How does bath application of KCl depolarize a neuron?

Membrane potential (measured electrophysiologically, or calculated using the Goldman equation) depends on two things: concentrations and permeabilities. In the Goldman equation you see this directly: concentrations multiplied by permeability, in both the numerator and denominator.

If the membrane is not permeable to an ion (PIon=0), that ion will not affect the reversal potential. In a typical resting neuron, in the absence of any synaptic activity, Chloride conductance is near zero compared to ions like potassium.

I'm not as clear what you are asking about patch clamp experiments, I will try to just describe the process and hopefully that helps.

In a whole-cell patch clamp, the inside of the cell is continuous with the patch pipette solution, which usually contains high concentrations of potassium, like the normal intracellular environment. This is done on purpose, to try to record from cells in the most natural condition that can be replicated simply.

During the process of making a whole-cell recording, however, the experimenter has to first place a patch pipette down near the cell. While doing this, some solution is leaking out of the pipette and increasing extracellular potassium concentrations, which can depolarize surrounding cells. So, patch quickly my friends, you are making it uncomfortable for everybody before you make a good seal.

(the process would be similar for inside-in patches; for on-cell or inside-out patches, one would use different ionic concentrations in the pipette to mimic the extracellular space, or these would vary depending on the exact experiment performed)

edit: Just wanted to note that a statement in your question is mostly wrong; "the pipette is loaded with KCl and injected into neurons that leads to depolarization" - KCl inside a cell would not depolarize that cell, unless the concentration of K+ was lower than the typical K+ concentration of the cell, in which case you would probably have other issues and a dead cell from osmolarity problems.


What type of CCD system is required to take photos of luciferase

You are looking for a bioluminescence imaging device. These have very sensitive CCD camera and exposure times are around 5 minutes in complete darkness.


How important is non-binding site of protein?

As it seems with about everything in protein science, the answer is it depends on the protein.  Many proteins will lose activity if they are truncated; however, I've worked with GPCR's that were truncated down to the extracellular portion only and they showed consistent kinetic results.  Antibodies have been cut into pretty tiny chunks (scFv's) to create some drugs like Pexelizumab. Some proteins can be hacked down quite a bit, some can't be at all.


The "crash" effect is typically perceived as a deterioration in affect. With drugs, this deterioration happens as the drug is cleared from blood circulation, particularly cerebral circulation. With the ingestion of amphetamines, there is a brief reuptake of certain neurotransmitters, particularly dopamine and norepinephrine. Amphetamines also temporarily prevent the 'recycling' of said neurotransmitters, so the reuptake effect can last anywhere from 4 to 24 hours. The brain regulates internal homeostasis of mood based on perceived 'high' and 'low' elevations; thus, after an extended elevation in mood, there must be a 'comedown' period, or a deterioration in affect.

Further essential to this idea of homeostasis are the stress hormones, cortisol and adrenaline. Upon release, these hormones may raise blood sugar levels, blood pressure, and/or heart rate. As heart rate increases, the flow of blood goes to the heart, with less going to the brain. This causes the groggy and tired feeling afterwards that might be associated with a 'crash'. Stress hormones also impact the thyroid (which controls how fast the body uses energy, and controls hormonal sensitivity) as well as the central nervous system.

Exercise also leads to increased heart rate, as well as muscle fatigue. However, exercise itself doesn't typically lead to a depressed, lethargic state, as exercise promotes the release of endorphins (which are known to improve general sense of well-being). However, it is not uncommon for some people to experience "endorphin withdrawal" after suddenly stopping excessive exercise, which could mirror the crash that comes from the 'comedown' after drug use.


Might as well make it into an answer. As I said in the comments, Albert's  "Molecular Biology of the Cell" is the classic textbook for Biology undergraduates. It has been so for decades now.

It starts from the basics and builds up. Anyone with a high-school science education and willingness to learn should be able to understand it. Just work your way through it :).


I'm going to focus on the why do carnivores exist part of this question, which should be extendible to answer why humans eat meat.

Let's start a thought experiment in which we only allow the consumption of vegetation (plants). In the simple system, we have our plants (lettuce) and our herbivores (rabbits). The lettuces have a constant population size and can support a limited population of rabbits. The rabbits satisfy their energetic and nutritional requirements by eating lettuces.

We then introduce a new species (humans) which are capable of eating both lettuce and rabbits (omnivores). If the humans limited themselves to only the lettuces as a food source they would have to compete with the rabbits in order to survive. Alternatively, the humans could hunt rabbits, as rabbits are also a potential source of energy and nutrition. The point being that, if a strategy has the potential to satisfy the energetic and nutritional requirements of a species, then that strategy has the potential to evolve. Because both plants and animals carry energetic and nutritional value, herbivory and carnivory/omnivory can evolve.

  "All behaviour takes time. All behaviour consumes energy." [1]

Now consider the nutritional and energetic value of two the two food sources, plants and meat. Meat is typically richer in calories than vegetation, particularly those coming from fat and protein. 100 grams of lettuce contains around 14 calories, while 100 grams of beef contains about 200 calories. Protein is used by the body for growth, to repair tissues, produce hormones and enzymes and much more. Fat has a high energy content per gram (roughly twice as many calories per gram than protein or carbohydrate), is essential for the digestion of some vitamins,  and is an effective insulator. Given that behaviour takes time and energy, it is perhaps not hard to see that consuming meat can help to satisfy the energy requirements more quickly than consuming plants, allowing meat eaters more time for other essential activity like sleep and reproduction. Consider the activity of two large mammals, elephants and lions. Elephants spend a lot of time eating, some 12-18 hours per day (fortunately for them are quite able to eat on the move). Lions on the other hand typically hunt for short periods of the day (dawn and dusk), allowing them to avoid the heat (reducing water requirements), to rest, and reproduce.

Consider also that vegetation is often hard to digest — it is often is rich in cellulose. Many herbivorous species have complex adaptations to help digestion. Therefore, it's not necessarily easy, or easier, to evolve to eat only vegetation. Improved energy acquisition can evolve by both eating more energy rich foods and by more efficiently extracting energy.

Carnivory is also present in plants. According to this paper [2], such plants may be an adaptation to nutrient-poor conditions, where the ability to digest insects (and other small animals) would be a massive benefit, allowing carnivory to evolve rapidly.

  Botanical carnivory is thought to have evolved in nutrient-poor and
  well-lit habitats such as bogs because the marginal benefits accruing
  from carnivory exceed the marginal photosynthetic costs associated
  with the maintenance of carnivorous organs.

The Egyptian mongoose is an omnivore. This species varies its diet across the year, according to what is available. For example, insects are the major component of its diet in spring, while no fish are eaten during summer (because of dry canals in the summer) and fish are a major component in the winter. This illustrates that allowing omnivory/carnivory can increase the resources available, potentially allowing better survival and reproduction relative to a herbivorous/narrow foraging strategy in the same species. Consider this problem in, for example, boreal or temperate climates, where winter can cover ground vegetation in snow and tree's will reduce foliage. Consuming animals would allow the acquisition of energy and nutrients through the winter.

In summary, carnivory can evolve because animals are a good and plentiful source of energy and nutrition, and may allow diversification of strategies, improving survival and reproduction. If animals were bad food sources then carnivory would be less common as it would be a more difficult/problematic behaviour to evolve.

While many people & organisations (including PETA) try to claim that we are not well adapted to being carnivores, many of the claimed adaptations to herbivory/lack of adaptations to omnivory are overstated, misleadingly presented, and even false, and are used in order to promote their own agenda. It's also worth noting that we are not well adapted to being herbivores (e.g. gut flora) and chimpanzees, one of our closest ancestors, are also omnivores.

[1] Krebs & Davies Behavioural Ecology, An evolutionary approach.* ISBN-10: 0865427313.

[2] Ellison, Aaron M., and Nicholas J. Gotelli. "Nitrogen availability alters the expression of carnivory in the northern pitcher plant, Sarracenia purpurea." Proc Natl Acad Sci, USA 99.7 (2002): 4409-4412.


Interesting protein structure trivia question!

Disulfide bonds form more or less spontaneously when two sulfhydryl groups from cysteines are close enough to each other in the proper orientation in a reducing environment.  So given this, its possible for them to exist, even though in most cases the distance between the cysteines in a disufide bridge is small and intra-domain.

Inter-domain disulfide bonds are rare.  The most common example is that some immunoglobulin domains in antibodies have an intrachain disulfide bridge.  I also found reference to one in a starch synthetase from rice.

In tertiary structure, the overall shape is an important one.  Globular shapes are the most common, but elongated protein folds, triangular folds,  rings, disk-like structures made out of wedges are popular examples of how protein structures can do amazing things when selection requires them to.


If people with colorblindness lack one type of cone cells, shouldn't they be unable to recognize one particular color?

Cones do not literally interpret colors.  The three cones work together to encode a signal that is abstractly interpreted by your brain in higher processing centers.  Here is what neuroscientists currently think the decoding scheme looks like:

This leads to what's called opponent process, an antagonist mechanism whereby the perception of green/red are a matter of the contrast between the two.  In a deuteranopes, the mechanism of antagonism is missing, so the colors can not be differentiated.

What this implies is that (to some extent) a single color has no meaning.  Colors are only meaningful in the context of other colors.


So there are a couple of things to bear in mind.

pluripotent does not mean that all genes are active. It means that the stem cells have the ability to form different cell types. However, it still needs to keep the cellular programme of a neuron for example silent. So the epigenome is still present to keep other cell type programmes silent until there is a transition.

DNA methylation is not the only source of epigenetics. Active and inactive genes also correspond to particular post translational modifications on tails of histone proteins. In the cell, DNA is wrapped around histones to form what is known as chromatin.

Hope that is a starting point to answer your question


Everything you state is correct, except that I disagree with your statement that a "[...] virus variant itself is a protein, which is composed of peptides.

A virus is typically composed of a protein capsule with genetic material on the inside. So technically, a virus is not a protein, but its outer shell is composed of proteins. Further, a protein does not necessarily have to be composed of (multiple) peptides - it can be a single amino acid chain.


What's the purpose of segregating a virus from the blood and growing it in the lab?

2019-NCoV was first cultured by a Chinese group, as published here on January 24. China has not shared samples, but did share sequencing data in the linked paper and via GISAID. The Australian group at the Doherty Institute hasn't published yet, but did put out a press release today (January 29), and appears to be the first group outside of China to have cultured 2019-NCoV.

Viral isolation, and in particular, culture, is an important, and often difficult step in characterizing a novel virus. Once characterized, viral culture serves as a gold standard for diagnosis. Generally speaking, the ability to grow virus in cell culture allows for a broad range of pre-clinical studies that can lead to clinical advances including prevention, diagnosis, and treatment. Consider how difficult it may be to study a pathogen if you are not able to manipulate it in a living culture. You can read about this in Murray Medical Microbiology, Ch 50. This article, which does not require a subscription, may also be of interest. The article describes a variety of historical and modern methods, but also includes some discussion about the use of viral culture.


Can a hinge joint technically allow rotatory motion?

It is about the movement of the bone along its major axis of movement. A hinge joint moves like a lever while a pivot joint involves rotation side to side like an axle.
It helps if you look at a example of a bone that has both types of joints. The radial head is part of both a pivot and hinge joint, with the ulna it rotates allowing the hand to pronate and is a pivot joint, while with the humerus it is a hinge allowing the arm to swing through an arc.
Keep in mind these are biological terms and not strict engineering descriptions, biology is more interested in how tissues move relative to each other. Biological terms are not interchangeable with geometry and engineering, nor are they designed to be perfectly rigorous, they are descriptive in nature. In biology rotation is a term reserved for more wheel and axle type motion where a bone is revolving around its own axis.

Find more help here.


Clatherin Mediated endocytosis is pinocytosis or phagocytosis?

My answer would be pinocytosis
Eukaryotic cells are also able to take up macromolecules and particles from the surrounding medium by a distinct process called endocytosis. In endocytosis, the material to be internalized is surrounded by an area of the plasma membrane, which then buds off inside the cell to form a vesicle containing the ingested material. The term “endocytosis” was coined by Christian de Duve in 1963 to include both the ingestion of large particles (such as bacteria) and the uptake of fluids or macromolecules in small vesicles. The former of these activities is known as phagocytosis (cell eating) and the latter as pinocytosis (cell drinking).

During phagocytosis, cells engulf large particles such as bacteria, cell debris, or even intact cells.In contrast to phagocytosis, which plays only specialized roles, pinocytosis is common among eukaryotic cells. The best-characterized form of this process is receptor-mediated endocytosis, which provides a mechanism for the selective uptake of specific macromolecules.The macromolecules to be internalized the first bind to specific cell surface receptors. These receptors are concentrated in specialized regions of the plasma membrane, called clathrin-coated pits. These pits bud from the membrane to form small clathrin-coated vesicles containing the receptors and their bound macromolecules (ligands). The clathrin-coated vesicles then fuse with early endosomes, in which their contents are sorted for transport to lysosomes or recycling to the plasma membrane.

For more information please see this link https://www.ncbi.nlm.nih.gov/books/NBK9831/

Hope this helps!


How can cane sugar sucrose be different from beet sugar in regard to carbon-13 content?

The differential uptake of different isotopes of carbon is covered well at:
https://en.m.wikipedia.org/wiki/Fractionation_of_carbon_isotopes_in_oxygenic_photosynthesis
Plants have a lower proportion of C-13 than atmospheric CO2.
The two mechanisms that cause this are the reduced diffusion speed of the heavier C-13, and an energetic difference in the chemical reactions that favours C-12.
In sugar cane (C4 photosynthesis) the carbon dioxide is captured in an additional step compared with sugar beet (C3 plant).
This capture step in C4 plants (using phosphoenolpyruvate carboxylase) is less exclusive toward C-13, so the carbon in these plants has detectably more C-13 than C3 plants.
This subsequently affects the isotopic proportion of all the carbon in the plant


Why doesn't enzyme reaction rate rise linearly with substrate concentration?

Disclaimer
This answer is a conceptual explanation, as appears to be the request, rather than a repetition of the derivation of the Michaelis–Menten equation, which I feel inappropriate, partly because it can be found elsewhere, e.g. in Wikipedia and Berg et al.. I appreciate that, like the derivations on which it is based, some of its assumptions do not always hold, or do not hold for all enzymes, and that some with an expert knowledge of enzyme kinetics will feel that it would be better to say nothing than present a conceptual simplification. Although I welcome corrections — I am not an enzymologist — but disagree with this point of view.
Summary
The reason that increasing the substrate concentration of an enzymic reaction does not increase the reaction rate beyond a certain maximum (Vmax) is that the reaction rate is dependent on the concentration of enzyme-substrate complex, not its rate of formation. Increasing substrate concentration only affects the reaction rate in so far is it affects the proportion of enzyme molecules involved in enzyme–substrate complex, which reaches a maximum when all of the enzyme is in such complexes.
More detailed explanation
The question presents a rate constant for only one of the reactions involved in an enzyme-catalysed reaction. In fact there are four that must be considered: the forward and backward reactions for the formation of a complex, ES, between enzyme (E) and substrate (S); and the forward and backward reactions for the formation of product (P).

The Michaelis–Menten treatment considers the initial velocity of reactions, at which time little product has formed so that it is assumed that the back reaction from product can be ignored, simplifying the situation to a consideration of the rates of three reactions:

A key assumption — the steady state assumption — in Michaelis and Menten’s original derivation is that there is that there is a considerable excess of substrate over enzyme so that the substrate is in instantaneous equilibrium with the ES complex. So, in effect, at a particular concentration of substrate the concentration of ES is constant. The implication in the question that the rate of formation of this complex would determine the reaction rate is incorrect.
The rate of the reaction depends only on the ES concentration and k2, the rate constant for the formation of products, also known as kcat, which is a characteristic of any enzyme and can be thought of as representing its catalytic capability:

d[P]/dt = kcat[ES]

What the substrate concentration does affect is the position of equilibrium for the formation of ES from E and S, i.e. how much enzyme is converted into complex. However there is obviously a maximum, approached asymptotically, equivalent to the total enzyme present. This explains† the hyperbolic nature of the curve for reaction rate.
The concentration of substrate needed to reach this saturation (more easily measurable as that to achieve half maximum initial velocity) is another characteristic of the enzyme (and substrate) and can be thought of as reflecting the affinity of the enzyme for substrate (the dissociation constant). The hyperbolic nature of the rate curve is similar to that for binding of small molecules to non-catalytic proteins such as the oxygen-carrier, myoglobin, and hormone receptor proteins.
Just as not all proteins in this latter class (e.g. haemoglobin) show simple hyperbolic binding of their ligand, so not all enzymes (e.g. allosteric enzymes) show hyperbolic kinetics. But that’s another story, which has been told many times on this site.

† I have given a more extensive explanation of the hyperbolic nature of the curve in an answer to a previous question, which I must admit I had forgotten about.


As @terdon comments, dormant organisms can survive in vacuum. This includes lichens, bacteria, and even an animal: the ever-amazing and adorable tardigrade (Jönnson et al 2008). In 2006, tardigrades survived exposure to the vacuum of outer space with no appreciable difference in mortality compared to controls.

Tardigrade Hypsibius dujardini, a different genus than the ones sent into space, but probably equally hardy. Photo by Bob Goldstein & Vicky Madden (CC by-nc-ca via Goldstein lab - tardigrades on flickr).

Jönsson, K. I. et al (2008). Tardigrades survive exposure to space in low Earth orbit. Current Biology 18(17):R729–R731


How to estimate the DNA density in human sperm head?

Find, or calculate, a value for the volume of the sperm head.

Find a value for the size of the human genome (haploid or diploid?)

Convert the genome size, which will probably in Giga basepairs, into mass (I suggest picograms).

Divide mass by volume to get a density, pg μm-3

Refinement - does the sperm nucleus take up all of the head volume? Do you need to factor this in?


Zinc supplements are usually used to treat zinc deficiency or other chronic conditions, so it is not that important in what time they are absorbed but what percent of them is absorbed.

They are certain nutrients, such as calcium (for example, in milk) that can bind to zinc and partially prevent its absorption. This is why it is usually recommended to take zinc on an empty stomach (Mayo Clinic):

  Zinc supplements are most effective if they are taken at least 1 hour
  before or 2 hours after meals. However, if zinc supplements cause
  stomach upset, they may be taken with a meal.

Usually there should be no significant difference between taking a pill with food, 2 minutes before or 2 minutes after the food, because in all cases the pill and the food will mix in the stomach. This is because every pill, even if you take it with water, will probably stay in the stomach for at least few minutes before it will be emptied into the small intestine.


Homoplasy just refers to the fact that the mutation happened independently. While several sources only discuss homoplasy as a phenotypic characteristic, and in contrast to homology (and thus suggest an adaptive implication), in general,  there is no assumption that the mutation gave increase in fitness (see this paper).


How are the two ATPs (properly 1.5 though) formed from oxidation of 1 FADH2?

FADH2 substrate does increase the H+ gradient by 6, and so increases the ATP Synthesization "potential" by about 1.5 (6/3.3). the difference between the NADH and the FADH2 substrats are mainly the different path in the electron chain. NADH uses Complex1, and FADH2 is part of Complex2, which have different ability to to pump H+ out. (but of course there are many other differences).

About the second question, it's a really broad subject involving the Krebs cycle and Glycolysis among other subjects. it is mainly a matter of enzyme regulation. The regulation affect both the electron chain and the ATP synthase.


Sure generally any cell that expresses MHCII will also express MHCI. Most cells in the body express MHCI as a self-identifier and to present intracellular proteins to T cells as a sort of a status update i.e. the cell will constantly be presenting peptides (pieces of endogenous proteins) on its surface bound to MHCI, if the cell becomes infected it could also present viral proteins on its surface with MHCI, which can potentially be recognized by a T cell specific for that particular epitope. B cells and antigen presenting cells such as dendritic cells and macrophages express MHCII but also need to be able to be identified as self through their basal level of MHCI presentation of self-peptides. The two MHC molecules are recognized by different cell types, MHCI by CD8 T cells and MHCII by CD4 T cells. So you could consider them to work independently from one another. The source of antigens (peptides here) and process for presenting them via MHCI and MHCII are somewhat different from one another.


Are neural connections one-way?

Yes. Action potentials travel only from dendrites towards axon.

  typically shown in pictures as an electric pulse traveling along a long, thin connective tissue.

What connective tissue? That thin "wire" which carries the action potential is a part of the neural cell body called axon.

Depending on what the axon connects to, there are 6 types of synapses:

"Blausen 0843 SynapseTypes" by BruceBlaus. When using this image in external sources it can be cited as:
Blausen.com staff. "Blausen gallery 2014". Wikiversity Journal of Medicine. DOI:10.15347/wjm/2014.010. ISSN 20018762. - Own work. Licensed under CC BY 3.0 via Wikimedia Commons.

A synapse is the connection between two structures: the axon of a neuron which "outputs" a signal (chemical or electrical) and the other structure ("input") that can be:

a dendrite or any other specific receptor from a cell
a neural body (can receive both electrical and chemical stimuli)

  what happens if both neurons fire at the same time on that connection?

In the situation of an axoaxonic synapse (example 2 and even 5 and 6 from the above illustration), the presynaptic neuron can have inhibitory action (nicely explained on michaeldmann.net at Presynaptic inhibition) from where I quote:

  Activity at the axoaxonic synapse partially hypopolarizes the terminal so that, when an action potential comes down the [...] afferent fiber into that terminal, its amplitude is reduced. Because the amount of transmitter substance released by a bouton is proportional to the amplitude of the action potential in it, less transmitter substance is released, resulting in a smaller EPSP and less excitation of the postsynaptic cell [...]

Links:

http://en.wikipedia.org/wiki/Synapse
http://www.getbodysmart.com/ap/nervoussystem/neurophysiology/synapses/introduction/synaptic_contacts/tutorial.html
http://michaeldmann.net/mann13.html


According to this article:

  Wet or moist wound treatment significantly reduces the time required for re-epithelialization

Since the lips are (normally) constantly being moistened by saliva, this could be the reason you experience accelerated cut healing.


Are (muscle) satellite cells the same as muscle stem cells?

Based on this review, satellite cells can replenish injured muscles, but among satellite cells there are satellite stem cells to maintain the pool of satellite cells.


What is the motivation behind the AAAAGCAUAU GACUAAAAAA of the mRNA SARS-CoV-2 vaccine when encoding its polyadenylated ending?

To enhance stability and translation efficiency according to {1}:

The 5′UTR (TEV) [8,21] and 3′ UTR (F-I) of this construct have been shown to enhance stability and translation efficiency, as has the 100-nucleotide poly(A) tail interrupted by a short linker (A30LA70, where L = GCAUAUGACU) [22]

References:

{1}
Stadler, C., Bähr-Mahmud, H., Celik, L. et al. Elimination of large tumors in mice by mRNA-encoded bispecific antibodies. Nat Med 23, 815–817 (2017). https://doi.org/10.1038/nm.4356 https://www.nature.com/articles/nm.4356
{21} Gallie, D.R., Tanguay, R.L. & Leathers, V. Gene 165, 233–238 (1995).
{22} Vallazza B, Petri S, Poleganov MA, Eberle F, Kuhn AN, Sahin U. Recombinant messenger RNA technology and its application in cancer immunotherapy, transcript replacement therapies, pluripotent stem cell induction, and beyond. Wiley Interdiscip Rev RNA. 2015 Sep-Oct;6(5):471-99. doi: 10.1002/wrna.1288. Epub 2015 Jun 9. PMID: 26061157. https://pubmed.ncbi.nlm.nih.gov/26061157/


EDITS - I appreciate the comments and have incorporated them here.  Thanks to    @Superbest and @user22406 for raising them.  I hope this makes a better answer for the community.

Under normal circumstances, genomic (self) or mtDNA released into your cell or body cause absolutely no (known) problems.   I'll explain why that is, how the body can detect bacterial DNA, and finally the circumstances in which DNA can cause problems.

Self-DNA generally causes no problems

Almost from conception, cells in your body die.  Sometimes as part of pre-programmed sequence (eg inter-digital cells of the fetal limb paddle die and form fingers) or normal replenishment of cells such as the white blood cell (hundreds of millions of neutrophils die each day) or your gut epithelium.

Macrophages consume liberated DNA, and the reticulo-endothelial system in the spleen, liver and lungs filters the blood for cellular fragments.  This paper (from @Superbest) shows that bacterial DNA, and not normal human genomic DNA, can activate macrophages.

So your immune system develops, and is constantly being exposed to, virtually every cell type and cell component (proteins, lipids, DNA and RNA etc).  If self-DNA could spark an immune reaction, normal life would be difficult.  We don't make antibodies (from B-cells) or T-cells that react with self-components due to a process called anergy in which any developing T- or B- cells that could react to self-components during their maturation are instructed to shut down and/or die.   Yes, mitochondrial are inherited matrilinearly, but they still lyse and cause anergy, preventing an auto-immune response.

(Not all cell death is harmless- @Superbest's comment reminds us that apoptosis (involved in finger formation and other tissue remodelling and cell turnover) can package cellular components into self-contained vesicles.  On the other hand, damaged or lysed cells can liberate cytoplasmic components that can be pro-inflammatory or pro-coagulant.)

Macrophages' vacuoles contain DNAse II, an enzyme that degrades DNA it encounters following phagocytosing/endocytosing fragments of dead cells.  More about that later....

Our bodies can detect bacterial DNA.  Same DNA, different decoration

However, invaders (bacterial, viruses, worms etc) may activate a family of receptors called Toll-like receptors (TLRs).   TLRs have evolved to have specificity for antigens not seen in mammals e.g cell walls, bacterial flagella and so on.  Some TLRs do recognise DNA or RNA.  You may know that DNA contains 4 nucleotide bases, A,T,G and C.  In mammals, special sequences of two bases, C-G, (called "CpG"s) can be enzymatically modified by a methyl group.  In bacterial CpGs are not typically methylated and so a TLR (e.g TLR-9) that detects un-methylated CpGs is generally detecting bacterial DNA.

Mitochondria are different

Mitochondria have features that resemble bacteria: a cell wall, a genome and the production of proteins that begin with the amino acid N-formyl-Methionine (f-Met).  Mammalian proteins don't have f-Met at the start ("N-terminus").  Macrophages have a receptor that can recognize f-Met sequences (especially f-Met-Leu-Phe, fMLP) and activation of the fMLP receptor stimulates phagocytosis.

This 2013 paper describes the controversy whether mammalian  mtDNA is methylated (at CpGs) and offers strong evidence that it is methylated.    In contrast, the Oka paper  gives 5 citations where mtDNA is not CpG-methylated.

So..do mitochondria look like bacteria to our innate immune system?

@user22406 flagged this paper by Oka et al which cites this paper by Zhang et al as evidence that mtDNA can be pro-inflammatory.  The Zhang paper provides evidence that mitochondria can stimulate the immune system's receptors for (1) f-Met-peptides (i.e detecting mitochondrial proteins that look 'bacterial") and (2) receptors for un-methylated CpGs, the TLR-9 receptor.  The Commentary on the article has a great figure of how mito components might promote inflammation which copyright prevents me adding.

The Oka paper uses 2 key techniques: (1) surgical constriction of the aorta to cause heart enlargement (cardiac hypertrophy) and (2) a mouse strain with the gene for DNAse II deleted (noted as -/-, two minuses, both alleles gone).  In the hearts of DNAse II -/- mice, they observe higher levels of deposition of mtDNA in the damaged heart (Supplemental Fig 2), greater heart damage and many animals die.  This suggests that excessive levels of DNA (not degraded in these DNAse -/-  mice) may be driving the damage. (The general phenotype of DNAse -/- mice was studied by Kawane et al  and the mice get an arthritis).  In Oka's DNAse II -/- mice, the degree of heart damage can be reduced by blocking TLR-9 (using an inhibitory oligo).  In aortic constricted mice where the DNAse II gene is intact (+/+), adding the TLR-9 blocking oligo gave some improvement, suggesting that the level of unmethylated DNA liberated in tissue damage may stimulate TLR-9 in normal animals.
The authors also examined aortic constriction in TLR-9 -/- mice and found they had less lung and heart damage compared to controls.

In summary, the Oka paper suggests something is signalling  via TLR-9 to drive inflammation and damage in this model and implies (but does not prove) that the 'something' is mtDNA.

mtDNA in the plasma

Another Zhang paper  detects up to 1ug/ml of mtDNA in the blood following major trauma (car and motorcycle crashes, falling 4 stories etc).  Their paper shows that this level of liberated mitochondria could stimulate immune cells (via TLR-9 and f-Met receptor).

mtDNA won't get back inside the cell

Extracellular DNA and RNA is generally broken down and cleared rapidly.  DNA, being a large, negatively charged molecule, will have extreme difficulty passing through an intact cell membrane.  In the laboratory, cells need to be exposed to high voltage electric shocks to make transient 'pores' in the cell membrane to allow DNA to enter or have the DNA formulated in liposomes.  Even if endocytosed, there is no known pathway to direct endocytosed DNA to the nucleus or an new mitochondrial 'host'.  So mtDNA would be extremely unlikely to re-seed into a new cell or a mitochondria.

But self-DNA can be harmful if released in large quantities

During successful cancer chemotherapy, large numbers of tumor cells lyse and may give rise to tumor lysis syndrome.  Among the products released when a tumor is killed is DNA. A and G - the 'purine bases' - can be further metabolized into uric acid.    Uric acid can crystallize in the kidney and cause damage.

Summary

Mitochondria may be the remnants of endosymbiotic bacteria but, absent major trauma or mutations in both of your DNAse II genes, mitochondria come (and stay) in peace.


Do we get 1/4 of our genes from each grandparent?

I have answered a similar question before: "How many genes do we share with our mother?".

It is not that you "get half your genes" from each parent, and thus a quarter from each grandparent, it is that you inherit the versions of the genes (we all have the 'same' genes).

The method that determines which traits are inherited from each parent by the offspring is known as homologous recombination, and this process is (essentially) random, and thus you end with ~50% of your traits (the alleles of the genes) from each parent, and ~25% from each grandparent, so you are right in this respect.

This is, however, a generalization; due to the chance nature of the recombination it is entirely plausible that you may inherit more traits from one grandparent in comparison to another, but this is unique to each individual (with the exception of course of genetically identical twins).


Discrete vs Continuous Replicator Dynamics

To make this derivation, it is better to focus on the population size of a strategy as opposed to the frequency of a strategy. Let $N_i$ be the population size of the strategy $i$. Strategies in the replicator dynamics change exponentially. The equation for continuous exponential growth is $\dot N_i = f_i N_i$. Since $x_i=N_i/N$ and $\dot N = \bar f N$, calculating $\dot x_i$ by using the quotient rule gives us the continuous replicator eqn.


Can we say it's hybridisation if it's the same species?

The question boils down to the definition of species and hybridization.

In general, we use the term hybridization to talk about mating between individuals from different species but really the term species does not mean as much as most people would think it does. Some people may use the term hybridization to talk about mating between lineages that are usually considered belonging to the asme species.

Have a look at How could humans have interbred with Neanderthals if we're a different species? for more information on the problems of definition of species.

Edit

Here are terms and concepts that are related and may help you

gene flow
introgression
interspecific mating
secondary contact
partial reproductive isolation


How do you derive steady-state conditions from the open-state differential equation of ion channels?

These are really math problems (algebra and basic calculus) rather than biology problems.

Oinf comes from solving algebraically the first equation you posted for steady state: i.e., when dO/dt = 0; just solve for O.

The time constant comes because this is a first-order exponential decay, which you get when you solve an equation (calculate an integral) of the form dO/dT = -lambda * O. The solution to that equation is an exponential decay of the form O(t) = O(0) * exp(-lambda*t)

tau is defined as 1/lambda and gives you the decay rate(relaxation time constant).


Cardiac output is the amount of blood pumped only by the left ventricle, per minute.


Why do classic psychedelics not cause withdrawal, despite high tolerance?

Short answer
Withdrawal effects are generally associated with drugs that induce feelings of euphoria by stimulating the reward center of the brain, either directly (cocaine, morphine) or indirectly (alcohol, nicotine). The classic hallucinogens have little effect on the dopaminergic pathways and hence do not cause serious withdrawal effects as observed with other classes of psychoactive drugs.

Background
Withdrawal is defined by the WHO as:

  a group of symptoms [that] occur on cessation or reduction of use of a
  psychoactive substance that has been taken repeatedly, usually for a
  prolonged period and/ or in high doses.

The typical drugs that are associated with withdrawal are alcohol and other sedatives, opioids, and stimulants.

Alcohol and sedative withdrawal can lead to anxiety, agitation, and depression. Opioid withdrawal results in drug-seeking behavior that may continue after the physical symptoms have abated. Stimulant withdrawal (the ''crash") is associated with depression, malaise, inertia, and instability (source: WHO).

All these characteristic symptoms are basically caused by the fact that the nervous system counteracts the drugs effects and downregulates the receptor systems activated by the drug. Therefore, more and more of the drug is needed. Indeed, downregulation is one of the physilogical mechanisms underlying tolerance (Stewart, 1993):

  Tolerance refers to the decreased effectiveness of a given drug with repeated administration.

There are many factors underlying tolerance. For example, there is acute, short-term tolerance seen with cocaine use, but also a long-term tolerance form example seen in opioids. One factor in developing (long-term) tolerance is a downregulation of the receptor systems involved. Alcohol and other sedatives target the GABAA system. GABA being the primary inhibitory neurotransmitter in the central nervous system, it's not surprising that abstinence in a situation of tolerance results in over-stimulation of the nervous system (anxiety, agitation). Likewise, opioid tolerance results in mu-opioid receptor downregulation (Stafford et al., 2011). Given that mu receptors mediate positive reinforcement following direct (e.g.., morphine and other opioids), or indirect (e.g., alcohol, cannabinoids, nicotine) activation it is readily apparent why opioid abstinence results in the craving for the drug, as it is thought that after prolonged use, the user is unable to experience pleasure without the drug. At this point, the person is addicted (source: The Treatment Center). According to the NIH

  Addiction is defined as a chronic, relapsing brain disease that is characterized by compulsive drug seeking and use, despite harmful consequences.

Now we come to the conclusion that dopamine is central to addiction, also for drugs not directly activating it, such as alcohol and nicotine. The latter group indirectly release dopamine in the brain's reward center (the limbic system).

The classic hallucinogens stimulate the serotinergic system, and specifically the 5HT2A receptors (López-Giménez, González-Maeso, 2017), but fail to activate the reward centers in the brain. Indeed, all addictive drugs activate the reward circuitry of the brain, thereby producing the subjective “high” that the drug abuser seeks (Gardner, 2011). Tolerance to these drugs has rarely been reported (Smith et al., 1999) and LSD  rarely produces serious withdrawal symptoms (source: LSD Abuse Help. But in rare cases, tolerance can develop and is associated with 5HT2A receptor downregulation (Gresch et al., 2005) and the development of hallucinogen persisting perception disorder (HPPD). An LSD tolerance can be developed quickly, although it usually dissipates within just a few days depending on the user, their dosages and frequency of use. Long term tolerances are uncommon because users do not frequently repeat doses of LSD without taking breaks in between (source: Hallucinogens).

The SSRIs you mention basically work by downregulation of presynaptic 5HT1A receptors (Celeda et al., 2004), which are unrelated to the effects of hallucinogens.

References
- Celeda et al., J Psychiatry Neurosci (2004); 29(4): 252–65
- Gardner, Adv Psychosom Med (2011); 30: 22–60
- Gresch et al., Neuropsychopharmacology (2005); 30: 1693–1702
- López-Giménez, González-Maeso, Curr Top Behav Neurosci (in press)
- Smith et al., Psychopharmacology (1999); 144(3): 248–54
- Stafford et al., Pharmacol Biochem Behav (2001); 69(1-2):233-7
- Stewart & Baidani, Behav Pharmacol (1993); 4(4): 289-312


The primary activity of the thyroid gland is to concentrate iodine from the blood to make thyroid hormone. The gland cannot make enough thyroid hormone if it does not have enough iodine. Therefore, with iodine deficiency the individual will become hypothyroid. Consequently, the pituitary gland in the brain senses the thyroid hormone level is too low and sends a signal to the thyroid. This signal is called thyroid stimulating hormone (TSH). As the name implies, this hormone stimulates the thyroid to produce thyroid hormone and to grow in size.
In Graves' disease one’s immune system produces a protein, called thyroid stimulating immunoglobulin (TSI). As with TSH, TSI stimulates the thyroid gland to enlarge producing a goiter. However, TSI also stimulates the thyroid to make too much thyroid hormone (causes hyperthyroidism). Since the pituitary senses too much thyroid hormone, it stops secreting TSH. In spite of this the thyroid gland continues to grow and make thyroid hormone. Therefore, Graves’ disease produces a goiter and hyperthyroidism.

Source: American Thyroid Association. What is a Goiter - Causes


Why does resting potential not become continually more negative?

The resting membrane potential is due to internal/external differences in ion concentrations and very importantly differences in permeability to those ions.
The fact that the sodium/potassium pump does not move an equal number of ions in each direction hardly matters at all for resting membrane potential; the resting membrane potential would be almost the same if that wasn't true. What is important is just the overall concentration of the two ion species, and the permeability of the membrane to different ions (almost all of this permeability is through specialized ion channels, because ions don't otherwise flow easily through a lipid bilayer).
You can calculate the resting potential/equilibrium potential using the Goldman equation - note that nothing in this equation involves the sodium/potassium pump moving different numbers of sodium and potassium ions.
The reason the membrane potential is negative is because the membrane at rest is most permeable to potassium, and because there is more potassium inside the cell than outside. Therefore, there will be a net flow of positive ions out of the cell, until enough ions have left that there is some negative charge inside the cell to counteract that net flow.


Are we evolving as fast as the oxygen is depleting?

Good estimates from ice core samples put the decrease in oxygen concentration at 0.7% over the last 800,000 years. At sea level, currently, inspired $P_{O2}$ is (760 mm Hg - 47) * 0.21, approximately 150mm Hg. Human physiology easily adapts to lower $P_{O2}$ levels, with approximately 140 million people living at elevations over 2500 m, with inspired $P_{O2}$ at 108mm Hg, and many permanent human settlements higher than 5000 m, with inspired $P_{O2}$ approximately half what it is at sea level (see West Respiratory Physiology, Ch. 9). A 0.7% decline over 800,000 years isn't going to be much of a challenge.


By selecting sex cells after meiosis, would it be possible to create two offspring with inverse parental DNA of one another?

Theoretically? Yes. Very theoretically possible.
In practice? It's difficult to isolate the exact daughter cells (sperm) from the same meiotic event, have these cells complete maturation, and only then have them fertilize an egg. Normally you need quite a lot of sperm cells even with in vitro fertilization, but also in principle all you need would be a single sperm cell to make a zygote!
To address some misconception: when you say "inherited from both parents but completely different", that applies also for regular sex cells and fertilized eggs. You don't need to fish for the precise 2 daughter cells following meiosis to get this outcome. Mitosis produces 2 genetic copies, while meiosis in humans produces 4 unique daughter cells. All individuals, as diploid as we are as humans, are products of genomes that have been very well shuffled (recombined).
Reality: the real-life reasons to perform such a procedure would be taken as very dubious, so I don't think realistically anyone would perform this. But in the designer baby era of the future, who knows!


How do B and T cells work incorrectly in a person with Systemic Lupus Erythematosus?

The initial trigger for the disease is unknown and can be different from person to person. However, we do know that there can be environmental or infectious triggers that are further potentiated by genetic and hormonal factors.

The pathology of SLE is associated with the development of "auto-antibodies" or "anti-nuclear antibodies," so saying that B cells and T cells attack healthy cells is not exactly correct - More accurately they produce antibodies against proteins on healthy cells, which form immune complexes, activate complement and induce apoptosis.  To produce auto-antibodies, events occur as follows:

The trigger causes macrophages or antigen-presenting cells (APCs) to display self- or auto-antigens
APCs recruit B cells to start producing antibodies against the antigen
APCs activate T helper cells, which stimulate inflammation and perpetually activate the B cells to produce auto-antibodies

The following immune abnormalities are associated with SLE (particular focus on B cells and T cells)

High levels of circulating B cells
Decreased levels of T suppressor cells, which would otherwise regulate the immune system and auto-antibody production
Abnormal B cell signalling and persistent activation of B cells (IL-6, IL-10)
Prolonged life span of B cells, possibly due to poor immunoregulation (#2)

Reference:
Schur PH, Hahn BH, Pisetsky DS, Ramirez Curtis M. Epidemiology and pathogenesis of systemic lupus erythematosus. Up to date. Topic last updated: Feb 5 2016. Subscription access only.


How can mammalian red blood cells live without a nucleus?

It depends on what you call "to live". RBCs cannot divide, for instance. They cannot synthesise proteins either, so they are decaying after their nucleus is expelled. But they produce ATP using anaerobic glycolysis (as they lack mitochondria), which you may take as a characteristic of "living".


Is alternative splicing possible in the same cell?

In complex eukaryotes like humans, alternative splicing is the rule, rather than the exception.
Eukaryotic splicing is managed by a complex regulatory system, including more than 100 different elements, some of which are enhancers and regulators.
Thus, while one form will often be dominant, one should generally expect at least some alternatives to be present in a cell.
While the amount of work on population-level heterogeneity is still much larger than that on variation within single cells, studies of splicing heterogeneity have identified that multiple forms are often present simultaneously within a single cell. For example, in this recent study, Figure 2 shows that although the distribution between two splicing alternatives is bimodal, single cells exist with the full range of fractional mixes between the two forms.


How could be the concentration of airborne pathogens in a specific indoor space be measured?

I have no idea how practical it would be for your intended application, but people do estimate airborne concentrations of fungi and bacteria by sampling aerosols (i.e., filtering a volume of area to extract dust etc. that can carry the target organisms) and then using quantitative PCR with primers targeted at generic fungal or bacterial DNA sequences to estimate concentrations of particular classes of organisms.

Luhung, Irvan, Yan Wu, Chun Kiat Ng, Dana Miller, Bin Cao, and Victor Wei-Chung Chang. “Protocol Improvements for Low Concentration DNA-Based Bioaerosol Sampling and Analysis.” PLoS ONE 10, no. 11 (November 30, 2015). https://doi.org/10.1371/journal.pone.0141158.


What is the meaning of multicellularity?

Bacteria are, as a general rule, unicellular.  However, there are some, like the cyanobacteria which you referenced, which are kind of border line.  Wikipedia's definition of multicellularity is a very broad sweeping definition, and its statement that bacteria are unicellular is also a broad sweeping statement.
The fact is, that as a general rule, bacteria are unicellular, but at times, like you said, they can undergo filamentation.  When they do, they end up with several connected cells which are generally considered functionally independent.  In certain circumstances, however, the cells can be dependent on each other for survival, and because they didn't separate completely, it's hard to define whether we're looking at multicellularity or symbiosis.
It is generally accepted that cyaonbacteria are truly multicellular.  In order to be multicellular, an organism generally has to fulfill 5 basic requirements:

More than one cell
Cells stick together
Cells communicate
Cells are dependent on each other
Cells are differentiated

By these requirements, some cyaonbacteria technically are multicellular bacteria, defying frequent claims that all bacteria are unicellular.  That said, wikipedia isn't totally wrong, since as a general rule, bacteria are unicellular.  Cyanobacteria are an odd (debatably) exception to the rule.

Sources:

Bacteria with bodies - multicellular prokaryotes, Gould, S.E.
Multicellularity in Cyanobacteria, Paleontology Podcasts
Introduction to Cyaonbacteria, University of California Museum of Paleontology
Wikipedia: Multicellularity, Cyanobacteria, Filamentation


What is this strange horned, slug-like coral reef dwelling creature?

Here is your animal in Blue Planet II trailer:

This is a sea cucumber (Phylum Echinodermata, Class Holothuroidea).

More specifically, this is a sea cucumber from the Species Pearsonothuria graeffei, the Graeffe's sea cucumber.

Here are other images of Pearsonothuria graeffei for comparison:

Sea cucumbers have an antero-posterior elongated body, as you can see in this image of the whole animal:

Those black structures you see are the tube feet, a distinctive feature of Echinoderms.

Here is a detailed image of the tube feet in Pearsonothuria graeffei:


How to derive rate of product formation for an allosterically inhibited enzyme?

If you apply quasi-steady state approximation for the complexes then you will get three equations for each of the complexes. Then you have to use the conservation law for enzyme to obtain the equation with respect to just substrate and inhibitor. If you try solving these algebraic equations, it gets very complex and difficult to solve by hand. However, in this system of chemical reactions, you can notice one thing: the binding of the inhibitor is not affected by the binding of substrate. In other words, the amount of enzyme inhibited will not depend on the amount of substrate present. So, in the absence of substrate:
$$\frac{d}{dt}(EI)=k_3I.E - k_{-3}EI = 0$$

So the total uninhibited enzyme ($E_u$) would be:
$$E_u=\frac{E_0}{1+\frac{I}{K_I}}$$

When the substrate is present, the amount of total enzyme available for catalysis would be $E_u$. Now, apply the Michaelis-Menten equation for uninhibited enzyme but substitute total enzyme ($E_0$) with total available enzyme ($E_u$):

$$V=\frac{k_2S\left(\frac{E_0}{1+\frac{I}{K_I}}\right)}{K_M+S}$$

From here you can get the equation given in the book.

The above logic works only if the rate of inhibitor binding is much faster than that of substrate binding. If not, the dynamics of product formation will depend on the different reaction rates and this simplistic equation would not be valid.


If humans had cellulase would they be able to digest grass?

No. Even for an herbivore, digesting grass, or plants to be more general, is hard, because they contain cellulose. Herbivores have different parts of a stomach, whereas humans only have one compartment, so in herbivores, the plants (or grass) enter the first part of their stomachs called the rumen, which contains a salty solution that breaks down cellulose, then, the herbivore will regurgitate the processed food, or cud, from the rumen, into their mouths, and break down the cellulose even MORE. The cud then enters back into the rumen and then digests as normal. So even if a human had cellulase, they would need a rumen, to break down the cellulose further.


looks most like a Meta ovalis with a span of about 10 CM.


What proves that speciation is a pairwise process?

I offer this perspective in addition to what WYSIWYG has provided.

Phylogenetic trees are tools to model what has actually happened, or what some evidence implies has happened, to a population of entities that exchange genetic material.

These models fail, for instance, when describing the phenomenon of horizontal gene transfer since a tree is acyclic by definition. Consider a viral genome that has integrated into a host genome. The host now contains DNA from its ancestral lineage and the viral lineage. This process cannot be modeled by a tree.

Some founder population that is susceptible to exogenous genetic transformation may give rise to many distinct lineages, some of which your species concept may qualify as "new" species.


Whence fecal E. coli (et al.) if swallowing it is dangerous?

E. coli is mostly harmless; only a few strains are harmful.

I don't believe the route by which gut biota is established has been entirely established for any species but, for example, koala feed their faeces to their offspring to help them establish biota capable of digesting eucalyptus. It seems that a small proportion of ingested bacteria somehow survive passage through the stomach to the gut and then begin multiplying and colonising the intestines.

It's also important to realise that just because an organism is sometimes harmful doesn't mean it always is. There are many microorganisms that are pretty much ubiquitously found on or in your body which are capable of causing disease but only do so very rarely; usually when the body's defences have already been compromised (e.g. Pseudomonas aeruginosa, Candida albicans aka thrush, and so on).


You mean generation time?

There are several definitions in use, but one is "the average difference in age between parent and offspring" (or "age at which members of a given cohort are expected to reproduce") which would be the same as the time period you're asking about.

(The difference between these two depends whether the population is at equilibrium or not.)

The two above are 'shortest generation time'; a third definition (which is the first in the link) is a little more complex but is more useful where individuals reproduce over a prolonged period.


Identify chromosome location from gene nucleotide or amino acid number

Option 1: You can use the SNP database, to see if it has (and it usually is) characterised before: The tutorial is here (http://www.sciencebuddies.org/science-fair-projects/project_ideas/BioMed_Bioinformatics_NCBIGene_SNP.shtml)

Option 2: is to use a go to character function in a few text editors. If you are on windows, You can do it in Notepad++ (https://superuser.com/questions/487507/how-can-i-find-nth-character-in-notepad); if in Linux/mac, you probably know how to do it in vim (https://stackoverflow.com/questions/22862558/go-to-a-specific-offset-in-a-document). If using other text editors in Linux, ask around that community, and they'll tell you how to go about it.

Option 3: One another labour intensive but easy way to do it is to use the tools available online. I personally use NCBI for this, and play around with the region shown. This prevents you from counting. Once you get the local region, select a  few nucleotides  to the left and right, and use that as a search term in your sequence (find text and replace text)

Option 4: And my personal favourite, get the computer to do it for you like this: https://stackoverflow.com/questions/23662748/replace-a-nucleotide-at-a-certain-position-in-a-dna-sequence-file

If you are using IGV, it is said in the documentation here (https://www.broadinstitute.org/igv/Navigate) on how to search for regions and even insert mutations. Were you not able to make this work ?


What is the fastest but not venomous snake?

The fastest non venomous snake is arguably the Eastern Coachwhip with a top speed of upto 10 mph (reference). If it feels cornered, it will attack with bites but otherwise, it prefers to flee.


This is a caddisfly larvae (Trichoptera). They live in streams and other water that are rich in oxygen.
They protect themselves by building there own 'house', with whatever is available, e.g. plant or wood fragments, gravel or even snail shells (see picture below)

Picture from Dutch wiki

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

Id to species level probably requires microscopic work.


Thousands of Reporters Integrated in Parallel (TRIP) barcodes

From the paper and user manual it seems that barcodes are random sequences of pre-defined length of 16-20bp ± 1bp. On data analysis step they are combined and all barcodes 2 Hamming distance apart (it means that two words have difference in one letter from each other) will be discarded from the list of genuine barcodes.


Is homosexuality an adaptation in humans?

Barnard's wonderful text "Animal Behavior: Mechanism, Development, Function and Evolution" offers some enlightening summary to the discussion of homosexuality in a biological context!

Brief Summary to ch 12, page 606:

  What we know so far:

  homosexual behavior is recorded all throughout animal kingdom
  there are evidence for genetic basis to homosexuality in various species including humans

  Three interrelated schools of thoughts:

  Homosexuality is maladaptive - external stress creates homosexuality

  reduce resource stress on family unit, youngest child tend to be gay (E.M. Miller 2000)
  *** mitochondrial DNA carries male killing genes, with male being a dead-end (Hurst 1991)

  Homosexuality as an adaptive early phase of development - homosexual acts are just target practice

  homosexuality is just males practicing sex on each other, most homosexual acts are performed by bisexuals with just as high fertility
  as straight males (Baker & Bellis 1995)

  Homosexuality advantages in other aspects of reproduction - homosexuality may imply better parenting

  homosexual genes induces feminine attributes in males such as sensitivity, empathy and kindness hereby increasing likelihood of long
  term pair bonding and paternal care (E.M. Miller 2000)

*** original text:

  A completely different suggestion is that homosexuality may reflect
  the interests of selfish genetic elements (see 2.4.3.2) inherited
  maternally on mitochondrial DNA for which males are effectively a dead
  end. Some insects have been shown to carry 'male-killing' genes on
  their mitochondrial DNA, so perhaps homosexuality is a similar, if
  more benign, rout to sidelining males (Hurst 1991)


I am colorblind, but I did not know that before I was 22 (!!). I got to know it by doing the Ishihara test. There are other tests you can do to test for colorblindness, such as the reverse colorblindness test (http://www.cs.unm.edu/~aaron/creative/colorTest.htm), where a "normal vision" person will not see the two patterns shown there.

Anyway, there is no test where you cannot ask "what do you see?" to the subject. On the other hand, I saw a photo where they were showing a northern light in both colorblind and normal vision (https://www.facebook.com/nlblog/photos/pb.236481989828593.-2207520000.1415264974./416457851831005/?type=1&theater) -I hope facebook links are OK in this site-, where I see no difference between the two photos. You could for example show that photo pair to your test subject and ask a set of questions (e.g. which one do you like more?). If he/she is colorblind, then the answer will be "they are the same", so you have a strong indication, or if they are able to point out differences, then they most likely have normal vision.

I could think of an experiment where you just show several photos with different contrasts/saturations, and then add the northern light photo (maybe the author has some other photos you could use), so they are not aware of the underlying question.

I hope this helps


Species identification, tree from Ecuador

Your plant appears to be Chionanthus pubescens, the pink fringe tree, which is native to Ecuador and Peru. The genus has a number of species. It belongs to the family Oleaceae, which includes well known plants like jasmine, forsythia, ash trees and olives. I could not find much biological information on the pink fringe tree but plantlist.org contains a number of links to various databases that may be helpful if you want to dig deeper.


If a cell has two different GPCRs, how does the cell differentiate between the phosphorylation cascade caused by each?

First, it would be an oversimplification to say that GPCRs act only through increases in cytosolic cAMP. This is true for receptors coupled to Gs proteins, but there are other G proteins like Gi, Go and Gq which act differently [1].

Now, a cell can have receptors coupled to many different G proteins. Vascular smooth muscle, for instance, has Gs, Gi and Gq-coupled receptors [2]. Further, a cell can have different receptors coupling to G proteins of the same type (e.g., hepatocytes have glucagon and beta adrenergic receptors [3], which both couple to Gs).

In such situations, the effects of different hormones add up. The final effect is a function of the total cytosolic concentration of second messenger (e.g., cAMP). Thus glycogen breakdown in a hepatocyte depends on the overall effects of glucagon and epinephrine [3]. The hepatocyte has no way of 'knowing' which cAMP molecule was formed by which hormone.

References

https://en.wikipedia.org/wiki/Heterotrimeric_G_protein
https://cvphysiology.com/Blood%20Pressure/BP026
https://www.nature.com/articles/emm2015122


Why do ladybugs have a different number of points on their backs

The spots on the back of Ladybugs over the surface is defense mechanism to avoid predators. The spots come in different shapes and different numbers. Some say that those dots tell us their age. Since some ladybugs have 24 spots which means its age would be 24 years and that is not at all possible. So this is a popular misconception running around us.

But the real truth about the number of spots on the ladybugs' back is:

  The number of spots on a ladybug does have significance. The spots and other markings do help you identify the species of ladybug. Some species have no spots at all. The record-holder for most spots is the 24-spot ladybug ( Subcoccinella 24-punctata), which has 24 spots, of course. Ladybugs aren't always red with black spots, either. The twice-stabbed ladybug ( Chilocorus stigma) is black with two red spots.

So now we know that the number of spots on the back of Ladybugs will help us to identify what species it belongs to. To give an insight into different species of them you can refer to this Identifying Ladybugs.

The above image shows different species of Ladybugs where you can see the varying number of spots in each bugs' back. More information can be found here Stripes on Ladybugs.


Short Answer : You can not pinpoint any single step for this delay. It is a combination of multiple processes.

Long Answer : I think there are multiple factors that can contribute to this. Dermal Wound healing is a multi-step and complex process typically includes inflammation, new tissue formation and remodeling (Gurtner et al 2008). Each of these stages involved very complex signaling pathways of various components. In addition, there are multiple types of fibroblast cells involved in this process. You are most likely talking about Myofibroblasts who bring the edges of a wound together. However, this itself is a very complex process involving interaction with the proliferation and migration of both mesenchymal and epithelial cells. This is further tightly controlled by Keratinocyte-fibroblast interactions (Werner et al 2007).

So what can you do? : The the physical analogy, which you are trying to implement here, has to apply within some assumptions. You can declare some fitting parameter(s) which can contribute to all the process and validate it according to good experimental data, probably with some kind of mutant data where the wound healing process is slowed down or accelerated. While deciding your assumptions, use as fewer assumptions as possible else you will end up creating Spherical Cow.


Scanning various reviews it seems that everyone who mentions the possibility of a human chymosin refers to a single paper. So for example this 2014 review has a single reference to a human chymosin:

  Henschel et al. detected a
  protease in the gastric aspirates of newborn infants within 6–10 h postpartum that was not
  pepsin [62]. The electrophoretic mobility and immunoreactivity are similar to that of calf
  chymosin, a protease that cleaves κ-casein and causes casein curdling. This protease is
  unique in that it disappears from gastric fluid at 10 days postpartum and is not found in adult gastric fluid.

I don't have access to the Henschel et al. paper (from 1987) but here is the abstract:

  The electrophoretic mobilities of proteases present in gastric juice taken within 10 h of birth from 5 healthy, premature infants were compared with calf chymosin, pig pepsin A and human adult gastric juice. The juice from 2 infants contained predominantly a chymosin-like enzyme, another had almost exclusively pepsins similar to those of the adult juice, while the other two contained a mixture of both. The pepsins consisted of two elements, probably pepsin A (EC 3.4.23.1), and pepsin C (EC 3.4.23.3). Single radial immunodiffusion gave a definite reaction to calf anti-chymosin serum in five samples taken from a further 17 infants. These results indicate that some human infants secrete chymosin. The reaction in the immunodiffusion assay indicated a much lower enzyme activity than that implied from electrophoretic separations. It is suggested that species differences resulted in poor cross-reactivity of the antiserum.

Now, obviously, without seeing the data it isn't possible to be conclusively critical, but the quality of the evidence seems to be rather weak, being based upon similar electrophoretic mobilities and an immunodiffusion assay (why not a Western blot?) with an overt apology for weak cross-reactivity of the antiserum used.

However, leaving all of that to one side, the strangest thing about this is the sporadic appearance of the proposed chymosin: although 4/5 were scored as chymosin positive in the 1st experiment, is it likely that 2 of these would apparently contain little pepsin? And in the second experiment (the immunoassay) only 5/17 scored positive for chymosin.

Evidently no-one has ever reproduced this result, and the evidence for the pseudogene (but no active gene) is very strong. I vote that humans do not produce a chymosin.

Update
Having read Bryan Krause's answer: if the human gene product was lacking an exon's worth of amino acid sequence then presumably it wouldn't have an electrophoretic mobility that was closely similar to the calf protein.


This is a polyclad flatworm.

Here is a video of notoplana vitrea moving similarly to the one in the video that you linked:
https://www.asturnatura.com/especie/notoplana-vitrea.html
Here is a gallery of polyclad flatworms observed in India:
https://inaturalist.ca/observations?place_id=6681&subview=grid&taxon_id=52318
A number of the images in this gallery look similar to the one in your video, but very few of them are identified beyond this order taxon of polyclad flatworm.


Why do coronavirus cases graphs have a sinusoidal like shape?

It's a weekly cycle due to reporting disruptions over the weekend.
Use a 7-day moving average to get a better picture. Holidays and such can still be disruptive but the 7-day average solves most of it.


This lizard is likely a Roughtail Rock Agama (Stellagama stellio or Laudakia stellio). They are colloquially referred to as hardon (or hardun) lizards.

According to Wikipedia:

  Like many agamids, stellions can change color to express their moods. They bask on stone walls, rocks, and trees. They are usually found in rocky habitats, and are quite shy, being very ready to dive into cracks to hide from potential predators.

More from natureisreal:

  The most commonly seen local lizard where I live in central Israel is probably the roughtail rock agama (laudakia stellio stellio), known locally as a hardon or hardun. They are rather sinister looking with rough dark armoured skin, but perfectly harmless. If frightened they run away and hide in the crevice of a rock or tree, inflating their skin and opening their mouth wide to wedge themsevles into the space, making it impossible to dislodge them. Sometimes I see a large dark male surveying his territory from the top of the nearby water tower.More usually they are to be seen during the warmest times of day sunning themselves on rocks, to the extent that it seems that each rocks has its own resident hardon, and believe me, this country is full of rocks, and that makes for a lot of these lizards...


It's not a single grass cell, but this does indeed appear to be a micrograph of a leaf of grass—so it actually contains numerous cells. Here's another image I was able to find with a much more clear description of exactly what you're seeing:

  Marram grass leaf. Light micrograph of a cross section through a closed (unravelled) leaf of Marram grass, Ammophila arenaria. The deeply grooved leaf is thrown into folds (seen here) and it uncurls when mature so that the folds do not face the centre. The folds conserve water and withstand salt, and prevent excessive evaporation. Round vascular bundles are visible inside each fold, serving to transport food and water through the leaf. Spines on the surface discourage animals from eating the leaf. Marram grass is important in coastal ecology, since it is one of the commonest grass species in Britain to stabilize sand dunes. Magnification: x22 at 35mm size. (Emphasis added)

  Source: http://www.sciencephoto.com/media/30161/view

And here's another:

  Transverse section of Marram Grass leaf , showing adaptations to prevent water loss; outer thick cuticle, curling by means of hinge cells to protect inner epidermis, stomata
  sunken into surface to maintain high humidity

  Source: http://www.eplantscience.com/index/principles_of_horticulture/minerals.php

The coloration yielding the yellow 'happy faces' is artificial, either due to staining or direct post-processing of the image.


Where do the bacteria within the vagina originate from?

Most of the initial colonisation is said to be coincidental ('happenstance' as the textbook puts it!) exposure.

It's then fairly predictable depending on:

type of delivery (as Larry commented);
feeding; and
receipt of antibiotics.

In terms of feeding, there are differences in flora between babies fed human milk and those that are given cow's milk.

There's a section called 'Establishment and Composition of Normal Flora' in chapter 187 of Principles and Practice of Pediatric Infectious Diseases (3rd ed) by Long which discusses the above.

It's also said that hormones may influence indigenous flora. For example, premenarcheal and postmenopausal vaginal flora are very different to those present during the childbearing period.[1].

Mandell, Douglas, and Bennett's Principles and Practice of Infectious Diseases. 7th ed. 2009. Churchill Livingstone.


Will a polyclonal antibody attach to proteins of different kDA?

If the sequence of the 26 kDa form is included within the sequence of the 28 kDa form then the answer is 'probably yes'.

However if the N- or C-terminus of the short form is an important/dominant epitope and it is masked in the long form (by being extended) then the activity of the serum against the long form could be significantly reduced.


Does AMP/ATP ratio affect lifespan in vertebrates?

There are many papers suggesting a link between AMPK (the major cellular sensor of the AMP/ATP ratio) and lifespan.  As with most of these sorts of experiments, I think it is currently unclear precisely what the mechanism for this is, but AMPK regulates TORC1 and autophagy, both of which are also important for lifespan regulation.  Here is a PubMed link to search results.


What causes Paresthesia (Pins and Needles) at a cellular level?

Underneath the superficial layers of your skin there are receptors which sense pressure, temperature and pain. These receptors are part of the peripheral nervous system which senses stimuli and they take the message conveying details about the stimulus to the somatosensory cortex of the brain. Here is where the perception of pain, burning, pressure etc is ultimately made. To take the simplest example, if you stop blood flow for a short amount of time in a limb, these receptors are activated, and will send signals to the brain that are interpreted as tingling or numbness. With more severe pain, different receptors are activated which , again, project to the same brain area but a different message is read out. If the pressure from one limb is removed, the receptors will go back to normal function as blood flow is restored.

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

http://www.scholarpedia.org/article/Mammalian_mechanoreception


What are in common between transcription factors?

Transcription factors are a very heterogeneous group of proteins. Their two main objectives are to bind DNA & to recruit polymerase to that site. There are a of ways for them to accomplish these tasks.

To bind DNA, all they need is a pocket of positive charge, which are found in several structural motifs across many proteins. The wikipedia page actually provides a good sample of this diversity: https://en.wikipedia.org/wiki/Transcription_factor#Structural

The other co-factors that transcription factors recruit to get polymerase to the DNA strand also vary pretty widely. They link together through structurally complementary pockets of opposite charge, but beyond that, the details get pretty messy and there are a lot of details. Even reviews of transcription factors tend to focus on a specific class. If you want more than that very simplified explanation, I would actually recommend reading some reviews on the subject. Here are a couple:

http://www.ncbi.nlm.nih.gov/pubmed/25755661

http://www.ncbi.nlm.nih.gov/pubmed/25640595


Where do amino acids get attached to tRNA and where is it synthesized?

A pre-tRNA is transcribed from tRNA genes in DNA by RNA polymerase III. Processing occurs in the nucleus, where a 5' sequence is cleaved by RNase P, the 3's CCA motif is added, and ~10% of the nucleotides are substituted. The tRNA are transported out via the pore complexes. Aminoacyl-tRNA synthetase enzymes attach amino acids in the cytoplasm in a 2-step reaction that requires ATP. You'll find there's a unique splicing mechanism in tRNA that additionally splices out an anticodon intron which is abesnt in mature tRNA's:

The wikipedia article notes RNA Pol III generally recognizes internal control elements rather than upstream control elements as in a normal gene.

Source: Qiagen

Source: Molecular Cell Biology. 4th edition.

Addendum: I said in my post that tRNA is charged in the cytoplasm, this is somewhat true. In mammalian cells, we also see that tRNA are charged in the nucleus as well, and it might aid in the export of some of these charged tRNAs. (Source)


Why does milk contained in cartons of milk expand?

The likeliest culprit here is fermentation carried out by bacteria present in the milk. Fermentation of a sugar, for example glucose, releases carbon dioxide (a gas) :

$$C_{6}H_{12}O_{6} \rightarrow 2 C_{2}H_{5}OH + 2 CO_{2}$$

Since this reaction produces a gas, the gas builds up in the milk carton causing it to bulge. This is not, generally, a good sign, make sure to smell the milk before drinking it!


What are the chances that Tyrannosaurus Rex could roar?

Careful now: T Rex was not a bird, it was a non-avian theropod. Birds are dinosaurs but not all dinosaurs are birds. In the same way, tigers are cats but not all cats are tigers.

The argument that T Rex could not roar is not only based on none of its closest relatives being able to as you seem to indicate. Dinosaurs (and by extension birds) are archosaurs, a clade that includes crocodilians too and crocodilians are quite a bit more close to the basal form of archosaurs than T Rex was. Crocodilians can only sort of "hiss", not roar in the colloquial sense. And birds cannot roar. This is a decent start to a thought process but this isn't really the argument for why dinosaurs likely didn't roar in the past.

Researchers who have studied the potential vocalizations of prehistoric, non-avian dinosaurs have found indications that similar closed-mouth vocalization to those found in other living archosaurs are very probable: https://news.utexas.edu/2016/07/11/dinosaurs-may-have-cooed-like-doves

Closed-mouth vocalization is not really compatible with what people typically think of as roaring. It still allows a variety of sounds that don't necessarily (though perhaps probably) somewhat resembled crocodialian or simple bird vocalizations. So no, it's not impossible that some non-avian dinosaurs could roar but the current state of our knowledge is that they very likely could not.


Why is electroporation not the prefered choice transforming for Mammalian Cells (HEK)?

Viral methods are just more efficient and give you a higher viability in the end. Electroporation works but you'll have a low yield of viable cells after. Here's a nice paper looking at the effects of buffer composition on cell viability/transfection efficiency: https://www.nature.com/articles/s41598-020-59790-x with the general take away being, if electroporation is working well enough to transfect the cells, it will also kill a fair percentage as well.
Hek cells in particular are pretty easy to transfect through viral methods for stable integration of your plasmid or Fugene/lipofectamine for transient expression.


How to attain a deep conceptual grasp of key atomic/molecular/genetic/ notions?

I'm assuming you have a reasonable high school education otherwise you probably wouldn't have posted your question.

Do a basic science course and/or read - maths, physics, chemistry, biology texts. 1st year university level should be good.

If there is anything you don't understand in these texts, go to more basic books - plus Wikipedia is good for the sciences (I wouldn´t like to read them on, say, the Arab-Israeli question), but I've never seen any egregious errors in the scientific area!

Then read Klug and Cummins "Concepts of Genetics" from cover to cover.

If there is anything you don't understand in Klug and Cummins, go back to basic texts.

I had a good background in the  sciences and then majored in Genetics with minors in Biochem, Microbiology and Immunology. I read that book from cover to cover taking notes in 3rd year (of a 4 year degree programme) and have done very well in the field.

The book covers the history of the discoveries in a very readable and approachable fashion. Obviously it is no substitute for doing a degree in the subject, but if you really wish to at least have a good understanding of the science, you could do worse than read that text!

You could also read popular science books aimed at the "interested and educated layperson" - Stephen Jay Gould, Richard Dawkins for example. Try National Geographic and even Scientific American or New Scientist. You, at least intially, will have to make a real effort, but it is very rewarding - there is nothing more fascinating than biology generally and molecular biology/genetics in particular! Best of luck on your journey!


Which Receptors are Involved in the antidepressant effects of SSRIs?

You're right, those are all important! There are several good reviews on the mechanism of action antidepressants. I like Molecular Pharmacology, by Nestler, or even Principles of Neural Science, by Kandel. I think a textbook is going to be your best bet, in terms of getting up to speed here, as this is largely an already-researched issue, but here are some good review articles as well:

Bonhomme et al., 1988
Charney et al., 1981
Norbert & Esposito, 1998
Spencer, 2012

If you have a more specific question, let me know!


When do fireflies glow in their lifetime?

Fireflies 'glow' in larval and adult stages but for very different reasons. It is thought that glowing behaviour first evolved in larvae to deter predators(Branham and Wenzel (2003)). This is an example of an aposematic warning, which uses bright colours, smells, sounds, or in this case light, to tell predators they are undesirable as prey. Sometimes a prey animal will use an aposematic warning to tell predators they are poisonous, or simply to mimic a prey that is poisonous. In the case of firefly larvae, they don't taste good to predators because of a steroid compound in their bodies (Branham (2005)).

Adults also glow, but do so in a synchronized pattern of flashes to communicate with mates (Carlson and Copeland (1985)). Mates will time their flashing with physiological fluctuations and even respond directly to another individual's flashing pattern with appropriate delays and timing of responses.

So to answer your first question, fireflies are not continuously glowing, but flash at night as larvae to deter predators, and during active mating as adults.

Your second question can get into a long-winded explanation of how certain traits evolve in response to a pressure, but to simplify, it's likely that fireflies evolved glowing because it relieved predation pressure. This ability then evolved further to communicate the quality of mates more efficiently than phermone signalling.


How to prevent a old promoter region from attaching onto a plasmid instead of a new one during ligation?

Run it out on a gel after digestion  and extract the vector only.
Treat with a phosphatase after digestion. This will prevent religation since you need at least one of your fragments to be phosphorylated for the ligation to work.
(A must regardless) sequence several colonies at the end.

I recommend doing all three.

Edit: option 4: digest with a third enzyme that cuts in your old promoter but not the vector or the new promoter.


How to characterize stability of a protein from Trp fluorescence vs [denaturant] curves?

Papers I've seen using this method show it's possible to calculate the fraction of denatured protein by analyzing displacement in peak emission wavelength.

Have you tried doing that with your data? What do you get if you plot peak emission wavelength as a function of denaturing agent concentration? If these look like sigmoidal curves (you might need a log scale on the X axis) with a clear upper plateau, then you can apply the method mentioned by these papers because the signal you observe is correlated to the fraction of denatured protein and saturates (this part is important: the signal must saturate past a certain concentration of denaturing agent, because all protein molecules are fully denatured and therefore adding more denaturing agent won't give further signal change; if your signal doesn't saturate, something is wrong).

  However, they use monomeric proteins with few Trp, whereas I have a dimer with several Trp

Oligomeric state and number of Trp residues should not matter, because peak emission wavelength is only correlated to the fraction of denatured protein. Total intensity will increase with more Trp residues, but you're not using intensity as a measure of the fraction of denatured protein (and if anything, it's good to have more intensity to begin with given the quenching effect you observe with increasing denaturing agent concentration).

  plus some additional variability introduced by the different ligands.

To take care of this concern, you need two controls that:

prove that none of the ligands alters the fluorescence of your protein,
prove that none of the ligands emits fluorescence between 300 and 450 nm, or if they do then you need to measure it to be able to subtract it from your total spectra, in order to recover the protein contribution to the total fluorescence.

For 1, record fluorescence emission spectra of the protein without denaturing agent but as a function of ligand concentration (span a few orders of magnitude) and see if the peak emission wavelength changes with ligand binding (it might change, which means the same assay can yield binding curves and Kd values for your ligands, which could also be useful!). Full ligand titration curves would be the most robust control, but you can simply use the same ligand concentrations as used in the denaturation experiments.

For 2, the simplest case would be that your ligands are not fluorescent, but you cannot simply assume that. Therefore, an important control you also need is to record emission spectra for each of your ligands at the concentrations used in the denaturation experiments, and this at each concentration of denaturing agent (or simply at 0 and max concentration: if there's no difference between these two spectra, you don't need to record one at every concentration in between). If the ligands emit fluorescence between 300 and 450 nm, you need to subtract that from your total spectra to recover the fluorescence arising from the protein only.


This looks like a Common Garden Skink (Lampropholis guichenoti)

Further information can be found here and here

The description is a quote from the first source:

  The colour of the skin of a common garden skink is mostly a brown-grey colour, and it usually has a black or dark coloured stripe down either side of its body and a copper coloured head. The diet of common garden skinks generally consists of insects and vegetation, and can include caterpillars, spiders, slugs, cockroaches, crickets, worms and ants, and fruit and vegetables. Small and enclosed spaces, such as rocks or trees, are the sought after home for common garden skinks, and they are commonly found in urban gardens, hiding in among plants or leaves. Common garden skinks generally grow to a length of 9 centimetres (3.5 inches), and they have five toes on each of their four legs, as well as a long tail. Common garden skinks can release their tails when caught by predators, such as birds, cats and larger reptiles like snakes.


What is the difference between sequence alignment and sequence assembly?

Sequence alignment
It is done for checking sequence similarity between two or more different sequences. This will give information about how two sequences are different, what is their evolutionary relationship, which residues are conserved etc. Take a look at following sequence alignment between different sequences. (Image courtesy: Wikimedia Commons)

You can see conversation of different amino acid residues in variety of organisms like human, mouse, rat etc.
Sequence Assembly
It is done for creating long consensus sequence from short fragments of same sequence. Generally you would do sequence assembly after sequencing some genome or large DNA fragment. Take a look at following representative image of sequence assembly (Image courtesy: Wikimedia Commons)

Here black sequence is your original sequence which you wanted to sequence. However because of technical difficulties you can't sequence all at once. Hence you fragment and sequence different fragments 9which are shown in red, blue and green). Looking at overlapping region between different sequenced fragments you calculate consensus (shown in Cyan). Here you are ideally sequencing only one large sequence and assembling it.


Modern research or study on patterns in nerve signals

You might want to read about event related potentials (recorded by EEG) or event related fields (recorder by MEG). The idea is simple:

1) Pick some stimulus, e.g. a person touching the hand of a subject. Pick another stimulus, e.g. the subject seeing a person touching the hand of another subject. Record EEG/MEG.

2) Repeat each condition for at least few hundred times. Throw away bad data, and average the repetitions. You do the averaging because the signal-to-noise ratio is low in all non-invasive electrical measurements, and the signals are always riddled with movement, cardiac, and eye-blink artefacts.

3) Compare the conditions in each sensor. Rest is statistics, though not very easy.

Actually, the experiment above would be about mirror neurons, a relatively hot topic in neuroscience. (See e.g. recent issue from Nature)

The more general situation is that using pattern recognition/machine learning algorithms to study brain signals is already a standard thing to do. There are for example graduate/undergraduate programs in computational neuroscience.

If you would study some other signal (e.g. measure from a hand, leg), they are going to dull. Very dull. Mostly because then you have 1 time-series, instead of several hundreds of time-series to analyse.

  For example I would want to know if applying hot/cold object to skin of both right and left limbs would cause the sensory neuron to send the same or similar signal (electrical impulse) to the spinal cord.

This you could too study with the event related fields/potentials.


Why are some chemical dangerous to aquatic environment only?

From some of the MSDS (1, 2) I come across, a major component of thermal grease is aluminum oxide.

Risk Management for Hazardous Chemicals by Jeffrey Wayne Vincoli states in page 101 that aluminum oxide has both acute and chronic toxic effects to aquatic life; it also states that aluminum oxide has a half-life longer than 200 days in water; finally, it acknowledges that the short term toxicity data for non-aquatic animals are insufficient.

From this, the reason thermal greases have special notification regarding to fishes can be attributed to those following points:

The long half life makes fishes exposure to it longer and therefore makes them more susceptible.
We simply do not understand how aluminum oxide effect non-aquatic animals.

(According to Risk Management for Hazardous Chemicals, bioaccumulation in food chain might not be the concern.)


How many species of mites live on the human body?

The answer is 2-3 human mites.

This page says that 2 mites specialize on humans:
http://www.bbc.com/earth/story/20150508-these-mites-live-on-your-face
https://link.springer.com/article/10.1007/s10493-009-9272-0

Another page I found said there are 3 common human mites, adding scabies to the list.

This page talks about bites from a variety of dust and house mites:
https://link.springer.com/article/10.1007/s10493-009-9272-0

My biology lecturer from university of Edinburgh told us that we have hundreds of species of detrital nematodes living on and inside us and that nematodes can be a few microns long. About 800 million humans have a 30cm large nematode inside them according to the WHO.


To take the easiest bit first: Red blood cells are destroyed because lacking a nucleus, they aren't quite as powerful as other cells when it comes to self-repair and longevity.

As for where; it really is all over the body. They are swallowed up (literally) by macrophages lining the blood vessels, which are particularly concentrated in the liver, spleen and bone marrow, but present everywhere.

As they age, they deform, and the macrophages are capable of recognising this deformation and reacting to it (by eating the red blood cells).

When the macrophages have eaten and destroyed the red blood cells, the nutrients they contain are returned to the blood plasma, and captured in the bone marrow for production of new blood cells.

(This pattern is common in a lot of systems, by the way: Even though the liver is the primary organ to break down toxins, for instance, most cells in the body has some limited capability for doing so; this is true of many functions.)

Ref:

http://bril2002.narod.ru/bllod56.html
https://en.wikipedia.org/wiki/Drug_metabolism#Sites