Why don't self pollinated crops show inbreeding depression?

Yes, self pollination does lead to inbreeding depression:

  However, we found substantial inbreeding depression, with seeds per fruit, progeny survival and progeny growth being lower after self- than after cross-pollination. Progeny arising from self-pollination also had a higher frequency of certain traits ... which were associated with lower rates of survival. ... high inbreeding depression has also been reported in other self-compatible trees ...

--Self-pollination and inbreeding depression in Acacia dealbata: Can selfing promote invasion in trees?

  Inbreeding depression is one of the leading factors preventing the evolution of self-fertilization in plants.

--Inbreeding depression in self-incompatible and self-compatible populations of Leavenworthia alabamica.

  The strategy for breeding F1 hybrid squash is to develop parental lines through self-pollination. However, it increases plant mean homozygosis, which is not the natural genetic state of a cross-pollinated species, and can cause "inbreeding depression".

--Depression by inbreeding after four sucessive self-pollination squash generations

So why don't all crops that self-pollinate show decreases in productivity? In part, they do, but the reduction in productivity caused by inbreeding is outweighed by the increases in productivity caused by inbreeding (i.e. selection for productive traits via inbreeding leads to both positive and negative results, and the total outcome is the sum of the positive and negative effects).

And partly because the deleterious effects of inbreeding can be partially overcome through "purging". The negative genes that lead to inbreeding depression when homozygous can be removed from a population as the affected individuals die (or fail to breed) and take their negative genes with them. Purging is most common when a population has a moderate degree of inbreeding over a longish time, which is what you'd expect with a crop that typically self-pollinates. It's an effect in many but not all common crops:

  Several plant species, E. g alfalfa (M. sativa) carrot (D. carota) , hayfield, tarweed etc show very high inbreeding depression. ... Many crops species, such as maize, jowar, bajara etc. shows moderate inbreeding depression. ... Several crop plants, E. g onion (A. cepa), many cucurbits, rye (S. cereale), sunflower (Hannus), hemp etc show only a small degree of inbreeding depression. Only a small proportion of the plants show lethal or subvital characteristics. The loss in vigour and fertility is small; rarely a line cannot be maintained due to poor fertility. The reduction in yield due to inbreeding is small or absent. Some of the inbreds lines may yields as much as the open pollinated varieties from which they were developed.

--Degree of Inbreeding Depression


How does isopropyl alcohol disinfect less in higher concentration?

The main reason why alcohols (isopropanol and ethanol mostly) can be used as disinfectants is that they denature (bacterial) proteins. This is also the reason why they work on such a broad spectrum of microorganisms (bacteria, fungi, viruses), but not on spores, as these are better protected.

The higher the concentration of the alcohol is, the faster this denaturation is happening. And this can cause problems: When you denature the proteins of the bacterial cell wall, they will form some kind of protective layer around some of the cells which allows their survival. Diluting the alcohols makes the disinfection happening slower and thus gives the alcohols more time to get into the cell.

For more information about concentrations and also for a ton of references, have a look into the CDC's disinfection guidelines in the subchapter on alcohols.
More details can be found in this review:

Antiseptics and Disinfectants: Activity, Action, and Resistance


Is there a difference between sleeping late and waking up late vs sleeping early and waking up early?

There is a popular theory that each person has a certain "chronotype" [Ref 1]. Based on your genetics, you could be naturally an early person ("Lark") or a late person ("Owl") [Ref. 2].  What will negatively affect your health is actually fighting what you naturally are.  You probably know which chronotype you are, and if not you can go by what time you naturally sleep/wake when you don't have school/job scheduling such as at the weekend.

[Ref. 1]:Chronotype Review
[Ref. 2]:Social jetlag paper


Can pheromones be received other than by odor?

We have only 5 senses, a 6th sense has been controversial, and some 6th senses are sometimes reported in new research in newspapers, but none have been conclusively been added to the clearly known 5. There is a second olfactory organ that deals with social signals in other animals, that we possess, the vomeronasal organ.

Pheromones are only olfactory molecules, so you can't get them other than by catching molecules and analysing them, i.e. smelling.

Humans react very strongly by attraction to some perfumes other than pheremones, and you arent supposed to block all your smells, only make them containable, a bit is probably a good thing.

Scientists did publish a study claiming that people can tell if they make a good immune response / metabolic genetic combo with a partner from smelling a potential partner's t-shirt.


What limits our ability to grow enamel rods?

Chandra's Textbook of Dental and Oral Histology and Embryology with MCQs p40-42 explains the complexity of enamel, and provides diagrams and images of real enamel.

What I didn't know before was that the hydroxyapatite is in the form of very small crystallites packed inside the key-like structure of the rods. The rods are packed together with a cement-like material. The rods themselves are segmented.

This small design and lack of vital parts suggest to me that bioglasses like Novamin would at least not recreate the natural enamel structure.

What isn't so easy to guess is whether crystallites from the components of the bioglass are formed on the existing crystallites, and if so, whether this can continue indefinitely, and with what qualities.


Is a variable domain in immunoglobulin's heavy chain different from the one in light chain?

You are correct. In an IgG antibody, there are a total of four protein chains — two identical heavy chains, and two identical light chains, each heavy pairing with a light to form one of the two "arms" of the molecule. Each heavy chain has three CDR regions — H1, H2, and H3 — as do each light chain (L1, L2, and L3). When the full molecule is assembled, three "full" CDRs are formed — 1, 2, and 3 — from the "partial" CDRs in the respective heavy and light chains.

from novimmune

You can see on the left the six individual heavy and light CDR loops separately, and on the right they are combined into the full CDR1, CDR2, and CDR3.

Here is a slightly more molecular view:


It's creepy ... something I find fascinating.

Creepy & fascinating indeed!

  Could someone tell me what this cactus-y, bed of vines-like plant is?

This is a cactus, and I believe it belongs to the genus Hylocereus, possibly the species H. undatus.

As for distribution, Hylocereus are quite prevalent throughout Hawaii, and can also be found scattered throughout the globe.

Hawaii is the leftmost blue dot. image source

More information about this plant can be found here.


What is the meaning of deep winter mixing?

The winter mixing of stratified layers in lakes and seas due to temperature changes can vary in depth, so scientists sometimes say "deeper winter mixing" and "deep winter mixing". Scientists measure the water arising from 300 or from 800 meters depending on the year, so the deeper winter mixing is a relative term. i.e.:
1992, associated with more stormy weather and higher precipitation than usual. This anomaly was the cause for the deeper winter mixing in the Cyprus Eddy (>500 m) than the typical 350 to 400 m reported by Brenner et al. (1991). Exceptionally deep vertical mixing (>850 m) was reported that winter also in the Gulf of Aqaba https://www.int-res.com/articles/meps/167/m167p047.pdf
Here is basic description of winter mixing:
https://teara.govt.nz/en/diagram/11817/water-circulation-in-a-lake

and here is a science paper:
https://www.jstor.org/stable/2259960?seq=1
A wiki page on lake stratification:
https://en.wikipedia.org/wiki/Lake_stratification


High Current (Speed) Transfer Buffer Recipe

So after a lot of work in optimization, I thought I would post what worked best for me.  This buffer recipe was able to successfully transfer EGFR and insulin from the same lysate, and a clear band for both (large and small protein respectively). 10% SDS-PAGE gels were transferred at 1A for 10 min.

High Current Transfer Buffer

48 mM Tris
15 mM HEPPS
1.0 mM EDTA
1.3 mM NaHSO3
1.3 mM N,N-dimethylformamide
25 Mm gLY-GLY
20% Methanol (v/v)

I do hope this can help someone else, and want to site Garic et al as wonderful starting point.  Their publication was made after I asked the question, as @user4148 pointed out.


How is Glycophorin A and straphylococcal related to Escherichia coli and what does readily purified mean in this context?

Basically, they engineered a vector which, when transfected to E. coli, produces transcripts of -and thus proteins to- a fusion gene which produces these transmembrane α helices conjugated to the staphylococcal nuclease. In other words, the E. coli are just factories for producing proteins:

  Expression, Extraction, and Purification of SN/GpA - For high
  levels of SN/GpA production, pT7SN/GpA was transformed into E.
  coli MGT7 (kindly provided by D. LeMaster), containing the plasmid
  pLYS-S.

And the reasoning therein was proposed in the discussion,

  We report here the use of a chimeric protein to show that
  the presence of just the transmembrane domain of GpA, fused
  to a normally monomeric soluble protein, is sufficient to
  mediate the dimerization of this artificial membrane protein
  -in SDS

What they mean by readily purified is that the protein can be extracted relatively easily, and in the experimental method they explain some commonplace methods of purification:

  One-step purification of milligram quantities of SN/GpA from the
  extract could be achieved by reversed-phase HPLC utilizing an acetonitrile/isopropyl
  alcohol/water gradient on a semipreparative Vydac
  C4 column. Alternatively, purification of larger quantities was
  achieved using two rounds of cation-exchange chromatography...

  ...The chimera SN/GpA131, but not truncated forms, could alterNaCl,
  50 mM Tris-HC1, 5 mM EDTA, 1 mM PMSF, 0.025% NaNa,
  natively be extracted by sonication of the pellet after cell lysis in 1 M
  pH 7.9, containing no detergent. This extraction was of similar
  efficiency to that with Lubrol, and was utilized in the preparation of
  material for generation of transmembrane peptide by trypsin treatment.


How are 23 chromosomes in human sperm chosen?

They are not chosen, they represent an even half, a complete set of chromosomes.

The entirity of a cells genes (found on the chromosomes) is called a genome.

Somatic cells are the cells in our bodies that exclude sperm and egg. Sperm and egg are called germline cells.

The billions of somatic cells in a homo sapien have the same 46 chromosomes. 23 ( half) of them came from dad and 23 from mom. Thus we say somatic cells have two copies of each chromosome and it is abbreviated 2n. The germline cells are 1n or just n.

So your sperm has 23 chromosomes and after sexy time one of them can combine with an egg (which also has 23) to produce a cell(called a zygote) that has an entire complete genome (46). Then that zygote splits, and splits and splits.... And each time before it splits, all 46 chromosomes are copied (the copies are called sisters, or sister chromatids, respective to each other). The cells split into two new cells called  daughter cell and each daughter has an entire genome. This form of cell splitting is called mitosis.

Probably the most important event in the cell cycle is the duplication of every DNA stand. This is called a Synthesis (S) phase. This is not a component of mitosis! It's a required event that happens before mitosis. So all 46 chromosomes get copied and then during mitosis each copy (an identical copy) is attached to each other at a region called the kinetachor. A kinetachor attaches sister chromatids (each sister is a copy of each other).

At the beginning of mitosis a web forms in the cell and you can think of the strands that make the web as sliding chains that can pull stuff from the center of the cell to 1 of two perimeter locations (poles) of the cell.

The chain like web attaches to the kinetachor and it rips apart the pair of chromosomes, rips apart the sisters. So that one sister goes to one side of the cell and the other sister chromosome goes to the other side of the cell. So now at opposite sides of the cell you have a complete genome (which will become the new daughter cells).

An identical process occurs in meiosis (specifically meiosis II) which is part of the  process that forms the sperm and the egg. During meiosis however there's additional separation (separation of homologs which occurs in meiosis I) that occurs but it's really not pertinent to your question.


How do beneficial features evolve in species without progressing through detrimental stages?

There are some interesting hypotheses that wings initially evolved for display, not flight.  Then at some point, the winged dinosaurs also had a locomotive advantage, at which point the wings could further evolve with selection for even better locomotion and eventually full flight.

Here is an article about Darla Zelenitsky's work on this:  http://phenomena.nationalgeographic.com/2012/10/25/bird-mimic-dinosaur-hints-that-wings-evolved-for-show-not-flight/

There is also an article by Richard Prum in a recent Scientific American that mentions this.https://www.scientificamerican.com/article/dinosaur-feathers-came-before-birds-and-flight/


How does changing the shape of ATP synthase specifically prevent the enzyme from working any longer?

If you look at an enzyme and its substrate you can also see this as a lock (the enzyme) and the key (the substrate). The key fits the lock and opens it, the substrate fits into the active pocket of the enzyme and a reaction takes place. See this figure for illustration (from here):

If the enzyme (or the substrate) changes its outer shape (this is what happens when amino acids of a protein are changed), this fit will not happen anymore and the reaction which is catalysed by the enzyme will not take place (the lock will not open).


Redox potentials in photosynthesis light dependent stage

You are right about the conditions in the chloroplast stroma vs. standard conditions. The pH is high (i.e., low H+) in the chloroplast compartment where the reaction takes place (within the stroma), so the pE is shifted from the nominal "pE0", which is +1.23V (effectively you push the equation to the right by low concentration of H+).

See this for a textbook-like summary of the important reactions and this for a quick problem on the math behind pE in different conditions, as well as this for more on the stroma.


By brain cells, I'll assume you mean neurons (the other type are called glial cells). Yes, new neurons arise in a least certain parts of the brain, and yes, they do cause memories to weaken or disappear. This has been shown in mice, guinea pigs and degus.

It would be wrong to assume that neurogenesis occurs with the frequency of, say, gastric cell or skin turnover. Up until recently, it was not thought to occur at all.

Learning and remembering use various cortical structures, including the hippocampus.Throughout life, new neurons (neurogenesis) are continuously added to the dentate gyrus. These additions remodel hippocampal circuits, and when this occurs after memory formation, this neurogenesis leads to degradation or forgetting of established memories. This was shown in adult mice. Conversely, decreasing neurogenesis after memory formation decreased forgetting.[1]

It is not only plasticity that makes the brain adaptable to continuous changes in environmental demands. Adult-born neurons integrate into preexisting neuronal networks and participate in information processing. Adult neurogenesis itself is a type of circuit plasticity required for hippocampus-dependent learning and memory recall. Adult hippocampal neurogenesis may also promote forgetting.[2]

The more neurogenesis there is, the more memories are broken down. Since we retain many memories over our lifetime, it's pretty safe to say out brains don't "turn over" every five years (or even over longer periods); some parts of our brain don't seem to undergo neurogenesis at all.[3]

[1] Hippocampal Neurogenesis Regulates Forgetting During Adulthood and Infancy Science 9 May 2014
[2] A Price to Pay for Adult Neurogenesis Science 9 May 2014
[3] Neurogenesis in the Adult Brain The Journal of Neuroscience February 1, 2002


This is what I think. Does it help? Let me know if you need more information.


Are there known functions of AST, ALT, and amylase in the blood?

These enzymes, while useful markers of disease, are not only produced during the disease state, and are not only produced in one organ. It is therefore not surprising that there are always low levels released into the biochemical milieu that is the blood. If there are not even low levels of the enzymes then that might indicate that the organ is not doing it's job properly.

I'll approach this from a veterinary viewpoint but I imagine it is much the same in humans. My preferred source for information about veterinary clinical pathology is Cornell's EClinpath site.

The major tissue sources of AST are liver, skeletal muscle, and cardiac muscle. A small amount is produced by erythrocytes. In lesser concentrations it is also found in renal epithelial cells and brain tissue. It therefore should be no surprise that low levels are found in blood. It is not difficult to picture a small amount of leakage from erythrocytes in the normal state, even without pathologic haemolysis, given the regular turnover of cells and permeability of erythrocytes – although I suspect this is a minor source. Just due to the fact that the liver's normal function is to deal with many cytotoxic compounds, even in the completely healthy patient there always is going to be some low level of hepatocellular damage. As a result, a very low serum level of AST might be indicative of a poorly functioning liver (e.g. with a chronic hepatitis).

Among veterinary species there is considerable variation in the clinical usefulness of ALT. For example, it is a very useful indicator of liver disease in dogs and cats, much less so in horses. Much like AST, ALT is also produced in liver, muscle, kidney, and erythrocytes.

Amylase is known to be produced by cells in the pancreas, salivary gland, duodenum, ileum, ovary, and testes. Of course, the pancreas produces the most of this enzyme, which is why it is somewhat clinically useful (though I can't say I like it much at least for veterinary species).

The bottom line is that these enzymes play an important role in biochemical reactions of many different tissues. While the enzymes may be produced in predominance in one tissue, they have the same function (at a biochemical level) in all these tissues (i.e. they convert the same reactions). I view it more as a difference of the tissue need for these enzymes rather than a difference in function between tissues.


Which part of a female mantises's DNA causes her to be a few times larger than a male mantis?

Insects and spiders have tremendous sexual dimorphism, with males often being much smaller than females.  They are pretty much just sperm carriers and sometimes do not eat.  Insects may have two or one sex chromosome, where males my have only one chromosome.   As is pointed out in the comments, not all mantis' species display this dimorphism.

Since such dimorphism is probably due to small changes in the genome due to environmental selection pressures and the genetic mechanisms of control are probably not simple.

Its difficult to say which genes are responsible for size per-se.  Recent studies of human height indicate that scores of genes may be involved in human size and insects have at least as many genes as humans do; it is pretty hard to look at a human genome sequence and say what height that person is without some other help.  I imagine for specific insect species this too would be difficult.


High Glucose vs Low Glucose DMEM for Cell Culture

We typically use High Glucose as cells grow faster.  One caveat is that there are concerns that certain protein modifications (specifically OGlnAc-ylation) may be upregulated in non-physiological (25mM or high glucose) media.


Could not fit in a comment....

To make sure we all understand your question...

Is your question how many (eukaryote) species are currently living? or How many (eukaryote) cells are currently living??

Just a hint to answer the question

Micheal Lynch, in his book (On the Origin of Genome Architecture) at page 3, Box 1.1 tries to answer the question How much DNA is there on earth?. He ends up with an estimation of a total length of DNA on earth of $10^{24}$ km for procaryotes, $10^{25}$ km for eukaryote (of which $\frac{1}{1000}$% is accounted to humans). This sums up to a total DNA length of $10^{12}$ light-years, or 10 times the diameter of the known universe!

In his calculations, he estimates that the total number of procaryote cells at $10^{30}$ (citing Whitman et al. 1998 as you did). He estimates the total number of eukaryote species to $10^7$, i.e. 6 times the number of known eukaryote species. However, he doesn't directly give any reference for this estimate but he refers to different chapters in the book that contain lots of references.

...I hope that helps...


The short answer is the transcription machinery will only bind on the correct orientation.  The binding of proteins and such to the promoter DNA strand is determined by the sequence of the DNA, the sequence is not correct on the anti-sense strand for a given gene.


Is "muscular attachment" synonymous to tendon? (when talking about the insertion of glutei medius and minimus to greater trochanter of the femur)

The tendon and muscle attachment are not the same. In your example, both are affected, so they are described separately.

A muscle extends into a tendon and this into an enthesis - an actual attachment site where the muscle is attached to the bone (PubMed).


Which processes are during the latent period of ventricular contraction?

During the latent period of ventricular contraction, excitation-contraction coupling takes place.

There may be other processes, but I think most are these from Wikipedia:

An action potential is initiated by pacemaker cells in the Sinoatrial node or Atrioventricular node and conducted to all cells in the heart via gap junctions.
The action potential travels along the surface membrane into T-tubules (the latter are not seen in all cardiac cell types) and the depolarisation causes Ca2+
to enter the cell via L-type calcium channels (also known as Dihydropyridine receptors) and possibly sodium-calcium exchanger during the early part of the plateau phase. This Ca2+
influx causes a small local increase in intracellular Ca2+
.
The increase in Ca2+
is detected by ryanodine receptors in the membrane of the sarcoplasmic reticulum which releases Ca2+
in a positive feedback physiological response. This positive feedback is known as calcium-induced calcium release and gives rise to Calcium sparks.
The spatial and temporal summation of ~30,000 Ca2+
sparks gives a cell-wide increase in cytoplasmic calcium concentration.
Contractile mechanism similar as in skeletal muscle about cytoplasmic calcium binding to troponin C and so on.

Note that to fully answer this question you should include figures about mechanisms of excitation-contraction coupling, cardiac action potential -figure and permeabilities of different ions.


Dry Bulb Temperature VS Dew Point, which one is most relevant to insects?

Insect development and activity are strongly associated with dry-bulb temperature. Development rate is usually predicted using degree-days (Links here: http://ipm.ucanr.edu/WEATHER/ddconcepts.html and https://entomology.ca.uky.edu/ef123). Basically this takes advantage of the nearly linear relationship between development rate and temperature in almost all insects (in some the type of food available can also be limiting). At temperatures above a certain threshold -- usually around 50 F or 10 C --  the warmer it is, the faster development will take place, up to a certain temperature cut-off above which development is drastically slowed (varies widely from species to species).

Insect activity is also strongly associated with dry-bulb temperature. In general most insects cannot fly at temperatures much below about 50 F or 10 C. They cannot generate energy fast enough at lower temperatures. The species that do fly at lower temps are generally Hymenoptera or Lepidoptera that use group or individual muscle movement to generate heat. Those that do fly in cooler weather or at night are often covered with fur or hair, which allows them to retain more of the heat generated by their flight muscles.

Wet bulb temperature generally relates to relative humidity, which has little to do with insect activity except in extremely hot, dry environments, wherein insects will be much more active during higher relative humidity (as it helps them retain more moisture) times of day such as morning or evening.

I hope this helps.


Why in some cells is GTP made in citric acid cycle and in some ATP?

This step is catalyzed by succinyl-CoA synthase which has two different isoforms- one which produces GTP while the other produced ATP.
It seems from this study that predominantly anabolic tissues prefer the GTP-producing form whereas the predominantly catabolic tissues use the ATP-producing from.
In the same paper they discuss that GTP is important for protein synthesis and it is also involved in production of phospho-enolpyruvate by PEP-carboxykinase in mitochondria; therefore playing an important role in anabolic processes.


Gibson Assembly is not ideal for short fragments; chances are that the T5 Exonuclease will digest your entire fragment before it has the chance to hybridize with the backbone. For fragments shorter than 200 bp NEB recommends a 5-fold excess to compensate for this, but in your case the fragment would only be around 130 bp long. It might work, but efficiency will be very low.
Either way, based on my understanding that you don't have the 3xtag-TEV sequence available as PCR template, what you would need is two long primers designed such that they overlap by 20-25 nt at their 3' ends (orange), and with the backbone at their 5' ends (blue) as shown below:

You would then run PCR cycles with the primers alone to generate your double-stranded fragment, which you can then use in the Gibson Assembly reaction.
If you're not using a commercial Gibson Assembly kit, but instead add the enzymes yourself, you can also try an alternative method called TEDA cloning. The procedure is practically the same as that of Gibson Assembly, but TEDA uses only T5 Exonuclease. Instead of relying on (very expensive!) Phusion DNA Polymerase and Taq DNA Ligase for sealing the plasmid, plasmid repair in TEDA happens after transformation into bacteria, taking advantage of E. coli's own DNA repair machinery.
In your case, the advantage with TEDA is that you can try different incubation times with T5 Exonuclease to find a short enough incubation time such that single-stranded 5' homology ends are generated without digesting your entire fragment; or even incubate your backbone first and add your short fragment later in the TEDA reaction. As an extra bonus, TEDA cloning costs a fraction of the price of a Gibson Assembly reaction.


Validation of houskeeping genes in a mixture of cDNAs of two species

Two possibilities:

Design primers based on differences in the sequences of the gene for the same protein between the two organisms. (Suggested by @Artem)
Identify an aspect of the metabolism of your parasite that is not present in the host, then use enzymes from that pathway. If the parasite is a worm and the host a mammal, for example, you should surely be able to find something.


What is the biological basis for the perception of time?

I'm no expert on the topic, but was about to find the following;

In mammals, the hippocampus region of the brain is one of only 2 regions with the capacity for lifelong neurogenesis (the creation of new neurons). This happens continuously with the creation of new memories and experiences (neurons are even created just to mark time passing - even if no memories are stored alongside - so that a perception of 10mins and 10secs is possible, even if nothing memorable happens). As new clusters of neurons are generated, they gradually differentiate and mature to become fully functional, and in this way time and memory are interlinked, and experiences are clustered together [1].

In a human study where individuals were asked to recall whether news events occurred within 1 week of each other (some related, some not), same-week and separation judgements were more far more accurate for related events. Unrelated events were essentially guesses, whereas deductions could be made about related events. [2]. This lends weight to the above argument that memories are clustered in the brain with temporal information embedded within.

The hippocampus is also involved in imaging the future. (Inconsistent) findings suggest that activation of the hippocampus allows mammals to conceive a scenario constructed from previous memories and experiences, and to store these for later use [3].

Refs

Aimone, J. B., Wiles, J., & Gage, F. H. (2006). Potential role for adult neurogenesis in the encoding of time in new memories. Nature neuroscience, 9(6), 723-7. doi:10.1038/nn1707
Friedman, W. J., & Janssen, S. M. J. (2010). Do people remember the temporal proximity of unrelated events? Memory & cognition, 38(8), 1122-36. doi:10.3758/MC.38.8.1122
Addis, D. R., & Schacter, D. L. (2011). The hippocampus and imagining the future: where do we stand? Frontiers in human neuroscience, 5, 173. doi:10.3389/fnhum.2011.00173


For fluorescence immunocytochemistry, there are 3 main incubations that determine duration of the procedure. Generally it takes 2 days to stain your cells before you can visualize them. Once cells or tissue are fixed onto glass, you first incubate with a primary antibody to directly target a specific antigen(s), usually overnight. After primary labelling, a secondary antibody is applied to target the primary antibody, which usually takes a few hours. These secondary antibodies come conjugated to some fluorescent dye (Cy5, TRITC, FITC, AlexaFluors, etc). A nuclear counterstain is really quick, only 5 minutes. After all the labelling and nuclear stain, you can mount the coverslip with mounting media and once it cures you can visualize them.

Abcam has one of many quick reference guides.


Previously frozen papaya seeds sprouted. How will it affect the plants?

Seeds are generally made in order to stand dry/cold conditions.
I don't see any reason to believe that the DNA got damaged during freezing (that could cause mutation and phenotypic changes). So, if they have germinated, the plants should not be any different from the controls.


Under what circumstances will a human neuron divide?

Mature, differentiated neurons do not divide (undergo mitosis), but apparently there is a small population of self-renewing neural stem cells in adults that can produce new neurons. Neurogenesis predominantly occurs in the subventricular and subgranular zones of the brain.

Peripheral nerves can regenerate along its axon as long as the endoneurial tube and the Schwann cells are intact. Here's a picture of a neuron regenerating.


Why not self pollination for finding the genotype instead of test cross?

Because for test cross you need to phenotype far less progeny to be reasonably sure about parent genotype. Lets say you decide to phenotype N progeny. If the tested parent is heterozygote the random chance of you getting all N plants tall is (1/2)N for test cross and (3/4)N for self pollination.

So for example if you decide to phenotype N=8 progeny plants in case of self pollination (3/4)8=10% of your heterozygous parents will be wrongly assigned as homozygous which is error too high for almost anything serious. In case of test cross (1/2)8=0.4% of your heterozygous parents will be wrongly assigned as homozygous. To achieve the similar level of accuracy with self pollination you would have to phenotype N=19 or N=20 progeny plants.

The difference does not seem like much when testing one parrent but if you need to test many the costs will add up.


What purpose does the wax coating on blueberries serve?

My uneducated guess is that the wax is called Epicuticular wax.

  The main functions of the epicuticular wax are to decrease surface
  wetting and moisture loss. Other functions include reflection of
  ultraviolet light, assisting in the formation of an ultrahydrophobic
  and self-cleaning surface and acting as an anti-climb surface.


An assay may be thought of as a trial or test that is designed to quantitatively determine the amount of a substance in a sample.

Thus a biochemist might use a protein assay to quantitatively determine the amount of protein in a sample, or a pharmacologist might assay a sample to quantitatively determine the amount of drug present, or an enzymologist might carry out an enzyme assay to determine the amount of enzyme activity in a sample.

Let's take the case of the enzymologist. I take a liver sample, homogenize it, centrifuge and take the supernatant (soluble) fraction. I want to quantitatively determine the amount of a given enzyme activity.

I do this by performing a test by (say) adding a sample of the supernatant to a cocktail that 'does something' only if the enzyme of interest is present.  The 'do something' could be a color change, where the cocktail  contains  everything needed for the enzyme to work (all substrates, cofactors etc) and where the enzyme transforms one of the substrates to a coloured product.  I now have an enzyme assay which tells me if the enzyme is present (the trial), which may be made quantitative with reference to the amount of color produced in a given time.

As I remember things, Sherlock Homes was pretty good at the assays, using them to make trials of his geological samples, but I cannot find the quote.


What can we infer from Warburg's Flashing Light experiment?

according to my understanding, if we compare two situation 1. one hour continuous illumination and other 2. alternating period of light and dark (but the illumination time remain same). the rate of photosynthesis will be more in second case which indicate that even in dark, photosynthesis is taking place (ie. dark reaction)...just my thought...


What processes are responsible for focusing on an image only seen by one of the eyes?

Short answer
Image blur on the retina is the most important monocular cue for lens accommodation.

Background
Focussing of an image on the retina is mediated by the lens. Re-shaping of the lens to focus the image on the retina is called accommodation. In general , the main cues for focussing are retinal disparity and blur, and to a lesser extent proximal cues such as looming, motion parallax and overlay of contours.

When looking with two eyes (binocularly) at an object, retinal disparity is by far the most important depth cue for accommodation. The two eyes look at an object from slightly different angles, so they get slightly different views of it. This difference is the disparity (imperfect match) between the two views. The visual system normally fuses these two images into a single perception and converts the disparity between the two images into perception of depth (Source: Indiana university).

When only one eye is available (monocular focussing), use of retinal disparity isn't possible, and retinal blur becomes the most important factor for lens accommodation. When an image is out of focus, its representation on the retina is blurry. By adjusting the shape of the lens the visual system adjusts the image projection to bring it into focus such that blur is minimized (Horwood & Riddell, 2008). Looming (incoming object becomes apparently bigger), motion parallax (objects further away move slower across the field of view) and overlay of contours (objects closer by obscure things further away) also provide monocular cues for accommodation.

Reference
Horwood & Riddell, Vis Res (2008); 48:1613–24


What is the significance and method behind Ramachandran plots?

Ramachandran plots show the relationship between the phi and psi angles of a protein referring to dihedral angles between the N and the C-alpha and the C-alpha and the C-beta. As an aside, the omega angle between the C-beta and the N tends to be fixed due to pi-pi interactions.

Dihedral Angles

There are limits to possible distributions of phi and psi angles due to steric clashes between the side chains. Furthermore other limitations from higher order structure will result in the adoption of defined phi-psi angles. Using data from solved crystal structures, it can be seen that the dihedral angles will adopt specific conformations in a protein.

RAMACHANDRAN PLOT from Lovell et al.

Furthermore, it can be noted that some of these conformations relate to specific secondary structures. As seen above, peptides in alpha-helices and beta-sheets adopt a even more limited set of phi-psi angles. Certain amino acids like glycine and proline, which differ from from canonical amino acids have an unique Ramachandran plot.

The angles from a Ramachandran plot are useful not only for determining a amino acids' role in secondary structure but can also be used to verify the solution to a crystal structure. Furthermore, it assists with constraining structure prediction simulations and helps with defining energy functions.


Why do mammals in the wild retain the "trait" of menstruating with blood?

I would guess that the answer is something like this: ever since the development of the placenta enabled females to carry their offspring longer and to develop more fully.  Upon birth they were stronger and/or their brains were more fully developed (in the case of humans).  The increased gestation time, made possible by the structures of the womb and placenta is probably an adaptation whose advantages are much greater than the increased risk from menstruation once a month.

Some anthropological studies indicate that in preindustrial societies that women do not menstruate very much as adults though.  If you subtract out the time that they are carrying infants and nursing, which both prevent menstrual cycles, females will miss years of menstruation with only a few months in between. I would assume this is a factor in the risk of menstruation for many animals.


Why does sulfonamid not inhibit the growth of Rickettsia?

Sulfonamides competitively inhibit the enzyme dihydropteroate synthase, which is involved in the tetrahydrofolate synthesis pathway in most bacteria. Rickettsia lack this enzyme target, and thus possess a natural resistance to the antibiotic. As tetrahydrofolate is an essential compound, it is believed that Rickettsia possess an alternative enzymatic process which is not susceptible to sulfonamides, or the bacteria simply acquire the compound (or its immediate precursors) from their environment.


Why do some proteins "use" a beta barrel structure instead of alpha helices in transmembrane space?

As you can see on the wikipedia page you linked yourself that beta barrels have far larger diameters (in some cases up to 40 angstroms as stated in this paper) depending on the numbers of beta sheets that make up the barrel, compared to the diameter of an alpha helix (that is fixed) of 6 angstroms. (source http://www.chem.uwec.edu/Modeling/GGProteinStructures/Pages/alpha_helix/helix.html). Alpha helices are good to anchor proteins into the membrane, or forming small holes that is suitable for compounds like ions, while with beta barrels larger compounds such as sugars, or various drugs can be transported.

There's a good list of proteins with different functions for both types on wikipedia


What is the significance of and biological mechanisms demonstrated in lac operon?

The lac operon in E coli is a set of four genes which work together to allow the bacterium to make use of lactose for energy. An Operon is a set of genes which are co-transcribed on a single mRNA, controlled from a common promoter.  While operons are nearly always found in bacteria, eukaryotes (and viruses that infect eukaryotes) do have some sets of genes organized into operons.

lacZ and lacY is the business end of the lac operon. They are the only 2 genes necessary for lactose usage in the cell.

lacZ codes for beta-galactosidase, an enzyme that cleaves the lactose disaccharide into D-galactose and D-glucose.  Most of know that glucose is an important source or energy via the glycolysis pathway, which is highly connected energy usage in the cell.  Galactose is readily converted by an enzyme (galactose mutarotase) into glucose, making lactose an efficient source of energy.

lacY codes for a protein found in the cell membrane called lactose permease which pumps lactose into the cell from the outside using the proton gradient inside the cell for its motive force.

The lacA gene codes for an enzyme which transfers an acetyl group to galactose, which may prevent the buildup of galactose in the cell.

The way the operon works is more important than what it does.  the lac operon was one of the first examples of transcription regulation every studied.  lacI is not in the lac operon, but it is the single gene which controls whether the operon is copied to RNA from the chromosome.  lacI is translated to the lac repressor protein (LacI), which binds to one of three sites in front of the lac operon.

lacI is a repressor gene - when it is active, it prevents the lac operon from being transcribed into RNA.  LacI is a tetramer - four copies of the protein form a complex.  LacI binds to allolactose, a derivative of lactose, when it is present in sufficient quantities, which then causes it to release itself from the chromosomal DNA, allowing transcription to occur and the lac genes may be expressed.


The human brain white balances, the eyes do not, but the process is not instantaneous.

the easiest way to see this is to make a person wear colored lenses they will soon see colors normally again, but will need to readjust, taking a similar length of time,  once the glasses are removed.

Your eyes will balance an image back to white , but it takes time, and may happen faster in a landscape image.
https://www.sciencedaily.com/releases/2005/10/051026082313.htm

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3820566/

there is a great ted talk showing a major aspect of this visually.

https://www.ted.com/talks/beau_lotto_optical_illusions_show_how_we_see?language=en

you can also see it with common photo negative color illusions.

Stare at the center dot on this for a minute then look at the second image.

you will see that the as the brain adjusts color balance you can use the lag as the eye readjusts to see false color in black and white images.


What is the maximum altitude where humans can survive?

Short answer
Between 62,000 and 63,500 feet (18,900 and 19,350 meters) blood begins to boil at body temperature. This altitude, referred to as the Armstrong limit, is generally considered to be the absolute limit compatible with life. At this point, humans cannot survive without pressurization measures.

Background
Atmospheric pressure drops at higher altitudes. As you go higher into the atmosphere, gases start to expand due to the lower atmospheric pressure. This is what causes your ears to pop when driving up in the mountains or when an airjet lifts off. At altitudes higher than 10,000 feet (3.5 km) people unaccustomed to the reduced atmospheric pressure may become short of breath or experience dizziness. At altitudes above 20,000 ft (6.1 km) supplemental oxygen is required to support life and at 34,000 ft (10.4 km), 100% oxygen is necessary to equal the partial pressure of oxygen in sea level air. Above 40,000 ft (12.2 km), 100% oxygen must be administered pressurized (NASA).

Altitudes above 50,000 ft (15.2 km) are considered near-space and man requires a pressurized suit to be safe. At 55,000 ft (16.8 km), atmospheric pressure is so low that water vapor in the body starts to boil at ambient temperatures, causing the skin to inflate. At 63,000 ft (19.2 km) blood at normal body temperature (98 F / 37oC) starts to boil. At altitudes above 65,000 ft atmospheric pressure approaches that of space, i.e., a vacuum (NASA).

Between 62,000 and 63,500 ft (18.9 - 19.4 km), blood at body temperature (37oC) begins to boil. This is the point beyond which humans absolutely cannot survive in an unpressurized environment. This point is named the Armstrong limit, after Harry George Armstrong, who founded the U.S. Air Force’s Department of Space Medicine in 1947. On Earth, the Armstrong limit is somewhere between 62,000 and 63,500 feet (18.9 and 19,4 km), or about 12 miles.

As a reference, the highest point on earth is the peak of the Mt. Everest at 29,000 ft (8,8 km).

Above the Armstrong limit, water in the soft tissues of your body vaporizes, causing gross swelling, though the tight seal of your skin would prevent you from actually bursting apart. Your eyes, likewise, would refrain from exploding, but continued escape of gas and water vapor leads to rapid cooling of the mouth and airways (Goslin, 2008).

Water and dissolved gas in the blood forms bubbles in the major veins, which travel throughout the circulatory system and block blood flow. After about one minute circulation effectively stops. The lack of oxygen to the brain renders you unconscious in less than 15 seconds, eventually killing you. When the pressure gets very low there is just not enough oxygen, which is thought to be the first and most important concern (Goslin, 2008).

Note that under conditions of near-vacuum, death is not instantaneous. At one three-hundred-eightieth of atmospheric pressure at sea level, dogs were shown to survive up to 90 seconds. During their exposure they weren't in a great state (the dogs were bloated, ice covered their tongue, and many more horrible facts to be read in (Goslin, 2008)). Monkeys were even shown to cope for 3.5 minutes under these conditions.

Reference
- Goslin, Sci Am February 2008


The traces you have come from Sanger sequencing. N in genetics means nucleotide (surprising right?). N is used when the base at a given location is unknown (or could be any base pairs).

In your case you have Ns because the base-calling software is unable to determine the nucleotide. The first N is due to two peaks overlapping (G and A signals) and the second one should be a C rather than a N.

From what I can see, you have no apparent mutations so no those changes are unlikely to be pathogenic. A mutation can be called when you know a base in the reference is modified in your sample, which is not the case here (simply N -> G and a N -> C). The signals for your Ns look very similar between your reference and your sample therefore not suggesting a mutation.

For the reading frame, you have to look for a start (ATG) and a stop codon (TAG,TAA or TGA) to identify the open reading frame (ORF). Multiple software do that and here a link to an online NCBI tool called ORF Finder.

As you pointed out the ORF can also be in the reverse strand. You don't want to look at the reverse sequence but at the reverse complementary sequence. Usually tools to detect ORFs have the option to look at both strands.


The fruit strongly resembles immature lychee (Litchi chinensis). Since I have only seen the fruit, I cannot comment on whether the flower looks correct. The flowers appear to be slightly different from those in Wikipedia, especially in the number of "stamens"(?) per flower.


Concerning the first question, it is very well possible to alter human genetics by injecting a highly radio-active substance that will eventually cause mutations almost all cells. The lifespan will be dramatically reduced, however and the condition is known as "radiation sickness"(link to Wikipedia).

But the person probably means so-called "directed mutations" (link to Wikipedia), when the changes of genetic information is not random, but rather at a certain place and towards a certain function.

Second point, this is the area of extensive research: if we could specifically cure a gene than many diseases that are incurable now (like cystic fibrosis) could be effectively treated.  The complete nanotechnology (link to Wikipedia) is all about it.

As to the third point, this is also a very old discussion about the role of nature (=genetics) and nurture (environment). Answering this question in the scope of other questions I can suggest that (genetic) knocking-out some inhibiting receptor systems in brain can lead to certain malfunctions and deceases, including the lymbic system that is responsible for emotions and perception.


What is this pink angiosperm from Morocco?

This is a species of morning glory (fairly obvious from the flower). It is a member of the angiosperm family Convolvulaceae. The flower and the leaves together identify it as Convolvulus althaeoides. It is a Mediterranean native.  Links provided.

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

https://www.google.com/search?q=convolvulus+althaeoides&source=lnms&tbm=isch&sa=X&ved=0ahUKEwit1P3t7L7aAhVPmVkKHZIJD_gQ_AUICigB&biw=1097&bih=642


Methods for microbial identification in soil

16S and ITS techniques try to identify organisms in your samples by amplifying short, 'barcode' sequences from each organism's DNA, and using those short sequences to try to identify the organism they came from.

16S can be useful for distinguishing between prokaryotes (bacteria), at least to genus level.  It will not always give enough information to determine exact species though.  ITS can be particularly useful for distinguishing between some eukaryotes (plants, fungi, etc), even down to species level.  If you are interested in both bacteria and fungi you would need to carry out both analyses on your samples.

A different approach is to use shotgun metagenomics, where rather than amplify only the 16S or ITS region, you extract and sequence any DNA you can from the sample, and then try to assign each sequence read to a species/genus by alignment with a reference collection (e.g. MEGAN pipeline) or by kmer analysis (e.g. Kraken).

There are some packaged approaches for dealing with 16S. Qiime2 is popular, and will likely involve some amount of work in python to get it working.  There is an R package microbiome, but I don't have experience with this.  Mothur is a long-standing stand-alone package that is resonably easy to use, and MG-RAST is a web-based version that is also reasonably easy.

ITS analysis is less fully developed as pipelines, but I am sure you can find some in the literature by searching for other people's studies of soil microbiomes.

This review of techniques and approaches might be helpful if you are interested to learn more about the whole genome/metagenomics approaches: http://ccb.jhu.edu/people/salzberg/docs/Breitwieser-etal-2017-Metagenomics-review-reprint.pdf


Do proteins contain phosphorous? If its true then how alfred hershey and martha chase used the statement that proteins do not contain phosphorous?

Yes some of the proteins contain phosphorus but in the experiment (Hershey and chase experiment) they used bacteriophage it's protein sheath contains carbon,hydrogen,nitrogen and sulphur while the DNA in the bacteriophage contains carbon,hydrogen,nitrogen and phosphorus(in the acid) so they selected this for that experiment moreover sulphur is absent in the DNA but phosphorus is not so one can conclude that DNA is the thing that was transferred
Reference:NCERT


In the lysogenic cycle, does the provirus split from the cell's main genetic material for replication?

When the virus is integrated into the hosts genome (and becomes a provirus) it is replicated with the cell genome, since it is now part of it. When the provirus gets activated (this happens by changes in the host's environmental conditions or health), it will get transcribed.
This is followed by the translation of the viral proteins which then leads to a cell which exclusively produces viruses until its resources are exhausted and the cell gets destroyed.


What is the meaning of the following: " completion of open rounds of DNA replication"?

From the context of the article I found from an internet search:

Cell cycle exit in bacteria encompass four general steps:
(i) inhibition of inappropriate reinitiation of DNA replication,
(ii) completion of open rounds of DNA replication,
(iii) segregation and compaction of daughter chromosomes, and
(iv) septation.

I would assume that ‘open rounds’ means ‘DNA replication that has already been started’ (‘open’ signifying already started, and a ‘round’ has the sense of one event of a series). ‘Completion’ is obviously ‘finishing’, ‘ending’ — the cell cycle doesn’t end until all the replication that has started has finished.
I have not seen the adjective ‘open’ used in this way previously, and suspect it is uncommon, but as this is not my field I stand to be corrected.


What are the effects of muscle and fat mass on survivability?

For car crashes, it's a mixed bag:

Better
Better
Worse
Worse

Basically, it looks like, if wearing a seat belt, slightly overweight is more likely to survive a car crash, but if no seat belts are worn they are at a disadvantage; the very obese are always more likely to die, however.  Also, some of this was found only for males, not females.


Transcription of Genes: Are Specific Transcription Factors + Enhancers Necessary?

enhancers, activators, silencers, repressors are necessary in controlling of the transcriptional process. Utilization of enhancers/silencers plays a part in differentiation of developmental processes (i.e. maturation, growth)

https://en.wikipedia.org/wiki/Enhancer_(genetics)


Western blotting with multiple antibodies

What you can do depends on your proteins: If both proteins (your target protein and the loading control) are seperated far enough, you can detect both of them in the same step by adding both primary antibodies and both secondary ABs into the buffer at the same time. They will bind only to their specific epitope and you will get nice signals. This is something I have done several time. This avoids the stripping process (which can be tricky sometimes) and you have both signals on the same film. Additionally you save chemicals, film and time.

There is another way with which you can come around the stripping: Do you first primary/secondary antibody combination and then incubate the blot with a buffer containing sodium azide. This inhibits the enzyme irreversibly, you have to make to wash very carefully afterwards. Then you can proceed with the second antibody combination.

If you want work with a marked primary antibody (which is unusual, but will of course work) and your loading control at the same time, I would definitely make sure that the secondary antibody with the HRP is not binding to your marked primary, otherwise the signal might get very strong (from the primary and also from the bound secondary), but I don't think it would cause other problems.


The ermine's colour and geographical range

The color change of Mustela erminea (more commonly known as ermine/stoat/short-tailed weasel) is both temperature-dependent and photoperiodic (depending on the length of the day). Bissonette 1943 and King and Moody 2012 show that the molting of the ermine happens as a result of the change in daylight lengths.  The King and Moody paper addresses the temperature dependence, using stoats (ermines) in New Zealand as an example:

  In temperate countries such as New Zealand, stoats frequently fail to complete the full change to white. Such animals are not necessarily all caught in the process of moulting. If ambient temperature fell below the threshold for whitening of the lower part of the body but not the rest, new hair would grow white on the tail and flanks and brown on the head and back.

This is a chemical effect of lower temperature (King and Moody):

  Experimental work has established that production of brown hair depends on melanocyte-stimulating hormone (MSH); in cold climates in autumn the synthesis of MSH by the pituitary is inhibited.

They don't provide a specific temperature at which the white color change does or doesn't occur, but I suspect that in nature it'd be very difficult to create a map since temperature is not constant year-to-year. There would most likely be an intermediate zone of partially white animals (both in terms of a mixture of brown and white animals, and a single animal that is not fully white).


What is the point in the Neuromuscular Junction?

After much searching on the internet I've found an answer to this question: the neuromuscular junction facilitates amplification of the motor neurone potential to generate a large enough current to depolarise a muscle fibre as muscle fibres have a much larger area of membrane (ie a larger capacitance) than neurons.
Source: Encyclopedia of Neuroscience: Volume One

The reason is the tremendous amplification of the neuromuscular junction. The amplification occurs since a small current is generated in a nerve can rekease large amounts of molecules of the transmitter acetyl-choline ($\require{mhchem} \ce{ACh}$), each of which can open channels in the much larger muscle membrane and can create much larger currents. In addition, a motor nerve fiber often branches profusely to innervate hundreds of muscle fibers, thus providing further amplification.
Finally, the capacitance of the muscular membrane has long been known to be much greater than the capacitance of the nerve membrane, because of the additional membranous systems, such as the transverse tubules in muscular fibers. Thus the capacity of the muscle to store charge is much greater than that of a nerve membrane and much more current must be supplied to depolarize muscle cells directly.


Does the biosphere have infinite resources and are they infinitely renewable?

No, it is not infinite.

The sun has not an infinite mass neither does the earth. So energy is not infinite. But we probably don't really care about that as it applies at a scale we're not really concerned with. What is important at our scale is the rate at which is the rate at which the biomass we're destroying (eating, building houses with) is produced. The rate at which we consume this biomass has to not overpass the rate at which this biomass is produced. Than, practically speaking, biomass will be produced infinitely. Of course, ecosystem stability is not that easy but it is not within the scope of the post to talk about that.


Short answer
The key word in EEG-driven mind control is brain-computer interface (BCI). In contrast, eye blinks can simply be detected with an eye tracker.

Background
As far as I know, EEG-driven computer control (The force is strong in you) is based on recording the EEG while thinking of certain actions, or simply doing them. As you likely understand by now, thinking of moving your arm activates much of the same brain circuitry as actually making the move, up until the pre-motor cortex. The motor cortex itself stays silent (otherwise you would actually make the move (Griggs, 2013).

So EEG correlates of motor activity can be translated into digitized electrical brain activity. In turn, these brain waves can be put to use from playing pong by mind force, to state-of-the-art applications like driving artificial (bionic) limbs for the lame. By using artificial neural networks / deep learning techniques / and multiple EEG electrodes, the combined activity can be registered of many brain regions and certain signatures may pop out and be trained for a computer to learn them. In tun, that can be used to, say, play a computer game.

For a commercial alternative, delivered with an SDK, check out (Pogue, 2012):

Emotiv's EPOC

References
- Griggs, New Scientist, January 2013
- Pogue, Sci Am, December 2012)


It could be a cockroach nimph. Distinctive characteristics:The overall shape and size, the long antenae, the segmented abdomen and the visible rear cerci.


Probably not. An immediate defense against predators requires an immediate response. The sting of Hymenoptera like the wasps and bees has an immediately painful reaction.  In addition, in the eusocial (colony-forming) species, multiple individuals typically contribute to defense of their nest. One sting may not deter a predator or invader but dozens or hundreds of stings would create an immediate deterrent.  See for example this paper by [Breed et al. (2004)] on the defense behavior of honey bees.  Animal bites that are immediately painful, such as an ant bite or dog bite create an immediate response in the organism being bitten. Spines and thorns on plants deter organisms from biting the plant. Odors released by skunks and some insect provide an immediate response.

The bite of blood-sucking mosquitoes does not provide an immediate deterrent. (Not all mosquitoes suck blood.) This paper by Ramasubramanian et al. (2008) provides a detailed explanation of how a mosquito penetrates the skin.  The paper is related to microneedle design but they are using the mosquito as a comparison for painless needle design. Go to page 3 to get a description of the mosquito anatomy and piercing behavior. Comparison of painless microneedle design to the mosquito's proboscis is instructive.

The proboscis is the set of modified mouth parts the mosquito uses to penetrate the skin and suck the blood.  The study states that microneedles that penetrate human skin less than 1.5mm is usually painless or effectively so. These needles have a very small diameter, only about 40-100 micrometers in diameter, similar to the width of a human hair. The mosquito's proboscis is about 1.5-2.0 mm long. The diameter of the various structures used to cut through the skin and suck the blood are all less than 40 micrometers in diameter. Thus, the size of the mosquito's proboscis is so small that it does not cause immediate pain, or the pain is so little that it is an annoyance at best. In addition, the proboscis is weak enough that the moquito may have to probe the skin several times before a spot suitable for penetration can be found.

Finally, only the females of blood-sucking mosquitoes feed on blood and have the penetrating mouth parts. Males do not. They feed entirely on nectar and water. Males would thus not be capable of such defense.


The two commonly put-forward explanations for spiral growth of tree trunks related to stress-loading and damage-tolerance.

The stress-loading explanation states that spiral-grained trees flex more than straight-grained trees before they break. Flexibility under stress-loading is useful in areas with heavy snowfall (as the tree can flex until the snow falls off) and in areas with heavy wind (as the tree can flex in response to wind-buffeting instead of breaking).

The damage-tolerance explanation states that in trees with straight grain, the leaves (or needles, etc) have water delivered to them, via the xylem, from the roots on the same side of the trunk. In spiral-grained trees with several years of growth, water and nutrients from a given root can be transported to branches on all sides of the trunk. Therefore in spiral-grained trees, if one section of the tree's root system is damaged, it does not necessarily mean that a corresponding part of the canopy will have to die off.

Kubler (1991) discusses both the stress-loading and damage-tolerance explanations in much more detail, if you're interested in further reading.


Lineages have many levels, it is like using the word groups in some ways, they are stacked inside each other like the worlds biggest branching Russian nesting doll. All vertebrates is a lineage, all birds is another lineage, as is chickens, as is just rhode island reds. Two individuals of any earth life will always share some lineages. Lineage is not the same as clade however since they do not have to be monophyletic and usually refers to a stem line leading to a group, because of how lineage is named, it can be confusing. For instance the gorilla/human lineage could refer to basically all the great apes minus orangutans or it could refer to the sequence organisms leading to their common ancestor, or it could refer to the genetic lines to their common ancestor and back to themselves. And easy way to think of it is the outer boundaries of a lineage is not well defined. What is used to denote the lineage will help with what it is referring too.

You have to look at context. In paleontology because it is assumed you never have a direct ancestor it is used more vaguely almost like a "stem clade", in microbiology however it will be a far more precise term referring to one or more genetic lines.

The concept of species is misleading because people are trying to use our instinctual categorical thinking to describe a continuous series. It is like trying to define a color any category we invent to split the spectrum up will have many problems because it is not something with discrete differences.


Why is urea not converted to ammonia in the body?

The answer to this question is quite simply this:

  The activation energy for the uncatalysed reaction is such that the
  amount of decomposition of urea in aqueous solution at blood temperature and
  pH is negligible in the time taken for the transfer of urea to the
  kidney.

The literature supporting this is very old, so I shall first cite a relatively recent (2004) and (I think) freely available paper by Robert P. Hausinger on urease in which he writes:

  The substrate [i.e. urea]  is highly resonance stabilized (30 to 40 kcal/mol), thus
  decreasing the reactivity of its carbonyl carbon so that spontaneous
  hydrolysis of urea has never been observed. Rather, urea decomposes
  in solution (with an estimated half-life of 3.6 years at 38°C) by
  the slow elimination of ammonia to form cyanic acid (17)

Reference [17] is a paper by Zerner in Bio-organic Chemistry from 1991 which requires a library subscription. In effect it quotes the same half-life:

  The urea molecule is very stable. Between pH 2 and pH 12, the
  nonenzymatic decomposition of urea in aqueous media is independent of
  pH and has a half-life of 3.6 years at 38°C (36-38).

References 36 is a book written in 1923, and references 37 and 38 date from 1942 and 1955, respectively. I have not checked the latter, but can if anyone demands it.

All of which is not surprising, as the purpose of the urea cycle in mammals (etc.) is to eliminate toxic ammonia, and, as @Fizz points out, the enzyme urease is needed by bacteria that utilize the compound.


How does transpiration help in sucking water up?

The benefit is not in taking up more water but in transporting the things that water contains.
Plants rely on bulk transport in water flowing though specialized tissue (xylem), somewhat analogous to blood flow in an animal. Water flows through the xylem using capillary action; when water is lost at the top, capillary action pulls water into the vacated space and the flow continues down the entire height of the plant. Water removed for other uses like photosynthesis also contributes, but transpiration is important for many plants to increase the flow rate.


The National Cancer Institute (NCI) has a list of doubling times for a variety of commonly used cell lines, see
https://dtp.cancer.gov/discovery_development/nci-60/cell_list.htm

I my experience, these doubling times are quite stable/reproducible, provided that cells are kept in standard culture conditions. While doubling times differ a lot between cell lines, they are also very different in size, and larger cells tend to have longer doubling times so that the biomass growth rate is actually rather similar between lines.

Note: these doubling times refer to cell culture conditions. Actual tumors in vivo grow much more slowly, due to lack of nutrients, suppression by immune cells, and what not. Estimating cell growth rates in tumors is a much more complicated business, and I don't know of any database for that.


Does "Garbage Enzyme cleaner" contain cleaning enzymes?

The discussion you linked (here) shows that both researchers agree that 'garbage enzymes' are mostly acetic acid or vinegar, with a low pH(3-4). Fresh papayas contain papain, but roughly 2% of the enzyme self-digests per day in aqueous solution. Bromelain from pineapples is still active at acidic pH. Like most other proteases, it self-digests much more rapidly than papain. As a result, any digestive enzymes present when the mixture was made would destroy themselves by the time the mixture matured.

((Those among you quick at math will note that perhaps 1/5 of the papain activity would remain after ninety days. While true, there's evidence yeast cultures eat gluten for sustenance, and if they can digest gluten they'll digest papain. There's no reason to expect yeast to leave a delicious protein source unused.))

If the solution acquired proteases somehow, they would self-digest under the conditions the 'garbage enzyme' solution is stored at(room temperature, aqueous solution, nothing exotic like formaldehyde, months). The yeast itself by the time the fermentation is complete has died, destroyed by the acetic acid(or ethanol, depending) they created. Any digestive enzymes used by the yeast to dissolve proteins destroy themselves as the mixture matures and the yeast die off.

If the mixture starts with no digestive enzymes, there's no mechanism to get appreciable amounts active digestive enzymes. If the mixture does start with digestive enzymes(papaya or pineapple), either the yeast will eat them and then die or they will digest themselves and the yeast will eat the byproducts. Finally, the yeast will die.

It's a vinegar/alcohol blend, depending on how much oxygen is available during the fermentation, and it smells like whatever you put in it. If you used orange peels, it probably smells pretty okay. That's why it cleans.

If you are anxious to use real live proteases, there are powdered papaya/pineapple/etc powders you could reconstitute in water right before use. They are usually sold as meat tenderizer among other things. There are also blends of enzymes sold for pet urine deodorizing, and general purpose cleaning fluid with bacterial and enzymatic action. Formulating those at home is going to be fairly involved, but if you wanted an enzymatic cleaner you made yourself that's how to do it.


Why do we feel numbness and an electric sensation in our legs after standing for too long?

This relates more to nerves than muscles. Each nerve has a small artery supplying it with nutrients and oxygen. A good example is the sciatic nerve, which is the largest nerve in the human body and requires a relatively large artery to supply it with blood:

http://article.sciencepublishinggroup.com/html/10.11648.j.ijcda.20150103.14.html

When we sit in a particular way that causes pressure over that nerve, or stand for a long while in a way that stretches the nerve, we effectively reduce or block its blood supply. This may result in temporary loss of signal leading to numbness, weakness or even temporary paralysis. If the pressure on the nerve is prolonged beyond a certain point, there will be irreversible necrosis of the nerve causing permanent nerve damage. An example of this is when a drunk person sleeps on the floor with pressure on the outside of the knee over the "Peroneal Nerve", causing "Peroneal Nerve Palsy" or "Zenker Paralysis".

https://en.wikipedia.org/wiki/Zenker%27s_paralysis

As for the electric sensation we might feel as a result of nerve damage, the answer is more interesting:

The transmission of signal in the nerves requires variable amounts of energy depending on the type of nerve fibre. Nerve fibres are mainly divided into "Myelinated" and "Demyelinated" ones, with further subdivisions. To put it simply, myelinated nerves have a coating of myeline formed by specialist cells called Schwann cells. Myeline allows the nerve fibre to act as a super conductor to transmit signal faster, but needs more energy to do so compared with demyelinated fibres, which are thiner, slower and more energy efficient.

One of the functions of the super-conducting large fibres is to modulate the pain signal. The damage or loss of these fibres results in "neuropathic pain", which is felt as sharp electric shocks or pins and needles along with many other reported descriptions. This is thought to be the result of the small pain fibres working uncontrolled, leading to the perception of pain without an actual painful stimulus. The super conductors "Myelinated Fibres" are much more vulnerable to injury due to reduced oxygen, while the smaller fibres, some of which conduct pain, are more resilient. This is why we might feel neuropathic pain as a result of reduction in signal rather than due to a painful stimulation. A good example is what happens in an auto-immune disease called Guillain-Barre Syndrome, where the immune cells attack and destroy Schwann cells, leading to significant neuropathic pains as a result of the loss of signal in the corresponding nerve:

https://en.wikipedia.org/wiki/Guillain–Barré_syndrome

Another common example is first degree burns, where the pain continues for a few days following a minor burn due to selective damage of the highly sensitive myelinated fibres leaving the non-myelinated ones intact. Pain improves gradually as the Schwann cells regenerate, improving the signal speed.


Yes, you could imagine a situation where two functional alleles could produce a recombinant which was non-functional.

chromosome 1 has A and B at positions x and y - functional
chromosome 2 has C and D at positions x and y - functional
Recombination between positions x and y produces A/D and C/B versions of the gene. Either or both of these could be non-functional.

Nothing prevents this from happening, but natural selection will act on the recombinants.


The path is correct. The safest reading is to say that the lion shares a set of characteristics with the lungfish. You can also say that lion and carps are bony vertebrates (Euteleostomes).

In evolutionary taxonomy, each taxon does not need to consist of a single ancestral node and all its descendants: it allows for groups to be excluded from their parent taxa (in other words, not "being part of" but, as you said, "having evolved from"). Thus, lungfishes are closer to the lions than they are from, e.g., sharks or trout. In other words (even if this is too simplistic to say so), their "common ancestor" is more "recent".

In the Linnaean taxonomic system, all fishes were in the same class. This corresponds to our "everyday life" classification of fishes but not to the most recents findings about the "common ancestors".

To make things clearer, you need to understand the concept of paraphyly. The bony fishes group is paraphyletic with respect to the tetrapoda. In other words, it consists of the group's last common ancestor and all descendants of that ancestor excluding the tetrapoda. "Bony fish" is therefore not a clade, but "Osteichthyes/Euteleostomes" is a clade (= a monophyletic group of the bony vertebrate with a common ancestor that looked like our "modern" fishes).


What is the benefit of near-emptying the bloodstream in the mammalian kidney?

Probably because it's easier to retain what the body wants than get rid of what the body doesn't want.

What does your body want to keep from your Urine? Pretty much water and selective ions (Cl-, K+, Na+, Ca+2, etc.). Maybe a few other things, depending on how healthy you are.

Now, what does your body want to get rid of in your Urine? Well, anything it can't get rid of in your solid waste. That includes pretty much anything water soluble that could harm you, whether it's Urea, chelating agents for heavy metals, ions your body doesn't want (excess minerals), excess vitamins, sugars (to maintain insulin levels), hormones, liver byproducts, and whatever dark horrors mother nature is concocting for us in the forms of virii or whatever else.

That's just the beginning of the list, but already you should start to see the impracticality of having active transport or coupled transport for everything. The list of transmembrane proteins needed to ferry all of the items your body wants to get rid of is a lot longer than the list of transmembrane proteins needed to keep what the body needs.

Then you have the "unknowns" - whatever else your body hasn't encountered yet, but will still be water-soluble. If the body required some sort of transport across membranes for everything it didn't want, then it would need to adapt to every single new compound it encounters. Given the relatively slow generation periods for humans, if a new compound turned out to be significantly fatal then the slow adaptation could spell disaster for any small populations and create serial bottlenecking events.

So, while it may not be energetically favorable to let water and ions pass into the Nephron and subsequent tubules to be reclaimed, Evolutionarily speaking it's probably strongly selected for. We may expend a lot of energy reclaiming water against its concentration gradient, along with whatever else we want from Urine, but at the same time we get rid of everything else we don't need that's filtered through the glomerulus. It doesn't matter what the "everything else" is - but we know we don't need it, and that's the big key.

With my current level of knowledge (B.S. - Biology) this is the best explanation I could think of, but I haven't read any specific papers nor heard any particular theories on why the kidney's components act as they do.


Scutella refers to shield or plate-like structure on animals (dictionary.com), such as the scutes of a turtle shell.  I have never seen reference to scutes or scutella or anything similar on any type of deer, including reindeer.

I have not seen the movie so I do not know the context of usage. My gut reaction is the person was trying to make something sound important or "scientific" when a much simpler (and perhaps more accurate) word would have sufficed.


Are there animals who do things just for pleasure like humans?

I see that Gerardo has said effectively what I was going to: animals don't do things because they have reasoned out that these things will help them survive; they engage in behaviors because these behaviors lead to reward circuitry response and animals who find general categories of behavior rewarding have tended to survive better. Sometimes behaviors that are not directly related to survival trigger the same circuitry.

(P.S.: this is exactly what is happening in humans, too.)

Masturbation is one example, as above; so are animals that 'adopt' either conspecific or heterospecific juveniles who don't belong to them, which is not uncommon in many species. (Barn cats in particular do this often; aside from all the cute Youtube pictures of cats who think ducklings are kittens, it's very common for queens with kittens about the same age to co-nurse them.) You can argue that sociality and taking pleasure in altruistic activities with no immediate personal benefit is a survival adaptation, but that's not a calculation the animal is consciously making at the time.

Animals often have strong aesthetic preferences, especially for conspecifics; female and male animals often prefer traits that don't have anything obvious to do with survival in potential mates, and there is an entire discipline of sexual selection in biology devoted to teasing out why. It's worth noting, however, that in many species it turns out that females have preferences that vary widely for a number of traits, and that female preferences do not always line up to male reality...

Outside of naturalistic social behavior, numerous examples of elephants and chimpanzees creating drawings or paintings in their enclosures without any conscious reinforcement from their keepers have proved interesting reading. There are also examples of animals who keep "pets", including the famous case of Koko the gorilla and her pet kittens. You may find this article, with descriptions and citations of several animals who may or may not be engaging "art" for its own sake, to be a useful read.


Is complete dominance actually a genotypic process?

"Or are all alleles actually codominant at the transcription/protein level?"

Yes this is the right idea. Generally all alleles are transcribed independently (with some exceptions like in females where one X chromosome is inactivated). And the dominant and recessive phenotypes are in a sense extreme cases of codominance. The terms are used for describing phenotypes and depend on thresholds of activity. In the snapdragons example we can associate 2 functional enzymes EE with the red phenotype and white (lack of red pigment) associated with 2 nonfunctional enzymes ee. But one E is not enough to make the red pigment so we see some red pigment and a pink phenotype.

Now consider a yeast cell with 2 hexokinase genes (H). With two inactive proteins (h/h), the cell will grow slowly. Now let's say that H is a very efficient protein and that glucose transport into the cell is rate limiting so one active H has the same phenotype as having 2 H/H, so H/H is the same as H/h thus H is a dominant allele and h is recessive because one H is past the threshold of activity for fast growth on glucose. h is recessive because h/h genotype is needed to see the h phenotype. Hope that helps.


Are there animal models for Clostridium difficile that better replicate human infection than hamsters?

Hamsters are considered the best animal model, most studied.
C. difficile has been found in calves, ostriches, chickens, elephants, dogs, horses, and pigs, but its role in infection and its pathogenesis in animals are largely poorly understood and possibly underestimated


Theranos blood test's Specificity and Accuracy?

Which patents are relevant for their device?

They currently only have about 27 issued patents (US)
Of those patents about 10 of them are related to network/internet/health record/algorithm (so not really about their device)
The remaining patents focus on a few areas: sample acquisition (getting the blood drop and handling of it), Patch based technology (before they pivoted), sample quality analysis (this is key to making sure the small sample is good quality), microfluidics/modular device (these are the patents relating to the actual testing and device)

What are the limitations of multiplying so little blood?

From a molecular standpoint (PCR) the smaller sample you start with, the less of the original nucleic acid template you have to start with.  Lower end PCR testing uses 10uL of sample.  This is ok when you are trying to bring molecular diagnostics to the point of care or developing markets, but the best PCR tests use 50uL of sample (more than a drop of blood which is traditionally 25uL or so),  regardless of how good your device is, at some point you start amplifying junk. The better the primers and other reagents the less junk you amplify, but at the end of the day you want more sample to be more sensitive.
From a NON-molecular standpoint (chemistries, cellular analysis, coag, etc.), they aren't/can't multiply the analyte of interest.  In these tests, they rely more on dilution or small volumes to perform detection.  This is where their ability to reliably dilute and correct for the dilution comes into play. Although there is certain limits to this.  Coagulation tests would not be representative if you diluted the sample so in this case they will have to rely on working with a small volume.  Cellular analysis can only be diluted so much as you get to a point where you miss important but less common cell types.  Take eosinophils (a type of WBC) while they can get to 15 or 20 percent of all WBC cell types, in general they only make up a couple percent.  Assume that 2% of all your WBCs are eosinophils.  If you only have 3500 WBCs per 1uL of blood (which is on the lower end of normal), you have approximately only 70 of these cells in that same volume.  If you dilute the sample so that way there is more of it available for other tests like electrolytes, but you still analyze 1uL, The number of those cells is even less.  If you had perfect detection you might be ok, but you generally want to analyze more blood so that statistics work in your favor and your performance goes up. Most of the other chemistries, proteins, and as mentioned earlier, electrolytes will probably be ok for dilution and detection and in fact this is why there are plenty of small devices already out there that use a drop of blood and perform the same tests.
Their issue in diluting or amplifying analytes of interest is that biology still is governed by the laws of physics and even though technology may allow you to analyze samples down to 10nL, that just isn't use full in biology, and limits their their capability to perform the supposed menu of tests from one microtainer of blood.  They don't publicize that they may need to draw a venous sample (needle in your arm) for some tests and depending on what tests you order, you may need a separate finger prick for each test.

How can Theranos blood test's be specific and accurate compared to conventional full blood test?

If they reliably control dilution of the small sample, they maybe able to provide high quality results for some tests.
Finger pricks actually can be easily skewed via technique.  Theranos has specially trained people to draw these samples, but it is time consuming >5 mins and until it is fully automated this is one variable that no matter how good sensors are, you can't correct for variation pre-analytically when you have that small sample.  Finger pricks also skew certain tests even when technique is good such as platelet and WBC values in the CBC.
I discussed the sample volume issue above regarding PCR amplification and how good tests use up to 50uL.  So if they compare to a 10uL test, they may be able to compete, but not full lab quality.
A lot of the future techniques they have regarding small techniques (in their applications) like their coagulation tests work great in an academic setting, but they fail to be able to handle the full range of blood samples they will see, so it will be interesting to see how that plays out.

Takeaway

Theranos is working on modular micofluidic devices/cartridges that will use small sample
There are certain biological limitations that stand in the way of them performing all the tests in their catalog with only a drop of blood
The FDA will eventually be requiring them to submit their tests for approval as they are currently doing tests that are available on commercially and FDA approved devices already (this makes sense because LDTs were never ment to be used in place of standard tests and equipment and since there is NO published data on their performance it can be worrisome to providers and payer)
Their true business plan has yet to be elucidated, but if they really did have a box that did all this, they would be selling them to physicians and clincs where those results could actually be used in diagnosis rather than 4 hours later.
I hope they succeed, but there is just way too much hype to buy in on it yet.

I am sorry I don't have sources, most of this is from intimate knowledge of the space and from the little info available on them so I could definitely be wrong on some of this.  I hope this helps!


Standard practice for generating rarefaction curves from Next Generation Sequencing data

I actually work in the same group as Chris (QIIME author), so I hope this helps: An explanation he gave to us a while back about the basis of rarefaction curves is just to give an indication of whether your sampling is reaching saturated diversity, when comparing 2 unequal samples.

If you compare 2 samples, where sample x has less information (reads/amplicons etc) supporting it, you can't be sure you've sampled all the possible diversity.

Thus, you plot the number of OTUs you see for increasing numbers of reads. If you're saturating the diversity you should see it plateau.

To bring the 2 samples inline with the 'amount of supporting data' they have, you randomly sample the data of the larger dataset, so that it is equivalent to the smaller, and then compare the number of OTUs each is reporting.


Why are the organs for reproduction and urinary excretion combined?

Developmentally, the urinary and genital systems (typically you will hear them referred to as "urogenital system") are derived from the same embryonic tissue, the intermediate mesoderm. The embryonic kidneys are drained by the mesonephric duct in both females and males. This embryonic tissue also gives rise to the ovaries and testes. The mesonephric duct degenerates in females, and becomes the ductus deferens in males. A second tube, the paramesonephric duct develops in both, but degenerates in males. The female paramesonephric duct becomes the uterine (Fallopian) tube.

Embryonically, the ureter, which drains the adult kidney is connected to the mesonephric duct. This connection is maintained in males, so that both urine and semen share a tube (urethra) for some of their exit pathway. In females, the paramesonephric duct and urethra are separate, so there are two openings.

In males, sphincter muscles and autonomic control prevent the simultaneous expulsion of urine and semen.

This system has worked acceptably well in mammals for at least about 200 million years (and in humans for the last 4 million or so), so I think it's not correct to call it a mistake. It's not how you would consciously design such a system, but evolution doesn't have a conscious designer.

Here are some slides that cover the embryology of the human urogenital system.


How can I create a microcapillary for manipulation of single cells?

It is very difficult to establish what kind of tip you will get from pulling a capillary on a Bunsen burner.
There are many variables to consider, including the glass you are using, the temperature you reach before pulling, the pulling strenght, speed and time, whether you pull once or make multiple pulls etc.

If you do not want to invest into a micropipette puller (they are indeed VERY expensive) you could at least build some mechanism to obtain a constant pull in terms of time and force.

The following paper may be of help:

An Instrument for Controlled, Automated Production of Micrometer Scale Fused Silica Pipettes

It seems you would need a fairly high speed (0.8-1 m/s) to get a tip size of <50um.

I could not really find a specific reference for pulling over a Bunsen.


Amount of reverse transcriptase in µg or mM for qRT-PCR

Reverse transcriptase (and most other commercial enzymes these days) is made recombinantly, then purified to varying degrees, using varying methods, among different suppliers (and sometimes between different lots from the same supplier). Some enzymes actually have multiple functional units combined in a complex, others may require a post-translation activation step like phosphorylation by a separate kinase in order to be fully functional. All of these variables can yield preparations of different molar concentration, but very similar activity. Therefore, companies like New England Biolabs have unit definitions for their various products based on activity.

Having dealt with NEB in the past, I know that they generally have a concentration for their products as well, so if you're doing experiments like an enzyme inhibition assay, you can dose for concentration as well as activity. It will vary from enzyme to enzyme whether your inhibitor will even bind to any inactive protein that may be present, in which case activity would be the better attribute to use in your calculations.


Additive genetic variance $V_A= 2pqa^2$ ... what is $a$?

This information is given in p.118.

In essence $a$ represents the deviation from the population mean due additive genetic effects.

Say a trait is controlled solely by locus X with the effect alleles X impacting the phenotype Y in an additive manner (no dominance and epistasis effect), then we can calculate the effect size of carrying the X allele, called $a$, and representing the distance from the population phenotypic mean of homozygote XX. Based on this definition, the distance from the mean for individual with the following genotype is given by:

XX: $a$
Xx : 0
xx: $-a$

This makes more sense using the genetic model:

$P=G+E=BV+I+E=A+D+I+E$ (parameters listed at the bottom)

In the example, the locus has only an additive effect then D=0 and assuming there is no epistasis then I=0 as well which gives $P=BV+E=A+E$ therefore $BV=A$

In this case $a$ can be computed directly from the BV, with p=f(X) and q=f(x), as:

$BV(XX)=2qa$
$BV(Xx)=(q-p)a$
$BV(xx)=-2pa$

Now for the complete case of both additive and dominant effects, i.e. $BV=A+D$, you can refer to table 7.3 in p.118 which describe that XX individuals are given the value $a$, Xx -> $d$ and xx -> $-a$ with the corresponding relationship to the BV given by (care here it's not $a$ but alpha $\alpha$):

$BV(XX)=2q\alpha$
$BV(Xx)=(q-p)\alpha$
$BV(xx)=-2p\alpha$

with $\alpha=a+d(q-p)$

P=phenotype
BV=A+D=Breeding value
G=Genotypic effect
E=Environmental effect
A=Additive genetic effect quantified by $a$
D=Dominant genetic effect quantified by $d$
I=Epistasis effect


What's a good reference for learning about recombinant proteins?

i would start by searching PubMed literature database for relevant articles using this query:

"protein"[Title/Abstract] and "expression"[Title/Abstract] and "purification"[Title/Abstract] and "recombinant"[Title/Abstract] and "mammalian"[Title/Abstract] and ("E. coli"[Title/Abstract] or "CHO"[Title/Abstract] or "Sf9"[Title/Abstract])

which returns 116 articles (including 7 reviews).


What chemical conversions are involved , and what's the name for the process, when the muscles use lactate as an energy source?

I see you've already got an answer in the comments, so this is rather a collection (with more proper formulation) of comments. As is known, lactate is produced by muscles (generally) during exercise due to absence of oxygen. However, the lactate produced can be used again in following two ways:

Conversion of lactate to glucose in the liver via a process known as Cori's cycle. Basically, the lactate produced from the muscles is released into the bloodstream, through which it reaches liver. There, it is converted back to glucose and again released into the bloodstream, through which muscles can use it again as fuel. The basic cycle looks like:

Conversion of lactate to pyruvate is the one you are concerned about. However, this process does not have a special name, because this reaction can be catalyzed both in forward and reverse direction. In the absence of oxygen, an enzyme lactate dehydrogenase convertes pyruvate into lactate, consuming 2 H+ during the process. However, when the envrionment is rich in oxygen, or the concentration of lactate is high, the same enzyme converts lactate into pyruvate, producing 2 H+ in the process. The reaction can be shown as: $$\ce{CH_3COCOO^- + NADH + H^+ \leftrightharpoons CH_3CH(OH)COO^- + NAD^+}$$

Thus, when the concentration of lactate increases, the enzyme lactate dehydrogenase catalyzes the (above) reaction in the reverse direction. After this, the pyruvate produced can be used in the TCA cycle.

PS: there have been studies which now suggest that indeed lactate, not glucose, is the primary energy source of neurons. As per the lactate-shuttle hypothesis, the glial cells neighboruing neurons convert glucose into lactate, which is then used by the neurons. This fits with the observation that the extracellular fluid immediately surrounding the neurons is richer in lactate as compared with blood and cerebrospinal fluid, as shown in microdialysis studies. These studies suggest that glucose is not the actual primary energy source of neurons.

EDIT: As you see, the first reaction in both the cases is $\ce{lactate \rightarrow pyruvate}$. However, the main difference arises after this reaction. In muscle cells, this pyruvate is used in Krebs cycle, for which the first enzyme is pyruvate dehydrogenase converting pyruvate to acetyl-coA. However, in gluconeogenesis i.e. formation of new glucose molecule (a part of Cori's cycle), the first step is conversion of pyruvate to oxaloacetate, and is catalyzed by the enzyme pyruvate carboxylase. Thus, although the first step in both processes is the same, the end product is quite different.

References:

Lactic Acid - Wikipedia
Lactate Dehydrogenase - Wikipedia
Cori's Cycle - Wikipedia


Why is liquefactive necrosis only seen in brain?

Liquefactive necrosis is indeed only seen in the brain in the absence of infection, but it is also seen in the case of some bacterial infections.  The reason is that liquefactive necrosis is, as you said, caused by the release of digestive enzymes and constituents of neutrophils.  Bacteria will, under some circumstances, release those enzymes, causing the cells to be devoured.
The fact that liquefactive necrosis is seen in the brain in the absence of bacterial infection is in part due to the fact that neurons have a higher lysosomal content, leading to a higher tendency toward autolysis, and in part due to a high concentration of neutrophils which swarm into an affected area.

Sources:

What happens after brain tissue dies?, PathologyStudent.com, 2012
Liquefecative necrosis, Medigoo.com, 2016
Necrosis, Cell (Liquefactive, Coagulative, Caseous, Fat, Fibrinoid, and Gangrenous), Rotimi Adigun1; Steve S. Bhimj, 2017