Are fluoroquinolone antibiotics (Cipro, Levaquin, etc) chemotherapy drugs?

Short answer: Yes, fluoroquinolones are chemotherapy drugs
In layman's terms, fluoroquinolone antibiotics kill human cells as they divide. Fluoroquinolones are a class of drug called "topoisomerase interrupters." Every drug in this class is directly labeled as a chemotherapy drug except fluoroquinolones.
This is not well known by the medical community and is in part why irreversible damage from fluoroquinolone antibiotics is not well understood.
Long answer: Fluoroquinolones are definitely chemotherapy drugs, and they're dangerous
A refresher on how fluoroquinolones work, in case you slept through molecular pharmacology :
If you want you can skip this first section and instead watch YouTube: Fluoroquinolones: Mechanisms of Action and Resistance
How topoisomerase works
Bacterial cells have double helix DNA, meaning two strands twisted around each other. When bacterial cells divide, the two DNA strands are separated (untwisted), and eventually each side is turned back into a full double helix, making two copies.
If you think of a tightly twisted rope (representing double helix DNA) and start to pull the two ends apart, the rope will twist tighter and tighter and eventually you can't untwist it further. Nature's fairly primitive solution is an enzyme called topoisomerase.

topo-: dealing with topology, as in the structure of the DNA
-isomerase: a class of enzymes (enzymes are usually bundles of proteins)

The job of topoisomerase is to cut the the double helix DNA strand, untwist it, and then glue it back together.
There are several types of topoisomerase, which we'll come back to.
How fluoroquinolones kill bacteria
Fluoroquinolones bind to the glueing action of topoisomerase. So, as part of normal cell division, topoisomerase cuts a DNA strand, untwists it, then tries to glue it back together. However, fluoroquinolones block the gluing action ("plug the glue bottle"), so the cell literally cuts up its own DNA. Insidious, isn't it?
Don't human cells have topoisomerase?
Yes, since humans have two sets of DNA, let's focus on one at a time.
How fluoroquinolones kill human mitochondria
Human mitochondria are bacteria, and they do contain double helix DNA and topoisomerase. So why don't fluoroquinolones kill mitochondria? Trick question: they do, and it's worse than that.
Human mitochondria keep around backup copies of their mtDNA (we often call mitochondrial DNA "mtDNA" to distinguish it) to use when there are replication errors in DNA synthesis. Fluoroquinolones "deplete" mtDNA, meaning irreversibly destroy backup copies. The organelle desperately tries to pull in backup copies as it cuts up its own mtDNA during replication, and may die, or may become permanently damaged.
Insidious, isn't it?
Many other studies have proven that fluoroquinolones kill human mitochondria as they divide. Interrupting topoisomerase isn't the only way they kill mitochondria, but it's an important one.
How fluoroquinolones kill human eukaryotic cells
Human "eukaryotic" cells (cells with a nucleus, such as tissue cells) also have topoisomerase. So why don't fluoroquinolones kill eukaryotic cells? Trick question, they do:

Compared to an [actual DNA poison], ciprofloxacin produced comparable dose-dependent SCE frequency increases

(an SCE, "sister chromatid exchange" is a marker for how genetically damaged a cell is)
and

topoisomerase type II and DNA gyrase are physiological targets for [ciprofloxacin]

Insidious, isn't it?
Like mitochondria, topo binding is a small part of the kaleidoscope of how fluoroquinolones cause permanent cellular damage, but it's an important one.
As you can imagine, fluoroquinolones killing a cell's main source of energy (mitochondria), while also causing the cell to irreversibly destroy its own DNA lead to human cells dying as they try to divide divide
Even clearer: Compared to other chemo drugs
There are several oral chemotherapy drugs on the market, one of which is Topotecan (notice the topo-?). Here's how they work:

Topoisomerase I inhibitors:  Ironotecan, topotecan
Topoisomerase II inhibitors:  Amsacrine, etoposide, etoposide phosphate, teniposide

And, as linked in the earlier study, fluoroquinolones are topoisomerase II inhibitors. (They probably bind to other forms of topo, but we don't know for sure).
Even clearer: Fluoroquinolones are used for chemotherapy
There are a few
"novel" studies using fluoroquinolones as chemotherapy drugs. In this study, ciprofloxacin is used to target leukemia cells.
Why are chemotherapy drugs used as antibiotics?
When (non-fluorinated) quinolone antibiotics were first invented in the 60s-70s, we didn't know about mitochondrial DNA, and certainly not how fluoroquinolones affect mitochondria.
Don't fluoroquinolones have a good safety profile?
No.
Fluoroquinolones were released in the 70s, but the FDA warning for permanent nerve damage wasn't added until 2013. Because the symptoms of permanent fluoroquinolone damage are so outrageous (permanent nerve damage, tendons spontaneously rupturing, organ failure, psychosis, and dozens more). Doctors simply didn't know (and still don't know) to look for the symptoms, so they aren't documented.
There have been other fluoroquinolones that had "good" safety profiles, passed all medical standards, and then were promptly removed from the market after they started killing patients outright. One such drug, temifloxacin, was removed because it caused so many cells to die that the kidneys became clogged, killing patients.
The fluoroquinolones on the market are all able to, and have, killed patients through multiple mechanisms, but it's more rare, and the permanent damage symptoms are not connected by doctors.
All fluoroquinolones have the same core method of action, and all have a fluorine moiety allowing them to penetrate anywhere in the human body ("hard to reach" infections), so even though the current ones haven't been removed from the market, it doesn't follow that they are safe.
Why continue to prescribe them?
I sincerely believe that if doctors understood how fluoroquinolones worked, they would stop prescribing them, and use them only in life or death situations. The FDA has already advised never to use fluoroquinolones for "uncomplicated" infections, but this advice is not known nor heeded.
If only doctors read studies from over 10 years ago:

In view of the present genotoxicity, ciprofloxacin should be administered with caution.


Are there plants that produce (audible) sound?

Plants make noise all the time as they transport water but that is believed to be an unintentional by-effect. As to the possibility of plants intentionally making noise,
my intuitive answer was no but I might well be wrong, there is actually increasing evidence that plants might produce vibrations for communication.

Two examples: Gagliano (2012) discovered that young maize roots subjected to a 220 Hz sound (check out the figure, not sure if I'm allowed to copy it here) grow towards the sound source and additionally emit periodic bursts of sound themselves for as of yet unclear reasons.  Gagliano, Renton, et al. (2012) demonstrated that chili plant seedlings grow faster in the presence of an adult fennel plant even though this adult plant was isolated in a such a way that it could not communicate via any known mechanism (chemical, light) with the seedlings, indicating influence through an unknown mechanism. The authors consider both magnetism and sound as possible unknown communication methods.

I don't think any of these sounds would be audible for humans though.

Acoustic emission analysis and experiments with physical model systems
reveal a peculiar nature of the xylem tension.
Laschimke, R., Burger, M., & Vallen, H. (2006).
Journal of plant physiology, 163(10), 996-1007.

Towards understanding plant bioacoustics
Gagliano, Monica et al.
Trends in Plant Science , Volume 17 , Issue 6 , 323 - 325

Out of Sight but Not out of Mind: Alternative Means of Communication in Plants.
Gagliano M, Renton M, Duvdevani N, Timmins M, Mancuso S (2012)
PLoS ONE 7(5): e37382. doi:10.1371/journal.pone.0037382


Geographical distribution of malaria and tuberculosis

The statement in the question about the current distribution of these diseases is not strictly accurate, as shown by the graphic below.

[Malaria graphic: Wikipedia user, Percherie (2006); TB graphic: Corbett et al. (2003)]

However there is no disputing that the contemporary and historical geographical distribution of these diseases differ. Why?

The crux of the answer is that this is because of the different agents that cause these diseases. Malaria is transmitted by certain mosquitoes and is therefore restricted to places in which these mosquitoes are found. TB is a bacterial disease, the geographical range of which is determined by human contact under conditions which favour its transmission.

To expand:

Malaria is transmitted by Anopheles mosquitoes, especially in Africa by Anopheles gambia together with the Plasmodium falciparum parasite. One of the factors determining the mosquito habitat is standing water and the elimination of malaria from Southern Europe followed drainage of the marches and swamps in which it breeds.

That is not to say that this is the only factor in the elimination of the malarial mosquitos from certain parts of the world in recent historic times. For example malaria has not been eliminated from Africa partly because of the cost and logistic problems of implementing programmes of eradication using drugs etc.

Tuberculosis (TB) in humans is caused by the bacterium, Mycobacterium tuberculosis. Its airborne spread was favoured by the crowded conditions in cities following the industrial revolution, and its elimination fostered by improved living conditions and the development of antibiotics in the twentieth century.

Footnote: Some Factors affecting Malarial Outbreaks in Africa

A section from an article by Tarekegn A. Abeku, entitled Response to Malaria Epidemics in Africa, is relevant:

  In highlands, transmission is unstable due to fluctuations in temperatures that are normally low. Temperature affects duration of the sporogonic cycle of the Plasmodium parasite within the Anopheles vector, survival and feeding frequency of the adult female, and duration of the aquatic stages.

and

  Semi-arid areas, on the other hand, have mostly warm climates, and epidemics are associated with anomalous rainfall, which causes increases in vector breeding and survival.


Are we more attracted to people of the same ethnicity?

The answer in extreme brief is yes.  Only about 9% of whites and 16% of blacks engage in interracial marriage in the U.S.

But really this deserves a fuller discussion.

The predominant pattern of mate selection in human beings is to marry within their ethnic group.  I say 'ethnic group' rather than 'race' because 'race' has no strong scientific definition. Racial groups as usually understood have about the same genetic variance as the overall species.  I need to point out here that races can have a strong geographical point of origin and thus races can in some cases be genetically identified, but these correlate poorly often with, say health risks or other clinical data.

Because its clear that interracial marriages are on the rise in the US, mating choices are often argued to be socially defined preferences.  Social attitudes affect men and women differently and different cultures too, as tracked by regional differences. Not the least is a limit of opportunities.  Being comfortable with people from other cultures or who simply look different.

Interestingly, Women at least in American studies are much more likely to state a same-race preference (see p17), while men are likely to demur from stating a preference, but act out a bias unconsciously, making both genders equally biased.

As mentioned in the comments by @AliceD, Mating preferences as described in traditional population biology are adapted from availability.  That's to say people don't meet because of ethnic boundaries such as geography, socioeconomic or social strata. Then there are socialized preferences.  I.e. growing up we are imprinted by the sorts of people we see, which can create preferences later in life.

Lastly there may be genetically conveyed preferences. The human race has been spreading out over the past 200,000 years or so.  That's a pretty small amount of time.

There are cases where such mating preferences have evolved.  There are 17 species of arctic penguins, species caused by migration around the globe.  Each species can actually mate with others nearby, but where the penguins met at the far end of the globe, the species do not mate because they have been separated for so long they have diverged.

But speciation events can take millions of years.  Its clear that human beings from the far corners of the globe can produce offspring - we are one species.  It seems as if we are only a fraction of the way towards two neighboring penguin species in the example above.  There doesn't seem to be any evidence that we are genetically predisposed to ethinic self mating.

Only by way of example (not to offend anyone!) you can choose an ethnic group which has divergent behavior and try to get an estimate of how big a role the social context plays.  Looking at the jewish community we see that 47% of jewish people have married out of group in recent statistics.  They are thinly distributed over a wide geographical region and availability is high for out-group marriage.  All this while orthodox jews have a practically non-existent out-group marriage rate. Not judging here, but only for illustrative purposes we can guess that social attitudes and behaviors are playing a large role here.

As and endnote, I'd also like to point out that since whites are about 50% of the US population and african americans are about 10%, the percentages not so disparate as they seem - all things being equal the average person one meets in the US is white.  For caucasians, approximately 50% of the population the average interracial marriage rate with no racial biases is is 50%.  For blacks its 90%.  Again, just using random shuffling for statistical point of view.


What does the nucleus look like in S phase of Meiosis?

In terms of chromosome number
During meiosis, the meiocyte is a diploid cell ( 46 chromosomes for human). So during the S-phase , the meiocyte would contain 46 chromosomes.
At the end of meiosis I, the divided meiocyte contains 23 chromosomes so it's called the reductional division
At the end of meiosis II each cell contains 23 chromosomes.
In terms of chromatid number and number of DNA molecules
Meiocyte in S phase contains 2 chromatid in each chromosome, so the number of DNA molecules is doubled (if you consider that each chromatid is composed of a pair of DNA strands like in Watson Crick Model, then each chromosome of S phase contains 4 strands... So 46×4 strands of DNA is present. Often each helix / duplex is considered one DNA molecule , so in that case you have 46×2 molecules. So you have to be careful with the terminology mentioned.
After meiosis I there are 23 chromosomes in each divided cell with 2 chromatids in each chromosome...So there are 23×2 DNA molecules.
After meiosis II there are 23 chromosomes with 1 chromatid...So they contain only 23 DNA molecules.


What do the names of Immunoglobulin subtypes mean?

Ig stands for immunoglobulin. The isotype names have various origins. This paper provides an interesting story:

Black CA. 1997. A brief history of the discovery of the immunoglobulins and the origin of the modern immunoglobulin nomenclature. Immunol Cell Biol 75:65-68.

A brief summary, in order of characterization and naming:

IgG - named gamma globulin because it migrated in the gamma band of electrophoresed blood plasma (the bands were named in order of mobility: alpha, beta, etc)
IgM - named macroglobulin because it sedimented faster than IgG (ie was larger)
IgA - found in the beta and gamma bands of electrophoresed plasma and initially named β2A and γ1A, later renamed to alpha globulin
IgD - named by process of elimination: IgA was taken, murine immunoglobulins were expected to be named beta, the letter C has no Greek equivalent
IgE - named because it was most reactive with a fraction of pollen proteins (fraction E because it induced erythema)


Can sugar alcohols, and glycerol in particular, cause intoxication?

Well, I was intrigued by this, and my intuitive response was that it would never be toxic at reasonable doses, but I was wrong.
A quick Google search led me to this paper:

Andresen, H. et al. (2009) Severe glycerol intoxication after Menière's disease diagnostic--case report and overview of kinetic data. Clin. Toxicol. 47: 312 - 6

Apparently in the Klockhoff test for Menière's disease the patient is given an oral glycerol dose of 1.2 - 1.5 g/kg (50% in water) then observed over a period of 4-5 h. The other details of the test don't concern us here. In this case report a patient suffering neurological symptoms was found to have previously undergone a Klockhoff test at another hospital, and it was estimated that he must have received a dose of 3.88 –3.95 g/kg.
Here are two sections from the paper's introduction (references removed).

Glycerol is well known as a nontoxic substance (LD50 > 25 g/kg in the rat). Possible side effects of the Klockhoff test include headache and nausea. During treatment of brain edema, additional adverse effects such as diarrhea and vomiting were reported, symptoms comparable to those reported for intensive osmolar diuretics. The GESTIS database ranks glycerol in general as a substance with very low toxicity. However, severe symptoms after oral ingestion of glycerol have been reported to occur. Doses exceeding 0.7 g/kg BW have been regarded as potentially toxic for adults. After doses of up to 1.4 g/kg BW, only mild symptoms such as headache, nausea, and diuresis appear. Reportedly, these symptoms are also associated with glycerol treatment of brain edema. In individual cases, an oral dose of 100 g of glycerol has been reported to cause drowsiness, cyanosis, renal pain, and bloody diarrhea.
Martindale Reference Desk reports headache, thirst, nausea, and hyperglycemia as adverse effects. Glycerol may also produce cardiac arrhythmia and hyperosmolar nonketonic coma. These effects are mainly based on its dehydrating properties. Hemolysis has been reported to exclusively occur after intravenous infusion. In fact, most of the major toxic effects of glycerol, such as hemolysis, hemoglobinuria, and renal failure, seem to strictly correlate with serum concentration of glycerol and the route of administration.

It appears then that any toxic effects of glycerol are not due to its alcohol nature per se but rather because it can become elevated in the blood leading to osmotic effects. The authors estimated that 10 h after administraion of the glycerol the concentration in the patient's serum was approximately 39 mM, compared to a physiological basal level in the range 0.05–0.3 mmol/L. The patient's serum level fell to the basal level over a period of 30 hours.
Just to put this in some perspective, in the UK the legal alcohol limit for drivers is 80 mg/100 mL which corresponds to 17.4 mmol/L.
I think that recommending sugar alcohols would fall under the heading of medical advice (not that I have any such recommendations).


Why are prokaryotic promoter sequences written 5' to 3', when transcription proceeds from 3' to 5'?

DNA sequence by convention is written starting at the 5' position so the directionality is assumed without explicitly writing the 5' and 3'. As for why its not the template strand sequence. I would say that's also a convention for simplicity because you only need to write one sequence if you want to discuss genes and regulatory elements.


How has the use and subsequent ban of DDT affected insect populations?

The most thorough study on the matter appears to be entitled "Anthropogenic impacts on mosquito populations in North America over the past century". Their broad conclusion is that various mosquito populations decreased in abundance and variety during heavy DDT usage years. However they have revived in the past few decades. The only species that seemed to have a permanent decline is Ae. Stimulans.  While this study was only on mosquitos, it may be representative of wider insects - most revived but a small fraction faced permanent damage.

There is a large amount of more associative evidence that observes a large decline in insect biomass and can only predict pesticides, such as DDT, as the culprit. The NYTimes had a good article on this.


What is the ratio of breathing rate to heart rate?

"This is because the heart is connected to the lungs via the pulmonary artery." It's not like heart rate or breathing rate are regulated by pulmonary arteries. The relation is more sophisticated than that. For example heart rate is controlled by nerves and hormones, and neither comes straight from the lung. But fast breathing leads to changes in blood oxygen and pH, which are picked up by sensors such as the carotid body, which informs the medulla, which then talks to the sinoatrial node. There is also more direct influence, because ample breathing increases pressure in the thorax.

But at each step, there are many other factors interfering, meaning the correlation between the two gets ever looser. There isn't really a "normal" ratio of heart rate to respiration rate. There is a healthy heart rate and a healthy respiratory rate, but they are both wide intervals (60-100 and 12-20, respectively). Dividing one by the other, you get a very wide interval, from 60 beats per minute / 20 breaths per minute = 3, to 100 beats per minute / 12 breaths per minute = 8.

Perhaps in practice the most common values for beats per breath are in a narrower interval. But "normal" values are defined in relationship to abnormal conditions, and there is no disease in which a change in this ratio is a cardinal feature. It makes little sense for clinicians to define a normal range for beats per breath, and therefore it makes little sense for epidemiologists to estimate most common values.


My answer may be a little basic, but I think it is comprehensive:
Many elements are special; for instance, many metal ions such as iron or cobalt are required as cofactors or in catalytic sites due to their chemistry. Oxygen is highly electronegative, that also grants it some of its functions. But... without delving too much into things... chloride is the most basic constituent of saline, without which it would not be saline. Here are 3 very, very important and yet

It works well with alkali and alkaline earth metals, hydrogen, and many compounds... it's a natural pairing!
You cannot separate positive and negative charges in a solution at a macroscopic level. It's not a feasible thing to avoid harboring chlorine atoms as part of biochemistry.
It accounts for a large portion of extracellular fluid tonicity.
etc...

Thus, most inter- and extra-cellular fluid is relatively chloride ion rich, across the entire bush of life. To my knowledge there is no life, tissue or cell on this planet that does not contain chloride ions as part of its makeup by necessity. It is simply heavily constrained in evolution as a basic component. It's just not practical to obtain K+ or Na+ or Ca2+ ions without Cl-, it is so common in nature.
If you want specific examples, you can always mention its indispensable roles in neuron firing (transmission of axon potentials) and general cellular homeostasis, which is dependent on electrochemistry and osmolarity and stuff like that which is heavily influenced and dependent on the presence of a regulated concentration of solvated Cl-.


What are the dimensions in angstrom of bacteria?

According to Wikipedia: 3 um long with a diameter of 0.5 um. That equates to a length of 30 000 A and a diameter of 5 000 A.

http://en.m.wikipedia.org/wiki/Helicobacter_pylori


How are melatonin levels measured in humans?

On the analytics of melatonin I have here a german language text by the RKI with references. Translated quote:

  Assay of melatonin is done by serum or sputum using RIA or ELISA.
  Alternatively, to infer the nightly amount of melatonin secretion it
  is possible to look for the melatonin catabolic metabolite 6-hydroxy
  melatonin sulfate (6-OHMS) in urine.[1,2] ... standardized
  conditions of sample taking are a must to get good results.[3,4]

Ref.:

P. Levallois, M. Dumont et al: Effects of electric and magnetic fields from high-power lines on female urinary excretion of 6-sulfatoxymelatonin. In: American journal of epidemiology. 154, 7, October 2001, 601–609. PMID 11581093
D. H. Pfluger, C. E. Minder: Effects of exposure to 16.7 Hz magnetic fields on urinary 6-hydroxymelatonin sulfate excretion of Swiss railway workers. In: Journal of pineal research. 21, 2, September 1996, 91–100. PMID 8912234
E. Gilad, N. Zisapel: High-affinity binding of melatonin to hemoglobin. In: Biochemical and molecular medicine. 56, 2, December 1995, 115–120. PMID 8825074
D. K. Lahiri, D. Davis et al: Factors that influence radioimmunoassay of human plasma melatonin: a modified column procedure to eliminate interference. In: Biochemical medicine and metabolic biology. 49, 1, February 1993, 36–50. PMID 8439449


Diffusion of Hypotonic solution into solution with glucose and starch

The bag will swell.

Diffusion results in molecules moving down their concentration gradient.

In the set-up described only glucose and water are able to diffuse. Glucose is at the same concentration inside and out so there will be no changes in glucose concentration. Water will move into the bag because it is effectively at a lower concentration (more correctly  - chemical potential) inside due to the presence of the starch. As water moves into the bag, increasing the volume, glucose will also move so that the glucose concentration remains equal on both sides. Thus there will be net movement of water and glucose into the bag.

@WYSIWYG has raised the spectre of colloids in the comments. I don't understand colloids so cannot comment, but I think that in the context of problems like this we are usually dealing with "soluble" starch. Here is an example of a calculation in which starch is treated as an osmolyte.


Under what circumstances does Batesian mimicry evolve?

While the attempt to consider this in a mathematical framework perhaps isn't so useful, it seems that the biological essence of your question is along the lines of:

  Does a Batesian mimic initially need to be initially quite similar in morphology to the different species which it evolves to mimic?

The answer is no, morphology does not need to be similar, but it does help make mimicry likely. The only requisite to evolution is the presence of heritable genetic information with the potential for change, and this prerequisite is the same for any trait. Selection is not a prerequisite but mimicry is more likely to evolve by adaptive evolution than random evolution. Given that phenotype is often strongly affected by the DNA and that DNA has a potential to mutate, then any distance in phenotypic space can be covered so long as sufficient mutations occur. Sufficient mutations are more likely to occur when

a) the distance in phenotypic space between the two initial species is small (the ancestral form of the mimic species is similar to the species it will mimic)

b) a large amount of time is allowed to elapse (more mutations can occur)

The first of these is simply stating that there are fewer (or less extreme) mutations required to get the species to be perfect mimics. The latter simply states that time allows for a greater number of mutations to occurs, making it more likely that large phenotypic spaces can be bridged.

Consequently, allowing identical time, mutation rates, mutation effect sizes, and selection coefficients, two species that initially look similar are more likely to evolve mimicry than two species that initially look very different, because fewer steps need to be taken for convergence of phenotypes.

This is the same for any trait. One could ask can humans evolve to be ten feet tall, the answer is yes, as long as the genetic variance arises. One could ask can humans evolve to be 20 feet tall, and again the answer is yes. However, the latter is less likely because it requires a greater movement in phenotypic space. More time also makes both results more likely.


Should the sum of RPKMs be constant over experiments

I guess this arises because of the default cufflinks option --total-hits-norm in which it normalizes the FPKMs with total reads including the ones that are not mapped to a known gene or a predicted gene from the assembly. In the genes.fpkm_tracking file the FPKM values are reported for known/predicted genes. It is certainly possible that the number of genes are different in a certain sample compared to the other and perhaps therefore the sums are different. If you are not interested in finding new transcripts then you can run cufflinks with a reference GTF/GFF file provided using --GFF along with using --compatible-hits-norm.

You can also try this:

Assemble with cufflinks, merge the GTFs with cuffmerge and run cuffquant with the merged GTF.

You can subsequently use cuffnorm to normalize the expression values. It has been observed by me and others that the FPKM value reported by cuffdiff and cufflinks are different which is most likely because of differences in default parameters (see this). The inner operations of cufflinks are not very clearly documented; so I cannot conclusively answer your question.


When you estimate a phylogenetic tree, be it by likelihood, parsimony, or distance (like NJ), the lengths will be given in units of substitutions per site, with no time information. For example from here:

  The units of branch length are usually nucleotide substitutions per
  site – that is the number of changes or 'substitutions' divided by the
  length of the sequence (although they may be given as % change, i.e.,
  the number of changes per 100 nucleotide sites).

To transform these lengths into a time scale, further information is necessary. For example assuming that the molecular clock is valid, or instead using relaxed clock models that describe how each branch length l=r x t can be decomposed into a rate r and a time t. Since in many cases the rate is not constant along the tree (i.e. the clock is not valid), an inferred phylogenetic tree is not ultrametric (i.e. the sum of branch lengths from the leaves to their MRCA is not constant).

There are software packages, most notably BEAST, that explicitly model a strict or relaxed clock for you, and then can return the branch lengths in arbitrary time units. "Arbitrary" means that the numbers by themselves do not have special meaning, and will reflect your choice for instance of the prior. In which case they can represent year, million years or generations (http://beast.bio.ed.ac.uk/faq#Evolutionary_rates_and_time_scales).


Is the "Great Pacific Garbage Patch" beneficial for marine wildlife?

There are very few things in the world that aren't beneficial to some lifeform.  Even if you were to, say, spill a mixture of persistent broad-spectrum poisons on an area that killed off 99.9% of all species there, the remaining 0.1% that did survive would benefit from the lack of competition.

The "great garbage patch" is hardly so extreme a phenomenon, but similar effects can be seen there: some species suffer, others benefit.  In that sense, it's no different from any other changing habitat.

From a conservation viewpoint, there are two issues here that one might find worrying:

First, novel, extreme or rapidly changing habitats tend to have lower than average biodiversity, at least initially: the few species that thrive in the new environment tend to proliferate at the expense of others, forming a relatively simple (and often not very stable) food web.  Of course, over evolutionary timescales we'd expect the surviving species to adapt and diversify and the ecosystem to settle into a more stable state, but that tends to take a long time compared to the human timescale on which such novel habitats are created.
Also, the effects of the "garbage patch", or ecological changes in general, are not limited to the directly changed area.  Creating a new habitat in one part of the ocean is one thing; disrupting the ecosystem of the entire ocean is something else, as doing so leaves no unaffected refuge for the species that are harmed.

For example, fish, birds and marine mammals passing even just occasionally through the patch might end up swallowing plastic and accumulating it in their gut; meanwhile, even for less motile organisms, the patch might act as a population sink, depleting their population density in nearby areas.  And if some organisms, such as the sea skaters mentioned in the article you cite, thrive in the patch, the increased population will likely spill into other areas, potentially harming their competitors or prey species.

As for why the news are focusing on the beneficial effects of the garbage to the sea skaters, well, that's what the study that prompted this current batch of news stories was about.  It's also seen as newsworthy precisely because it seems so unexpected: we've all heard stories of plastic flotsam harming wildlife, so finding out that some species are actually benefiting from it has some "man bites dog" style news value.

Also, it's a lot easier and more convincing to observe something that is there than something that isn't: we can directly see these insects laying their eggs on the bits of plastic, giving direct and incontrovertible proof of a causal connection.  Meanwhile, simply observing that some species used to be more common in the area of the patch than it is now is a lot less direct and informative: we might never be sure just how the patch is harming that species, and it always leaves skeptics an opening to claim that the decline might be caused by other factors.  With the sea skates, on the other hand, we're not just observing the effect, but the direct mechanism as well.


Can too low oncotic pressure lead to Third spacing and Edema?

Yes it can! Its a very important cause of third spacing a.k.a. peripheral oedema, mainly due to decreased protein.

Below is a list of causes of peripheral oedema due to fluid moving from the vascular bed to the peripheral spaces gathered from the following source: http://www.patient.co.uk/doctor/Peripheral-Oedema.htm

Immobility: Increased fluid pressure from venous stasis. Varicose veins.

Obesity: Increased fluid pressure from sodium and water retention; should not to be confused with non-pitting lymphoedema.

Cardiac: Increased fluid pressure: right heart failure, constrictive pericarditis.

Drugs: Increased fluid pressure from sodium and water retention: calcium antagonists, non-steroidal anti-inflammatory drugs (NSAIDs), prolonged steroid therapy, insulin.[1]

Hepatic: Decreased oncotic pressure: cirrhosis causing hypoalbuminaemia.

Renal: Decreased oncotic pressure from protein loss, and increased fluid pressure from sodium and water retention: acute nephritic syndrome, nephrotic syndrome.

Gastrointestinal: Decreased oncotic pressure: starvation, malabsorption, protein-losing enteropathy (eg Crohn's disease, ulcerative colitis, tumours of stomach and colon, coeliac disease and other intestinal allergies).

Pregnancy: Increased fluid pressure both from sodium and water retention and venous stasis from pelvic obstruction.

High-altitude illness: Oedema of face, hands and ankles may occur.

Idiopathic oedema: Associated with cyclical high lymph volume overload, or dynamic insufficiency: usually in a woman aged 20-40 years. Variable and not related to menstrual periods. Diagnosis is based on the exclusion of other causes of oedema.

Post-thrombotic syndrome: Late complication of deep vein thrombosis (DVT) which occurs in up to two-thirds of patients. May present with pain, oedema, hyperpigmentation, and even skin ulceration. May result from remaining venous obstructions, from reflux, or both. Rate of reflux is highest during the 6-12 months after an acute DVT. It may be temporary and self-limiting or not resolve and persist at variable severity.

Pitting localised limb oedema:

DVT: Compression of large veins by tumour or lymph nodes.

Following hip replacement or knee replacement.

Local infection, trauma (including burns, which may also cause generalised oedema because of protein loss), animal bites or stings.


Do ant colonies prioritize survival of particular members above others?

I couldn't find any information about ants starving in times of plenty, most likely since it's difficult to determine whether an ant colony is "letting" certain members starve or whether the ants have just died for whatever reason. To your second question, though, yes! This paper, The Effect of Colony Size and Starvation on Food Flow in the Fire Ant by Howard and Tschinkel, shows the effects of different lengths of starvation on the passing of radioactive food through different sized ant colonies. First, the queen:

  Generally, queens received radioactive food earlier in starved colonies than in well-fed ones

Starved foraging ants distributed food more quickly than forager ants who had not been starved:

And interestingly, in large colonies, larger worker ants were more likely to receive food (radioactivity) than smaller ants. Very cool paper.


Picking up Plasmid DNA using Nanodrop, but not using Electrophoresis

Having a positive reading on the Nanodrop but no band on the gel can be due to a number of different issues (not exhaustive):

An incorrectly zeroed sample
Incomplete staining of the gel
Contamination of the sample
Human errors in loading of samples

You should try to exclude these possibilities by positive controls in order to find out the true reason behind the inconsistent results.


They look like seeds from palm trees. It reminds me of seeds from Phoenix canariensis which I once planted. However, since this particular species is not native to India, they could be seeds from another Phoenix palm species. Do you have Phoenix palm species in your area in India?


Do intestinal flora have the same DNA as their host?

Could you suggest a good source for beginners. - Louis Somers

The interactions between the human body and its microbiome are quite complex. I am going to provide you with an answer that will be based on your comment that you would like an answer from a beginners perspective.

For simplicity sake I will keep the answer to humans as the host organism, though pretty much any multicellular organism can act as a host for microscopic organisms.

Note: A number or the references I use come from Janeway's Immunobiology. The links provided are to the 2001 edition that is on the NCBI bookshelf. The issue, however, is that over the past decade we have learned a great deal more about the immune system since then, and some of the things I refer to were not represented in that edition of the text.

  Do intestinal fauna have the same DNA as their host?

The short answer to this question is no. Also, we generally identify microbes of this nature as flora instead of fauna, so you would say intestinal flora.

The human microbiome (microbiota), as it is often referred to, is made up of hundreds of trillions of microorganisms that live in the niche of our digestive tract, airways, urogenital tract, and skin. In fact, the estimate is that there are 10 times as many microbial cells that live on the human body than there are human cells that make up the body itself (1). The difference is that human cells are immense when compared to most of the microbial cells that colonize us (2).

The vast majority of the microorganisms that populate us are single-celled organisms, such as bacteria or fungi (yeasts). Each of these cells is its own entity, in other words is an independent living organism, and they have their own genome (the complete genetic material of an organism) that encodes for their own proteins.

There is a good reference tool, though maybe a little advanced from The University of Utah, The Human Microbiome. This interactive presentation gives a layman's overview. The American Museum of Natural History has also curated an exhibit called The Secret World Inside You.

To add a point for clarification, while the genetic codes of these microbes are different in different species and are different from that of the human host, the molecules that hold the information, namely DNA, are all made of the same nucleic acid building blocks (5). To use an analogy, it is like using the same letters but writing in two different languages. We may use mostly the same characters, but the way we arrange those letters to form words in Spanish or words in English create different meaning.

When these single-celled organisms reproduce, they copy their own DNA and they divide into two new cells, each receiving one copy of that DNA (6).

Since yeast and other fungi are evolutionarily closer ancestors to humans than are bacteria, some of their genes, the sections of DNA that are functional and encode for proteins and RNAs, have a very similar sequence to our own (referred to as having homology) and often perform similar or the same function (7). When this is the case, we say that the genes are evolutionarily conserved, but for the most part evolutionarily conserved genes will vary in sequence from organism to organism, and the variation will usually increase the farther back you go in order to find a common ancestor between the organisms.

The human body is made up of about 37.2 trillion cells, on average (8). Almost all of these cells, with the exception of Red Blood Cells, have a copy of the hosts genome (9). All of these cells arose from a single egg produced by the mother and fertilized by the father's sperm (10). The egg and the sperm contained half the genome necessary for the embryo to develop. The DNA from the mother and the DNA from the father come together when the nuclei fuse. So we have our own genome that came from our mother and father, and the microbes have their own genome which they inherited from the ancestral cells that gave rise to them.

That is a slightly simplified answer as there can be different ways that the DNA can be passed between the organisms, but for the most part, we have our own DNA and, even though they live on us and in us, the microbes have their own DNA.

  Your first paragraph.

I cannot tell you necessarily why seed that we swallow and digest do not germinate inside of us. It is likely that the seeds are not receiving the proper signals from the environment of our digestive track to initiate the genetic program to begin germination and development into a plant.

  I also heard that the immune system uses the same technique to detect intruders (and subsequently attack donor-organs).

The vertebrate immune system is a diverse, highly-tuned system of surveillance that monitors for pathogens or foreign bodies that are introduced into the body that may be dangerous to the survival of the organism (11).

For humans, the first set of defense are barrier defenses (12). The surface of our skin consists of several layers of dead, keratinized cells that form an impermeable barrier. As long as this layer is not breached, it does an excellent job of keeping yeast and bacteria outside, away from tissue that they could damage.

On the interior surfaces, our airways, gastrointestinal tract, and genitourinary tracts contain specialized cells that produce large amounts of mucus that will coat the surfaces of these tissue. Mucus serves multiple roles. First it keeps the tissue moist, so that it does not dehydrate. Next it keeps the microbes at a distance from our cells, so that they do not come in direct contact with our epithelial cells (The cells that make up the linings of our digestive tract, genitourinary tract, and airways). Third, it can trap microbes in it. The epithelium is able to "sweep" the mucus along and as a result it is able to clear bacteria out of the body (13).

Included in the barrier defenses are actually the microbial organisms themselves. The interaction between the host and an organism which is neither detrimental or actively beneficial is known as commensalism (13). Basically, all of these trillions of microorganisms that life on us do not hurt us. In return, they get an environment in which they can live. As a result of this, commensal organisms will grow on these surfaces, will take up all of the space, and will use up the nutrients that could be used by pathogenic organisms (organisms that are actively able to cause an infection) to establish an infection.

The next level of defense comes from the cells of the innate immune system (14). In innate immunity, specialized cells monitor the area they are in for Pathogen-Associated Molecular Patterns (PAMPs). PAMPs can be sugars that make up the cell walls of the microbe or proteins that get expressed on the surface of the organism, such as Flagellin, a protein only found in the flagella of certain pathogen. The innate immune cells have pattern recognition receptors (PRR) that have a general specificity for recognizing and responding to the PAMPs. Our cells even have PRRs for DNA and Double Stranded RNA's, however those are usually found in vesicles on the inside of the cell. These interactions are very general, however once PRRs bind to the PAMP, they are able to signal into the cytoplasm, which can lead to the production of proteins, among other possible responses.

Here you can think of PRRs like a motion detector in a security system; the dog, or your two year old, or an intruder are going to set off the alarm just the same. It is not specific. The motion sensor "knows" that something that it is supposed to recognize, i.e. a moving object larger than a mouse passed by and it triggered the response, but it cannot tell you which moving object triggered it, only that it was triggered.

The innate immune cells are also able to respond by "eating" the pathogen in a process called phagocytosis. Here, they break up the bacteria, yeast, or the remnants of other dead host cells or large pathogens, things like worms, and put the broken up pieces on protein molecules on their surface.

When innate immune cells do this, they are presenting molecules to specialized immune cells (adaptive immune cells (14)), B-Cells and T-Cells, that are highly specific as to what they will react to. These cells can also cause a lot of damage to the host, so they are tightly regulated. Think of the interactions as keys and locks. A protein from a bacteria should turn a few of these cells on, but a protein from the host should not fit the lock.

All of these immune cells also respond to diffused chemical signals called cytokines. These molecules are secreted by some cells and are received by receptors on the host cells. Sometimes the secretion is by another immune cell, sometimes it is from a non-immune system host cell, and sometimes these molecules can be secreted by the bacteria, fungi, or worms themselves.

Depending on the chemical signals that are secreted, and how the cells are interacting at the time of the message, and which cells are receiving the message, will determine the response to the message. It is contextual. Think of the phrase "You're killing me." If someone says it, while laughing, to a good friend who is telling jokes, it means one thing. If it is screamed as someone is being choked by an attacker, it means something very different.

To summarize, the immune cells are surveilling the environment and trying to pick up what is friend and what is foe and they try to respond accordingly.

Over time and coevolution, our microbiomes have developed ways of communicating with our immune system to let it know that these microbes do not mean any harm. They are able to "train" the immune cells using chemical signaling to temper the immune systems response to them (15), and this is how they are able to coexist within our body and with an immune system that is constantly on seek an destroy missions. Also because of the mucus, our microbiome usually isn't in direct contact with our cells, so it is a different kind of interaction than if an infecting pathogen were to breech the barriers and gain access to sterile areas where no bacteria or fungi should be found, and as a result, the immune system reacts differently.

As for organ and tissue rejections (16), the issue here is that each of our cells, except for Red Blood Cells, present molecules on their surface that identify it as being a cell that was made by the body itself. You can almost think of it as a sport's teams jersey. The immune cells can survey the proteins displayed on the surface of our cells and tell that they are ours instead of from a pathogen. The problem is that each person makes a different array of these proteins, so if I were to give you a kidney, the proteins that the cells from my kidney make and put on their surface for immune cells to look at will be different from yours. In this case, because the keys do not fit the locks, the immune system reacts to the donated organ as an intruder and begins to attack it. Immune cells are extremely lethal and will kill the donated organ if they are not suppressed. That is why transplant recipients need to have their immune systems suppressed in order to survive with the donated organ. You might ask "well what if we just took all these proteins off of the surface so that they don't get recognized?" Well, the problem is that we have another class of immune cells known as Natural Killer Cells that patrol the body looking for cells that are not presenting these proteins, so the immune system is pretty adept and finding and killing things that it does not recognize specifically as self.

  I was wondering, when a baby gets weaned (starts eating regular food), where do these fauna come from? Does the baby produce them, or are they provided in the food and survive the defense system?

To be honest, the majority of the microbiome is laid down during vaginal birth and breast feeding. Passing through the birth canal, microbes from the mother's vagina and feces are ingested by the newborn and this is their first real dose of microbiome, though some research is suggesting that the microbiome begins to form in the fetus before birth and is transferred through the placenta from the mother to the fetus.

Assuming we do not kill these bacteria with antibiotics, have other pathogenic bacteria take over the territory (yes, bacteria and fungi, like gangs, have turf wars; that is why we often find our antibiotics as compounds secreted by these organisms), or have a disease that wipes out the microbiome, and provide it with a health diet, then the microbiome pretty much is maintained by the microbial cells reproducing by cell division.

Also we will pick up these bacteria from the environment. We are constantly shedding enormous amounts of these cells into our environment. Babies touch things and put their hands in their mouths. This transfers good microbes as well as bad ones, and it is really just a natural part of the process. That is why the overuse of antibiotics and antibacterial soaps can cause unintended consequences. We are killing the good as well as the bad.

This reference, Your Changing Microbiome, again from The University of Utah is a good resource.

So to summarize, babies get the microbiome at birth through vaginal flora and maternal feces. They are also getting daily doses from the microbes that colonize the mother's skin when she nurses the child. Then these bacteria are also in the environment, so babies touch things, then they put their hands (or feet, the little contortionists) in their mouths and they get doses this way. Raw fruits and vegetables will also have microbes on them that will be taken in. As for the microbes, they have cell walls that allow them to live in environments that would be hostile if they did not have the cell walls. They also communicate with our immune system and "train" it not to kill them, and as long as nothing that we do, such as take antibiotics or get a disease, the microbiome will pretty much maintain itself through replication.


No.  Nobody considers red blood cells to be prokaryotic, perhaps most importantly because they are part of a eukaryotic organism.  Red blood cells begin life with the full complement of organelles, including a nucleus and mitochondria, but our RBCs shed their organelles during maturation.  In actuality, though, only mammalian RBCs lack nuclei; other animals' RBCs still hold on to their traditional eukaryotic characteristics.

As an analogy, apoptotic or necrotic cells don't have intact organelles, but they are still considered eukaryotic.


Why don't fish get hurt with so many sharp fish bones?

Connective tissues prevent fish from being hurt by its bones. They surround the sharp bones so that the bones do not hurt its organs/flesh.

However Of course the bones can hurt the fish, but the situation is quite imaginable.

If a fish is smashed or gets too much force, its connective tissues cannot protect its organs much(like our clothes cannot protect us from bullets, or our broken bones penetrating our organs when we encounter a serious car accident despite our connective tissues covering the bones - the bones just damage our connective tissues and organs, and so on...) and its organs get hurt.

Your worry can happen in human case too (but much weaker version), we can think of our hip bones sometimes pressing our flesh between the bones and the chair we are on.


When contracting a muscle will the muscle spindle stretch or contract?

The muscle spindle normally stretches/contracts in concert with the muscle fibres in order to maintain detection of changes in length.

This image should demonstrate it clearly:

  When the muscle spindle is stretched and excited it sends impulses to the spinal cord more rapidly (increased frequency). The sensory neurons synapse with alpha motor neurons in the spinal cord, which stimulate the extrafusal muscle fibers of the stretched muscle to contract and resist further stretching.
  Contraction of the muscle (extrafusal fibers) would cause the muscle spindle to become slack and stop transmitting impulses, however descending fibers of motor pathways synapse with both alpha and gamma motor neurons (alpha - gamma coactivation) so the ends of the intrafusal fibers contract and maintain muscle spindle sensitivity when the muscle contracts.

Further reading: here.


Gene & Protein nomenclature: N-Myc, c-Myc, et. al

There is a useful set of links to nomenclature guidelines for all of the main genetic systems at this Wikipedia page. Personally, I think that the Saccharomyces cerevisiae system works best: it manages to cover dominant and recessive alleles of a gene, the name of the protein, how to refer to a related phenotype, and the use of a parallel convention for the designation of ORFs.

Unfortunately there is now no going back - there are many different systems and there is no hope of unifying them. When this plethora of naming conventions is combined with the reluctance of so many scientists to stick to the guidelines, we have a recipe for near anarchy.

Edit - On the specific topic of MYC nomenclature:

The v- and c- prefixes come from the early days of oncogene research. Viral oncogenes such as myc and src were found to be related to (derived from?) similar genes in normal cells. Thus v- means viral and c- means cellular.

This can be seen if you peruse the HUGO entries for the four MYC family members encoded in the human genome (extracts below). They all have an approved name which relates them back to a viral oncogene found in the genome of avian myelocyomatosis virus. This was the founder member of this gene family. Thus c-myc was the first myc-related gene found in the human genome, and is the one that is responsible for Burkitt's lymphoma. It is true, as @Leonardo says, that in tumours the expression of this this myc gene in lymphatic tissue changes due to chromosomal rearrangements, but this is not the origin of the designation c-myc.

  MYC
  Approved Symbol:      MYC
  Approved Name:   v-myc myelocytomatosis viral oncogene homolog (avian)
  Previous Symbols & Names:   "v-myc avian myelocytomatosis viral oncogene homolog"
  Synonyms:   bHLHe39, c-Myc
  Chromosomal Location: 8q24

  MYCL1
  Approved Symbol:      MYCL1
  Approved Name:   v-myc myelocytomatosis viral oncogene homolog 1, lung carcinoma derived (avian)
  Previous Symbols & Names:   MYCL, "v-myc avian myelocytomatosis viral oncogene homolog 1, lung carcinoma derived"
  Synonyms:   bHLHe38, "l-myc protein", LMYC, "myc-related gene from lung cancer", "oncogene lmyc"
  Chromosomal Location: 1p34.3

  MYCL2
  Approved Symbol:      MYCL2
  Approved Name:   v-myc myelocytomatosis viral oncogene homolog 2 (avian)
  Previous Symbols & Names:   "v-myc avian myelocytomatosis viral oncogene homolog 2"
  Synonyms:   bHLHe38
  Chromosomal Location: Xq22-q28

  MYCN
  Approved Symbol:      MYCN
  Approved Name:   v-myc myelocytomatosis viral related oncogene, neuroblastoma derived (avian)
  Previous Symbols & Names:   NMYC, "v-myc avian myelocytomatosis viral related oncogene, neuroblastoma derived"
  Synonyms:   bHLHe37, N-myc
  Chromosomal Location: 2p24.3


Cell Respiration and Oxidative Phosphorylation

The passage of protons through the FO (membrane) portion of the molecule (driven by the electrochemical gradient of protons across the respiratory membrane) generates torque at the interface between the a and c subunits. This mean that the ring of 10 c subunits rotates relative to the a subunit. The γ subunit in the stalk rotates along with the ring of c subunits, while the ring of α and β subunits in F1 is constrained to remain static with respect to the a subunit because of the interaction with the δ and b subunits (forming the peripheral stalk). So we have two portions of the molecule the "static" a-b2-δ-α3β3 part and the rotating c10-γ-ε part. The γ subunit rotates within the α3β3 part of F1 and drives a three-step cycle of conformational changes (via intersubunit interactions) which are linked to the phosphorylation of ADP.

There is a useful animation here illustrating the three step catalytic cycle being driven by the rotation of the γ subunit.

(image from Aksimentiev et al. (2004)
Insights into the molecular mechanism of rotation in the FO sector of ATP synthase. Biophys J. 86:1332-44)


I believe it is more of the fact that the organism gets stuck to the residual resin on the plant itself, and becomes encased and later fossilised in the amber.

From LiveScience.Com:

  A host of bugs, fungus and other life forms have been found trapped in amber from the time of the dinosaurs.  Bugs can become encased in amber if, while alive, they get stuck in the resin.

Although plant resin is slow-moving, the bug stands to be encased in it if it is already stuck to the tree itself, as there is a large amount of resin on the surface of the plant.  If they are crawling over the plant, or land on the surface, they would become stuck and later encased. It would be similar with other organisms as well, as plants and other organisms have been discovered preserved in this way.

  These fossils represent some of the earliest African fossil records for a variety of arthropods, including wasps, barklice, moths, beetles, a primitive ant, a rare insect called a zorapteran, and a sheet-web weaving spider. Parasitic fungi that lived on the resin-bearing trees were also found, as well as filaments of bacteria and the remains of flowering plants and ferns.


From my experience I would say that it is no problem to freeze the digested DNA, when the enzyme is inactivated (even when not, for this time period I wouldn't expect much damage).

However, if possible, I would rather opt to freeze the PCR product and make the digest fresh, since the overhanging ends are kind of sensitive to hydrolytic degradation. I have also frozen linearized vectors without problems.


What does this mutation notation mean: MAP2K41161fs*12

fs means frame shift and *12 gives the length of the new reading frame (ie the number of codons up to and including new stop codon). Usually before fs they give the first mutated amino acid, so I'm not sure what the number 41161 means (but apparently the OP does).


Low temperatures change the speed of different chemical reactions, throwing delicately balanced systems out of balance. How resilient a creature is to temperature changes is largely a function of how complex it is, and how buffered it is against this kind of change.

Tardigrades as kmm mentioned essentially can't be killed by cold, surviving down to almost absolute zero (absolute zero ≈ minus 273.15°C). Most unicellular organisms can be frozen (especially if frozen quickly or cryoprotected with something like DMSO) and revived later without any change. Most strain libraries of bacteria are kept frozen for cost reasons. Even human cell cultures can be frozen and thawed, even though some of the cells will die. (If even 10% of your cells died you as a person would probably die, so freezing is off the table unless you are very clever indeed.)

Humans and most mammals are pretty sensitive to temperature changes, even though reptiles are not. Most fish are cold-blooded and are adapted to cope with the relatively cold temperatures, but the human heart is not well adapted to even relatively warm temperatures. The atria and the ventricles of the heart stop communicating below 27°C (80.6°F)or so, and below 20°C (68°F) the heart can stop beating entirely. Nerves are complex systems, and absent regulation systems in the nerves themselves to compensate for the changes in temperature, they can stop firing completely. A simple heart can run with less sophisticated orchestration, and is, therefore, more resistant to temperature change. A complicated heart involving the coordination of the atria and the ventricles to produce effective pumping action is affected much more strongly by the drop in temperature.

So, in general, more complicated implies more vulnerable to temperature changes. There are exceptions, however. Bears can hibernate and drop their core body temperatures without any ill-effects, so it's possible to adapt to. Fish deal very well with cold temperatures if exposed gradually, and some fish could live quite happily in a slushie, salinity notwithstanding.


How do these triplets code for these proteins?

In the first image, AAG is the true codon for Lysine.  So when the ribosome hits "AAG" in the mRNA it recruits a Lysine-tRNA.

What can be confusing is the use of the term "coding strand" when talking about the DNA. The coding strand is illustrated in the second image you posted, and it is the coding strand of DNA that the first image is depicting. What "coding strand" means here is, this is the strand that looks like the mRNA will look. Depicting the DNA coding strand like this--i.e. as a series of codons--can be slightly misleading since we know codons really only mean anything when in the form of mRNA. Nevertheless, it is a common way of thinking about DNA.

Back to the first image. Because it is showing the "coding strand" of DNA, the "template strand" for 5'-AAG-3' then must be 5'-CTT-3'. Hence, when this strand is transcribed by RNA polymerase, the 5'-CTT-3'(DNA) becomes 5'-AAG-3'(mRNA).


What is the purpose of ultrahydrophobicity in lotus flower leaves?

Lotus benefits from hydrophobicity for that it decreases the likeliness of being infected by pathogens (found in "dirt") and increase the ability to perform photosynthesis.

According to a study by Darmanin and Guittard, the plants (not only lotus) with ultraphobicity benefits from these structure for :

  self cleaning

and

  these structures are able to stabilize the presence of air underwater and be submerged for several weeks

Let's talk a little about the second part : having a good access to gas is vital for plants to do photosynthesis. In an environment which is very wet (like the one the lotus lives in), it is better to be dry to maximise air/plant surface area.

Now, about the self cleaning.
First, lotus lives in backwater or muddy environment
In this study by W. Barthlott and C. Neinhuis, it is said that big particles can occlude stomas, the small "holes" that allows the plant to breath.
Wet environment is ideal for bacterial/fungal growth and different kind of disease. Unclean water could also block light and make photosynthesis less efficient.

  Again, wettability
  is important for the adhesion of microorganisms to
  leaf surfaces. In addition, on waterrepellent
  surfaces, spores and conidia are deprived of the water necessary for germination. Therefore, the epicuticular
  wax crystalloids and their physical properties
  may be regarded as the first line of defense against
  pathogens.


Does the bending of a tree's trunk in the wind stimulate and strengthen root growth?

In tree growth there is principle called The axiom of universal stress whereby the growth is in such a way as to equalise the stress across the whole of its structure. The roots, the stem and the branches are one continuous system and can not be thought of as separate.

On a simplistic level for a branch to grow, there must be a corresponding equal and opposite growth in the stem and roots. Of course it is not quite like this as the growth happens across the whole structure at the same time.

The trees on the edge of an even-age stand of trees will have grown to be more stable against wind. They are referred to as being a wind-firm edge to the stand. The trees that have grown up within a stand, with the shelter of their neighbours will not have the same stability in the face of wind, so that if the stand is opened up too quickly it can lead to wind-blow. In uneven-age woodlands, the same principle is true but the dynamics make it less pronounced.

The reason for mentioning this is just to illustrate that, absolutely the wind, and other external factors, gravity being the obvious one, will have an effect on the growth of the roots, as well as the rest of the tree. As the wind exerts a force on a tree that  force will travel through the structure and into the roots and into the ground.

To come back to the specific question then.

  Does some kind of mechanism exist within the tree that connects mechanical bending of the trunk with increased rate of root growth?

Yes, and no. Because the increased rate of growth will be across the whole structure, but not equally. It will put on growth at the points where the stresses are, in order to self-optimise the loading including within the root system.

The next time you cut either the stem of a leaning tree, or a branch of a tree, take a look at the orientation, and thickness of the rings. You will see that in broadleaf trees (or more correctly angiosperms) the rings on the side under tension will be thicker. In conifers (or gymnosperms) it is the opposite. The thicker growth is found on the compression side.

Here is a great photo of compression wood in a conifer from http://www.copperman.co.uk/didgeridoo/how_to_make_a_wooden_didgeridoo/what_is_wood_2.php

The same principle will be happening in the roots also.

As to the actual physiological mechanism that causes this response I have not yet come across a definitive answer. The consenus, at least as far as I know, is that it is not fully understood.

The closest I have come across so far is from this phd in 1994. http://etheses.whiterose.ac.uk/2438/1/DX184141.pdf

I dare say there has been more work done on this in the last couple of decades.


Is the Lucy fossil really what scientists claim it is?

Per the comments, the actual paper seems pretty like a pretty straightforward operation of normal science:

Somebody noticed something that looked off about one of the bones and decided they'd look into it more carefully.
They found that yes, that bone appears to have been an accidental inclusion, and in fact the rest of the skeleton makes more sense without it.
The original conclusions are not weakened in any way, but are in fact strengthened by cleaning up a minor mistake.

It might have come out otherwise, but in this case, as in most cases, careful criticism and examination of scientific work ends up making the whole enterprise more coherent.

It's frankly not even very interesting, scientifically, which is probably why you're finding discussion of it mostly on creationist sites.  Note also that the creationist article linked uses sloppy language like "proof" and "part ape, part human" that tend to indicate a massive lack of understanding of both science in general and evolution in particular.


Is Webmedcentral a reputable scientific publisher?

I checked this site and its journals in Scopus.com based on its "ISSN 2046-1690" but nothing was there. they are fast in submitting and publishing but it is not some thing great by it self. I think maybe its better to find some where better to publish your article(s).


Where can I find a global life expectancy table?

Not surprisingly, the WHO has a lot of data, I think especially interesting for you is this interactive figure, which you can find here:

Other data on this topic can be found on the WHO website here, in the Wikipedia or from the Worldbank.


I don't really understand why mRNA processing doesn't simply occur in the cytoplasm.

To be clear, P-bodies are in the cytoplasm (ie they are not separated by a membrane). There is also dynamic exchange of components between the ribonucleoprotein complex and free cytoplasmic pool (1):

  Most P-body components are distributed diffusely throughout the cytoplasm as well as being localized in P bodies. Quantitative information regarding the fractionation of these proteins between the cytoplasm and P bodies is still lacking, but given the volume of P bodies relative to that of the cytoplasm, the diffuse cytoplasmic fraction could be significantly larger, although the concentration of mRNA-decay factors might be much higher in P bodies. Also, P-body components dynamically exchange with the cytoplasmic pool, which indicates that decay enzymes and co-activators are not confined to P bodies. So, it is probable that mRNA decay also occurs, and might even be initiated, in the diffuse cytoplasm, and that P bodies arise by association of mRNA-decay intermediates induced by interactions between decay enzymes and cofactors. The concentration of mRNA-decay intermediates and mRNA-decay enzymes in P bodies would be expected to increase the speed of degradation and, in turn, reduce any potential competition between these RNA fragments and normal mRNAs for limiting cellular proteins involved in mRNA regulation.

I'm not clear on whether all mRNAs pass through P-bodies at some point, when not actively involved in translation.

mRNA can also be degraded by exosomes (1):

  In eukaryotic cells, degradation of bulk mRNA occurs by two alternative pathways, both of which are preceded by removal of the poly(A) tail by deadenylases. Following this first rate-limiting step, mRNAs can undergo 3'→5' exonucleolytic decay, which is catalysed by the exosome... Alternatively, after deadenylation, the cap structure is removed by the decapping enzyme DCP2, rendering the mRNA susceptible to 5'→3' digestion by XRN1 [a P-body associated protein].

Also see (2), and this image therein:

If the only requirement for recruitment to a P-body (and potentially degraded via RNAi) is to not be currently involved in translation, wouldn't that select for viral proteins to be more highly translated?

That is, in fact, not the requirement (3)

  Recruitment of mRNA to PBs is not an occurrence of non-translation, rather requires active silencing via miRNA or RNAi mechanisms.

They reference another paper (4):

  Recent studies with mammalian cells have shown that P-body integrity is not required for ARE-mediated mRNA decay or silencing mediated by fully or partially complementary exogenous, transfected small interfering RNAs (siRNAs). In this study, we investigated the requirement for P-body integrity in NMD, mRNA decay, and silencing mediated by miRNAs and long double-stranded RNAs (dsRNAs). We show that these pathways are unaffected in cells lacking detectable, wild-type P bodies. However, although P bodies are not required for silencing, active silencing pathways are required for P-body formation in Drosophila melanogaster cells, indicating that P bodies are not the cause but a consequence of silencing.

Is there is a separate step by which mRNAs of exogenous origin are specifically (or more rapidly) recruited to P-bodies - and, if this happens, how are they specifically targeted for this uptake?

The RISC complex can be involved in initial recognition and cleavage of viral RNA and the resulting fragments are subsequently degraded by the exosome or P-body associated proteins. RNAi associated components have been observed to be localised with P-bodies (1):

  Endonucleolytic cleavage of siRNA or plant miRNA targets is catalysed by the C-terminal PIWI domain of Argonaute proteins... Following this endonucleolytic cleavage, the resulting mRNA fragments are handed over to the general mRNA-decay machinery. In D. melanogaster, 5' and 3' mRNA fragments that are generated by Argonaute-mediated endonucleolytic cleavage are degraded by the exosome... and by XRN1, respectively.

You can also consider the R-gene viral defence mechanism in plants which induces P-body formation and suppression of translation in an RNAi independent manner (5):

  Plant NB-LRR proteins [R-genes] confer resistance to multiple pathogens, including viruses. Although the recognition of viruses by NB-LRR proteins is highly specific, previous studies have suggested that NB-LRR activation results in a response that targets all viruses in the infected cell... NB-LRR signaling does not result in the degradation of viral transcripts, but rather prevents them from associating with ribosomes and translating their genetic material. This indicates that defense against viruses involves the repression of viral RNA translation... As a consequence..., NB-LRR responses induce a dramatic increase in the biogenesis of RNA processing bodies (PBs). We demonstrate that other pathways that induce translational repression, such as UV irradiation and RNAi, also induce PBs. However, by investigating the phosphorylation status of eIF2α and by using suppressors of RNAi we show that the mechanisms leading to PB induction by NB-LRR signaling are different from these stimuli, thus defining a distinct type of translational control and anti-viral mechanism in plants.

There are many articles discussing how viruses subvert and/or repurpose P-body mediated decay if you want some further reading (3), (6), (7).


What happens if a non-diabetic receives an injection of insulin?

Blood sugar drops (Hypoglycaemia)
There are several other uses of insulin (other than diabetic treatment)

Some of those could be:

Diagnostics
Psychology (Narcoanalysis)
Parenteral nutrition
Cardiology (Glucose–insulin–potassium solution (GIP or GIK solution) is given   after a myocardial infarction)
Malignancy (Insulin potentiation therapy (IPT))
Psychiatry (Deep insulin coma therapy (DICT))

Sources:

Niazi, Asfandyar Khan, and Shaharyar Khan Niazi. "A Grand Dame
with Hidden Aces: The Non-diabetic Uses of Insulin." Indian Journal
of Endocrinology and Metabolism. Medknow Publications & Media Pvt
Ltd. Web. 06 Feb. 2016.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3354952/.
"Hypoglycemia." Hypoglycemia. Web. 06 Feb. 2016.
http://www.niddk.nih.gov/health-information/health-topics/Diabetes/hypoglycemia/Pages/index.aspx.


Earliest to use media after autoclaving?

There is a relatively simple (and yet logical) answer: You can use the media as soon as they are cold enough for your desired culture temperature. So if you want to use the media at 30°C, there is no need to wait longer. The media will only warm up again in the incubator until this temperature is reached.

The addition of antibiotics is also uncritical, since the media is ways to hot to be directly used when they still inactivate antibiotics. Your cells wouldn't survive this either.

There is also no waiting period necessary to use fresh media after autoclaving, since there are no processes going on when the autoclaving was done properly. If not, you will see contaminations pretty fast.


What if our whole body is made up of cancer cells?

No.

One aspect of cancer cells is that they no longer follow their programming, ie they stop doing all the work that a normal cell in that particular part of your body would do.

The next aspect is that cancer cells keep growing even when they are told to stop, even when there is no more space to grow.

Cancer cells also tend to destroy surrounding extracellular matrix in the quest for more nutrient. SO stuff like bone get deformed or just broken down leaving holes.

So if your entire body were made of cancer cells... well it would fall apart as cell stop doing their assigned job in the body, start growing without care and break down existing structure for better access to more nutrients.

What you want are immortal cells that still do their job.. stem cells.


Have we ever observed fertile offspring with a different number of chromosomes than the parents?

[..] have we ever observed a situation where the offspring of meiosis has a different number of chromosome pairs than the parents, the offspring lived, and the offspring was not sterile?

Yes!

While it may seem a detail, the difficulty is to know what exactly you mean by observation. Chromosomal abnormalities, gene duplication, chromosomal duplication, robertsonian translocations, whole genome duplication are not super common but common enough to be seen repeatedly. We see them happen again and again in different lineages, we can even investigate how our environment affect such chromosomal abnormalities (Merkatz et al. 1984). So below, I am citing a few papers that I more or less randomly selected among the decently large amount of work on the subject.

Chromosomal rearrangements are sometimes involve in speciation (Rieseberg 2001).

There are many genetic disease in humans that are related to such chromosomal duplication (e.g. Down Syndrome) and de novo mutations for these mutations, while rare, are not so rare that we can witness them only on geological time scale (Veltman and Brunner, 2012)

There are soo many articles on the question that I don't really know what to cite. Of course, there are reviews that can be of interest to you (such as Zhang 2003). I tried to find a video showing a meiosis leading to chromosomal duplication but unfortunately, I have failed to find that.

The mechanisms of these mutations leading to chromosomal rearrangements are pretty well understood. You should probably start with wikipedia > gene duplication # Mechanisms of duplication for an intro.

As you talk about the difference between the number of chromosomes in chimpanzee and humans, you might want to have a look at the post Evolutionarily speaking, why do humans have 46 chromosomes where it is explains (with plenty of citations) how did the change in chromosome number occurred in our lineage.

  I have read a lot about the idea of evolution

I do not want to seem pedantic but given that the vocabulary that you are using (change in kind,  concepts of transfer errors, concept of gradual change) it really suggests that all you read comes from the creationist propaganda and not from the evolution literature. Indeed nobody use these terms in the research. Those terms are mainly used as straw man from the creationist propaganda.

There are many free intro courses to evolutionary biology. You might want to have a look at Understanding Evolution by UC Berkeley.


What happens to the umblical cord inside the mother?

Labor is typically divided into 3 stages:

Stage 1: From the onset of contractions (true labor pains) to full dilatation of the cervix (which is about 10 cm) - this takes about 12 to 18 hours
Stage 2: From full dilatation of cervix to expulsion of fetus - This takes about ~ 30 minutes
Stage 3. From expulsion of fetus to expulsion of placenta - this takes about ~ 15 minutes. During the third stage, the umblical cord which is attached to placenta is expelled along with the placenta. This would be the answer to your question.

Source:Hympath.com


Nucleotide sequence for STRING protein sequence

Google is not a bad resource for such a question.

In this case I find that the Yeast Genome site has a button which returns the nucleotide sequence. You can select the genomic sequence for the locus or the coding (CDS) sequence.

http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=Q0010

They also give a link to NCBI at the bottom of the page.  I think the reason you were having such a hard time is that UniProt extracted the protein sequence from the mitochondrial genome record.  Like many genome ORF predictions, Q0010 does not seem to have a distinct nucleotide record assigned yet.

Summary:

In general  you can do a web search for the uniprot id to start.  In many cases, like this one you will find that the nucleotide seq is only a chromosomal sequence record.   Biodatabases are a bit of a maze - there are scores of them out there, you may find that someone has clipped the nucleotide sequence of the gene out, which is helpful if there are introns!


You will find various bioinformatics tutorials on: https://www.biostars.org/t/Tutorials/

As a computational biologist I would however strongly suggest to attend biology lectures, and read many textbooks that cover topics outside of the favorite topics of today's bioinformatics (Bruce Albert's "Molecular Biology of the Cell" would be a good start):

Technical aspects are easy to solve, and learn (and also to outsource). The difficult part is to find smart problems, and to understand how you can solve some things faster than your competitors by combining bioinformatics with other approaches.

BTW: I really like your idea to approach bioinformatics from the hard-ware side (also see evolvable hardware).


It is not about redundancy. There are evolutionary and developmental  reasons why we have two eyes or two legs and one heart. However just to give you short examples, two eyes are better than one because of our binocular vision while we have two legs because of its locomotor energetics.


Query for gene upregulation in cBioPortal

Well, I have worked with expression patterns. Unfortunately there is no clear cut or magical numbers for cutoffs . I agree with you that 0.5 is not stringent. However, to explore data usually one can parse it using lower cutoffs and later on you can rise the bar to see what happens.


In humans, are diseases inevitable during old age?

There is a thought that aging itself should be considered a disease. In which case, death by disease is inevitable with our current level of medical technology.

  During the last 25 years, by targeting the underlying processes of aging biomedical scientists have been able to improve the health and lifespan of model organisms, from worms and flies, to rodents and fish. We can now consistently improve the lifespan of C. elegans by more than ten-fold (Ayyadevara et al., 2008), more than double the lifespan of flies and mice (Bartke et al., 2001; Sun et al., 2002), and improve the lifespan of rats and killifish by 30 and 59%, respectively (Valenzano et al., 2006; Zha et al., 2008) (see Figure Figure11 and Supplementary Table 1). Currently, our treatment options for the underlying processes of aging in humans are limited. However, with current progress in the development of geroprotective drugs, regenerative medicine, and precision medicine interventions, we will soon have the potential to slow down aging (Bulterijs, 2011, 2012).


Do larger multicellular organisms have an increased risk of mutation and thus cancer?

As mentioned in the comments, this question is quite complicated. If the chance of a single cell from different organisms getting cancer was the same, then you would be correct, but this is not the case.

Different organisms have evolved to live different lengths of time. This is rather obvious when you think about it: mice have a maximum lifespan of ~3 years, humans ~80years (these figures are of course massive generalizations - but it doesn't really matter). Yet 'old' mice (> 2 years) still get age-related diseases such as cardiovascular disease, and cancer. It should be fairly clear that the risk of a 2 year old mouse getting (age-related) cancer is much higher than a 2 year old human.

The explanation for this isn't exactly concrete, but it goes something like this; mice invest a lot more resources in growing very fast and reaching a reproductive age very early, whereas humans develop much more slowly, and invest a higher proportion of their resources in maintaining tissue function, thereby reaching reproductive maturity much later than the mouse. The Hayflick limit for a mouse is about 10, whereas for humans this is closer to 60.

Thus the rate of aging in humans is much lower than that of the mouse, and it comes back to evolution: mortality in the wild is very high for the mouse, and thus mice that invest heavily in reaching early reproductive maturity are selected for - and those that invest in anti-cancer mechanisms take longer to reach reproductive maturity, and thus have less chance of actually doing it!

So to answer your question - smaller organisms tend to have higher risks of getting cancer because their lifespans are comparatively shorter, and thus they 'age' at a faster rate and invest less resources in maintaining function (e.g. genome integrity).


Is it possible to lose weight doing brain exercise?

No The amount of calories the brain consumes is basically the same whether it is doing anything or no. Best case only about 3% increase in calories consumed by the brain or about 50 calories per day, which is miniscule and most studies do not even show that much.
Additionally buring calories is only important for weight loss once consumption is controlled. It is too easy to out eat any amount of exercise.
https://www.scientificamerican.com/article/thinking-hard-calories/


Base-stacking interactions versus hydrogen bonds

For a direct reference on the contribution of these two forces see here.

If it helps, think of the double helix of dsDNA as a more rigid structure than ssDNA, which flops around and generally is capable of a lot of steric freedom that dsDNA doesn't have. This freedom means that the bases of the ssDNA backbone may not always be in the correct orientation for stacking, because the two strands of the helix aren't forcing the bases together into that orientation. "Usually the DNA double helix is considered to be a relatively rigid structure. Certainly it is much more rigid than its component single strands." (see the review for a much more detailed discussion of this issue)

It's true that base stacking still occurs in ssDNA, it's just not enforced in the same way. It also appears to be somewhat sequence-specific, occurring more in polypurines than polypyrimidines, possibly because purines are bulkier molecules with more steric hindrance.

For a related conversation see here.


How would substances that have anti bacterial characteristics interact with yeast?

Substances that exhibit antimicrobial activity do so because the microbe itself is susceptible to the mechanism of action. For example, some bacteria crosslink their peptidoglycan cell wall with a transpeptidase (aka penicillin-binding proteins), and penicillin antibiotics block this step. Other bacteria don't do this, and so if you use penicillin there will be no effect.

Likewise, some antimicrobial methods have very broad efficacy against everything, like drugs that inhibit ribosomes, or at the extreme end, bleach. Being said, ginger as in the homebrew link is shown to have a broad action on microbes as denoted in the following article. The question now is does ginger affect yeast?

Google search "gingerol antifungal" (gingerol is apparently one of the potent effector molecules in ginger) and you get a host of results detailing it's efficacy on C. albicans. This doesn't necessarily mean it has the same efficacy on S. cerevisiae, but it does mean that, and this is just a number out of the literature, but a 10% ginger solution may have deleterious effect on fungal growth.

Outside that, I can't really find anything on the actual antimicrobial mechanism of action for ginger, either, so it's difficult to say other than for some reason, they inhibit microbes. They did show that 6-gingerol induces ROS production in tumor cells, which results in DNA damage, but I'll continue to look for an explanation.

What remains, now, is too broad. The ways that antimicrobials interact with different microorganisms is a lot to consider and I can only be about as broad as I've written above without going into a novel worth of text. Hopefully this was helpful!

You can check out this Sigma page on antibacterial modes of action to get an idea of the ways different antibiotics are made to affect microbes.


"pLT63 contains 0.8 kb of the fem-1 gene inserted into the L4440 vector" (1). The gene fem-1 is involved in determining the male sexual trait in C. elegans (you can verify this on uniprot). It may be best, however, to stick to a "normal" plasmid like L4440 that'll just have your tph-1 insert ligated in.


I'm still not entirely sure what specifically you're asking about, but I have a guess. It is true that positively-charged hydrogen ions, or bare protons, are typically only observed in gaseous/plasma states and hard vacuums, and it is also true that cells routinely pump positively-charged hydrogen ions across membranes. This is not a paradox because in aqueous solutions, hydrogen ions exist as $H_3O^+$, also known as hydronium or hydroxonium.

Image from Wikimedia Commons


How many people in the world have bad eyesight?

I do know that the TED Ed episode linked (at 3:50) actually says that 500 million people have myopia or hyperopia, which is 1000 times what the question says, and which seems more reasonable for a world of 7.4 billion people (skewed towards the young).


I think its useful to say that nicotine is not very toxic to humans - cells don't die or get sick for typical smoking habits.  Secondary health effects are possible, but here is a toxicological profiles.

Nicotine is a toxin in large enough quantities and nicotine has an LD50 (lethal dose for 50% of individuals) of 0.5-1 mg Nicotine / kg of body weight.  So even a small spill on your skin of the chemical can be life threatening, but for smokers the nicotine itself is not dangerous.

Individuals who smoke intake about 1 mg per cigarette smoked.  So a small adult (110 lbs) can smoke 25 cigarettes in a short period of time (or all at once!) and just barely get to the bottom end of that limit.  Nicotine is water soluble and clears out through the urine at a fast rate though - half of the nicotine from a cigarette is cleared from  your system within 2 hours, which means that 4-5 pack a day smokers are not really killing themselves (from nicotine).

That being said, children are about 5-10 times more sensitive than adults, so even 5-6 cigarettes in an hour can be toxic.  That's quite a bit of smoking though.

Not all animals have the same relationship to the nicotinic acetylcholine receptors as humans do.  Nicotine is toxic to insects and will kill an insect in a matter of minutes or hours. Rats are about 50x less sensitive than people.

I think its comparable to the question of whether caffeine is harmful to people.  In the amount we consume it, sometimes up to grams a day, there is no obvious common side effect, but you figure that decades later it will show up as a problem - a difficult connection to prove.


How does adjuvant enhance the immunogenicity of antigen?

This is a quick answer to a very broad question since the mechanisms of adjuvants are very different. I'll try to summarize just a few. For a deeper understanding please start reading this paper and its references.

1) Aluminum salts (aluminum phosphate or hydroxide)

  Studies suggest alum salts work by causing the formation of an antigen
  depot at the inoculation site from where the antigen is released slowly.
  The trapping of soluble antigen in the alum gel may also increase the
  duration of antigen interaction with the immune system. Other
  mechanisms of action involve complement, eosinophil, and macrophage,
  activation and increased efficiency of antigen uptake by antigen
  presenting cells seen with particulate matter with a size under 10
  micron.

2) Calcium salts

They work pretty much like aluminum salts but they are much better tolerated by the organism.

3) Bacteria-derived (peptidoglycan or lipopolysaccharide)

They are naturally recognized by the immune system and for this reason, they are used to simply boost the immune response.

4) Emulsions

They form a depot at the injection site, enabling the slow release of antigen. The immune system has more time to recognize the antigen and react.

5) Liposomes

They help to extend the half-life of antigens in the blood leading to a higher antigen exposure to antigen presenting cells after vaccination. A Very similar effect is achieved using microbeads made of artificial polymers.


Why does ESR have to be waited for one hour?

Does it really make a difference how long they settle, or why they chose that amount of time? At one extreme, you haven't really given them adequate time, at the other, there's no more useful information to gather.

The tubes in which Sed Rates (or ESR) are measured are 200 mm in height. Why wait three hours for the result (which is still expressed as a rate, i.e. mm/hr)? In three hours, they may (depending on how quickly they settle) have all settled an hour and a half ago. (If an ESR is 100mm/hr, it will hit the settled cells at the bottom before it finishes settling if two hours is the length of the test.

The test is simple, cheap, easy, with good sensitivity and specificity. And the results come back in a little over an hour. The sooner the diagnostician gets the results back, the sooner the answer helps in the decision tree needed for the treatment of the patient. Longer wait times aren't helpful and may not be accurate with very elevated ESRs.

Acute Phase Proteins Molecular Biology, Biochemistry, and Clinical Applications By Andrzej Mackiewicz, Irving Kushner, Heinz Baumann, 1993


In which phenomena does one gene pair hide the effect of other unit?

The definition of "gene", according to The American Heritage Science Dictionary is:

"A segment of DNA, occupying a specific place on a chromosome, that is the basic unit of heredity. Genes act by directing the production of RNA, which determines the synthesis of proteins that make up living matter and are the catalysts of all cellular processes. The proteins that are determined by genetic DNA result in specific physical traits, such as the shape of a plant leaf, the coloration of an animal's coat, or the texture of a person's hair. Different forms of genes, called alleles, determine how these traits are expressed in a given individual. Humans are thought to have about 35,000 genes, while bacteria have between 500 and 6,000. See also dominant, recessive. See Note at Mendel."

So, when the question refers to genes, it must be referring to two different genes on two different loci. If the question was referring to alleles of the same gene on the same locus, the correct answer would be dominance, but since it is referring to two different genes, the answer is epistasis.


That is a cottonwood stage beetle. Lucanidae, Lucanus mazama https://bugguide.net/node/view/666700/bgimage


Why don't amino acids get linked in the functional groups of acidic and basic amino acids?

When the amino acid comes to the ribosome it is in the form of an aminoacyl tRNA in which the carboxyl group of the amino acid is esterified with the 3' OH group of the ribose moiety at the 3' end of the tRNA.

There is already a growing peptide bound in the P site of the ribosome with a free -COOH group which will react with the -NH2 group of the incoming amino acid in the A site to form the next peptide bond. This reaction takes place in the context of what is essentially an enzymic active site. The reactants will be held in the correct positions for catalysis to take place (in this case the catalysis is carried out by the ribozyme activity of the small ribosomal RNA).

So the answer is that the selectivity of this reaction is just another example of the way in which enzymes are able to carry out highly-specific reactions. So, for example, the enzyme hexokinase, which phosphorylates glucose at the 6 position has, potentially, four other -OH groups that, chemically speaking, could be phosphorylated.


Hardy-Weinberg Equilibrium: To compute probability of finding two siblings (random mating)

Are you sure it is 0.59 because I am getting 0.5625 for part (a) and this is how I computed.

To check genetic similarity of siblings we first have to pick up mating pairs. Six mating pairs possible with following offspring probabilities (choice of first mate x choice of second mate x same offspring genotype freq).

AA x AA : will always give same type of offspring: prob = 0.25x0.25x1
aa x aa : will always give same type of offspring: prob = 0.25x0.25x1
AA x aa : will always give same type of offspring: prob = 0.25x0.25x1
Aa x Aa : will give Aa in half the number of times: prob = 0.5x0.5x0.5
Aa x AA : will give two types of similar offsprings, half the number of times - AA and Aa: prob = 0.5x0.25x0.5x2
Aa x aa : will give two types of similar offsprings, half the number of times - aa and Aa: prob = 0.5x0.25x0.5x2

Total probability = 3x(0.5x0.5x0.5) + 3x(0.25x0.25) = 0.375+0.1875 = 0.5625

Assumptions:

Population is infinite
Population in equilibrium