Why does closing one eye in bright light allow me to open the other?

A couple of factors play into this. First, you're halving the number of nociceptors that are signaling the brain. Second, there is a psychosomatic effect. Your brain continuously combines the visual data from both eyes to form one image. With one eye closed, your brain combines the brightness of both inputs to form an image that is roughly half as bright as reality. As a result, your brain not only ignores a portion of the nociceptor signals from the open eye, but it also doesn't assume the presence of pain like it normally would.

I've no publicly accessible sources to cite, as this is something I learned in my EMT class. Someone actually asked your same question in class


Initial letters of the names of the amino acids were chosen where
  there was no ambiguity. There are six such cases: cysteine, histidine.
  isoleucine, methionine, serine and valine. All the other amino acids
  share the initial letters A, G, L, P or T, so arbitrary assignments
  were made. These letters were assigned to the most frequently
  occurring and structurally most simple of the amino acids with these
  initials, alanine (A), glycine (G), leucine (L), proline (P) and
  threonine (T).

  Other assignments were made on the basis of associations that might be
  helpful in remembering the code, e.g. the phonetic associations of F
  for phenylalanine and R for arginine. For tryptophan the double ring
  of the molecule is associated with the bulky letter W. The letters N
  and Q were assigned to asparagine and glutamine respectively; D and E
  to aspartic and glutamic acids respectively. K and Y were chosen for
  the two remaining amino acids, lysine and tyrosine, because, of the
  few remaining letters, they were close alphabetically to the initial
  letters of the names. U and O were avoided because U is easily
  confused with V in handwritten material, and O with G, Q, C and D in
  imperfect computer print-outs, and also with zero. J was avoided
  because it is absent from several languages.

  Two other symbols are often necessary in partly determined sequences,
  so B was assigned to aspartic acid or asparagine when these have not
  been distinguished; Z was similarly assigned to glutamic acid or
  glutamine. X means that the identity of an amino acid is undetermined,
  or that the amino acid is atypical. "Nomenclature and Symbolism for Amino Acids and Peptides"


Let's take a look at the magnified body of the insect (it is a nymphe btw) - we can see 2 brown dots one above the other along the body line. This pattern is very suggestive to Chelinidea species (the most common is Chelinidea vittiger aequoris):

I stop my search at Coreidae family, because multiple species (a lot of bugs actually) of this family have similar appearance, for example:

Gonocerus acuteangulatus:

But other enthusiasts can start from here (Coreidae family) and trace it down more precisely - I am sure they will succeed.


Autologous stem cell transplants are used to treat individuals who have had their bone marrow destroyed or damaged by diseases such as lymphomas or by irradiation or cancer treatments. As they are damaged and potentially cancerous, they are removed. They are then replaced in the transplant. The whole idea is to destroy all the cells before transplanting the marrow back.


Why does decreasing ion channel density result in an action potential not firing?

It is very straightforward. More the density of sodium channels, more the influx of sodium ions. More the influx of sodium ions, more the depolarization. If there are sufficient sodium channels, then the large influx of sodium ions will cause membrane depolarization above the threshold value, thus resulting in firing. If the density of channel is reduced, the depolarization value will not cross the threshold. Thus causing a net change in membrane potential, but not firing.

Potassium channel acts in coordination with sodium channel. Only if there is an influx of positive sodium ions into the cell, potassium channel will act and release potassium ions outside the cell in order to maintain the membrane potential. If sodium channel is reduced, no further processes happen, thus no firing.


Ahh entropy. The bane of many undergraduates. You won't need a lot of mathematical rigor needed to solve for absolute entropies in most biological fields so it's best to think of it abstractly.

Consider the atom. What can it do? Well if you remember from chemistry class, it can bounce around a process we call translate, and the electrons can basically switch spins. For the most part, if you had a single atom alone in the universe, that's all it could do. Move around and have its electrons switch states. It's best to think of these as "states" of the atom.

Let's see, the atom can move in the X direction and be in spin up. It can move in the x and y direction and be spin down...etc. But the point is, there is not a whole lot the single atom all by it's lonesome can do.

On the other hand, if we start adding other atoms to the mix, say across chemical bonds, then they can start to do more. If two atoms are bonded, they can stretch and contract (vibrational states), they can rotate around each other, and they can do everything the atom can do as well.

As you can see, there a lot more "things" or "states" that the two atoms can be defined in at any one time. They can be rotating one direction, vibrating in one way, moving in another... etc etc...even this sentence seems to be getting more chaotic! And that is really all entropy is. Adding up more and more ways for matter to get into all these possible configurations.

So the answer to your question is the macromolecule. It has tons of atoms and bonds. An uncountable number of ways to rotate, translate and vibrate, and be struck with photons, and emit light, and do all kinds of chaotic "stuff" (you can count it actually, it's just really hard).


How long ago did the mutation arise that gives rise to sickle-cell disease?

In a fairly recent review P W Hedrick surveys a number of gene variants associated with resistance to malaria.

He explains that:

  The impact of malaria is thought to have increased between 10,000 and 5,000 years ago when there were the beginnings of agriculture and consequently more human settlements. During this period, the numbers of both the human population and the mosquito vector increased, resulting in higher spread of malaria.
  Recent molecular studies suggest that malaria in humans from Plasmodium falciparum may have originated from gorillas. Using these data, an initial timeline for the origin of P. falciparum as a human pathogen suggests that it may be more recent than previously thought.

As you can see from his Table 1 (reproduced below), the S variant of β-globin is suggested to have arisen 1440 years ago.

The study of the origin of sickle cell anaemia is complicated by the fact that the allele responsible is found associated with five different β-globin haplotypes (four from Africa, one from Saudi Arabia/India). This has sometimes been interpreted as indicating that the allele arose on several independent occasions. However, the picture is complicated by patterns of human migration, and recent papers suggest that the observed distribution of the S variant is not inconsistent with a single origin, e.g. this paper.


Action potentials usually maintain muscle tone in skeletal muscles, but muscle cells are affected by other influences that can affect their contraction and thus the tone of the muscle.
Smooth muscle occurs in the walls of hollow organs, most notably the blood vessels and the GI tract, and in a few other places.  Contraction of smooth muscle is generally involuntary and can be stimulated by the APs from the autonomic nervous system, but often for the slow maintenance of muscle tone contraction is controlled by hormones, other external molecules, or external pressure.  The mechanisms that cause this contraction generally involve the phosphorylation of myosin light chains. (1) (2)


How to distinguish between a genetic bottleneck and directional selection?

Population bottleneck will have genome-wide effect while directional selection will affect only the locus (and closely linked loci via a selective sweep).

You can typically screen through the genome and calculate Tajima's D. Under a bottleneck scenario, Tajima's D will be expected to be negative everywhere. Under a directional selection scenario, Tajima's D would be negative only at the locus (and closely linked loci) to the one that is under selection.

There are of course a whole lot series of technics but the above is probably the simplest and most straight-forward (it probably lacks in power though).


Why replication collapse but not stall leads to DNA break?

Stalling precedes collapsing. And collapsing precedes breaking. Hence, both stalling and collapsing precede, and lead to, breaking; but not every stalling leads to collapsing, and not every collapsing leads to breaking.


Cultures of HeLa cells are used in many labs around the world, and were widely shared from very early on. From the Wiki:

  In the spring of 1953, a cell culture factory was established at
  Tuskegee University to supply Salk and other labs with HeLa cells.


There are two major factors that will affect the development of diversity, given the same starting point: The mutation frequency, and the strength of selection.

Mutation frequency is unlikely to change significantly, so you're left with the strength of selection as the deciding factor for how much diversity arises and how rapidly.

"Selection" means that less-fit individuals are removed from the population, so if the selection is strong enough, you're left with the race between evolution and extinction. With a small starting population and strong selection, the most likely scenario is extinction, but the right level of selection can lead to diversity.

An oversimplified view of selection is that a population will evolve toward some Platonic ideal. If long necks give more fitness than short necks, then the population will evolve toward having longer necks. The population changes, but isn't necessarily more diverse.

But there are several modes of evolution that drive a population toward increased diversity. In theory, you could imagine that the population does better with a 50/50 mix of long and short necks than either an all-short or an all-long necked population. Examples of drives toward population diversity include positive and negative frequency-dependent selection (also known as "balancing selection"), and overdominance.

Are there any examples of bottlenecked populations where one of these drivers has led to increased diversity? Yes, there are several. The best example might be the Channel Island fox:

  The San Nicolas Island fox (Urocyon littoralis dickeyi) is genetically the most monomorphic sexually reproducing animal population yet reported and has no variation in hypervariable genetic markers.  ... foxes colonized the three northern Channel Islands (San Miguel, Santa Rosa, and Santa Cruz) ≈16,000 years ago and, subsequently, were transported by Native Americans to the three southern Channel Islands (San Nicolas, Santa Catalina, and San Clemente) 800 to 4,300 years ago ... We examine variation of five loci within the MHC of San Nicolas Island foxes and find remarkably high levels of variation. Further, we show by simulation that genetic monomorphism at neutral loci and high MHC variation could arise only through an extreme population bottleneck of <10 individuals, ≈10–20 generations ago, accompanied by unprecedented selection coefficients of >0.5 on MHC loci. These results support the importance of balancing selection as a mechanism to maintain variation in natural populations and expose the difficulty of using neutral markers as surrogates for variation in fitness-related loci.

--High MHC diversity maintained by balancing selection in an otherwise genetically monomorphic mammal

The specific question "how long would it be before the population is free of problems related to a lack of genetic diversity?" is too broad to answer with any detail, but another point to keep in mind is that the problems of inbreeding are usually less to do with loss of diversity (although that can be one problem, as the San Nicolas foxes show) and more to do with deleterious recessives emerging as homozygotes; this can be softened by various factors, including chronic low-level inbreeding before the bottleneck occurs, which "purges" out the deleterious recessives and makes the population more resistant to inbreeding. One review: Do Plant Populations Purge Their Genetic Load? Effects of Population Size and Mating History on Inbreeding Depression


The family-level identification I had given I now see was unnecessary; the Wikipedia site for an economically important member of the genus (there called the Brown planthopper) is here: https://en.wikipedia.org/wiki/Brown_planthopper.  The species covered there has long- and short-winged forms; other members of the genus are probably similar.  All of the individuals in the photograph above are adult.  A late-instar nymph will have wing pads (not yet wings) which are fused to the thoracic segment to which they're attached (a life-cycle diagram with drawings of two nymphal instars -- there are probably more -- is found here: http://www.cpsskerala.in/OPC/pages/ricePestbrownplant.jsp [the eighth slide]).
 So nymphs and short-winged adults won't be flying out of danger -- they'll be hopping away.


Do histones constitute the largest proportion of the protein in chromosomes at mitosis?

If you are asking if histone mass represents a larger percentage of total chromosome mass then the answer is yes when considered at the level of the nucleosome. Each histone-octamer wraps ~147 base pairs of dna around 1.7 turns. The histone-octamer consists of  two copies of each of the four structural core proteins (H2A, H2B, H3 and H4). The sequence encoding for H2A histone family member B1 (H2AFB1) is 517 nucleotides long (RefSeq). Based on nucleotide length alone and inferring a consistent contribution to mass from nucleotides at the single base level and in triplet at the amino acid level, each nucleosome should be roughly 95% histone by mass. But this doesnt account for stochasticity in the mass and density due to DNA-methylation and to heterochromatin and euchromatin along the genome, respectively.

Consider DNA methylation, these features represent a non-zero contribution to total chromosomal mass that would decrease histone mass as a portion of the total and would not be considered if whole genome sequencing of a single organism was employed to answer this question at the genome level for a single sample. Now consider histone acetylation, this is another feature that represents a non-zero contribution to mass but swings the pendulum in the other direction. Beyond a local calculation at the nucleosome level this relationship would be nearly impossible to quantify.

During replication specifically, histone translation seems to be as tightly regulated as DNA replication.

Ma Y, Kanakousaki K, Buttitta L. How the cell cycle impacts chromatin architecture and influences cell fate. Front Genet. 2015;6:19. Published 2015 Feb 3. doi:10.3389/fgene.2015.00019
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4315090/

nature has a great open source overview related this topic.

https://www.nature.com/scitable/topicpage/chromatin-remodeling-in-eukaryotes-1082


As John mentioned, pyrokines such as IL1 and TNF affect the hypothalamus. Your hypothalamus is a thermostat, similar to central heating for example. So when you set your core temperature higher, your body thinks it is cold. To warm up it does several things:

Vasoconstriction directs blood to the core body and prevents heat
loss
Brown fat break down in infants makes heat
Shivering which requires respiration which produces a lot of heat. Metabolism also
increases in other ways - this is why it is commonly advised to
increase food consumption during illness
We wrap up warm - an often overlooked mechanism that is incredibly important.
Limited piloerection: if we are hairy our hair will stand up attempting to
create a barrier for heat loss
We stop sweating (breaking of a fever or when the hypothalamus is reset to normal causes us to sweat)
Hormonal regulation via (nor)adrenaline/epinephrine, thyroxine - these are related to the increased metabolism.


Why do birds that walk on the ground walk so "bumpy"?

If you mean the head bobbing displayed by many birds when walking: it is believed to help with visual stabilization.

  The term head-bobbing, used for the apparent back and forth movement
  of the head of some birds while walking on the ground (think pigeons),
  is a bit of a misnomer. These birds don't actually bob their heads
  back and forth – instead, they move their body forward, leaving the
  head behind, then thrust their head forward past their body (hold,
  high-speed thrust!). This innate behaviour is believed to help several
  key aspects of vision during locomotion and foraging. While the head
  is still, images are stabilized on the retina and moving objects
  become clear against the background, and during the thrust phase,
  depth perception becomes more accurate.

https://jeb.biologists.org/content/jexbio/217/11/1836.1.full.pdf

In this article you can find an stroboscopic photography that shows the particular bumpy walk.


Does the term "fitness advantage" or "fitness disadvantage" make sense?

What is unclear to you?

If you could highlight what is unclear to you, or what exactly are the semantic issues in your opinion, that would help to really address your misunderstanding. In absence of that, I will just give you a general explanation of their meaning.

What does 'fitness advantage' mean?

If a group of individuals has a fitness advantage, it means that this group of individuals has a higher fitness over some other group of individuals. The other group, then has a fitness disadvantage.

Natural selection

If we grouped these individuals based on genetics, then the genotypes having a fitness advantage will likely raise in frequency in the population. If we used phenotypic trait to group individuals and if the trait is heritable, then the frequency of these phenotypic traits is also likely to raise in frequency in the population.


Why might food spoil faster in Ireland than the US?

I would think added preservatives are the most likely candidate, for example, Azodicarbonamide is frequently added to bread in the US, but banned in Ireland and most of the rest of the EU. Since it has a preservative effect it is a reasonable candidate for a specific causal factor.

But as Keegan points out there are an awful lot of possible factors so it's impossible for us to say with any certainty.


When performing mutagenesis for an assay, how do you decide on the sample size of individuals to be mutated such that all genes are covered?

Don't think about mutagenized animals, think about mutagenized genomes. Depending on when the mutagenesis is carried out, and how efficient it is, a very small number of males could give rise to thousands of mutagenized F1 progeny, each carrying a uniquely mutagenized genome. That is the number to focus on. Typically, in fruit flies and soil nematodes the animals are hit "pretty hard" such that each F1 is carrying hundreds, if not thousands, of mutated sites, randomly throughout the genome. The trade-off is to not mutagenize them so much that they suffer a drastic decrease in fertility or viability, while at the same time minimizing the number of F2 homozygotes you have to screen for phenotypes.

In C. elegans exposed to 50 mM ethylmethane sulfonate for 4 hr, you might reasonably hope to recover 1 loss-of-function mutation after screening 2,000 mutagenized F1 genomes.

Are there good genetic markers along all of the salmon chromosomes?  If you are only interested in recovering dominant mutations then you can screen the F1 directly (however dominant alleles tend to be much rarer than recessive alleles, and interpretation of dominant phenotypes is challenging without lots of good genetic tools, like duplications and deficiencies). Otherwise you will have to mate the F1 to obtain male and female F2 and then set up brother-sister matings so that you can score the F3 for phenotypes of interest.

None of these numbers would apply to salmon because the genome is much larger, and unless someone has already done a dose-response curve on the optimal mutagenic dose for salmon, you would need to do that first.


What are some useful physical information of a protein?

All the information about a protein, biochemical or functional is encoded in its structure, which are primary (Amino Acid (AA) sequence), secondary (alpha helix or beta pleated sheet), tertiary (overall 3D structure of a single peptide) and quaternary (overall 3D-structure of a protein composed of multiple peptides which are attached together through various different bonds) structures (http://en.wikipedia.org/wiki/Protein_structure).

Obviously, the key determinants for all these structures is the AA sequence of a protein, since that determines the biochemical property of a protein as well as its function (e.g. enzymatic residues and active sites, functional domains, motifs, whether it is post-translationally modified or not by phosphorylation and whether that causes its activation or inactivation through conformational changes or its interaction with other proteins etc).


Why is it that guttation is most commonly observed in the morning?

Guttation is commonly seen at night and early morning. Plants release excess of water via the guttation. During day time as the transpiration rate increases, excess of water is released via transpiration and hence guttation decreases. Also due to high temperature these small droplets are quickly evaporated during day time.


This is too long for a comment, so I post my thoughts about this here:

This falls into different important parts here: One is an insufficient understanding of the techniques on which the method is based. This makes it hard to decide which steps are important and which are not. One prominent example would be the use of EDTA in DNA gel running buffers. This recipe originated from RNA research (where you need the EDTA) which where then simply used for DNA as well. Since it worked somehow, it was never really changed.I have seen enough people in the lab clinging to old photocopies of protocols without knowing why they do certain steps.

And the other (connected) issue is that protocols are usually passed down through labs. Things are then done in a certain way because they have always done in this way (with some changes in the protocol probably not even documented) and are not changed. People are even told to use the exact routine, even if this makes absolutely no sense.

In publications there may also be another thing which comes into play: The fear that someone uses the own methods and will then be faster than the own group. At least some groups only publish incomplete and vague methods because of this reason. Then it's a thing of space: There are character limitations in publications and when you need to save a few hundred characters when the article is too long, it's much easier to shave the methods than the discussion.


Cells scatter light in solution. Do they refract?

You're both correct. Turbidity is causes by excessive light reflection events from all of the particles, and is actually how it is measured in a sample. As to cells, they both both reflect light that is incident on a membrane, but they will also refract light that does manage to enter the cell because of the difference in refractive indices. A portion of the light will also be absorbed by the cells.


How does the shoulder joint stay in place?

Because it's

held together by muscles, tendons, and ligaments.

(image from Wikipedia.)
It's somewhat complicated how all these parts contribute to holding the joint in place because it depends on the position of the joint. E.g.

Shoulder muscle forces are usually powerful stabilizers of the glenohumeral joint, especially in mid-range positions when the passive stabilizers are lax. However, muscle forces can contribute to instability as well. Certain muscle forces decrease glenohumeral joint stability in end-range positions. We found this to be the case with both active and passive pectoralis major forces.

That study has some data based on computational models and actual tests on cadavers.


Suitable writings for self-study in general biology/chemistry

My personal favorite intro biology book is Campbell Biology. The new edition is a little pricy, but you can probably find one of the older editions for pretty cheap--my intro class used 9th edition, and I don't think much has changed other than some of the taxon names.

I'm not sure what branch of Bio you're interested in, but Campbell covers all of introductory cell biology, organismal/evolutionary and ecology. The "concept check" questions at the end of each chapter are fantastic open-ended responses, and I believe most (if not all) have answers in the back of the book

I'm not as solid in general chemistry, but some good ones I remember are Brown, Lemay, and Burston which got me through AP Chem, and Zumdhal which my university uses and I haven't heard any complaints. The Brown text is a pretty good intro though. It provides good information and I thought it was pretty enjoyable to read.


Is Hemoglobin binding to oxygen the same as Adsorption

From the Wikipedia article you cite the answer to your question is clearly NO. They seem very different: absorption is described as a surface phenomenon, whereas oxygen binding occurs in a single internal pocket in each globin subunit and forms a specific bond to an Fe(II) atom. The chemical nature of this pocket is quite different from that of the surface of the protein.

The Wikipedia article states:

  Adsorption is the adhesion of atoms, ions, or molecules from a gas, liquid, or dissolved solid to a surface.[1] This process creates a film of the adsorbate on the surface of the adsorbent.

and

  Similar to surface tension, adsorption is a consequence of surface energy. In a bulk material, all the bonding requirements (be they ionic, covalent, or metallic) of the constituent atoms of the material are filled by other atoms in the material. However, atoms on the surface of the adsorbent are not wholly surrounded by other adsorbent atoms and therefore can attract adsorbates.

However if you consult a text-book which describes the biochemistry of haemoglobin, such as Berg et al. you will find the specific chemical nature of the binding clearly described, as indicated by this extract:

  The iron atom lies in the center of the protoporphyrin, bonded to the four pyrrole nitrogen atoms. Under normal conditions, the iron is in the ferrous (Fe2+) oxidation state. The iron ion can form two additional bonds, one on each side of the heme plane. These binding sites are called the fifth and sixth coordination sites. In hemoglobin, the fifth coordination site is occupied by the imidazole ring of a histidine residue from the protein. In deoxyhemoglobin, the sixth coordination site remains unoccupied...The binding of the oxygen molecule at the sixth coordination site of the iron ion substantially rearranges the electrons within the iron so that the ion becomes effectively smaller, allowing it to move into the plane of the porphyrin (Figure 10.19).

The only similarity I can see is that in both processes the interaction of the gas with the material to which it binds is controlled by the pressure of the gas. However in the case of haemoglobin there is a distinct difference from absorption in that the dependency on pressure exhibits a sigmoidal curve, specifically suiting it for the role of quantitative delivery of oxygen to the tissues at a particular small reduced pressure range.

You sound as if you come from the physical sciences. If so, prepare to be surprised at how smart a chemist Mother Nature is.


Do corresponding areas in the two hemispheres arise from the same stem cells?

No, they don't. The stem cells of each cortical hemisphere are located far from each other, in the subplate below the developing cortex.


Why is 450 nm monochromatic light perceived as blue or violet depending on its intensity?

This is a general feature of human perception of blue-white mixtures. It's known as Abney effect. It's not limited to highly monochromatic blue colors (not even to blue colors). We can observe this blue-related phenomenon even with longer wavelength light than 450 nm – e.g. sRGB blue, whose dominant wavelength is about 464 nm. Here's what most people would undoubtedly call blue – in HTML notation #0000ff:

And here's a mixture of 60%† white with 40% blue (in HTML notation #cacaff):

To me, if I haven't stared at shades of truly violet a few moments ago, this mixture seems to have a considerable amount of violet — more than I'd expect looking at the primary blue. Naturally, shorter wavelength light should give even more violet perception, until it becomes violet even in its pure form.

† Percentage is given in linear scale, actual color presented is gamma-corrected to be displayed on sRGB monitors.


Great question! In fact, some of the most successful pathogens (Herpes viruses are a excellent examples) have evolved with precisely this strategy. Herpes viruses have very low virulence, but infect nearly every human on the planet, and stick around for life.

But there's an evolutionary trade-off to this strategy. Herpes viruses have giant genomes (for a virus), because they need a ton of genes that counteract the immune system and perform other feats of cellular control so that they can stay dormant for long periods of time. While dormant (the technical term is "latent"), the virus is not transmissible, so while it persists  for a long period of time, they actually don't transmit very often.

Other viruses (influenza is a good counter example), are readily transmissible throughout most of their life cycle, but end up being cleared in a few weeks by most people. And yet influenza also spreads around the globe each year, so this also seems to be a pretty effective strategy.

It's really hard to ask questions like "why doesn't influenza behave like herpes?" When it comes to evolution, there are many successful strategies. Might as well ask, "why don't fish have feathers?" "Why don't sea birds have gills so that they can stay under water?" "Why aren't humans single-celled organisms?"


Alternatives to NCBI BLAST during US government shutdowns?

b.nota is correct - Just further adding to his answer. The International Nucleotide Sequence Database Collaboration (INSDC) is a consortium between DNA Data-bank of Japan (DDBJ), EMBL-EBI and NCBI. Contributions to each of the 3 databases are shared on daily basis.

(Thanks to @KonradRudolph) Since EMBL-EBI is not directly accountable to any single government either financially or in terms of research directions so a (temporary) shutdown equivalent to that of the NCBI is vastly less likely. Rather, like CERN, it’s an international treaty organization and thus probably a lot more robust.

BLAST

Answering part 2 of your question: YES! BLAST is available in both DDBJ and EMBL-EBI on following links:

BLAST - DDBJ
NCBI BLAST+

Scope

Here is what INSDC's website says about its scope:

  INSDC covers the spectrum of data raw reads, though alignments and
  assemblies to functional annotation, enriched with contextual
  information relating to samples and experimental configurations.

Following table (taken from INSDC website) may help you have better understanding about respective data types comparison for 3 contributors:


If mCherry was successfully cloned replacing the stop codon, you would indeed expect a fusion protein that is about 27 kDa larger than the original protein.
However, with a PCR you are not testing for the full length protein, but rather for a part of the target gene sequence.

The length of the PCR product very much depends on the position of your primers: If both primers are targeted at your unmutated sequence, the product size will not change by adding mCherry behind the targeted sequence. The product size of the PCR would only change, if one primer is located before or in your unmutated protein and the other one behind mCherry. This would probably result in a very large PCR product and hinder the PCR reaction from being effective.

To check for correct integration of mCherry, you would need to design a primer pair with the forward primer in your unmutated protein and the reverse primer in mCherry. This should result in a product in the fusion protein colonies, but not in the unmutated ones.

Alternatively, you could sequence your products.


Youtube chemist NileRed chemically extracted DNA from strawberries in this video, he also tastes it if I remember correctly: https://www.youtube.com/watch?v=araeHtN_3Lk

TL;DW: He gets the DNA from the strawberries and says it has a slimy texture as it isn't soluble, and it tastes salty more than anything. Note though that this could be from leftover reactants from the reaction, so take this with a grain of salt.


What is the best color for a PPG signal (photoplethysmography)?

The reason red and infra-red are used is the difference in absorbance at those two frequencies between oxygenated and unoxygenated hemoglobin. Using the difference in these two frequencies allows the concentration of oxyhemoglobin to be calculated. (The red LED is at the frequency where oxyhemoglobin and hemoglobin have identical absorbance).

As far as I know, there's no reason why a green LED wouldn't work. You would only be able to measure the PPG signal and not the oximetry data (unless you used two different LEDs and did some math).

Absorption curves.


Does recombination increase the additive genetic variance for fitness?

This is a little tricky.

First of all lets be clear about 'bringing together favorable alleles' (or any alleles) represented by site mutations on 2 chromosomes:

--------A------------------
             X
------------------B--------

If the two dashed lines are two copies of the same chromosome, then a recombination event at X may produce:

--------A---------B--------

Allowing both A and B to be passed along to offspring.

Any given case of recombination might actually harm resulting offspring. But in cases where A and B together are beneficial, over the course of generations you will find AB genotype combinations show up more frequently in the population because of selection and competition.

Firstly each individual variant experiences some selection for fitness and many are lost.  Because of this, recombination will typically put two or more such variants together onto a single chromosome.  Recombination allows for individual mutations of benefit to pool together and collect into a single place.  This multiplies the chance that stronger combinations of mutations will show in the gene pool.  This increases the fitness variance - the most powerful combinations are more beneficial than any single variant alone.  On the other end detrimental combinations will also make some individuals exceptionally weak.

So its not just recombination, but recombination and selection which create favorable combinations of alleles in populations.  The link you give discusses how when selection is not strong, recombination is not so great, but we never seem to lose recombination where these conditions don't hold sway.

By comparison, consider a simple case where recombination does not occur where there is an A genotype and then one waits for B to show up on the same chromosome by random mutation.  That would take perhaps thousands or even millions of generations before such a thing happens at random.  Recombination is a powerful accelerator of evolution.


Spiders do curl up their legs when they die. Since they do not have muscles for extending the legs at their joints, they control the haemolymph pressure in the legs by using the blood pressure spike from their heartbeat to extend their legs out or walk. And with no heartbeat (when the spiders cease to exist), they curl up upon death.

Source: http://www.informationsociety.co.uk/why-do-spiders-curl-up-when-they-die/


The problem of off-targets in CRISPR/Cas is often discussed. It was shown that the system allows mismatches up to five basepairs. For your question, if it is helpful to elongate the gRNA: it was shown that truncating the RNA enhances the specificity more than elongating (see also here).

So what can we do? Well, there are different methods to improve the specificity. The simplest may be the usage of lower dosages of the CRISPR/Cas system. Another method is to use altered PAM motifs.

A more complicated method is to convert the Cas9 into a nickase. In this strategy you would use two different gRNAs for two different target sites and introduce ssbreaks. A modification of this method is to completely knock-out the enzymatic activity of Cas9 and fuse it to a FokI nuclease which will cut the DNA only when it dimerizes.

There are several advantages in these methods, however, you may also loose on-target effects.

There is another method which, in my opinion, is really awesome. It is possible to alter the energetics of the DNA binding site resulting in high-fidelity variants of Cas9 (HF1 and HF2)

So, I hope I could help you. There are other and even more effective ways to increase CRISPR/Cas specificity instead of altering the gRNA. If you're interested, have a look on the references.


How does a pinched nerve cause pain (at the molecular level)?

Typically nerve compression or a "pinched" nerve is due to inflammation in the tissue through which a nerve passes. The gap is already quite narrow so any inflammation is quite potent. Inflammation causes you to feel things as more painful (hyperalgesia). In a similar way to how of you burn your hand then poke it, it hurts, when cells are damaged the receptors surrounding them are sensitised to be more reactive. Binding of many ligands involved in inflammation leads to higher than normal sodium influxes which means you feel pain as this impulse is sent. I could be a lot more detailed but not sure what level you want, however for much more detail see this review.


Why only heterogeneous SNVs for validation using genotyping arrays?

The purpose of validating is to find genuine SNPs and not those caused by sequencing or amplification errors. It is extremely unlikely you will have a false homozygous SNP as a result of error. Just think about it. The same error, at the same base, occuring 80%+ of the time? Its not going to happen unless you have low coverage, and these SNPs should be thrown out anyway. You may have some cases where a genuine heterozygous SNP is called as a homozygous SNP. But that isnt much of a problem. It is still a genuine SNP. It would only be a problem if you were only interested in homozygous SNPs, in which case you will just need to validate everything biochemically, which you will need to do anyways.


Who creates first nitrogen compounds in the food supply chain

There are nitrogen fixing bacteria who turn N2 into NH3.  Some are free-living in soil, others live symbiotically with plants.

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


What makes us "tired" in the gym that forces us to rest?

I think you refer to the Muscle fatigue:

  A state of exhaustion or loss of strength and/or muscle endurance following strenuous activity associated with the accumulation of lactic acid in muscles. (Source)

So yeah, you're right about the lactic acid overproduction :)

How Muscle Fatigue Works ?

During short term (anaerobic) exercise, ATP and creatine phosphate (CP) are used up within the first 7 seconds of training. This signals the metabolism of glycogen to produce energy for your body. This process is known as glycolysis.

During glycolysis, glycogen (muscle sugar) is broken down to produce more CP. The breakdown of CP releases energy, which catalyzes a reaction to produce ATP. The production of more ATP allows movement of the muscle to continue.
Lactic acid is a product of glycolysis created by the breaking down of pyruvate.

Lactic acid is then disassociated to produce lactate. When lactic acid (C3H6O3) releases a hydrogen ion (H+), the remaining compound binds to a sodium ion (Na+) or a potassium ion (K+) to form a salt. It is this salt that is lactate.

Now the cell contains a lactate compound and a free H+ for each compound of lactic acid that is produced. It is this increase in cellular H+ that causes the pH to decrease, becoming more acidic. The acid in the muscle causes the fibers' calcium-binding capacity to decrease, thus limiting muscle contraction. This is the cause of muscle fatigue.

So the muscle Fatigue occurs when the muscle experiences a reduction in its ability to produce force and accomplish the desired movement.

Short term fatigue (failure to lift a heavy weight, do more push-ups, etc.) is different than long term fatigue such as as a marathon run, a 100 mile bicycle ride, or a full-day hike through the Rocky Mountains of Colorado.

Muscles become fatigued during high intensity exercise, most notably that the demand for oxygen can be greater than the supply. The blood flow to the muscle can be reduced because of :

muscles intensely contracting can reduce blood flow and thus oxygen availability, or
the muscle is simply working so intensely that there literally is not enough oxygen to meet demand (a sprint at top speed).

The factors that explain fatigue are complex and after more than 100 years of investigation are still a topic of active research, you can check those articles for more informatoins :

Experiment: EMGs during Muscle Fatigue
All About Muscle Fatigue
Skeletal Muscle Fatigue: Cellular Mechanisms


Hypothalamic breakdown and effect of temperature on membrane lipids

If you supply heat to a system, the entropy increases which results in destabilization of order. This is a general thermodynamic principle and you can refer any basic book on that topic. However, it is not essential that all molecules would be affected equally. There are heat-stable enzymes in thermophiles such as Thermus aquaticus which are resistant to heat. Also the membranes in these organisms are made up of stronger and more rigid isoprenoid lipids.

Even in mesophiles, lipid membranes with higher content of cholesterol are rigid and more resistant to thermal movements.

On Breakdown of thermostat:
The body can regulate the temperature only in a certain range; at higher temperatures these mechanisms will fail as well.


An extension of com.prehensible's comment -- your sapling could be a bur oak.  It is older than the seedling pictured below, but retains a similar cotyledon.  The range of this species includes Ontario.

bur oak seedling
Photo by Todd Dwyer, via Flickr
(please ignore the image artifact -- an effect of resizing)

Your photo appears to show the tree at a stage after the seedling shown above and before the more mature sapling shown here:

bur oak sapling
Photo by John T. Fowler, Alamy Stock Photo


Your image is not correct.

According to Lehninger (2000):

  At relatively low concentrations of substrate, V0 increases almost linearly with an increase in [S]. At higher substrate concentrations, V0 increases by smaller and smaller amounts in response to increases in [S]. Finally, a point is reached beyond which increases in V0 are vanishingly small as [S] increases. This plateau-like V0 region is close to the maximum velocity, Vmax. (emphasis mine)

This is the image that comes after that paragraph:

FIGURE 6–11 Effect of substrate concentration on the initial velocity of an enzyme-catalyzed reaction. Vmax is extrapolated from the plot, because V0 approaches but never quite reaches Vmax. The substrate concentration at which V0 is half maximal is Km, the Michaelis constant.

Thus, regarding your questions ("Why don't we achieve enzyme saturation linearly? Why do we go through that curved phase( region B )?"), the answer is: there is no line, it's all curved.

Source:

Lehninger, A., Nelson, D. and Cox, M. (2000). Principles of biochemistry. New York: Worth Publishers.


What type of fish is this- Cabo San Lucas, Gulf of California side

That is a giant hawkfish, Cirrhitus rivulatus. It is identified by its unique markings from other species in the same region. This individual looks slightly young to me from the size, however it is most certainly this species. Giant hawkfish on mexican-fish.com


Correct/complete representation of RTPCR statistics

I think you can follow this method:

Test the statistical significance of a single experiment by comparing technical replicates (lets say Tests: T1, T2, T3 and Controls: C1, C2, C3). This will tell you if the instrument can reliably detect difference or not. Note that you should compare the relative expression (i.e. wrt your reference gene) and not the CT values. The ΔΔCt method is fine but you should note that it is not necessarily a power of 2; 2 denotes perfect PCR efficiency. See these posts:

Real time PCR normalization algorithm
Real time PCR standard curve

If the difference is found significant in all technical replicates then test the difference between biological replicates by using the means of the technical replicates in each experiment; for example mean of T1, T2 and T3 in biological replicate-a ($\bar{T_a}$) used as the sample value for that replicate. You can proceed with t-test for computing statistical significance which will tell you if the difference in expression is because of a random cellular behaviour or not. You can also do an ANOVA to compare the variance between technical replicates (within an experiment) and biological replicates (mean of the technical replicates between experiments). ANOVA lets you know some aspects of reproducibility of a measurement technique.
Fold changes (FC) are a problematic issue because many biologists seem to mess up with the interpretation of the data. First of all a t-test cannot be applied to FC directly (especially if FC is calculated pairwise for each replicate). Now all you have is a single random variable i.e fold change that you cannot statistically compare with anything. Fold changes are not really bad but I would recommend that a t-test be done between the control and the test samples and if the difference is found statistically relevant then report the FC. I personally know many people who do the other way round and set variance of the control sample as zero (because pairwise FC would be = 1 in all cases): This is a blunder.


You can find a great article about this here.

basically, these two groups are very similar in their effects, however they work through different pathways.

Mitogens directly promote cell to get through G1 checkpoint through highering the activity of cyclin D/cdk4 (the complex needed to get through the checkpoint.) and according to the article above, also the cyclin E/cdk2 complex (which helps cell to get into S phase). By activating the MAPK (mitogen-activated protein kinase) pathway leading to production of transcription factors (Elk-1, jun, fos), which then promote specific transcription of proteins needed to get through cell cycle.
The mitogen pathway also causes phosphorylation of Rb (Retinoblastom) protein, which then dissociates from E2F transcription factor. This activates the E2F, which in turn helps synthesise proteins needed to promote S phase.

Growth factors usually stimulates mTOR receptor, which is a "serine/threonine protein kinase that regulates cell growth, cell proliferation, cell motility, cell survival, protein synthesis, autophagy, and transcription." Source

mTORC complex generally promotes translation. It plays role in "cell growth via the modulation of protein synthesis in yeast and mammals, it and its yeast homologs strongly stimulate transcription from all genes involved in ribosome biogenesis, transcription of rRNA genes by RNA polymerase I (Pol I), transcription of ribosomal protein genes by RNA polymerase II (Pol II), and transcription of tRNA and 5S genes by RNA polymerase III" and many other effects. Source.

Although all of this, in practice, I've seen many people use this categories interchangeably or referring to mitogens as a subgroup of growth factors.

I hope this helps.


The answer to this question has its reason in the hair cycle. Our hair goes through a cycle of growth. At the end of this cycle, the cells in the hair follicle die and have to be replenished before a new hair cycle starts, also the hair falls out eventually. See the figure from reference 1:

The replenishment process is done by to two cell types: Epithelial stem cells which replenish the hair follice itself and melanocyte stem cells (MCSC) which replenish the melanocytes in the follicle and produce the pigment of the hair.

The MCSC are located in the bulge region of the hair, to be able to successfully replenish the pool of pigment cells the MCSC need to do things: proliferate and also differentiate. Proliferation makes sure that there are enough cells in the bulge region to repeat this process in further hair cycles, while the differentiation generates the cells who actually produce the pigment. When the MCSC are lost, no further pigment producing cells and hence no pigment can be made.

It has now shown that with age this pool of MCSC is not replenished completely anymore, eventually resulting in the loss of the melanocyte stem cells. The reason that our skin does not become gray at some point is that this process doesn't happen there, so pigment cells are not depleted. Reference 1 summarizes this topic nicely, while reference 2 is the original paper.

References

Melanocyte Stem Cell Maintenance and Hair Graying
Mechanisms of Hair Graying: Incomplete Melanocyte Stem Cell
Maintenance in the Niche


It is indeed a Crane fly, superfamily Tipuloidea, which is part of two-winged insects (Diptera). There are >15000 species worldwide. Their systematics is somewhat uncertain (used to be a single family, now a superfamily). They are placed in the same suborder as mosquitoes (Nematocera). The adults feed on nectar or not at all (they do not prey on mosquitoes), and the larvae usually feeds on litter, roots, fungi etc, but some aquatic species are predatory. Larvae of some species develop in soil and others in water. Adults of many species are attracted by light, which is why you often find them inside houses. I dont know why you find so many this year where you live, but winter conditions affecting survival is a possible explanation.


What is meant with “the chest wall and lungs are coupled together”?

How are the lung and chest wall coupled?

You have your answer in the text:

  the surface tension between the lungs and the chest wall

And as you say, it is very much

  like there is a physical-contact adhesion force between the lungs and the chest wall

A good, medical school level anatomy textbook will walk you through this. Moore's Clinically Oriented Anatomy gives the appropriate level of detail. Lets refer to Fig 1.30 (pg 107 of the 6th edition):

Below, you can see that there is a bag of fluid (the pleura) around the lung itself, like an under inflated balloon wrapped around the lung (see the picture of the fist, representing the lung, wrapped in a balloon, representing the pleural sac). The space inside the bag of fluid is very small, very thin, in a normal lung. The size of that space is exaggerated in the figure below in order to show the layers more clearly. In fact, in medical images of a healthy chest, it doesn't even appear as a space. The thin layer of fluid provides surface tension, keeping the two pleural walls close together. Since the chest and lungs are physically attached to the pleural walls on either side, that surface tension pulls the elastic lung outward (expanding it), and the chest wall inward (collapsing it, slightly). If the pleura is punctured, blood or air can enter, surface tension can no longer keep the two pleural walls next to each other, the chest wall returns to its preferred state (slightly more expanded than it would otherwise be), and the lung returns to its preferred state (substantially more collapsed than it would otherwise be).


How do fatty acid and polyketide synthases handle the varying size of their substrates?

Although the substrate is different at each stage of chain extension,
  the part involved in the reactions — and recognized by the enzyme — is
  the same. This is a common feature of polymerization reactions,
  whether the catalysis is by a single module (ribosomes, DNA
  polymerase) or multiple modules (polyketide and fatty acid synthesis).

This is illustrated by the modification made below to a part of Figure 1 of the paper cited in the question. An overlay in yellow has been made to indicate the common structural features of the polyketides of different length.

Of course, the rest of the chain may well interact with the enzymes, but as this is not at their active sites it can be in a less specific manner, perhaps in a ‘groove’ containing appropriate interating chemical groups.

The question of substrate specificity is not the point of interest in the paper on polyketide synthase where the focus is on the way the elongating substrate is passed from enzyme to enzyme and module to module (the resolution is also too low). It has, in any case, been addressed in previous work on mammalian fatty acyid synthase, where exactly the same single (dimeric) multidomain complex acts on each intermediate until the chain length is 16-18 C atoms. However the question of chain length is taken for granted and the discussion is about discrimination between chemically different intermediates. Thus in a 2008 paper by Maier et al. a substrate tunnel in the ketoacyl synthase (KS) module of the fatty acid synthase (mFAS) is compared with that in polyketide synthase (PKS):

  “Despite the pronounced structural similarity between the KS domains of mFAS and PKS, the selectivity of FAS for saturated acyl chains can be explained by a considerable constriction at the base of the active site phosphopantetheine binding pocket leading into the large acyl chain substrate binding tunnel, which connects both active sites of the KS dimer (Fig. 4, A and B). A number of residues lining this narrow tunnel are highly conserved in mFAS but are substituted with smaller residues in all DEBS (6-deoxyerythronolide B synthase) PKS modules (Fig. 4B), resulting in a wider, more permissive tunnel in the KS of DEBS.”

It is important to think of substrate specificity in molecular terms — e.g. what part of the substrate binds to the enzyme and how specific has the binding to be. In this case the substrate is attached to the long phosphopantetheine chain of acyl carrier protein, so that recognition of that and the part of the fatty acid or polyketide attached to the sulphur may be enough to discriminate against ‘free’ extraneous molecules. And a tunnel is permissive as a binding site: if the chemistry and radius are right, there is no need for the whole of the tunnel to be occupied.

Tunnels of various types are found in other enzymes or organelles involved in elongating molecular ‘chains’, e.g. polypeptides and nucleic acids. The tunnel on the ribosome and that through which RNA or DNA passes has to accomodate chemical disparate molecules (four different bases, 20 different amino acids).


What's the fastest legal way for the nutrients in a dead body to re-enter the ecosystem?

The Parsis and other Zoroastrians dispose of their dead in a so-called Tower of Silence, where the body is left on a raised platform to be eaten by scavengers, particularly birds such as vultures.

This is possibly (probably?) the quickest way for nutrients to re-enter the wider ecosystem, as scavengers usually work a whole lot quicker than microbes.

Tibetan tradition also contains a ritual known as the Sky Burial, which achieves the same sort of thing. The Tibetan version may be even quicker, as once the scavengers have stripped the body, the bones are ground into a paste along with flour and yak's milk/butter to be fed to a second round of scavenging birds.


You're asking about the C-value enigma, in particular this kind of diagram:1

The quick answer is that there is no "why" in evolution; things happen and if they're beneficial they tend to stick around more than the deleterious things.  The longer, (slightly) more satisfying answer is non-coding DNA.  Thanks to non-coding DNA the size of a genome doesn't even correlate to the number of genes.  The human genome, for example, has over 20,000 genes but is less than two percent protein-coding; the flower Utricularia gibba, however, has over 28,000 genes with about two orders of magnitude smaller of a genome, due to the fact that its genome is 97% protein-coding.  In short, there is no real meaning to be found in genome size variation due to non-coding portions, which while they are sometimes important regulators can often be just transposons (40% of our genome).  I will also point out that all of those groups you mention have species with significant polyploidy.

The are a number of other interesting ideas.  In the process of researching this, I stumbled upon the Animal Genome Size Database, which is an absolute gem of a treasure trove.  It's an unbelievable mine where I've spent a good half-hour just reading.  In particular, the statistics pages list interesting correlations for certain groups.  Mammalian genome size, for example, correlates:

Positively with red blood cell size, despite lack of nuclei
Negatively with metabolic rate
Not at all with developmental rate or longevity

For amphibians, however, there is:

Positive correlation with red blood cell and nucleus sizes in both frogs and salamanders
Negative correlation with developmental rate in many groups
Negative correlation with brain complexity in both frogs and salamanders
No strong relationship with metabolic rate in either frogs or salamanders
Some association with intensity and frequency of metamorphosis

If you have time, I highly recommend reading through T. Ryan Gregory's PhD thesis entitled The C-Value Enigma.  It's around 350 pages, but each chapter is in separate pdfs and is the most in-depth treatment I've seen, despite being about a decade old.  It's been moderately life-changing for me to read, some of the interpretations he presents challenged my thinking on the subject of genome evolution entirely.  Should genomes be treated as individuals, and what would that mean?  I digress.  Chapters 3, 4, 6, and 7 are what you'll want, in particular the last twenty or so pages of chapter 7.

Dr. Gregory now has a faculty position and his lab's research page is a little easier to read.  I love this image:

  As genome size increases in eukaryotes, the percentage of the genome composed of genes (white circles) becomes smaller. Conversely, the percentage of the genome made up of transposable elements (black circles) increases with genome size.

It seems like the best way to look at genome size and find some meaning is within a specific group.  There are correlations, for example, that are present in frogs and salamanders, but not in either group alone.  Some of the groups are very unbalanced; in insects, only Orthoptera tend to have very large genomes.  Interestingly, a number of those groups also undergo some form of metamorphosis, but the correlations aren't what you might have expected:  insects that develop quickly and metamorphose have smaller genomes, but "[i]n a more general sense, small genome size seems linked to rapid diversification... Conversely, insects without metamorphosis may possess very large genomes..."


Short answer
My best bet is D)

Background
A) seems incorrect as lipases break down fats. However, one has to realize there quite some fat in milk (up to 3.5% in untreated milk). Digestive lipases in man are secreted by the pancreas into the duodenum.

B) Might be a correct answer, as trypsin is released in the small intestine and...

  [Trypsinized] peptide products are further hydrolyzed into
  amino acids via other proteases, rendering them available for
  absorption into the blood stream. Tryptic digestion is a necessary
  [first] step in protein absorption as proteins are generally too large
  to be absorbed through the lining of the small intestine.

C) Chymosin, known also as rennin, is a proteolytic enzyme synthesized by chief cells in the stomach. Its role is thought to be in digestion is to curdle or coagulate milk in the stomach, a process important in young animals. If milk were not coagulated, it would rapidly flow through the stomach, impairing protein digestion. So this is a enzyme in the stomach and active earliest in the digestive system (answers A and B concern enzymes in the duodenum, which is later down in the digestive tract). However, in humans there is only a chymosin pseudogene present, and since the answer specifically deals with humans, answer C) is incorrect.

D) Pepsin is

  ...[] one of three principal proteases in the human digestive system, the other two being chymotrypsin and trypsin. [These] enzymes [...] break down dietary proteins into [...] amino acids, which can be readily absorbed by the small intestine. Pepsin [mainly] cleav[es] peptide bonds between hydrophobic and [..] aromatic amino acids [...The other two proteases have different targets].

  Pepsin's proenzyme, pepsinogen, is released [...] in the
  stomach [...], and upon mixing with the [...]
  gastric juice, [it is] activate[d] to [...] pepsin.

Here we have the adult equivalent of rennin, also active early in the digestive tract, namely the stomach. So D) is the enzyme present in humans (as opposed to C) and active already in the stomach (as opposed to later in the duodenum in answers A and B). So D is the answer.


What are "intrinsic hypothalamic fibers"? (From an article on neuronal mechanisms of sexual desire)

"Intrinsic hypothalamic fibers" are fibers instrinsic to the hypothalamus; so yes, these are fibers either projecting from somewhere in the hypothalamus to somewhere else in the hypothalamus, or locally in the hypothalamus (the hypothalamus itself is a pretty complex structure containing many distinct nuclei). The paper you reference specifically mentions the medial preoptic area, mPOA, as a target:

Infusions of mu opioid receptor agonists to the mPOA inhibit sexual behavior in male rats

and

infusions of a mu antagonist to the mPOA, but not NAcc, block sexually conditioned place preference

"Fibers" does not necessarily refer to myelinated axons, just axons of any sort.


meaning of abbreviations h and m in Na channels

Those initials were proposed by Hodgkin and Huxley in their original paper modeling the action potential in nerve cells: https://en.wikipedia.org/wiki/Hodgkin%E2%80%93Huxley_model

They are not names for subunits, domains or motifs in the sodium channel, as your question may imply. Instead,

  n, m, and h are dimensionless quantities between 0 and 1 that are associated with potassium channel activation, sodium channel activation, and sodium channel inactivation, respectively.

However, there is no indication of what those initials mean (if anything), apparently being just letters they chose to name the variables in their equations.


Good question! I had never really though about it, so thank you!

Echinodermata have a pentaradial symmetry

Echinodermata actually don't have a radial symmetry like jellyfish do. They have a pentaradial symmetry as they systematically have 5 arms.

Parsimony

Even if Echinodermata were radially symmetric, then it would actually be unlikely that bilateral symmetry evolved, was then lost and evolved again. It is much more parsimonious that bilateral symmetry evolved once and was later lost in the echinodermata lineage.

Developmental and Genetics of pentaradial symmetry

As one would expect modifications of hox genes are involved into the evolution of this peculiar body plan. From Lowe and Wray 1997

  Here we report the expression domains in echinoderms of three important developmental regulatory genes ( distal-less, engrailed and orthodenticle ), all of which encode transcription factors that contain a homeodomain. Our findings show that the reorganization of body architecture involved extensive changes in the deployment and roles of homeobox genes. These changes include modifications in the symmetry of expression domains and the evolution of several new developmental roles, as well as the loss of roles conserved between arthropods and chordates. Some of these modifications seem to have evolved very early in the history of echinoderms, whereas others probably evolved during the subsequent diversification of adult and larval morphology.

Here is the whole abstract of Mooi and David 2008

  The strangeness of echinoderm pentaradiality results from superposition of radial symmetry onto ancestral deuterostome bilaterality. The Extraxial-Axial Theory shows that echinoderms also have an anterior/posterior (A/P) axis developed independently and ontogenetically before radiality. The A/P axis is first established via coelomic stacking in the extraxial region, with ensuing development of the pentamerous hydrocoel in the axial region. This is strongly correlated with a variety of gene expression patterns. The echinoid Hox cluster is disordered into two different sets of genes. During embryogenesis, members of the posterior class demonstrate temporal, spatial, and genetic colinearity within the extraxial region. We suggest that displacement of genes from the more anterior Hox classes toward the 5′ end of the chromosome leads to control of the later-developing, radially symmetric axial region. Genetic disorder is therefore another way of using colinearity to build the unique echinoderm symmetry.

As insinuated above, note that (in most echinodermata species at least) only adults have a radial symmetry. Larvea have a bilateral symmetry. Here are a bunch of picturesand schema.

Larvea

Adults


The probability meaning of Covid variants

The studies referenced do not have any such specifics about transmission probability.
What they observe is that a variant is becoming more common. Modeling the spread gives a different R0 value for the variants vs the reference strains:

In line with previous
modelling studies, the R0 for VOC-202012/01 was estimated as 75% more transmissible than other variants [35].
Davies et al. modelled data from three English regions to estimate that VOC 202012/01 is 56% more transmissible
(95% credible interval (CrI): 50-74%) than previously identified SARS-CoV-2 variants [32]. Danish modelling
studies performed in January 2021 estimated that VOC 202012/01 was 36% more transmissible than other
variants [ECDC communication with Danish authorities].

(from your second reference)
They infer that the variant is more transmissible because the modeled number of people subsequently infected per infected person is greater. The reasons for this cannot be easily determined by the methodology they refer to, and there is no simple way to map this onto probability of infection given some exposure; they are just describing what happens in real-world conditions, on average.
What you can infer is that there are some types of contact that occur in the real world that wouldn't result in transmission with the old strain that do result in transmission of the variant. This could be because more infected people produce enough virus to spread to others, it could be because shorter contacts lead to infection, it could be because infected people have different behavior that leads to more contact with people to potentially get infected; you can't tell the difference from these data.


In terms of cell bodies? Zero.  There are autonomic projections from the spinal cord (sympathetic) and vagus nerve (parasympathetic) to the sinoatrial node, the atrioventricular node, and at discrete points in the atria and ventricles.


What kind of bug is this? I found it on my Cleome plant in Atlanta Georgia

This is an instar (nymph) of a shield or stink  bug (order Hemiptera, family [Pentatomidae])(https://en.wikipedia.org/wiki/Pentatomidae).

Specifically, it appears quite similar to a later juvenile stage (~4th instar) of Chinavia hilaris, the Green Stink Bug.

 4th instar; Source: Oregon Dept of Agriculture

 4th instar; Source: UF IFAS; Credit: Herb Pilcher, USDA-ARS, Bugwood.org.

Alain Hogue also captured a wonderful picture of this species at bugguide.net

From UF IFAS:

  Distribution
  The green stink bug occurs in most of eastern North America, from Quebec and New England west through southern Canada and the northern U.S. to the Pacific Coast, and southwest from Florida though California. This is the most commonly encountered stink bug species in North America.


Data repositories for data on the Tumor Microenvironment?

Have you seen the St Jude Children's Research Hospital Pediatric Cancer data repository PeCan?
They have a bunch of data on a wide range of different types of pediatric cancers. These are all in the form of genomes and RNA-seq. However, they also have a bunch of visualizations set up so that you can see how these profiles work from a perspective of mutations and RNA in tumours of all sorts.


Is there an evolutionary purpose to armpit perspiration?

There may be an evolutionary purpose to underarm perspiration, as alluded to in the "hidden hint" link of @DevashishDas, and also hinted at by the answer by @Chris. The apocrine sweat glands of our armpits produce steroids. One group of steroids secreted by the axillary apocrine glands are sex pheromones.  Although we may not consciously notice the chemical odors of sex pheromones, they do likely affect our behaviors.

For example, Wedekind et al. showed that females showed distinct preferences for certain male odors. Women tended to prefer the odors of males that were genetically different at the major histocompatibility complex (MHC) loci, a group of genes associated with our immune response system. Greater genetic variation of MHC genes generally translates to greater ability to combat disease.  Females that select males that are genetically different at the MHC would produce offspring with greater genetic variability at the complex, and therefore more likely to have greater resistance to disease or ability to fight disease.

These results suggest that the pheromones secreted in underarm perspiration is a sexually selected trait in humans. If so, underarm perspiration would have an evolutionary (fitness) advantage.


The idea that bacteria thrive in warm places is mostly biased from a human perspective. Human researchers will tend to care more about bacteria that cause human disease. These pathogenic bacteria can replicate in/on humans at ~37 °C (which is warm). As Dexter points out, bacteria can grow at other temperatures.

But I'd go deeper and consider proteins (and other macromolecules) in the cell. For example, the enzymes that carry out many important processes for the bacteria (such as DNA polymerases that build the DNA) are most active at certain temperatures: in E. coli or humans or dogs that's ~37 °C; for a thermophile it's warmer. See below:


Pitch perception - why is the missing fundamental not directly detected in the cochlea?

The basilar membrane in the inner ear (cochlea) is a place-dependent Fourier transformer (Fig. 1). This means that there is an orderly tonotopic map projected on the basilar membrane (BM). Traveling waves imposed on the BM via the ossicle chain and the oval window start of at the base and travel all the way to the apex. Along the way the resonance frequency of the BM gradually decreases, as the BM gets wider and more flexible (like piano strings).

Now, if a certain frequency is missing, the BM is not moving at that frequency location, and hence the hair cells do not become activated, and the neurons with that specific characteristic are not activated either. How on earth can you still hear that frequency?

It is the harmonic structure that determines our perception of pitch, rather than the lowest harmonic alone. Our brains are sensitive to the frequency difference from one harmonic to the next and base the "real" pitch of the tone on that difference. This is referred to as the "difference tone". When you hear two pure tones, the ear and brain subtract one frequency from the other, and you "hear" a tone with a frequency of this difference (source: National Taiwan University).

Fig. 1. Frequency tuning in the cochlea. source: New York University


What repairs faster when injured: white matter or grey matter?

Short answer
As @BryanKrause indicates, neither answer really makes sense.

Background
This is basically per the answer of @BryanKrause. Myelin is the stuff that forms the main characteristic component of white matter. White matter being

  [the tissue] found in the deeper [in] the brain (subcortical). It contains nerve fibers (axons), which are extensions of nerve cells (neurons). Many of these nerve fibers are surrounded by a type of sheath or covering called myelin. Myelin gives the white matter its color. It also protects the nerve fibers from injury. Also, it improves the speed and transmission of electrical nerve signals

I think what the question aimed to target was your understanding what a myelin sheath is for (and, hence, what it is not intended for). Quoting from (Morell & Quarles, 1999):

What

  [A] greatly extended and modified plasma membrane wrapped around the
  nerve axon in a spiral fashion. [It] originates from and are a part of
  the Schwann cells in the peripheral nervous system (PNS) and the
  oligodendroglial cells in the central nervous system (CNS)

What for

  Each myelin-generating cell furnishes myelin for only one segment of any given axon. The periodic interruptions where short portions of the axon are left uncovered by myelin are the nodes of Ranvier, and they are critical to the functioning of myelin.

How

  In myelinated axons, the excitable axonal membrane is exposed to the extracellular space only at the nodes of Ranvier; this is the location of sodium channels. When the membrane at the node is excited, the local circuit generated cannot flow through the high-resistance sheath and, therefore, flows out through and depolarizes the membrane at the next node, which might be 1 mm or farther away []. The low capacitance of the sheath means that little energy is required to depolarize the remaining membrane between the nodes, which results in local circuit spreading at an increased speed. Active excitation of the axonal membrane jumps from node to node; this form of impulse propagation is called saltatory conduction (Latin saltare, “to jump”). Such movement of the wave of depolarization is much more rapid than in unmyelinated fibers. Furthermore, because only the nodes of Ranvier are excited during conduction in myelinated fibers, Na+ flux into the nerve is much less than in unmyelinated fibers, where the entire membrane is involved.

What not
Although the myelin sheath is formed by a glial cell type, and although glial cells do structurally and metabollically support neurons, I would not say that this means myelinated tissue heals faster. Instead, myelin is more about the functional role of white matter, namely efficient, fast and reliable long-distance transfer of information across distant brain regions.

Reference
- Morell & Quarles. The Myelin Sheath. In: Siegel et al (eds); Basic Neurochemistry. 6th ed. Philadelphia: Lippincott-Raven (1999)


What are typical values for bone mass in humans?

I wonder what are typical bone mass values for adult males and females?

This seems hard to find. The only value I could find is on Bionumbers at it says that vertebrates compact bones have a mean density of 2 mg/cm$^3$ [1]. However in medical practice two scores are used to indicate the ratio between tested bone density and ideal bone density [2, 3] and absolute values are uncommon.

  And do they change significantly with workout and diet?

Bone mass is mainly influenced by genetic factors. Only up to 25 % may be influenced by environmental factors such as diet and exercise [4].

Among the medical conditions that influence bone mass, osteoporosis is the most frequent especially in women. Other conditions are: hyperparathyroidism, glucocorticoid therapy, other bone abnormalities and fractures [2].

References:

Brian Cotterell, Fracture and Life, Imperial College Press, 2010 p.77 bottom paragraph via http://bionumbers.hms.harvard.edu//bionumber.aspx?id=108642&ver=2
Bone density. (2014, September 15). In Wikipedia, The Free Encyclopedia. Retrieved 17:08, September 29, 2014, from http://en.wikipedia.org/w/index.php?title=Bone_density&oldid=625737182
http://www.niams.nih.gov/Health_Info/Bone/Bone_Health/bone_mass_measure.asp
http://www.niams.nih.gov/Health_Info/Bone/Osteoporosis/bone_mass.asp


blastn: What substitution matrix is used?

BLASTN does not use a substitution matrix. There are scores for match, mismatch and gaps which you can also define.

There is no feature available as of now to allow scoring of matches against unknowns. They are considered mismatches (as shown below). If these unknown are in the middle of a HSP, then you can probably re-score the HSP according to your scheme using a python script. If the N stretch is disrupting the HSP, then you can try relaxing the mismatch penalties and reduce word size (basically reduce stringency). I can't think of any other solution.

Query  1    CAGCGTCCANNTCCCGAGGTGCCGGGATTGCAGACGGAGTCTGGTTCACTCAGTGCTCAA  60
            |||||||||  |||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  8    CAGCGTCCACCTCCCGAGGTGCCGGGATTGCAGACGGAGTCTGGTTCACTCAGTGCTCAA  67

Query  61   TGGTGCCCAGGCTGGAGTGCAGTGGCGTGATCTCGGCTCGCTACANNCTCCACCTCCCAG  120
            |||||||||||||||||||||||||||||||||||||||||||||  |||||||||||||
Sbjct  68   TGGTGCCCAGGCTGGAGTGCAGTGGCGTGATCTCGGCTCGCTACAACCTCCACCTCCCAG  127

Query  121  CCGCCTGCCCTGGCCTCCCAAAGTGCCGAGATTGCAGCCTCTGCCCAGCCGCCACCCC  178
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  128  CCGCCTGCCCTGGCCTCCCAAAGTGCCGAGATTGCAGCCTCTGCCCAGCCGCCACCCC  18


Why do nerve cells convert electric signals to chemical signals?

There are two types of synapses:

Chemical synapse
Electrical synapse

The first one is the one you are asking about.  The second one corresponds to the faster synapse you are imagining. It consists of two neurones connected by a gap junction. Gap junction form a cytoplasmic bridge between the neurones and thereby allow electrical signal to directly go from one neuron to the next through ion diffusion without converting to chemical signal.

The second one implies release of chemicals (neurotransmitter) in the synaptic cleft, the extracellular space between the two neurons. It is indeed slower than the electrical synapse. However, unlike the electrical synapse, it enables a variety of postsynaptic effects. Some neurotransmitter elicit excitatory effects, some elicit inhibitory effects (electrical synapses where the presynaptic side is an axon only allow excitatory effects). Some postsynaptic receptors to neurotransmitter are ionotropic whereas some are metabotropic. The former are neurotransmitter-gated ion channels, which means that they let specific ion cross the postsynaptic plasma membrane when they bind neurotransmitter. The latter trigger intracellular chemical reactions, such as production of cAMP, which is a companent of a signalling pathway and can for example influence the expression level of specific genes.

This more diverse set of postsynaptic response enabled by chemical synapses explains why they dominate our nervous system.

Reference: Purves et al., Neuroscience, 5th ed., 2012 ISBN 978-0-87893-695-3


How much does a typical biologist know about signal processing, machine learning, and (theoretical) computer science?

I don't know what a "typical" biologist is, but I'd guess they don't know much about computers, because the population in general is computer illiterate. In my department, we do have a lab that does a lot of computational work on proteins. And of course bioinformatics relies on computers.

I can see where programming would come in handy for an ecologist, and maybe hardware and electronics too. Lets say you want to track animals in the woods. Traditionally, you'd give them a radio collar, then you'd have to triangulate their position in the woods, and at the end of the day all you'd have is location data. You could use something like a Raspberry Pi or Arduino to create a device that has GPS, a camera, and cell phone antenna, which could record much more information about the animal's location and activity and send it back you without as much effort.

In our modern computerized age, knowing some programming is always a plus, no matter what field you're in. Finding ways to apply that skill aren't always easy. I know both Java and C++, but I've really only written a few programs that I've used in research, 1 to calculate number of possible peptides given a size and some amino acids that won't change, and one to calculate how much DNA to use in ligation reactions.


I presume the aptamer is biotinylated; if not, that’s a likely reason for the outcome.
Have you used a biotinylated positive control to confirm the surface is functional with PBS? I understand you want to buffer exchange to Tris, but this positive control in PBS buffer is important.
Amine coupling involves covalent attachment of the 1-Ethyl-3-(3-dimethylaminopropyl) carbodiimide (EDC) to carboxylate on the chip surface, followed by replacement of this adduct with N-hydroxysuccinimide (NHS), thus creating an active surface to crosslink primary amines at slightly acidic pH. Then the unreacted active surface is quenched with ETH. Residual active surface would react with Tris that contains a primary amine.
Perhaps the ethanolamine blocking agent may not have completely inactivated the active surface following streptavidin amine coupling, enabling crosslinking of Tris buffer to that surface and impacting the ‘Protein’ capture?
Other possible reasons: Binding of the aptamer to streptavidin may sterically hinder binding of the 'Protein.' Also, the loss of the proper secondary structure of the aptamer may impact the 'Protein' binding. Perhaps refolding the aptamer prior to streptavidin capture may help?
Edit: Differences in pH and ionic strength may impact 'Protein' binding to aptamer when tested in Tris versus PBS buffers.


How did viruses learn to utilize the workings of a cell?

It's a numbers game.  Viruses can produce thousands, millions, even billions of copies every day, and only one of them needs to be slightly better to get ahead.  Rhinoviruses make roughly one error every time the genome is replicated; over many, many replications a single change can arise giving an advantageous effect.  As another example, it's been said that HIV mutates every single spot on its genome every single day.  Evolution is simply a waiting game.

This article is a pretty cool write up detailing the process.  It says exactly what I said: large numbers, high mutation rate.  Besides, the virus only has to take advantage of cellular processes, not make new ones every time.  That's much more efficient.  It also details some specific changes that explain some differences between similar viruses.  It's amazing, but a single base change can mean a single protein is different which can mean a different receptor is used for binding, which can make all the difference.

And there's this cool quote:

  [T]here may well be more viruses in a single common cold infection than there have been primates in the entire history of life on Earth.


Is the number of legs in myriapoda determined entirely by the genome?

Three factors that influence the number of legs are:

1) Sex : In some species of myriapoda, the females have been found to have more leg segments than males (reference) eg: Himantarium gabrielis

2) age

  Growth is by adding segments and legs with successive molts
  (anamorphic), and myriapods continue to add additional segments and
  legs after they have reached sexual maturity (reference).

3) Working of a "segmentation clock" (set of genes) that periodically adds segments (reference).


What is the current molecular explanation of Mendel's pea cross?

The article you have linked to does explain everything thoroughly, though in a somewhat complex way. I did not know how much genetics you actually know, so I tried to answer very thoroughly.

So the article states that the gene Mendel studied and that was responsible for the white color of the pea flower is ANTHOCYANIN1 (in the article it is also called - bHLH, that is the name of the protein family that ANTHOCYANIN1 belongs to). So, ANTHOCYANIN1 is a transcription factor - a molecule that activates the transcription (making of mRNA) of other genes, basically it activates other genes.

The white flowered peas have a mutation (Guanine to Adenine transition) in the sixed intron of the gene ANTHOCYANIN1. Introns are sequences of non-coding DNA, that does not encode amino acids, and is removed from the RNA transcript by a process called splicing. The mutation occurs at a binding site for the Spliceosome (a protein and RNA molecule) that splices the RNA, because of this the RNA transcript is not spliced correctly. The faulty RNA transcript for the gene ANTHOCYANIN1 contains 8 extra nucleotides and because the genetic code is a triplet, a frame shift occurs. When a frame shift occurs all of the codons bellow the frame shift sight get changed. In this case, this leads to a premature stop codon. The translation of the ANTHOCYANIN1 RNA get stopped before a full protein can get synthesized and a non-functional protein is made.

If ANTHOCYANIN1 does not function, no genes are activated and no pigment is synthesized.

To summarize - the white pea flower color is a consequence of a nucleotide mutation (Guanine to Adenine) in a intron sequence of the gene ANTHOCYANIN1, this leads to incorrect splicing of the ANTHOCYANIN1 RNA (a frame shift) and to the production of a shorter protein that is non-functional.


Why pellet and resuspend E. coli for plasmid prep

The reason this centrifugation/resuspension step is done has a simple reason: It concentrates the bacteria in a much smaller volume which is much easier to handle afterwards.

For a maxiprep you typically have a culture volume between 250 and 500ml, depending on the copy number of the plasmid. After centrifugation the pellet is resuspended in 10ml of Buffer P1, for lysis another 10ml of buffer P2 are added, for neutralization 10ml of P3.

Imagine doing this with 500ml culture volume - adding 500ml of each P2 and P3. This might work for a miniprep, but definitely not for larger volumes. Additionally, the centrifugation steps are carried out at high g numbers - typically something around 15.000xg. Doing this with this really high volumes is complicated and needs big centrifuges, which a lot of people are not trained anymore to operate or have available.


Is a corpse more flexible than a living person?

According to the science in this article: healthunify.com/why-cant-everybody-cant-do-a-split/, not really. Flexibility such as splits are only possible by lengthening the skeletal muscle fibers (in the case of splits, this includes the hamstring and iliopsoas). Which means that splits aren't solely dependent on how your CNS functions.
Furthermore, with death eventually comes rigor mortis where due to the body's chemical changes after death (lack of ATP production etc... https://biologydictionary.net/rigor-mortis/), the body becomes rigid which makes it even more difficult for a dead person to do splits than a live one without seriously damaging the dead person's body/muscles.


Historical recovery from mass extinction events

I think the concept of adaptive radiation is what you may be thinking about, since adaptive radiations have been observed following historic mass extinctions.

When organisms are placed in environments with low diversity (either due to mass extinction or the recent creation of the environment) they can undergo adaptive radiation.  This generally occurs when there are lots of unoccupied niches in the environment - essentially there are lots of potential ways to make a living that are not being exploited by an existing organism.

In this situation, any organism with a heritable trait that was able to utilize a niche better than other organisms would have a selective advantage and would increase in frequency.  Over time this process can result in new species of organisms.

There is nothing really different about adaptive radiation and the normal process of evolution and speciation except that in an environment with lots of unoccupied niches, the probability of having a trait that gives you a selective advantage is greater so speciation occurs at a faster rate.

It is the normal processes of evolution and speciation that give the biome the capacity to increase diversity based on the remaining species.


The drugs you are referring to are called receptor mimics or peptide inhibitors.  Yes, molecular mimics for human ACE2 can and have been synthesized.  Binding of these mimics to coronavirus spike proteins leads to sequestration or inactivation of viral particles.

Relevant literature:
Romano M, Ruggiero A, Squeglia F, Berisio R. An engineered stable mini-protein to plug SARS-Cov-2 Spikes. bioRxiv. 2020.
Han Y and Král P. Computational Design of ACE2-Based Peptide Inhibitors of SARS-CoV-2. ACS Nano. 2020;14(4): 5143-5147.
Walls AC, Xiong X, Park YJ, et al. Unexpected Receptor Functional Mimicry Elucidates Activation of Coronavirus Fusion. Cell. 2019;176(5):1026-1039.e15.


What is the efficacy of Pertussis booster vaccine among different age groups?

No, it is not true, see references 1 and 2 for this purpose. From these articles which followed up booster vaccinations for pertussis it seems that there is at least some protection 5 and 8 years after the boost.

There is another study, which says that 10 years are relatively safe to assume, as the reduction in antibody levels over time estimated from the 5 year study would still allow protective levels of antibodies. See reference 3 for details.

One of the problems to make statements about the duration of the protection is the lack of data. Additionally there was a change in the vaccine from whole cell (which is pretty immungenic, but has higher number unwanted side effects) against a acellular vaccine. This change happened in the 90s, so there are no longterm data available. See reference four for more details.

The common recommendation at the moment for adults is to repeat the booster vaccination every 10 years (together with tetanus and diphteria) and for people which have close contact to unvaccinated persons every 5 years to prevent infections (see reference 4).

References:

Immunity to pertussis 5 years after booster immunization during
adolescence.
Immune responses to pertussis antigens eight years after booster
immunization with acellular vaccines in adults.
How long can we expect pertussis protection to last after the
adolescent booster dose of tetanus-diphtheria-pertussis (Tdap)
vaccines?
Acellular pertussis vaccine use in risk groups (adolescents,
pregnant women, newborns and health care workers): A review of
evidences and recommendations


Cold/warm blooded are misleading categories

The terms cold blooded and warm blooded is very misleading as it gives one the sensation that animals may warm up their internal temperature for the only reason of warming it up.

The terms homeo-, poikilo-, exo- and endo- terms are much more useful in thinking about control of body temperature. Have a look at this post and this post to understand these terms. Make sure to really read these posts to correctly understand these terms and how they interact.

Reformulating your question

What people, in general mean by cold vs warm blooded animals is whether they actively control their body temperature or not. That is cold blooded would mean exotherm while warm blooded would mean endotherm. As such the question becomes "why would any animal care about being endotherm if the body temperature won't go under freezing point anyway?"

Answer

Any metabolic pathway is affected by temperature. A change of temperature of only a few degrees can drastically affect the rate of chemical reactions. Homeotherm individuals (often homeotherm thanks to endothermy) are able to keep a quasi constant level of activity despite external change in temperature. It allow them to forage during hot and cold whether for example. This is a very important advantage but it often comes at the important energy cost. It is a trade-off between the benefit of homeothermy vs the energy cost of endothermy that will define the best interest of an organism.


Why isn't the DNA in bacteria always split up and replicating?

Bacterial DNA replication is initiated at the oriC by DnaA in E. coli. Think about ways in which DnaA binding or activity can be regulated in a way that inhibits or permits DNA replication. In recently replicated bacterial DNA, the DNA is hemimethylated (parental strand has a methyl group, daughter strand doesn't): An inhibiting protein binds to hemimethylated DNA, that can block DnaA activity at the oriC. A DAM methylase adds methyl groups after a while to the newly synthesized DNA, in which case DnaA may bind. Due to the lag between replication and methylation, DNA replication can't be continuously initiated! This is one of many examples (for example, DnaA must bind ATP for it's mechanism of action), but the take home point is DNA replication must be initiated and if it can't be, then it doesn't take place!

THE INITIATION OF BACTERIAL DNA REPLICATION

Breaking that down: (note, this is in E. coli)

DnaA is a protein with DNA-binding activity. When many DnaA bind at the oriC, it causes the DNA to bend open and loop. At this point, DnaB would have access to the DNA, and this is the helicase that unwinds everything for replication (you'll also see that DnaB must be loaded onto the DNA by DnaC, a helicase loader). So blunty enough, oriC is an origin of replication, everything starts here. There are repeats of AT rich regions denoted 13mer and 9mer in the oriC (number of bases in the region if you will). We know that this is beneficial because AT rich regions are easiest to pull apart due to the number of hydrogen bonds between A and T.

In the example I provided, the assumption is that the DNA of E. coli is methylated on adenines on both strands. When replication occurs, the new DNA doesn't have this methyl group on it's adenines like the parental strand. A protein that recognizes and binds so-called hemimethylated (half methylated) DNA, SeqA, binds where it can, including in the oriC. It blocks DnaA subsequently for a short time, and falls off the DNA on its own. The DAM methylase adds the methyl groups when it can, and once it does the SeqA can no longer bind, but the replication-initiation complex thus can.

There are other modulators of DNA replication, and the concentration of the DnaA itself is a big factor because you need many units of DnaA to bind to facilitate initiation. So then you have to consider is DnaA being expressed strongly enough? And this has it's own pathway outside the scope of this question.


What kind of microscope for ML/biological research?

I agree with @Jeremias Brand's answer.

Pretty much you will have to forget about fluorescence microscopy... you can probably find some dusty old one on eBay in your price range, but it probably won't be any good.

However, the good news is that seen that in your comment you mention

  a) plants, b) blood, c) liquids such as wine, d) food?

transmitted light (white light) would be perfect for a start.

eBay is surely a good place for finding used objectives at a cheap price. You may end up with a good collection of objectives for less than 100€.
That is surely tempting, and it may actually be OK as a start.
However, I personally think that it is better to own a good lower magnification objective than a cheap high-magnification one, so be always be a bit wary about offers that look too good to be true (especially for new piece of equipment).

I would strongly suggest getting a binocular microscope (so with two eyepieces), rather than a monocular one. Makes life much easier.
Also, be sure to have a camera attachment. While a camera may not be strictly necessary, especially at the beginning, it's better to have an attachment so that you can add one in the future, if you feel the need of taking pictures. Although many microscopes have specialized attachments for microscope cameras, you can get away with using your own normal camera, or even your cellphone, if you position it correctly (may need some DIY depending on the situation).
This page has very detailed explanations on how to connect a camera to a microscope.

As for your samples, plants are a very good and easy thing to start observing. Onions are probably one of the best samples to start with.

You may also want to stain your samples. Probably the easiest thing to get is methylene blue, which should be a few euros for 20-30 ml. However, fountain pen ink works as well.

Whenever you use chemicals, remember to look for their safety data sheet (MSDS). Methylene blue is pretty safe to work with, provided you don't swallow it (doh...) and use gloves (standard latex gloves are OK). Be careful because it stains and can be a bit messy, which is true for pen ink as well!

Crystals are also pretty cool to watch under a microscope: take a coverslip, put on a drop of sugary or salty water and wait for it to dry!