Which wavelength to use to determine algae using a colorimeter?

From Biotek I learned the following:

  Spectral scans of algae cultures demonstrate significant absorbance below 400 nm as well as two distinct absorbance peaks at 440 nm and 675 nm (Figure 1). Cell number determination is most consistent when light scatter is used rather than absorbance by cellular constituents. In order to avoid influence from absorbing material 600 nm [is best] to monitor growth.

Figure 1. Absorbance spectral curve of Microcystis aeruginosa suspension cultures.Source: Biotek


Why outgroups are supposed to be ancestral?

Yes, sister taxa are, by definition, of equal age. So they evolve independently after the two groups diverge. You are asking about character polarity, and you are exactly right. That is why multiple outgroups are better for inferring which state is ancestral. If an outgroup is state A, and a second more distant outgroup (an out-outgroup) is also state A, and the ingroup has state B, then you can be fairly confident that state A is ancestral. If you look at dozens of characters this way, you will find that any of the three taxa in any combination may have the ancestral state. Imagine the distant outgroup (the out-outgroup) is state A, and both the close outgroup and the ingroup are state B. Then again, you could not know which state is ancestral, and would need a further outgroup. These are inferences, not measurements.


What do blue cone cells add to visual function?

Short answer
Primate color vision started off with photosensitive cells detecting medium to long wavelengths (M/L cones detecting greens and reds) and short wavelengths (S cones most sensitive to blue). By neurophysiologically weighing their relative contributions the full spectrum (red, orange, yellow, green, blue and indigo) can be detected by dichromats. Addition of a slightly different M/L cone and generating separate M and L cones increases the resolution of color vision in the medium and long wavelengths, which is thought to enhance color discrimination useful for foraging fruits. Indeed, blue in itself is not needed for this task. However, missing the blue cones would eliminate a large proportion of the visual spectrum.

Background
Evolutionary spoken, primate vision started off with dichromatic vision. These early dichromats had retinas with one type of cone sensitive to medium-to-long wavelengths (M/L cones) and one type sensitive to short wavelengths (S cones) (Jacobs, 1996). This organization determines the dynamic range of color vision, i.e., to see colors from short wavelengths (greens and blues) to long wavelengths (red and yellows). Weighing their relative contributions by neural networks in the retina allows the intermediate wavelengths to be resolved.

Later in evolution, some diurnal species had a gene duplication on their X chromosome, generating a M/L duplicate gene (Jacobs, 2009). Small mutations in these genes eventually paved the way for two closely related M/L opsins, namely one a little more sensitive to longer wavelengths (L opsin) and one to slightly shorter wavelengths (M opsin). The dynamic range of color vision still depends heavily on the S opsin in the blue cones, as the M and L opsins have absorbance spectra much closer to each other (Fig. 1). The benefit of two opsins with nearly identical absorbance spectra is a higher color discrimination ability (higher color resolution) in the medium to long wavelengths. High discriminating power in the red-yellow-green part of the spectrum is thought to be beneficial for diurnal fruit foraging primate species (Jacobs, 1996). Note that cones need a lot of photons to operate; nocturnal primates are typically dichromats and they will not benefit anyway from another M/L cone.

For fruit foraging alone, the L and M cones do a pretty good job, as your example shows. However, there is more to the eye than food alone. Eliminating the blue cones would substantially narrow down the dynamic range of color vision. Further, evolution started off with S and L/M cones and added another M/L cone to that existing system. Evolution didn't start off with a blind ape and the goal to generate the perfect fruit forager; no it started off with a dichromat and over time improved its ability to seek food during daylight.

Fig. 1. Absorbance spectra of the different opsins. source: Kevin MD

References
- Jacobs, PNAS (1996); 93: 577-81
- Jacobs, Philos Trans R Soc Lond B Biol Sci (2009); 364(1531): 2957–67


How do you merge SNP data with a reference genome?

First, you need to know which genome sequence does the SNP file refer to. They must have mentioned the reference sequence that they used.

As others mentioned the case of CT is heterozygosity. If you just want to mark the changes then discard the residue that is already present in the reference genome and use the other allele. However, you want to keep a track of the haplotype then you have make sure that a set of SNPs come from the same chromatid. This is difficult- you might still be able to know it for SNPs that are close enough to be mapped by a single read but it is almost impossible for SNPs that are separated well enough.

As Endre said, you have to start from the first nucleotide. However, it seems dubious that you are getting $\ (NNNN)_n$ in the beginning of chromosome 1. Complete assembled chromosomes do not have such stretches. Below are the first 10 lines of the chromosome 1 fasta file. See for yourself.

>gi|568815364|ref|NT_077402.3| Homo sapiens chromosome 1 genomic scaffold, GRCh38 Primary Assembly HSCHR1_CTG1
TAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC
CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCAACCCTAACCCTAACCCTAACCCTAACCCTAA
CCCTAACCCCTAACCCTAACCCTAACCCTAACCCTAACCTAACCCTAACCCTAACCCTAACCCTAACCCT
AACCCTAACCCTAACCCTAACCCCTAACCCTAACCCTAAACCCTAAACCCTAACCCTAACCCTAACCCTA
ACCCTAACCCCAACCCCAACCCCAACCCCAACCCCAACCCCAACCCTAACCCCTAACCCTAACCCTAACC
CTACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCCTAACCCCTAACCCTAACCCTAACCCTA
ACCCTAACCCTAACCCTAACCCCTAACCCTAACCCTAACCCTAACCCTCGCGGTACCCTCAGCCGGCCCG
CCCGCCCGGGTCTGACCTGAGGAGAACTGTGCTCCGCCTTCAGAGTACCACCGAAATCTGTGCAGAGGAC
AACGCAGCTCCGCCCTCGCGGTGCTCTCCGGGTCTGTGCTGAGGAGAACGCAACTCCGCCGTTGCAAAGG

How to replace $N^{th}$ residue is quite a straightforward task. But that is a programming question and not the scope of this forum. Assuming that you have solved the part 1 problem and have a tab separated sorted file like this:

chromosome  position    residue
 1           79989           G
 1           100232          T
 3           341342          A

This script may not be the best but would work in a linux/*nix/Cygwin terminal, to replace the residues (ensure that you have gawk version >=4.0):

gawk -F "\t" '(FNR==1){x++} (x==1){a[$1][$2]=$3;next} (x==2){if($0~/>/){h=$0;sub(/^.*chromosome /,"",h);sub(/ .*/,"",h)} else{seq[h]=seq[h]$0}} END{for(i in a){s=0; for(j in a[i]){m=m substr(seq[i],s,j-1) a[i][j];s=j+1} m=m substr(seq[i],s); print ">Chr"i"\n"m}}' SNP_file Genome.fa | fold -w 60


Is an X ml dose of a drug at 50% bioavailability roughly equivalent to a 2X ml dose at 25% bioavailability?

All things being equal, does that mean an administration of a drug will be twice as potent if the bioavailability is doubled?

Bioavailability is initially taught, and sometimes reported as a proportion, $F$, the concentration in drug in plasma under a test condition (typically oral administration) over the concentration of of the same dose of the drug under a reference condition (typically IV administration).

In the simplest case, under zero order kinetics (the rates of all reactions that cause a change in concentration of the drug are independent of that drug's concentration), you can substitue $F\cdot D$, for a dose, where $F$ is the bioavailability and $D$ is the dose (see equation 2-16 in Goodman and Gilman's The Pharmacological Basis of Therapeutics, Chapter 2).

So, for your question, you can write down the state with equal plasma concentrations, $0.5\cdot D_1 = 0.25 \cdot D_2$, which reduces to $2D_1 = D_2$

Potency is a hairy term, defined in many different ways (some with more hand waving than others), but lets say for the purposes of this question that potency is the oral dose $D$ required to produce a measurable effect, $E$, and relative potency is the oral dose of formulation 1, $D_1$ required for a set effect, $E$, over the oral dose of formulation 2, $D_2$ for the same effect (modified from Goodman and Gilman Chapter 3). So, if the effect of your drug is directly proportional to its concentration in plasma ($E = kC$), then yes, the formulation with twice the bioavailability will be twice as potent.

I was going to write a long treatise on why this is not necessarily going to be the case, but since you were so specific about all things being equal, I'll just say this: bioavailability is often not reducible to a single $F$, which is why the FDA requires a lot of information on Bioavailability. This is for good reason, because kinetics are often not zero order, and even once we get to plasma concentration, the concentration term that drives efficacy can be $AUC$, $C_{max}$, time above a threshold, and sometimes even hard to correlate directly to plasma concentration at all. But, in the simplest case, all things being equal, your answer is yes.


Is it possible to affect a brain with electromagnetic waves?

One can use transcranial magnetic stimulation to modulate neural activity. This is effectively inducing a current in the tissue under a magnetic coil.


Fingerprints form in the womb at 22 weeks and after that, all they will do is expand as you grow. Therefore, it is possible that a fingerprint 22 weeks after conception could be used to identify a 50-year-old criminal.


1) Can cells survive without any of the different cytoskeletal components?

Yes, most certainly. At least for actin and microtubules (MTs) there are plenty of eukaryotic cell types that can survive without them. MTs can be disrupted by cold-shock (see for example here https://www.ncbi.nlm.nih.gov/pubmed/16505977). How well the cell survives depends on the type of cell, but the ability to survive without MTs can range from minutes to hours as far as I'm aware. Once the temperature goes back to normal, the MTs just grow back. Of course, the cells won't behave normally in the meantime, because many processes do depend on MTs. Actin can be disrupted using various drugs or genetic constructs, or they can be cut using femtosecond lasers (see for example https://www.ncbi.nlm.nih.gov/pubmed/28324605). Again, many processes are disrupted, particularly cell motility, but most cells can survive without actin for a while.

I'm not aware whether any eukaryotic cells exist that have no intermediate filaments or can survive at least for some time without them.

2) Could a cell function normally while lacking one type of cytoskeletal component?

First, to my awareness there is no eukaryotic cell without MTs or actin. We do commonly use actin and tubulin promoters for transgenes and assume that all cells will express them. So I'm taking this question hypothetically.

As with every hypothetical question, the answer then purely depends on the restrictions that you define. Can the cell possess arbitrary new proteins that currently don't exist? Then yes, definitely you could get eukaryotic cells with just MTs or just actin or just intermediate filaments. You just have to bend all the other things the cell does to fit with that filament type, and then enjoy arguing whether that's still a eukaryotic cell or not.

But I think actin would find it easier to take over the other filaments' jobs compared to the other way round.

MTs are large and rigid. They can't operate on scales below 25nm like actin can, and the individual tubulin dimers can't do anything useful until a tube of some minimal length has been formed out of many dimers. Intermediate filament monomers are pretty thin, but very long. Actin monomers are small and globular, and a supershort actin filament made of a handful of monomers can already function as a filament, branch out, form networks, pull on things etc. Actin-mediated endocytosis crucially depends on this (https://www.ncbi.nlm.nih.gov/pubmed/25675087 for example). It would be difficult to find workarounds for these small-scale functions of actin if MTs or IFs were to replace it. On the other hand, actin filaments can very easily be made into large, thick, rigid rods like microtubules. Many cell types do this constantly when they form filopodia. Actin meshworks can also provide similar mechanical support (both stable and flexible) as IF meshes. With minor shifts in the regulation of where, when and how to organise filaments, actin could probably take over the other cytoskeletons' functions. It would probably require a quite sophisticated regulatory system though to perform all the different functions at the same time in one cell.


The basic concept of the immune system is that it has to discriminate between self and foreign and that is only allowed to launch an immune reaction against something foreign. This is called immune tolerance which basically makes sure that all immune cells which are directed against the own organism are destroyed.

If these antibodies survive, they can attack the own body (and are hence called self immunoreactive) and cause damage. Self-immunoreativity is a reaction of the body against itself. Problems with the immune tolerance are called autoimmune diseases, examples would be  systemic lupus erythematosus, rheumatoid arthritis or type 1 diabetes.


Has any research lab done serious work to engineer new bacteria which assemble graphene wafers?

Surprisingly, the answer is yes. In 2012 Tanizawa et al published a paper titled Microorganism mediated synthesis of reduced graphene oxide films. The gist of it is that most of the steps (including the structuring of the graphene sheet) were carried out with chemical synthesis, but a final reduction step from graphene oxide to graphene was carried out using bacteria from a local river.

Probably not quite what you were thinking of, but I imagine this is the closest you'll get for right now.


Do trees have no set lifespan and
"quite"immortal?

There are certain annual(eg.peas) and biennial plants(eg.carrot) also which die at fixed times.

But for perennial plants :

From this

  Trees endure as long as they do basically because they're
  nonhierarchical organisms. In animals, all vital functions are
  controlled by the central nervous system, the guiding element of which
  is the brain. When the brain dies, so does the animal. By contrast,
  vital functions in trees are decentralized. A large part of the tree
  can die, and indeed routinely does die, without killing off the tree
  as a whole. Most of a mature tree is dead except for a few layers
  under the bark.....

  All trees die eventually, of course. Four thousand years is old
  compared to the life spans of gossamer creatures like ourselves, but
  in the context of geologic time it's the blink of an eye. As they get
  older trees become more susceptible to disease, pests, and other
  perils, and inevitably these take their toll.


How does your body ultimately recover from a cold?

Great question.
Rhino Virus
For the rhinovirus in particular, it is eradicated.
Integrase
However for some of the retroviruses and other virus that contain an enzyme called 'integrase', they actually integrate their DNA with yours. That way as your cells go about their business, they make the virus genes too. However, you have some white blood cells called CD8 T Cells that mark these 'compromised cells' for death.
Evading
Some viruses though can remain cleverly hidden and don't turn on their own genes in your genome until the immune response goes down, or you stop taking anti-retroviral drugs.  HIV is a great example of a virus you can also 'live' with but never actually eradicate. The medicines you take can kill all the circulating virus down to a non detectable level. However, when you stop taking your meds, the DNA integrated in your genome will start making the virus again, thus you will always 'live' and can never eradicate it.


Why do reptiles still move even after death?

In warm-blooded animals, our high metabolisms are a significant disadvantage when being decapitated. Just a few minutes without oxygen and a mammal's brain is caput—the result of a massive cascading cellular die-off. Not so with cold-blooded reptiles. Their slow metabolism sustains their internal organs for far longer than a mammals causing them to completely die far more slowly. Essentially, cutting off their heads only makes them "mostly dead".


What is the impact of selection on orthologous and paralogous genes? How would this impact differ in different regions of protein coding genes?

Exactly .
Paralogs and orthologs , both go under natural selection. But harmful mutations tend to have a less fatal effect if they happen to paralogs as there would  be a backup for the malfunctioning protein. In paralogs, if a bad mutation happens to a protein, the paralogous protein will compensate and help the organism maintain its function but in orthologs one mistake is enough to do harm because there are no other proteins to perform the function of the wild protein.

All the different members of the tubulin family of genes (and
proteins) are sufficiently similar in sequence to suggest a common
ancestral sequence. Thus all these sequences are considered to be
homologous. More specifically, sequences that presumably diverged as a
result of gene duplication (e.g., the α- and β-tubulin sequences) are
described as paralogous. Sequences that arose because of speciation
(e.g., the α-tubulin genes in different species) are described as
orthologous

Reference : Molecular Cell Biology of Lodish et al 8th edition page 325
Also see Campbell Biology 9th edition chapter 26 section 26-4


Can one use a hemocytometer on a compound upright microscope?

Yes it can. You will want to use a thin hemocytometer and the working distance of the objective (20x) needs to be long enough to focus both the cells under the cover glass and the grid under the hemocytometer. Because you are looking at it from the top it would be helpful probably to have some phase on the scope to increase your contrast so that you can more clearly see the grid.

Hemocytometers are most commonly used with inverted microscopes because inverted microscopes are the most convenient microscope for performing tissue culture, and 's a commonly used to count cells when passaging or setting up an experiment etc, as they allow you to view cells in a culture plate. Upright microscopes require that you make a slide.


This review 22 proteins in the NOD like human repetoire. It was published in 2013...

The families are broken down into 9 general groups according to their domain composition in Figure 1 from that review.  Most of them are not named "NOD".


How is transport of glucose into prokaryotic cells different from transport into eukaryotic cells?

In prokaryotes the glucose transporter is always present in the cell membrane; in cells whose glucose uptake is insulin-regulated the transporter is only present in the plama membrane when hormone levels are high.

GLUT4 is the isulin-regulated glucose transporter found in muscle and adipose tissue. When insulin levels are low the GLUT4 protein is in the membrane of small vesicles inside the cell. The appearance of insulin signals the fusion of these vesicles with the plasma membrane. In this way the number of GLUT4 molecules in the plasma membrane is increased, raising the capacity of the cell for glucose transport. GLUT4 transports glucose into the cell by facilitated diffusion.

More information about the GLUT family of glucose transporters can be found here.


Cross section through the right arm question

Based on the location of that cross section in the upper arm the vein in question appears to be the basilic vein. The basilic and cephalic veins are the largest veins (most of the time) in the upper arm. Here is a nice diagram from wikipedia that shows both. The cephalic vein is much more superficial than the basilic vein, as you can somewhat appreciate in the diagram below.

I think the label "brachial vein" is probably an honest case of mislabeling.

This is another figure that supports that vein in the image in the question as the basilic vein as well:

From this image (Gray's Anatomy), you can appreciate that the basilic vein is the large and deeper vein that runs near the brachial artery. In the case of many arteries and veins there are similar names, but that does not appear to be the case in this instance.

Clinical Correlate: In vascular and/or transplant surgery, when making an arteriovenous fistula for dialysis access (for kidney failure), there are a number of common routes of access. Two of the most common are the (1) brachiocephalic fistula, which is formed by surgically connecting the brachial artery to the cephalic vein, and (2) brachiobasilic fistula, which is created by connecting the brachial artery to the basilic vein. Some additional information and a picture can be found in this open access article from Maya et al entitled Outcomes of Brachiocephalic Fistulas, Transposed Brachiobasilic Fistulas, and Upper Arm Grafts .


Reverse transcriptase, as the name suggests, uses an RNA template to create a DNA transcript (i.e., complement). Once the DNA complement has been made, DNA polymerase is used because it uses a DNA template to produce a DNA complementary strand.

In your specific example, HIV contains a positive-stranded, RNA genome. The HIV RT can use either RNA or DNA templates to produce DNA complements, and this is how the single-stranded RNA genome is transcribed into double-stranded DNA, before integration.

To my knowledge, the RT enzymes sold commercially (for applications like RT-PCR) are typically a mix of an RT enzyme and a DNA polymerase, isolated from other retroviruses, such as murine leukemia virus. An important consideration for lab application is the production of cDNA that truly represents the RNA template of interest. Since RT enzymes typically lack a 3'->5' exonuclease activity, they are unable to "proof-read" the complement strand as it is being produced. In contrast, there are very efficient proof-reading DNA polymerase, and this is why a DNA polymerase (with high proof-reading ability) is used after first-strand synthesis by RT.


What are the essential criteria for sleep in living organisms?

I take it you did not even read the article. The article quite nicely expounds on this question. The whole idea is that sleep used to be considered as a human or psychological phenomenon that could only be studied by EEG, and clearly sleep was a phenomenon that goes deeper and wider in biology than just EEG waves. From the same article, just a little below:

She distilled a set of behavioral criteria to identify sleep without the EEG. A sleeping animal does not move around. It is harder to rouse than one that’s simply resting. It may take on a different pose than when awake, or it may seek out a specific location for sleep. Once awakened it behaves normally rather than sluggishly. And Tobler added a criterion of her own, drawn from her work with rats: A sleeping animal that has been disturbed will later sleep longer or more deeply than usual, a phenomenon called sleep homeostasis.

The keyword is behavioral criteria.
This is cited, I recommend a read-through.
I also recommend reading the rest of the article, it guides you through the status quo in sleep science which may further answer more of your questions. At the end, there is an exposition on animals without brains that seem to be sleeping. The hydra is one of them.


What might a supposed “tree enzyme” be — injected into a Morton Bay Fig tree?

So eventually I decided to email the City of Fremantle, who put me in contact with their Parks Department, who gave me the name of the company who had handled the tree, who replied with a most informative letter.
And the answer is…

Glutathione

Most animal biochemists, like me, will be more familiar with the importance of glutathione (reducing sulphydryl group highlighted in yellow, above) as a reducing agent in erythrocytes, the constituents of which are subject to oxidation damage.
What was wrong with the tree?

“…the figs in Kings Square… had quite elevated levels of heavy metals Cd, Cr, and metalloids Hg and As.
We traced this back to the colonial past, where in the 1830s – 1840s, when gold had been discovered south east of Fremantle, a battery operated (by the Crown) in Fremantle. In those days, gold was commonly lixiviated using mercury. Kings Square had a pit cut earlier for mining limestone. A good place to dispose of battery mullock is a pit.The earliest gold deposits were mafic ores, so often contained Cd and Cr.”

Why use glutathione to treat the trees?

“Firstly, it stimulates the jasmonate pathway, thereby alters transpiration and root growth.
Secondly, it assists in the isolation and immobilisation of heavy metals.
Thirdly, if assists in the breakdown of triazine herbicides by ring cleavage…”

And my correspondent kindly provided a review by Hossain et al. in the Journal of Botany, which elaborates on the second point.
And why the “tree enzyme” business?
This did not come from the company that handled the treatment, but from someone (unknown or nameless) who was handling the public relations, and who wished to provide reassurance that the treatment was ‘natural’:

“I guess in the world of snake oil, “enzymes” are benign, natural things, rather than usually ephemeral catalytic proteins.”


Why does alum work on blisters in the mouth/cold sores?

Alum has been shown to be effective in treating aphthous stomatitis (canker sores) and it is believed to be due to the compound's significant drying effect. Alum is known as an astringent - a chemical compound that tends to shrink or constrict body tissues. More information on alum's astringent properties are reported in this paper. As the infected tissue shrinks there is a decrease in pressure due to swelling and this less pressure around the nerves in the affected area. The exact mechanism is still under question.


Some species of Eupithecia perhaps. A type of moth, the larvae tend to resemble twigs. According to this relatively old text, Eupithecia miserulata is the most commonly distributed species in Texas, but I'm sure identifications stem largely from expertise and adult specimens, both of which I lack. The larvae for E. miserulata don't seem to visually match what you have, there.

In essence, though, it's a caterpillar that will turn into a moth.


Why does SDS-PAGE use for protein, and agarose use for nucleic acid?

You can use polyacrylamide gels for RNA and DNA, and this is the common way to examine shorter nucleic acids. Agarose gels can be used for larger nucleic acids like plasmids that are a few thousand base pairs long, polyacrylamide gels work better for shorter nucleic acids around a hundred nucleotides long.

You don't need SDS for nucleic acids, they already have a negative charge at the phosphate backbone. Polyacrylamide gels for nucleic acids also don't use a separate stacking gel like in SDS-PAGE, it is just one single gel.


How many polynucleotides are there in one molecule of DNA?

In general, it is right since with the term DNA you commonly refer to the double-stranded DNA. However, you need to be aware that DNA may exist in different forms.

Single-stranded DNA (ssDNA), for example, is composed of only one strand of DNA, so one chain of nucleotides or one polynucleotide molecule.

Double-stranded DNA (dsDNA) is the common form of DNA found in cells and it is composed of two polynucleotide molecules.

Triple-stranded DNA (tsDNA ?) also exist, which of course, is composed of 3 polynucleotide molecules.


Chemical methods to detect cell division

The most common indicator for the growth of any kind of cell (population) I know of is the amount of DNA in that cell. There are a number of (fluorescent) dyes that bind to DNA in a stoichiometric fashion and can therefore be used to determine the (relative) amount of DNA inside a cell (is hope that's what you mean with 'biochromatic indicator'). The most common dye used in this way is probably DAPI.

In order to determine which cells are dividing, you'll obviously need a device that can measure the fluorescence of each cell individually- so either a microscope or a flow cytometer. Because growing mammalian cells (it seems to me that's what you want to look at) multiply their full set of diploid chromosomes in the S-phase of the cell cycle, you can discriminate growing cells from others by their relative DNA amounts:

A non-growing cell has only the diploid chromosomes (1x relative DNA)
A growing cell will have either the doubled set of chromosomes (2x relative DNA) if it sompleteded S-phase or an intermediate amount (1-2x relative DNA) if it's currently in S-phase

Figure 1 of this (really old) paper also shows, how DNA amounts can indicate at which point of the cell cycle a cell is (which tells you if its growing) works.

A note on cell viability:

Staining any kind of cell with DAPI (or most other dyes that bind to DNA) will most likely kill it or at least act as a very strong mutagen. Based on your answer to my comment this should not be a problem.

While not really part of your question, you mentioned that you want to preserve cells using lyopreservation, which basically means drying them. You should consider, that mammalian cells will most likely not to survive this process (unlike plants and some invertebrates there are no mechanisms in mammalian cells to protect them against the water loss). Without sorting the live cells from the dead ones first, your measurements may detect cells that were dividing prior to the preservation.


How to set up a slow cooling on an AB Veriti thermal cycler?

If I recall correctly (from when I interned at ABI), you can't directly set this in the Veriti interface.  However, (again, I'm not 100% certain -- I couldn't find anything to confirm this after 30 minutes of googling,) the ramp rate percent refers to the percent of maximum ramp rate for the heating block.

According to the product website, the max heating block ramp rate is 5 °C/s while the max sample ramp rate is 4.25 °C/s, so you need a ramp rate between 2% and 2.4%.


In my mind, pipette and pipettor are generally* synonymous in the life sciences. Pipetman, which is actually a trademark, is also commonly used to refer to these instruments.

Gilson UK
That being said, there are some other things that you need to differentiate between. A pipette tip is the (usually plastic) thingy that goes on the end of the pipette, shown in the image above as clear white plastic on the left end. There are also serological pipettes

Argos Tech
and volumetric pipettes

Pro Lab Supply
together also referred to as transfer pipettes. These can be made of plastic or glass, and are used in conjunction with an electrical or mechanical pipettor, or a bulb (not your mouth!). Just to be confusing, sometimes lab personnel will refer to serological pipettes as just pipettes, even though they refer to the things pictured above in image 1 as pipettes as well.
Some people, such as SeRe above, distinguish between pipettes (the first image above) and pipettors, such as those used with serological pipettes:

Drummond
These are also known as Pipet-Aids or by other brand names.

However, in case I come across a Russian 'pipetka' that really means "pipettor", how to distinguish between the two? Maybe the terms are largely synonymous?

So yes, the two terms can be synonymous, so just be consistent, whichever you choose. I would stick with pipette unless it's clear from the text that the authors are transferring larger volumes than 1 ml, in which case they're probably using a pipettor in conjunction with a transfer pipette. If it's unclear, sticking with pipette should be good enough. If your readers are familiar with lab techniques, they'll understand what's going on.


PSI-BLAST is an iterative algorithm. Each cycle it uses a model (the position-specific scoring matrix, or PSSM) to search for sequences matching the model, next updates the model with the sequences found, and then runs the search again with the updated model. That P-value controls which of the sequences found in each iteration should be included in the new model (i.e. only include those sequences satisfying the P-value).

Regarding the pseudocounts, this is a value to be added to each column in the PSSM. The reason is to avoid zero count entries, which may give problems later. But as the help suggests:

  Pseduocount parameter. If zero is specified, then the parameter is automatically determined through a minimum length description principle (PMID 19088134). A value of 30 is suggested in order to obtain the approximate behavior before the minimum length principle was implemented.

It is probably OK to leave the default option unless you have some reason to change it.


What's the duration between the binding of adrenaline to β-AR and the first translated protein?

Things can certainly vary for different ligands and different levels of cascading but these are the reactions that you may consider.

Receptor activation
Nuclear translocation (lets assume it is just a part of the receptor. You can assume secondary messengers; it will add an extra step)
DNA-binding and Transcription activation
Transcription
Nuclear export of mRNA
Translation

Finally I guess what you really want is to know when steady state is reached. This will also depend on other factors such as:

Receptor deactivation rate
mRNA and protein degradation rates
Nuclear export of activated TF
Network architecture (some networks can speed up response times). This factor can be ignored and we can consider an open loop.

Phosphorylation reactions are generally much faster than transcription/translation/translocation rates and can also assumed to be equilibrium with dephosphorylation reactions.

Nuclear import rates are also dependent on cell volumes and for polarized cells like neurons it will be much higher. The average import rate is around 0.2 - 1.2 s-1 NPC-1 µM-1(cargo) [where NPC is number of Nuclear pore complexes which is again on an average 120 ] [1].
It can be, for ease, assumed to be ~0.02 min-1 [2].

In most modeling papers the transcription rate is assumed (based on experimental reports) to be 1 per min (Average polymerase speed of ~1000nt/min and gene length of 1000nt. This can vary with gene length)

Translation rates are somewhat trickier. The translation rate per ribosome translation elongation rate is ~5 codons/sec (15aa/sec)[3] or perhaps may even be lower — 3 - 9aa/s[4] ( [3] is a more recent finding). However, the overall translation rate will be dependent on number of ribosomes (Ribosomes can be assumed to be infinite unless it is some condition like stress or starvation. By no of ribosomes I meant polysomes per mRNA, which can also vary). Also, the protein synthesis rate will depend on length of mRNA. This is one parameter that can have a broad range of values (0.6-100 min-1 × mRNA).

You can set up mathematical model (based on reaction rate equations) and calculate the response times (Depending on parameters it can be 8-20 hours). Steady states can generally reach by 8 hours (based on my own experiment. But I used tetracycline to induce luciferase). Another experiment (unpublished) using IFNγ induction caused a peak in the reporter at ~12h. I am not linking all references (you can easily look up for these). Usually, for cell culture applications, there is some sort of unsaid rule to assume 12h as a general response time to persistent stimuli. Response times are also dependent on initial conditions.

Note: Response time means the time required to achieve steady state. This does not mean the delay between signal onset and protein synthesis. Other metric that is used generally is max-peaking time.


Sequencing inaccurate at the primer site

The very extremities of sequencing reads obtained by most if not all sequencing technologies are usually of lower quality, though more often so in the 5' region. You should disregard this data, or better yet design additional primers further away to encapsulate that region too if you desperately need it.

Below is a fairly typical output from FASTQC analysis of Illumina sequencing data. You can see how the quality is at its peak in the middle of the read (base index on the x axis. You'd likely see a similar thing for Sanger sequencing which is presumably what you're using.


What is the meaning of depth relation and EM in this excerpt?

EM is Electron Microscopy; the definition is found earlier in the passage in the normal form where the whole term is given followed by the abbreviation in quotes; you should look for this in the future.

  ...suited to connectomic approaches using electron microscopy (EM; Lacalli, 2009).

I'm not super familiar with invertebrate morphology, but from context in terms of "depth relation" they are talking about inferring directions of connectivity based on their locations in EM sections. If you find axon terminals from one cell type and dendrites from another at the same depth, you can infer they are likely connected. The passage explains that this doesn't work well in invertebrates that do not have a axon -> dendrite connectivity pattern. Dendrites synapse on other dendrites, and you can't easily tell what the direction of connectivity is from EM alone.


What dangers would the wireless transmission of power through microwaves pose to living organisms?

Whether wireless power transfer is safe depends on the type of power transfer. Inductive coupling is generally safe, but only works across small distances (i.e., millimeters to centimeters). The other option is far-field or radiative technology, where either visible light (from lasers) or microwaves are used. The latter has not been applied much, some uses have been found in space technology. Their safety in general will depend mainly on the power being transmitted. For example, a laser can be destructive if it is powerful enough.

I will focus on inductive coupling, because it is not only safe, it is commonplace. The prime example being cochlear implants. Cochlear implants are basically electrode arrays implanted in the inner ear to directly electrically stimulate the auditory nerve in deaf people where the hair cells have degenerated (or were never there). The implant is powered by an external battery worn behind the ear. It is coupled to a head-worn external coil that wirelessly transfers the power needed to drive the implant to an internal, surgically implanted coil. I'm not entirely sure about the exact numbers, but more than 100,000 folks around the globe have received one or two cochlear implants.

Cochlear implant showing the external and internal coil to transcranially transmit power to the implant.Source: Extreme Technology

Very similar technology is used in retinal implants. Retinal implants electrically stimulate the degenerate retina to [partly] restore vision in the blind. For example, the Argus II deploys an external coil mounted on a pair of glasses that wirelessly couples to a surgically implanted coil in the eye to power the implant. Being newer technology, there are not more than two hundred or so people implanted worldwide as we speak, but this number will definitely sore in the near future, all, or at least many relying on wireless power transfer.

Schematic of the Argus II retinal prosthesis showing the wireless link. Source: Ars Technica.

These examples may not be exhaustive. For example, transcranial magnetic stimulation of the brain is another example of wireless energy transfer across the skull, making use of magnetic induction to stimulate the cortex. However, these examples do show that medical bionics is already making use of wireless power transmission technology.


Do birds change their diet before migration?

Apparently, yes. This article underlines the changes in diet in semipalmated sandpiper before its 3000 km-long migration:

  Near the beginning of their journey, sandpipers stop at the Bay of Fundy on Canada's eastern coast to gorge on mud shrimp, 1-cm-long crustaceans loaded with omega-3 fatty acids. Over 2 weeks, the frantic feeding doubles each sandpiper's body mass [and i]t makes sandpipers' muscles use oxygen more efficiently, enhancing the birds' endurance.

The authors experimented the diet on a similar species to disentangle the effects of the different diet from other effects, for example due to hormonal changes:

  To isolate diet's role, Weber and colleagues took exercise and migration out of the equation. They turned to the bobwhite quail, an unrelated sedentary bird that doesn't migrate and seldom flies. For 6 weeks, the scientists fed 40 couch-potato quails a combination of omega-3 fatty acids from fish oil. To the researchers' surprise, the quail's oxidative capacity - their muscles' efficiency at using fuel - shot up 58% to 90%.

This paper reviews the effects of diet changes on the digestive trait of migratory birds; however, it's quite old (2001).

I couldn't find any indication on mallard feeding prior to migration, but these links can be a start for further research.


How does cancer of the larynx (laryngeal cancer) affect the respiratory system?

According to this website:

http://www.spirometry.guru/fvc.html

it causes difficulty with inhalation but exhalation is normal...

  "Typically the expiratory part of the F/V-loop is normal: the
  obstruction is pushed outwards by the force of the expiration."
  "During inspiration the obstruction is sucked into the trachea with
  partial obstruction and flattening of the inspiratory part of the
  flow-volume loop."

the exact symptoms of a laryngeal tumor depends on where it is located on the larynx... above the vocal cords, on the vocal cords, or below the vocal cords...

but more generally:

anatomy:
mouth/nose-->pharynx-->larynx-->trachea-->bronchi-->lungs

a tracheostomy may be necessary... basically the surgeon makes a connection between the skin outside the throat and the trachea... this bypasses the larynx (as well as pharynx and nose/mouth)...


Is there some branch of biology that deals with the entire organism?

I was thinking of Systems/Integrative/Predictive Biology reading your question. Studying the wikipedia entry it looks like a research approach with many problems trying to understand organisms from a biochemical perspective, identifying control circuits and macro-quantities like temperature and its relation to such biochemical control circuits. Basically you have to give up reductionism and use holistic/systemic perspectives and methods. While physics was successful with such research approaches (climate simulation, many particle systems,...), biology is lacking very accurate and proven mathematical theories to implement and test reasonable models of an organism, not surprising when biological systems have so many degrees of freedom compared to something like a ideal gas in physics. The wikipedia link doesn't show a lot of proven knowledge that this field/research approach has already created.


16s rRNA Sequencing From Gut Microbiome (stool)

In general, you extract DNA, then PCR out the 16rRNA coding regions and finally sequence them.
Here some links

http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/16s/

http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0068739

https://support.illumina.com/content/dam/illumina-marketing/documents/products/other/16s-metagenomics-faq-1270-2014-003.pdf


Action Potential Distribution On Synapses

I think you are really wondering how axonal morphology affects the voltage along the axon. The short answer to your question is that each synaptic terminal sees the same voltage because that voltage is generated "fresh" at each site. This has nothing to do with synaptic strength, which determines the amount of voltage deflection in the postsynaptic terminal but not in the presynaptic terminal.

The axon has two major properties that allow for this even activation across its branches. First, as @Armatus said, the axon is an active structure, meaning that the action potential (AP) regenerates as it travels along the axon. This means that there is essentially no decay of the voltage as the AP propagates.

Second, the axonal geometry appears to be carefully regulated. As you seem to have guessed, there has to be sufficient current flow to activate an action potential in the neighbouring patches of membrane or else there is a propagation failure and the AP stops. This is a problem at axonal branch points (see Box 1 in Debanne, 2004), where the diameters of daughter branches have to be correctly sized so that there is little or no extra electrical load. (For instance, if one branch stays the same size as the mother, the other branch is an extra load that will "steal" current and leave less current travelling down the mother branch). Recent work using voltage-sensitive dyes have shown that in mammalian neurons, in practice, propagation failures are rare (Foust et al, 2010). This suggests that there is fine regulation to ensure that the geometry is "just right." (Those "just right" rules are basically governed by cable theory, which I've previously described here.)

To your last question, yes, there is time-dependent decay of subthreshold potentials because the membrane is a capacitor (~1 uF / cm^2). I wouldn't call this "storage" exactly, but it does work just like a capacitor in a circuit. Many people think of the membrane as a capacitor and a resistor in parallel.

Debanne, D., 2004. Information processing in the axon. Nature Reviews Neuroscience 5, 304–316.

Foust, A., Popovic, M., Zecevic, D., McCormick, D.A., 2010. Action Potentials Initiate in the Axon Initial Segment and Propagate through Axon Collaterals Reliably in Cerebellar Purkinje Neurons. J. Neurosci. 30, 6891–6902.


Below is a figure showing the sequence of events during an action potential (AP). While the resting potential is characterized by an equilibrium, during an AP this balance is markedly 'disturbed'. The action potential is characterized by a specific timed series of events, namely the opening of Na+ channels in the initial depolarization phase, followed by an opening of K+ channels in the subsequent repolarization phase. During these phases, the Na+ and K+ currents are anything, but balanced.

Fig. 1. Series of events during an AP. source: Brigham Young University-Idaho


Why are GC-rich regions less condensed than GC-poor regions?

@ThoH.Ho and @Thawn. When banding chromosomes they are first treated with trypsin before staining with Giemsa dye. My understanding, and I have worked in the field of cytogenetics for quite a while, is that chromatin condensation due to gene content IS the reason for differential banding patterns. Gene rich/ high GC content areas, with more open chromatin, are more readily digested by the trypsin enzyme and therefore less protein is then present to stain with Giemsa. Vice versa for the gene poor/ low GC content regions. This is why non coding regions such as heterochromatin stain very dark and gene rich chromosomes such as chromosome 19 are pale. So although chromosomes may be at their most condensed stage of the cell cycle in pro metaphase, there is obviously still a relative difference between chromatin condensation of the GC rich and GC poor regions.


Why does regular bread yeast fail to thrive in pond water?

A few random thoughts.

I think that one problem here is that by using dried yeast you aren't really measuring growth or survival. Over a short time period much of the fermentation that you see probably has very little to do with viable cells. Dead cells in dried yeast act as permeable packages of enzymes and can promote fermentation.

Following on from that, it may be that components of the pond water can poison the fermentation carried out by the dead cells.

Thirdly, if you are using frothing as a measure of CO₂ production it is possible that there are components of the pond water that collapse that foam by removing stabilisers (probably protein).

Next, Saccharomyces isn't an obvious choice for use as an aquatic micro-organism since it is adapted/selected for growth in high sugar concentrations.

If I was trying to do this I think I would try to culture from the dried yeast under conditions where you do see activity, add lots more sugar (as if you were brewing), and look for actual production of yeast cells. Yeast settles out of suspension very easily so you might be able to pour off most of the liquid and add the cells to your pond. But I have no idea how well such cells will do in a pond.


The group tries to predict possible epitope sequences for the generation of antibodies. This includes also non-linear epitopes where not all amino acids of the epitope are line up behind each other, but come in close contact due to a 3D-structure. To train their algorithm, they use data, where the boundaries of the epitopes and the non-epitopes are known and clearly mapped.

The "Dataset and Preparation" section in this paper contains the following:

  In this article, we used several different datasets to train and
  benchmark COBEpro. These datasets were derived from several different
  previously published sources: BciPep (Saha et al., 2005), Pellequer
  (Pellequer et al., 1993) and HIV (Korber et al., 2003). The BciPep
  datasets consist of epitope/non-epitope sequence fragments. The
  Pellequer and HIV datasets consist of whole antigen proteins annotated
  with precise epitope boundaries.

The "positive epitope fragments" are known and verified ("positive") epitopes from these datasets in the training database. The fragment refers to restriction of length to 20 amino acids which they choose to apply. Shorter epitopes got amino acids added so they get 20 aa long, longer got truncated.


In percentage, how much is the human genome (DNA) similar to the mouse genome?

This question cannot be answered as simply as you put it, but it's not too much to elaborate on.

The order of the base pairs will be drastically different, but the same proteins and amino acids will be coded for in genes, just at different points along the DNA. For example, you may find the same sequence to code for a protein in a mouse as in a human, but they will not be found in the same place along the DNA code (although they will still be read and eventually produce the same protein).

http://www.nature.com/nature/journal/v420/n6915/full/nature01262.html
Additionally, this article shows that, if we take your question literally, "at the nucleotide level, approximately 40% of the human genome can be aligned to the mouse genome", that is, if human and mouse DNA was lined up side-by-side, and a percentage of identical match-ups was calculated.

However, taking a 'looser' approach, it is worth noting that about 5 percent of both of genomes consist of protein-coding genes (https://www.genome.gov/10001345), and the remaining 90%+ is non-coding. If we only count the protein-coding genes, the average similarity of genes between humans and mice in only protein-coding genes is 85%. The link above says that some are 99%, and some are 60% - there is a clear similarity here between humans and mice, albeit not 100% identical.

If you wish to know the explanation, simply it is because mice and humans both have a common ancestor (the last link also explains this) about 80 million years ago. Due to these similarities, and the striking similarities, scientists simulate genetic changes in mice that can occur to humans, and have used computers to analyse the similarities in mouse genome.

I hope this is understandable, if you need any clarification on terms, please ask :)


Why is the penicillin/ceftriaxone hypersensitivity test only done once?

Because developing a hypersensitivity takes time. If you get exposed to an allergen, the body first has to produce those antibodies that then get used in the hypersensitivity response at the second, or subsequent, exposure.

If you are talking about taking a second test just minutes after the first one, how would your body even "know" that this is a second exposure? Two exposures within minutes are not distinguishable from one exposure for the body.

Usually, an allergic reaction shows the second time a patient takes a full course of antibiotics. It does not show at the second oral dose or injection, which are way too close to the first dose to have already lead to the developing of a hypersensitivity.

So, why test you in the first place? Because you might have been exposed previously without remembering it - people misremember what medication they got during their childhood all the time, I imagine, and your doctor/nurse seem to just routinely do the test before giving these antibiotics.

Sources/Reading

Drug allergies

Update on the Management of Antibiotic Allergy


Why are certain baby (water)fowl yellow?

Wild ducklings, like these baby Mallard ducks, are in fact typically only partly yellow:

Photo by TheBrockenInaGlory via Wikimedia Commons, used under the CC-By-SA 3.0 license.

While I'm no expert, I would guess that the mottled yellow-brown coloring of the juveniles is, at least partially, protective coloration, just like the somewhat similar pattern on the adult female's feathers.  While it may appear conspicuous on open water, ducks in their natural habitat will often seek shelter among reeds and other vegetation, where the irregular pattern of light and shadow would create a very effective camouflage for the ducklings.

As for the all-yellow ducklings of domestic ducks, these presumably arose via elimination of the darker parts of the coloring as a result of selective breeding, perhaps as a side effect of artificial selection for the white adult plumage found in many domestic ducks today.

Specifically, according to a recent study of domestic duck genetics, it appears that the all-white plumage of domestic Pekin ducks is caused by a single recessive mutation to the MITF gene, which regulates melanin production.  The mutation, when homozygous, causes the normal melanin production pathway in the skin to be almost entirely shut off, so that the adult plumage is pure white regardless of what other plumage color genes the bird may be carrying (a fact apparently known for a long time from cross-breeding experiments, even though the specific mutation behind this effect was not determined until recently).

Apparently, however, the yellow base pigmentation in young ducklings is not affected by the MITF mutation, and thus appears even in individuals homozygous for it.  Presumably this is because the yellow color is produced via some other pathway, which is active in young ducks but gets shut off as they develop their adult plumage.  The brown pigmentation pattern overlaid on top of it in wild-type ducklings, however, is controlled by MITF, and thus fails to appear in ducklings with two copies of the mutated version of the gene, leaving their juvenile plumage pure yellow.

As far as I can tell, the specific reason why the yellow pigmentation in ducklings is not controlled by the MITF gene still remains unknown.  Or, if it is known, my Google search skills were not good enough to find it.


I think it's Scutigera coleoptrata.

Source of the image.


Why are trichromat cone cells unable to sense ultraviolet and infrared radiation?

The range of color perception in humans is primarily limited by the sensitivity of cone cells (specifically, the opsin proteins in cone cells) to various frequencies of light.  This sensitivity drops off at 700 nm on one side and 380 nm on the other, which is where infrared and ultraviolet begin, respectively.

Even with hypothetical infrared or ultraviolet cones, we wouldn't necessarily be able to perceive color much further beyond our current range anyway.  The various parts of the eye (cornea, lens, and the liquid inside) block both ultraviolet (starting around 400 nm) and infrared (starting maybe at 1400 nm) beyond certain wavelenghts.

http://en.wikipedia.org/wiki/Color_vision

Tetrachromaticity, at least in humans, does NOT confer an extended spectrum of color perception.  Tetrachromaticity results from a mutation on one of the light sensing proteins, changing its peak sensitivity by a few nanometers. So a tetrachromat can't see beyond the normal color spectrum, but they can probably distinguish shades of green and blue more precisely than trichromats. This has been an area of active scientific research recently; I think most scientists didn't think they existed.  Now studies suggest they're 2-50% of the population.  Humans with 5+ cone types are also hypothesized, and with the ubiquity of genome sequencing I imagine we'll be learning a lot more about that soon.

Other species have more diverse color perception, with ultraviolet being especially common in insects and birds. The mantis shrimp has an astounding 16 different kinds of photo receptors, plus a few specialized eyes for detecting polarized light. For a loving account of mantis shrimp, I recommend this comic. http://theoatmeal.com/comics/mantis_shrimp


What are the binding sites (or receptors) of cortisol?

The intracellular receptor for cortisol is called NR3C1.
http://www.uniprot.org/uniprot/P04150

To my knowledge, a direct (competitive) effect of anabolic steroids on the binding of cortisol to NR3C1 has never been proven. The anabolic effects can easily be explained by other targets. A good starting point for further reading might be this review:
https://www.ncbi.nlm.nih.gov/pubmed/22101547


Is the innate immune system capable of identifying all foreign antigens?

TL;DR the huge block of text:

The innate immune system only recognizes certain antigens, called PAMPs.
The activate immune system usually requires the immune system, but it can get around this in some cases.

You're on the right track.
Pathogen-associated molecular patterns (PAMPs)
Innate immune cells such as macrophages and denritic cells (DCs) only recognize certain pathogen-associated molecular patterns (PAMPs), and this occurs primarily through membrane-bound receptors called Toll-Like Receptors (TLRs). Diversity of PAMPs is extremely limited compared to the extraordinary diversity in recognition by the active immune system. However, they include many molecules and classes of molecules that are essential for certain pathogens, such as flagellin, lipopolysaccharide, and viral double-stranded RNA.
To answer some of your question right away, the immune system can't adapt, but it can recognize antigens that the body hasn't seen before, because the set of antigens it can recognize (the PAMPs) are dictated by the genes associated with Toll-Like Receptors and other "Pattern-Recognition Receptors".
Exception 1: T cell anergy
The major link between the innate and active immune systems that you mentioned is through the presentation of antigens to T helper cells in lymph nodes by DCs: DCs present antigens (digested parts of pathogens) to T helper cells through a process called antigen cross-presentation.
When this happens, the T helper cell is activated through a series of chemical exchanges between the DC and the T helper cell, with two that are important to mention here: 1) the T cell recognizes the antigen–MHC class II complex on the DC (called T cell stimulation), and 2) the T cell receives a signal (called co-stimulation). The first signal only requires cross-presentation and recognition by a T cell. But for the DC to release the co-stimulatory signal, Toll-Like Receptors (TLRs) on its surface need to have recognized a PAMP.
With these interactions (plus some more), the T cell will begin proliferating. However, immunology is very nuanced; you can probably find exceptions to every sentence I just wrote (I see a lot even while writing this). It turns out that a T cell can still be activated even without co-stimulation if its own stimulation is strong enough. This occurs through a process called T cell anergy. Activation of an anergic T cell—that is, one that was activated but did not receive a co-stimulation signal—has to do with the autocrine and paracrine nature of a signal called IL-2, which T cells normally produce only small amounts of but produce much more when fully stimulated.
Exception 2: B cells T-independent activation
But T cells are only half of the active immune system. It turns out that B cell activation follows similar rules, though not through DCs. B cell activation usually occurs with help from activated T helper cells (only one that recognizes the antigen the B cell is specific for). However, B cells can become activated without T cell help in two situations: an antigen binds to the B cell receptor and to a TLR, or 2) the B cell receptors become saturated with highly repetitive epitopes. Situation #2 technically occurs without help of the innate immune system.
So you're mostly correct that the active immune system requires innate immune system help, except that there are these two exceptions. And since immunology has so many exceptions, there are likely to be more.


What is this red and white striped wasp?

First of all, it isn't a wasp, but a true bug. After a long search in the databases about Hong-Kong's insects, I found that it is a red cotton stainer. Wikipedia says "Dysdercus cingulatus occurs in Sri Lanka, northeastern India, Bangladesh, Thailand, the Philippines, Sumatra, Borneo, Papua New Guinea and northern Australia".  iNaturalist.org has a number of photos, including some that match the one in the question, and confirms that the bug occurs in Hong Kong.

These insects are serious pests of cotton and there are several other species of them, some of which occur in North America:

  The cotton stainer is most common in southern Florida and in Cuba. It has been reported in Jamaica and Puerto Rico, Alabama, Georgia, and South Carolina. In view of its scarcity in north Florida, it must be presumed rare in the other three states mentioned. Dysdercus andreae ranges from southern Florida to most of the Antilles and Surinam. Dysdercus mimulus ranges from southern Florida, Texas, and Mexico into Central America and the West Indies. The fourth, undetermined species is known in the United States from two specimens taken at Key Largo Key and Homestead, Florida.

--University of Florida

Here are some pictures to compare with these one in the question:


Breakdown of energy expenditure at the level of a single cell

I was musing on this and did some strange googling, and have some ballpark figures  for a bunch of different organisms. It's far from a complete answer but it's at least a start, and all this won't fit in a comment.

DNA replication, I assumed, was a huge metabolic drain on the cell. Turns out that is far from the case. Many helicases are passive, requiring no ATP, and the amount of ATP-equivalent triphosphates to synthesize the entire genome is pretty small compared to the amount that gets used and recycled every day.

According to these guys humans go through their bodyweight in ATP every day, about 50% of which is actin turnover, and 30% is synthesis (60% or more in rapid bacteria). Proteins cost about 4-5 ATP per AA to break down and rebuild.

You're not going to get a really good general breakdown, I don't think, but in crop plants or E. coli there are numbers for this, sort of. A lot of them are based on indirect measurements of protein uptake/turnover and ATP cost per AA or BP. They're fascinating but insane and often contradictory.


Have there been any theories put forward as to the reasons behind Temperature-Dependant Sex Determination in reptiles?

Welcome to Biology StackExchange!

Environmental sex determination is tremendously interesting.
It looks like the most common explanation is that temperature-dependent sex determination (TSD) is the original form of sex determination, and genetic sex determination has evolved multiple times in different animal groups since then. Reptiles are a mish-mash of different mechanisms.

If TSD came first, then the real question is not why did it evolve, but why is it still around. And the answer is likely because it works well enough. I couldn't find a lot of evidence that females make varying choices for next temperature, so in "real life" it might mostly be that plenty of males and females are always born. There is also recent evidence that genes affect when the temperature has an effect, so again, temperature alone is unlikely to drive sex ratios.

As far as possible advantages of TSD there is no definitive explanation that has held up to testing. It is possible that ideal female development has slightly different requirements than male development, so nest location choice by the parent may act to produce more females if the current environment supports them more than males. For instance, it has been shown that having more female offspring when temperatures are higher results in larger females.

Sorry to not have a simple answer for you. The whole idea is fascinating, along with other environmental triggers to development, like worker ant larvae becoming a winged queen if given the right nutrition, or butterflies that add "eyespot" pigmentation to their wings in wet years with increased predators.


Could Junk DNA be used as a Turing Machine by nature?

Perhaps this question is whether the regions between genes sometimes known as 'junk DNA' has any function.

In the human genome, out of ~5 billion bases there are something like 20-30,000 genes which take up perhaps 10s of millions of base pairs, depending on how you count it. 1% of all human DNA is the common figure.

It is sometimes asked as if biologists commonly think of it as having no use, but in fact this is a researched topic, and few feel that it has no evolutionary or biological function at all.

Some of the most common uses for intergenic DNA in eukaryotes (bacteria are an entirely different topic with very different responses.

Transcriptional Regulation

Outside the coding sequences of the gene, there can be an extensive set of binding sities for proteins which regulate the gene.  In this paper in Figure 1 the celebrated regulatory sequence of ENDO16 is can be seen in Figure 1. As you can see for almoat 2000 bp there are numerous binding sites for many sorts of promotors and inhibitory factors, as well as factors which may splice the gene in various ways.

As I recall, ENDO16 only  turns on for a brief period in the development of the sea urchin and so its very tightly controlled, which means that its got a lot of regulatory elements upstream of it, controlling transcription. Its one of the most exhaustively studied genes ever and the believe they have most of it.  Other human genes ive seen perusing medical literature have seen 20kb are necessary to reproduce the regulation of a gene. Still all this might at best only triple the amount of DNA actively involved.

Centromeres and Telomeres
The physiology of the chromosomes have large regions as Deniz mentions are necessary for cell reproduction and for development.  In animals (like humans) the regions are devoid of transcribed genes and might be 10-15% of the genome length (I'm eyeballing this from the UCSC genome browser on chr21 - in some organisms like yeast the centromere can be just a few hundred base pairs.  So anyway we are getting somewhere now!
Non translated genes.
There are lots of pieces of DNA that might be copied into RNA and then do not function as templates for proteins.  some folks say there is a lot of this stuff.  The typical view is that there are a few thousand of these sorts of beasts known, and humans are currently thought to have about 1500 of them.  A small tweak in the number of genes, but they are there nonetheless.
Chromatin binding and organization sites
Although Centromeres are places where chromatin binds, the several families of proteins which bind DNA and wrap them into organized coiled coils thought to be like spools of telephone wire to form the Nucleosome which makes the chromosomes look like the little stick men you see in text books.  Chromatin can spool up just about any sort of DNA but seems to have a preference for regions which are at the ends of genes.  They can be modified by enzymes (acylated, methylated) to modulate their affinity for some classes of DNA sequence.  This is a hot topic of research.  The ability for RNA polymerase to find transcribe a gene is not good if its wound onto chromatin and though its not a precise binding like a transcription factor, chromatin binding and regulation must be affected greatly by changes in the distance between genes and the DNA sequences which surround a gene for thousands of base pairs, which is one of the main differences between species.

Of all biological systems (at least that I know of) this one accounts for the most bulk DNA sequence and is probably as related to the difference between different species as transcription factors and almost certainly is an older system of gene regulation, if you think about it.

Copy Number Variations and repetitive regions
just a side note, but small and very long repeat sequences can show up in the intergenic regions as well as inside a gene boundary to account for some of the differences between individuals.  they can be quite short or quite long.

Well hope this helps?


Is there an evolutionary advantage to crying when sad?

First, here is a link to an article that discussion the answer to your question:
Why Cry? Evolutionary Biologists Show Crying Can Strengthen Relationships

The original article to which it refers can be found here:
Emotional Tears as Biological Signals

To speculate a bit on Jez's question, crying in adults could be a result of our possible Neoteny. Crying in infant animals is extremely common as a way to elicit attention and sympathy from the mother. If we are neotenous apes, crying could be a left-over behavior that was seized by evolution, instead of being discarded.


Is a flower having 12 petals trimerous or tetramerous?

Suppose if a flower has 12 petals. Then 12 is a multiple of both 3 and 4. So which category of flower is it? Is it trimerous or tetramerous?

Merosity, in the context of your question, is the number of petals in the corolla.
Refer to "Gray's Botanical Textbook: Structural botany", on page 176, section 322:

"322. To designate the particular plan, such familiar terms of Latin derivation as binary, ternary, quaternary, quinary, unary, &c., are sometimes employed, denoting that the parts of the flower are in twos, threes, fours, fives, or sixes. More technical and precise terms, equivalent to these, are composed of the Greek numerals prefixed to the word meaning parts or members, as Alonomerous, for the case of a flower of one member of each ; Dimerous, of two, or on the plan of two members of each ; Trimerous, of three, or on the plan of three members ; Tetramerous, of four, or on the quaternary plan ; Pentamerous, of five, or on the quinary plan ; Ilexamerous,$^{[1]}$ of six, or on the plan of six members to each circle. But, in Monocotyledons, so-called hexamerous blossoms are really trimerous, the sixes being double sets of three.
[1] These may be shortly written 1-merous, 2-merous, 3-merous, and so on up to 10-merous (decamerous), 12-merous (dodecamerous), &c.".

Because counting is done using Greek cardinals a corolla with 12 petals is dodecamerous. One with 4 sets of 3 is trimerous, and one with 3 sets of 4 is tetramerous.


Whole Genome Sequencing and Chromosome Counts

I'm pretty sure that it relies on a reference genome. As in, since the original human genome sequencing, most of the techniques used today rely on that original construction (with modifications).

That's how people use it to detect copy number variations (CNVs) and single nucleotide polymorphisms (SNPs) with these sequencing techniques (and aneuploidy as well).

The reads from the sequencing run are compared to the reference genome and if statistically significant differences in the number of reads are seen, then they are noted as differences in the genome. If there is extra unmapped DNA, then it would likely just not know where to put it and call it "extra material".

So #1.


Plants without bacteria? is it theoretically possible?

This is the sort of question that should be considered from more than one perspective.  Since this is speculation, take it as a given that there is a lot of 'what if' here.

I doubt most animals and plants can do entirely without bacteria - as you say most of the essential nutrients come from bacteria, who fix nitrogen.  If only plants were left on earth, eventually the plants would use up all the nitrogen and they would have to find a way to fix more.

Can bacteria emerge from just a world of plants?  I don't think viruses arise spontaneously, but since genomes often have viruses embedded in them, over the course of a billion years or so, its possible since bacteria and viruses continue to be impressed upon our genomes.  Would it happen in time?  Most would be skeptical whether that timing could work out.

In practice it would be hard to create a world like this.  I would be interested to see whether you could sterilize the microorganisms off of seeds without killing the plant for instance.  If you're asking about a small sterile environment with only plants, you could do it by adding the nutrients the plants need and giving them sunlight.  Such self sustaining systems have been made with cyanobacteria and i'd be surprised if plants could not be included.  But these are closed systems and judged by limited amounts of time, so whether this is an answer to your question is not clear.  Here it looks like some water plants and fish have been done.  If there was a plant that created CO₂ at an adequate rate its possible.

At one time there were no animals at all.  Its thought that for a while there might have only been photosynthetic structures that lay in the water and soaked up the rays.  Its not clear whether as some say there were colony formations of cyanobacteria as we see today, or whether there may have been larger pre-cellular or proto-cellular structures.  But recovering the pre-cambrian configurations of genes from just plant genomes seems like a gambler's bet to me.


Can a cell start a mitosis if it lacks energy or molecules to complete it?

The short answer: no. First, let's get an understanding of the cell cycle control system, as there are some important molecules involved in this system that regulate mitosis. Think of the control system as a series of stoplights: as you mention, there is one stoplight at the G2 phase. There are two additional checkpoints: one at G1 and one in the M (mitotic) phase, just before Anaphase. Why before anaphase? At this stage in mitosis, the cell checks to determine if all of the kinetochores of the duplicated sister chromatids have microtubules attached to them. This is to ensure proper distribution of chromatids in anaphase.

Ok, so back to your question: what are some of the molecules involved, or what are some molecules that the cell might need before it proceeds?

Cyclins - these are proteins that are produced in the late S-G2 phases of Interphase. They activate cyclin dependent kinases (Cdks)
Cyclin Dependent Kinases - as the name suggests, these proteins (kinases) are dependent on cyclin in order to operate. The best known Cdk is called MPF, short for maturation promoting factor.

Throughout the cell cycle, these Cdks, together with their bound cyclins, are able to phosphorylate various proteins in the cell as it undergoes mitosis. For instance, the MPF would phosphorylate lamins, which are proteins on the nuclear envelope that can initiate degradation of the laminar matrix. This is essential in Prophase, when the nucleus is disassembling. There are many other things it can phosphorylate. For a more complete list, look under "Targets of MPF" in the above link for MPF. Take a look at this diagram, taken from Campbell's Biology (9th Ed):

There is one other molecule worth mentioning:

Growth factors - these are proteins specifically released by neighboring cells (relative to the cell that is preparing to undergo mitosis). These are crucial for mitosis to even initiate. A great example of a growth factor is PDGF, which stands for "Platelet Derived Growth Factor". These PDGFs are released by platelets at sites of injury, such as a cut on your knee. The PDGFs stimulate cell division and help your skin to reheal!

There are many other essential nutrients that cells require before they can initiate mitosis; not all have been listed here. Also, I know I didn't necessarily answer the "energy" part of your question, but I hope this helps for your first part.


How to define drug-resistant or -sensitive cell line when knowing the IC50 values?

From this post.

The IC50 is the concentration of inhibitor required to reduce the activity of a molecule/protein by one-half. It is the inverse of EC50. Usually inhibition curves looks sigmoidal so the IC50 is the middle point of the S curve. Here an example. (Note that the Y-axis can be pretty much anything, like enzyme activity and the X-axis is the concentration in a logarithmic scale).

Now for your actual question. The IC50 you got is by plotting a measure of the cell death rate vs the concentration of the drug. IC50 is expressed as a concentration so the higher the concentration of drug needed to kill the cell line the more resistant that cell line is. If the IC50 is very low then the concentration (or amount) of drug needed to kill the cell line is also very low which means the cell line is more sensitive.


Why do asparagine and glutamine have two different abbreviations?

The abbreviation Asx (B) is used if it is uncertain whether the amino acid at a given position in a peptide sequence is Asparagine or Aspartate. Similarly, Glx (Z) is used when there is uncertainty between Glutamine / Glutamate.

These two pairs of amino acids can be ambiguous in peptide sequences because Asp/Asn and Glu/Gln differs only by a terminal amide (-NH2) group in the side chain, and this amide group can be spontaneously lost from proteins by a deamidation reaction. When this occurs, asparagine is converted to aspartate/isoaspartate, and glutamine to glutamate/glutamate. These cannot be distinguished from "real" aspartate or glutamate by classic peptide sequencing, nor by mass spectrometry, since their mass is identical. Hence, protein sequences obtained directly from protein frequently contains Asx/Glx entries.


Besides X. morgani praedicta, are there any species whose existence was predicted before they were discovered?

I'd imagine there would be numerous examples of this. One species I can think of is Monocercomonoides sp., before the discovery of which we didn't know any examples of eukaryotes that had completely lost their mitochondria, or the derived forms of these organelles, such as hydrogenosomes and mitosomes. A prediction wasn't necessarily coined by any particular person like in your example, although there might be some papers somewhere that make such a prediction, I'm sure many people hypothesised that it was probably possible for eukaryotes to completely lose mitochondria if their iron-sulfur cluster biogenesis pathway was replaced by a cytosolic system that could fulfil the same role but we didn't know of any that had.

See paper: http://dx.doi.org/10.1016/j.cub.2016.03.053


Can cancer grow forever if supplied with unlimited resources?

Yes. The very first cells used to study cancer are still around (HeLa Immortal Cells - Named for the subject Henrietta Lacks) and are basically immortal as long as they're fed.

As for tumors, whether cancerous or not they most definitely can continue to grow until they become a serious medical issue (WARNING: GRAPHIC - 3 Largest Tumors Recorded). One of the largest recorded tumors was 300lbs (~140kg) in a woman's abdomen that sprouted off of an ovary. They had to operate with her laying on her side, otherwise it would have crushed her abdomen and killed her.

Not all forms of cancer are immortal or produce large tumors (the 300lb tumor was benign), but it's definitely within the realm of plausibility.


The process you propose is called 'stocking', and has been carried out for many different fish species for many years. The practice is, as you suggest, complicated, and more than a little contentious.

In the specific case of Atlantic salmon, Young et al. (2014) provide a non-technical overview of the conservation, population-genetic, and infectious-disease factors at play in stocking decisions. In general, fish raised in hatcheries are often wild-caught, which decreases the wild population, and once they are released, they sometimes have lower survival rates and reproductive success than truly-wild fish. If fish are raised in captivity for multiple generations, they can show evolutionary adaptations for captivity, and once released, captive-adapted fish can introduce harmful genes to the wild population. Similarly, captive-reared fish may be at an increased risk of communicable disease, and may introduce diseases to wild fish after their release.

A further complication from stocking is the impact of the stocked species on the local ecosystem. Many commonly-stocked species are non-native in the areas where they are released, and have negative impacts on the native species in that area. For example, brown trout have been introduced to many waterways in New Zealand, and they are predators of many native species, and compete for food with others. The New Zealand government has trialled an eradication of brown trout from some high-value conservation waterways in order to minimise the ecological damage caused by trout.


There was a paper by: Donald I. Williamson, published in the Proceedings of the National Academy of Science (PNAS) August 28, 2009 https://doi.org/10.1073/pnas.0908357106, and communicated by Lynn Margulis.

Lynn Margulis, as a member of the National Academy of Sciences, could publish papers in PNAS without adequate peer review. Members of the academy were afforded this honor, because they have achieved the highest levels of science, and supposedly, have few peers who can review their work.

Margulis was known for her work on the origin of mitochondria from the engulfment of prokaryotes, and also the Gaia hypothesis (that the Earth is itself, a living organism). That may have predisposed her to the ludicrous idea that butterflies were the result of some strange symbiosis from onycophorans (Velvet worms).

The whole thing was a huge embarrassment to PNAS, and Margulis. It would never have been published if it had been objectively peer reviewed, and was formally rebutted as wrong, and without any merit whatsoever. See: https://blogs.scientificamerican.com/observations/controversial-caterpillar-evolution-study-formally-rebutted/


This is a fruiticose lichen, meaning one with a bushy growth habit. They are common in my native state of Texas (USA), where they hang off of oak trees. Your photos look much like them. I have seen other examples in the rainforests of the Pacific Northwest, in both Oregon and Washington. I can't name the species.

In the upper left of your first photo, I see a thick, stem-like structure. This looks to me like the holdfast, the place the lichen attaches to the tree or other support.


Well to well variation in thermal cycler fluorescence?

There can be several reasons for variability and since you said that the machine has not been serviced for a long time, I guess that should be one main source of errors. Multichannel pipettes can also sometimes cause problems (based on personal experience) and it is mostly because the tips don't fit properly in all channels.

Try varying some parameter (for e.g. concentration of RNA) and see the effect on melting temperature; if the inter-replicate variability is not high enough to make the inter-sample difference insignificant then you can continue with your experiment. Take more number of replicates to minimize variance.

If the variability is very high then I guess you would need to get your machine repaired or use more sensitive equipments designed specifically for these kind of studies.


Voltage-gated Potassium channels in the action potential of cardiomyocyte?

Two main types of action potentials occur in the heart . One type, the fast response, occurs in normal atrial and ventricular myocytes and in the specialized conducting fibers (Purkinje fibers of the heart)and is divided into five phases. The rapid upstroke of the action potential is designated phase 0.The upstroke is followed by a brief period of partial, early repolarization (phase 1) and then by a plateau (phase 2) that persists for about 0.1 to 0.2 second. The membrane then repolarizes(phase 3) until the resting state of polarization (phase 4) is again attained (at point e). Final repolarization (phase 3) develops more slowly than depolarization (phase 0).

Genesis of the Upstroke (Phase 0)

The action potential amplitude (the potential change during phase 0) is dependent on [Na+ ]o.
The Na+ channels open very rapidly or activate (in about 0.1 msec), thereby resulting in an abrupt increase in gNa . However, once open, the Na+ channels inactivate (time course ˜1 to 2 msec), and gNa rapidly decreases.

Genesis of Early Repolarization (Phase 1)

In many cardiac cells that have a prominent plateau, phase 1 is an early, brief period of limited repolarization. This brief repolarization results in the notch between the end of the upstroke and the beginning of the plateau . Repolarization is brief because of activation of a transient outward current (ito ) carried mainly by K+ . Activation of K+ channels during phase 1 causes a brief efflux of K+ from the cell because the cell interior is positively charged and [K+ ]i greatly exceeds [K+ ]o . The cell is briefly and partially repolarized as a result of this transient efflux of K+ .The size of the phase 1 notch varies among cardiac cells.

Genesis of the Plateau (Phase 2)

During the action potential plateau, Ca++ enters myocardial cells through calcium channels During the flat portion of phase 2 , this influx of Ca++ is counterbalanced by the efflux of K+ . K+ exits through channels that conduct mainly the ito , iK , and iK1 currents. The ito current is responsible for phase 1, as described previously, but it is not completely inactivated until after phase 2 has expired.
During the plateau (phase 2) of the action potential, the concentration gradient for K+ across the cell membrane is virtually the same as it is during phase 4. However, Vm is now positive. Therefore, there is a large gradient that favors efflux of K+ from the cell. If gK were the same during the plateau as it is during phase 4, efflux of K+ during phase2 would greatly exceed the influx of Ca++ , and a sustained plateau could not be achieved. However, as Vm approaches and then attains positive values near the peak of the action potential upstroke, gK suddenly decreases . The diminished K+ current associated with the reduction in gK
prevents excessive loss of K+ from the cell during the plateau. This reduction in gK at both positive and low negative values of Vm is called inward rectification. Inward rectification is a characteristic of several K+ currents, including the iK1 current For these channels, large K+ currents flow at negative values of Vm (i.e., gK is large). However, when Vm is near 0 mV, or positive, as occurs during the plateau (phase 2), little or no K+ current flows (i.e., gK is low). Thus, the substantial gK that prevails during phase 4 of the cardiac action potential is largely due to the iK1 channels, but current through these channels is greatly diminished during the plateau.

Other K+ channels play a role in phase 2 of the action potential. These are characterized as delayed rectifier (iK ) channels. These K+ channels are closed during phase 4 and are activated very slowly by the potentials that prevail toward the end of phase 0. Hence, activation of these channels tends to increase gK very gradually during phase 2. These channels play only a minor role during phase 2, but they contribute to the process of final repolarization (phase 3), as described later. Two types of iK channels exist, depending on their rates of activation. The more slowly activating channel is designated the iKs channel, whereas the more rapidly activating channel is designated the iKr channel . The duration of the action potential in myocytes in various regions of the ventricular myocardium is determined in part by the relative distributions of these iKr and iKs channels.
Genesis of Final Repolarization (Phase 3)

The process of final repolarization (phase 3) starts at the end of phase 2, when efflux of K+ from the cardiac cell begins to exceed influx of Ca++ . As noted, at least three outward K+ currents (ito , iK , and iK1 ) contribute to the final repolarization (phase 3) of the cardiac cell.
Restoration of Ionic Concentrations (Phase 4)

The steady inward leak of Na+ that enters the cell rapidly during phase 0 and more slowly throughout the cardiac cycle would gradually depolarize the resting membrane voltage were it not for Na+ ,K+ -ATPase, which is located in the cell membrane. Similarly, most of the excess Ca++ ions that had entered the cell mainly during phase 2 are eliminated principally by a 3Na+ -1Ca++ antiporter, which exchanges 3 Na+ ions for 1 Ca++ ion. However, some of the Ca++ ions are eliminated by an ATP-driven Ca++ pump.


interpreting enhancer and promoter regions of a target gene

The NCBI nucleotide page does not have information on regulatory regions.

UCSC browser also displays regulatory regions mostly based on the ENCODE ChIP-Seq data. ENCODE project has MEF2 ChIP-Seq experiment for human cell lines. You can have a look at that. There is a MEF2 ChIP-seq experiment for mouse too.

You can analyse these data for a more detailed information.


Does TSH and Growth hormone have any role in menstruation?

TSH has an effect slightly similar to that of FSH and LH. This is found to be problematic in thyroid diorders. For example, in hypothyroidism the TSH overflow causes children to become fertile at an earlier stage, compared to the norm [1].

[1] Ann N Y Acad Sci. 1997 Jun 17;816:280-4. PMID: 9238278. http://www.ncbi.nlm.nih.gov/pubmed/9238278


Is there an enzyme for the transformation of the hydroxyl group?

It is possible to search for enzymes or a series of enzymes that will take similar reactants to similar products.

ReBIT allows you to query enzymes by your molecular structures of interest using their SMILES code. Unfortunately, a quick search using coumarin didn't produce any results but searches for phenol and phenolate gave some hits.

If you're seeking to do a more extensive search, I would suggest BRENDA. There you can search for reaction substrates and reaction products and even both. Both strategies may provide you with an enzyme that does the transformation chemistry that you're looking for.

Lastly there is always ENZYME, The Enzyme Data Bank. There you can search for chemical compounds. I did a search of coumarin and there are a few hits but they are for methyl-transferases and hydrolases. A more extensive search may give you a few leads.

Most of the concepts that I just suggested are explained in the following review: De novo biosynthetic pathways: rational design of microbial chemical factories.


If wolves (or foxes) are fitter than rabbits, why rabbits have not become extinct?

Simple: wolves and foxes are not fitter than rabbits. If they were, rabbits would be extinct.

This question is like asking "If Gary Kasparov is better than Michael Jordan, why hasn't he won a chess championship against him?"

And the answers are the same:
- "what do you mean, 'better'? Better how? At what?"
- "either way, they've never played in a chess championship against each other, so..."

"Fitter" in evolutionary theory means "better at something"; in general it will be "better at surviving", but better at surviving under what circumstances? There isn't a single "fit" or "fitter". Maybe you thought that wolves are better at surviving than rabbits because wolves kill rabbits and not vice-versa, but I could as easily argue that rabbits are better at surviving than wolves because rabbits would survive fine without wolves, but wolves would go extinct without rabbits (not completely true because they have other prey, but you get the idea). The truth is, as far as we can tell wolves and rabbits are equally good at surviving because both have survived.

So you can only talk about fitness if you focus on one specific circumstance to be fit in. But then there is the other implied idea in your question, which is that fitter species drive less-fit ones to extinction. This is true only if the species are in competition. Two species (or individuals, or anything) are in competition when if one species does badly, the other will do well as a result, and vice-versa. For example, maybe they eat the same food, and there is only so much to go around, so every additional bit of food A gets is less food for B, and vice-versa. In that case it is clear that one species being better at surviving than another is bad for the other species, and can (and, according to theory, will) drive it to extinction. Like fitness however two species can be in competition in some ways but not others. For example, two species might compete for food, but have a mutually-beneficial relationship with respect  to predators, where if there is more of A the predators will go for them which is good for B, and vice-versa.

Wolves and rabbits are clearly not competitors: things that lead to more wolves will indeed lead to fewer rabbits, but things that lead to more rabbits will also lead to more wolves. As such, even if one were measurably fitter than the other by some metric, it would not necessarily lead the other to extinction. For example rabbits being better against the cold than wolves could promote the existence of wolves in cold places, because a lot of them might freeze but the abundance of food might make it worth it.

This does involve an interesting ecological paradox, which is that according to theoretical models, if you have X species in perfect competition, all but one will eventually go extinct. There is a lot of research in how and why our world's massive biodiversity exists despite this. A big factor is that as I have pointed out, perfect competition is extremely rare in nature. Most species aren't competitors at all, and those that do compete usually don't compete on everything, everywhere and at all times. But when they do or close enough, yes, one should drive the other to extinction. Whether this is why the Neanderthals went extinct is another question


Help with identifying creature found in brazilian beach

Those are gooseneck barnacles possibly pelagic gooseneck barnacles (Lepas_anatifera).

For comparison:

A beautiful picture and description can be seen here.


What are the differences between G+ and G- bacteria?

I didn't know there were distinct differences between gram-positive and gram-negative bacteria when it came to quorum sensing, but it seems as though there are:

  In gram negative bacteria, acyl-homoserine lactone type molecules serve as the main signalling molecules while lipid, peptide, and amino acid based signalling molecules infrequently serve as signalling molecules. Furthermore, in gram-negative bacteria, there is one well conserved mechanism for controlling quorum response. Gram-positive bacteria, on the other hand, use peptides or modified peptides as the primary means of signaling; and also differing from gram-negative bacteria, there are several different mechanisms found within the class which are used to gain quorum responses.

Source.

In G+ bacteria, the two main quorum sensing mechanisms are apparently as follows:

Two-component signal transduction, in which the peptide signal works by binding to a sensor protein, histidine kinase, located in the cell membrane of the bacterium. The activation of the histidine kinase leads to phosphorylation of response-regulating protein, and interaction with another regulatory protein facilitates transcriptional activation.
Internalization, in which the signal molecules are transported into the responder cell to interact with intracellular effectors.

G- bacteria on the other hand, synthesize autoinducers, effector molecules that can diffuse freely through the cell membrane and trigger cell response when a certain concentration threshold is reached. I do not know how or if these differences are related to cell wall structure.

When it comes to endospore formation, all I know of the difference between the two is that this is by far most common in gram-positive bacteria.


Why do we see colours when we close our eyes and press our hands against them?

Yes, this is a biological phenomenon, not a physical one, because the phenomenon depends on a cellular response. Pressing your eyeballs (mechanically stimulating them) causes you to see phosphenes.

  What is the cause of this phenomenon?

The increased pressure in the eye causes activation and inhibition of cells in your retina (retinal ganglion cells). These cells are intermediates between the light-sensitive sensory neurons and the brain which interprets information into an image.

Quoting a well known study from 1989:

  Eyeball deformation [pressing] in total darkness led to an activation of the
  on-center ganglion cells, while the off-center ganglion cells were
  inhibited. The latency and strength of this activation or inhibition
  varied considerably between different neurons, but were fairly
  constant in the same neuron when the eyeball indentation was repeated
  after a pause of 1-3 min. The latency and strength of neuronal
  activation or inhibition seemed to be dependent mainly upon the neuron
  location relative to the point of eyeball indentation. Some on-center
  neurons also exhibited a short activation at "deformation off". [...] We assume that the activation of on-center and inhibition of off-center ganglion cells by eyeball deformation are caused by retinal stretching, which also leads to horizontal cell stretch. Stretching the horizontal cell membrane probably generates an increase in membrane sodium conductivity and a depolarization of the membrane potential [neuron firing]. This depolarization of the horizontal cell membrane potential is transmitted either directly or indirectly (via receptor synapses) from the horizontal to the bipolar cells.

This is a phenomenon at the retina (periphery), i.e. not in the brain region associated with vision processing (occipital lobe). You can achieve the same visual effect by vigorously sneezing or blowing your nose, stimulating the same cells electrically (by injecting current with electrodes) or magnetically (with coils that generates a local magnetic flux, whereby currents are locally induced). It is also possible to duplicate the effect by stimulating only the visual cortex, but it is likely due to the fact you are simply approximately replicating the retinal firing patterns coming to the brain via the visual nerve.