Why is it unlikely that bathroom smells can pose health risks?

Mostly, what you're smelling are volatile small molecules: stuff like butyrate, indole, mercaptans, hydrogen sulfide, etc. These molecules are thousands of times smaller than even the smallest pathogens, being measured in Angstrom vs. nanometer scales. Pathogens are just too large to be actually volatile, in the sense of freely escaping into the air. And fortunately, these volatile organics are not nearly as reactive as something like chlorine gas. (If they were, imagine the damage they would do, at a much higher concentration, to the person they were just inside.)

Now, if someone had literally just projectile-vomited (or if excreta were churned around, e.g., by flushing), it's possible that a very small pathogen like norovirus could spray outwards in an aerosol. Since norovirus has a very small infectious dose (on the orders of tens of viral particles) this could be enough to make you sick, and indeed, aerosols have been implicated in norovirus transmission, though it's not that common. But the smell would remain long after any viral particles in aerosols had settled down onto surfaces.


Is the water-splitting enzyme a component of photosystem II?

The name of the protein (actually, three proteins) you are referring to is Oxygen-evolving Complex.

And yes, it is part of Photosystem II.

According to Lodish (2002):

  An Oxygen-Evolving Complex in PSII Regenerates P680: The splitting of H2O, which provides the electrons for reduction of P680+, is catalyzed by a three-protein complex, the oxygen-evolving complex, located on the luminal surface of the thylakoid membrane. The oxygen-evolving complex contains four manganese (Mn) ions as well as bound Cl- and Ca2+ ions (see Figure 16-44); this is one of the very few cases in which Mn plays a role in a biological system.

You can see the complex in this diagram of PSII, also from Lodish:

Figure 16-44: In a reaction center, two integral proteins, D1 and D2, bind the special-pair chlorophylls (P680), two other chlorophylls (Chl), two pheophytins (Pheo), one Fe atom, and two quinones (QA and QB). All of these are used for electron transport following light absorption by an associated lightharvesting complex (see Figure 16-42). Three extrinsic proteins (33, 23, and 17 kDa) comprise the oxygen-evolving complex; they bind the four Mn2+ ions and the Ca2+ and Cl− ions that function in the splitting of H2O, and they maintain the environment essential for high rates of O2 evolution.

As you can see, all proteins coloured green in the image above are part of PSII. However, since the oxygen-evolving complex is made of extrinsic proteins, it can be easily separated from the rest of PSII:

  The Mn ions together with the three extrinsic proteins can be removed from the reaction center by treatment with solutions of concentrated salts; this abolishes O2 formation but does not affect light absorption or the initial stages of electron transport.

Source:

Lodish, H. (2002). Molecular cell biology. 4th ed. New York, N.Y.: Freeman.


Why should collected blood from patients be analyzed as soon as possible?

Biological samples, including whole blood, are not at equilibrium. Biological processes, e.g., cellular metabolism, continue. Cells interact with their environment and a tube is not the same thing as the human vascular system. For one, in humans, on average, the entire volume of blood recirculates once every minute (see Costanzo Physiology Ch 4). Recirculation, with the associated access to nutrients, waste drop off, and exposure to various different compartments doesn't happen in a specimen tube. Nutrients are consumed, waste collects, cellular stress occurs, intracellular components leak out, cellular morphology changes... You can slow this down by putting samples on ice and collecting blood in a tube with components that preserve the sample for the specific test. There's a nice discussion of this in Lange's Guide to Diagnostic Tests, Chapter 1.

Given ongoing biological process in a very different environment, you can understand how interpretation of a particular test result depends on consistent collection and storage methods. Different tests are going to be more or less sensitive to time since collection and storage methods. There's a good deal of data on this for whole blood in this review.


Cysteine deficiencies are possible, and one cause is the genetic disorder homocystinuria. Cysteine can be produced from methionine through a homocysteine intermediate, and defective genes for the enzymes involved can prevent proper cysteine production and cause a buildup of homocysteine. Patients have to eat a very carefully controlled diet with very low amounts of protein. This prevents homocysteine buildup by avoiding methionine exposure, but also requires that the patient take vitamin B6 and  B12 supplements and betaine. They might need to take cysteine supplements as well. The symptoms affect many organ systems, including the brain, nerves, and blood vessels, with about 25% of patients dying due to blood clots by age 30.


Software to model and analyse protein–ligand interactions

I don't know precisely what you mean by "analyze", which could be anything from simply "view" or "measure distances", to evaluating an energy function on a crystal structure or molecular dynamics simulation, to prediction of binding sites de novo. The tools are different for each case, though some can do several things.

For simply viewing, measuring distances, and creating "pretty pictures" like the ones you included with the question, PyMOL and UCSF Chimera are the most popular tools. Chimera is highly scriptable and can perform molecular dynamics simulations (i.e. simulate movement of atoms based on an energy function), though its capability in this regard is somewhat limited. The NAMD/VMD software suite (which was used in the study cited in the question) is more full-featured, as is CHARMM (the latter of which is also the name of an energy function). For prediction of binding sites de novo (without a bound experimental structure), i.e. "docking", there are DOCK and AutoDock (both with long academic histories) as well as more industry-oriented ones like Glide.

Be careful though what you're getting into — while simply viewing structures and making geometric statements by direct observation is well within reach of the average biochemist with reasonable knowledge of protein structure (provided you trust the lab that solved the structure in the first place!), simulation of proteins using energy functions requires considerable computational expertise, though the "black box" nature of some software glosses over this. It may be relatively easy to run a simulation using questionably appropriate parameters, but the adage "garbage in garbage out" applies very much here. This is somewhat true with docking as well.


How does rho-dependent termination occur?

There is no dichotomy in the two sources you have described. The text book you linked to says, exactly (emphasis added):

  Rho appears to bind to a stretch of 72 nucleotides near the 3'-end of the nascent RNA...

It doesn't say at the 3'-end, which is obviously impossible since the 3'-end forms a double-stranded hybrid within the transcription bubble.
Rho is not loaded at the 5'-end of RNA, either, but rather binds internally at cytidine-rich Rho utilization (rut) sites, which will be somewhere 5' of the actual point of transcription termination. As you mentioned, there is a lot of uncertainty in the process and, while a lot is known about rut sites, as far as I can tell there is no consensus sequence, thus making it difficult to systematically identify rut sites throughout the genome. I have found papers which identify rut sites in the 5'-UTR (1) as well as within the 3'-UTR, intercistronic regions and coding sequences (2, 3, 4).

Mechanism of internal Rho loading:

Koslover DJ, Fazal FM, Mooney RA, Landick R, Block SM. 2012. Binding and Translocation of Termination Factor Rho Studied at the Single-Molecule Level. J Mol Biol 423:664-676


How to recover all protein ses into refseq database

As with most things, there are multiple ways to do this. Here are two of them:

Download from the NCBI Assembly portal

Go to https://www.ncbi.nlm.nih.gov/assembly/ and search for 'Viruses[Organism]'. For our purposes, I am going to restrict this search to Virus assemblies that are latest RefSeq and reference genomes. The query for this will be: "Viruses"[Organism] AND "latest refseq"[filter] AND "reference genome"[filter]. It will return 46 results.
To download the protein FASTA sequences for all of these, click on the big blue Download Assemblies button, choose RefSeq as source and Protein FASTA as File Type.
Click the Download button and a tarball with FASTA files - one for each assembly - will be created for you to download. You will then have to combine them all into a single file.

Download using wget

Go to ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/viral and download the assembly_summary.txt file. This is a tab-delimited file with information about every RefSeq viral assembly located in that FTP path. Column 20 has the FTP path for the assembly which you can parse out and use wget to download the protein FASTA file for each assembly, followed by combining them into a single gzipped file as shown below:

## download the assembly_summary.txt file
wget ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/viral/assembly_summary.txt
## download the protein FASTA files
grep -v '^#' assembly_summary.txt \
    | cut -f20 \
    | while read -r url ; do wget $url/*_protein.faa.gz ; done
## combine all files into a single one
zcat *_protein.faa.gz | gzip > all_viral_proteins.faa.gz


Autophagy is a cellular process that is occurring all the time, but it can be elevated during times of need (see below).

In autophagy, cargo (can be anything - mostly macromolecules but also bacteria/viruses etc) is taken up by a lipid membrane which folds on itself to form an autophagosome, which is like a vesicle but have markers on it that makes it specialized in carrying out autophagy. These autophagosomes are then transported to, and merge with, lysosomes, releasing the cargo into the lysosome to be degraded. The broken down materials are then released back into the cytosol, where other processes can make use of them. That is the "some kind of recycling" you are referring to.

There are two types of autophagy - selective and general. In selective autophagy, receptors on the membrane of the autophagosome specifically selects for ligands (e.g. p62, ndp52 selects for ubiquinylated substrates, which usually marks molecules for degradation). In general autophagy, the uptake into the autophagosome is random.

So, you can think of general autophagy as maintaining a basic level of turnover - to ensure everything in the cell is not worn out; and selective autophagy as a response to specific ligands that needs to be degraded.

By this logic, autophagy activity increases during infection because those infectious agents, once gaining entry into the cell (either through phagocytosis or by forced entry), will need the autophagy machinery to transport it to the lysosome to be degraded. Interestingly, some bacteria actualy hi-jacks this process to ensure its survival in the cell. Here's a good review to get you started if you are interested.

Note that the proteasome also recycles macromolecules, although the things it can recycle is limited by size.


Looks like Pseudorhiza haeckeli. Based on cross motif, and long tail. Grows over a metre across. There is a photo at https://www.abc.net.au/science/photos/2012/01/11/3406019.htm?xml=3406019.mediarss.xml#bigpicturepos
but dont copy it here - copyright.


Have any mutations or genetic loci been associated with exceptional longevity in humans?

It looks like you have uncovered the majority of the corpus of molecular genetics related to aging.  There is a follow up analysis just published this year by Sebastiani et al.  Pubmed has a feature that you can look at the publications that reference the paper you are looking at, and there are only reviews.  Nobody else seems to have done another yet.

You are probably right to feel that the power of the study is not great.  The researchers did try though. The Centenarians have long lived relatives and the controls had both parents die before they were 73.  Although the controls were 68 y.o. and older.  Yes not great.  The controls are very difficult because you don't want people who would die from heart attacks, hypertension and all sorts of things that would color the background.  Its a hard study to do.

No single gene will convey a phenotype like longevity.  Its basically impossible as the advantages would propogate through the population v quickly.  We could talk about how this trait is post-reproductive and about the grandmother effect, but I'm setting that aside for now.

The lack of statistical power of the study is also hampered because a mere 800 centenarians probably reflects dozens of different combinations of longevity groups.  (this is another reason all of these people are of specific european ancestry - to keep the number of variations in combinations down).  There are 281 significant mutations they found.   APOE is by far the most significant (fig1) but given the situation, just focusing on that one is not enough.

For example, even in flies it looks like the sir2-1 gene is not a single mutant anti aging phenotype.  When they cross the mutant strain with wildtype, the sir2.1 mutants live 15% longer.  Its at least one other mutation they had not detected in that caused a 50% longevity bump in the mutants.  Its probable that if there were 5 other important mutations, that the average crossover has one or more of these mutations with it too.

In order to try to understand how these loci might work together to expand life span, they created clusters of these SNPs (interestingly half of them are in genes which is relatively rare).  these clusters of genes look like they affect the lifespan together.  the paper is open and all the 281 genes are downloadable, each one of them has a known biological property you can look at.  how they fit together is still to be determined, but their clusters might point the way for now.


Why do we blink instead of winking each eye independently?

Looking at it completely in terms of evolutionary pressure:

1.1 The whole idea of binocular vision for humans, (and some other species) is depth perception. If you suggest continuous, alternate winking, the cognition of the individual would be seriously affected.
The 'wink as needed' mechanism (assuming all other visual processes are as they have evolved today) would be like continuously alternating between a pair of binoculars and a telescope while still trying to move forward.

1.2 If you are suggesting that there would still be an evolutionary pressure for winking, then its very likely that the evolutionary pressure for coordinated motion/ efficient cognition acting together with the evolutionary pressure for depth perception would be much higher as compared to it. (This would especially be true if eye-brain coordination evolved before the blinking mechanism, as is seen to be the case, which explains your point on 'how we are rather than how we got here'. Obviously fish have evolved some eye-brain coordination, but don't blink)

This link explains evolutionary pressure for depth perception/stereopsis to an extent
https://en.wikipedia.org/wiki/Depth_perception#Survival

2.1 As for the chameleon, the winking/ eye rolling mechanism might be very closely linked to the evolution of chameleon vision. It is seen as the link for studying evolution of binocular vision and stereopsis(depth perception) from monocular vision.

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


In what ways, if any, does administration of rapamycin *not* mimic calorie restriction?

Rapamycin specifically inhibits the mTOR pathway (mTOR = mammalian target of rapamycin), which has numerous downstream functions including protein biogenesis, regulation of cell cycle, immune function and apoptosis. The upstream effectors of mTOR include growth factors and amino acid availability, so you can certainly see that the lifespan enhancing effects of caloric restriction will be (at least in part) mediated by the mTOR pathway.

But there are key differences. mTOR also receives signals relating to DNA damage and inflammatory changes (to name just 2) that are essential for healthy survival. So any direct inhibition of this pathway will affect all the functions - I can't find the reference now, but I have definitel read in one of the numerous rodent studies that rapamycin treated mice have reduced immune function (i.e. the lifespan increased effects can only be seen in a controlled lab environment - in the wild mTOR-inhibition to this degree would be a disadvantage).

I think therefore it is fair to say that the effects of caloric restriction on longevity are mediated by mTOR, but administration of rapamycin is not an equivalent treatment.

Update

Really great review came out last month (http://www.ncbi.nlm.nih.gov/pubmed/22500797) - I recommend you give that a skim if you want detail!


Why can nervous inflammation radiate symmetrically in the limbs?

Padua et al. (1998) did find that 87% of followed patients developed bilateral CTS (i.e., carpal tunnel syndrome in both hands).

Most patients that develop unilateral symptoms, eventually have the symptoms spread to the contralateral (opposite) arm.

Bagatur & Zorer (2011) found that 59% of patients they followed reported bilateral symptoms initially, while 73% of remaining patients had symptoms eventually develop in the contralateral arm (even after receiving surgery on the first!)

So why? From what I could gather, we don't really know. From Bagatur & Zorer (2011):

  we assume that bilaterality may be time-dependent... [but] a definite conclusion could not be drawn.

However, research regarding "double crush syndrome" suggests that perhaps issues closer to the cervical spinal cord may play some role:

Pierre-Jerome & Bekkelund (2003) found that cervical intervertebral foramina were narrower in observed patients and affected nerve roots.

Although their research provided evidence for ipsilateral double crush symptoms, their study provides credence to the fact that more cervically-oriented issues (often which should show up bilaterally) could lead to CTS symptoms.

Not the greatest of answers, but a thorough search really didin;t turn up anything more recent or helpful. I'll update if I find additional info.

Citations

Bagatur, A. E., & Zorer, G. (2001). The carpal tunnel syndrome is a bilateral disorder. Bone & Joint Journal, 83(5), 655-658.
Padua, L., Padua, R., Nazzaro, M., & Tonali, P. (1998). Incidence of bilateral symptoms in carpal tunnel syndrome. The Journal of Hand Surgery: British & European Volume, 23(5), 603-606.
Pierre-Jerome, C., Bekkelund, S. I., Pierre-Jerome, C., & Bekkelund, S. I. (2003). Magnetic resonance assessment of the double-crush phenomenon in patients with carpal tunnel syndrome: a bilateral quantitative study. Scandinavian journal of plastic and reconstructive surgery and hand surgery, 37(1), 46-53.


Amylase is an enzyme that breaks down starches to simpler sugars. Only living organisms can produce amylase. Animals produce only alpha-amylase. Plants, bacteria, and fungi produce both beta- and alpha- amylases. Like all proteins, the presence of amylase in food depends on if it is permanently denatured by high enough temperatures or extremes in pH. Interestingly, amylases can be classified into high/intermediate/low thermostability groups, depending on whether they become inactivated at a certain temperature. Taking this into consideration, saliva would definitely have alpha-amylase. Bread and biscuits may have alpha or beta amylase (depending on baking temperatures/pH, if amylase was added at all, and if it comes from a grain). Of the rest of your list, banana, corn, milk, and sweet potato would have amylase. Honey (not listed) would also have it. Tomato seems to amylase activity as well. For ketchup, it seems to be an added ingredient to speed processing.

Sources:

http://www.gmo-compass.org/eng/database/enzymes/80.amylase.html
http://www.lallemand.com/BakerYeastNA/eng/PDFs/LBU%20PDF%20FILES/2_7SOFT.PDF
http://www.ehow.com/info_12013063_plants-contain-amylase.html
http://www.ajofai.info/Abstract/Detection%20of%20amylase%20activity%20from%20vegetables%20and%20fruit%20in%20an%20undergraduate%20classroom.pdf


How is the transcription direction of RNA polymerase determined?

Transcription always proceeds in the direction 5' (5-prime) to 3' (3-prime) on the coding strand of DNA. Binding of both transcription factors and RNA polymerase to DNA depends on sequence motifs in the DNA. Transcription always happens in the same direction with respect to the chemical structure of the coding DNA strand, while the transcription direction with respect to the structure of the chromosome depends on which strand the coding sequence is found on (and thus which strand is defined as the coding strand for that gene).


The birds in question appear to be fledgling eared doves, which belong to the species Zenaida auriculata. The beak color, eye markings, and overall feather coloration were most indicative when IDing.

Here's a few images of what the doves may look like once matured:


Evolution, self organization and neuroscience

I don't fully understand your question. I hope the following will help a bit.

I'd like to pinpoint what seems to me to be one important mistake in your text. Reading you we have the feeling that selection acts on wires so to select the best combination. If this is what you meant, then it is obviously wrong. The thing is that the change that get inherited are alleles. An allele is a variant of a gene. For example: gene codes for eyes color. A bi-allelic gene has an allele which codes for blue eyes while the other codes for brown eyes. Assuming that there is genetic variance underlying the wire connection variance in the population, then yes selection will select for the best genetic variant. This does not necessarily mean that this best genetic variant is the most optimal possible to imagine solution. The most optimal allele might have never been created just because of the randomness nature of mutations.

EDIT:

To answer:

  Do natural selection always bring a particular phenotypic (loosly speaking, phenotype = morphological) trait to its optimal state?

No! It does not.

The main reason is that the genetic variant coding for this optimal trait does not necessarily exist because of the randomness of mutational process. Also, because of the metabolic pathway bringing some variance to a trait, it is often very hard to even imagine a  mutation that would allow creating a new, more optimal, phenotypic variant. So indeed developmental biology has to be taken in account to.
Because in absence of genetic drift (infinite population), selection can only bring genotypes uphill in the fitness landscape. If a very high peak exist somewhere in the fitness landscape but in order to reach such peak, 10 mutations are needed were all of them in any other genetic background are deleterious (correspond to valleys in fitness landscape), then the optimal high will probably never be reached (except if all 10 mutations appear suddenly in the same individual).
Because selection might be weaker than genetic drift. Also, different subpopulations might be in different environments were different traits correspond to optimal traits and because of migration (gene flow) between subpopulations, it is possible that no optimal phenotypic trait can be ever seen although all the genotypic variance exist.
The seemingly most optimal trait might actually not be really optimal. For example: Peripheral vision might be limited by the brain rather than by the eye because it would be an important energy cost for the brain to process more information, a cost that might outweight the benefit of having a better peripheral vision.


How does the immune system recognize pathogens?

Pathogens will often have non-peptide antigens, peptide antigens, and pathogen-associated molecular patterns that are recognized by innate and adaptive immunity mechanisms. Useful bacteria are not differentiated, and often sit beyond the grasp of our immune system, or have mechanisms to escape an immune response. When contacted they do, however, produce an immune response and due to their location, this often involves mucosal immunity:

This portion of the immune system varies greatly in response to the systemic immune response because it is constantly stimulated, and in a way trained, by the presence of all microbes, such as gut flora. As a result, it often resolves infection quickly with low severity, and little lasting tissue damage. Keep in mind that self cells have mechanisms which desensitize them to autoreactivity with immunity. Microbes don't share these same mechanisms, but can evade or escape the immune response through their own methods. But by no means are microbes of any sort, for the average immune system, disregarded.

Unfortunately, to respond more specifically would go into textbook chapters of material so to that end I'm going to cut the explanation here, and recommend you do some research of your own.


Depends if your talking about interstitial fluid or lymph:

As per starling forces: the oncotic pressure of the late capillary plus hydrostatic pressure of interstitial space, would be higher than oncotic pressure of interstitium [though I dunno why since intertitial GAGs are very water hungry and they are responsible for the negative (hydrostatic?) pressures found in interstitium... Read lots of articles, still makes no sense to me] and hydrostatic pressure of the capillary... Thus there would be a net influx of interstitial fluid in the very ending part of the capillary, toward the venous side...

I say interstitial fluid, because it's not lymph yet since the interstitial fluid hasn't yet entered the adjacent lymph capillaries... if the interstitial fluid entered the lymph capillary then it would be stuck there, the mechanism of this one way flow is the junctions between the endothelial cells in these blind ended lymph capillary... These junctions which only opens up gaps between these endothelial cells when the interstitial pressure outside the lymph capillaries is higher than pressure inside the lymph capillaries...

The lymph then goes forward through lymphatic vessels/nodes because external pressure (pulsing of adjacent artery, contraction of adjacent skeletal muscle, changes in thoracic pressuring during breathing, etc) and there is little back flow because of valves (just like venous valves which prevent back flow in the low pressure venous system)... Ultimately the lymph returns by either thoracic duct (in the angle between left subclavian and left jugular vein) or right lymphatic duct  (in the angle between right subclavian and right jugular vein)...

There are some sweet review articles from University of Bergen, Norway that go much more in depth on the physiology of interstitial fluid...
Here is one of their more recent review articles:
http://m.physrev.physiology.org/content/92/3/1005 it's free

IN SUMMARY: the starling forces bring interstitial fluid into the blood (the "peripheral part" right after the capillary)... The thoracic and right lymphatic duct drain lymph into the blood (I'm assuming this does not apply by your definition of peripheral, since this venous blood is about to be drained into the right atrium and is destined for the lungs)...

P.S. aqueous humor (in the eye), endolymph (cochlea aka inner ear) and CSF are also absorbed back into the blood... Also the brain has an interstitial fluid that is different from the CSF found in the subarachnoid spce of the meninges, i actually don't know how that drains... But anyway, the head is so special, I'm sure you weren't wondering about these specifics...


Average dimensions of the human back (anthropometry)

This doesn't really answer the question and I only post it at the asker's request.

NASA has measured the dimensions of the back in 40 year old American males and 40 year old Japanese females in the year 2000 at 1G. Of course gravity matters to NASA…

From figure 3.3.1.3-1 (American male). All data in centimetres:

921 Waist back

5th percentile: 43.7
50th percentile: 47.6
95th percentile: 51.6

506 Interscye

5th percentile: 32.9
50th percentile: 39.2
95th percentile: 45.4


How big is the change in proteins due to alternative splicing?

For your first question, They can vary dramatically.

I did not originally post as a formal answer because my statement below is hard to cite a source and would therefore be somewhat subjective, although I am pretty confident in the assertion. It is based on my own experience in both GWAS and EWAS literature reading. My research concerns methods for analysis of such data.

To answer your second question, the main focus has shifted from genetic variation (still done though) to expression variation and epigenetic variation. The expression research focuses exactly on the type of issue you are discussing with alternative splicing, and this is largely possible because of the decrease of the cost of RNAseq. We aren't as fixated on sequence anymore; the advent of GWAS, once thought to be a panacea for the explanation of disease susceptibility has only ended up explaining a fraction of genetic heritability estimates. Not to say it isn't focused on, just in the context of other types of variation and environmental exposures.


No, they may not sense Earthquake by an organ but due to other reasons. This may be any other physical factors which can be measured.

  "...There is therefore
  little reason to believe that these ants react to earthquake
  precursors other, perhaps, than those that may affect colonies
  directly, by altering physical variables that can be directly measured
  by other means..."

Fascinating though the behavior and physiology of ants may be, they cannot be employed as reliable predictors or even sensors of earthquakes.

Source: Shaken, not stirred: a serendipitous study of ants and earthquakes


Forward versus backward numerical simulations in population genetics

Your intuitions all seem correct. Coalescent simulation should be faster, because you don't track the entire population history over all t generations as you do in the forward simulation. Rather, as you work backwards in time you are tracking a smaller and small population. And with coalescent simulations it is probably very hard to incorporate the full range of evolutionary processes whereas doing so is more or less trivial with forward simulations.

A 2008 paper by Carvajal-Rodriguez reviews some of the issues in more detail that I have here.


Why do people have darker skin in sunnier climates?

One of the important pigments that the earlier answer hinted at is melanin.  Melanin is a brown pigment with photoprotectant properties.

As you correctly identified in your question, exposure to EM radiation (particularly UV and shorter λ waves) is damaging (indirectly) to DNA, which can cause mutations and therefore possibly cancer.  Melanin production is one of the defence mechanisms the body has evolved to deal with this threat.

When DNA is damaged by the UV-B radiation, melanogenesis (the increased production of melanin pigment) is induced.(1)  Therefore, people often exposed to more UVB (i.e. in sunnier climates) are likely to have more melanin in their skin, which makes it appear darker in colour.  It is likely to be the increased incidence of melanin proteins in your skin which leads to the formation of a tan.

Melanin and its derivatives work as photo-protectors (protecting the body from the damaging effects of ultra-violet exposure) by absorbing UV-B photons and converting them into much less damaging infra-red wavelengths (heat energy).  It does this extremely rapidly by internal conversion and extremely efficiently - efficiency in excess of 99.9% has been reported.

As the melanin removes the danger posed by the UV within a few femtoseconds (x10-15 s), the more melanin that is present in skin tissues (and consequently the darker the skin), the lesser the chance of the UV damaging molecules in the skin so the lesser the risk of developing skin cancer.


Are there two varities of dandelion leaves?

Although the leaves are similar, these are both not Dandelions Taraxacum species, because:
1. Dandelions have leaves in a rosette, not distributed along a stem.
2. Dandelions have a stem with a single flower at the end, not multiple flowers.
3. The shape of the closed flower heads after flowering is too pointed.     Dandelions usually have the pappus (white hairs) sticking out a little.

These distinctions can be clearly seen in the picture below:

I am not familiair with the flora of India, but I think these could be Sonchus species. Sonchus is known to have  variable leaves.

For comparative purposes, see how Sonchus looks like


What is the difference between ferritin and hemoglobin?

Does hemoglobin get sourced from ferritin?

Yes, of course it is. Ferritin is the superior Group.

  Is it possible for a person to be low on ferritin but normal on
  hemoglobin?

Yes, since these things don't have something in common.

  Will he feel any symptoms of anaemia, if so?
  Why should he?? No, he won't get any crazy feelings from this.


I don't imagine a frog is going to go hopping over a hill to get to a marsh on the other side, is it?

Why not? In wet weather, the conditions would be just fine for an enterprising amphibian to go exploring, perhaps driven by predators or lack of available resources, not to mention Ro Siv's comment about wind-borne dispersal of animals. Birds of prey may also pick up small animals, fly away with them, then drop them for whatever reason.

You are also neglecting the fact that these organisms have existed for millions of years, and the landscape has changed tremendously in that time, with glacial periods interspersed with interglacials every 20-50,000 years or so. As glaciers melt, large lakes form, and as those dried the organisms were dispersed across the land into smaller bodies of water. Streams and rivers form, transporting aquatic life forms, and may dry out and form isolated ponds, or they may be blocked for any number of reasons (mudslides, earthquakes, volcanic eruptions, beaver dams, fallen trees, etc.). As erosion and landscape remodeling occur, all traces of the original body of water may be erased, except for the wide distribution of similar organisms.


The Taq polymerase is a rather fast enzyme (the synthesis rate is around 1 kb/min), but the backdraw is that it has no 3'- 5'exonuclease activity which would enable to proofread the newly synthesized DNA. This leads to the introduction of errors and the chance of getting these is higher the longer the DNA you want to synthesize is.

Polymerases which are able to proofread (which have the exonuclease activity) like Pfu have a much lower error rate, but are on the other hand also much slower, typically around 0,5 kb/min. Pfu is also more expensive than the Taq polymerase. See table 1 from reference 1 below:

To combine the advantages of both polymerases, you typically use a blend of Taq and Pfu. Then you get the high processivity of the Taq combined with the proofreading capacity of the Pfu and get good yields of DNA with a low amount of mutations. See also reference 2 for details on this system.

References:

Error Rate Comparison during Polymerase Chain Reaction by DNA
Polymerase
Effective amplification of long targets from cloned inserts and
human genomic DNA.


What was the biological mechanism that allowed Tarrare to eat so much?

Tarrare

Tarrare was a showman who was renowned for his insatiable appetite including eating cats, dogs, and snakes sometimes raw.
He is also said to have eaten many inedible items.
At the time, he was alleged to have committed cannibalism of a 14-month-old baby and was caught in the act of cannibalising cadavers by hospital staff.

He was given away as a child by his parents and served in the French Revolutionary Army.

Tarrare died at the age of around 26.
From the book "Anomalies and Curiosities of Medicine" originally published in 1896 by Gould and Pyle:

  He was of middle height and was always heated and sweating. He died of a purulent diarrhea, all his intestines and peritoneum being in a suppurating condition.

This record is 100 years after Tarreres death and is largely based on the 1819  London Medical and Physical Journal.
The earlier record claims:

  At seventeen years of age, Tarrare weighed only one hundred pounds,
  and was already able to eat, in twenty-four hours, a quarter of a
  bullock of that weight.

From these accounts, I form the opinion that Tarrare ate an incredibly poor diet of raw meat and offal and countless inedible objects.
There are references to throwing up after consuming raw animals and chronic diarrhoea. There are references to sleeping for large periods of time after eating large quantities of food.

Autopsy

A passage from the 1819 London Medical and Physical Journal:

This is the closest article we have to a contemporary record.
From this account we gather that his stomach was enlarged and ulcerated, his gall bladder was enlarged, and his liver was diseased and enlarged.
Also, it might be a factor that his appetite was lost during these final days, common among patients with diarrhoea.
The record at the time, as quoted above, attributes the cause of death to diarrhoea.

Although the picture is painted that the autopsy occurred soon after death, we have no idea if this was hours, days, weeks, and conditions were much less sterile than modern morgues. I am not sure if the  "corruption" mentioned is significant.
One source claims Tarrare died of TB, however, I cannot find any corroborating evidence.
Another source recounts Tarrare blaming his demise on eating a golden fork.

These post mortem observations could have developed from 20 years of eating an exceptionally poor, unhygienic, and often inedible diet and may or may not have been the cause of his underlying condition.

Summary

So we have a few things to consider.

Polyphagia including inedible object consumption
Died young
Gastrointestinal abnormalities identified post mortum
Chronic fever and sweating
Chronic diarrhoea and vomiting
Periods of prolonged sleep

Polyphagia

The London Medical and Physical Journal describes Tarrare as having polyphagia which in his case could not be cured by acids, opium, or tobacco.

Colloquially, polyphagia means ingesting a wide variety of items.
However, if they meant "polyphagia" medically, it could be a symptom.

Polyphagia is a medical symptom defined as excessive hunger.
In modern times, this can indicate a disorder such as diabetes (improper production or reception of insulin) or Kleine–Levin syndrome (a disorder of the hypothalamus).
It could also indicate a genetic condition Prader–Willi syndrome and Bardet–Biedl syndrome.

The full list of causes from Wikipedia is:

Anxiety
Stress
Depression
Orexigenic drugs
Diabetes mellitus
Hyperthyroidism
Hypoglycemia
Fatigue
Premenstrual syndrome
Prader–Willi syndrome

From the
NHS:
Prader-Willi syndrome is a rare genetic condition that causes a wide range of physical symptoms, learning difficulties and behavioural
problems.

Bulimia
Graves' disease

Autoimmune thyroid disorder that can lead to an intolerance of heat

Kleine–Levin syndrome

A sleep disorder

We cannot know if Tarrare's polyphagia was brought on by his stressful exhausting life, his poor diet, or some genetic condition.
We cannot even be sure if his condition was responsible directly or indirectly for his death.
We cannot know if his sweating was related to; his underlying condition, or a chronic state of infection.
The only cause for his eating we can rule out from the above list of underlying causes is premenstrual syndrome (PMS) and orexigenic drugs (which are not documented).
There could be a case made for most of the other causes.

Concluding remarks

Given the scarceness of good quality medical records, the anecdotal nature of what was recorded, and the relatively poor diagnostic power of medical practitioners of the time, it would be, in my non-medical opinion, impossible to conclusively form a diagnosis.


Because your textbook is probably worded poorly.

It appears that the Japanese (and several other ethnic groups) apparently have a higher proclivity for the 10th rib to be a true floating rib, but every ethnic group has the chance of having a floating 10th rib.

With that said, the one McGraw-Hill book cited in the Wiki article is the only source I've seen for this higher morphology rate. I, personally, wouldn't trust just one source, and (if true) the rate may not be much higher.


There is.

At a first approximation the total lung capacity is the anatomical dead space(the volume of your trachea, more or less) + the tidal volume(the volume of each breath). It's slightly more complicated than that based on the differences in how deep you breathe and how often you can breathe, but at a first approximation exhaled air + half a liter(plusminus) = lung capacity.


Generally speaking, structure prediction programs look only at the thermodynamic minimum, without consideration of the kinetic trajectory of folding.

The main reason for this is mostly time considerations. It's very difficult to accurately model the true folding pathway of even a moderately sized protein. With special tricks and a bunch of computing power, we're barely able to simulate a folding trajectory of small, simple proteins. We aren't (yet) able to do so with anything of reasonable size.

Instead, what protein structure prediction programs do is take a shortcut, skip the physically-realistic folding simulation, and instead look for low energy models, with the assumption that these low energy states will look like the natively folded proteins.

(One such program I'm familiar with - Rosetta - effectively takes small backbone structures already seen in crystallized proteins, stitches them together and asks if that looks like a reasonable structure for the sequence. If not, it tweaks which backbone fragments it uses, repeating until it gets something it thinks looks good.)

This assumption - that the native structure of the protein is the global energy minimum - is called Anfinsen's hypothesis. One rationale is related to Levinthal's paradox: unlike simple chemical reactions, a protein folding trajectory has too many degrees of freedom for even nature to exhaustively sample all conformations. This implies that stably folded proteins evolved with well defined "energy funnels" - that is, the energy landscape of well-folded proteins is such that the folded form is "downhill" from a large number of potential states. Since a large number of potential states need to point toward the folded form, this implies that the local minimum of energy which is the folded form is also likely the global minimum of folding.

The energy differences in protein folding also tend to be small - it's relatively easy for proteins to climb back up of local minimums and go elsewhere. Without the strong, global energy funnel to direct them toward a stable state, it's difficult to keep proteins from unfolding and refolding. This is why kinetic considerations like controlling the trajectory of folding from a ribosome, or having special chaperonins don't really work. Because chaperonins are catalysists, they change the rate of the reaction they're involved in, but not the equilibrium. Microscopic reversibility means that any protein which randomly collect enough energy can use the chaperonin to escape the dead end it was put in: it's not a one-way gate.

Now having the kinetic minimum be the thermodynamic minimum doesn't have to be the case - it's just the case for the vast majority of proteins we've seen. There are certain systems where we're pretty sure the normal folded form is in a local kinetic trap, and with time it can escape into a more stably folded version. Amyloid fibrils and prion proteins are thought to be one such instance. The normally produced version is in a low-energy kinetic minimum, but over time or through various interactions with amyloid or other prion proteins those proteins can relax into an alternative, lower energy conformation.

The keyword here for future literature searches is "kinetic trap". Some kinetic traps are very short lived (microseconds), but other may be longer.

Finally, I'll point you to the paper "The Protein Folding Problem" by Dill et al., which is a good review on the topic of protein folding.


For all types of athlete, their ability is determined by both genetic and environmental factors (nature and nurture). The degree to which each contributes ultimately depends on the demands of the sport.

As an example let's compare basketball and golf.

Basketball is likely to have a strong genetic component because players tend to be exceptionally tall (average is over 2 metres and there are only a handful who have played NBA under 1.75m). Because height is strongly genetically (but not entirely) determined by the genes, they have a big influence on whether someone can poses the physical qualities to play in the NBA. However, a large part of their technical capabilities are due to their environment. If you give a basketball to someone who has played 2 games a week their entire lives and ask them to take 10 shots it is likely they would score more than someone who has never seen a basketball!

Comparing basketball to golf, there are all sorts of body types within the PGA tour, and they is no/few obvious genetic traits which golfers tend to have over other people. This would suggest that golfing ability is more affected by environment.

So an easy way to get a rudimentary test of genetic contributions to sporting ability would be to compare frequency distributions of focal traits in the athletes to distributions of regular people. Obviously the phenotypic trait you measure has both genetic and environmental contributions (e.g. childhood diet) which could affect them but it would be a good starting indicator which could give some candidate traits to test.

As a scientist I would also consider sequencing some athletes and some non athletes and seeing which genes the athletes have more often then the regular person's genome. However, such studies are likely to be complex - linking phenotypes (in polygenic traits) to the single allele variants relies on large sample sizes. Generally it will be more difficult if:

There is large variance in the trait
The gene has a small effect (see major and minor effect genes)

Both of these problems going to be positively correlated with the number of genes affecting a trait (how polygenic is it?) which for athletic ability is probably quite a substantial amount of genes.

EDIT:  Here are some possible studies for your further exploration of the topic-

Candidate genes for Specific Genetic Markers of Endurance Performance and o2max

Rowers have an excess of the ACE I allele

Elite Italian footballers with "explosive" leg strength also reveal ACE and other genetic markers

A precautionary tale about Genetic tests for athletic ability


What is the pH of the mitochondrial intermembrane space?

According to the authorities Roos and Boron the difference of pH across the inner-membrane of mitochondrion is  0.5 with pH outside the membrane equal 7.0 and inside the pH is 7.5 (pH-mit = 7.5, pH-out = 7.0) according to Intracellular pH


Found a larva in my broccoli, is it a Small White (Pieris rapae)?

It definately looks like a Pieris rapae larvae, which are distinct from larvae in closely related common species as e.g. Pieris napi and Pieris brassicae. However, I'm not a lepidopterist and there might be related rarer species I'm not aware of, especially since you don't know where the broccoli is from. However, Pieris rapae is found basically all over the world as native or introduced (native in Europe, Asia, Africa and introduced in e.g. Ameria and Australia) and is a pest species of cabbage (including broccoli) so it is a very good fit.


How does this small brown crescent-headed land planarian(?) "look around" and sense its envirnoment?

Given that "hammerhead worms" are Bipaliinae, I expect you can find your species from this bibliography1.  Bipalium or Diversibipalium ruteofulvum and cosmopolitan Bipalium kewense are mentioned, but I did not find images of these species online just now.
A paper about the sense organs of B. kewense (Abdel-Haleem, 2014) mentions many small pigment cup eyespots, as well as papillae and pits that may be chemosensory in nature.

1Kawakatsu et al. 2004 An Annotated Bibliography of Taiwan Land Planarians, with Lists of Linked Papers on This Animal Group


Are humans the only animal that requires "clean water"?

I wouldn't say that a human is "likely" to get sick by drinking from a puddle, I'd say "at some risk". It isn't desperately dangerous, although don't take that as a recommendation. There are many infections you can get from water (bacterial, viral, amoebal, and I presume fungal). You don't want to risk them, but probably won't actually encounter them in that puddle in your garden you see your dog drinking from. If the water is stagnant then the list of things in it that might hurt you is longer than if it's flowing. If you can avoid the mud, and anything that's been standing long enough to grow algae, fresh rainwater is a pretty good bet as these things go.

The same is true of other species, but the risk per drink is lower, since they drink it more and develop resistance to more of the things on the list. Humans are no different. For example some areas tend to have Hepatitis A in the tap water. The local population is immune after they've been infected once, and most childhood infections cause no symptoms, so it's not a problem for the locals. But to an unvaccinated visitor, the water's not safe. Hep A normally won't kill you, but is still well worth avoiding since it will make you sick for several weeks.

So basically, humans drink clean water because we can, not because we absolutely need to.

The lifespan of humans living "in the wild" (that is, populations prior to or independent of human agriculture) is pretty well agreed to be rather less than that of typical modern lifestyles. Water-borne disease is only one of many things responsible for that. The expected lifespan of a person used to purified water and so on, dropped into "the wild", is even lower again.

The "clean-water" problem in developing countries is primarily one of high population, relative to what the same area could possibly support in the absence of agriculture and other technology. The biggest risk of water-borne disease comes from contamination by human waste (although there are other sources, for example rats can contaminate water with Weil's disease). A small group of humans living in a large area doesn't have to worry about human contamination, they just drink upstream of where they defecate. This strategy doesn't help much once the population is dense enough that someone else is doing the same thing 20 metres away from you.

And of course, human agriculture also supports a much higher rat population than would otherwise be present (they're omnivores too, so they'll eat pretty much any food humans do). I suspect most human disease can be blamed on agriculture one way or another: if not on the animals then on the close-quarters living. If the population of humans was closer to what it was in the palaeolithic (a few thousand or tens of thousands of people in Europe), and was used to drinking from natural sources, then the water would be mostly (not entirely) safe.

So it's not so much that humans need perfectly clean water, it's that humans have figured out how to live in populations so large that we tend to make all the nearby water particularly dirty. Other species aren't completely unaffected by this, but they are less affected because our waste is specifically contaminating the water with diseases that affect us.


Biochemical coupling between two enzymatic reactions - Enzymes physically associated?

The enzymes don't need physical interactions to couple reactions. Some enzymes do share subunits which are physically associated, but this is a special case. The following review gives a sort of general example during glycolysis,

  For example, in the biochemical pathway that breaks down glucose for energy, two enzymes work one after the other to create a high-energy ATP molecule:

We can also look at the peptidyltransferase reaction during the elongation step in translation. Earlier, an aminoacyl tRNA synthetase catalyzed the covalent addition of an amino acid to it's associated tRNA. The energy from breaking this bond in the ribosome provides energy for the peptidyltransferase to link the two amino acids together. This isn't assuming the ATP/GTP needed by elongation factors, etc.


As there are many insects, there are also a number of different strategies. As you already said, insects depend on the temperature of the environment and cannot produce enough heat with their metabolism. The major strategies are:

Migration,
Communal living
Cold tolerance (by means of antifreeze proteins)

Only some of the insects can opt for " Migration" , those which are big enough to travel long distances. A good examples for this migration of insects is the monarch butterfly which migrates from summer habitat in the north-eastern US and southern Canada to Mexico in the fall. Using this strategy the insects avoid live threatening temperatures.

"Communal living" helps insects to get over the winter, as the colony produces enough heat to survive. A prominent example are bees, which maintain relatively high temperatures in their hives, another would be ants.

"Antifreeze proteins" are also employed by a few. Some insects contain special proteins or glycerol in their hemolymph (the equivalent to blood) which either prevents it from freezing and/or prevents the formation of ice crystals which destroy the cells. An example for such an animal would be the New Zealand Mountain Stone Weta which can stay frozen for month until the temperature gets high enough for living again. Some insects go into some kind of winter sleep, in which they survive the cold temperatures. Their living cycle is synchronized with the seasons of the year.

The answer is based on this and this article, have a look for further information and references.


Human evolution: Where *exactly* did the first human come from, whose parents were not?

but I get lost on the 'border' cases.

Not surprisingly, since there are no borders, and this is probably the greatest misunderstanding: Evolution is gradual. It’s not generally possible to say where a complex feature (or a species) starts and another one ends. We could in theory say, for individual mutations on the genetic level, in which generation they first occurred, or when they became fixed in the population. But we cannot infer from these atomic changes where our ancestors started becoming humans. So the whole concept of “first human” is not biologically meaningful.

The best analogy remains a gradient between two colours. Going from the left, where does blue end and red start?

By the way, you spotted this very well by yourself:

  [if there is no first human] then that necessarily means that the definition of a species is itself fuzzy

Exactly, that’s the case. For more details on definitions of species, refer to MCM’s answer. But it’s indeed crucial to note that the definition of species (or any other biological classification) is an ever-changing approximation which tries to fit a definitive yes/no answer onto a gradually changing scale.


Spider Identification: Is this an Arizona Recluse?

I don't think it's an Arizona recluse. Characteristic of all recluse spiders (including the five varieties found in Arizona):

  Long thin legs
  Oval shaped abdomen
  6 eyes in dyads (pairs)
  Uniformly colored abdoment with fine hairs
  No spines on legs
  Legs are uniformly colored
  Light tan to dark brown in color
  Distinct violin-shaped mark on on the back points to the posterior of the spider (less obvious on Arizona recluses)
  Body not more that 3/8" in length

Your spider has spiny legs. That, plus the fact that Arizona recluses are even less likely to live where humans do (as your article states), and are attracted to dry places, makes your spider an unlikely candidate, but I could be wrong.

Loxascelidae, Loxosceles reclusa


Yes (reference)

While I found your question interesting this was pretty much the first hit when I typed "CMV yeast" in google scholar. You should really look there first before you ask!


Some sort of passionflower (genus Passiflora). They have very distinctive flowers.

Could possibly be Passiflora miniata.


The basis of this question is a common misconception, and unfortunately the accepted answer by @CHM is also based on this common misconception. The misconception is based on the homunculus falacy: the tendency for people to think that the image that lands on the retina is somehow 'assembled' and presented for something (the 'consciousness') to view. This is not the case.

As the comment by @mgkrebbs explains, there is no orientation (up or down) in the brain, there is only neural firing. The information of the visual scene is distributed over the brain, and information does not have physical properties like orientation. Although as @nico pointed out the neurons that process the information do have a spatial structure that mimics that of the retina, this is a topological property (i.e. stimuli that are close on the retina are processes by neurons that are close in V1) and such a topological property does not induce an orientation.

The root of the problem is really that the question "How do we know the brain flips images projected on the retina back around?" is a pseudo-question. Although it is grammatically well-formed, it makes no semantic sense. When the image is 'in the' (i.e. being processed by the) brain it no longer has physical properties like orientation. Thus you cannot ask if it has been flipped or not.


Difference between medicinal caffeine and regular caffeine

From a pharmacology point of view, there is no difference between caffeine in caffeine pills and in a cup of coffee. It doesn't matter, how a chemical substance (in this case caffeine) is made, the effect of the substance is the same. What can make a difference is the presence of secondary plant ingredients.

For pure caffeine there are two possible sources: By chemical synthesis ("A Novel Method of Caffeine Synthesis from Uracil") and as a byproduct of the decaffeination process when producing decaffeinated coffee.

What is also different is the amount of caffeine. While pills contain standardized amounts of caffeine, the amount for caffeine in brewed coffee varies between different kinds of coffee beans as well as for different brewing methods. See this figure (from here):


It depends entirely on where the fossils were dug up. In the US fossils on private land belong to whomever owns the mineral rights to the land, that landowner can do with the fossils as they will. On public land the fossils belong to the government and to get a permit to dig them a paleontologist must have a place to store them, this is part of the permitting process (digging on public land without a permit is a felony). Most of the time this place is something called a repository, a public institution that has facilities to store and care for fossils, usually a museum or university and has contingencies so that the fossils will not be lost if the facility were to fail or close. Now this is for vertebrate fossils becasue of the nature of invertebrate fossils (chalk for instance is made entirely of fossils) the laws can be a bit more lax.

Private collectors can only collect on private land, which usually involves making an agreement with the landowner. Keeping collection records is always a good idea if for no other reason than to show where a fossil was found.

I have worked with both types of collectors private and public, good private fossil hunters will differentiate rare fossils and common ones and will donate rare ones to museums while selling common ones. Bad one will sell everything, which often does lead to fossils disappearing or in some cases being outright destroyed by those who disapprove of evolution and the fossil evidence for it. For this reason most journals will not accept publication made using private collections, becasue it makes repeatability impossible.

Now this is all in the US, other countries have different laws some more strict some less so.


Does the dissociation of serotonin receptors and their ligands really take hours?

That paper is describing the binding between the 5HT3 receptor and some high-affinity ligand, not serotonin.

Numbers of serotonin probably vary according to the precise receptor (species, subunits, etc), but for a ballpark figure this source says 1.7/s, giving half time of ~400 ms. That estimate is based on solution changes, so I'd say it's an upper bound.

Remember from the other questions you have asked and I have answered, serotonin is a slower-acting neurotransmitter, and clearance of serotonin is not as fast as for other, faster-acting neurotransmitters. However you are correct that your initial calculation of a ~4-hour dissociation time is unreasonable.


First off all let me say something about this tree.

Turkish hazelnut (Corylus colurna) is a slow growing pyramidal tree approximately around 25 m (82ft) tall, with a stout trunk up to 1.5 m (4 ft 11 in) in diameter. Leaves are deciduous, rounded, 6-15 cm long and 5-13 cm across, softly hairy on both surfaces. Corylus colurna is actually the largest species of hazel. The name Korylos (korys) comes from Greek and means helmet. The tree is dioecious.

Nuts are about 1-2 cm long, surrounded by a thick, softly spiny and bristly involucre (husk) 3cm diameter. The nuts are born in cluster of 3-8 together. The nuts mature in September and are edible, with a taste similar to common hazel (Corylus avellana). The nuts have a very hard shell, approximately 3 mm thick, which it makes them a little hard to open. Nut production is very irregular and occurs every two to three years.

Source

https://en.wikipedia.org/wiki/Corylus_colurna
http://www.missouribotanicalgarden.org/PlantFinder/PlantFinderDetails.aspx?taxonid=277856
https://www.chicagobotanic.org/plantinfo/tree_alternatives/turkish_hazelnut


Why when measuring turbidity do we use the minimum wavelength?

Usually when measuring materials in a spectrophotometer we want to use the absorption maxima to minimize the signal-to-noise ratio, that's why for pigment measurement you'll use the maximum point. But when you measure two materials you want to take two measurements with as little correlation as possible, that is to avoid one material influencing  your measurements of the other.
Imagine you are trying to breed C. marina for more pigment. Obviously more algae = more pigment so you want to measure how much algae you have and normalize by it. If you'd measure alga density in a wavelength correlated with chlorophyll content you'll get inaccurate results.
I think the question is ill-worded. You should measure at the pigment's absorption minima and not at the alga absorption minima. As the alga can have other peaks unrelated to chlorophyll. When doing this you should remember that chlorophyll and many other pigments are insoluble in water but your measurements of live cells are, usually, in water media.
The best in my opinion and that is the method I'm currently using is to build your own curve by counting cells in some manner (like hemacytometer) and measuring the full spectrum (Your graph stops at 750nm, I got up to 1000nm).


Mendel published his results 1866 but they were rediscovered only in 1900. The Hardy-Weinberg model is an application of Mendel's rules to a population that is not under selection forces. So the one builds on the other, and Hardy-Weinberg is a simplification model-wise, and Mendel's rules are not detailed enough either. It's the same relation as with a physical law like gravitation and a mathematical model of its consequences applied on many entities, like models of a solar system's gravitational behaviour.


How large is the range of 'same origin' when determining whether two organs are analogous or homologous?

There is no limit: the ribosomes in your cells and the ribosomes in a palm tree are homologous structures, because both you and a palm tree inherited that structure from your last common ancestor, an unicellular eukaryote, more than 1 billion years ago.
That being said, the question in your link (and several other sources) gives an incorrect definition of homology and homoplasy (or analogy). Homology and homoplasy are not defined for "the function of the organ" or anything like that.
First, both terms apply to structures, which have a different meaning in phylogenetic systematics and evolutionary biology. A structure can be:

Morphological
Physiological
Biochemical
Comportamental (ethological)

Thus, we are not necessarily talking about organs or morphology when we define homology and homoplasy.
The difference between homology and homoplasy is very simple:

Homology: a similarity due to common ancestry.
Homoplasy: a similarity not due to common ancestry.

So, in my example using ribosomes, that similarity ("presence of 80S ribosome") regarding you and a palm tree is due to your (ours) common ancestry.
On the other hand, the thermoregulation in mammals and in birds (and probably other dinosaurs, not only birds) is an example of homoplasy, because the common ancestor of mammals and birds, an early amniote, was probably not capable of thermoregulation. Notice that here the structure is not a morphological one, but a physiological one. Another example using physiology is the pH of the blood: the pH of my blood and the pH of your blood is the same (7.4) because we inherited that feature from our common ancestor. Thus, it's a homology.
Sometimes the situation is tricky. Is the wing of a bat and the wing of a pigeon an example of homology or homoplasy? Since the common ancestor of bats and birds didn't have wings, and both bats and birds developed wings independently in their evolutionary histories, it's an case of homoplasy (analogy). What causes confusion here is that, in both cases, the wing is a modified anterior limb, and the presence of an anterior limb in bats and pigeons is an homology. The "limb" is a homology, not the "wing".
And that brings us to the case of sharks and whales. If the pectoral fin of a shark derives from the same structure that formed the anterior limb of the first sarcopterygii, then you can say (as several systematists say) that the pectoral fin of a shark and the anterior limb of a whale are homologous structures.
Summarising: given two organisms, Y and X

X and Y share a given feature;
find the last common ancestor of X and Y (it doesn't matter how long ago in the past)
did that ancestor have the feature? Did it transmit the feature to both its descendants?

If the answer to that last question is "yes", it's an homology. If "no", it's an homoplasy (analogy).


The pictures aren't very clear, but I would put this down as a book louse, not a bed bug nymph, as the body is quite elongated, which is atypical of the bed bugs and more typical of book lice.
Book louse:

Bed bug:

Courtesy of  bedbugger.com.
Check out also this page from the University of Minnesota Extension; the picture nicely matches the photo you posted in body shape.


RNA seq and using of Poly(A) or non-Poly(A) based amplification of RNA

Yes, it was odd that they said that. The second protocol with the polyA based method had another purpose though, which was "examine the reproducibility of period-regulated genes in an independent genetic background". I would suspect this was its main purpose, and not so much to look at fragment bias, which has already been done in other papers. They didnt even publish this data in the main paper, they put it in the supplement.
Yes, this would remove any transcript without a polyA tail.
One way of purifying is by using oligos that are antisense specifically to rRNA. The oligos will be attached to some solid phase, on a column or a bead or something, and the rRNA will stick to it and everything that doesnt is what will remain in your sample
It is not safe to say that you lose information with polyA based kits. The polyA based technique had reads that were single end and only 75bp long. This is compared to the other protocol which was 100bp paired. Reads that are 75bp will align much more easily than 200 bp (100 x 2 since its paired). However, there will not be as much certainty in the alignments, as there is a greater chance it will align to multiple locations in the genome, or align to the wrong location. So yes they have more reads aligned but I would be hesitant to make any conclusions from this. And if you look at total numbers of reads, the non-polyA method aligned more. Again, I dont think the main purpose was to show that one method is better than another.

Basically the method you choose depends on your experiment and your samples. Random hexamers will give you non-coding RNA which is important in some experiments, and that is its main advantage. It will also give more uniform coverage across the gene (no 3' bias). Poly(A) selection will give you only mRNA, however you will miss any transcripts that are degraded or partially degraded. If you have a high quality sample or a large amount of starting material this is less of a concern. As mentioned before you end up missing parts of the 5' end on some transcripts with this method. If you have a low abundance transcript that you are trying to find, polyA selection is probably best, as it is more likely to be captured and you will capture the whole thing, rather than just getting bits and pieces of it with random hexamers. They both have advantages and disadvantages. Hopefully this helps you or someone make a decision.


According to InterPro, a paired domain is a DNA-binding element consisting of paired N-terminal and C-terminal subdomains, separated by a linker. PAX proteins follow this motif, and as such typically represent a class of helix-turn-helix transcription factors.

Box is the more interesting term here. In genetics, a box can be used to describe any regulatory element of a gene, including its promoter, UTRs and any enhancer or silencer elements. More loosely they also use box to describe coding segments of a gene, but in older publications.

Going back to Drosophila, however, studies in embryogenesis initially identified a protein called paired, a.k.a. prd. Homology studies into mammalian transcription factors found the presence of a prd-like domain in human HUP transcription factors, and these were renamed to PAX (ref). Thus, the naming of PAX family proteins classicaly denotes the presence not of a PRD regulatory element, but of a coding region for a prd-like domain in the gene product.


Reference for the bite force for Nile Crocodile

Here is a video by Brady Barr (video in YouTube) measuring 5000 lbf for an adult Nile Crocodile. This is equivalent to 22.24 kN (more than 2.2 tonnes of force). This result is also refered here (Getty Images).

 Source: Gianfranco Gori, Wikipedia


Twins reproducing with each other ( just hypothetical)

Monozygotic twins won't be able to reproduce (naturally), because they are of the same sex. Dizygotic twins may or may not be of the same sex, just as regular siblings; genetically speaking, they are just siblings, not twins, so this case is out of the scope of your question.


Examples of plant families that contain species that are safe for human consumption and species that are poisonous to humans?

The most classic example if you want to win this argument would be the family Solanaceae.

Also referred to as the Nightshade family, it includes the deadly nightshade or Atropa belladonna and many other plants not safe to eat.

Other members of the family are tomatoes, peppers, potatoes, and more.

Plant families can be massively diverse, and toxicity doesn't really have much relationship to family. Most of the compounds that are found in plants that are toxic are found in other non-toxic plants as well: dose is crucial.


Can an argument be made that humans are 90% bacterial?

I am not sure what you read as you have not supplied any references, but humans are not 90% bacterial cells. (OP subsequently provided; see Edit 2)

Humans are 100% human cells, however for every one human cell, approximately 10 single celled organisms (Bacteria or Fungi) live in (colloquially) or on the human body. This is referred to as the microbiome. You can find more information in the link I provided or in the answers to the following questions on Biology SE.

Do intestinal flora have the same DNA as their host?
How many diseases can be linked to disruption in the microbiome of a human?
What is the function of E-coli bacteria in our stomach?
How heavy are all foreign microorganisms in and on the human body?

Think of it this way; just because the human body provides these organisms with a home does not mean that it is composed of them, that would be like saying an apartment building is made up of x percent of humans or pets or mice or insects just because that is where they live.

You may also find some interesting information at The Secret World Inside You from the American Museum of Natural History.

Edit

  As bacteria helps us in making many enzymes for us, can we say that we are symbiotic creatures?

The definition of symbiosis is:

  The interaction between two different organisms living in close physical association, typically to the advantage of both.

Given that definition, and given the fact that there are some bacteria in our microbiome that are able to produce metabolites that our cells cannot, and we provide them with a "home" with the necessary nutrients for their propagation, then you can say that this is in fact a symbiotic relationship.

The more technical description that is often used for the microbiome is that these organisms that populate the human body are commensal.

Commensalism is defined as:

  An association between two organisms in which one benefits and the other derives neither benefit nor harm.

In this respect, the majority of our microbiome are commensals, they live on us, but give us nothing in return, and for the most part do us no harm.

Some of the organisms can be opportunistic pathogens in the sense that if they are able to gain access to normally sterile areas of our body, such as in peritonitis arising when the intestines are perforated, then they can be harmful, but in their general niche, they are just there.

As we learn more about the microbiome, we are beginning to see that there is a far more complex relationship between host and microbe than we anticipated, so over time, the views on the microbiome are likely to change from the understanding that we have today.

Edit 2

To address the source that you added All about Scientist in Microword: Microbiology, I would say that the blogger is guilty of hyperbole. While Steven Gill, the molecular biologist that the blogger quoted, may not have chosen his words carefully, he was not implying that humans are 90% bacteria, as the blogger then posits.

Gill makes the mistake of using the word "in" when he states "There are some estimates that say 90% of the cells in our body are actually bacteria...." The microbiome exists on the surfaces of our body not in it.

We forget that the gastrointestinal tract, urogenital tract, and respiratory tract are lined with epithelial cells and are thus external surfaces, just as our skin is an external surface. So the microbiome lives on our body, and not in it or as a part of it.

No place in our body do we have organs or tissue that is a homogenate of human cells and bacterial cells functioning together normally. And while there are bacteria that are able to infiltrate cells and live within vesicles or the cytoplasm, this is a pathogenic condition and not what we would normally expect to see in a healthy human.

We know that this is the case, because developmentally all of our body cells and germ cells arise for the fertilized egg. It isn't until much later in development or at the moment of birth (there are some reports that microbiome begins to cross the placenta prior to birth) that we acquire our microbiome. If it were the case that humans, or any eukaryotic organism for that matter, were 90% bacteria, then we would not develop in the sterile environment of the amniotic sac. The lack of bacteria during development would be fatal.


I am going to try to walk through this problem, in a step-by-step manner in relation to exercise, starting from at rest, and ending at the point in which the body is no longer able to maintain its energy-charge.

At Rest

The body mainly utilises oxidative phosphorylation to maintain its energy-demands. In cells where great amounts of energy need to be produced very quickly, eg. cells that are actively replicating, glycolysis is the preferred mode of energy production because this pathway is able to very quickly produce large amounts of ATP, and lactate is able to quickly diffuse in to the bloodstream. Lactate will travel in the bloodstream, to the liver, to be recycled back to glucose through an anabolic process called gluconeogenesis. This recycling pathway is known as the Cori-cycle. Essentially, what is happening is, parts of the body that are in need of high amounts of energy, will "dump" their wastes to the bloodstream, to be dealt with by other organs.

Science and Skiing VI, 2015, pp 17-30. George Brooks of the University of California summarises lactate recycling quite nicely here.

Beginning Exercise

Muscle cells will begin to quickly utilise ATP-stores, and release glucose from the glycogen-stores, and release oxygen-stores from myoglobin.

As these stores begin to become depleted, the body will begin to go in to overdrive, in an attempt to restore itself to a resting-state. Thus, your heart-rate will increase, breathing will become faster, and glycolytic pathways will be activated through feed-forward mechanisms.

During Exercise

I have touched on this before, in another post that you may find interesting. I believe that if you read through this though, that you will understand why there is low levels of oxygen, and what the body does to attempt to circumvent this.

There will be very low levels of oxygen throughout the active tissues. The body will do everything it can to try to restore this, but it will ultimately fail to do so. Thus, the only real option it has is to rely on glycolysis in the tissues that are causing "problems". The rate of ATP-production is most dependent on the rate at which a cell can take glucose in to the cell.

The electron-transport-chain is only able to synthesise ATP at its maximum velocity - this maximum velocity is proportional to the concentration of oxygen. The rate of glycolysis is, however, essentially, only affected by the rate at which lactate can be removed from the cell and the rate at which glucose can be absorbed by the cell.

Of course, the muscles that are being used will only be concerned with producing energy. Therefore, all of the lactate that they produce will be dumped in to the bloodstream, where it will travel to the liver, in the previously mentioned cori cycle.

Overall, the issue is not in the muscle-cell's ability to regenerate NAD+. This is the easy part, seeing as there is no net-change in the concentration of NAD+ when glucose is converted to lactic acid. And also, things such as malate-aspartate shuttles, citrate-pyruvate shuttles, and glycerol 3-Phosphate shuttles can be used to maintain redox-balance. These are only but a few examples of how to maintain redox-balance.

You must also remember that carbohydrates are not the only class of molecules involved in these cycles; degraded proteins and fats can also be used to supply the TCA-cycle with alternative means of energy-production. Pyruvate probably would not even be able to be converted in to acetyl-CoA anyway, since pyruvate dehydrogenase requires the presence of oxygen to function.

Problems however do arise once the body is unable to deal with all of the waste that it is producing. There will reach a point, where the liver cells will be physically incapable of accepting any new lactate-molecules. And so, lactate will accumulate in the bloodstream. With an accumulation of lactate in the bloodstream, lactate will be unable to diffuse to the outside of the cell. Thus, cells will be unable to convert pyruvate in to lactate.

The reason why ATP-regeneration eventually fails to keep up with the rate of ATP-usage, is because the rate of conversion to lactate decreases. The rate of conversion to lactate decreases, because the concentration of lactate increases

I tried to make a little illustration of what I mean above, below. Hope this helps to conceptualize it.

In this second picture, there is too much lactate for diffusion to occur.

Supporting information

Taken from Quantifying intracellular rates of glycolytic and oxidative ATP production and consumption using extracellular flux measurements; Mookerjee et al. 2017

"These maximum values of JATPglyc and JATPox define the bioenergetic capacity of the cells. As shown in Fig. 5D, the maximum individual capacities of JATPglyc and JATPox in the bioenergetic space plot intersect at (62.5, 46.5) for a theoretical maximum bioenergetic capacity of 62.5 + 46.5 = 109.0 pmol of ATP/min/μg of protein. At this maximum point, the glycolytic index (GImax capacity) would be 62.5/109 = 57.3%, making C2C12 myoblasts primarily glycolytic when running at their maximum ATP production rate. Compared with the actual value of JATP production in the presence of glucose (55.2), the bioenergetic capacity was 109/55.2 = 197% of the rate with glucose (Fig. 5D). This bioenergetic capacity of 197% of the rate with glucose (alternatively, a reserve capacity of 109.0 − 55.2 = 53.8 pmol of ATP/min/μg of protein) reveals that the C2C12 cells under our experimental assay conditions with added glucose were operating comfortably within their capacity to generate ATP and were well set up to respond to any acute increases in ATP demand by increasing either glycolytic or oxidative ATP production, or both."

In these experiments, the researchers were trying to figure out what proportion of ATP would be created by glycolytic and oxidative pathways in muscle cells (and other cell-types). Their findings, were that, indeed, the majority of ATP production in muscle cells comes from glycolysis.

During exercise, this difference in amounts of ATP production between glycolysis and oxidative phosphorylation would probably be even greater.


Why do many cells together survive better than one cell alone?

Cells can communicate with each other using chemical signals.

But do you also know about gap junctions? These are tunnels that connect cells in tissues.

Water, ions etc. can travel to and fro.

Or maybe a tight junction can connect cells together to form an an organ. No fluids pass through, which is good: The bladder is an example.


As you point out human beings (and other organisms) have hundreds of retroviruses and many can be seen in the human genome, some of which appear to be the remains of deactivated viruses, others which may be active.   Most retroviruses are not pathogenic - they don't cause disease.

This is because many retroviruses replicate slowly, budding and secreting from the cell surface in small numbers without killing their host cell.

There are several disease-causing retroviruses.  Human T-cell Leukemia Virus (HTLV) can cause T-cells to replicate in an uncontrolled fashion, resulting in leukemia.  This is not a necessary result for HTLV to replicate, but it is a result of viral infection as viral replication tweaks the cell machinery to replicate.

While it's not clear exactly how, Human Immunodeficiency Virus (HIV) kills its hosts cells.  Unfortunately HIV's hosts are CD4 immune cells.  The fact that sporadic replication of HIV can cause all host immune cells to die entirely makes HIV a pathogen.

Disease is usually thought of as a lack of adaptation of a pathogen and host: viruses do better if they do not kill their host.  Both these cases are possibly not the future for either virus: either could adapt to reproduce without causing a disease. Or they might have already , having spun off some strains into the pool of quiet retroviruses medical science does not concern itself with.


Let's start with your definition.

"Selection for traits that would be beneficial to a population of units at the expense of an individual unit possessing the trait"

This is not a good definition of group selection. In reality, selection can act on groups regardless of the direction of selection at the individual level. This definition sounds to me (your link is directing me to somewhere unpleasant) like one that has been set up in order to study whether group selection can act as an explanatory principle for the evolution of individual-level altruism, which is an altogether different question than the title of your post (the two questions are often conflated for historical reasons).

To expand the debate, I will introduce two formal definitions of group selection both of which are defined by alternative forms of Price's equation (See Okasha's book Evolution and the levels of selection for a thorough analysis).

Interdemic group selection

Interdemic selection occurs when selection acts on both groups and individuals within groups separately. That is, both groups and individuals within those groups must be units of selection in their own right. We must be able to assign fitness to both levels of selection some way, and track the offspring produced at each level. In this form of group selection, group fitness corresponds to the ability of a group to survive and produce more groups of a similar kind, and individual fitness corresponds to the ability of an individual within a group to survive and produce more individuals of a similar kind within that group. A good example  is selection on multicelullar organisms and selection on cells within those organisms. If there are greater than two levels of selection, interdemic selection is commonly referred to as multi-level selection 2 (MLS2) (see Okasha).

'The extinction of some groups and the ``reproduction'' of others are essential features of evolution by group selection. If groups are the units of selection, then they must have the properties of variation, multiplication, and heredity required if natural selection is to operate on them.' Maynard Smith

Intrademic group selection

Intrademic selection occurs strictly among individuals within a meta-population. That is, individuals are the only units of selection we study. The groups in which individuals reside are seen as part of the structure of the environment in which individuals live. In this form of group selection, individual fitness corresponds to the ability of an individual to survive and produce more individuals of a similar kind, given that they reside in a particular group. A good example of this perspective on group selection is selection cells of the quasi-multicellular organism Dictyostelium. Cells of this species are units of selection in their own right that occasionally group together into bodies that may also act as units of selection. If there are greater than two levels of selection, intrademic selection is commonly referred to as multi-level selection 1 (MLS1) (see Okasha).

'A way of looking at this is that the [intrademic] group selection approach looks at the evolution of individual characters in a group structured population, whereas the [interademic] group selection approach looks at the evolution of group characters.' West et al

Equivalence

It is worth pointing out that there is currently equivocation in the field about whether these two selective processes are different perspectives on the same underlying biology or distinct causal processes.

Another important point to note is that it is the intrademic form of group selection that leads to the conclusion that kin selection and group selection are really just different perspectives on the same selective process. This has been shown mathematically by Queller.

There is not yet a conclusive proof either way showing that interdemic group selection and kin selection are equivalent or not. Some evolutionary theorists feel that they are, while many feel that they are not.

Group selection versus group adaptation

It is also important to point out the distinction between the process of selection acting on groups (which most evolutionary theorists accept - I mean, it definitely does happen!), and whether or not this selection gives rise to group adaptations (which evolutionary theorists are equivocal about). Some argue that all adaptation can be explained from selection acting on lower-level units (right down to the gene, remember Dawkins?), whereas others think there may be nested levels of causality that cannot be reduced in this way.

Empirical research

There are many examples of laboratory and field based studies of group selection. Too many to list here. In a response to a theoretical paper by Gardner, a history of empirical research on group selection was given by Goodnight. The original paper, its response, and its counter response are worth a read to understand some of the different perspectives on the debates. In particular, two different perspectives on the evolutionary dynamics of cancer are presented that nicely illustrate the differences between MLS1 and MLS2 thinking.


How to pipe Bwa-mem output without saving SAM file

I never used CIRI2 but I think you can do the same way as I used to pipe with samtools:

bwa mem genome.fa reads.fastq | samtools sort -O BAM -o output.bam -

So it would be something like:

bwa mem genome.fa reads.fastq | CIRI2 <your options>

I think you will need to precise that CIRI2 input is STDIN.
I hope it will help,


Can saltwater fishes survive in sugar solution?

No, the chloride cells in the gills rely on the relationship  between chloride and sodium to remove salts out of the body against the gradient. Switching the environment to sugar would cause the chloride cells to not be able to maintain ionic regulation. See the below link for basic info on chloride cells: https://en.m.wikipedia.org/wiki/Chloride_cell


On the molecular level, genes most often encode proteins which perform some function for the cell: For example, they could be enzymes and catalyze chemical reactions. They could also have some structural function, such as make up the "muscle" part of your muscle cells... You get the idea.

In the most simple case, the dominant allele encodes a protein that can perform its function. For example, the dominant allele for the CFTR gene encodes a channel that can let chloride into and out of the cells. The recessive allele, on the other hand encodes a protein that cannot do its job correctly (this also called a loss-of-function mutation). So if you inherit a functional copy from one parent and a non-functional copy from the other parent, you will still have one copy of the protein that can do its job. Only if you get a nonfunctional copy from both parents will you have a recessive condition called cystic fybrosis.

On the molecular level a gene can also encode a dominant-negative variant of a protein. In this case the protein cannot do its job and also prevents the functional version of the protein to do its job too.

A third way this could work is by a gain-of-function mutation. In this case, the gene encoding a protein acquires a mutation that gives a new function to the protein. For example, in Huntington's disease, the mutant Huntingtin protein acquires the ability to clump together in large plaques, which are poisonous to some neurons in the brain. Since it takes only one copy of the protein to perform the new function, the gain-of-function allele is a dominant one.

These are only a few examples that deal with simple dominant and recessive inheritance. Most often there are more complex mechanisms of inheritance at play.


what is the active ingredient in cymbopogon citratus that repels mosquitoes?

I think the problem isn't a hoax; it's just that people are overly excited about 'natural' as opposed to synthetic remedies.

C. citratus might be hazardous - the active ingredient is citral α-pinene.

C. nardus might be hazardous, too - the active ingredient is citronellal or citronella. [There's confusion, in the article, about whether citronella has other plant chemicals in addition to citronellal.]

They're both partially effective as insect repellents.

"It is commonly assumed that plant-based repellents are safer than DEET because they are natural. However, some natural repellents are safer than others, and it cannot be assumed that natural equates to safe."

This info all comes from a 2011 scientific article about plant-based insect repellents:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3059459/

Here's a link to a table with the results, summarized below:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3059459/table/T1/?report=objectonly

And a table with possible toxicities:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3059459/table/T2/?report=objectonly

Citronella has found its way into many commercial preparations through its familiarity, rather than its efficacy. Citronella was originally extracted for use in perfumery,..."

C.nardus is at least somewhat effective in 3 lab studies; citronellal    is the active ingredient.

C. citratus - the active ingredient is citral α-pinene.  Again, it's at least partially effective in 3-4 studies, e.g., "74% protection against An. darlingi for 2.5h"

Here's a scientific article from 2011 about the scientific basis for the therapeutic use of Cymbopogon citratus, stapf (Lemon grass):
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3217679/

But it doesn't mention 'insect repellent' among its possible uses!:

"Studies indicate that Cymbopogon citratus possesses various pharmacological activities such as anti-amoebic, antibacterial, antidiarrheal, antifilarial, antifungal and anti-inflammatory properties. Various other effects like antimalarial, antimutagenicity, antimycobacterial, antioxidants, hypoglycemic and neurobehaviorial have also been studied."


Classic symptoms of untreated diabetes include excessive thirst and urination, and glycosuria. Think about the solute gradient. At some arbitrary number the level of glucose becomes saturated. The kidneys are forced to get rid of the extra glucose in urine. This increases the concentration of solutes in the urine, so where does the water go? Right? So that high blood glucose concentration translates into frequent trips to the bathroom, and frequent need to consume fluids. This can also lead to a fluid/electrolyte imbalance, which is potentially dangerous.

There's actually a limit to what can be reabsorbed, denoted the transport maximum,
but, you can only eliminate so much solute over time, so here's a figure from a Pearson physiology chapter:

Source

You've got your renal threshold around that 180 mg/dL but look at that excretion kinetic. It's known that the excretion rate increases linearly with the filtration rate above the renal threshold (ref). So say i'm an average male with 400 mg/dL plasma glucose and 50 dL of blood or 20 g of net plasma glucose. All other things held equal, it looks like it could take around 2 hours to clear that glucose on excretion alone, which doesn't typically happen. Clearance is also outlined in that Pearson chapter, and you can measure that by knowing the excretion rate, and the concentration of glucose in the urine and in the plasma.

Data shows, however, that the filtration/reabsorbtion process is maladapted in a diabetes model, and increased plasma glucose levels are maintained by an up-regulation in glucose transporters (thus an increase in the transport maximum), and an increase in the renal threshold (and thus the kidneys only begin to excrete glucose at a significantly higher level) (ref).


Why is Sanger sequencing inferior for detecting SNPs in cancer cells?

In the Sanger approach, DNA would be isolated from the biopsy and would contain both normal alleles and mutant alleles of genes associated with the development of the tumour. If, for example, PCR amplification was then used to derive a sample of a target template region, this material would end up being sequenced as a mixed population: the derived sequence would be an average of that population of sequences, and rare alleles would be masked.
The key difference in most next generation approaches is that the template DNA is "cloned" physically (e.g. by sequestering individual molecules into droplets, or by binding them to a surface) so that the sequences of these individual molecules can be determined in parallel. This approach would reveal tumour-associated polymorphisms when the sequences of the individual template molecules were compared.
Added later as supplementary information.
I have now looked at the paper cited in the question. This quotation from the Introduction bears out my main point about sequencing a mixture of templates differing at just a few key positions.

Although commonly used in many clinical settings, dideoxynucleotide chain termination (or ‘Sanger’) sequencing of PCR products often lacks sufficient sensitivity for detecting mutant alleles in tumor biopsies, where the failure rate has reached 75% in some cases. Gain-of-function oncogenic mutations are frequently heterozygous events or may represent a single allele of an amplified gene; thus, the signal for mutated residues is typically reduced relative to neighboring bases. Moreover, the ability to detect single base mutations or small insertions or deletions in biopsy material by Sanger sequencing depends heavily on sample purity (for example, the extent of contaminating stromal DNA) and genomic DNA integrity. Furthermore, resistance to kinase inhibitors may correlate with low-frequency second-site mutations. These observations underscore the challenges for accurate mutation detection in cancer specimens.
A massively parallel sequencing-by-synthesis approach, ‘picotiter plate pyrosequencing,’ provides a new alternative to Sanger sequencing. This approach relies on emulsion PCR-based clonal amplification of a DNA library adapted onto micron-sized beads and subsequent pyrosequencing-by-synthesis of each clonally amplified template in a picotiter plate, generating over 200,000 unique clonal sequencing reads per experiment. Sequence variants that represent a fraction of a complex sample can be vastly oversampled, thus enabling statistically meaningful quantification of low-abundance variants.