Manipulation of gene expression using VP16 fusion and engrailed fusion to a transcription factor?

VP16 is a herpesvirus derived protein transcription factor, which activates the early genes of the viral infection cycle. The activation domain (AD) which is formed by the 78-amino acids from the C-terminal, can be fused to DNA binding domain of other protein transcription factors, such as GAL4, to make a hybrid protein that constitutively and strongly activates transcription, without the requirement of any ligands. VP16-AD interacts with TBP, TFIID, SAGA histone acetyltransferase complex, and PC4 (transcriptional coactivator positive cofactor 4) to drive transcription.

The engrailed gene, from Drosophila, is a transcriptional repressor.  When the repressor domain is fused to transcription factors, the fusion results in trans-dominant negative functions of the transcription factor (phenocopying loss of function mutations in the target genes).


How can we calculate the minimum sustainable number of the panda population?

Minimum viable population (MVP) can be predicted in two ways.

Computer simulations.
Population viability analyses (PVA)

PVA is considered generally more common practice by ecologists and without a reference to the 1600 panda population you mention, my guess would be that this is what they did. PVAs work well for endangered species prediction.

A typical example of PVA was carried out on an endangered species Fender's blue butterfly an endangered species (Schultz et al., 2003). However there is currently no scientific standard on how a PVA should be done.

Schultz, Cheryl B.; Hammond, Paul C. (October 2003). "Using Population Viability Analysis to Develop Recovery Criteria for Endangered Insects: Case Study of the Fender's Blue Butterfly". Conservation Biology 17 (5): 1372–1385.


How do changes in temperature affect body weight in humans?

You would see moderate weight gain in both subjects.

Since humans thermoregulate and aren't terribly "adapted" to any extreme for either very hot or very cold climates, anything outside of short range of temperatures will cause us to either sweat or shiver.

Sweating or shivering will cost kcals ("Calories", "Joules"), and the extra energy expenditure will keep the subjects' weights lower than they would otherwise be.

Once the subjects enter an environment where they no longer need to sweat, shiver, or basically maintain a wide gap between the outside temperature and their body temperatures (which is the real driver here - the difference between the two), they will no longer expend as much energy maintaining human body temperature.

How much energy are they saving? Not much. I wish I could find the article again, but you're talking an extra 50kcal or so an hour saved - or a few pounds until the energy required to maintain the extra weight reaches equilibrium with the energy saved.

There are a few assumptions built into the above, which sees the question as more of a physics-oriented hypothetical than real-world example. In reality you have some large complications - getting anything done in cold temperatures is going to require a much larger energy expenditure, as you're usually carrying 30-50lbs of gear to not freeze to death, for example. A person used to wearing a dozen kilograms of animal furs during their weekly routine would gain a lot more weight than hypothesized above if they suddenly entered a mild climate with similar food intake, but without the constant load on their muscles.


Safranin is retained, very much like Crystal violet, by the peptidoglycans in the cell wall. However, the main difference is the thickness of the peptidoglycan layers in Gram positive and Gram negative bacteria.

Gram positive bacteria, due to their thicker peptidoglycan layer, have a higher affinity to and retention rate of crystal violet. On the other hand, Gram negative bacteria, due to a thinner peptidoglycan layer cannot retain crystal violet as well and are more likely to retain safranin.


Why do red blood cells maintain Iron in the Haem group in the +2 (ferrous) oxidation state?

Q. “What problems (if any) arise when the iron is oxidised?”

  A. Haemoglobin will be converted to methaemoglobin which cannot bind oxygen.

To quote from the article on Methaemoglobin in Wikipedia:

  Methemoglobin (English: methaemoglobin) (pronounced "met-hemoglobin") is a form of the oxygen-carrying metalloprotein hemoglobin, in which the iron in the heme group is in the Fe3+ (ferric) state, not the Fe2+ (ferrous) of normal hemoglobin. Methemoglobin cannot bind oxygen, unlike oxyhemoglobin. It is bluish chocolate-brown in color. In human blood a trace amount of methemoglobin is normally produced spontaneously, but when present in excess the blood becomes abnormally dark bluish brown. The NADH-dependent enzyme methemoglobin reductase (diaphorase I) is responsible for converting methemoglobin back to hemoglobin.

The question also asks:

  “…the higher the oxidation state of the cation, the higher its
  polarising power… hence stronger the bond.So wouldn't
  iron in the Ferric state be able to bind with oxygen better…”

which can be transformed into:

  “Why can‘t methaemoglobin bind oxygen?”

The answer is chemically rather complex, but one thing you should be aware of is that in haemoglobin (and myoglobin) the oxygen Fe(II) is five-coordinated (as shown in the diagram below where Fe is black) and binds oxygen in the sixth position (to the right).

In simple terms, the electronic change in oxidation to Fe(III) causes a change in the geometry of the haem pocket such that oxygen no longer can bind (although now water can). This page elaborates the point, without providing a full chemical answer.

Footnote: Fe(II) or Fe2+ ?

Some readers may be wondering why I have referred to the ferrous state of Fe in haem as Fe(II) and not Fe2+ (which the Wikipedia entry uses). This is to avoid implying that there is an overall charge of 2+ on haem groups in haemglobin and myoglobin. Inspection of the structure of haem (above) will show that the formation of two covalent bonds to imidazole nitrogens has left haem with a zero net charge.


Heated Honey and HMF

In this paper, Studies on the physicochemical characteristics of heated honey, honey mixed with ghee and their food consumption pattern by rats, by Annapoorani, et.al.;International Quarterly Journal of Research in Ayurveda, 2010 Apr-Jun; 31(2): 141–146.doi:  10.4103/0974-8520.72363, the report finds a statistically significant increase in the compound hydroxymethyl furfuraldehyde (HMF).

The compound was studied by the National Toxicology Program of the U.S. Department of Health and Human Services in Mice and Rats and the results were published in a report dated June of 2010.

  5-(Hydroxymethyl)-2-furfural is formed when reducing sugars such as fructose and sucrose are heated in the presence of amino acids. 5-(Hydroxymethyl)-2-furfural is ubiquitous in the human diet and occurs at concentrations greater than 1 g/kg in dried fruits, caramel products, certain types of fruit juices, and up to 6.2 g/kg in instant coffee. 5-(Hydroxymethyl)-2-furfural also occurs naturally and has been identified in honey, apple juice, citrus juices, beer, brandy, milk, breakfast cereal, baked foods, tomato products, and home cooking of sugar and carbohydrates.

- NTP toxicology and carcinogenesis studies of 5-(Hydroxymethyl)-2-furfural (CAS No. 67-47-0) in F344/N rats and B6C3F1 mice (gavage studies).; Natl Toxicol Program Tech Rep Ser. 2010 Jun;(554):7-13, 15-9, 21-31 passim.

HMF is a breakdown product of Fructose, Glucose, and Cellulose (hexoses) and is found in many products, especially high fructose corn syrup, after heating, and is excreted in the urine. However, it has not been correlated to any diseases in humans (4). In the NTF toxicology and carcinogenesis studies, the conclusions were that

  under the conditions of these 2-year gavage studies, there was no evidence of carcinogenic activity of 5-(hydroxymethyl)-2-furfural in male or female F344/N rats administered 188, 375, or 750 mg/kg. There was no evidence of carcinogenic activity of 5-(hydroxymethyl)-2-furfural in male B6C3F1 mice administered 188 or 375 mg/kg. There was some evidence of carcinogenic activity of 5-(hydroxymethyl)-2-furfural in female B6C3F1 mice based on increased incidences of hepatocellular adenoma in the 188 and 375 mg/kg groups. Administration of 5-(hydroxymethyl)-2-furfural was associated with increased incidences of lesions of the olfactory and respiratory epithelium of the nose in male and female rats and mice.

- NTP toxicology and carcinogenesis studies of 5-(Hydroxymethyl)-2-furfural (CAS No. 67-47-0) in F344/N rats and B6C3F1 mice (gavage studies).; Natl Toxicol Program Tech Rep Ser. 2010 Jun;(554):7-13, 15-9, 21-31 passim.

As is shown in the NTP report and the other sources above, HMF is not only found in honey. It will be found in any product that contained sugar or high fructose corn syrup that has been heated, such as baked goods. The reason you are likely to encounter it in honey is foremost that honey is 70-80% reducing sugars (5) and also that bee keepers often supplement HFCS for actual flower nectar when there is not enough flower nectar available for the bees to use to produce honey.

Toxic Honey

One thing to note is that there are toxic forms of honey, just as there are poisonous mushrooms and edible mushrooms. Honey derived from rhododendrons can contain Grayanotoxin, however it is rarely fatal in humans. If you are buying your honey from a supermarket or a reputable keeper, then there is almost no chance that your honey will contain grayanotoxin.

Why is Honey Harmful to Infants?

The issue with honey is that it can contain Clostridium botulinum spores. If the spores germinate, the resulting bacteria release botulinum toxin.

Botulinum toxin, which is the cause of botulism, is a neurotoxin that causes dystonia, and can be lethal in minute doses (ng/kg doses).

For most adults, the risk of botulism from the spores found in honey is minute. The gut microbiome and immune system proteins such as defensins will prevent C. botulinum colonization, so even if the spores germinate, they will not grow to a critical mass to produce enough toxin to do harm and will be excreted.

This however is not the case for infants less than six months of age. Their microbiome is still developing and their immune system is not fully formed. Also, as they have less mass, it takes a lesser absolute amount of the toxin to cause illness and death.

C. botulinum spores are heat resistant, though they can be killed by boiling (7), which means that the internal temperature of the spore needs to reach >85°C for over 5 minutes. Pasteurized honey should already have had this treatment, however you will still see the warnings to not feed to infants less than six months to one year of age, as commercial heat pasteurization may not kill all of the spores (7).

So unless you are immunocompromised, have no gut microbiome, are an infant less than six months of age, or your boiled water does not stay at a temperature greater than >85°C for longer than 5 minutes, and are using raw honey, then you shouldn't be at too much risk.

Edit

Information has been reorganized to better reflect edit to question.


Body temperature results from a balance between the heat generated by our cells and the heat “lost” to the environment. Heat created by our cells comes from the energy used to keep us alive. Heat is lost through our skin and the air we breathe out. Human beings have an average temperature of 98.6 degrees Fahrenheit. The brain monitors body temperature and controls our bodies to keep our temperature within the normal range.

If you get a fever when you’re sick, it’s because your brain has told your body to get hotter. It directs the body to make a number of changes to correct the imbalance. Those changes include increasing heat production within the body (by shivering, for example) and reducing heat loss to the environment. Heat loss is reduced by decreasing blood flow to the skin.


Is it possible to make a cancer cell that doesn’t encode any neoantigens?

Immunosurveillance of cancer cells is predicated upon multiple "signals" derived from the cancerous cells and their microenvironment.

I should point out tumor mutational load (Figure 1). A sort of take-home point here is that certain indications have less mutations and thus less neoantigens than others. You also have to take into consideration the stage of the tumor, though. Stage IV tumors have amassed more mutations than stage I/II.

Figure 1. Mutational prevalence by indication. A higher prevalence predicts a higher neoantigen frequency or mutational load for that cancer histology. (1, 2)

It's interesting to point out the bottom part of figure 1 where the authors of a separate review note for us where it's believed the disconnect between traditional checkpoint blockade immunotherapy and CAR-T immunotherapy exists. Just to educate a bit on the subject, checkpoint blockade targets T cells, the drivers of antigen-dependent cell killing. T cells naturally infiltrate the tumor as it develops and attempt to mount an attack. One of the methods tumors use to evade T cell killing is through persistent antigen, expression of inhibitory receptors and secretion of inhibitory molecules. Checkpoint blockade immunotherapy uses antibodies against the inhibitory receptors such as PD-1 (Opdivo, Keytruda), it's ligand PD-L1, CTLA-4 (Yervoy), Tim3, Lag3, and so forth. This attempts to lift the dampening effect these receptors have on T cells so that they may resume killing. The T-antigen-dependent paradigm is also supported by such publications which look at checkpoint blockade in the setting of clonal T cell diversity and confirm that (1) a diverse repertoire of T cell clones result in successful checkpoint blockade, and (2) enrichment of certain clonotypes within the repertoire, presumably the antigen-specific clonotypes, further indicates a response (3).

So below that are indications circled in red, notably the histologies with a low neoantigen frequency. The idea behind CAR T cells is that I can take advantage of T cell biology, notably that T cells recognize antigen with a receptor and kill the target cell. So just backing up to checkpoint blockade immunotherapy real quick, say a patient has melanoma which can consist of 1000s of mutations and 100s of neoantigens. There is a greater chance that an infiltrated T cell has specificity for any particular antigen. So how about a glioblastoma patient? They may have 10-20 neoantigens, or as you said they may have no neoantigens, at least none that their T cells are specific against. So checkpoint blockade may not be so effective. CAR stands for chimeric antigen receptor. It's essentially a monoclonal antibody against one target connected to a linker connected to the intracellular domain of a T cell receptor. Hematologic malignancies such as NHL like diffuse large B-cell lymphoma are commonly targeted for a B cell receptor known as CD19. So all you have to do is make your CAR CD19 specific and transfect the T cells with it in place of their own T cell receptor or TCR. So the basic process behind CAR is I isolate your T cells as with leukapheresis, lentivirally transfect with my anti-CD19 CAR, expand, and infuse. There are two CD19 CAR T products with great response rates on the market (Kymriah, YESCARTA). The whole reason these are good is because we can direct them to whatever antigen we want (of course be careful about self-antigens, see autoimmunity).

Figure 2. Schematic of CAR T cell therapy. (4)

The CAR T approach is in fact because the neoantigen load is low or non-existent, which is problematic for un-modified T cells, and thus problematic for standard-of-care treatments like checkpoint blockade.

As such, there are other ways, and other cells that can handle some of the abnormalities presented by tumors as a whole. This includes the presence of danger/damage-associated molecular patterns (DAMPs) and the regulation of surface receptors, for example, NK receptor ligands such as MIC.

The way DAMPs work is that a milieu of molecules are secreted by cells that are damaged or transformed, signaling cells of the innate immune system. One of the issues is that the DAMPs promote an inflammatory environment. This means that yes, you get immune cells checking out the situation, but that some of these are good immune cells and some are "bad" (myeloid-derived suppressor cells (MDSC), tumor-associated M2 macrophages (TAM), or T-regulatory cells (Treg)). These dampen the immune response both through inhibitory cytokine release like IL-10, and expression of inhibitory receptors like PD-L1.

Figure 5. The molecules secreted by the inflammatory tumor microenvironment both help and hurt the immune response. (5).

And then the idea behind NKR ligands is pretty straightforward: Natural killer (NK) cells patrol your body routinely for abnormalities and are licensed to kill cells that are abnormal. For example, all nucleated cells express class I major histocompatibility complex (MHC-I) on their surface. Some receptors like MIC are also present on the cell surface that engage receptors on the NK cells like NKG2D in distress. So what do cancers do? They sometimes express truncated and thus inactive MIC, express no MHC but also express inhibitory receptors to NK cells, and so forth.

Everything is summed nicely in the following figure on cancer immunoediting (Figure 7). Note that while things are working normally, the immune system can handle the tumor load. As the scales tip, and this could be for example, your T cell response edits out an immunoantigen but doesn't take care of the whole tumor, resulting in growth that those T cells no longer respond to. As this happens, the cancer becomes increasingly invasive.

Figure 7. Cancer immunoediting. (7).

So just to clarify at the end, there probably isn't a case where the immune system isn't responding at all unless you had chemotherapy that destroyed your immune system. Inflammatory environments alone are sufficient for your immune cells to at least check out the tumor. In fact, and I cant find the paper now but I'll try, investigators even found naïve T cells in the tumor microenvironment simply due to the inflammation. We could also get into "hot" and "cold" tumors, but that's out of scope here (take-home point, cold tumors aren't inflamed and are known to contain less immune infiltrate). I used immunotherapy as a vehicle to get my point across, note that this answer isn't about immunotherapy but rather about immune escape and mutational load theory.


Why are there not effective pharmaceutical treatments to prevent weight gain?

The two main factors are:

Hunger is more complex to treat than pain (more pathways, more potential targets), and I would argue against your suggestion that we are good at treating pain: despite the term "painkiller" we aren't great at blocking pain except for with local anesthetics that block all nervous activity (lidocaine for example). For systemic pain relief, there are lots of long-term efficacy issues with either opiates or NSAIDs, and that isn't even taking into account:
Side effects. Amphetamines are great for suppressing appetite. They also mess with the cardiovascular system, are habit-forming, and cause psychological issues. "Fen-phen" is a famous example of an anti-obesity drug that had major side effects leading to massive lawsuits. A more recent supplement, Ephedra, had many of the same problems and was banned by the US FDA for those reasons.

There are some drugs that are used to treat obesity, but many of these have come into regulatory issues with side effects and are only used in special cases like in diabetics or as an absolute last resort.


This is a slime mold of the genus Stemonitis, and I'm thinking the species is axifera. They tend to form on dead wood, of which seems to be the case in your picture (assuming that we are in fact looking at the wall just next to your actual window, since the bottom left of your window can be seen at the top right of the picture).


How can microarrays be used to quantitatively determine level of gene expression?

From the comments:

MattDMo:

  You can compare different samples, which may have started out as
  different amounts of tissue, by using control genes. The numbers
  reported by most standard microarray experiments are not absolutely
  quantitative (There are 2450 copies of this RNA per cell in this
  sample), but are rather a proportion as compared to a set of
  housekeeping genes whose levels are not expected to vary much between
  the samples you are analyzing.

cagliari2005:

  For PCR amplification, you are right, this is a random process and
  while you would expect most RNAs to be similarly amplified, biases can
  and will occur. Amplification biases are usually assumed to be
  identical between similar samples and therefore will (mostly) cancel
  out during the differential analysis.


Typical cellular respiration lab with a respirometer -- why is potassium hydroxide (KOH) necessary?

The solid precipitate does not contribute as much to the pressure inside the vial as the gas does. Intuitively, the gaseous molecule contributes to the pressure by collisions that exert force on the vessel (which would push the water out). By contrast, the solid precipitate only contributes to the pressure insofar as it decreases the volume of the vessel, which is negligible in comparison to the loss of kinetic energy per gas molecule.

Basically, just because they both occupy space, doesn't mean they occupy the same amount of space (or rather, they don't contribute equally to the pressure in the vial). Gases tend to occupy more space than liquid or solid phase molecules of identical size, due to their kinetic energy of motion and the force of their collisions on their surroundings. The KOH reacts with the CO2 to remove it from the pool of high energy gas molecules, converting them to low energy molecules in the solid. With the lower number of molecules contributing to the pressure (ideal gas law), the pressure is lowered and the force of the water becomes greater than the force of the gas, and the water enters the respirometer.


Are humans still competing in the same way now that the first life forms did?

It's important to realise that evolutionatry competition and the common usage of the word competition do not mean quite the same thing. For example, you could talk about Usain Bolt competing in the 100m but this is only evolutionary competition with the other athletes in they are in competition in terms of evolutionary fitness. Evolutionary fitness encompasses ideas of survival, reproduction and the nurturing of offspring. The only thing that matters, from an evolutionary point of view, is how many successful offspring are produced1. Where human competition does not relate to this, it is not related to competition in the evolutionary sense.

People certainly do still compete in the evolutionary sense for mates, resources, etc. but in the West, in particular, much of human competition has become a very long way removed from anything that relates to evolutionary competition except in the most tangential of ways.

1 - my favoured definition for fitness is number of grandchildren.


What is a coupled reaction and why do cells couple reactions?

A reaction where the the free energy of a thermodynamically favorable transformation, such as the hydrolysis of ATP, and a thermodynamically unfavorable one, are mechanistically joined  into a new reaction (or may be envisaged to be so joined) is known as a coupled reaction.

To put it another way, two or more reactions may be combined mechanistically such that a spontaneous reaction may be made 'drive' a non-spontaneous one,   and we may speak of the combined reaction as being 'coupled' (see, for example, Silby & Alberty (2001), quoted below). The combined reaction may be catalyzed by an enzyme, in which case the 'thermodynamic push' is provided by the coupling agent (such as ATP) and the 'kinetic push' is provided by the enzyme.

We need to take into account a very important point. As pointed out by Atkinson (1977),  the coupled reaction is a different reaction to the reaction we are trying to 'drive', with different overall stoichiometry and hence a different overall equilibrium constant (Atkinson, 1977, p52).

A coupled reaction does not "push a reaction past its equilibrium" (see Atkinson, 1977, p52). No enzyme, for example, can push any reaction past its position of equilibrium. This is forbidden by the second law. (If your favourite kinetic mechanism does not obey the second law there is, as Eddington put it, "no hope"). An enzyme (or enzymes) can however, cause a reaction to proceed further than it normally would by catalyzing a different reaction (or series of reactions).

Perhaps (in lysine biosynthesis from aspartate), nature requires the the (NADH-linked) reduction of a carboxylic acid to an aldehyde, a reaction normally considered  irreversible. And lets spell this one out: the equilibrium constant for a reaction such as the following:

        NADH + carboxylic acid = NAD+ + aldehyde        (1)

greatly favors aldehyde dehydrogenation so much so that the left-to-right transformation has never (to the best of my knowledge) been demonstrated (more on this below).

Lets first phosphorylate the carboxylic acid using ATP as coupling agent to give aspartyl-phosphate (aspartate kinase):

         aspartate + ATP = aspartate-4-phosphate + ADP        (2)

Now let's reduce the 'activated' acid (aspartate-4-phosphate) using NADPH as electron donor, where the equilibrium constant of the following reaction is  very much to the right  (aspartate semialdehyde dehydrogenase):

  aspartate-4-phosphate + NADPH + H+ ⇌ L-aspartate 4-semialdehyde + Pi + NADP+

So we have got our product (the aldehyde) from our 'starting material' (the carboxylic acid), but at the 'expense' (as we would see it) of  ATP hydrolysis.

We may think of the above reactions as being 'mechanistially coupled' by the formation of aspartyl-phosphate such that the overall equilibrium constant for the following reaction is much more favourable than that of Eqn (1)

  aspartate + ATP + NADPH + H+ ⇌ L-aspartate 4-semialdehyde + Pi + NADP+

Or, perhaps in more abstract terms, the coupled reaction may be represented as folows:

  carboxylic acid + ATP + NADPH + H+ ⇌  aldeyde + Pi + NADP+

The reduction of a carboxylic acid to an aldehyde has been given a thermodynamic 'push' by the coupling agent  (and a kinetic 'push' by the enzymes).

Before we move on to some specific examples let's consider three further points.

(i) What makes ATP a good coupling agent? To again quote Atkinson (1977, p48), a good coupling agent has two requirements: firstly, it must be thermodynamically unstable. That is, it must be "far from equilibrium in terms of some useful conversion" (Atkinson, 1977, p48). The hydrolysis of ATP nicely fills this criterion. Secondly, a good coupling agent must be kinetically stable. Again ATP 'fits the bill': solutions of ATP in water are stable (Atkinson, 1977, p48).

ATP (-39.7 kJ/mol), of course, is not the only useful coupling agent, or even the 'best' one. phosphoenol-pyruvate (-61.9 kJ/mol) , creatine-phosphate (-43.5 kJ/mol)  and acetyl-phosphate (-43.1 kJ/mol) are others. The figures in brackets refer to free energy of hydrolysis and are taken from Silby and Alberty (2001, p 282).

(ii) The coupled reaction need not involve direct hydrolysis of coupling agent. Any reaction in which ATP is converted to ADP has received a 'thermodynamic push equivalent to the free energy of hydrolysis of ATP' (Atkinson, 1977, p49). In essence, the concept of a coupled reaction is an abstraction, created by us for our convenience.

(iii) To state the obvious, a coupled reaction is exactly that: coupled.  The coupling may be 'chemical', as in many of the examples below, or may be conformational (as in ATP synthase), but there must be in some sense a mechanistic joining into a new (real) reaction. Two reactions occurring in isolation, even if one is ATP hydrolysis, are not coupled.

Specific Examples

An example of a coupled reaction is the  glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12; GAPDH) reaction [see here] .

 Glyceraldehyde-3-phosphate + NAD+ + Pi → 1,3-diPhosphoGlycerate + NADH + H+

We can think of this reaction in terms of two separate reactions which are coupled mechanistically by the enzyme. (i) The NAD+ linked oxidation of an aldehyde to a carboxylic acid (the aldehyde dehydrogenase reaction) and (ii) the phosphorylation of a carboxylic acid. (Like ATP, a phosphorylated carboxylic acid may be considered a 'high energy' compound, that is one where the equilibrium for hydrolysis lies very much to the left in reaction 2 below).

Reaction 1

 RCHO + NAD+ + H2O → RCOOH + NADH + H+

Reaction 2 (Pi is inorganic phosphate).

 RCOOH + Pi → RC(=O)(O-Pi) + H2O

As stated above, the NAD+-linked oxidation of an aldehyde (reaction 1) is practically irreversible. That is, at equilibrium it has proceeded almost totally to the right. As stated above, the position of equilibrium of reaction 2 lies very much to the left.

How can one 'drive' the formation of a phosphorylated carboxylic acid by coupling it to the (spontaneous) NAD+-linked oxidation of an aldehyde?

A simplified version of the GAPDH reaction is as follows (a more complete mechanism, supported by a lot of experimental evidence, may be found in Fersht (1999), which I quote below).

Step 1.  Formation on an enzyme-linked thiohemiacetal.

 E-SH + RCHO → E-S-C(R)(H)(OH)

A sulphydryl on the enzyme (part of a Cys residue) reacts with the aldehyde group on the substrate to give a thiohemiacetal.  (In the representation above, groups in brackets are all connected to a single (tetrahedral) carbon atom).

Step 2. The thiohemiacetal is oxidized by enzyme-bound NAD+ to a thiol-ester (the key step).

 E-S-C(R)(H)(OH) + NAD+ → E-S-C(=O)(R) + NADH + H+

This (enzyme-bound) thiol-ester is a 'high energy' intermediate wherein, it may be envisaged, the free energy of aldehyde oxidation has been 'trapped'.

The final step of the GAPDH reaction is now spontaneous (proceeds to the right).

Step 3. Attack on the thiol-ester by inorganic phosphate (Pi is inorganic phosphate)

E-S-C(=O)(R) + Pi → E-SH + R-C(=O)(O-Pi)

Thus, the free energy of NAD+-linked aldehyde oxidation has been 'sequestered' and used to 'drive' the thermodynamically unfavourable phosphorylation of a carboxylic acid, by coupling the two reactions via a ('high energy') thiol-ester: the coupled reaction is a different reaction.

The 'thermodynamic price' is that the GAPDH reaction (unlike NAD+-linked aldehyde oxidation) is freely reversible: the coupled reaction has a different overall equilibrium constant.

As stated above, this is a simplified version of the GAPDH reaction.  The (tetrameric) enzyme contains a tightly bound NAD+ for a start, and this needs to be taken account of.  A fuller account may be found in the following reference:

Fersht, Alan. (1999) Structure and Mechanism in Protein Science, pp 469 - 471, W.H. Freeman & Co.

For a fuller treatment of coupled biochemical reactions, see

Silbey, R.J. & Alberty, R.A. (2001) Physical Chemistry (3rd Edn) pp 281 - 283.
Atkinson, D. E. (1977) Cellular Energy Metabolism and Its Regulation.
Academic Press, New York

Pyruvate kinase (EC 2.7.1.40) [see here] is another great example of a coupled biochemical reaction.  In this case the reaction is almost irreversible in the direction of ATP synthesis!

The standard transformed free energy (ΔGo') for the hydrolysis of phosphoenol-pyruvate (PEP) to pyruvate and phosphate is ~ - 62 kJ/mol.  This represents an equilibrium constant of about 1010 in favour of hydrolysis! (see Walsh, quoted below, pp 229-230).

For comparison,  ΔGo' for ATP + H2O → ADP + Pi is about - 40 kJ/mol.

Thus the pyruvate kinase reaction may be viewed as a coupled biochemical reaction where the free energy of PEP hydrolysis is coupled to (almost irreversible) ATP synthesis.

Why does PEP have such a large negative ΔGo'? The enol form of pyruvate does not exist in appreciable quantites in aqueous solution at pH 7 (Pocker et al., 1969; Damitio et al., 1992).  PEP may be considered a 'trapped' form of a thermodynamically unstable enol which is released upon hydrolysis, thus 'pulling' the equilibrium to the right. (see Walsh, quoted below, p 230, for a more thorough explanation).

Personally, I have always considered the reaction catalyzed by PK to be pretty amazing.

Edit

In response to this question on the standard free energy of hydrolysis of phosphoenolpyruvate (PEP), I'll add the following.

The thermodynamically stable form of PEP in solution at 'physiological' pH is the enol form.  That is, the enol from predominates.

PEP hydrolysis may be formally divided  into two parts:
(i) the hydrolysis of the phosphate ester to give the enol form of pyruvate,
followed by (ii) tautomerization to the (thermodynamically stable)  keto form of pyruvate (Chiang et al., 1992).
Thus it is the enol form of PEP that predominates in aqueous solution at pH 7, but pyruvate exists predominately in the keto form under similar conditions.

In their in-depth study, Chiang and co-workers attribute 47% of
the free energy liberated by  the hydrolysis PEP to the ketonization of the enol form of pyruvate, and
conclude that "nearly half of the high energy content of this molecule resides in its masked  enol function" (And of course, they mean 'high energy' in the Lipmann ('squiggle') sense, that is PEP has a high standard free energy of hydrolysis).

We need to be careful with the following and acknowledge that the language is somewhat loose: we may
think of PEP as a molecule where the thermodynamically unstable form of pyruvate (the enol form)
is 'trapped' in a (thermodynamically stable) phosphate-ester linkage, which will be 'released' on hydrolysis. And to emphasize, the thermodynamically stable form of PEP is the enol form.

IMO, Chiang et al. (1992) is a very nice paper that rigorously backs up conclusions with strong experimental evidence, but it is surprising that they did not quote Walsh
 who (again, IMO) is the first to give the correct explanation?

References

Chiang,Y., Kresge, A. J. & Pruszynski, P. (1992) Keto-Enol Equilibria in the Pyruvic Acid System: Determination of the
Keto-Enol Equilibrium Constants of Pyruvic Acid and Pyruvate and the
Acidity Constant of Pyruvate Enol in Aqueous Solution  J. Am. Chem. Soc. 114, 3103-3107
Damitio, J.,  Smith , G.,  Meany , J. E.,  Pocker, Y. (1992).  A comparative study of the enolization of pyruvate and the reversible dehydration of pyruvate hydrate
J. Am. Chem. Soc.,  114, 3081–3087
Lipmann, F. (1941). Metabolic generation and utilization of phosphate bond energy.  Adv. Enzymol. 1, 99 - 162.
Pocker, Y., Meany, J. E., Nist, B. J., &  Zadorojny, C.  (1969) The Reversible Hydration of Pyruvic Acid. I. Equilibrium Studies.  J. Phys. Chem.
76, 2879 – 2882.
Walsh, C. (1979) Enzymatic Reaction Mechanisms.  W.H. Freeman & Co.

Oxidative Phosphorylation

Perhaps the most important coupled reaction is that which occurs in oxidative phosphorylation where the oxidation of  fuels via the respiratory redox chain is coupled to  the  'synthesis' of ATP.

I have 'steered clear' up to this point, as it is a very complex area and difficult to do justice to in a few lines.

In the chemiosmotic theory of oxidative phosphorylation (due primarily to Peter Mitchell)  electron transport via the respiratory chain to molecular oxygen creates a proton  gradient across the inner mitochondrial membrane by pumping protons outwards. This proton gradient, or protonmotive force, is used to 'drive' the following  reaction to the right:

ADP + Pi ⇌  ATP + H2O

This is commonly referred to as 'ATP synthesis' but, more correctly perhaps, it  maintains our coupling agent  "far from equilibrium in terms of some useful conversion" (Atkinson, 1977, p48), that is far from equilibrium in the hydrolysis of ATP.

Although all of oxidative phosphorylation may be considered a coupled reaction, all that will be (very briefly) looked at here is the reaction catalyzed by ATP synthase, which may be considered to catalyze the following coupled reaction.

 ADP + Pi + H+(Out) ⇌ ATP + H2O + H+(In)

This is an example of vectorial catalysis, but it is much more. The ATP synthetase has been described as a "splendid molecular machine" (Boyer, 1997b).

It is an example of sequential, cooperative catalysis between 3 active sites where the the release of products (ATP) at one site is dependent on binding of substrates (ADP and Pi ) at another.
It is an example of indirect conformational coupling where the proton gradient effects the release of of tightly bound ATP by eliciting sequential conformational changes in all active sites .
It is an example of a binding-change mechanism, where the proton gradient is responsible release of ATP from the enzyme, but plays no role in its synthesis.
Perhaps most dramatically,  it is an example of rotational catalysis, where the indirect rotation of a protein subunit brings about the sequential conformational  changes in the active sites.

Much of the mechanism of ATP synthetase is due to Boyer: this includes the prediction of rotational catalysis and the formulation (and defense) of the binding-change mechanism (see Boyer, 1997a,b). For some nice dynamic diagrams on the mechanism of action, see this SO answer.

Perhaps the most important considerations from the standpoint of the present discussion is the subtlety  of the coupling effect or 'mechanistic joining': it is brought about by a conformational change due to rotation of a protein subunit, and it is mediated though the dissociation of ATP from a subunit and not through its 'synthesis' from ADP and Pi at an active site.

[Aside] In a most famous experiment, rotary catalysis was 'physically' demonstrated by Kinoshita and  co-workers by attaching an actin filament to the rotating subunit of the enzyme and viewing under a fluorescent microscope (see here), which showed that rotation is anti-clockwise (viewing the enzyme from the 'membrane' side) when the enzyme is hydrolyzing ATP. A nice YouTube video, which seems to be base on the original Noji experiment, may be found here .

References

Abeles, R.H., Frey, P.A. & Jencks, W.P. (1992) Biochemistry.  Jones & Barlett, Publishers.
Boyer, P. D. (1997a) [Nobel Lecture] Energy, Life, and ATP (pdf available here)
Boyer, P. D. (1997b) The ATP Synthase. A splendid molecular machine Annu. Rev. Biochem.  66, 717–749
Mitchell, P. (1978) [Nobel Lecture] David Keilin's Respiratory Chain Concept and Its Chemiosmotic Consequences (pdf available here)
Walker, J. E. (1997) [Nobel Lecture] ATP Synthesis by Rotary Catalysis (pdf available  here)


What is the name of this type of inflorescence?

That is a woody compound umbel. A compound umbel is one with more than one set of pedicels between the peduncle and the flower. Hydrangeas also exhibit this type of inflorescence, although not necessarily woody.

In the picture below, I've marked all the levels where the pedicels branch.

End of peduncle, beginning of primary pedicels
Beginning of secondary pedicels
Beginning of tertiary pedicels
Beginning of quaternary pedicels, which bear flowers


How Does The Presence of Livestock on Land Increase Net Methane Production?

Ruminant digestion produces a lot of methane.
Cows are ruminants, and ruminants produce a LOT of methane. Sheep and goats are also ruminants but their are far fewer of them. Ruminants use methanogenic bacteria to breakdown their food, these bacteria, as there name implies release methane as a byproduct.  Ruminants produce a lot more methane than other herbivores becasue of this.
Decaying grass normally produces CO2 as do many native herbivores. Cows like most herbivores only convert a very small amount of the grass they eat into cow. Herbivore digestion is not terribly efficient, not surprising the grass does not what to be easy to digest.
Farming also puts a lot more herbivore mass on a piece of land than it would normally have, further increasing the effect, that is the purpose of farming to get more out of the land than simple hunter/gathering could. This is an issue becasue methane is a FAR more effective greenhouse gas than CO2.
Feeding cattle often involves replacing existing ecosystems which high yield feed crops and this can release a lot of CO2 and/or Methane depending on the original ecosystem just from the change, but it also means that feed is now producing methane instead of CO2 it would be if eat by non-ruminants.
Source
Source 2


Sexual reproduction in organisms with 1 parent

Your second piece is correct: dissimilarity is produced through meiosis.

from The evolution of meiotic sex and its alternatives

  Strikingly, almost all forms of uniparental reproduction do maintain
  meiosis, but abandon just outcrossing. Hence, the paradox of sex in
  eukaryotes must focus on the purpose of meiosis.


Any examples of animal behavior in response to meteor showers?

There are a significant number of major meteor showers in the earth's orbit, especially in the Northern Hemisphere. Nocturnal animals have good night vision (obviously) and their acclimation to the dark plus time spent awake at night (if they look up at all) means they see many, many more meteors on average than humans do.

The year's parade starts with the Quadrantid shower.

  January overall has good meteor rates restricted to the last third of the night. Rates to 20/hour can be obtained.

Meteor "showers" (if they can be called that) continue until mid-march, when they drop off to a "very poor" rate of 10/hour or less, continuing this pattern into early June, except for the Lyrids (max: April 22/23) and the Eta Aquariids (max: May 7/8).

  February, March, and April evenings have another notable feature. An unusual number of sporadic fireballs come in this interval, possibly one every few nights.

In the last half of July, we get the Delta Aquariids (July 29/30) and Alpha Capricornids (July 27-28).  Then the Perseids (maximum: August 12/13), rich to our eyes at about 100/hr at their peak, moon and weather permitting.

From September to the first half of December is pretty rich.

  Mid-October to mid-December is a nearly continuous period of heavy meteor activity. The Orionids (max: October 21/22) during the second half of October have a prolonged, plateau maximum for several nights, usually rich. The Taurids (max: October 11 for S. Taurids, November 13/14 for N. Taurids), active for two months, are most numerous in November’s first half, and can be rather variable in strength. This period is the best for a couple of Taurid fireballs each night, if the shower is not too weak. The Leonids of mid-November (max: November 17-19) are quite unpredictable, with rich displays occuring roughly every 33 years.

Finally there's the Geminids of mid-December (max: December 13/14) with "the strongest dependable and observable display" (usually passing 60-70/hour at maximum.)

  Finally, the oft-overlooked Ursids complete the year’s activity, reaching maximum on December 22/23. Nearly half the year’s visual meteor activity is crammed into the two-month interval just described.

What does all this have to do with biology and your question? I'm guessing here that the Perseids, though rich for humans, are probably nothing exciting for animals. The diurnals and crepusculars don't see them at all (they're soundless and certainly not bright enough to wake anyone up). The nocturnals see the (or not, depending on where they're looking) all the time. So a study wouldn't likely detect much, would be challenging to design well, would cost some big bucks, and wouldn't really help humans like studying animal behavior before earthquakes and such.

As a child, I once saw some very funny chicken behavior on my grandmother's farm during a total eclipse of the sun. It was so funny that I remembered it all the years since.

I searched, as I'm sure you did, and the first hit on regular Google was this question. A scholar search brought up possible animal behavioral changes before fireballs.

Major Meteor Showers


What is the difference between "lineage restriction" and "differentiated" in terms of stem cell biology

When you look at the development of the embryo, at the beginning all cells are totipotent, meaning they can develop into any cell type of the body. This changes relatively fast by differentiation, which means that the totipotent cells develop into more specialized cell types, which then can not give rise to all cell types. So the different germ layers (meso, ecto- and endoderm) develop and from these all the cell types in our body. See the first figure for clarification (from here):

Lineage restriction means that you have a differentiated cell line, which can only further develop into cells of this line. So hematipoietic stem cells can only further develop into cells of the hematopietic line (lymphocytes, erythrocytes, basophiles and so on), like shown in the figure below (taken from here):


In the endomembrane system, after a protein leaves the rough ER, where does it go?

I'm no expert at this but will do my best to answer your question based on the title. It depends on the protein! proteins can either be cytoplasmic, nuclear, transmembrane or secretory. Cytoplasmic proteins (as far as I know) get released to the cytoplasm after they have been folded correctly (through chaperones) and gone through the quality control mechanism. Nuclear proteins get transported through the nuclear pores, across the nuclear envelope through chaperones. Now for the transmembrane or secretory proteins, the fate of these proteins and where they go is decided by the ER (but obviously the information is there in the protein sequence). Transmembrane proteins have a signalling peptide and a transmembrane domain signal anchor sequence which ER recognises and through fancy looping and elongation across the ER membrane, the proteins is further translated by the ribosomes and eventually gets translocated to the cell membrane. There is very very nice nature review paper (Rapoport, 2007) about this and if you look at Figure 5, you will get a good ideas as to what goes on. For the secretory protein again its the interaction of the protein sequence with the ER membrane, helped with the ribosomes (in fact the groves in the ribosomes are key for making these fancy looping happen as the protein residues in ribosomes interact with peptide residues (amino acids) that are being produced on the fly), that processes it and sends it for secretion (Rapoport, 2007) and trans-golgi network is also important in the secretion process (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1424219/).

Hopefully these information would provide you with some hints.


Can the human eye axial length decrease?

Generally the axial length doesn't decrease:
graph
Although there is discussion of various conditions where it has been observed to decrease, i.e. nanophthalmos, microphthalmos, and retinoblastoma... A review of current research is here: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5501611/ quote:
It is considered that the axial length reaches adult length by the age of 13 years, showing no further increase in length. Recent cross-sectional studies found that the axial length in older adults tended to be shorter, suggesting that it may decrease with aging. However, in a recent longitudinal study by He et al., slight increase of the axial length in adults (mean refractive error, −0.44 ± 2.21 diopters) was reported. Conversely, an increase in the axial length in adults with highly myopic eyes is common and has been previously shown in longitudinal studies [5–7]. However, to the best of our knowledge, there have been no studies directly comparing the increase in the axial length in adults with non-highly myopic eyes or highly myopic eyes. In addition, because previous studies on the axial length in highly myopic eyes have not compared between eyes with and without macular complications, their influence on the axial length remains unknown.
Can myopia be treated with a reduction in axial length? Presumably, yes it could, if opticians had figured a way to do it... Do you suggest that a drug or a medical intervention can flatten the entire eyeball a bit? perhaps a drug could but it would reduce the entire eyeball, you'd have to find a way to administer it. Apparently doctors haven't researched that option, but perhaps they will in future. Laser currently seems like a better way.
https://www.google.com/search?hl=en&biw=1706&bih=951&sxsrf=ALeKk01GuiHpl6-_fRp-Bg_UdsYOdqVzbg%3A1596509065944&ei=icsoX9aRObLMgweX6KboCQ&q=%22decrease+in+axial+length%22+of+optical
https://www.google.com/search?hl=en&biw=1706&bih=951&sxsrf=ALeKk03b75zOsA6CN_Ypqdv5v7hqfVWLbA%3A1596509091797&ei=o8soX8ySMIyqUP2dtvgI&q=%22reduction+in+axial+length%22+of+optical&oq=%22reduction+in+axial+length%22+of+optical


According to the article Why do we love music?, "No one knows why we love music, or what function, if any, it serves."

Of course, that article was published in 2013, so it's possible someone has found an answer since then. ;)

Some have argued that music is merely an evolutionary byproduct that serves no really important purpose. (Type "auditory cheesecake" into Google.) In a similar vein, one might speculate that music did serve an important purpose at one time (e.g. a mating ritual).

In this spirit, we might ask how one defines music and then ask if we humans are the only species that makes music. When we hear frogs croaking or crickets chirping, are they merely communicating, or are they making music - or are they doing both at the same time?

Though your question focuses on music people listen to, a similar question could be asked about dance. Except I think music is more universally popular than dance, which doesn't interest everyone.

In summary, I haven't really answered your question - which probably can't be answered with any accuracy at this time. But there are actually lots of references on the Internet that offer clues to the puzzle. I suspect there's some overlap between the love of music and the love of poetry, painting, etc.

I just discovered an interesting term - evolutionary musicology - along with another theory to explain music's popularity: It may simply be a welcome break from silence, which may be associated with danger.

Yikes, I know I'm doing a lot of rambling, but here's another thought:

Some researchers believe music served as a sort of group bonding tool. In other words, a particular tribe might have produced a certain kind of music that helped unite members of that tribe. In other words, music could be a form of symbolism, similar to flags.

As a huge fan of Latin music, I've come to appreciate the association between specific genres and their places of origin. For example, flamenco is a product of Spain, while cha-cha-cha and mambo are forever linked with Cuba. There's a fierce debate about the origins of salsa, which was officially born in New York City but which is clearly derived from mambo.

No one can deny that country music sucks. Yet I love a lot of country music, which I was exposed to when I was growing up in rural West Dakota.

What I'm trying to say is that music probably helps us identify with a particular group and connect with our roots.

P.S. It's worth noting that other species do indeed enjoy music. Check out the article What type of music do pets like?


Online course on Plant Taxonomy and Physiology

Well, I wasn't able to find an online video course. The closest I came was this site, which links to courses that put their material online. Most of these are compilations of the lecture notes. There's also this page from the University of British Columbia, that has a nice little overview of the field of plant taxonomy.

In my experience, botany and plant identification are subjects where one really needs to learn by doing. You really need to grab a plant and take a close look at it while noting why its in the group that its in. A great way to get started might be to join a local gardening club or native plant society. The people in those groups can provide their tips for ID-ing plants.

One of the primary skills you'll want to learn is identifying what family a plant is in. Plant families have (mostly) consistent characters, and learning how to spot the most common families in your area will be a big help.


What is the name of a gene whose effect comes from the dominant and recessive alleles

Allelic effects

  What is the name of a gene whose effect [..]

The concept of dominance make sense for alleles. The gene has no name to refer to the allelic interaction.

Patterns of dominance

Patterns of dominance and recessivity are typically used for quantitative traits. Can you somehow put a a number into the phenotypes of all three genotypes? Making some kind of association table would help even if the phenotypes are not quantitative. See below.

Attempt to answer the question

It looks like you are considering a case where the phenotypes

aa -> healthy
Aa -> sick
AA -> very sick

Under this model, it is hard to tell whether you would consider sick half way through healthy and very sick or not. It feels like you want to consider sick as being closer to very sick than to healthy so if we put numbers we could get something like

aa -> 1 (healthy)
Aa -> 2 (sick)
AA -> 2.5 (very sick)

As such, A shows partial dominance (aka incomplete dominance or semi-dominance).


How do you estimate global species richness?

You might be interested in the below works as well as the references that they cite.

May, R. M. (1988). How many species are there on Earth? Science, 241(4872), 1441–1449.

Millennium Ecosystem Assessment. (2005). Ecosystems and Human Well-Being: Synthesis (p. 137). Washington, D.C.: Island Press.

It's worth noting that many estimates of species richness at large scales are based on the use of the species-area relationship to upscale richness measurements from small scales to large scales.


Do effects of caffeine on human body change with habitual use?

I don't have any references off hand (though if you like, I will find them). The body acclimates to caffeine intake, becoming desensitized to chronic caffeine use, analogous to chronic narcotic use. Habitual coffee drinkers, soda drinkers, and so forth must achieve the same level of daily caffeine intake to maintain a normal state of being. Taking in less caffeine leads to withdrawal symptoms, and taking in more caffeine leads to the familiar stimulatory effects. As for time frame of addiction, this likely varies, but I hazard a guess it's on the order of a few days to a week. Fortunately, caffeine is not nearly as strong and addictive as narcotics, however it is the most widespread.

Edit: Caffeine exerts high-affinity and low-specificity for adenosine receptors. This was a review article I fould that may help you out.

Dunwiddie TV, Masino SA. The role and regulation of adenosine in the central nervous system. Annu Rev Neurosci. 2001;24:31-55.


Name of neurons affecting or being affected by a neuron?

At the simplest level, the terms 'pre-synaptic'/'post-synaptic' neurons should cover what you wish to describe.
'Afferent'/'efferent' are usually used to refer to axonal projections, usually between functionally distinct areas, or nerves. However, I wouldn't be too surprised if someone used these terms to refer to synaptically connected populations although I would consider it unusual. Simply, 'connected neurons' is also a term frequently used.

I will now go into a tangent to give you some background that should help you formulate an informed view about the vocabulary being used:

In areas that display a high degree of local connectivity, like the cerebral cortex and the hippocampus, any given neuron is connected with many different neurons. Hebb's theory of cell assemblies posits that a group of highly connected neurons may form over time in order to subsist a specific function. Given the high degree of connectivity, any given neuron will be able to participate in many different assemblies. It is often thought that these assemblies constitute the substrate of engrams, the physiological correlates of memory, at the level of the neuronal network. Hence, the concept of cell assemblies is prominent in our thinking about groups of synaptically connected neurons.

Setting aside the questions of the definition of the engram, recent efforts have claimed to identify engram cells under this or that experimental paradigm, although the connectivity of those cells has not been established. While we know that functionally similar neurons display a higher degree of connectivity and that groups of cells with correlated activity patterns can be formed by artifically-induced synchrony, the direct link between increased connectivity and behaviourally relevance has not been established.

On the other hand, only a handful of studies have directly measured the connectivity between more than two neurons (Song et al., Perin et al.), revealing the intricate properties of neuronal network structure. Depending on the level of description they may refer to distributed cell assemblies, synaptic clusters of neurons, $n$-vertex cliques, and motifs.

All this is to say that as soon as you start considering more than a pair of neurons, it makes little sense to talk about neurons that are exclusively connected with each other. As every neuron is connected to almost all other neurons in its immediate neighbourhood we often focus on the functional implications of their connectivity. Under this light, the concept of cell assemblies is central in modern neuroscience.


(B) is incorrect. I think the answer is (C) but to my mind those other two options are badly worded.

Here is an explanation.

The classic example of isozymes is the case of lactate dehydrogenase.

As you will see if you visit the Wikipedia page the enzyme is a tetramer, and there are two subunit types, the muscle or M type and the heart or H type. Consequently there are 5 isozymes, ranging from M4 to H4 with all possible combinations in between. Different tissues express these two subunit types to different degrees and so are characterised by a different pattern of isozymes.

The M type is encoded by the LDHA gene and the H type by the LDHB gene. I obtained the sequences of the two proteins and analysed them:

LDHA: 332 amino acids; 36.7 kD; pI=8.45

LDHB: 334 amino acids; 36.6 kD; pI=5.93

You can see from this that the ability to separate these isozymes depends upon charge and not molecular weight. That big difference in pI (isoelectric point) means that at neutral pH the LDHA protein will carry a net positive charge while the LDHB protein will be negatively charged. Consequently each tetramer will have a unique overall charge. You can find some details and an image of an electrophoresis result here.

In general, protein electrophoresis is much more sensitive to charge differences than it is to molecular mass except in the special case of SDS-PAGE when the large amount of negatively-charged detergent that binds to the proteins masks their intrinsic charge differences.

Another classic example of this is the ability to separate haemoglobin S in sickle cell patients from haemoglobin A in normal blood. In this case the only difference between the two molecules is a single Glu>Val substitution in two of the monomers in each tetramer.


How many abdominal sclerites would be there in a cockroach?

Tergal plates:

There are ten tergal plates. The $8^{th}$ tergum in the male and both $8^{th}$ and $9^{th}$ terga in the female are not visible  as they are overlapped by the $7^{th}$ tergum.

The $10^{th}$ tergum extends beyond the posterior end of the body and has a deep groove in the middle of its free end.

Sternal plates:

Only nine sterna are present as the $10^{th}$ sternum is absent.
In the male, nine sterna are visible whereas in the female, only seven sterna are visible.

In females, the $7^{th}$, $8^{th}$ and $9^{th}$ sterna together forma brood pouch. The brood pouch has two parts: the anterior – genital chamber or gynatrium  and the posterior – gothecal chamber.

(source: lander.edu)

(source: lander.edu)

Sources:

http://www.slideshare.net/prof_aarif/animal-types-cockroach
https://learnzoology.wordpress.com/category/periplaneta-americana/page/15/
http://zoologybaburao.in/pdfs/7.%20Unit%20VII.pdf (Best)
http://www.eskool.com/files/subject/ppt/103_11_07_04_01.pdf
http://www.sakshieducation.com/(S(clpea355rwddux55iuci1cer))/Inter(New)/Material/IstYearEM/Zoology/07_01_ARTHROPODA_COCKROACH_UPTO_LOCOMOTION.pdf

Update:

Youtube links for Cockroach dissection:

https://youtube.com/watch?v=ZwvG69ICnps
https://youtube.com/watch?v=wF7ew2w24as


What is the smallest molecule that can present as an antigen to the immune system in the context of allergies?

At one of my previous companies that raised antibodies to proteins and post-translational modifications, we found that 6-8 amino acids was generally the smallest peptide length required for an epitope. Anything much smaller than that won't induce the cross-linking or conformational changes required for signal transduction and an allergic response. As WYSIWYG notes, allergies to small molecules/atoms are formed via hapten-carrier interactions. These can be covalent, as in the nickel-transferrin example, or as a result of denaturation/chemical modification, as likely happens with people who are allergic to things like isopropanol or bleach.

I very much doubt that there can be such a thing as a glucose allergy, as it is so ubiquitous in the body that such antibodies/T-cells would be negatively selected long before they could do any damage.


Can you see the coloration of Sinosauropteryx with the naked eye?

Is it just a coincidence that that's exactly what I would have guessed by looking at the color of feathers in the fossil? Am I falling prey to hindsight bias?

Hmm.. TBH, I don't think anyone can tell you that! However, after taking a look at it, I myself may have suggested reddish feathers along the neck and back, with some kind of red/purple coloration going down the tail (though I have no significant expertise in this field).

  Or is it the case that the feathers are so well preserved that their color is visible to the naked eye?

Melanosomes are actually fairly large; about 500 nm (source). Relatively speaking, this is somewhere between the size of the flu virus, and of mitochondria; see here for scale. According to this book, written by the Swiss Institute of Bioinformatics, it states:

  ... besides [zebrafish] being vertebrates like us - their epidermis and their eggs are transparent, and embryonic development can be overved and tinkered with at every stage. Likewise, even melanocytes and their melanosomes are visible to the naked eye.

So, it would seem that it's possible to observe melanosomes with the naked eye, given a high enough (melanosome) concentration. It should also be noted though that, although the fossil did preserve the melanosomes (here), I'm not necessarily sure that that means the color observed in the fossil is the same color that would have been observed in the living organism. If anyone can comment/add to this, that would be quite welcomed.

Here's an image that suggests what this dinosaur would look like, given the discovery and analysis of the Sinosauroterpyx's melanosomes, acquired from the fossil you provided a picture of.


The following answer was giving by Michael D. Dryden from https://chemistry.stackexchange.com/questions/24797/what-is-a-triglyceride/24799#24799

There is some minor argument as far as nomenclature goes for these lipids. Most sources I can find, including IUPAC have glycerides as only including esters of glycerol with fatty acids. Monoglycerides have a single fatty acid ester with two free OH groups, diglycerides have two fatty acid esters, and triglycerides have three. Phosphoglycerides are defined separately as esterified derivatives of phosphatidic acids, so you can think of them like glycerides where for one of the substituents, instead of a fatty acid, some derivative of phosphoric acid is present. However, the way the two terms are defined, they don't encompass any common molecules, i.e. there are no molecules that are both glycerides and phosphoglicerides and neither group is a subset of the other.

So: mono-, di-, and triglycerides are subsets of glycerides while phosphoglycerides are a different group altogether, though structurally similar.


Genes, chromosomes, base pairs and the 23 pairs

I will start from the small and go to the big organisational unit:
All of this is constructed by DNA, the sequence of the four bases: adenosine, thymidine, cytidine and guanosine.  They are abbreviated G, A, T and C and are called the letters of DNA.

Genes are organisational units formed by a specific sequence of the four "letters". Genes encode for all the proteins (in fact this is a simple view, but should be enough for the moment) and are the way the information of how the protein sequence looks is conserved.

All DNA is organised in the form of a long string of bases, which would be very long in higher organisms. To come around this problem, the DNA is organised in chromosomes, in which the DNA is wound around special proteins (the histones) and further wound up to get a compact form.  The image below (from here) shows the relationship:

The 23 chromosome pairs are the 23 organisational units in humans, in which our genetic information is stored and organised.  A picture of them looks like this (image from the same website as above):

Please note that the chromosomes are not X-shaped, although they might look like on the image. They are pairs of long DNA molecules, which are not connected.


How to model species interactions on population size dynamic?

You can write these equations in the form of ODEs but it is not really essential.

This is my analysis (just the model formulation and not literature):

The effects of interactor species may or may not be dependent on the population of the species that is being analysed (recipient). Now you have to model based on how you would realistically expect the interactions to have an effect on a species. A simple assumption would be that the interaction improves or reduces fitness (growth rate), additively. So you can model the effects as:

$$N_{t+1} = (r_0 + \beta_a + \beta_b + \beta_c) N_t$$

where $\beta_x$ denotes the effect of species $x$ which in turn you can model as dependent ($N_tN_{x_t}\alpha_x$) or independent ($N_{x_t}\alpha_x$) of the recipient population. Now, you can also impose a condition that the growth rate cannot increase beyond a certain value and so you can model it as a saturating function. A logistic or a Michaelis-Menten like function would work. For e.g:

$$\begin{align} r &= \frac{r'}{K+r'}\\[1em]
 r' &= r_0 +  \beta_a + \beta_b + \beta_c\end{align}$$

You can likewise adapt model using the logistic equation.


If I am myself not mistaken, the table shows the paths of least resistance. There are many paths through this table and all of them are not shown only the ones that cost the least. You need to understand that a mismatch between the letters costs -1 (eg - AT), but an empty square  costs -2 (-A or -T). So your solution would cost = -1-3-4-3-2-4 which sums up too -17.
This is a full alignment table. The top value is going diagonal, the second value is going down and the third value is going right.


Do men have significant hormonal cycles?

Short answer: yes.

Although clearly the infradian changes in steroid hormones in females are quite "obvious", other changes are less evident, but happen nonetheless in males as well as in females.

Most of the hormones produced by endocrine organs such as the hypothalamus (a region at the base of the brain) or the hypophisis are not secreted in a continuous manner but rather in pulses. The exact frequency/amplitude etc. of these pulses can be different depending on the species considered, but (as fare as we know) the undelying mechanism are fairly conserved.*

In general, you can find circadian (~24 h), ultradian (<24h) and infradian (>24h) rhythms.

For instance these graphs show the concentration of cortisol, aldosteron and renin in a man, showing a strong circadian rhythm.

From: Charloux et al. - Am J Physiol Endocrinol Metab 1999

You can see that on top of the circadian rhythm, an ultradian pulsatility (every ~2-3h) is also quite clear.

Another example is that of GH (growth hormone): here you see secretion of GH in an healthy women (top) and an healthy men (bottom)

From: van den Bergh et al. - J Clin Endocrinol Metab. 1996

Many other hormones show this type of rhythmicity in males, such as testosterone, LH, GnRH, and probably many other.

I am not aware of long term studies on this matter.

* Actually, the mechanisms underlying pulsatility are still poorly understood.


First: what is inflammation.  From wikipedia
https://en.wikipedia.org/wiki/Inflammation

  Acute inflammation is the initial response of the body to harmful
  stimuli and is achieved by the increased movement of plasma and
  leukocytes (especially granulocytes) from the blood into the injured
  tissues. A series of biochemical events propagates and matures the
  inflammatory response, involving the local vascular system, the immune
  system, and various cells within the injured tissue.

Second re shock: why does it happen?  If I go into shock from blood loss after a terrible knife juggling accident I will probably not have the inflammatory piece: I am dying from lack of blood and consequent low blood pressure.

What if I am in septic shock?  That means shock caused by organisms, usually bacteria, in the blood stream.  Bacteria are the ancient enemy and we have layers upon layer of defense accumulated over evolutionary time.  The reason we have them is that somehow, our ancestors that had them had some fitness advantage - probably because they survived having bacteria in the blood.

Some of the stuff that comes with that package does not seem very adaptive - like the leaky vessels and lungs filling up with fluid.  Maybe we see the wild extreme of this reaction but to a lesser degree (lesser infections?) those inflammatory responses are good?  Maybe releasing a storm of neutrophils has unavoidable side effects for the surroundings - like the Avengers fighting an alien army in NYC?  It was tough on NYC.  Maybe those extreme shock reactions save the organism 1 time in 10, which is better than the odds otherwise with an overwhelming bacterial infection.

Bottom line though is that bacteria in the blood in great numbers is an existential threat to the organism.  Desperate times call for desperate measures.


Did you say warm-blooded?

Despite the definition you cite from Merriam-Webstre Dictionnary, the term warm-blood is very unclear. The correct terms are endo-, exo-, poikilo- and homeo- therm. In short…

Source of heat

endo = inside
exo = outside

Variation in inside temperature

Poikilo = varies
homeo = does not vary

Please note, that these terms refer to extreme cases. There are organism which temperature are extremely constant (homeotherm), organisms which temperature are extremely variable (poikilotherm) and anything in between.

Any combination of these two axes exist. For example: If the temperature in the environment never varies you can be homeotherm without needing to be endotherm. Also, some organisms manage to keep a quasi constant body temperature via behavioural actions (moving to the sun when cold, going into the water when it's hot). A fun example (although debated to what I've heard) are the large dinosaurs that are thought to be homeotherms because their metabolism produce some heat and they are so large that they remain warm thanks to this heat source. However, they were probably not able to regulate actively their temperature. Therefore, I would tend to qualify dinosaurs as homeo-exo-therm but I wouldn't be surprised if someone prefers to call large dinosaur homeo-endo-therm individuals.

Opah fish

From what your second quote, it sounds like the Opah fish is endotherm. It is unclear from the quotes whether Opah fish are homeothermic.

Wegner et al. (2015) is a great read on the subject. Below is their abstract but I recommend reading the whole paper, it is easy to read and is very short (3 pages).

  Endothermy (the metabolic production and retention of heat to warm body temperature above ambient) enhances physiological function, and whole-body endothermy generally sets mammals and birds apart from other animals. Here, we describe a whole-body form of endothermy in a fish, the opah (Lampris guttatus), that produces heat through the constant “flapping” of wing-like pectoral fins and minimizes heat loss through a series of counter-current heat exchangers within its gills. Unlike other fish, opah distribute warmed blood throughout the body, including to the heart, enhancing physiological performance and buffering internal organ function while foraging in the cold, nutrient-rich waters below the ocean thermocline.

In the whole, paper, I could not find a mention of how much variation in body temperature there is. They highlight however that the point of such adaptation is for foraging in cold waters suggesting that they would just make a boost of temperature in extreme cases but not necessarily actively maintained a constant temperature otherwise. I would tend to think that Opah fish are much more variable than birds or mammals. To reinforce my believes, in the wikipedia > Opah fish it is written (without reference unfortunately) "The opah is not homeothermic like birds and mammals".

FYI, this answer was written by partially recycling this other answer of mine.


Such projections are more formally known as spiculations. Most commonly, we talk about spiculations with respect to the radiographic appearance of malignant breast and lung lesions. This paper* describes the correlation between the mammorgraphic appearance of spiculated breast lesions and their pathology (microscopic appearance), which is a reasonable start at addressing the "why" question you pose. The authors define spiculations as follows:

  A spiculated breast lesion is defined as a mass or an architectural distortion characterized by thin lines radiating from its margins.

Here is a picture taken from that paper which shows the mammographic appearance on the left and the microscopic appearance on the right, with the arrows pointing to the spiculations.

The linked paper gives many other examples of the microscopic and radiographic analysis of such tumors. It also explains that the two primary reasons for the spiculated shape are:

desmoplastic response
tumor infiltration (which occurs along anatomic ductal structures)

According to this report, the first explanation is more common. To understand the why behind the shape, we need to know the mechanism of this desmoplastic response. As described in the linked Wikipedia article, desmoplasia is not actually the tumor itself but dense fibrous tissue that is induced with malignant tumors invade healthy tissue. The mechanism of this is not entirely clear, but the Wikipedia article sets forth two theories:

The reactive stroma hypothesis postulates that tumor cells cause the proliferation of fibroblasts and subsequent secretion of collagen that acts as a scaffold. This scaffold apparently forms the outline of the "crablegs".
The tumor-induced stromal change hypothesis states that tumor cells themselves differentiate into fibroblasts and secrete the collagen that forms the spiculated scaffold.

*Franquet T, De Miguel C, Cozcolluela R, Donoso L. Radiographics. Spiculated lesions of the breast: mammographic-pathologic correlation. 1993 Jul;13(4):841-52.


What are the biochemical processes occurring when food spoils?

During putrefaction of animal tissue, lysine is decarboxylated into cadaverine and arginine is decarboxylated into putrescine. These compounds are deemed to be toxic.

A serving of meat contains 8 g of protein, corresponding to 640 mg lysine and a little bit less of arginine. Let's go straight and say that a spoiled meat serving contains 640 mg cadaverine and a little bit less of putrescine.

In rats, the acute oral toxicity for both polyamines is around 2000 mg/kg, let'assume that this is valid for humans also. According to these rough calculations, to have an acute toxic effect, a 70kg man that is resistant to the direct toxic effects of microbes, should eat 140 grams of cadaverine, corresponding to 218 smelly rotten meat servings.

[composition and toxicity data taken from wikipedia]


How does CO2 gets diffused into the red blood cells?

The red cell membrane is highly permeable to gases because the molecules of gases are small, uncharged, and soluble in lipids, such as those of a bilayer.The effect of 4,4′-diisothiocyanato-stilbene-2,2′-disulfonate on CO2 permeability of the red blood cell membrane Remember red blood cells are  cells like any other cells only that they have hemoglobin and no nucleus. Because they have an ordinary cell membrane, it follows that the laws of diffusion which apply in gases and other cells will also apply with gases and RBCs. Oxygen is the major gas which gets into RBCs, so is carbon monoxide and others


How to best conserve a beetle inside a jar?

The answer to this question depends on how you want to preserve it - as a pinned specimen (also dry preservation, most common) or in a liquid. If you want to pin it, placing it in a jar with a cottonball soaked with ethyl acetate (also used in killing jars) is good because it softens the muscles and makes the insect easier to pin and mount. Beetles are then usually pinned with a needle through the right elytra (wing cover), but there are also other ways to pin them. You can also glue the beetle to a piece of cardboard, which is then pinned. Gluing insects generally helps to protect them (so that legs and antennas dont fall of when handling them), but makes it more difficult to see the ventral side and it can also be cumbersome to have large glued beetles in a collection.

If you want to keep it in a liquid, 70-80% alcohol (ethanol) is a good choice, but not stronger (95% alcohol makes the insect stiff and brittle and might distort smaller insects). As you say, formaldehyde is generally not used since it's very toxic and it can also make the insect stiff.

Here are some more good tips on collecting and conserving insects from the University of Minnesota.


Forum on synthetic biology and hypothetical biology?

Your best bet might be the sub forum on reddit specialized in synthetic biology. Have a look here

Happy science!


Fatty acids are usually not considered polymers.

From a biological viewpoint this is simply because there is only a very limited set of chain lengths that exists in nature (~2-20 or so) and also even numbered chains are much more common than uneven numbered ones. In contrast to this 'true' polymers can have an arbitrary length of chain length (of course there is still a limit in biology, but not a super strict one) and no specific lengths are favoured.

From a chemical viewpoint fatty acids are also not really a polymer: you can't just take a bunch of alkyl monomers and fuse them to one long fatty acid  chain, because simple alkyl monomers don't have chemical groups that allow this reaction to take place (making C-C bonds is chemically not the easiest thing to do).


Why doesn't blood remain on a mosquito's proboscis in quantities that could spread blood-borne diseases?

A mosquito's proboscis isn't like that of a butterfly, which could easily have nectar clinging to it when it is coiled up; instead, consider that the part of the mosquito's proboscis that enters a blood vessle is probably wiped clean when it is retracts outward through the epithelium. A a dirty needle or razor is many, many times larger than the sucking parts of a mosquito, and a razor is an unlikely vector of HIV.

Epithelial tissue consists of cells very tightly bound together; it has to be to prevent constant invasion by bacteria, fungi, etc. It takes some considerable force or sharpness to penetrate. If you've ever watched someone give you an injection (a vaccine, for example), the needle is never bloody upon withdrawal. You might get a bead of blood from the wound, but the needle itself will be quite clean. The reverse is also true due to essentially the same reasons: the likelihood of introducing a pathogen by dragging it from the surface into the subcutaneous area is so low that there is no absolute need to swab visibly clean skin before giving a subcutaneous injection:

  Although skin that is visibly soiled or dirty must be washed, swabbing the clean skin of a patient before giving an injection is unnecessary. Studies suggest that there is no increased risk of infection when injections were given in the absence of skin preparation. (WHO Bulletin)

HIV is the most serious virus (aside from Ebola, about which much is still unknown) which can be transmitted by needlestick. Sharps injuries - needles, suture needles, scalpels, lancets, etc. - are very common in the medical field, estimated to be much higher than 350,000/year due to underreporting and occurrence in non-hospital settings, e.g. nursing homes, etc. Of course, in the majority of sharps injuries, the sharp wasn't likely to have been used on someone with HIV. Still. HIV is not rare.

Even with a potential half-million exposures a year to sharps, as of December 31, 2013, only 58 confirmed occupational transmissions of HIV and 150 possible transmissions had been reported in the United States. Of these, the vast majority follow hollow needle sticks (88%), where blood drawn from a patient still remains in the bore of the needle which can be reinjected into the unfortunate recipient. If the patient is terminally ill with AIDS, the incidence of transmission by hollow needlestick is increased, meaning the viral load in the blood is important. A solid needle, even a bloody one, presents a very low risk (the risk is, in fact, unknown*.) Getting blood splashed in the eye is a higher risk than a sharp solid (i.e. suture or lancet) needle.

The piercing mouthparts (The mandibles and the maxillae) are solid, akin to a solid sharp. Only the twin tubes (the hypopharynx and the labrum) actually reach blood.

So, given the combined factors of limited survival of HIV on exposed surfaces, the small size of the proboscis (compared to a suturing needle or a lancet, both of which have a higher surface area, yet not known for certain ever to have transmitted HIV), the low probability that the mouth parts have HIV-laden droplets of blood on it, the fact that only the tip of the hypopharynx and labrum encounter blood (the fluid most likely to contain virus) and the extremely low probability that there are enough actual HIV viruses to cause an infection anywhere on the proboscis, I hope this answers your question.

Edited to add: I've focused on HIV here, because it's not known to infect mosquitoes. Mosquitoes are considered by many to be the most dangerous animal in the world. They transmit a significant number of viruses and parasites (like dog heartworm, elephantiasis, dengue fever, equine encephalitis, etc.), but (hypothesized from those diseases that have been studied in mosquitoes) only after being infected by the pathogens themselves. Some die of the infection; some die before the infection spreads through the mosquito's body, some don't harm the mosquito. But transmission is from infected saliva injected into or onto the bite site, not virus particles on the proboscis, as evidenced by the need for adequate incubation time between the bite that takes up the virus to the bite that transmits the virus. If there was sufficient virus on the surface of the proboscis, that incubation time would not be necessary.

Best infection control practices for intradermal, subcutaneous, and intramuscular needle injections
Workbook for Designing, Implementing and Evaluating a Sharps Injury Prevention Program
Occupational HIV infection among health care workers exposed to blood and body fluids in Brazil
Needlesticks: What you must know


Is there any evidence of increased life expectancy for animal species?

As far evolution is concerned, there is no benefit whatsoever in having long lived individuals. Evolution only "cares" about individuals while they are capable of reproducing. Survival past the maximum age of reproduction is irrelevant from the evolutionary point of view since it does not make you any better at reproducing, and therefore your genes will not be selected for.

This is highlighted by the various species that die to give birth to or feed their young. One of my favorite examples is the giant pacific octopus (Enteroctopus dofleini) whose females lay their eggs and then die, leaving their body to feed the emerging young.

Now, a mutation that makes an individual both longer lived and capable of reproducing at a greater age could well be selected for. It just always needs to be combined with the ability to reproduce. By itself, dying older will confer no selective advantage unless it is combined with producing more offspring.


Highly spherical Radiolaria; does this image accurately depict the organism?

According to the Marine Species Identification portal, the presence of these thorns is variable.  They also vary in size, shape, and the presence of polygonal frames.  I don't think there is anything about the imaging process described that would result in the uniform loss of spines (unless the sieve/microsplitter broke them all, but I think that would be a non-uniform loss).

Re: whether it's hollow or not, that appears to be variable too.  One species is filled with oil, while another appears to be hollow.


Gestation period of African savanna elephants?

The African bush elephant and the African savannah elephant are the same species (i.e., they are just different names for Loxodonta africana).

According to here and here, the African savanna/bush elephant (Loxodonta africana) has a gestation period of 22 months.

The only other African species of elephant, the African forest elephant (*Loxodonta cyclotis), has a gestation period of 20 - 22 months (see here). Both Wikipedia and this source corroborate this higher expected range of 22 months, but with the latter source adding:

  from zoo data a gestation length averaging 660 days has been determined while the average in one wild population (Amboseli) was 656 days.

And for fun, click below for a video of an elephant fetus!


How can there be a one-to-one correspondence between RNA and genes?

Very few things are that clear cut in biology. There are three main things to consider here.
1. Gene to RNA
Most eukaryotic genes are spliced. This is basically a process by which a single gene can be transcribed to multiple, different, mRNAs each of which will then be translated to a different protein.
Therefore, there is usually (some genes aren't spliced) not a one-to-one correspondance between a gene and the mRNAs it can produce.
2. RNA to Gene
The next issue is that some genes exist in multiple, similar copies in the genome. For such genes, it is not always possible to know which of the duplicates was actually read to produce a given mRNA.
There is, therefore, not always a direct one-to-one correspondance between an mRNA and the gene it was transcribed from. This, however, is far less common than the splicing issue mentioned above and can, in most cases, be ignored.
3. Each gene is only on a single strand
Each gene is only on a single strand of DNA. Yes, DNA is double stranded, but each gene resides on only one of the two strands (the other strand will be the reverse complement of the gene).

Despite the points made above, it is actually usually possible to map an mRNA molecule to the gene that produced it. In the case of duplicate genes you'll just get multiple hits. The programs that exist to do this sort of analysis can mostly deal with splicing. So, for example, if you have the sequence of the human chromosome 21 and the mRNA sequence of the ERG gene, you can do (on a *nix system with exonerate installed):
exonerate -m coding2genome -t chr21.fasta -q dscam.fasta > out

Which will produce:
Command line: [exonerate -m est2genome -n 1 -t chr21.fasta -q erg.fasta]
Hostname: [oregano]

C4 Alignment:
------------
         Query: gi|609878487|ref|NM_001291391.1| Homo sapiens ERG, ETS transcription factor (ERG), transcript variant 8, mRNA
        Target: gi|528476536|ref|NC_018932.2| Homo sapiens chromosome 21, alternate assembly CHM1_1.1, whole genome shotgun sequence:[revcomp]
         Model: est2genome
     Raw score: 7669
   Query range: 0 -> 1546
  Target range: 39594417 -> 39332536

        1 : GTTTTCACTTGGTCGGAATGGGGAGAGTGTGCAAGAGATCGCTGCGGGACAGGT :       54
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||
 39594417 : GTTTTCACTTGGTCGGAATGGGGAGAGTGTGCAAGAGATCGCTGCGGGACAGGT : 39594364

       55 : TCCTAGAGATCGCTCCGGGACGGTCGTGACGGCCCCCGAGGGACATGAGAGAAG :      108
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||
 39594363 : TCCTAGAGATCGCTCCGGGACGGTCGTGACGGCCCCCGAGGGACATGAGAGAAG : 39594310

      109 : AGGAGCGGCGCTCAG  >>>> Target Intron 1 >>>>  GTTATTCCAG :      133
            |||||||||||||||++         76685 bp        ++||||||||||
 39594309 : AGGAGCGGCGCTCAGgt.........................agGTTATTCCAG : 39517600

      134 : GATCTTTGGAGACCCGAGGAAAGCCGTGTTGACCAAAAGCAAGACAAATGACTC :      187
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||
 39517599 : GATCTTTGGAGACCCGAGGAAAGCCGTGTTGACCAAAAGCAAGACAAATGACTC : 39517546

      188 : ACAGAGAAAAAAGATGGCAGAACCAAGGGCAACTAAAG  >>>> Target In :      226
            ||||||||||||||||||||||||||||||||||||||++         9093
 39517545 : ACAGAGAAAAAAGATGGCAGAACCAAGGGCAACTAAAGgt.............. : 39517505

      227 : tron 2 >>>>  CCGTCAGGTTCTGAACAGCTGGTAGATGGGCTGGCTTACTG :      266
            bp         ++|||||||||||||||||||||||||||||||||||||||||
 39517504 : ...........agCCGTCAGGTTCTGAACAGCTGGTAGATGGGCTGGCTTACTG : 39508374

      267 : AAGGACATGATTCAGACTGTCCCGGACCCAGCAGCTCATATCAAG  >>>> Ta :      312
            |||||||||||||||||||||||||||||||||||||||||||||++
 39508373 : AAGGACATGATTCAGACTGTCCCGGACCCAGCAGCTCATATCAAGgt....... : 39508326

      313 : rget Intron 3 >>>>  GAAGCCTTATCAGTTGTGAGTGAGGACCAGTCGT :      345
             130340 bp        ++||||||||||||||||||||||||||||||||||
 39508325 : ..................agGAAGCCTTATCAGTTGTGAGTGAGGACCAGTCGT : 39377955

      346 : TGTTTGAGTGTGCCTACGGAACGCCACACCTGGCTAAGACAGAGATGACCGCGT :      399
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||
 39377954 : TGTTTGAGTGTGCCTACGGAACGCCACACCTGGCTAAGACAGAGATGACCGCGT : 39377901

      400 : CCTCCTCCAGCGACTATGGACAGACTTCCAAGATGAGCCCACGCGTCCCTCAGC :      453
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||
 39377900 : CCTCCTCCAGCGACTATGGACAGACTTCCAAGATGAGCCCACGCGTCCCTCAGC : 39377847

      454 : AGGATTGGCTGTCTCAACCCCCAGCCAGGGTCACCATCAAAATGGAATGTAACC :      507
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||
 39377846 : AGGATTGGCTGTCTCAACCCCCAGCCAGGGTCACCATCAAAATGGAATGTAACC : 39377793

      508 : CTAGCCAGGTGAATGGCTCAAG  >>>> Target Intron 4 >>>>  GAA :      532
            ||||||||||||||||||||||++         21741 bp        ++|||
 39377792 : CTAGCCAGGTGAATGGCTCAAGgt.........................agGAA : 39356027

      533 : CTCTCCTGATGAATGCAGTGTGGCCAAAGGCGGGAAGATGGTGGGCAGCCCAGA :      586
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||
 39356026 : CTCTCCTGATGAATGCAGTGTGGCCAAAGGCGGGAAGATGGTGGGCAGCCCAGA : 39355973

      587 : CACCGTTGGGATGAACTACGGCAGCTACATGGAGGAGAAGCACATGCCACCCCC :      640
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||
 39355972 : CACCGTTGGGATGAACTACGGCAGCTACATGGAGGAGAAGCACATGCCACCCCC : 39355919

      641 : AAACATGACCACGAACGAGCGCAGAGTTATCGTGCCAGCAG  >>>> Target :      682
            |||||||||||||||||||||||||||||||||||||||||++         19
 39355918 : AAACATGACCACGAACGAGCGCAGAGTTATCGTGCCAGCAGgt........... : 39355875

      683 :  Intron 5 >>>>  ATCCTACGCTATGGAGTACAGACCATGTGCGGCAGTGG :      719
            698 bp        ++||||||||||||||||||||||||||||||||||||||
 39355874 : ..............agATCCTACGCTATGGAGTACAGACCATGTGCGGCAGTGG : 39336142

      720 : CTGGAGTGGGCGGTGAAAGAATATGGCCTTCCAGACGTCAACATCTTGTTATTC :      773
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||
 39336141 : CTGGAGTGGGCGGTGAAAGAATATGGCCTTCCAGACGTCAACATCTTGTTATTC : 39336088

      774 : CAGAACATCGATGGGAAGGAACTGTGCAAGATGACCAAGGACGACTTCCAGAGG :      827
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||
 39336087 : CAGAACATCGATGGGAAGGAACTGTGCAAGATGACCAAGGACGACTTCCAGAGG : 39336034

      828 : CTCACCCCCAGCTACAACGCCGACATCCTTCTCTCACATCTCCACTACCTCAGA :      881
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||
 39336033 : CTCACCCCCAGCTACAACGCCGACATCCTTCTCTCACATCTCCACTACCTCAGA : 39335980

      882 : GAGA  >>>> Target Intron 6 >>>>  CTCCTCTTCCACATTTGACTT :      906
            ||||++          867 bp         ++|||||||||||||||||||||
 39335979 : GAGAgt.........................agCTCCTCTTCCACATTTGACTT : 39335088

      907 : CAGATGATGTTGATAAAGCCTTACAAAACTCTCCACGGTTAATGCATGCTAGAA :      960
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||
 39335087 : CAGATGATGTTGATAAAGCCTTACAAAACTCTCCACGGTTAATGCATGCTAGAA : 39335034

      961 : ACACAG  >>>> Target Intron 7 >>>>  GGGGTGCAGCTTTTATTTT :      985
            ||||||++         1911 bp         ++|||||||||||||||||||
 39335033 : ACACAGgt.........................agGGGGTGCAGCTTTTATTTT : 39333098

      986 : CCCAAATACTTCAGTATATCCTGAAGCTACGCAAAGAATTACAACTAGGCCAGG :     1039
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||
 39333097 : CCCAAATACTTCAGTATATCCTGAAGCTACGCAAAGAATTACAACTAGGCCAGG : 39333044

     1040 : TACGAAAACACCCCTGTGTGATCTCTTCATTGAGAGACATCCCAGATGTCCTGC :     1093
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||
 39333043 : TACGAAAACACCCCTGTGTGATCTCTTCATTGAGAGACATCCCAGATGTCCTGC : 39332990

     1094 : TGAGATCCGTGCCCTAAGTCACGTGATACAAAGAGAGCTGATCCCGGAGCTGAA :     1147
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||
 39332989 : TGAGATCCGTGCCCTAAGTCACGTGATACAAAGAGAGCTGATCCCGGAGCTGAA : 39332936

     1148 : GCCAGTCCCAGACAGTCTTATTCTGCCTCTGTTGATTTGGAGACTAAATCCACT :     1201
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||
 39332935 : GCCAGTCCCAGACAGTCTTATTCTGCCTCTGTTGATTTGGAGACTAAATCCACT : 39332882

     1202 : CAAACCATTTCATTCAAAGACCACACTAAAGGAATTAAGAGCAGATTAGCCCTT :     1255
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||
 39332881 : CAAACCATTTCATTCAAAGACCACACTAAAGGAATTAAGAGCAGATTAGCCCTT : 39332828

     1256 : TAACTAGCTTTTCAGAAAGACAGATGGGCAAAGAAGGCATCCTGGATGCCTGGC :     1309
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||
 39332827 : TAACTAGCTTTTCAGAAAGACAGATGGGCAAAGAAGGCATCCTGGATGCCTGGC : 39332774

     1310 : AGTTAGGAATAGGCCGACTTTTGAACTAACAGAAGGATCTGTCCCTCCTCGGGG :     1363
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||
 39332773 : AGTTAGGAATAGGCCGACTTTTGAACTAACAGAAGGATCTGTCCCTCCTCGGGG : 39332720

     1364 : GAAGAGCACAAAACAAGGACACTCCCCAGATTCACAGTGACCGATTATCAGTAT :     1417
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||
 39332719 : GAAGAGCACAAAACAAGGACACTCCCCAGATTCACAGTGACCGATTATCAGTAT : 39332666

     1418 : GTCACAAGAAGCCAGTCTTGCAGAGCAGAAGCATGCAACCAGTAGTATTTACAT :     1471
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||
 39332665 : GTCACAAGAAGCCAGTCTTGCAGAGCAGAAGCATGCAACCAGTAGTATTTACAT : 39332612

     1472 : CTGAATCTTACTGCCTGTCCTCCAAATGATTTAATTAGGTAATAAATTTACATG :     1525
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||
 39332611 : CTGAATCTTACTGCCTGTCCTCCAAATGATTTAATTAGGTAATAAATTTACATG : 39332558

     1526 : CCATTCATGCAAAAAAAAAAA :     1546
            ||||||||||||||| ||| |
 39332557 : CCATTCATGCAAAAATAAACA : 39332537

vulgar: gi|609878487|ref|NM_001291391.1| 0 1546 + gi|528476536|ref|NC_018932.2| 39594417 39332536 - 7669 M 123 123 5 0 2 I 0 76681 3 0 2 M 102 102 5 0 2 I 0 9089 3 0 2 M 86 86 5 0 2 I 0 130336 3 0 2 M 218 218 5 0 2 I 0 21737 3 0 2 M 152 152 5 0 2 I 0 19694 3 0 2 M 204 204 5 0 2 I 0 863 3 0 2 M 81 81 5 0 2 I 0 1907 3 0 2 M 580 580
-- completed exonerate analysis

Alternatively, you can use an online resource like the UCSC's BLAT page to align the mRNA against the genome. You can see the results here and in the image below:

As you can see, our query mRNA sequence (NM_001291391.1) overlaps perfectly with the ERC gene.


It looks like the common Geranium sylvaticum (also called wood cranesbill or Mayflower), and it is at least a close relative (member of the Geranium genus). This plant is commonly found across Europe and in parts of Asia (see map below), and it is sometimes planted in gardens. It is a perennial herb that grows in many types of habitats (woods, meadows, road sides, mountain areas), and the flowers are most commonly violet to blue, but can also be white. Geranium pratense is very similar, but usually has more narrow leaf lobes and bent flower stalks. However, it might not be possible to separate these two species based on your picture.

There are also similar relatives found in North America (e.g. Geranium maculatum) and Asia (e.g. Geranium himalayense) and many hybrids of plants from within this genus are cultivated.

(picture from Swedish Wikipedia)

(distribution map from the Swedish Museum of Natural History: Den virtuella floran)


How does further hybridization affect fertility?

Some first generation hybrids[f1] are viable and fertile, but when they mate with each other or back to either parental species[P}, the successive generations[f2] are sterile or feeble.  this concept is known as hybrid breakdown.  This is often seen in hybridized forms of domestic crops.  I am aware that some female tiger/lion hybrids are fertile, but I'm unaware of successful breeding of the f2 generations.  It could be a case of hybrid breakdown.

Article about hybrid breakdown in rice

Hybrid breakdown in Cichlid Fish


Enzyme Inhibition in relation to Aspirin

‘Reversible’ and ‘Irreversible’ are standard designations in enzyme kinetics. It may be that your instructor was using the word in this sense.

As already commented, irreversible inhibitors bind the enzyme in such a way that they don't dissociate from it. Either they form a covalent bond or their affinity for the binding site is extremely high. Reversible inhibition is generally found with competitive inhibitors — those that resemble substrate enough to bind to the active site and compete with the substrate for it. Unless they have an extremely high affinity there will be an equilibrium between bound and unbound inhibitor, and the inhibitor can be competed out by substrate — i.e. the binding is reversible.

You can read about this in more detail, but still at an introductory level, in the Wikipedia article on Enzyme Inhibitors  or this section in the online version of Berg et al.


The primer is incorporated into the start of the new strand. The number of dna strands produced is limited by the number of primers.