Differences between neurotransmitters and neuromodulators

Key points:

Neurotransmitters directly stimulate or inhibit ionotropic receptors (the receptors of ion channels) in the postsynaptic membrane within a single synapse.
Neuromodulators act on metabotropic receptors within or outside the synapses of many neurons at the same time; they modulate the release of neurotransmitters and excitability of ionotropic receptors; the signaling between metaboreceptors and ionoreceptors usually involves a cascade of secondary messengers.

Neurotransmitters

"Classical neurotransmitters" stimulate or inhibit the fast-acting ionotropic receptors of ion channels. Their actions last few milliseconds and are limited to a single synapse, which means they are released from a presynaptic membrane of one neuron and they target the postsynaptic membrane of one (or, sometimes two or maybe more) postsynaptic membranes of the neurons involved in the same synapse, or a single muscle cell or other target cell (Oxford Scholarship, The Revisionist).

Examples of neurotransmitters: noradrenaline, acetylcholine, dopamine.

Neuromodulators

Neuromodulators act on the slow-acting metabotropic receptors inside or outside the synapse of "thousands" of neurons at the same time. In long-term (minutes), they modulate the release of neurotransmitters and excitability of ionotropic receptors. They are usually (but not necessary) released from presynaptic membranes into the synapse by the same mechanisms as classical neurotransmitters but can then leave the synapse through "spillover" and act on the neurons other than those involved in the synapse. So, their action is diffuse, but usually still limited to to certain neural pathways. (International Encyclopedia of the Social & Behavioral Sciences, 2001, Encyclopaedia Britannica, Wikipedia, Current Opinion in Neurobiology)

Examples of neuromodulators: dopamine (D receptors), serotonin (5HT receptors), acetylcholine (M and nicotinic receptors), noradrenaline (alpha and beta receptors), histamine (H receptors), endorphins and neuropeptides (Wikipedia, Journal of Chemical Neuroanatomy, 2011.)

Neurohormones are released from neurons into the bloodstream and have a systemic effect, for example:

Oxytocin and vasopressin, which are produced in the hypothalamus travel to neurohypophysis from where they are secreted into the blood and act on the mammary glands and uterus.
Adrenaline, which is secreted from adrenal medulla acts, via sympathetic nervous system on various tissues, usually on the smooth muscles of the blood vessels, heart, gut, etc.

Can a certain molecule can be a neurotransmitter, neuoromodulator and neurohormone at the same time?

Yes, for example:

Noradrenaline acts as a classical neurotransmitter and neuromodulator in the postganglionic neurons of the sympathetic nervous system and as a neurohormone secreted from the adrenal medulla (International Encyclopedia of the Social & Behavioral Sciences, 2015)

Dopamine acts as a classical neurotransmitter and neuromodulator in the dopaminergic pathways in the deep areas of the brain, such as thalamus and pituitary gland (picture); as a hormone, it inhibits the secretion of prolactin from the pituitary gland.

Are both neurotransmitters and neuromodulators stored in and released from vesicles by similar mechanisms?

Yes or no. Neurotransmitters are always released into the synapse, while neuromodulators may or may not be released into the synapse (Oxford Scholarship).

Do both neurotransmitters and neuromodulators get effective by interacting with receptors and affect if a ligand-gated ion channel opens or not?

Neurotransmitters can be effective if the ligand-gated ion channel are open and neuromodulators can open or close the ion channels.

Since the same molecule can be both a neurotransmitter and neuromodulator, it may not be that important to define the differences between the both in detail:

  It could, therefore, be concluded that the aspect of defining
  neurotransmitters has taken a back seat to the investigation of the
  actions of individual signaling molecules. (International Encyclopedia of the Social & Behavioral Sciences, 2015)


At what point do scientists consider something sentient vs random and/or genetic?

if you have 300 neurons and 10 of them can put you in a depressed state, you are a sad eukariote.

To compare the logic gates of a worm and a mouse? which one is sentient? a slug literally has 10k neurons and a fly has 250k. that would make a slug 25 time sless sentient than a human, and a dog less sentient than a human, but a human is equally as sentient as a dog so numerically there may be now lower bounds.

Logic Gates are electronic switches which provide routing for AND/OR/NOT/EQUALS of data types, or objects. They come into existence when you have the first cilia and sensory cells. 20 nerves are a signal routing engine, logic system.

A neuron can roughly represented by 4-8 transistors, and a logic gate is a simple transistor routing/instruction, so a worm has about 2000 logic gate equivalents. https://en.wikipedia.org/wiki/List_of_animals_by_number_of_neurons

A logic gate is digital, a brain is analogue, no software, , so you inadvertantly weave smoke and mirrors to clarify your question.

The question evokes electrical sentience, synapses are electrochemical, slower than electricity and can varied in many ways chemically, and they are self organizing.

feeling, aware and knowing (reductionism of sentience) are much more debated topics in science. Relative to random and genetic logic gates for intelligence, that's unclear and you are discussing free will and decision (philosophy), intelligence has unclear relation to sentience/emotion.

Your question is confusing a vast range of scientific measures by using the term sentience, which is rarely used in science. Scientists write informally about sentience as an ethical issue based on their experience, but there's only fringe research on animal sentience. https://scholar.google.fr/scholar?hl=en&as_sdt=0%2C5&q=sentience+fish&btnG=

Animal psychology is a scientific topic, and sentience is metaphysical, it means feeling, aware and knowing, it's incommensurate and imprecise.

So scientists don't consider there to be such a point of sentience. They measure certain markers of sentience, such as

self awareness,

stress response,

emotional queues,

counting,

comparing,

memory,

puzzle solving,

social behaviour,

hormones, that kind of thing.

There are perhaps a 2 publications about sentience in fish, none about lizards or insects, and there are thousands of books and opinions about sentience in insects and other animals.

The brain increases in size from a dozens to billions of neurons. So the progression is in stages, so awareness is likely to be a complex series of steps.

A good animal psychologist can give you an entire book about the onsent of emotions and knowing in animals.


Limited space for animals - how is that bad?

The building of a bridge on a river seems like an example of habitat fragmentation. There are a number of reasons why this may be detrimental to the animals.

Reduced resources available. I'm not too familiar with dolphins, but all animals need food, shelter and a place to raise their young. A smaller habitat can't support as many animals due to limited resources.
Isolation from other habitats. The bridge may cut off the dolphins on one side of the bridge from the other side, meaning they can't mate with dolphins on the other side or migrate. The fact that dolphins on one side of the bridge can only mate with the other dolphins that share that size causes a decrease in the genetic variability on both sides of the bridge. Decreased genetic variability means an increase in inbreeding depression and reduced ability to adapt to disease and environmental changes.
The edge effect. This means that areas next to the edge of the habitat (i.e. next to the bridge) will be even less suitable than they were before


Is Natural Selection like a Copy Editor?

Evolution, in the Darwinian sense, can be broadly described as the interaction of three processes: inheritance, mutation and selection.

Of those three processes, mutation is the one that produces novel innovation, by occasionally producing new alleles that did not exist in the parent population.  It is, however, a blind innovator — the novel genotypes produced by mutation are essentially random, and no more likely to be advantageous to the organisms carrying them than one would expect by change (i.e. not very likely at all).

Selection, whether natural or artificial, is what happens when the organisms carrying the diverse genomes produced by mutation end up competing for survival and reproductive opportunities against each other and against their environment.  It acts on the diversity generated and replenished by mutation, favoring those mutations that happen to confer a survival advantage.

Finally, inheritance ensures that the beneficial alleles generated by mutation and filtered by selection get passed on to successive generations, allowing them to spread in the population and to be further modified by successive mutations.  In a sense, inheritance and mutation can be seen as opposite sides of the same coin: the more faithfully genes are inherited, the less mutations there are.  Yet both are necessary for evolution; an organism that never mutates obviously could not evolve, but neither could one that mutated so much that all of its genes were totally scrambled in each generation.

Of course, this whole process is stochastic in nature — even the best adapted individual may die without offspring due to simple bad luck, just as even a maladapted individual may get lucky and prosper.  But over generations, there is nonetheless a statistical tendency for individuals carrying certain alleles, or combinations of them, to be more fecund than others, and those will be the alleles that will eventually come to dominate the population (assuming they're not it turn displaced by even more successful mutants).

Thus, I would personally say that, of these three components of evolution, (natural) selection indeed "works only with what is already present in a population."  However, it's not really like a copy editor, since it does not seek to "correct errors" in the genome; it's more akin to a slush reader, who just sorts the incoming texts into ones to keep and ones to throw away.


I think the answer to this one is a most definite 'yes'.  Almost all aminotransferases proceed via a ping-pong mechanism where a schiff base involving pyridoxal phosphate is an obligate intermediate, and where  the 'half-reation' modified enzyme form has often been isolated. An example is aspartate aminotransferase.

Let's also remind ourselves that a transition state is not an intermediate on the reaction pathway (in the TS bonds are in the process of being broken and formed), but may resemble one.


How do nutrients get to the cells they need to get to?

Broadly speaking, nutrients that enter the blood from the gut, and those that are released into the blood by the liver, are available to any cells that require them. So there is no "guiding to the correct location" in the sense that you suggest.

Lipids for example are present in the various lipoproteins and can be acquired from these by all cells. Iron is bound to transferrin, and any cell with transferrin receptors can internalise the transferrin and take the iron. Glucose is available in solution in the plasma, and free fatty acids are bound to serum albumin in the blood. During starvation the liver produces ketones ("ketone bodies") which are taken up by many different tissues/cell types.


What could cause a forest of bent trees?

The phenomenon in question is probably related to geotropism.

If the hill soil is "on the move" it will cause the bend on the trees -

  If the soil in a slope is moving downward, the trees on this slope
  will tip downward.  As the tree continues to try to grow upward, the
  trunk will show a curve. The degree of bending could indicate the rate
  or amount of movement of the soil.

source


You are almost right. I modified you picture a little bit to answer it:

Structure I is indeed DNA, structure II is processed RNA.
This is because in I you see loop structures which have no complementary part in the RNA anymore, these are introns (structure Q and the flanking loop regions to P). P is an exon flanked by two introns.
The end of the RNA is not complementary to the DNA because the poly-A tail has been added here.

The DNA is eukaryotic since you have introns and exons (which are not present in bacteria) and since the processed RNA contains a poly-A tail (which is also not present in bacteria).


Validation by PCR of a lowly expressed gene in microarray

If it was detectable in a microarray, the odds are very good for RT-rtPCR. If you are designing your own primers, make sure they span an exon junction, or if the gene is intronless, then span the UTR to exon junction to avoid amplifying DNA.


The Nightman is giving you a headstart to understand and read about nail colour.

I would like to add a different view to this question from "Colour and Pathology" point of view. Finger nails have been an excellent source of evidence for the initial physical diagnosis process. Nail colour and texture can be an indiator for a wide range of medical conditions.

You may take a look at this link : The hand in Diagnosis Process and discusses about nail pathology.. However this diagnosis gets a little tedious if the patient has colourfully painted their nails with nail polish...

I see many of the answers do include an image - well at the end it's anatomy.

Here's a relative simple and fun to read article to clarify any doubts you have about Keratin in nails being dead or not, for its colour and why it's tough.

  The cuticle and matrix are white because the melanocytes there are inactive, so there is no pigment produced. The matrix cells divide and the new cells produce a lot of keratin protein.

  The older cells fill with keratin and die, and the new cells push them out of the way – this means toward the end of your finger. This is how your nails grow.

  But our fingernail doesn’t look like individual cells. You are
   sloughing millions of skin cells each day, but for a nail the dead
   cells all mass together. Nails only wear away or must be trimmed.
   Individual cells are not lost. The solidity of the nail comes from the
   connecting of the dead cells together by junctions between the cells
   called desmosomes, and by the interlocking of the cells like jigsaw
   puzzle pieces. But there’s more.

  Individual keratin protein filaments also become connected so that the entire mass of keratin becomes one solid structure. This is called cornification, like the stratum corneum (the outer, dead layers) of your skin.

  One of the two main forms of keratin in your nails is crystalline keratin, which is rigid, stronger, and has an ordered structure - like a tinker toy cube. Transmitted light is less likely to strike an atom and bounce back when the atoms are all lined up, so this is why many crystalline lattices appear translucent.


Goats are so fearless but sheep are not. Is there any genetic difference responsible?

1. Sheep are fearless

2. English common names are misleading when it comes to the genetic differences between goats and sheep

You posted a picture of Mountain Goats (Oreamnos americanus), which are a different genus than Domestic Goats (Capra aegagrus). Both Capra and Oreamnos are members of the Subfamily Caprinae, as are Domestic Sheep (Ovis aries).

Within Caprinae, Capra and Ovis are actually more related to each other than either one is to Oreamnos, despite the confusing way that we parcel out English common names. Oreamnos is, in fact, more closely related to the Musk Ox! (Here's the Tree of Life page that shows the phylogeny of Caprinae).

The Domestic Sheep genus Ovis also includes mountain species such as the Bighorn Sheep Ovis canadensis, which is plenty fearless. See the Bighorn Sheep above, and in this incredible photo. For what it's worth, the Domestic Goat genus Capra also includes cool mountain species, such as the Ibex.

Edit: the differences in behaviour between the domestic goat and sheep would be a combination of the initial differences between wild Ovis and Capra and the coevolutionary process of domestication; where humans shape niches to fit animals and animals to fit niches. It's possible that there has been more neotenization in the domestication of sheep, in which individuals who show immature characteristics are successfully selected for. See also this other question on apple and pear domestication.

(Bighorn Sheep photo by TwelveX, used under CC BY-NC-SA license.)


What is Colloidal biology and does it have any scientific background?

There are two antipodes: The molecular (or makromolecular) biology, which has the concept of large macromolecules which fulfill one task. This can for example be an enzyme which breaks down its subtrate. The properties and the structure of all molecules of the enzyme are the same and the factor determining the function of the enzyme.

The coloidal biology assumes that the function is granted by adding small amounts of an enzyme to water to form a colloid, which thenchanges the properties of the water in the way that it does break down the subtrate. Life was also explained as the sum of the functions of the colloids building the body.

This theory came up in a time when macromolecules and their functions where not very well understood. The better understanding of macromolecules rendered this theory irrelevant. This is also neatly sumarized in the conclusions section of the article you cite.


Phenoptosis, behavior evolved for good of species?

I don't really have an opinion on whether or not this is the main or even a reason for the evolution of senescence and death, but it is certainly not nonsense.

Death can indeed be good for a species. Diversity is always good and the death of the elders allows phenotypes that have been selected for more recently to take hold in the gene pool. If the young need to compete with the old, this will make it harder for them to grow and reproduce. In situations with a limited food supply, having to support old individuals who can no longer forage/hunt for themselves will be a strain on the species/society/pod or whatever it is we are looking at.

Therefore, genotypes that encourage the death of elders who are past the age of reproduction could be selected for. This does not contravene the selfish gene hypothesis at all, these individuals have already reproduced, the selfish gene no longer 'cares' about them. The main idea of the selfish gene hypothesis is that the genes themselves 'want' to be passed on, not that the genes 'want' to save themselves. Once their host has reproduced, they loose interest so to speak.

The selfish gene theory is just a conceptual tool, it should not be taken literally. It does not suggest that genes are actually selfish or in charge of their own evolution in any way. It is just a useful approach to take when studying evolution and was instrumental in our understanding that the gene (the nucleotide actually) and not the individual is the smallest unit of selection.

Anyway, in the strictest sense, the statement in your question is absolutely compatible with the selfish gene hypothesis. If you can no longer pass your genes along, you are useless and just a drain on the species, why should you keep living?


iodine: how did they manage without it in old ages? (People who were living far from the sea)

Iodine is naturally found in sea water and soil but it is not evenly distributed, with many areas in the world with low levels of iodine. Iodine accumulates naturally in fish, and plants growing in iodine-rich soil. Mammals that eat these plants get iodine from them, which then accumulates in the milk, making dairy and its products (e.g. cheese) another natural source of iodine. Table 1 from the Iodine deficiency section at the American Thyroid Association web page contains a brief list of iodine-rich food.
Quoting the web site:

What are the sources of iodine?
Iodine is present naturally in soil and seawater. The availability of iodine in foods differs in various regions of the world. Individuals in the United States can maintain adequate iodine in their diet by using iodized table salt (unless they have to restrict the amount of salt in their diet), by eating foods high in iodine, particularly dairy products, seafood, meat, some breads, and eggs, and by taking a multivitamin containing iodine (see below). However, the amount of iodine in foods is not listed on food packaging in the U.S., and it can be difficult to identify sources of iodine in foods.

As mentioned, the amount of iodine in some food depends on how much iodine is present in the water or soil. For example, in the International Council for the Control of Iodine Deficiency Disorders (ICCIDD) there is some mention about the natural sources of iodine and its limitations:

Most of the iodine we consume comes from what we eat and drink. Seafood is usually a good source because the ocean contains considerable iodine. Freshwater fish reflect the iodine content of the water where they swim, which may be deficient. Other foods vary tremendously in iodine content, depending on their source and what may have been added. Plants grown in iodine-deficient soil do not have much iodine, nor do meat or other products from animals fed on iodine-deficient plants. Because the breast concentrates iodine, dairy products are usually a good source, but only if the cows get enough iodine.

Iodine deficiency causes important health problems. Iodine is necessary to produce thyroid hormones. Lack of thyroid hormones causes hypothyroidism, cretinism and goiter. However, iodine deficiency is not mortal per se.
Conclusion
As a consequence, in the Middle Ages iodine deficiency was not an issue in places where water and/or soil was rich in iodine. In other places they would suffer of iodine deficiency, leading to a higher impact of the related diseases.
Nowadays, iodine is added artificially to food in order to prevent iodine deficiency. This practice has diminished the impact of iodine deficiency-related diseases. However, iodine deficiency is still an important issue today, as reported by the World Health Organization in its map describing the Degree of Public Health Significance of Iodine Nutrition. As shown in the map, in many places in the world there is still risk of severe iodine deficiency.

Sources:

Iodine deficiency - Wikipedia
American Thyroid Association
World Health Organization
International Council for the Control of Iodine Deficiency Disorders (ICCIDD)


If you look at the definition of a model organism as this can be found on the Nature Homepage, this clarifies quite a lot:

  An organism suitable for studying a specific trait, disease, or
  phenomenon, due to its short generation time, characterized genome, or
  similarity to humans; examples are a fly, fish, rodent or pig, whose
  biology is well known and accessible for laboratory studies.

So you want an organism, that:

can be bred in large numbers
has a sufficiently short generation time, so you can analyze several generations of it
is well characterized
sufficiently close to the organism you want to learn more about (mostly: Humans), so the findings can be transfered
can be mutated and has your gene/protein/etc. of interest
has been sequenced completely

Besides this general considerations, practical ones also play a role. If you don't have a fish facility on hand, you will most likely not start using zebrafish as your animal model.

There are certainly more requirements, see one of the references.

References:

Requirements and selection of an animal model.
Selecting appropriate animal models and strains: Making the best use
of research, information and outreach
Basic Principles in Selecting Animal Species for Research Projects


Is there a difference between any of these terms for proteins: "crystal structure," "NMR structure," "solution structure," and "complex structure"?

Depending on who you talk to (typically laymen and scientists who are not structural biochemists), the term "crystal structure" is frequently taken to mean "some determination of molecular structure, whether by actual crystallography or some other means".

For example, a graduate student is talking to her adviser, an immunologist, about the structure-function relationship between a certain viral capsid protein and the peptide antigens they are using to create families of antibodies to the virus. The adviser consistently refers to the recently-published "crystal structure" of the protein, even though the actual study was performed using a combination of NMR spectra obtained from solution, electron microscopy, and quantum mechanical computational chemistry modeling techniques, and no crystals were actually studied.

So, you probably want to talk to your teacher/professor and clarify what s/he is looking for. Most likely, if you're in some sort of undergrad or first-year graduate class, they're just looking for "structural determination" in general, but they may specifically be looking for those models that were generated using actual crystals, so asking is always best.

I should note that there are significant methodological and computational differences when determining structure via X-ray crystallography, various types of NMR, electron microscopy (with or without crystals as the target), so-called "complex" determinations, etc. Find a structural biologist to learn much, much more.


Expected number of SNPs in a sample of size `k`

Let $\theta = 4n\mu$, then $E(S) = \theta\sum\limits_{i=1}^{k-1}\frac{1}{i}$, assuming infinite sites model. This is indeed given by Watterson (1975).


Why do changes in preload not cause changes in end systolic pressure?

Preload is defined as the volume of blood that stretches the ventricle at the end of diastole. Therefore, when preload is increased, the end diastolic volume is increased. In simpler terms, there is more blood in the heart just prior to contraction. Even though there is more blood being ejected from the ventricle during systole (that is, there is an increased stroke volume), the increase in preload alone will not affect the end systole volume or pressure.

When preload is increased while afterload and inotropy are held constant, the cardiac muscle fibres will still shorten to the same length. This means that the end systolic volume is unchanged, therefore the end systolic pressure is unchanged. This is best visualized by a pressure-volume loop. On the first example on the diagram below, you can see that the end systolic pressure and volume at point 3 are unchanged with increased preload:

Since cardiac output is equal to the product of stroke volume and heart rate, with increased preload the cardiac output is increased due to the increase in stroke volume. The reason why the end systolic pressure is unchanged with the increased cardiac output is because the end diastolic volume is increased.


Why don't we develop immunity against common cold?

Long lasting immunity is obtained by means of the adaptive immune system, and mainly involves the development of antibodies that identify specific parts (epitopes) of the pathogen's proteins. Common cold is typically caused by a type of virus called rhinovirus. Viruses have very high mutation rates, which alter the sequence of the virus proteins, modifying their antigenic properties. This consequently alters the ability of antibodies to recognize a particular antigen.

In other words, we do develop long lasting immunity against the virus that causes us a cold today, but the virus that causes us a cold a few months later is somewhat different, and the adaptive immune system has to start from scratch.


When there is incomplete dominance of one allele, is one allele still considered recessive?

No - if we have a phenotype, in your case the tail, which we can measure and treat as a numeric variable, and if a heterozygote's phenotype is exactly half-way between that of the two homozygotes, the phenotype is considered not to exhibit. Dominance exists only when the heterozygote's phenotypic value lies closer to one homozygote than the other.


European hornet (Vespa crabro). In the Asian hornet, the black body bands are much wider and more uniform. For the European hornet, as in your specimen, the bands are thinner and appear as thin lines connecting triangular black dots. See this image for comparison:
https://www.sciencephoto.com/media/980933/view/asian-and-european-hornets-illustration


How can I save bacillus strains on filter paper without an -80 degree freezer?

Use agar stubs: pour some Nutrient agar (or any suitable agar medium) in a test tube (~10% of the tube volume) and punch your inoculum halfway into it using a pipette tip or inoculation loop. Store it in 4⁰C.

Glycerol stocks can be made and stored in -20⁰C also.


Literature about putative epigenetic state changes in mammal sequences after cloning steps in Escherichia coli

E.coli strains that have dam or dcm methylases can methylate plasmid at adenines or cytosines respectively. See here — It is a NEB web page but has links to the cited references.

DH5α has both the methylases- dam+ dcm+ , BL21 is dam+ dcm− and ET12567 is dam− dcm−


Could transfusion of a different blood type cure blood-based cancers?

No. When a different blood type is introduced in the body, the host immune system recognizes the foreign blood as non-self and attacks it. The transfused blood becomes useless, and the potentially massive immune reaction can cause shock, which itself can be fatal.

More details in the book Blood Groups and Red Cell Antigens, which can be found at the NCBI library.


The equilibrium constant $K$ is the quotient of the rate constants of forward ($k_1$) and backward reactions ($k_{-1}$) (for elementary reactions).

E.g., for an  equilibrium
$$\ce{A + B <=> C + D}$$
we get
$$\frac{[C][D]}{[A][B]} = K = \frac{k_1}{k_{-1}}$$

So,

If both rate constants are affected in the same way (multiplied by the same speed-up factor) so that the quotient doesn't change, then also the equilibrium constant does not change, no shifting, no change in Gibbs free energy.
That would be the case with your catalyst as that facilitates both forward and reverse reaction by lowering the energy of the transition state in the elementary reaction leading to just such a multiplicative increase in reaction rate - but no effect on the energy of educts or products (thus, no change in $\Delta G$).

This has an interesting link to the impossibility of constructing a "chemical" perpetuum mobile by use of a catalyst.
If the rate constant of either forward or reverse reaction (or both, but not by the same factor) change, the equilibrium shifts.
But, yes, that also means that Gibbs free energy has changed.
Thus, there must be a change in free energy of educts and/or products as the energy of the transition state does not affect $\Delta G$, it only affects the reaction rates.
Whether this is possible hinges on the question whether we consider it still the same reaction $\ce{A + B <=> C + D}$ or whether we say that now we have another equilibrium, say, $\ce{A' + B <=> C + D}$ or $\ce{A' + B' <=> C' + D'}$ which of course can have different equilibrium constants. An example where I think one may argue either way would be the dependency of equilibrium constants on solvent.
(And, btw, we still cannot build a perpetuum mobile: solvation energy makes the difference)


If a human takes antibiotics are all bacteria in the body killed?

No

There are several reasons why this might not be true, as Alexander has discussed. An antibiotic often has a molecular target that isn't present in all bacteria, it's extremely hard to get antibiotics to certain parts of your body, and some bacteria will be defended against a antibiotic attack by biofilms, resistance mechanisms, and sheer statistical probability.

That is not to say that many don't die. Indeed, one of the major causes of Clostridium difficile infection is that antibiotics kill most of your gut bacteria, allowing the somewhat better protected C. diff to proliferate, start producing toxins, and send you to the hospital with symptoms ranging from diarrhea to perforated colon and worse. That disease is a direct consequence of "Antibiotics kill some but not all bacteria in you".


Difference in reptile inner ear and otosclerosis

Good question. To understand it perfectly, you'll need a good reference to a text on detailed explanation of sound conduction by the ear ossicles in reptiles and humans. I couldn't find anything better than these here and here.

But these are partly inadequate in addressing your questions and are a bit involved in the physics used.
But, if we leave the physical details aside below is the possible reason as to why a single bone in case of reptile conducts just fine but in humans fails to conduct.
 The reptile ear has evolved such that it uses a single bone for conduction, while the human ear is functioning with three transmitting ossicles (the only example i could think of). This is similar to the working of a watch. You can create a time-keeping device by using a combination of three gears (old play watches) or a combination of a large number of gears (my Timex Retrogade). Both have the same function, but if we fuse several gears in the second case to equal the number in the first (hypothetically only), it will obviously stop working. In our analogy, the ear has evolved such that the sound is optimally transmitted due to several effects like, resonance, impedance, transformation and simple amplification along the ossicles, and all these functions depend very specifically on the shape and orientation of the various conducting elements of the system. And therefore, even a slight disfigurement might severely impair the conduction of sound. Therefore, had the human ear system evolved to work with one ossicle, it would have evaded osteosclerosis by being able to conduct with one ossicle also.


How long would you expect a designed plasmid to remain in a population of E. coli after transformation?

There isn't a simple answer.
There are a lot of factors which can influence how stable a plasmid will be. I'll describe what the main factors are, but to work out exactly how stable your plasmid is, unfortunately you'll just have to test it. I've given links to some studies which do this at the end.
Copy number
Copy number refers to how many copies of your plasmid are present in each cell. This can range from 1-10 for low copy number plasmids, to 300-500 for high copy number plasmids. Generally, low copy number plasmids can be lost easier than high copy number plasmids as there is a higher chance that the plasmid won't be present in one of cells after division. (https://www.nature.com/articles/s41598-017-05219-x)
Plasmid Size
Very large plasmids (in the mega base range) tend to be less stable than smaller plasmids as organisms, especially E. coli, can struggle to replicate them. This means that over time, less of the plasmid will be present in your system. (https://pubs.acs.org/doi/10.1021/acssynbio.0c00008)
Selection marker
Typically, synthetic plasmids will have a selection marker encoded which is used to provide selective pressure for keeping the plasmid. The exact marker used can affect the stability of the plasmid, as some are more effective than others. This paper has a good comparison of two different markers and measures the stability of plasmids for each: https://bmcbiotechnol.biomedcentral.com/articles/10.1186/1472-6750-8-61.
Burden
Plasmids normally contain an insert which encodes your system. Some inserts will have relatively low burden on the cell (for example low expression of a small protein). Others may involve high expression of many proteins, or proteins which are toxic to the cell. Mutations are much more likely in high burden plasmids compared to low burden plasmids. This is because cells containing plasmids with mutations which reduce/stop expression will have a much higher fitness advantage over those cells with unmutated plasmids. Other time, these mutated plasmids will become dominant and eventually you will lose your original plasmid. There's some good reading about cell burden here (https://2019.igem.org/Team:Austin_UTexas/Measurement) and here (https://pubmed.ncbi.nlm.nih.gov/25849635/).
This is anecdotal, but I've managed to run 24 hour experiments with plasmids about 5kb in size containing a low burden insert and without using any selection marker without seeing plasmid loss. I've also had trouble even cloning plasmids of about the same size but with antibiotic selection and a high burden insert without any mutations occurring. So it really does depend on what your plasmid is and what it's expressing.
Measuring plasmid stability
Here are some examples for how you can measure plasmid stability:

https://link.springer.com/protocol/10.1007/978-1-4939-9877-7_16
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3966108/ - This paper describes plasmid stability mathematically
https://academic.oup.com/femsle/article/232/1/45/490969


It looks to me like a male Argia fumipennis violacea


In my protein purification experience, affinity purification is the most selective purification strategy. This makes sense because affinity tends to be very specific, and only one protein should in theory be preferentially separated by the column. Think how specific the antibody-antigen interaction is compared to the differences in, say, charge between proteins (which could be very slight). When I was purifying proteins I would pretty much always start with affinity purification. If more purity was desired after the affinity purification step, I could perform salt precipitation or charge separation on the affinity-purified sample, which had already been cleared of major contaminants/nuisance proteins by affinity purification.


How is Na concentration re-established after action potential

Yes, there are Na-K pumps all over.

However, it is important to recognize that ion concentrations change very little during action potentials. The change in membrane potential is due to changes in ion conductances, very few ions actually flow. It is still necessary to maintain concentration gradients over many many action potentials, but the change in concentrations during the course of a single action potential is negligible.


Can a pyruvate reaction to acetyl coA be called as acetylation in any way?

Acetylation is defined as1:

  Acetylation (or in IUPAC nomenclature ethanoylation) describes a reaction that introduces an acetyl functional group into a chemical compound.

So, any reaction in which an acetyl (CH3CO-) group adds to another compound is an acetylation reaction. A common example is Friedel-Crafts acetylation reaction:

If the reaction is catalyzed by pyruvate dehydrogenase: In this case, first of all the reaction that you refer to is termed as pyruvate decarboxylation (rather than oxidation, although it won't hurt either). As @WYSIWYG has said in comments, it is not a simple reaction, it involves three steps (+ 2 steps for regeneration of complex), each catalyzed by different enzymes. The name given for the whole complex is pyruvate dehydrogenase complex (PDC)2. The steps involved are3:

The keto carbon of pyruvate reacts with the carbanion of TPP on E1 to yield an addition compound. The electron-pulling positively charged nitrogen of the thiazole ring promotes loss of CO2. What remains is hydroxyethyl-TPP.
The hydroxyethyl carbanion on TPP of E1 reacts with the disulfide of lipoamide on E2. What was the keto carbon of pyruvate is oxidized to a carboxylic acid, as the disulfide of lipoamide is reduced to a dithiol. The acetate formed by oxidation of the hydroxyethyl moiety is linked to one of the thiols of the reduced lipoamide as a thioester.
The acetate is transferred from the thiol of lipoamide to the thiol of coenzyme A, yielding acetyl CoA.

Now, pyruvic acid has the formula: $CH_3-CO-COOH$. So, if you look at the step C of reaction, then since CH3CO- has been added to coenzyme A, hence, in a way, it would be considered an acetylation reaction. Pay attention that the complete reaction will not be considered acetylation, only a part of it would be. This is also the reason why calling the complete reaction as oxidation won't hurt, because even decarboxylation is just a part of complete reaction.

If the reaction is not catalyzed by pyruvate dehydrogenase Taking the question out from pyruvate dehydrogenase (as you don't talk specifically about that), there is an enzyme Acetyl-coA synthetase whose job is catalyzing acetylation of coenzyme-A(!)4. The reaction looks like this:

$ATP + acetate + co-A \rightarrow AMP + pyrophosphate + acetyl-coA$

The enzyme is of two types: AMP forming and ADP forming5:

So, as long as the conversion is not one specifically catalyzed by pyruvate dehydrogenase, we can say that Yes, conversion of coenzyme-A to Acetyl-coA is an acetylation reaction.

References:

Acetylation - Wikipedia
Pyruvate Dehydrogenase - Wikipedia
Pyruvate Dehydrogenase and Krebs Cycle - Joyce J. Diwan; Rensselaer Polytechnic Institute
Acetyl-coA synthetase - Wikipedia
Hentchel KL, Escalante-Semerena JC. 15 July 2015. Acylation of biomolecules in prokaryotes: a widespread strategy for the control of biological function and metabolic stress. Microbiol Mol Biol Rev doi:10.1128/MMBR.00020-15


Looking for study/genome data for HIV in different organs

This website comes to my mind
https://www.hiv.lanl.gov/content/index
It is a HIV databases containing HIV sequence data and related immunologic information


In plant photosynthesis, in the light dependent reactions, why is 3 ATP produced per 2 H2O?

I remember being confused by the numbers when I first studies it primarily because most sources seem to differ on the stoichiometry. I have tried to explain why is it difficult to comment upon such large equations, hope it helps!

Short Answer

There are two faults in your assumptions.

The plastoquinone-cytochrome cycle actually pumps $2H^+$ per electron (terms and conditions apply)
ATP-synthase requires $\approx 4$ protons per ATP produced

So, 12 protons per 2 water molecules is what is pumped, which makes 3 ATP.

Full Answer

As you might notice, the above scheme does not account for many things. For starters, since the 4$H^+$ from water splitting are produced and not pumped, only 2 of those need to be pumped back via ATP-Synthase to restore equilibrium. So even if you account for the $2H^+$ consumed by $2NADP^+$, there is still something that doesn't quite fit. Furthermore, some sources also try to account for the acidity of the inorganic $Pi$ in the ATP-synthesis which will further allow for changes in the $H^+/e^-$ ratio.

Why the confusion?

Most of what we know of the stoichiometry is based on a conglomerate of experiments, beginning with experiments on isolated chloroplasts. As a result, some experiments give us some parts of the stoichiometry (we know that the $NADPH/ATP$ ratio is around $2/3$) and others give us the reactions. Often times, many possible reactions are proposed, from which, the ones which can best be integrated with results from different experiments are thought to represent the actual truth. But this process is often mangled with complications, unexplained patches in the theory and the like. Furthermore, biological processes often are stochastic and do not have perfect stoichiometries. This is all overlooking the actual disagreements between experiments (the $H^+/ATP$ ratio for the synthase had significant variations in different experiments).

Okay, so now what?

Don't loose hope. We do know quite a bit about photosynthesis. What we currently understand about photosynthesis (light reactions) is thus:

There are three distinct processes that can produce a chemiosmotic gradient of $H^+$.

a. Non-cyclic Photophosphorylation is the main method. This constitutes the popular Z-scheme involving a linear electron transport from water to the final acceptor $NADPH$, and this process pumps about $12H^+$ per $2H_2O$

b. Pseudo-cyclic Photophosphorylation which is basically the same as above, but the final acceptor is an $O_2$ molecule, with similar ratios.

c. Cyclic Photophosphorylation which allows for recycling an electron, that is, proton pumping without there being a final acceptor of electron solely by internal shuffling of the electron between different states (primarily involved Plastoquinone (Q) cycle. This can pump $2H^+$ extra for 1 electron.
The ATP-synthase is slightly different from that found in animal mitochondria. The number of protons per ATP depends on the rotational symmetry of the synthase. (details in the references below). Basically, initially, it was thought to have 12-fold symmetry (needing $12H^+$ per rotation, in which $3ATP$ is produced, hence $4H^+$ per $ATP$) but was later found to have 14-fold symmetry actually needing $14H^+$ for the observed $3/2$ ratio of $ATP/NADPH$.
The number of Photosystem 1 units(where the cyclic version operates) is more than that of Photosystem 2 units. This means, that cyclic photophosphorylation goes on simultaneously at these centres, and will account for the extra $2H^+$ required to meet the experimentally observed ratio (1 in every 5 electron is "recycled").

References

A good overall paper addressing all the main issues. Photosynthesis of ATP—Electrons, Proton Pumps, Rotors, and Poise; John F.Alle; Cell Volume 110, Issue 3, 9 August 2002, Pages 273-276
General resources on these reactions. Here, here and here.
Studies on the $H^+/ATP$ ratio.

a. Petersen, Jan et al. “Comparison of the H+/ATP ratios of the H+-ATP synthases from yeast and from chloroplast” Proceedings of the National Academy of Sciences of the United States of America vol. 109,28 (2012): 11150-5.

b. Watt IN, Montgomery MG, Runswick MJ, Leslie AG, Walker JE. Bioenergetic cost of making an adenosine triphosphate molecule in animal mitochondria. Proc Natl Acad Sci U S A. 2010;107(39):16823-7.
Old studies to illustrate the difficulty of explaining the results of many studies:

a. Function of the Two Cytochrome Components in Chloroplasts: A Working Hypothesis; R. HILL & FAY BENDALL; Nature - volume 186, pages136–137 (1960)

b. Photosynthesis by Isolated Chloroplasts; DANIEL I. ARNON, M. B. ALLEN & F. R. WHATLEY; Nature - volume 174, pages394–396 (1954)


A mutation is a change in the genomic sequence - this can either be in the DNA or for viruses also in the RNA which carries their genetic information. This can either happen due to external influences (chemicals, radiation) or internal (mistakes while copying the information) reasons. See the figure below which shows the principle:

DNA based lifeforms usually have pretty good proof reading functions which eliminate most mutations, as they are often causing problems. RNA based viruses (as the flu virus or the ebola virus) do not have a proof reading function which raises their mutation rate drastically. See the figure below, which shows the mutation rates of several organism groups (image from this paper):

These higher mutation rates indeed produce high number of mutated viruses which are different from the original form. This leads to a high number of viruses which are non-functional due to this mutations, but also to a few which are better adapted or look different due to this mutation. This can help in evading the immune system (when surface proteins of the virus change) or to adapt better to a host.
Since the number of viruses in an infected individual is very high (billions of viruses) it doesn't matter and the the mutations which are beneficial for the virus are positively selected for.

This can lead to difficulties in the production of vaccines when the proteins used in the vaccine mutate. Usually this is accounted for by using proteins for immunization which only mutate slowly or not (because their function is important and mutations disrupt it). For more information have a look at the following review:

RNA virus mutations and fitness for survival.


Does the palate truly house the sense of taste?

Anatomically speaking, the palate is the roof of the mouth, separating the oral cavity (mouth) from the nasal cavity (inner nose). While the palate may be sensitive to heat and spiciness (via the capsaicin receptor, for example), it does not contain any taste buds, which are located on the tongue, and are part of the taste-sensing system. The other part of this system, olfactory receptors, are responsible for sensing odors, and are mainly located in the nasal cavity, as well as partway down the back of the throat.

So, unfortunately, while your palate is figuratively the center of your sense of taste, in reality it has almost nothing to do with it.


How good is information transfer between the hemispheres of the brain?

Auditory information is routed to cerebral hemispheres via the brainstem and midbrain.  Structures in the midbrain receive information from both ears and combine it (including differencing it for spatial location) before sending the combined information on to both cerebral hemispheres.  Usually only the left hemisphere interprets the sound for language content, but it is doing so based on the sounds perceived from both ears.  The corpus callosum would not be involved in the hearing pathways.  So sound coming from the left ear should work as well as sound from the other if the perception level is adequate and not interfered with by sounds from the other ear.  It is likely the sound perception is somewhat better if both ears are receiving input from the source.


Hormones occur inside organisms as signaling factors, and arise from biological activities, the development or homeostasis of the organism.

Thus, they are considered neither biotic nor abiotic factors in ecology.

(Terrible analogy warning!) It's a bit like asking whether the wheel of a car is petrol- or diesel-based. It makes no sense!

Here's a helpful, comprehensive website.

Biotic (living) factors are living organisms in an ecosystem, that must share common resources or compete in a habitat one way or another. Abiotic (non-living) factors are things like temperature, wind, salinity, etc. that affect individuals or the community of an ecosystem.

As you can see, hormones are just one of many components of a living organism. They aren't living themselves. It's a silly question to ask, as I hope you can see now.


Can the activity of a specific gene in a cell artficially be increased?

There are technologies available for inducing higher (or lower) gene expression in cultured mammalian/human cells as well as in bacteria. The state of the art is CRISPR-mediated gene activation/repression, where you fuse a transcription activation domain to a Cas gene in a CRISPR-Cas system (usually Cas9), and provide a guide RNA to target genes of interest. This Cas gene is made "nuclease-dead" so that it can only target but not cut or degrade DNA (as opposed to natural CRISPR-Cas systems that do both), and serves to bring the transcription activation domain to your gene of interest, which leads to an increase in transcription of that gene.

Check out this paper for an earlier example of such a system in cultured cell lines. The field has advanced quite a bit since then, and people have successfully activated genes in mouse lines


Does sleeping fewer hours than needed cause common cold?

There have been some studies directly linking sleep deprivation to increased risk of catching a cold  ("Behaviorally Assessed Sleep and Susceptibility to the Common Cold Sleep". 2015;38:1353–9.).

Colds are caused by a family of viruses. There is pretty solid evidence that sleep deprivation has a significant weakening effect on your immune system. Given a weakened immune system, it would be more likely that you would catch a cold if you are exposed to one of the cold-causing viruses.


What contributes to the variation of protein sequence across different species?

I have found an acceptable answer for my question. Just post here if any interest in it. Pardon my English.

Source:

Nei et. al. 2010. The Neutral Theory of Molecular Evolution in the Genomic Era. Annu. Rev. Genom. Human Genet.

Evolution and point mutation cause the sequence difference of the same functional protein across species. Neutral theory of molecular evolution shows that speciation level of evolution is an accumulation of molecular level of neutral evolution. In neutral evolution, the mutation only occur at a scope of point mutation in sequence in the manner that the function of the protein is retained. Overtime, speciation occurs yet the function carried out by that specific protein is still necessary and is conserved across species. Difference in protein sequence of the same functional protein is the residuals of random point mutation.


How do omega-3 fatty acids reduce cholesterol at the molecular level?

I found this research paper (pdf) by D. Roger Illingworth, William S. Harris, and William E. Connor (Journal of the American Heart Association, 1984) that offers some help. Its abstract says:

Diets rich in omega-3 fatty acids derived from fish oils lower the plasma concentrations
of low density lipoproteins (LDL) and very low density lipoproteins in humans. The present study was designed to examine the mechanism(s) by which diets enriched in omega-3 fatty acids reduce plasma LDL cholesterol levels in normal subjects.

In the Dicussion part, you will find your answer:

Reductions in the plasma concentrations of LDL in human subjects consuming diets rich in long-chain omega-3 fatty acids from fish oils or omega-6 fatty acids from vegetable oils may be due to a reduction in LDL synthesis, an increased fractional rate of catabolism of LDL, or a combination of both... The present study indicates that the hypocholesterolemic effects of long-chain omega-3 fatty acids present in fish oils results from a reduction in the rate of LDL apoprotein B synthesis and that such oils do not stimulate the fractional rate of catabolism of LDL. These observations imply that the incorporation of omega-3 fatty acids into cellular or lipoprotein lipids does not enhance the rate of receptor-mediated catabolism of LDL as has been observed with omega-6 fatty acids in vitro.

I could not find a paper on its exact mechanism, so I'd rather say that the process is still not clear. Yet, as the paper suggests, the main effects of omega-3 fatty acids are reducing LDL synthesis and/or increasing fractional rate of catabolism (FRC) of LDL.
A similar article can be found here:

Omega-3 fatty acids have been shown to lower triglycerides, which are a type of fat in the bloodstream. Experts aren't sure of the exact mechanism. Omega-3 fatty acids may also slow down the growth of plaques in the arteries and reduce inflammation throughout the body.
A number of studies going back years have shown the benefits of fatty fish. In an important review of studies, researchers found that getting daily omega-3 fatty acids from fish oil could lower triglyceride levels by 25%-30%. The results were published in The American Journal of Clinical Nutrition in 1997.

BUT, I would also like to point out that the question itself "omega-3 fatty acids found in fish are a good way to prevent/reduce cholesterol problems" seems to be a matter of debate because of articles like this:

New data presented this week provide clues as to why eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA)--both components of omega-3 fatty acids--have differential effects on LDL cholesterol.
Presenting the results of the laboratory study here at the National Lipid Association (NLA) 2011 Scientific Sessions, senior investigator Dr Preston Mason (Brigham and Women's Hospital, Boston, MA) said that EPA is an inhibitor of lipid oxidation at normal and elevated cholesterol levels in the presence and absence of DHA, while DHA seems to have no real effect on lipid peroxidation. This trial was one of a number of studies that attempted to address the clinical question as to why LDL-cholesterol levels increase in patients treated with the triglyceride-lowering omega-3 fatty acids. In his trial, Mason et al compared the effects of EPA and DHA--alone or in combination with statins--on lipid peroxidation in polyunsaturated fatty-acid– and cholesterol-enriched vesicles.


I think I understand what your issue is here.

Often, in diagrams of lens systems and eyes, the diagram will only show rays parallel to the optical axis (see here). Although many optical systems are designed so they are optimal for this axis, off axis rays respond in a fairly predictable way too. This figure shows an off-axis point source, which focuses at a corresponding off-axis point on the other side of the lens.

So, there is "one focal point", as you say, for each position of the object relative to the optical axis. In optics we generally talk about a focal plane rather than a point, as the focal point only refers to cases of idealized point sources, lasers etc.

Now, the aperture (pupil) is a completely different matter. This provides a limit to how well an optical system can focus. When the aperture is small, it can focus really well, but not much light can get in. When it is large, the ability to focus is reduced but it allows one to see better in the dark (increasing the signal to noise ratio). Focusing requires all the rays from a source to end up at the same point on the retina/film, the aperture, when it is as small as possible "selects" only those rays that will end up focusing at exactly the right place (assuming the lens focuses to the right place, which it does not in the case of the short or long sighted). This selection cuts out a lot of the light, and often it is good to trade off the ability to focus for the amount of light. Without going into detail, this large aperture results in the focal ability of the optical being strongly dependent on how far away the object is (see this).

Your question is rather open ended, but I hope this is what you were getting at.


No, because temperature is a quantity related to the motion of molecules (or particles) in an ensemble (thus, kinetic energy) but such motion does not have a mechanism to transduce it into some form of useful energy for biological purposes. Chemical gradients are easily stored because of the highly specialized biological membranes (via specific ion channels, etc). Light (photons) can also be used via some proper transducers (photoreceptors), given that there is transduction into chemical energy (i.e. in photosynthesis). But there is no way to 'store' energy from temperature directly in biology because there is no transducer. Temperature differentials in purely physical applications exist, but there is no parallel for biology. All life forms depend heavily on chemical potential and physicochemical gradients, which is deeply rooted in the evolutionary history, you can find an interesting lecture on this topic here.


Manganese is part of the oxygen-evolving complex and is essentiell for the oxidation of the water to generate electrons, protons and oxygen. This is done by changing the oxidation state of the mangane from +2 to +4, as shown in the figure (from here):

These manganese atoms are the center of the reaction - important here are the different oxidation states they can take, other examples are copper (in tyrosinase for example) or iron (hemoglobin) which are also present in the active center of enzymes.
For more information see references 1 and 2.

Anoxygenic bacterial photosynthesis also needs metal ions in the bacteriochlorophyll, this is magnesium (as in the chlorophyll of green plants), the light harvesting complexes contain iron-sulphur complexes.
For a general overview see reference 3, for more detail on the reaction centers and their evolution, see reference 4.

References:

Where water is oxidized to dioxygen: structure of the photosynthetic
Mn4Ca cluster.
Reduction-induced inhibition and Mn(II) release from the photosystem
II oxygen-evolving complex by hydroquinone or NH2OH are consistent
with a Mn(III)/Mn(III)/Mn(IV)/Mn(IV) oxidation state for the
dark-adapted enzyme.
Bacterial Photosynthesis
Reaction centres: the structure and evolution of biological solar
power.


Are there animal species where some females have greater amounts of male-associated qualities than average males?

Spotted hyenas are a matriarchal society and female hyenas are larger than males. Also, female hyenas dominate males.


gene expression of tumor with different percentage of infiltrates

Consider that while a fair portion of your immune infiltrate will be T cells, that you can also have dendritic cells, macrophages, B cells, NK and NKT cells, and other cell types. I like to use this figure to demonstrate that fact, and also make note that the relative abundance of immune mRNA by cell type differs by indication (figure 1).

Source: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4852857/

Also consider that for T cell markers like CD4 or CD8, these are expressed by antigen-presenting cells, as well.


What causes the yellow and brown spots on our sour cherry tree?

The tree is most likely sick. Plant diseases take years to develop versus diseases in animals caused by either bacteria, viruses, or parasites. This is because the tree has thick cell walls that can be a huge barrier hindering viral infection. Another thing is that trees lack a circulatory system and rely on partial water pressure from the air to draw water from the roots up to the leaves.
Your tree might have a virus that is slowly killing it. Which insects are endemic to your region? We can deduce the virus if we know the main types of bugs living in your area.


What do the Clustal Alignment Symbols Mean?

From the FAQ for the Clustal-W2 program:

An * (asterisk) indicates positions which have a single, fully conserved residue.
A : (colon) indicates conservation between groups of strongly similar properties - scoring > 0.5 in the Gonnet PAM 250 matrix.
A . (period) indicates conservation between groups of weakly similar properties - scoring =< 0.5 in the Gonnet PAM 250 matrix.

Therefore the hierchy of conservation using these symbols is * (identical) > : (colon) > . (period).


Does the word "polymorphism" refer to the gene, the phenotype, or both?

The term "polymorphism" itself is more generally defined as "the quality or state of existing in or assuming different forms" (Merriam-Webster dictionary). So I guess semantically, it would be correct to say that there is polymorphism in a gene that can occur in different allelic variants, or polymorphism in phenotype because of variant traits (such as sexual dimorphism).

However, when biologists today speak of polymorphisms, often they refer to variations at the level of individual nucleotides (single nucleotide polymorphisms or SNPs; some people use the terms polymorphism and SNP interchangeably). These SNPs have become popular for genotyping and for correlation with a variety of diseases or other observable phenotypes.

And regarding the bonus question, I think "polymorphism in" is the most correct usage--it's definitely the most widely used. For example, you could say "there is a polymorphism in nucleotide 257 of..." or simply "there is polymorphism in nucleotide 257 of..." or even "nucleotide 257 of ... exhibits polymorphism".


Will omega 7 make it harder to produce high quality meat?

No. The only sure thing about omega-7 is that the suppliers are making money.

There's no evidence that it's doing anything more than just being an unsaturated fat in humans. This make it extremely unlikely that it would do anything after you put it through a pig.


Yes:

  That GH has an effect on glycaemic control is most evident from the abnormal glucose tolerance seen in acromegalics...

acromegaly is defined as abnormal growth of the hands, feet, and face, caused by overproduction of growth hormone by the pituitary gland.

Such an effect has been known for decades, which makes sense given how interrelated the axes are.  Although I think the best evidence is the fact that the side effects of growth hormone therapy says that Some patients have developed diabetes mellitus...


"Heterozygotic expection" - when heterozygote differs from both homozygotes, but homozygotes are similar

You question is a bit unclear, and I think there might be a couple of mistakes in your inequalities. However, I think you are looking for the terms Overdominance (also called Heterozygote advantage) and Heterosis (also Hybrid vigor). Both of these concepts imply that heterozygotes and/or hybrids have a phenotype that lies outside of the range described by the homozygotes (or, for heterosis, either parent or parent population).

Here is a section from "Genetic Dominance: Genotype-Phenotype Relationships" from Nature education - Scitable, which has a bit more information and a couple of references:

  In particular, the phenomenon known as overdominance occurs when a heterozygote has a more extreme phenotype than that of either of its parents. Indeed, in a few examples, a trait that shows overdominance sometimes confers a survival advantage in the heterozygote (Parsons & Bodmer, 1961).

You will find more information about overdominance and heterosis in any textbook on evolutionary biology, e.g. Futuyma's Evolution. There are also lots of relevant papers on the subject, and this one might be a nice example and starting point:

Frascaroli et al. 2007. Classical Genetic and Quantitative Trait Loci Analyses of Heterosis in a Maize Hybrid Between Two Elite Inbred Lines. Genetics 176(1): 625-644.


Does anyone have any TOPO directional cloning tips?

I have lots of experience with the TOPO TA kit which is very similar to the kit your using. Here's a link to the TOPO Directional cloning product page which shows a schematic of the enzymatic ligation.

From your comments, you said you have doubly-digested the PCR product. This is likely your point of failure unless you are absolutely confident that your enzymes work at blunt ended DNA (which I can almost guarantee does not work). Restriction digestion of PCR products will only work if there are at least a few bases on either side of the recognition site so that the restriction enzyme is able to "grab on" to the DNA. What you are mixing instead, is blunt-ended PCR product DNA + cohesive-ended vector. This will not work under any circumstances as is.

There is a simple solution.

Add 3'-A overhangs to your PCR product directly. The back of the TOPO manual tells you how to do this as well as many other sources. Ligate this using your TOPO kit to produce a shuttle vector that you can then doubly digest your insert out and gel purify it. Then you may ligate this purified, digested DNA with your previously digested destination vector.

Note that in my hands and in others in our lab, topoisomerase is unstable and has a short half-life. It is especially sensitive to temperature changes (warming from -20°C to 4°C) which you wouldn't expect since it is designed to work at room temperature. The vector is not affected, but without a working topoisomerase, the ligation step does not occur and the DNA does not transform.

As an aside: If you plan on doing more cloning in the future and need to replace the kit, I would recommend getting the basic TOPO TA cloning kit, clone your PCR product (with 3'-A overhangs) into the vector, transform, pick white/light blue colonies for screening then cut out from the TOPO vector (the shuttle vector) for downstream applications. The fact that it is directionally cloned or not into the TOPO vector is of no consequence unless it also happens to be your destination vector.


Can LSD in very small amounts increase mental ability?

The phenomenon you are referring to is called microdosing. It was brand-new in terms of research focus when you initially asked your question, and it is still a fairly novel and little-studied subject.

A lot of interest in this phenomenon stems from anecdotal evidence by microdosing users, who report beneficial effects. This is however not necessarily an indicator of neuroenhancing potential, since psychopharmacological agents are known to modulate subjective evaluations of performance more than constrained objective measures of it (compare tables 3 and 4 in this article, which does not discuss LSD or microdosing per se, but illustrates this psychopharmacological phenomenon).

Anecdotal findings regarding LSD are substantiated in an article, which found that microdosing LSD improved the self-reported mood of participants.
Additionally, this article showed an improvement of vigour (as per the POMS scale) at the highest dose.
This is, however, still not a behavioural effect, as POMS is a psychometric assessment method.
Still, this further substantiates the mood-enhancing effects beyond direct self-reporting.

Another article reported increases in creativity, focus, and well being, though again, it should be noted that all of these metrics were assessed using participant reporting, and not evaluated based on behaviour.

So to conclude, there is to date no convincing evidence that microdosing LSD improves “mental ability”.
There is however a growing amount of evidence that LSD microdosing improves mood, which in and of itself can be a desirable effect, and can further be argued to contribute to improved “ability” in more complex behaviours such as sustained deductive reasoning or social interaction.
Conjecturing from the first cited article on methylphenidate, modafinil, and caffeine, it is conceivable that a similar effect:

  In conjunction with results from neuropsychological testing we conclude that modifying effects of stimulants on complex cognitive tasks may in particular result from more reflective decision making processes. When not under time pressure, such effects may result in enhanced performance.

as the one seen with modafinil and methylphenidate could be present with LSD microdosing.
Appropriate data to address such complex evaluations is however very scant in general, and to date wholly absent for the emerging phenomenon of LSD microdosing.

TL;DR

No but maybe.


What is the water and fat composition of the human brain?

Whenever you see a percentage, you should think "Percentage of what?".  Not doing this is usually at the root of the trouble people get into with percentages.

The water and fat percentages mentioned in the question are certainly not percentages of the same thing.  The sources of the figures should make clear what the percentage is of, but non-scientific writing quite often fails to do this.

In the paper "Lipid composition of the normal human brain", there is a table giving percentages of water and lipids (fats), and at the bottom of the table it says:

  All values, except water, are expressed as a percentage of dry weight.

This is a common approach, as, for example in this table from a textbook the lipid percentages are also given as percent of dry weight. This is convenient because water is such a large part of most organisms, and also dry weight is what is usually measured in the laboratory.

Thus the water percentages you are seeing are presumably percentages of total weight, and the fat percentages are percentage of dry weight.  You can convert the latter to percent of total weight by multiplying by the dry percentage of the brain, which is what is left when you subtract the water percentage from 100%.

Thus, assuming say 73% of total brain weight is water, the 60% fat figure would translate to about 16% of total brain weight is fat.


The issue with Michaelis menten curves, is that they presume only one pathway the enzyme can act by. Therefore if an enzyme has multiple pathways the presumptions fail. An example of this is monoamine oxidase, (Ramsay, R. R., Olivieri, A. & Holt, A. An improved approach to steady-state analysis of monoamine oxidases. J. Neural Transm. 118, 1003–1019 (2011).) This paper has the enzyme specific kinetics for monoamine oxidase - the development of the models is incredibly complicated but if you look at the equations you can see how there are multiple pathways.

They also presume only one substrate, so multi-susbtrate reactions need to have the kinetics modified as such. For that the mechanism are: Ping-pong, ternary- ordered and random, all of which impact on the kinetics.If the concentration of the intermediate complex is presumed not to change with time, then another model is the Briggs-Haldane model, known as quasi-steady state kinetics.

Then there are the kinetic models for inhibition. Of which the michaelis menten, where the kinetics vary according to how the inhibitors binds. But as is seen with the above MAO paper, can vary depending on the pathways and binding affinities.  If an enzyme is irreversible then the kinetics also differ (Mcdonald, A. G. & Dublin, T. C. Enzymes : Irreversible Inhibition. 1–17 (2012). doi:10.1002/9780470015902.a0000601.pub2).

It is also worth noting, it is better to use non-linear regression to analyze kinetics as linearizing the data can lead to calculation errors (despite admittedly being the easier and clearer option).


A word that includes plants and fungi, but not animals

Short Answer
There is no such word that I can think of.
 Long Answer
Note: although fungi were once considered to be lumped with plants, such classifications fell out of favor 60+ years ago (or sooner). See here for a summary.
Nomenclature "dead ends"
Using the traditional taxonomic approach (including Woese's familiar 3-domain classification system)  will not provide the collective term you're looking for. Plants, Animals, and Fungi are all of the kingdoms rank in this system; the only higher rank than kingdom in this system is domain (in this case "Eukarya"), which would include all 3 kingdoms.
If we take a cladistics approach instead, we can investigate Phylogenetic nomenclature. This taxonomic approach lacks categorical ranks such as "kingdoms" and instead tends to use hierarchical group names based on nested ancestral synapomorphies. However, using this approach proves to be even less useful for finding the term you're looking for:

Generally ~6 (5-8) informal supergroups (sometimes called "suprakingdoms") have been recognized based on phylogenetic research. Importantly, 2 of these groups (i.e., clades) are the Opisthokonts (which include fungi and animals) and the Archaeplastids (which include plants). Since animals and fungi share a common ancestor more recently than plants, it's not possible to "lump" plants and fungi together without including animals (and a whole host of other organisms).
You can see a recent publication (Burki et al., 2020) discussing an even more recent proposed organization for classifying Eukaryotes that maintains this phylogenetic distinction and separation between animals/fungi and plants.

Comment on the usage of "flora"
FYI, "flora" has broader usage beyond plants. "flora" can also be used for fungi (e.g., search "fungal flora" on Google). In fact, in microbiology, "flora" (or sometimes "microflora") is used to describe microorganisms in/on a system/host, which would include fungi, bacteria, etc. (For example, see gut flora).
I don't think "flora" is what you're looking for. I think referring to "all plants and fungi" as "flora" is not clear and will likely not get across the meaning you intend without further annotation/clarification.
Other thoughts:
I momentarily considered if being sessile would be a possible trait to use for delineating these organisms the way you're trying since by definition animals are not sessile (at least not at all stages of their lifecycle). However, many "protists" are also sessile and therefore such delineation would not be exclusive to plants and fungi. Further, I'm not sure all fungi are in fact sessile (though I can't think of any reason why not).

The phrase "multi-cellular sessile organisms" is probably much more exclusive and encompassing, but probably not 100% perfect. (However, at the point you'd be considering such phrases, I'd just suggest sticking with "plants and fungi" :p).

Perhaps someone else can come up with something, but I couldn't think of any non-outdated ways to accomplish your goal off the top of my head.


What kind of event would cause the current Mitochondrial Eve to be replaced by a new one?

One possible scenario would be that a particular woman develops a mutation rendering her much more 'fit' (in the evolutionary sense) than her peers. For the sake of argument, lets take the very simplistic case of an X-linked recessive mutation causing the women who bear it to have say 10 children at each birth. If this mutation is then transferred to the offspring, it will very quickly spread across the entire population.

If this continues for a few generations, the crushing majority of the earth's population will be the descendants of that one woman who carried the original mutation, she would be the new mitochondrial Eve.

I want to stress that this is nothing but a very simplistic thought experiment. Such a mutation is i) very unlikely, probably impossible, ii) likely to render the carrying individual less fit rather than more as each birth would be exhausting, increasing the chances of dying during child birth.

Update:

I have specified that the mutation has to be X-linked and recessive. This means that it will only present a phenotype in women who are homozygous for it, women both of whose parents carried the mutation. This is because, as mgkrebbs very correctly pointed out in the comments below, otherwise her sons would mate with women who are not their sisters and their children would have the mutation but not her mDNA. If the phenotype is only expressed when the mutation is homozygous, only women whose mother carried the mutation (and Eve's mDNA) would show it and only then would a new mEve arise.


What is the genome size of Saffron (Crocus sativus)?

Neither NCBI nor Ensembl have a genome project listed for any crocus species, although individual ethidium bromide stained nuclei have been analyzed by flow cytometry, revealing approximately 11.4 pg of DNA per nucleus (warning, pay wall).

C. sativus is triploid, giving it a C-value of 3.8 pg which works out to a haploid genetic content of about 3.45 Gbp.

(full credit to canadianer for finding the Brandizzi paper)


Why are some protein sequences known but their 3D structure isn't?

Protein sequencing is a nicely constrained problem: you have a one-dimensional sequence of amino acid members, which come from a limited set of options (made a bit more complicated by post-translational modifications, but not much more so). Because it's one-dimensional, it's a problem you can easily solve by chopping up a protein into little bits, using mass differences between amino acids to understand their constituents, and determining the order from that distribution. If a DNA (or mRNA) sequence is known, it becomes even easier - you can skip the protein sequencing process and get the amino acid sequence directly from the nucleic acid sequence and the genetic code.
By comparison, protein folding is an absolute nightmare to solve for. Chemical bonds between amino acids are not rigid, they can bend and twist in all directions. The conformation of those bonds also depends not just on adjacent amino acids (as in a 1-D problem) but potentially on any other amino acid in the sequence (not to mention external influences..).
In a large molecule like a protein there is a massive massive degrees of freedom problem. From Wikipedia, describing Levinthal's paradox, bold mine:

In 1969, Cyrus Levinthal noted that, because of the very large number of degrees of freedom in an unfolded polypeptide chain, the molecule has an astronomical number of possible conformations. An estimate of 3300 or 10143 was made in one of his papers[1] (often incorrectly cited as the 1968 paper[2]). For example, a polypeptide of 100 residues will have 99 peptide bonds, and therefore 198 different phi and psi bond angles. If each of these bond angles can be in one of three stable conformations, the protein may misfold into a maximum of 3198 different conformations (including any possible folding redundancy). Therefore, if a protein were to attain its correctly folded configuration by sequentially sampling all the possible conformations, it would require a time longer than the age of the universe to arrive at its correct native conformation.

Now, of course that's not the actual process that proteins use to fold (they don't iterate through all possible combinations, they settle through an energy landscape where only certain intermediate conformations are realized), and we can use that in computational models to solve protein structures more quickly than the age of the universe, but it's still quite a slow process. Projects like Folding@home have aimed to distribute the computational load among unused processing power in devices around the world, including idle gaming consoles and personal computers, but there are many many protein structures to solve.
It's possible to get a general picture of protein shape using imaging techniques like X-ray crystallography or cryo-EM, and for some purposes these techniques give a lot of information, but these techniques are also by no means simple and can be prone to errors.


Can 12 mitotic divisions produce 6000 nuclei?

There are indeed some mistakes in that excerpt from Wolpert & Tickle. First of all, the blastoderm is not a syncytium, it is a cenocyte instead (have a look at my answer here). By the way, that's a wrong nomenclature used by all books on developmental biology I'm aware of... therefore, being so well established, that wrong nomenclature probably won't change anytime soon. We have to get used to it.

Back to the numbers:

The second mistake in that excerpt (also reproduced by most books on developmental biology) is the number of divisions: it's not 12, but 13. And that would give us 213, or 8192 nuclei. As you can see, that's more than the ubiquitous "6000" we see everywhere in the literature.

Now the question becomes inverted: what's the reason for the blastoderm having a smaller amount of nuclei compared to the expected number?

According to Miles et al. (2010), the number of nuclei depends on the size of the egg:

  The number of nuclei at the cellular blastoderm stage also changed in response to selection, with large-egg selected lines having more than 1000 additional nuclei relative to small-egg lines. This increase in nuclear number in larger eggs does not scale with egg size, however, as nuclear density is inversely correlated with egg length. (emphasis mine)

And the most important part of that paper, which addresses your (now inverted) question:

  After 13 mitotic divisions the maximum possible number of nuclei at the blastoderm stage is 213 or 8192 nuclei, considerably more than the classic value of ~6000 given in the literature (Zalokar and Erk 1976; Turner and Mahowald 1983). We found that cell number is not anywhere near constant at 6000 nuclei in the cycle 14 embryo, but rather is positively correlated with egg size. On average, our large-egg selected treatment had more than 1000 additional nuclei than the small-egg selected treatment, a difference that arose as a correlated response to selection for egg size. Yet, in comparing cell numbers in other (nonselected) lines and species, we conclude that cell number must not be entirely a consequence of egg size, but rather must itself be a genetically variable trait. For example, D. sechellia (mean cell number = 7448.7, some embryos approaching the 213 limit) and the Ind strain of D. melanogaster (mean cell number = 6569.1) have nearly non-overlapping distributions of cell number despite having almost identical egg length. (emphases mine)

Conclusion

213 (or 8192) is the upper limit when considering 13 divisions. The real number of nuclei is less than that and varies from blastoderm to blastoderm. The mechanical explanation for that smaller number is, probably, that some nuclei fail to divide.

Also, it's worth mentioning that, from the 14th cycle on, the divisions become asynchronous, that is, the nuclei do not divide at the same time: some of them divide faster and some of them divide slower, and the exponential 2n (where n is the number of divisions) for the total number of nuclei doesn't apply anymore (because, at a given moment, you have several different values for n).

Source:

Miles, C., Lott, S., Luengo Hendriks, C., Ludwig, M., Manu, Williams, C. and Kreitman, M. (2010). ARTIFICIAL SELECTION ON EGG SIZE PERTURBS EARLY PATTERN FORMATION IN DROSOPHILA MELANOGASTER. Evolution, 65(1), pp.33-42.


Why does the protection afforded by some vaccines last longer than for others?

The first thing I want to make clear is that, the B and T that "will only float around in circulation for a short period of time before dying and being replaced", are not the ones that have already learned to recognise a certain diseases (or vaccine) but rather the naive cells that haven't yet done so. This is also made clear later in the same answer you cited:

  As these injected protein sequences circulate through your blood they
  will eventually bump into a B or T cell that has a receptor that
  recognizes them. When this happens, the B or T cell will now start to
  divide and give rise to long lasting memory cells that express the
  exact same receptor and will therefore recognize the exact same
  protein sequence again in the future. These cells will float around in
  your blood for most of your life and make you 'immune' to the
  recognized pathogen.

In order to understand why some vaccines hold for your whole life, while some need a booster every few years we need to look at the life time or recycling of those memory cells, which stay in your body for much longer than the naive immune cells.

Now we come to the actual answer(s) to your question and there multiple  factors that (can) have an influence on this:

Initial strength of the immune response: Every vaccine (and/or disease) evokes an immune response with a different strength. Generally the stronger the first response is, the more memory cells will be created initially (those actually don't have correspond to the same molecular memory either, they might recognise different aspects of the vaccine/disease) and with more cells available it will take longer until none are left
Natural exposure: memory cells start proliferating when they encounter the molecule (protein/virus/bacteria) which they have 'memorised', if there is an acute infection they will do so a lot in order to produce a lot of antibodies against it. However, even a very small amount of virus/bacteria, that wouldn't actually make you sick, will allow induce them to proliferate and preserve their numbers. Therefore memory cells against a more common or prevalent disease should be more stable in your body, than ones against a very rare one.
There very likely more factors that either I or the whole scientific community don't really know about. Cellular systems and the immune system in generally are rather complicated ...


Will moth larvae pupate in response to food deprivation

Not officially an expert, but I have been watching clothes moths for years and haven't noticed any small ones, so dont expect early pupation. I would expect small pupae to give small moths (like with houseflies). I do see the hormone traps reduce population, but only with lots of them (2 per small room).


Your link that says "proven wrong" includes a hypothesis that Opabinia could have eaten trilobites during their molt, simply that it would not be able to eat through their armor (all the better reason to have armor).

The best evidence we are likely to have that trilobites had predators is that they have defenses; the fossil record is incomplete, and just because trilobites are well-preserved does not mean their predators must be. Unless other evidence surfaces for an alternative explanation, the simplest reason for why trilobites evolved armor is that trilobites with armor were protected from something and therefore selected for.

Injuries seen in fossil trilobites are similar to injuries from failed predation of modern related species (see for example Bicknell et al., 2018) and seem to be widely reported (Bicknell et al. 2018 cite a variety of other sources).

Bicknell, R. D., Pates, S., & Botton, M. L. (2018). Abnormal xiphosurids, with possible application to Cambrian trilobites. Palaeontologia Electronica, 21(2), 1-17.


Of course.

There is a famous set of experiments (Milner & Olds) in biology that basically started modern behavioral research in which a wire was inserted in to a rats brain allowing for direct electrical stimulation of the pleasure center. as long as the current continued the rats experienced extremely high levels of pleasure. To the point they were unwilling to engage in any voluntary behavior, including seeking food and water, even when right next to them if it would interrupt the pleasure. You could keep stimulating the pleasure center until the rats died of thirst.


Is it possible to get (an estimation of) reaction rates from the Michaelis constant?

$K_M$ is a ratio and for QSSA it is $\dfrac{k_{cat}+k_r}{k_f}$ and for equilibrium approximation it is $\dfrac{k_r}{k_f}$.

It is clear from the formula that you cannot obtain all the constants simulataneously. If you know two (in case of QSSA) you can get the third.


Are some virus loads introduced to human cell but never triggered?

There is viral DNA within our genomes. Embedded in the genomes of all vertebrates are the proviral remnants of previous retroviral infections. It is possible that some have conferred biological benefits.
Human endogenous retroviruses (HERVs) represent the proviral phase of exogenous retroviruses that have integrated into the germ line of their host. They are transmitted vertically through the germline and are thus inherited by successive generations in a Mendelian manner.
HERVs possess a similar genomic organisation to present day exogenous retroviruses such as human immunodeficiency virus (HIV) and human T cell leukaemia virus.
Although many are defective through the accumulation of mutations, deletions, and termination signals, some HERVs have been implicated in certain autoimmune diseases and cancers and might have a role in the etiology and pathology of disease.

Within humans, the most recently active ERVs are members of the HERV-K (HML2) family. This family first integrated into the genome of the common ancestor of humans and Old World monkeys at least 30 million years ago, and it contains >12 elements that have integrated since the divergence of humans and chimpanzees, as well as at least two that are polymorphic among humans.
Here we show that the HERV-K (HML2) family has increased in copy number predominantly via reinfection, and that the family has probably retained replication-competent and infectious members for >30 million years. We also present evidence for persistent reinfection by other ERV families within the human genome, and suggest that endogenous retrovirus families are often capable of extremely long periods of smoldering infection.

Long-term reinfection of the human genome by endogenous retroviruses
The viruses in all of us: characteristics and biological significance of human endogenous retrovirus sequences
Demystified . . . Human endogenous retroviruses


Do multiple axons innervate a single skeletal muscle fiber?

Until a better educated person contributes a more detailed answer, Hunt's article here from 1954 will likely be the best source,

  studies have shown that muscle fibres in the frog's sartorius are innervated in two major zones and most of the fibres receive motor
  endings at at least two regions along their length (Katz & Kuffler,
  1941). In this case a multiply-innervated muscle fibre may derive its
  several end-plates from the same motor nerve fibre. The possibility
  also exists that a muscle fibre may receive end-plates from more than
  one nerve fibre, i.e. polyneuronal innervation.

HUNT CC, KUFFLER SW. Motor innervation of skeletal muscle: multiple innervation of individual muscle fibres and motor unit function. J Physiol. 1954;126(2):293–303. doi:10.1113/jphysiol.1954.sp005210

He in turn references an article by Kats and Kuffler from 1941,

KATZ, B. & KUFFLER, S. W. (1941). Multiple motor innervation of the frog's sartorius muscle. J. Neurophysiol. 4, 209-223.

As those are both 70 years old, it is likely that more documentation has been produced, and that it could contribute to a competent answer to the question.


I think this question could basically be summarized as "What is apoptosis?"  I will attempt to give a brief answer to that question, answering the two aspects of the question along the way.

Apoptosis is at its root programmed cell death (PCD).  It is basically when a cell (healthy or not) dies so that it can be replaced.  It is happening all the time in multicellular organisms such as me, you, and the lion in the zoo.  Basically, it allows all the cells to be replaced as the tissues of the body grow.

For instance, as your skin grows, cells in the dermis are dividing to produce a new epidermal layer.  At the same time, cells on the outside are dying (at the stratum corneum) so that the skin does not grow infinitely and we aren't covered with 20 inches thick of skin by the ends of our lives.

The same thing is happening in, for instance, the liver.  As the liver cells split, old ones are also dying.  This allows us to rebuild the liver to its normal size after a surgery in which we remove a section of it.  We simply have to stimulate cell growth so that it counterbalances PCD (apoptosis) and the liver grows to its normal size.

Cell death is initiated, not by the DNA, but rather by caspase activity.  All cells have inactive procaspases which will destroy the cell as soon as they become active.  When what we call an initiator procaspase bonds with a procaspase within the cell, the procaspase is activated, and the signal is spread across the cell.  This initiator procaspase is usually triggered by a death receptor outside the cell.

More reading here


Can someone identify this species from the pea family?

The plant appears to be Medicago arborea. Common names include moon trefoil, shrub medick, alfalfa arborea, and tree medick. It is a member of the pea family Fabiaceae. The species is characterized by the woody stems, the leaves (three), and compressed, coiled seed pods.  See further description in the links below.  It is a native of the Mediterranean basin and apparently becoming rare in nature.

http://botanyphoto.botanicalgarden.ubc.ca/2015/09/medicago-arborea/

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


Streamside plant identification - Oregon

It's a plant in the family Ribes, which includes currants.

If it stinks when you crush the leaves, it is probably Stink Currant, or Ribes bracteosum, a plant found in the Pacific Northwest.

  Leaves are large, like maple leaves, sparsely hairy to smooth, with 5 to 7 lobes, stinky when crushed.  Flowers are numerous on mostly erect clusters; with white petals and brownish-purple to greenish-white calyces.  Berries are blue-black with a whitish bloom.

The leaf and berry are a good match. There are ~150 species, so it's a bit difficult.

It could also be Ribes acerifolium, or Maple-Leaved Currant.

  Shrub with spreading branches but no bristles. Leaves maple-like, 1–3 in. across, with 5–7 rounded, finely toothed lobes. Hanging stem of 8–12 greenish flowers, each less than 1/3 in. across with tiny red petals and stamen filaments broad at base. Berry black, coated with bluish powder. Grows from mid elevations to treeline in Cascade and Olympic mountains.

I could not find a photograph that was not copyrighted. The flower color was pinkish to brownish.

It's not a perfect identification, but it's closer than 'in the ballpark'. If you google "Ribes western Cascades", you'll see what I mean. :)


Why do Humans not produce Vitamin C like other mammals?

Humans do not produce Vitamin C due to a mutation in the GULO (gulonolactone oxidase) gene, which results in the inability to synthesize the protein.  Normal GULO is an enzyme that catalyses the reaction of D-glucuronolactone with oxygen to L-xylo-hex-3-gulonolactone.  This then spontaneously forms Ascorbic Acid (Vitamin C).  However without the GULO enzyme, no vitamin C is produced.

This has not been selected against in natural selection as we are able to consume more than enough vitamin C from our diet.  It is also suggested that organisms without a functional GULO gene have a method of "recycling" the vitamin C that they obtain from their diets using red blood cells (see Montel-Hagen et al. 2008).

A 2008 published study (Li et al. 2008) claimed to have successfully re-instated the ability to produce vitamin C in mice.

Simply as trivia: other than humans; guinea pigs, bats and dry-nosed primates have lost their ability to produce vitamin C in the same way.

References

Li, Y., Shi, C.-X., Mossman, K.L., Rosenfeld, J., Boo, Y.C. &
Schellhorn, H.E. (2008) Restoration of vitamin C synthesis in
transgenic Gulo-/- mice by helper-dependent adenovirus-based
expression of gulonolactone oxidase. Human gene therapy. [Online] 19
(12), 1349–1358. Available from: doi:10.1089/hgt.2008.106 [Accessed:
31 December 2011].
Montel-Hagen, A., Kinet, S., Manel, N., Mongellaz, C., Prohaska, R.,
Battini, J.-L., Delaunay, J., Sitbon, M. & Taylor, N. (2008)
Erythrocyte Glut1 Triggers Dehydroascorbic Acid Uptake in Mammals
Unable to Synthesize Vitamin C. Cell. [Online] 132 (6), 1039–1048.
Available from: doi:10.1016/j.cell.2008.01.042 [Accessed: 31 December
2011].


Insect identification: white spotted beetle

It is a longhorn beetle (Cerambycidae), most certainly from the subfamily Lamiinae (flat-faced longhorns). The overall apparence with a downward-pointing face, partially divided eyes, robust build and spined pronotum fits well with Lamiinae.
The beetle in you picture is very similar to species in the genus
Batocera, for instance Batocera rufomaculata (also called Mango trunk/stem borer), and the red spots on the elytra fit relatively well. This species is considered a pest on mango plantations in India and Nepal (Hill, 2008 and Insects in Indian Agrosystems), so it's probably not all that uncommon.

(picture from Insects in Indian Agrosystems, from the National Bureau of Agricultural Insect Resources.)
However, there are probably hundreds of species in Lamiinae found in India, and I cannot give you a certain answer.
The striped elytra with raised lines doesn't fit with the species I've seen in Monochamus (suggested in the other answers), so I don't think that is the correct genus.
References:

Hill. 2008. Pests of Crops in Warmer Climates and Their Control