's not easy to see from your photos whether this is true, but I'm going to say, yes, it does look like a member of the Brassicaceae family. The cross-shape of the petals would confirm this.
I don't think these plants are native to Illinois, and it also does look somewhat like a crop plant, rather than a weed, so maybe it is an escape from a farm/garden. It could be canola, possibly.
Wild cabbages are native to the Mediterranean and Atlantic coasts of Europe , so it is probably not a wild cabbage, unless someone planted it in Illinois.


A couple of comments, but maybe not an answer; I think misuse is the wrong word - alternative meaning is better. 'Evolve' as a word is much older than the theory of evolution, and has its origin in the Latin evolvere:

  evolve (v.)
      1640s, "to unfold, open out, expand," from Latin evolvere "to unroll, roll out, roll forth, unfold," especially of books; figuratively "to make clear, disclose; to produce, develop,"
  from assimilated form of ex- "out" (see ex-) + volvere "to roll" (see volvox). Meaning "to develop by natural processes to a higher state" is from 1832. Related: Evolved; evolving.

from Online Etymology Dictionary. Implicit in that definition is the laying out of something predetermined, which can relate to going from simpler to more complex.

Also note that Darwin only used the word 'evolve' once in On the Origin of Species (1859), in the final sentence:

  There is grandeur in this view of life, with its several
  powers, having been originally breathed into a few forms or into one;
  and that, whilst this planet has gone cycling on according to the fixed
  law of gravity, from so simple a beginning endless forms most beautiful
  and most wonderful have been, and are being, evolved.

The implication of progress was one reason why Darwin disliked the word 'evolve' and preferred "descent with modification".

The same root was then used as a name to the theory of Evolution, but then in a much more specific sense than the older, general meaning.

If you look back at the etymology above, it is quite clear that biological evolution (The Modern synthesis version) emphazise the connotations 'expand', 'produce' and 'develop', but not the 'unroll' and 'unfold' parts (which both to some extent imply something predetermined).


How do DNA viruses keep themselves in the nucleus without inserting themselves into genome?

Herpesviruses maintain themselves during the latent state as "episomes", circular DNA elements, with no capsid, that are in the nucleus but that are not integrated into the host genome. Host enzymes replicate these episomes, and different viruses have evolved different strategies for ensuring that the episomes are passed on to newly-divided cells.

  After they first infect cells, many herpesviruses establish a latent lifecycle with the viral genome existing as circular genetic elements called episomes inside the host cell’s nucleus that are closely associated with, but not integrated into, the host DNA. During latent infection, episomes are replicated during S phase, but new viral particles are not produced and the infected cell survives. The maintenance of herpesvirus genomes as episomes contrasts significantly with retroviruses, which insert their genome within the host cell genome to ensure their replication and inheritance by daughter cells and establish long-term infection. ... EBV uses a mechanism to tether the EBV genome to host DNA, facilitating the equal distribution of episomes in daughter cells with a larger number of cells having at least one EBV genome. In contrast, KSHV uses a clustering strategy that promotes a higher number of episomes per cell, but at the expense of not passing on the episome to some daughter cells

--How herpesviruses pass on their genomes

Another mechanism many herpesviruses use is to establish their latent infection in non-dividing cells, especially neurons, so that there's no concern about daughter cells.


What is the longest-lasting protein in a human body?

Crystallin proteins are found in the eye lens (where their main job is probably to define the refractive index of the medium); they are commonly considered to be non-regenerated. So, your crystallins are as old as you are!

Because of this absence of regeneration, the accumulate damage over time, including proteolysis, cross-linkings etc., which is one of the main reasons why visual acuity decays after a certain age: that is where cataracts come from. The cloudy lens is the result of years of degradation events in a limited pool of non-renewed proteins.

Edit: A few references:

This article shows that one can use 14C radiodating to determine the date of synthesis of lens proteins, because of their exceptionally low turnover: Lynnerup, "Radiocarbon Dating of the Human Eye Lens Crystallines Reveal Proteins without Carbon Turnover throughout Life", PLoS One (2008) 3:e1529

This excellent review suggested by iayork (thanks!) lists long-lived proteins (including crystallins) and how they were identified as such:
Toyama & Hetzer, "Protein homeostasis: live long, won’t prosper" Nat Rev Mol Cell Biol. (2013) 14:55–61


Why do the deoxyribonucleotides use T and ribonucleotides use U?

For the switch from thymine (T) to uracil (U), it actually doesn't have anything to do with the sugar backbone of the nucleotides. This article on Science Daily explains that U is more cost efficient to produce than T because it can be easily gotten from a chemical degradation of cytosine (C). Since RNA has a short life span and because the cell needs a lot of RNA it uses U. DNA, on the other hand, undergoes a lot of checks and repairs. If it were to use U, it wouldn't know if the U was really a U or if it was a C that got damaged. Since it is important to keep the number of mutations to a minimum, DNA uses the more costly T to ensure fidelity.

I would also like to point out @AMR's comment. It isn't just an oxygen atom. An oxygen atom is the difference between the air we breath and ozone that can kill you. It's the difference between water and highly flammable hydrogen gas.


Does chromosome cross occur over male and female or vice versa?

The question is unclear to me but hopefully that will help a little bit.

  My understanding is homologous chromosome pair, which means male and female chromosome

There is no male and female chromosome. Chromosomes have no sex. In humans, to the exception of chromosome Y all chromosome can be found in individuals of any sex.

There are paternally inherited chromosomes and maternally inherited chromosomes though. As you said the maternally inherited chromosome is indistinguishable from the paternally inherited chromosome when comparing their sequence (they may well differ in terms of epigenetic changes).

  chromosome inside the DNA.

A chromosome is not inside the DNA. DNA is the name of the very long molecule from which a chromosome is (mainly) made of. DNA can be organized in different forms one of which is into chromosomes (another one would be a plasmid for example). While it would still sound funny, it is more correct to talk about DNA inside a chromosome than talking about chromosome inside DNA.

  So if that's homologous how does male do with female?

This is very unclear...do what? Why would the paternally inherited chromosome (assuming this is what you mean by male chromosome) do anything with the maternally inherited chromosome rather than the other way around? While it is clear from the what follows that you would like to talk about recombination, I don't get where you're heading.

  does it flip over and change direction, that could not happen as male chromosome 1(say) is indistinguishable from female?

I don't get what kind of "flip" you are thinking about. You probably should have a look at the wikipedia article for cross-over.

In short, synapsis are formed during prophase I of meiosis and when segregation happen synapsis are resolved with a probability of $\frac{1}{2}$ of causing a recombination event. Synapsis occur as they allow matching pairs of homologous chromosomes together that will ensure their separation during anaphase 1. You should probably take some time to review the meaning of this paragraph.

  And what about the XY chromosome in male,say?

Sorry, that's a bit unclear too.

  I know some are pseudoautosomal, but most are normal sex chromosome nucleotides. So what about them?

Sounds like you misunderstand what a sex chromosome is and what pseudoautosomal mean.

In short, in humans, there is only one pair of sex chromosomes (XX or XY depending on the sex). The other 22 pairs of chromosomes are autosomes. There is no such thing as a pseudo-autosomal chromosome in humans but there is a pseudo-autosomal region on the Y-chromosome.

Most of the Y chromosome never recombine (while the X chromosome recombine in females only) as it is never present with another Y chromosome in the same cell. There is only a short sequence on top of the Y chromosome that recombines with the X chromosome, this region is called the pseudo-autosomal region. This region probably still exist to allow separation of X and Y chromosomes during anaphase I.

Please also note that you seem very focus on humans (without saying it and maybe without realizing it). The diversity of sex-determination is huge. You might want to have a look at Do males of all sexual species have Y chromosomes?


In animals, birds, reptiles and fish, is a male sometimes unnecessary for a female to have/extend a male

Rephrasing your question

The question is worded in a funny way. If I am not mistaken your question is

  Are there other means of reproduction than cloning that do not require mating with another individual? In particular, I am interested in such mean of reproduction that would allow an individual to create an offspring of another sex.

I will assume this is your question. I don't fully understand the point of the first paragraph though if this is your question.

Answer

Means of reproduction are much more diverse than we tend to think. So diverse that it is sometimes hard to really class each reproduction in non-arbitrary bucket.

Yes that exist! There are several modes of reproduction that may be of interest to you, the main one be selfing. Selfing is when an individual fertilizes itself. Now, by definition, such individuals need to be hermaphrodites, however it is not impossible that there are individuals that look males, others that look females and yet they (typically the females but not only) are able to self every so often.

Just to give a funny example to show how diverse system of reproduction might be. In social ants, the queen can either let the sperm of a male fertilize her eggs and produce a female worker (or a future queen depending on whether the larvae receive royal jelly) or chose to undergo normal meiosis but the gamete from the mother will directly develop into an individual without fertilization and make a male. This is not cloning because 1) only half of the genome is being transmitted and 2) recombination occur.

Related

What DNA does a self-fertile plant's seedling have?
Do males of all sexual species have Y chromosomes?


The difference between the beta-sheets and the quaternary structure of proteins

Quarternary structure is between separate protein chains or proteins themselves. Beta sheets are a form of secondary structure which is within a single polypeptide.

Sure, some of the structures in quarternary complexes will be between “two or more peptide chains”, but the stipulation that these not be part of the same polypeptide chain would be necessary.


What constitutes as the death of a bacteria?

When you talk about organisms like fungi and bacteria which can have a dormant form, and viruses, "dead" becomes somewhat harder to define. In fact, it has not been definitively defined for bacteria.

I would have guessed "when they are permanently unable to reproduce", but I may be wrong.

From one source[1]:

  The observed coordinated gene expression continued even after cell death, in other words after all bacteria permanently lost their ability to reproduce. Transcription of a very limited number of genes correlated with cell viability under the applied killing regime. The transcripts of the expressed genes in living bacteria – but silent in dead bacteria-include those of essential genes encoding chaperones of the protein folding machinery and can serve as molecular biomarkers for bacterial cell viability.

From another[2]:

  it is a challenge to determine if bacterial cells are dead, or viable but non-culturable (VBNC), and what is an agreed upon correct definition of dead bacteria.

Some viable but nonculturable cells (VBNC) can be "resuscitated" into dividing cells. [3]

Also4,

  However, the simple binary definition live/dead probably does not accurately describe the complex physiological states possible with microbial cells.

Unfortunately the actual conclusion is behind a paywall.

Finally, another country heard from5 :

  Programmed cell death is a gene-directed process involved in the development and homeostasis of multicellular organisms. The most common mode of programmed cell death is apoptosis, which is characterized by a stereotypical set of biochemical and morphological hallmarks. Here we report that Escherichia coli also exhibit characteristic markers of apoptosis—including phosphatidylserine exposure, chromosome condensation, and DNA fragmentation—when faced with cell death-triggering stress, namely bactericidal antibiotic treatment.

So, perhaps the answer is, a bacterium is dead when it is unable to reproduce, cannot be resuscitated, gene expression has ceased, and shows characteristic markers of apoptosis

[1] Transcriptional activity around bacterial cell death reveals molecular biomarkers for cell viability, Remco Kort, Bart J Keijser, Martien PM Caspers, Frank H Schuren and Roy Montijn, BMC Genomics 2008
[2] Can dead bacterial cells be defined and are genes expressed after cell death? Trevors JT1, J Microbiol Methods. 2012 Jul
[3] A matter of bacterial life and death Gregg Bogosian, Edward V Bourneuf
[4]Advances in microbial food safety: 23.
[5] Antibiotic-Induced Bacterial Cell Death Exhibits Physiological and Biochemical Hallmarks of Apoptosis, Daniel J. Dwyer, Diogo M. Camacho1, Michael A. Kohanski, Jarred M. Callura1, James J. Collins, Molecular Cell, Volume 46, Issue 5, 8 June 2012, Pages 561–572


I think the answer to your question is relatively unknown. The answer I have heard the most often, which is largely the most accepted, is that many insects orient themselves in space using light. So if they are flying at night, the soft light of the moon tells them which relative direction they are going. Light bulbs end up confusing them, because they think they can orient themselves to it, but they are wrong.

http://www.npr.org/templates/story/story.php?storyId=12903572

Additionally, insects do have very similar photoreceptors as humans and vertebrates. Fruit fly eyes are a major research topic because of the similarity of the photoreceptor proteins as well as the amazing genetics that can be done.


Example of a virus becoming symbiotic with an organism

In humans, endogenous retroviruses (HERVs) comprise a substantial fraction of the genome, as much as 8%.  While many historical viral incorporation events into the primate genome were likely neutral or detrimental (and therefore selected against), some were co-opted and are now functional elements in humans.  An example: human syncytin is the envelope gene of a defective HERV, and the protein has been co-opted for fusion during human placentation.  More HERV resources here.  The Feschotte Lab at Cornell studies the evolution of HERVs and other mobile elements in mammalian genomes, and their lab site provides more resources.

In bacteria, prophage (integrated bacteriophage) can be co-opted by their hosts for niche-specific transcriptional control.  A cool example is the pathogen Listeria monocytogenes, which utilizes prophage excision during intracellular growth to activate its Com system and escape from phagosomes.


Most animals are not afraid of the vet. When I was in practice, many dogs and cats waltzed in perfectly happily.

Of those that were afraid, I presume that many picked up expectations from their owner.  The owners who tell themselves "My dog is going to be afraid of the vet!" will be tense and nervous themselves, and of course their pet will detect this and react the same way. Many owners were far more distressed than their pets were, expecting some huge negative reaction to the vaccination or something (the pet often didn't even notice the injection, until the owner squealed or shrieked with anxiety).

Finally, animals that experienced something negative on a previous visit -- perhaps a bad interaction with another animal in the waiting room, or their owner being afraid of needles, or actually having some unpleasant procedure -- will of course remember this.


Possibly related to leafhoppers? .. Assuming it's within Hemiptera.

Your assumptions are correct! This insect is related to leafhoppers, in that it's a planthopper, and, is of the order Hemiptera -- it belongs to the species Scolops sulcipes.

According to the College of Agriculture & Natural Resources at the University of Delaware, this is one of eight species in Oregon that belong to the Dictyopharidae family. (source)


Are there any solitary species of ant or termite?

I do not know of any solitary ants, but there are species that form very small colonies.

One such species is Jerdon's Jumping Ant (Harpegnathos saltator). They usually live in colonies smaller than 100 individuals and workers may reproduce, so the colony can survive after the queen's death.


Is olfaction same among different individuals?

Humans generally have the same set up of olfactory receptors, since they are encoded by genes (there likely are minor differences between people, since there are a lot of these genes). Therefore chemically or physically  all humans can smell the same substances.
However, how a smell is perceived depends also a lot on how the brain reacts to a certain smell (or rather the activation of certain olfactory neurons). Therefore individual people can perceive the same chemical substance a different way - how different depends probably strongly on previous experiences.


I recommend the DESeq2 tutorial at:

http://www.bioconductor.org/help/workflows/rnaseqGene/

I think this is a good start for you because:

DESeq2 is a very popular package. You'll learn how exactly a bioinformatician works.
The workflow starts from alignments, and show you how to connect command-line tools with the R-package
It shows you how to generate MA plot, PCA plot etc. You'll appreciate how easy to do such things in R.
Testing for differential gene expression is very important
You'll learn how R does the programming. For example, in R it's a good idea to create a data set object, and do something like this:

obj <- .... # This is my R-object
obj <- fun1(obj) <- # Function 1 adds information to the object
obj <- fun2(obj) <- # Function 2 adds more information to the object


Synaptic connectivity in the newborn's brain

I wonder if in a newborn's brain the areas where learning will take place are equally weakly connected by synapses (so the pathways will be "built up") or are equally strongly (maximally) connected (so the pathways will be "carved out") or something inbetween. Or are there areas of both/all kinds?

According to a paper authored by Princeton researcher Deborah Sandoval:

  At the time of birth, the human brain consists of roughly 100 billion neurons in the cortex (The University of Maine, 2001). During the early stages of development (between infancy and adolescence), the weight and size of the brain increases significantly (by up to a factor of 5). This increase in density is not contributed to the creation of a large number of new neurons (neurogenesis), but rather an exponential increase in synaptic growth, known as exuberant synaptogenesis (Huttenlocher & Drabholkar, 1998). At infancy, each neuron averages around 2,500 synapses, and at the peak of exuberant synaptogenesis (around 2-3 years of age) the number increases to around 15,000 (The University of Maine, 2001).

..

  Shortly after this period of synaptic growth, the network experiences a decline in synaptic density as neuron connections that are used least-often are removed from the network. The process of eliminating/weakening the irrelevant and inefficient synapses during this developmental period is known as synaptic pruning. Synaptic pruning has been viewed as a learning mechanism, where the “pruning” or removal of a synapse is dependent on the neurons’ responses to environmental factors and external stimuli (Craika & Bialystokb, 2006). The processes of synaptogenesis and synaptic pruning in the developmental stages of the brain have been associated with an individual’s “critical period,” a time where an individual is highly receptive to environmental stimuli and, therefore, learning (Drachman, 2005).

Given the claims in those passages, it would seem that learning (for infants) takes place by initially developing an extremely large number of neuronal connections (most likely due to massive information exposure), and then selectively prunes synaptic sites due to a lack of various external stimuli keeping those axons/dendrites/synapses active; the remaining connections are then reinforced (continously excited). So, as you put it, it would seem that the infant brain both "builds up" and "carves out" neuronal connections for the sake of learning.

To further support this idea though, consider the following fMRI images that depict the functional connectivity of an infant's brain for the first year of life. (Function Connectivity of the Infant Human Brain)

Pay special notice to the coloration differences between rows, within a given column, for the infant (first five rows). With dark red being least functional, and bright yellow being most functional, it can easily be seen that, as the infant gets older (is learning), occurrences of yellow tend to form as clusters within regions of red, which indicate locations of highest functional network activity.

If you then continue this pattern and compare the most functional regions belonging to the 12 month infant scan, with that of the adult (bottom-most row), you can see that the concentrated yellow regions in the infant scan become the general (red) functional regions in the adult scan. This only further suggests that those initial, yellow-denoted functional regions (belonging to the infant), matured into the even more dense, functional regions of the adult brain, through the process of pruning unnecessary connections (which creates smaller functional regions), while at the same time increasing signaling strength amongst neighboring neurons (synaptogenesis).

Lastly, to assess the initial strength of each neuronal connection for an infant brain: when looking at the 1-month old scans, it appears that most all regions of the brain have a color that falls within an associated numerical range of .4 to .8, which would suggest that the brain, as a whole, begins at an almost "neutral" state.


All else being constant, velocity of the Venous blood will be reduced.

The Flow-Rate Equation: Q=AV

Q = Flow Rate
A = Area (of the "pipe")
V = Velocity of the Fluid

If we assume that the body will try to maintain a constant Q, then an increase in the A of the Arteriole means a reduced V to compensate and a corresponding drop in Venous fluid velocity.

If we start to assume that things are not constant, then the story becomes more complicated. Since Venous pressure is largely maintained by musculature and other actions, not heart contractions (though the system is essentially closed-loop), an increase in Arteriole flow-rate doesn't always correspond to an increase in Venous flow-rate. When there is an imbalance - either due to mechanical interference or something else - conditions like subcutaneous edemas can occur where the interstitial (between-tissues) fluid builds up enough to cause discomfort or damage.

*Normal Disclaimer: I am not a medical professional. The above us based upon an Undergraduate level of knowledge.


What is a selectively neutral genotypic change?

Mutations in DNA or RNA sequences do not necessarily result in significant changes in the functions of the proteins they encode (or in the case of RNA ribozymes, ribozyme function ). This is because, for a variety of reasons, the change in DNA/RNA sequence may not significantly alter the structure and function of the ribozyme/protein (the function that contributes to the fitness of the organism). If two alleles of a gene with different sequence have equivalent function (again with regard to the function of the gene that provides fitness) the differences between them are selectively neutral.

The neutral network consists of every variation in the sequence of the gene that can be reached from another sequence (of equivalent fitness) by a single base pair mutation (these aren't the only type of mutation, possible, but they are common and more likely to be neutral than more drastic changes). So for example (using an unrealistically short sequence), if I had a gene with the sequence  0 AACAATGCTGACTGA, and alleles 1 AACAATGCTGACTAA, 2 AACAATGCTGACAGA, 3 AACAATGCTGACTGG with equivalent function, 1, 2, and 3 would be directly linked to 0 in the neutral network as they all differ from 0 by a single base pair. The sequence 4 GACAATGCTGACTAA if of equivalent function would also be in the network as it differs by one base pair from sequence 1.

Each gene in the network being mutually accessible through mutations means that I could start out with any of the above sequences and reach any of the others through a series of single base pair mutations that traverse the network (i.e. I could mutate 0 into 4 by first mutating to 1, another network member, then to 4).

The genotypic space includes the sequences of all extant alleles of the gene. This paper suggests that there is a tendency for these sequences to form these networks and especially to evolve towards highly interconnected networks. This is the structural information the author refers to. It should be easy to imagine how this might confer robustness to deleterious mutation. Let's think about our sequences from above, imagine if every sequence was only linked to two other selectively neutral sequences forming a long chain. The sequence AACAATGCTGACTGA is 15 base pairs long with 45 possible single mutations, if only two of those are selectively neutral, the chance of mutating to a neutral network member is low, and even if you do hit on a neutral mutation, your chance of hitting another neutral mutation next time (reverting back or moving on down the chain) is still only 2/45. Now imagine that the neutral network is highly interconnected, with sequence 0 linked to sequences 1, 2, 3 and several other neutral 1 base pair changes, imagine those sequences are linked through each other by other neutral intermediates (being 2 base pair mutations away from 0). Not only is the chance of a single mutation being neutral higher, but subsequent mutations (remember that these include reversions from prior mutations) are more likely to stay within the network (you're more likely to come back around to 0.

Would you have more long-term success walking around a fitness plateau or walking across a fitness rope suspended over the abyss?


Why are Taurine and Arginine essential components of the feline diet?

From the Taurine Wikipedia article:

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

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

I could not find anything particularly special about Arginine as opposed to other EAA's for cats.


What is Luc Montagnier's research on electromagnetic signals from DNA about?

I think that ymar poses an excellent set of questions that should be discussed on these forums.  It brings back memories (sic) of the memory of water controversy.
I'll quote from Andy Coghlan's excellent article published in New Scientist in 2011
Draw your own conclusions.  (The emphases are mine).

... So what have
Montagnier and his team actually found? Full details of the
experiments are not yet available, but the basic set-up is as follows.
Two adjacent but physically separate test tubes were placed within a
copper coil and subjected to a very weak extremely low frequency
electromagnetic field of 7 hertz. The apparatus was isolated from
Earth's natural magnetic field to stop it interfering with the
experiment. One tube contained a fragment of DNA around 100 bases
long; the second tube contained pure water.
After 16 to 18 hours, both
samples were independently subjected to the polymerase chain reaction
(PCR), a method routinely used to amplify traces of DNA by using
enzymes to make many copies of the original material.
The gene
fragment was apparently recovered from both tubes, even though one
should have contained just water (see diagram).
DNA was only recovered
if the original solution of DNA - whose concentration has not been
revealed - had been subjected to several dilution cycles before being
placed in the magnetic field. In each cycle it was diluted 10-fold,
and "ghost" DNA was only recovered after between seven and 12
dilutions of the original. It was not found at the ultra-high
dilutions used in homeopathy.
Physicists in Montagnier's team suggest
that DNA emits low-frequency electromagnetic waves which imprint the
structure of the molecule onto the water.
This structure, they claim,
is preserved and amplified through quantum coherence effects, and
because it mimics the shape of the original DNA, the enzymes in the
PCR process mistake it for DNA itself, and somehow use it as a
template to make DNA matching that which "sent" the signal

I always knew there was something suspect about genetics!  Stick to biochemistry, that's what I say :-)


Menstrual cycle and luteinizing hormone (LH)

Luteinizing hormone (LH): A hormone released by the pituitary gland in response to luteinizing hormone- releasing hormone. It controls the length and sequence of the female menstrual cycle, including ovulation, preparation of the uterus for implantation of a fertilized egg, and ovarian production of both estrogen and progesterone. Theca cells in the ovary respond to LH stimulation by secretion of testosterone, which is converted into estrogen by adjacent granulosa cells. In women, ovulation of mature follicles on the ovary is induced by a large burst of LH secretion - the preovulatory LH surge. Residual cells within ovulated follicles proliferate to form corpora lutea, which secrete the steroid hormones - progesterone and estradiol. Progesterone is necessary for the maintenance of pregnancy, and, in most mammals, LH is required for continued development and function of corpora lutea.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3136063/


Can a human be made with ovum but without sperm?

Nice question! It is actually very difficult to do so because humans, obviously, are far more complex than some animal species which naturally show parthenogenesis. Just to mention, there are female-only animals also present in nature, such as New Mexico whiptail, which reproduce only by parthenogenesis, meaning that it is not as impractical as one might think.

There have been many parthenogenesis tests on mice and monkeys, but they usually result in abnormal development. This is because mammals have imprinted genetic regions, where either the maternal or the paternal chromosome is inactivated in the offspring in order for development to proceed normally. A mammal created by parthenogenesis would have double doses of maternally imprinted genes and lack paternally imprinted genes, leading to developmental abnormalities. It has been suggested that defects in placental folding or interdigitation are one cause of swine parthenote abortive development.

During oocyte development, high metaphase promoting factor (MPF) activity causes it to arrest at the metaphase II stage until a sperm fertilizes it. The fertilization event causes intracellular calcium oscillations, and targeted degradation of cyclin B, a regulatory subunit of MPF, thus permitting the oocyte to proceed through meiosis. The most precise and exact mechanism is not known yet.

But this does not mean that it is not possible. Actually, it has been done quite a few times; once on June 26, 2007 by International Stem Cell Corporation (ISCC), and once (controversially) on August 2, 2007 by Hwang Woo-Suk. Even the procedure for parthenogenesis (in swine though) in lab is available. To initiate parthenogenesis of swine oocytes, various methods exist to induce an artificial activation that mimics sperm entry, such as calcium ionophore treatment, microinjection of calcium ions, or electrical stimulation. Treatment with cycloheximide, a non-specific protein synthesis inhibitor, enhances parthenote development in swine presumably by continual inhibition of MPF/cyclin B As meiosis proceeds, extrusion of the second polar is blocked by exposure to cytochalasin B. This treatment results in a diploid (2 maternal genomes) parthenote Parthenotes can be surgically transferred to a recipient oviduct for further development, but will succumb to developmental failure after ≈30 days of gestation.

The major problem with parthenogenesis in humans is the abnormal development of embryo. This has been accounted by a phenomenon known as genomic imprinting. Genomic imprinting is the epigenetic phenomenon by which certain genes are expressed in a parent-of-origin-specific manner. For example, if the allele inherited from the father is imprinted, it is thereby silenced, and only the allele from the mother is expressed. The death of diploid parthenogenetic or androgenetic mammalian embryos is determined by the absence of expression of the genes of imprinted loci of the maternal or paternal genome, which leads to significant defects in development of tissues and organs. How this exactly works is not known yet, but it is supposed that it evolved to prevent parthenogenesis. Bi-parental reproduction is necessary due to parent-specific epigenetic modification of the genome during gametogenesis, which leads to non-equivalent expression of imprinted genes from the maternal and paternal alleles. Thus, genomic imprinting seems to be ineffective during normal reproduction.

As a side note, in the article you refer to, the researchers did not just mix two sperms and produce diploid zygote or something like that. In the procedure, they injected a normal sperm to the above explained abnormal embryo, which later on proved to be viable. They, thus, showed that these kind of embryos can also become viable if they get fertilized by a sperm within time.

References:

Abnormal development of embryonic and extraembryonic cell lineages in parthenogenetic mouse embryos; Karin S. Sturm, Margaret L. Flannery, Roger A. Pedersen
Parthenogenesis - Wikipedia
Patient-Specific Stem Cell Lines Derived from Human Parthenogenetic Blastocysts; E.S. Revazova, N.A. Turovets, O.D. Kochetkova, L.B. Kindarova, L.N. Kuzmichev, J.D. Janus, and M.V. Pryzhkova
Genomic imprinting is a barrier to parthenogenesis in mammals; Kono T.
Genomic Imprinting and Problem of Parthenogenesis in Mammals; E. S. Platonov
Mice produced by mitotic reprogramming of sperm injected into haploid parthenogenotes;
Toru Suzuki, Maki Asami, Martin Hoffmann, Xin Lu, Miodrag Gužvić, Christoph A. Klein & Anthony C. F. Perry
Stem cell fraudster made 'virgin birth' breakthrough; Silver lining for Korean science scandal; 3 Aug 2007, Christopher Williams


How do I improve expression using the GAL1 promoter in S. cerevisiae above the "leaky" level I'm currently seeing?

There are a couple of things that are strange here. First, you have low expression in the presence of galactose. The GAL1 promoter is really strong, so that strikes me as odd. Even if it was leaky, induced vs uninduced should be night and day. However, you should keep in mind you still may not be able to see it by eye. Second, it is weird that it would be leaky in the presence of glucose (or dextrose, in your case). The glucose should not only prevent the promoter from activating, but it should actually repress it.

A few potential fixes that come to mind:

1) Check your strain genotype. Some strains do not have gal4, the transcriptional activator of the GAL1 promoter, so if you don't have this, the system will not work in your strain. Likewise, you may not have an intact UAS, which would make the repression fail. Other issues may also arise which may make a strain unsuited for this system.

2) Sequence your promoter/gene. It is kind of a pain, but if you have a mutation in your Gal1 promoter, this could be the reason for all your problems. Also check the UAS, as this would create repression problems. Finally, check if the gene itself is inserted in the place you think it should be, if you got some recombination mishap this may be the problem. The appearance of an extra band at a low molecular weight makes me suspect this may be an issue.

3) On that note, try picking a different clone. Maybe you got unlucky and the colony you picked had a defect, and a different colony will be what you think it is.

4) If you haven't already, make fresh stocks of your galactose and glucose media. Maybe you got impurities or some other issue in your media, and therefore what you think you are giving the cells is not what you are giving the cells.

Anyway, that's all I got. Good luck!


Why would decrease in amount of proteins cause Edema?

Proteins in the blood (esp. albumin, because it's the most abundant one there) cause fluid to come from the interstitial space into the capillary. This phenomenon is called oncotic pressure. On the other side there is hydrostatic pressure on the vessel wall, which causes fluid to exit the capillaries. This hydrostatic pressure gets lower as the blood passes through the capillary, while the oncotic pressure stays the same, because under normal conditions, proteins don't exit the capillary very much compared to their amount in blood.

In the first part (closer to the arteriole), hydrostatic pressure is bigger, so the fluid exits the capillary site, while as you get closer to the venous site, the hydrostatic pressure gets lower than the oncotic pressure and the fluid flow is reversed. (see picture)

If you lower the amount of proteins in the blood drastically (as in Kwashiorkor) the oncotic pressure is lower and therefore less fluid is reabsorbed from the tissue, which leads to its accumulation there - this results in edema.

  Why doesn't it occur in Marasmus (which is both protein and energy deficiency)?

Sometimes, both features of kwashiorkor and marasmus are present in the patient, which is called marasmic kwashiorkor and the distinction between these two conditions isn't that easy.

However, normally in marasmus, there is also dehydratation present, which balances the effects of decreased oncotic pressure. Cardiac output is usually decreased too, which leads to decrease of hydrostatic pressure, so again, this can counterbalances the decrease of oncotic pressure.


Identifying a lone bone found newar Rowena Crest, Oregon (USA)

My guess is that it's a relatively young cow humerus. The strongly grooved trochleas are more characteristic of a humerus than a femur, which usually just has two condyles. The deep pit is where the olecranon process (your bony elbow) goes. The proximal end is missing, which indicates that the growth plate was not fused, suggesting juvenile.

And I guess cow because cows are very common and have robust bones compared to other artiodactyls.

Here's an image pulled from the web:


Can two populations of the same species pollinate during different times?

Yes, they can.  Consider an original population that produces pollen over a fairly long time, and then something happens to select earlier & later times for different populations.  This is actually quite common for domestic plants such as fruit trees, where different varieties are selected (by humans) to produce fruit at different times.

As far as the question itself goes, it's more a case of the other answers being either obviously wrong, or not supported by the information in the question.


How can neurons divide without centrioles?

You talk about memory loss. The hippocampus is involved in the formation and storage of memories and indeed one of the few places in the brain where new neurons are formed. The formation of new neurons here is indeed linked to the formation of memories (Coras et al., 2010).

Hippocampal neurons do not lack centrioles (Dotti & Banker, 1991; Poppov & Tsygunova, 1996). In fact, centrioles may not be necessary for cell division to occur (source: BSCB), although the lack of centrioles in cell models may result in aberrant cell division (Rodrigues-Martins et al., 2008).

In the hippocampus, however, it is not the neurons themselves that regenerate, but rather the resident neural stem cells and progenitor cells (Kirby et al., 2014).

References
- Coras et al., Brain (2010); 133(11): 3359-72
- Dotti & Banker, J Cell Sci (1991); S15: 75-84
- Kirby et al., PNAS (2014); 112(13): 4128–33
- Poppov & Tsygunova, Neuroscience Letters; 203(2): 135–8
- Rodrigues-Martins et al., Cell Cycle (2008); 7(1): 11-6


Looks like a six-spot burnet (Zygaena filipendulae)

Diurnal moth of the Zygaenidae family.

Description:

has a wingspan of 30–40 mm (1.2–1.6 in)...The fore wings are dark metallic green with six vivid red spots (sometimes the spots are merged causing possible confusion with other species such as the five-spot burnet). Occasionally, the spots are yellow or even black. The hind wings are red with a blackish fringe. The larva is plump and hairy with variable markings, usually pale green with rows of black spots.

Habitat:
meadows, woodland clearings, sea-cliffs and rich, grassy/flowery areas.
Range:
common throughout Europe, June - August.
Sources:
wikipedia


How are we able to find the specific sites at which DNA binding proteins bind?

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

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

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

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

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

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

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

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

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


Since RNA viruses and retroviruses all have high mutation rates, why do only a few viruses have the virtue of variability?

The high mutation rate is only a small part of the reason it's hard to make vaccines against those RNA viruses.  The real problem is not that they mutate rapidly, but that they can tolerate high levels of variation in their antigenic regions without losing fitness.  Viruses like polio and measles, as you say, have mutation rates easily on a par with influenza or HIV, but when they mutate antigenically significant regions, those new viruses are much less capable of infecting and transmitting between hosts.  Vaccines therefore either block the virus replication altogether, or force them into a much weaker form that is much less infectious.

Why do some viruses tolerate antigenic changes better than others? It's not known, but presumably there has been selection for it in those lineages.


Difference between "transcriptional activity" and "RNA expression"

In your case, RNA expression and transcriptional activity probably differ in the stage of processing. Transcriptional activity refers to the binding and processive activity of RNA polymerase. There are different ways to measure this experimentally, but with a microarray you are measuring the amount of actual transcripts relative to the control array.

RNA expression usually refers to the amount of mature transcripts but is often used interchangeably with transcriptional activity. The distinction is made at the sample extraction stage and whether or not the RNA was selectively recovered using poly-A selection or other methods that isolate mature transcripts.

What your microarray will measure depends on the probe library constructed on the array and whether you are applying total RNA or selective RNA. Probes matching mature transcripts report for RNA expression. Probes matching immature or nascent transcripts can be used to measure transcriptional activity.

Careful probe design is required to distinguish between the different levels of processing.


What's superposition and thread in RosettaCM?

Threading:
Start with a homologous protein. This protein can be thought of as two parts: (1) a backbone conformation and (2) a sequence of amino acids attached to the backbone. Threading occurs when you switch out the amino acids to those of your protein with unknown structure, but do not change the backbone conformation.
I believe the origin of the term is like beads on a string. The "string" does not change (the backbone geometry stays the same) but new "beads" (amino acids) are threaded onto certain positions.
The definition of superposition you found online is the correct definition for RosettaCM.


Can a small polypeptide fold over itself and have a tertiary structure?

Your instinct is valid, there are other molecules which can be defined as having tertiary structure.

The most common example is RNA, which can fold into a vast array of conformations. These can be part of ribonucleoprotein complexes like telomerases, spliceosomes, or ribosomes or they can function on their own like tRNAs and many ribozymes such as RNase P. An example of a common tertiary structural motif in RNA is the pseudoknot; a haripin loop in which some of the bases in the loop have base paired to another portion of the RNA molecule.

It is also possible for DNA to possess tertiary structure, though the term is used less often when referring to DNA. Usually DNA tertiary structure describes topological structures formed by supercoiling, protein scaffolding, etc. However, DNA can also form cruciform motifs similar to RNA hairpin loops (though it is less common). If multiple cruciform motifs and other structures were to interact in three dimensions, this could be another form of DNA tertiary structure.

You may also be interested in DNA origami, in which 3D building blocks made from DNA are assembled in desired ways by using sequence complementarity (generally).

I think that polysaccharides and oligosaccharides are also sometimes referred to as having tertiary structures, but I don't know as much about those. I encourage you to look into pectin, amylopectin, branched oligosaccharides, etc in the context of tertiary structures.


Yes they excrete uric acid which is stored in the allantois of the embryo; which acts as a reservoir of nitrogenous waste.

Uric acid is not very soluble in water, so it stays as a small solid mass.


In my view, thinking of entropy as something biological life has "wants" about is a bit mistaken. In general, entropy arguments regarding biology run into a major problem in that the interesting physical laws involving entropy required closed systems, and no biological system is closed, so it's a bit moot.

It makes more sense to think about what benefits "fighting against entropy" gives a biological organism, and I also think it makes more sense to think in terms of potential energy rather than entropy (even though they are of course related).

Neuronal signaling is best when it's rapid. By pumping ions against their gradient ahead of time, neurons establish a concentration gradient (which you can view as a decrease in entropy). This is indeed the active part. This also stores energy in the gradient, in that if a 'gate' were opened, the gradient would tend to equilibrate. Because the ions involved are charged, additional sensors in the membrane can respond to this changing electrical gradient.

  I would have hence found it more intuitive if signalling would be acquired by an active decrease in entropy (followed by some sort of "passive" restoration)

I think you might be mixing up the "action" verbs here. Think about pushing a rock up a cliff or lighting a firework. If you want that rock to be a signal, it's going to be a much more dramatic signal falling down the cliff than it was pushing it up the cliff. It's going to be much more dramatic lighting off the firework rather than extracting the needed ingredients from various places and assembling them. Processes that release stored energy tend to be a lot more dramatic and "active" despite being "passive" in terms of needing to add energy (besides activation).


Will the sex ratio of chickens become favourable to females?

Any chick has a mother and a father. Hence, the contribution to the gene pool of the following generation comes at 50% from males and at 50% from females. As a result there is no selection for biasing the sex-ratio among its offsprings. The variance in reproductive success might be higher among males than among females but that does not matter for the sex-ratio.

This is known as Fisher's principle. In the terms of W.D. Hamilton (Extraordinary sex ratios), copy-pasted from wikipedia:

  [..] given the condition that males and females cost equal amounts to
  produce:

  Suppose male births are less common than female.
  A newborn male then has better mating prospects than a newborn female, and therefore can expect to have more offspring.
  Therefore parents genetically disposed to produce males tend to have more than average numbers of grandchildren born to them.
  Therefore the genes for male-producing tendencies spread, and male births become more common.
  As the 1:1 sex ratio is approached, the advantage associated with producing males dies away.
  The same reasoning holds if females are substituted for males throughout. Therefore 1:1 is the equilibrium ratio.

To my knowledge, only kin/group selection can yield a sex-ratio different from 1:1 to be an ESS.


During what phase is the cell polyploid?

I assume that you mean phase of cell division. First off all i will write down a definition of word polyploid. Polyploid is cell which has two or more pairs of homologus chromozoms. There are two basic types of cell division are meiosis and mitosis

Technicly you can say that in reduction meiosis when chromozomes go from diploity to haploid state (which is first anaphase in this process), but ussually polyplidy occure when something goes wrong in cell division.

The major cause of polyploidy is found to the non disjunction of sister chromatids during the meiotic recombination events. Prior to meiosis chromosome numver doubles followed by chromosome separation during gamete formation (anaphase).
Artificial generation of polyploidy have been found to be useful both in research as well as economic purposes. Colchicine, the chemical which inhibits formation of spidle apparatus is widely used.

Unfortunately colchicine is only used in mitosis. Result of this process is new cultivars of plant specious.


Is this arthropod non-intrusive and recommended to be left alive?

This appears to be a silverfish, a very common household "pest" in the Lepismatidae family of insects.

 Photo Credit: Dong-Hwan Choe. Source: UC IPM

Silverfish are silver/grey and (like all members of the Zygentoma order) have three distinct, tail-like caudal appendages from their posterior end -- really, two large cerci with a central long filament.
 [Sources: 1, 2, 3].

According to Wikipedia, you can find them all arround the world:

  Silverfish are a cosmopolitan species, found in Africa, the Americas, Australia, Eurasia, and other parts of the Pacific.[8] They inhabit moist areas, requiring a relative humidity between 75% and 95%.[9] In urban areas, they can be found in attics, basements, bathtubs, sinks, kitchens, old books, classrooms, and showers.[3]

They are relatively harmless due to their weak jaws [source], and their presence is typically a larger nuisance than the damage or disruption that they cause.

We have a number of posts already identifying silverfish and asking about management advice. Try yping "silverfish" into the Search bar at the top of the page to search for more information.


Is it possible to determine what tissue a DNA sample came from based solely on its sequence?

The answer is in the question but I suppose you wanted to ensure you were not missing some info.

Answer

The DNA sequence is the same in all cells of a multicellular organism. Only the expression pattern varies among tissues. It is therefore impossible to tell from the DNA sequence alone what tissue a cell come from.

It would be feasible by looking at the transcriptome or the proteome or eventually by looking at epigenetic modifications.

Potential exception

Of course, as you talk about CNV, if you consider that the number of chromosome is part of the info present in a DNA sequence, then haploid cells (spermatozoids and ovules) are an exception and you could tell them apart. Similarly anucleated cells would be an exception as they contain no nuclear DNA.

Further potential exceptions are explained by @tsttst in his comment.


Can Coronaviridae mutate into something as dangerous as Flioviridae?

Each existing virus can mutate until it becomes ready to affect new species, organisms, cells or whatever.

Coronaviruses too are capable of mutating, so they could become more dangerous.

But can coronaviruses (which cause respiratory tract diseases) mutate into filoviruses (which cause hemorrhagic fevers)?

Of course not.

Filoviridae and coronaviridae are two different families of viruses, like felidae and canidae are two different families of mammals, in the order carnivora.

And you would never ask if cats can mutate in dogs!


Why do skinny people live for shorter than the norm even though calorie restriction extends life expectancy?

This is an interesting point you raise, and as the study you linked to states, "the link between physique and life expectancy is not clearly understood," which is certainly true at the moment. The relationship between BMI and lifespan in humans is a very different story to controlled dietary restriction in model organisms.

Dietary restriction is defined as "undernutrition without malnutrition" [1], and by definition model organisms live in controlled environments. In contrast, humans have confounding factors that may reduce weight and health (for instance smoking status, early-life diseases, malnutrition, etc) that are not modelled in these experiments.

In addition, the relationship between BMI and mortality is complicated in older humans, known as the 'obesity paradox'; overweight and obese elderly hospital patients have a lower mortality risk than low-normal weight patients [2]. There are a number of hypotheses regarding this, but the favoured one appears to be that the association is not actually paradoxial, but that higher BMI only appears protective because losing weight is associated with many diseases of ageing, so after accounting for many of these confounding factors (e.g. dementia, cancer, etc) high BMI no longer appears protective.

Therefore the study you found only appears to be contradictory to the dietary restriction experiments; in human populations the situation is much more complicated. Additionally, there is conflicting evidence as to whether dietary restriction even works in primates [3], let alone in humans (the largest effects are observed in worms and drosophila).

Weindruch et al. The retardation of aging in mice by dietary restriction: longevity, cancer, immunity and lifetime energy intake. (1986) J Nutrition; 116(4):641-54
Yamauchi et al. Paradoxical association between body mass index and in-hospital mortality in elderly patients with chronic obstructive pulmonary disease in Japan. (2014) Int J Chron Obstruct Pulmon Dis; 9:1337-46
Maxmen. Calorie restriction falters in the long run. (2012) Nature; 488, 569


Why does a Urinary Tract Infection cause a strong, persistent urge to urinate?

Nerve endings exist in a more or less homeostatic interstitial fluid medium which when disturbed in certain ways result in depolarization. This is a very simple explanation, but basically correct. Depending on the nerves being discussed, a change in the medium can be the presence/absence of neurotransmitters (serotonin, GABA, etc.), chemicals released from damaged tissue, pH differences, etc. etc.

Very simply put, anything causing irritation of the bladder or urethral mucosa will cause some of the nerve endings to depolarize; these are some of the same nerves that depolarize when the bladder is full, and therefore the sensation is of urgency (the feeling that one needs to urinate). The substances can be substances excreted by bacteria, released by neutrophils, or some other.

Simply administering a topical anesthetic - something that decreases the depolarization of nerve endings by reversibly binding to/inactivating sodium channels - (lidocaine, for example) will instantly alleviate this sensation. In the case of UTIs, a commonly given medication is the bladder anesthetic phenazopyridine hydrochloride.

The more complex answer is that no one exactly knows. The complexity is more important in the treatment of non-infectious causes of urinary urgency and in the investigation of why catheter-related UTI are often asymptomatic.

Edited to add: If you're looking for a more teleological reason (such as, it hurts so that you'll get flush out the bacteria faster, that's not actually what happens. When it hurts to urinate, very many women intuitively stop drinking fluids in an attempt to avoid the pain of urination, allowing the infection to get much worse. The counterintuitive measure is to drink more, not less, to flush out bacteria.


Are there oligocellular organisms in nature and, if so, what are they like?

Various colonial and multicellular forms of cyanobacterial species are reviewed in:

Beardall, J et al. (2009) Allometry and stoichiometry of unicellular, colonial and multicellular phytoplankton. New Phytologist 181: 295-309

Nostoc and Volvox are some of the simplest true multicellular organisms known (usually 3-4 cell types), but in both cases the differentiated colonies (filaments in Nostoc, spheres in Volvox) typically consist of hundreds of cells.
The paper below reports the emergence of a colonial form of a unicellular organism. Since there is no evidence that the individual cells within a colony have specialised functions this doesn't really count as 'oligocellular' but it is an interesting angle on the question nevertheless.

Boraas, ME et al. (1998)Phagotrophy by a flagellate selects for colonial prey: A possible origin of multicellularity. Evolutionary Ecology 12: 153-164
Abstract: Predation was a powerful selective force promoting increased morphological complexity in a unicellular prey held in constant environmental conditions. The green alga, Chlorella vulgaris, is a well-studied eukaryote, which has retained its normal unicellular form in cultures in our laboratories for thousands of generations. For the experiments reported here, steady-state unicellular C. vulgaris continuous cultures were inoculated with the predator Ochromonas vallescia, a phagotrophic flagellated protist (`flagellate'). Within less than 100 generations of the prey, a multicellular Chlorella growth form became dominant in the culture (subsequently repeated in other cultures). The prey Chlorella first formed globose clusters of tens to hundreds of cells. After about 10-20 generations in the presence of the phagotroph, eight-celled colonies predominated. These colonies retained the eight-celled form indefinitely in continuous culture and when plated onto agar. These self-replicating, stable colonies were virtually immune to predation by the flagellate, but small enough that each Chlorella cell was exposed directly to the nutrient medium.


No, it is not possible. The problem is the fertilization which takes place near the ovary. It takes the new forming blastocyst about 4-5 days to wander through the fallopian tube to reach the uterus and 8-9 days in total to implant itself into the uterine wall. See the picture below (from the Wikipedia article on fertilization):

You would have to get the blastocyst out of the right fallopian tube, make sure it survives the procedure and then implant it into the uterus of a woman which is about in the same phase of their period (otherwise the uterus is not ready to allow implantation).
It is already hard enough to do in vitro fertilization where you can control the environment.


Conversion of ATP to NADH without creating a proton motive force?

I am not aware of any enzymes that both oxidize NADH and generate ATP.

However, in the absence of oxygen, many bacteria ferment ethanol and acetate (among other products) to oxidize NADH and produce ATP. ATP is produced by acetate kinase and NADH is consumed by dehydrogenases in the parallel ethanol secretion pathway. Together, these pathways consume (or more accurately, recycle) NADH and generate ATP.

http://mmbr.asm.org/content/69/1/124/F6.expansion.html


In the most basic sense you want to kill the most cancerous cells whilst minimizing the regular somatic cell death. Almost all cancer medications affect regular cells, too - though the better ones do so at a minimum whilst being effective. In reality, it's also nearly impossible to kill all of the cancerous cells. The goal is to bring them below detectable levels, which can allow the body to finish the job. Leaving significant amounts of cancerous cells alive won't do the patient any good - they'll just continue to proliferate and the patient will be back for more operations or treatments soon.

So, with the goal of minimizing benign cell cost and completely eradicating the cancerous line, on your crude chart that falls at about "4".