Amount of blunt force to kill a person In short, if I were to whack someone over the head, what factors play a role in whether the victim survives? Force? Pressure? Location? Something else?

TL;DR: It's highly variable. Don't go whacking people over the head.

All of those things are factors, yes; the two most important ones being force and location. There are subsidiary factors, but most of the time, insofar as there is and identifiable proximate cause of death, it boils down to force and location.

There are two primary paths to death when whacking someone over the head: trauma to the brain, and trauma to the spine. Trauma to the brain is caused by significant force applied to the cerebellum; either in one-off high-impact events, or repeated blows; and trauma to the spine is much the same, injuries caused by shear force to (in particular) the cervical spine; again either in one-off high-impact events or repeated blows.

(There are also secondary paths to death, such as blood loss or infections associated with lacerations of the scalp, face or neck.)

Blows to the top of the head, or blows delivered when prone tend to introduce direct damage to the brain, whereas blows to the side and back of the head tend to introduce damage to the spine. Either is fatal, but for different reasons: Cervical spine injuries hamper communication between the central nervous system and vital organs such as the heart and lungs, leading to hypoxia and suffocation, as well as cascade effects with lesser injuries, whereas brain injuries are more directly deleterious and fatal.

All of that being said, however: While cervical spine injuries can be debilitating, they can be ameliorated by muscles associated with the damaged structures. Direct brain injuries aren't nearly as forgiving, but some people do have Simpson Syndrome to varying degrees.

In addition, there are various somewhat common congenital defects that due to the relatively peaceful nature of our day-to-day are never discovered, but can have a significant effect on response to blows to the head. (This is part of why, if you're ever in a car accident, paramedics will be very keen to evaluate you, even if you have no outwards signs of injury.)

Long story short: Punching someone in the head is a bad idea, unless they pose a very direct threat to you; and you mean to incapacitate them; and you don't mind said incapacitation being potentially permanent (to the point of death).


Do plant-plant interactions inhibit growth? Plants produce lots of compounds that inhibit (kill or irritate) microorganisms and insects.  They have defenses against plant viruses and infections.

What kinds of compounds or hormones to plants use to regulate the growth of other nearby plants?  I have hear of ethylene, but I would like to hear about more specific compounds that might be known that work against specific species or kinds of plants?

The phenomenon you are asking about is allelopathy.
Remarkably, it has its own journal - Allelopathy Journal (ISSN:
0971-4693) published since 2009 and currently at volume 30, issue 1.
Here are the titles of the papers from the most recent issue:

In-vitro assessment of allelopathic effects of wheat on potato.
Allelopathic effects of sunflower on seed germination and seedling growth of Trianthema portulacastrum.
Effects of simulated acid rain on the allelopathic potential of invasive weed Wedelia trilobata.
Allelopathic effects of Brachiaria ruziziensis and aconitic acid on Ipomoea triloba weed.
Effects of Butia capitata pyrenes extracts on the germination of lettuce seeds.
Effects of root exudates from crop plants on the growth of Fusarium oxysporum f.sp. niveum.

So, if you have specific questions, this might be the place to look.


what species moth is this? found in garden in wiltshire, england. about 15mm-20mm long. Resting at 6pm on raspberry plant.

You have found Smerinthus ocellata, the Eyed hawk moth. It is name comes from the eyes on the hindwing, which do not show at your photo. It is known to show these eyes if disturbed, to scare of attackers.

Photo from wikipedia commons:

The forewing shows considerable variability, as you can see here


Why are so many recreational drugs serotonin 5-HT1A partial agonists? I found out that many psychoactive drugs partially activate the 5HT1A receptor. Looking at Wikipedia, these include MDMA, LSD, CBD, Psliocybin/Psilocin, amphetamine and various other psychedelics, and they appear to all be serotonin 5-HT1A partial agonists.

Why is this receptor so popular for recreational drugs? Why are all these partial instead of full agonists? I looked at 5-HT1B and there weren't any recreational drugs that used this listed. I looked at other 5-HT receptors, and only 5-HT2A had other recreational drugs as agonists.

Why do so many recreational drugs affect these two 5-HT receptors?

Interesting notion. However, the main effects of the indoleamine-class of psychoactive compounds, including psilocybin and LSD (Shulgin, 1997), are generally ascribed to 5-HT2A receptors and the glutamatergic system (Aghajanian & Marek, 1999). The stimulant effects of the phenetylamines (PEAs) such as amphetamine and related compounds (Shulgin, 1991) mainly target the dopamine (DA) and noradrenergic (NE) systems. I reckon that the 5HT1A effects are 'side effects', or secondary effects.

Antidepressants, such as the selective serotonin-reuptake inhibitors,  target the 5HT1A system and mainly do so by downregulating the pre-synaptic variant of the 5HT1A receptors, which have a regulatory role by decreasing 5HT release. Downregulating them takes about 2 weeks. After that time 5HT release is disinhibited and 5HT release is enhanced, which has antidepressant actions (source: Sci Am, 2013). Because many recreational drugs are not taken that long, my educated guess is that acute activation of 5HT1A by recreational drugs limits the drug's effect more than anything else.

Why are they partial agonists? Because they target other receptors better; the main effects of e.g., PEAs as described above shows you why. Many of those compounds mainly target the DA and NE system. Because they are aspecific ('dirty') drugs, they also target a variety of other receptor systems. Perhaps altering the main effect, perhaps not doing anything substantial to the trip.

Note that the PEA MDMA is kind of a one-of-a-kind psychoactive compound (Shulgin, 1991) that releases massive amounts of 5HT (Gartside et al., 1997).

On a side note, Wikipedia tends to list all available information on an item in a cluttered way that obscures the relevance of that information to the global picture.

References
- Aghajanian & Marek, Neuropsychopharmacology (1999); 21(2 Suppl): 16S-23S
- Gartside et al., Neuropharmacology (1997); 36(11-12): 1697-703
- Shulgin, Pihkal (1991), Transform Press
- Shulgin, Tihkal (1997), Transform Press


Correct term for initially neutral mutations that subsequently cannot be reversed Can anyone tell me what the correct name is for a neutral mutation to a protein that occurs when that mutation becomes "locked in" due to a subsequent mutation?

For example: mutation A is neutral initially and can be reversed with no deleterious effects, but after mutation B, the reversal of mutation A would now become deleterious. What is the correct terminology for a mutation of A's type?

Mutation A is a suppressor of Mutation B. The Wikipedia article on the topic (https://en.wikipedia.org/wiki/Suppressor_mutation) mostly describes situations where Mutation A occurs after B and reverses B's deleterious effects, but the principle is the same.


How to find suitable qRTPCR reference gene for a inflammatory response experiment? I have tried several housekeeping genes – Hprt, β-actin and GAPDH, to analyze the relative expression of a cytokine for measuring the inflammatory local response in mice ears. However, all these housekeeping genes show significant variation in both within and between different experimental conditions.

I really don't know how to solve this. I take the same amount of RNA (quantified by  nanodrop) to make cDNA so I guess I have the same concentration in all the samples.

Any suggestion of what can happens and how to solve it? Could I use something different to measure the relative quantification? (My cytokine of interest is TNF).

You don't say how you're measuring but I'll guess that you're using quantitative PCR. A typical approach to handling housekeeping gene normalization in qPCR experiments is described in

Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes.

  We outline a robust and innovative strategy to identify the most stably expressed control genes in a given set of tissues, and to determine the minimum number of genes required to calculate a reliable normalization factor. We have evaluated ten housekeeping genes from different abundance and functional classes in various human tissues, and demonstrated that the conventional use of a single gene for normalization leads to relatively large errors in a significant proportion of samples tested. The geometric mean of multiple carefully selected housekeeping genes was validated as an accurate normalization factor by analyzing publicly available microarray data.

There is an R package called NormqPCR that implements this approach (publication here).

Briefly, the approach required measuring multiple housekeeping genes and iteratively removing the ones that are most variable, ending up with two genes that are jointly least variable, and making a sort of pseudo-housekeeping gene from them with which to normalize your other genes.

This doesn't magically turn bad data into good data, but it helps clean up some intrinsic problems with housekeeping genes.


Relationship between immunologic response to specific gluten epitopes and clinical antibody testing Celiac disease is understood to be an immune response to certain proteins which occur in a group of cereals; most commonly they are glutens (wheat), secalins (rye) and hordeins (barley). A clinical test for celiac examines serum levels of two specific antibodies: Deamidated Gliadin peptide Ab IgG and Tissue Transglutaminase Ab IgA.

Is it possible to test positive for the above antibodies while being sensitive (raise an immune response) only to hordeins?

There are two components to this question:

Can a person be sensitive to hordeins while being unaffected by either wheat gluten or rye (secalins)?
Would the above test produce a positive result given only hordein-specific antibodies? In other words, is the test specific to wheat gluten antibodies or will antibodies to any gluten epitope produce a positive result?

The reason behind this question in a short case history:

Mature adult subject experienced mild/intermittent IBS symptoms, onset vaguely extending back several years. Diet notably included regular/daily consumption of wheat/rye products as well as intermittent (2-3/week) beer (barley).
Recent clinical screening for celiac (serum levels of Deamidated Gliadin peptide Ab IgG and Tissue Transglutaminase Ab IgA) performed to investigate cause of suspected osteoporosis; both antibody levels assessed as positive.
Symptoms apparently abated within about one week following an initial dietary change successfully removing only barley gluten (beer), while regular consumption of wheat/rye continued.

Observations suggest a specific response only to barley, and raises the question about specificity of the clinical antibody test.

1) Can a person be sensitive to barley hordeins, while being unaffected by wheat gluten or rye secalins?

Possibly, but I haven't found a documented case.

According to What is gluten? (Journal of Gastroenterology and Hepatology, 2017):

  A variety of sequences from α, γ, and ω gliadins, as well as from the
  glutenins, have been identified to activate coeliac disease. However,
  several hundred gluten peptides are predicted to be immunogenic and
  trigger the T-cell mediated response.6 The most immunodominant T-cell
  epitope is from α gliadin, although T-cell cross-reactivity against
  gluten-derived, secalin-derived, and hordein-derived peptides have
  been confirmed. Additionally, within each grain, there exists a
  distinct hierarchy of immunostimulatory gluten peptides.6 Of all the
  peptides known to stimulate the T-cell response in coeliac disease, a
  given patient may react to only a few.

However, according to Coeliac disease: immunogenicity studies of barley hordein and rye secalin‐derived peptides (International Journal of Experiemntal Pathology, 2016):

  In conclusion, barley hordein and rye secalin appear to contain CD
  toxic epitopes that are found in wheat gluten, as demonstrated by the
  observed cross‐reactivity of CD‐derived gluten‐sensitive small
  intestinal T‐cell lines to wheat gliadin, barley hordein and rye
  secalin‐derived peptides.

2) Are the blood tests specific to wheat gluten antibodies?

I can't say for deamidated gliadin peptide Ab IgG test, but tissue transglutaminase antibodies IgA test (anti-tTG IgA) is not specific for wheat gluten; antibodies can be triggered by wheat gliadins, barley hordeins and rye secalins.

Gluten peptides (gliadins, hordeins, secalins) bind to tissue transglutaminase which deamidates them. Individuals with celiac disease have HLA DQ2/DQ8 dendritic cells, which present deamidated peptides to T cells, which stimulate B cells to produce antibodies against tissue transglutaminase:

  In CD, deamidation of gluten by tissue transglutaminase (tTG) in the
  small-bowel lamina propria promotes presentation of gluten peptides
  (gliadin in wheat, secalin in rye and hordein in barley) by
  HLA-DQ2 or HLA-DQ8 dendritic cells to pathogenic local CD4+ T
  cells...The most widely used serological test is anti-tTG IgA
  (Medscape)

3) Can barley affect the gut differently than wheat?

Possibly.

Nutrition and Celiac Disease (Nutrients, 2014):

  There is very limited data looking at the effect of barley hordein or
  rye secalin on CD outcomes in the published literature (e.g.,
  [66,67]), but evidence exists that these prolamins induce effects
  different to wheat gluten, at least at an immunologic level.

4) Do positive DGP and TTG test confirm celiac disease?

The specificity of IgG deaminated gliadin peptide (DGP) is 98% and of IgA tissue transglutaminase (TTG) 95% (American Family Physician, 2014), so when both tests are positive, celiac disease is very likely. The final diagnosis is by histological examination of a tissue sample obtained by duodenal biopsy.

5) Is it possible that, in celiac disease, symptoms disappear after removing only beer, but not wheat and rye from the diet?

It could be possible to have celiac disease confirmed by blood tests without any symptoms despite consuming wheat, barley and rye. Beer could trigger symptoms by irritating the bowel, not by gluten, but by alcohol or other substances, like in people with irritable bowel syndrome (American Journal of Gastroenterology, 2013).


Is there any relation between weight class and extreme lifting performance in O-lifting? We usually thought that weightlifting is a tough game. It is only for great physique.

There are 6 man in history who lifted  3 times their body weight. Check here.

3 of them are Bantamweight(56kg), 2 of them are Featherweight(60kg), and 1 is at Lightweight(67.5kg).

All of them are light. Is there are fact that light weighted are more efficient in weight lifting?

I suspect that such might partially result from both an inherent advantage and a coincidental advantage of lower height.  The former would be an effect of strength being roughly proportional to the cross-sectional area of muscle (square of a linear measure) and mass being proportional to the body volume (cube of linear measure).  This would make a 182cm person 10% stronger by body weight than a 200cm person of the same build (when one might initially think that having the same build would imply the same strength per unit weight).

The second advantage might be from taller individuals tending to have a more slender frame.  A more slender frame might be associated with lower muscle bulk (cross-sectional area) even with intensive training (more "ectomorphic"?).  Since there is a limit to thickness, to increase mass height must be increased, and if taller individuals tend to be more slender in build then as mass increases the build would tend to become more slender reducing muscle cross-sectional area (strength) in proportion to mass.


What spider species is this? I saw this spider yesterday and it was the first time I saw one. It had a log slender body and an almost tail like end. It also can apparently jump. Just wanted to know what species this is. Location (Cavite, Philippines)

It's one of the more unusual Jumping Spiders - similar, as Charles said above, to the North American spider Marpissa pikei, the Slender Jumping Spider (see second link below).  Yours is even thinner and more stretched out, but still clearly a Jumping Spider, from the long, heavy front legs and the big eyes on the front of its head.
Your species appears to be a spider called Mantisatta logicauda (first link below)

http://www.peckhamia.com/salticidae/diagnost/mantisat/longi-ph.htm

http://bugeric.blogspot.com/2012/07/spider-sunday-pike-slender-jumper.html


Why does caffeine give you so much energy, while being so low on calories? There's definitely something I'm missing here.

Since calories is a unit of measurement for energy, and caffeine seemingly gives you a lot, how can the labels on caffeinated products have such a low calory count?

I would presume that caffeine doesn't really have as much energy as it seems to give you? In which case, what does it do?

Thanks in advance!

I agree with @inf3rno: caffeine is a stimulant that acts on the brain and various other parts of the body (Snyder et al., 1981) and I wish to elaborate on its psychopharmacology. Caffeine's effects in the brain are mediated through adenosine A1 and A2 receptors (Daly et al., 1983). This results in a variety of actions (Fredholm et al., 1999). Most notably, adenosine inhibits neurotransmitter release in various brain structures including the acetylcholine release in the mesopontine projection neurons. Caffeine blocks these adenosine receptors, in turn leading to an increase in acetylcholine release in the cortex and hippocampus. This increases vigilance and information processing. Increased acetylcholine release in the prefrontal cortex may lead to increased attentional abilities. Adenosine also inhibits the effects of dopamine released by the striatium, ultimately leading to disinhibition of motor output in the brainstem. This in turn increases motor activity (Fisone et al., 1997). In all, caffeine does not exert its stimulant effects through its metabolic energy content, but due to its pharmacologic effects on adenosine receptors.


How is Taq polymerase produced? I've seen Taq polymerase being marketed as either "native" or "recombinant". I understand that the recombinant version is produced by specially modified Escherichia coli strains that have the gene for polymerase production spliced in them, but I am wondering about the "native" variant. I imagine that Thermus aquaticus is rather difficult to culture in a medium; is it thus true that the archaeans have to be extracted from the springs they came from for producing "native" polymerase?

For recombinant Taq polymerase, industrial-scale production produces liters of highly concentrated enzyme in a single run.  It comes in such small, dilute quantities when sold that only a few preps a year would be necessary to satisfy research lab demand.

I don't know the Thermus aquaticus protocol, but considering the achievements in yield for E. coli, and the minimal price difference between the two enzymes, I'd imagine that yields are similar there.  That would say to me that nobody's farming hot springs for T. aquaticus.


H₂S as a source of electrons for plants The first electron source for plants was H2S, but now most modern plants use H2O as an electron source.

What is the advantage of using H2O instead of H2S?

The major reason for this is because H20 can cause hydrogen bonding. Hydrogen bonding is what allows for plants to transport "this electron source" from their roots through their stems an further.

The stronger polarity of H20 also allows for stronger interactions. Such as ionic interactions (not fully bound but 2 polar atoms interacting). This kind of ionic interaction also allows for other types of material interactions such as cohesion and adhesion.

Overall, aside from the discussion of abundance as mentioned above (which is a very good point), it also allowed the plants to grow in directions that were more advantageous (darwinian) for their survival.


relative-rate of evolution I am supposed to calculate the relative rate of evolution of two sequences (human and sheep) with a chicken serving as the outgroup. The sequences are pretty long, so I will just create a short example since I just want to learn the process (we are expected to use online resources to figure out our homework problems since it is an online class, but I can't find any examples).

Human:   GGATGCGCCT
Sheep:   GGACGCGCCT
Chicken: GGACACGCCT

Can someone show me how to do this? Here is my guess from the limited info I found, but I have little to no confidence that it is correct:

p-distance of human/chicken = 2
p-distance of sheep/chicken = 1
relative rate of evolution = 2/1 = 2

Is this correct? If not, can someone show me how to do it correctly?

This kind of thing is normally calculated using the $K_{a}/K_{s}$ ratio, the ratio of synonymous to non-synonymous substitutions. It is not enough to count mutations for coding sequences, you should also take into account whether or not that mutation will actually change the resulting product.

There are various online tools that can help you do this, for example Phylemon:

http://phylemon.bioinfo.cipf.es/evolutionary.html


What buffer should I choose for IEX chromatography for purifying IgY I will use ion exchange chromatography with an anion exchange column to purify chicken IgY. Prior to this I did dialysis to remove salts from previous purification steps, is it possible after this step to just change buffer system?

The pI of IgY is 5.6-7.6, and so, what buffer should I use for the chromatography? I know I want the IgY to be negative, so I would want pH in start buffer to be higher than pI?

I bought a column but it has not arrived yet. Does it come with recommendations on preferred buffer system for the chromatography or can I use any one I want? And also, what buffer should I use to elute my protein?
Do you have any recommendations?

In previous steps, prior to dialysis, I used phosphate buffered saline with pH 7.

Thanks in advance

Your column manual will probably come with buffer recommendations (these manuals are also often available online). You can also search for publications that have purified IgY by anion exchange chromatography and use their procedure as a starting point.

Some generalities to keep in mind for buffer selection:

Buffers are most effective when the desired pH is close to their pKa. A rule of thumb is to choose a buffer with a pKa within 1 unit of the desired pH.
For anion exchange, the pH should be higher than the pI of the protein so that it carries an overall negative charge and will bind to the positively charged column. Another rule of thumb is to keep the pH about 1 unit above the pI. If the pH is too low, the protein will not bind. If the pH is too high, the protein will require more salt to elute, which can cause instability/precipitation.
For anion exchange, the buffer itself should be neutral or positively charged so it does not bind to the column. This can affect binding of the target protein both by its ionic strength and localized changes in pH.
Choice of pH depends on whether your column is "strong" or "weak". The charge on the functional group of a strong ion exchanger will not appreciably change over a wide range of pH whereas the charge on a weak ion exchanger is only maintained over a relatively narrow pH range.
This may go without saying, but make sure that your protein is stable in the buffer and pH you select. You may also want to keep in mind the buffer requirements of any downstream applications and choose one that is compatible to simplify purification.

Elution is generally done with a salt gradient, though a pH gradient can also be used. In a typical setup, you would have two solutions, both with the same buffer and pH but one with high salt (let's call it B) and one with no salt (let's call it A). The sample is applied in buffer A and then a gradient from 0 to 100% buffer B is applied to the column with fractions collected periodically. The most commonly used salt for ion exchange is sodium chloride (so the counterion for anion exchange would be chloride). Since relatively high concentrations of salt are often used for elution, in general you want to avoid counterions like sulfate that have a stronger salting-out effect.


Where do the lysines come from during ubiquitination? I know that Ub forms an isopeptide bond with lysine, but where do the lysine come from?

Are they just always available for the Ub to find to during the ubiquitination process? Is there a free lysine available on each of the additional Ub added to the chain? After the first Ub is added onto the target protein, does the E2/E3 complex still have to bind each time a Ub is added to the chain?

The Wikipedia article on Ubiquitin gives a pretty good answer to your questions. Look at the referenced articles if you want to get more detailed answers.

  Are they just always available for the Ub to find to during the ubiquitination process?

Yes, This [Ubiquitination] process most commonly binds the last amino acid of ubiquitin (glycine 76) to a lysine residue on the substrate.

  Is there a free lysine available on each of the additional Ub added to the chain?

Ubiquitin has seven lysines and each one of them can be bound to the N-terminal glycine of the next ubiquitin.

  After the first Ub is added onto the target protein, does the E2/E3 complex still have to bind each time a Ub is added to the chain?

Yes, but this is more complicated than the general mechanism. A poly-ubiquitin chain can be attached just like a single ubiquitin or one more ubiquitins can be conjuated to an exisiting ubiquitin-protein complex. See for example Brown et al and David et al.


Is there a difference between "Alpha Helix" and "Alpha subunit"? In my biochemistry textbook the terms alpha helix and alpha subunit are both used. Are these two terms synonymous? For instance, hemoglobin has an alpha and beta subunit, are these the same thing as alpha helix and beta pleated sheet?

These terms are completely unrelated. Alpha-subunit is an arbitrary name for a protein subunit in a multi-subunit protein complex (one having a quaternary structure like haemoglobin or G-protein etc).

Alpha-helix is a type of secondary structure.

Addition by David:

For those who may be unfamiliar with this, alpha, beta, gamma etc. are Greek letters of the alphabet (equivalent to English a, b, c) — also written α, β, γ. They are sometimes used in science to enumerate or differentiate between a series of related things — proteins, small molecules etc.


Phospholipid Bilayer structural reversal What would happen if the phospholipids in the phospholipid bi-layer were reversed, the fatty acid tails now facing outwards and the phosphate heads facing inwards? I'm assuming this will not affect the protein channels, but perhaps the loss of cholesterol in the structure of the bi-layer. Would this then mean that the fluid mosaic model no longer holds?

This would have quite dramatic consequences. The layers are ordered in the way they are, because of their polarity. In the way they are ordered, the hydrophobic tails are inside and directed towards each other, the hydrophilic heads are orientated to the outside and inside. Since both sides of the membrane are surrounded by aqueous solutions, this is necessary to allow a contact between solution and cell membrane and to allow an exchange of molecules between them. If the layers would be oriented the other way, this contact and exchange wouldn't be possible. Proteins channels in the membrane wouldn't be possible as well, since the intermembrane domains are composed preferrably of amino acids with hydrophobic sidechains, while the domains on the outside of the membrane contain more hydrophilic amino acids.
A turn like this would need a completely different composition of life - meaning it couldn't be based on water like it is.


Acetone–butanol–ethanol fermentation Source

Source

Source

Acetoacetyl-CoA is a C3 unit.

3-Hydroxybutyryl-CoA / Butyryl is a C4 unit.

Where does the additional C atom come from? I'm suspecting it's another Acetyl-CoA -> CoA reaction, but I don't see it in the images.

Well, I’m not sure I should answer this, as your question is predicated by an incorrect supposition:

Acetoacetyl-CoA is a C3 unit.
3-Hydroxybutyryl-CoA / Butyryl is a C4 unit.

Not according to Kegg:

However, my answer is worthwhile if I explain how I found this out. One way to check this sort of thing is to go to the Kegg website and search for the compounds of interest, find the appropriate pathway (shown below) and then click to check compounds and reactions.

There is also the Metacyc website for metabolic pathways, and you can check the formulae on Wikipedia.


Can you change your gut microbiota by changing your diet? Would that affect calorie uptake? I have seen peer-reviewed papers mentioning the daily changes in gut microbiota composition according to dietary changes. See for example this paper:

http://genomebiology.com/2014/15/7/R89

My question is related to this one:

Relationship between our microbiome and personalized nutrition

If, according to these recently published scientific results, it takes a day to change the gut microbiota to adjust to the dietary change, and the presence of certain microbes makes food assimilation more effective,

Does this mean that alternating a protein-rich meat and dairy diet with a carbs-rich diet every day would make our microbiota switch daily and not have time to increase calorie uptake?

Firstly, it should be noted that a stable, healthy microbiome is generally thought to be a marker of health; actively disrupting it through diet in an attempt to fight with it over nutrients is therefore not necessarily a good idea, as it can affect the health of not only your gut but also your immune system, etc.
Dysfunctional microbiomes are for example associated with behavioral problems in eating disorders.
Nonetheless, diet shifts have been used as a tool to attempt to control the microbiome and put it in a "healthy state". You can indeed use consumption of some foods to shift microbiome composition. Presumably if you did this in a sufficiently disjointed way, you could throw your microbiome into a sort of ecological chaos.
However, it would be much simpler to just constantly take antibiotics to ensure that your gut load of microbes was generally low. This still isn't a good idea, as it can lead to Clostridium difficile or E. coli infections or other bad things, but it would be a much more straightforward way of getting to the desired end state.


Would it be possible to eat things from another planet Although at first glance my question is perhaps better suited for a space exploration or sci-fi forum I looked  and felt this forum was more appropriate.

What makes plants and animals edible and allows us to gain nutrition from them? If life evolved separately from life on earth would any of it be edible to us or to any other creature that evolved on this planet.

My question is not about stuff being toxic, its about if anything other than life on earth, would be digestible? Do we need to evolve side by side with our food? I know of convergent evolution, that may make things look similar, but is there something at a cellular level that makes things edible. Does everything edible have DNA?

I don't have an academic background in biology so apologies if this question sounds silly. It's been bugging me for ages. My gut feeling tells me that nothing will be edible but I don't have any science to back that up.

I'm a vegetarian so I'm not just thinking about hunting and eating aliens either!

Thanks.

Short Answer- No, chances are negligible.

Long Answer- Digestion is a chemical process which is mediated by enzymes. Enzymes are highly choosy molecules so that they only perform the work they're made for. In digestion, enzymes like proteases (for breaking down proteins), lipases (for breaking down lipids), amylases (for breaking down starch), DNAses (for breaking down DNA), etc. are involved. For example, amylase is specialized to break down polysaccharides (carbohydrate polymers) into mono/di/tri/oligo-saccharides. See this from wikipedia:

  The α-amylases are calcium metalloenzymes, completely unable to function in the absence of calcium. By acting at random locations along the starch chain, α-amylase breaks down long-chain carbohydrates, ultimately yielding maltotriose and maltose from amylose, or maltose, glucose and "limit dextrin" from amylopectin.

And this image from here:

Lets forget the "completely unable to function in absence of calcium" part as it is out of the scope of this question. But it is necessary to know how specialized enzymes are to answer your question. They are so specialized that amylase can break starch, but not cellulose. See this image:

Source

You must have noticed, in the diagram above, the minute difference between starch, cellulose and glycogen (BTW glycogen is another polysaccharide), but even that difference is enough for enzymes to tear apart one and pass on the other molecule.

The above explanation was necessary to tell why the answer is no. If we eat something, enzymes are needed to break it down. But if enzymes cannot recognize something, then they can simply not work on it. So, if you even want to eat space grass, forget about being able to digest it. Because even if we confirm that life on earth came from space through meteorites billions of years ago, then also during this time period of billions of years both that life of space and this life on earth would have evolved so much that they might not match, even chemically!

Hope this helps. Tell me if you want any more details :)


What is a false crocodile? On the wikipedia page about crocodiles crocodiles are called true crocodiles. Does this mean there are (or where) false crocodiles as well?

  Crocodiles (subfamily Crocodylinae) or true crocodiles are large semiaquatic reptiles that live throughout the tropics in Africa, Asia, the Americas and Australia. Crocodylinae, all of whose members are considered true crocodiles, is classified as a biological subfamily.https://en.wikipedia.org/wiki/Crocodile

The only "false crocodile" I found was the False gharial.

What is a false crocodile? if it exists at all. If not what is the reasoning behind the naming of a true crocodile?

If you keep reading the next sentence it makes clear what is meant (emphasis mine):

  Crocodiles (subfamily Crocodylinae) or true crocodiles are large semiaquatic reptiles that live throughout the tropics in Africa, Asia, the Americas and Australia. Crocodylinae, all of whose members are considered true crocodiles, is classified as a biological subfamily. A broader sense of the term crocodile, Crocodylidae that includes Tomistoma, is not used in this article

So, the Crocodylidae family refers to crocodiles, the Crocodylinae subfamily are the true crocodiles which includes almost everything known as a crocodile, and indeed, you found the one that gets left out:

  The crocodylian family Crocodylidae includes the true crocodiles, which are the members of the subfamily Crocodylinae, as well as potentially the false gharial, the only extant member of the subfamily Tomistominae. The latter is a subject of controversy as to whether it is a crocodile or actually belongs in the family Gavialidae.

(via Wikipedia)

Wikipedia further states:

  Gavialidae have conventionally consisted of only one surviving species, the gharial (Gavialis gangeticus), which is native to India and Nepal. Many extinct species are also known

and also

  Tomistominae is a subfamily of crocodylians that includes one living species, the false gharial. Many more extinct species are known, extending the range of the subfamily back to the Eocene epoch. In contrast to the false gharial, which is a freshwater species that lives only in southeast Asia, extinct tomistomines had a global distribution and lived in estuaries and along coastlines.

So there are many other extinct relatives of crocodiles in these groups; the question is to which the extant false gharial belongs. In either case, the other Tomistominae would be non-true crocodiles, according to a definition that subfamily Crocodylinae are the true crocodiles.

The words "true" and "false" are not necessarily used in their boolean meaning here, but rather, "true" in taxonomy fits better with other definitions, for example from Merriam-Webster: "typical" (Merriam-Webster explicitly references the "true cats" as a use for this meaning). A synonym would be more like "archetypal" or refer to a clade or other more robust grouping, rather than a linguistic/non-scientific grouping.


Change in synthesis rate of a molecule changes equilibrium concentration I was reading the topic of 'The concentration of the molecule can be adjusted quickly only if the lifetime of a molecule is short' from Molecular Biology of the Cell by Alberts.

At the end of pg-837 (this part can also be found here), the author says -

  "In fact, after a molecule's synthesis rate has been either increased
  or decreased abruptly, the time required for the molecule to shift
  halfway from its old to its new equilibrium concentration is equal to
  its normal half-life—that is, equal to the time that would be required
  for its concentration to fall by half if all synthesis were stopped."

What do they exactly mean by 'shift halfway'? I am not able to understand quite clearly what the above sentence means. I hope some of you may be able to help me. Thanks.

Note: The term equilibrium is different from steady-state w.r.t chemical reactions. Steady state is the right term for the above example. Equilibrium is used in the sense of forward and reverse reactions in a single reversible reaction. The above example considers two irreversible reactions — production and degradation.

  ... ... the time required for the molecule to shift halfway from its old to its new equilibrium concentration is equal to its normal half-life

This is not true if the degradation reaction is zeroth order or if these reactions are nonlinear. But for a linear production degradation set of reactions ($X$ is a biomolecule formed at a constant rate $\alpha$ and degraded at a first order rate  $\beta$ ), the reaction rate can be represented by the following equation.

$$\frac{d[X]}{dt}\bigg|_1=\alpha _1 - \beta [X]$$

At steady state $\frac{d[X]}{dt}=0$, which means $[X_{ss_1}]=\Large\frac{\alpha _1}{\beta}$

Half life as defined, by setting $\alpha$=0 and solving the differential equation = ${\Large \frac{log(2)}{\beta}}$

When the formation rate is changed to a new value:

$$\frac{d[X]}{dt}\bigg|_2=\alpha _2 - \beta [X]$$

and $[X_{ss_2}]=\Large\frac{\alpha _2}{\beta}$

From the above equation following equation can be deduced (by integrating the differential equation):

$$-\frac{1}{\beta}.log(\alpha _2 - \beta [X]){\large|}_{X_{initial}} ^{X_{final}}= t_{\frac{1}{2}} $$

when you substitute $X_{initial}=X_{ss_1}=\frac{\alpha _1}{\beta}$ and $X_{final}=\Large\frac{\frac{\alpha _2}{\beta} - \frac{\alpha _1}{\beta}}{2}$ (halfway between new steady state and old steady state)

you would obtain: $$t_{\frac{1}{2}}= -\frac{1}{\beta}log\left(\frac{\alpha _2 -\beta\frac{\alpha _1}{\beta}}{\alpha _2 - \beta \frac{\frac{\alpha _2}{\beta} - \frac{\alpha _1}{\beta}}{2}}\right) = \frac{log(2)}{\beta} $$


Is half-a-tablet of X a substitute for a tablet of X/2? This may be anecdotal.

At the pharmacy earlier, the prescription called for a drug with X mg of the target chemical. The pharmacy however only had stock of a higher potency of the same brand.

E.g. A prescription may call for 25mg of a particular chemical, whereas the pharmacy could only service a request for 50mg of that chemical in the same brand.

According to the pharmacist, and the medic - a proportional fraction of higher potency drug of the same brand may be substituted for the lower potency. Thus in the example above, half-a-tablet of 50mg may serve in lieu of a single tablet of 25mg.

For a given brand

Is half-a-tablet of X a substitute for a full tablet of X/2?
Does the corollary scale upwards too?

This website gives a nice overview, including how the FDA approve drugs that they expect will be spit and some practical issues of pill cutting.

Yes, half a tablet of (2x dose) is, absent other issues, equivalent to one intact tablet of (1x) dose.  The main exceptions are practical ones.. where the tablet cannot easily be cut; where the dosing is so specific that slight variations of dose (uneven tablet fragments) matter, or where the dose is in a capsule or has some special coating so that cleavage might alter the release of drug into the body.

Yes, dosing scales upwards.  Two pills give twice the total dose of one pill.

All prescriptions are dispensed with specific dosing regimens (i.e how much you take and when you take them) to ensure the drug reaches effective concentrations in the body. You should not try to 'boost' the drugs effectiveness by taking more drug, or taking drug more frequently than your physician has prescribed.  As noted in the weblink above, it can be tricky to keep track of dosing and timing if your pill bottle contains whole and cut pills.  (i.e what does "take one pill every NN hours" mean ?).

This is NOT MEDICAL ADVICE . Always consult your physician and/or pharmacist for your particular case.


Mitochondrial donation - why is the second woman needed? Mitochondrial donation or the latest case procedure describes that an egg of the second woman is used as a host with healthy mtDNA.

Being a complete layman I'm interested in whether it is a restriction of the method or some fundamental requirement. Is it in principle possible to replace broken mtDNAs of a mother with mtDNAs of a father, which are mtDNAs of his mother?

It looks like the current techniques might better be described as "nuclear donation".  You take an ovum with healthy mitochondria, remove the nucleus, and insert the desired nucleus from the woman with bad mitochrondria.  So yes, currently, the mitochonrdria have to come from an ovum, and therefore a woman.


Is there an animal which, when eaten by other animal, poisons the predator and gets out of it's stomach? It was a question in one competition, but it remained unanswered and i am curious about an answer.
There was a hint: American bullfrog
but i can not find any example of this behaviour on the web.

The closest I can think of with that hint is a Middle Eastern beetle that hunts frogs and other amphibians:

  In almost 400 face-offs, the amphibians only managed to get the larvae in their mouths seven times. Even then, they soon spat out the larvae, which quickly turned on them (first video below). One toad even managed to swallow a larva, which moved inside its stomach for two hours. For some reason, the toad eventually regurgitated its catch, and the larva, apparently unharmed, killed and ate the animal that had just eaten it (second video below).

However, it's only a pseudo-fit to the clue. The beetle doesn't hunt American bullfrogs, but ones native to its area of the world.


How is Microenvironment strictly defined? I started to think this definition of Wikipedia:

  Microenvironment (biology), a small or relatively small usually
  distinctly specialized and effectively isolated biophysical
  environment (as of a nerve cell)

and I started to think which environments can be examples of its.
Joints, synovial joints with capsule, hyaline cartilage in capsules, ...?
I would like to get more examples of environments so I can think better definition.

What is Microenvironment?

The meaning of the term microenvironment depends on the scale of the system that you're looking at. It's a sort of weasel word that loosely means "context" or "stuff in the immediate surroundings of the system of interest that has some kind of an effect on it". I've seen it used to describe everything from the chemical microenvironment of a cell (e.g. a hormone gradient) to the electrostatic microenvironment of a single amino acid residue in a protein (e.g. the field from nearby charged residues).

Conceptually it's similar to the "surroundings" in the "system and surroundings" framework from statistical physics.


How did shellfish and coral survive acidic oceans in earlier eras? Throughout most of Earth's history, the planet has had more CO2 in its atmosphere, correct?  Therefore th pH of the oceans was even lower, right?  So how did CaCO3-using animals create their shells back then?

They didn't survive when carbon dioxide levels in the atmosphere passed certain thresholds in the history and increased ocean acidity significantly; leaving less carbonate for marine life to use for shells or skeletons. For example, up to 96% of marine life (including organisms with CaCO3 skeletons) went extinct in the Earth's most severe known extinction event, Permian–Triassic extinction. Another event called Paleocene–Eocene Thermal Maximum caused a mass extinction of benthic foraminifera.

  Five times in the Phanerozoic [the past 542 million years (My)], more than three-fourths of marine animal species have vanished in mass extinctions. Each of these events is associated with a significant change in Earth’s carbon cycle. However, there are a great many disturbances of the carbon cycle  whose imprint in the geologic record is almost exclusively environmental. These other events are relatively benign, with extinction rates barely, if at all rising, above background levels.

  Two well-studied examples illustrate these distinctions. The end-Permian extinction [~252 million years ago (Ma)], the most severe mass extinction in the Phanerozoic, plays out over a period of 104 to 105 years; the extinction interval immediately follows a perturbation of the carbon cycle of similar duration. The Paleocene-Eocene Thermal Maximum (~55.5 Ma) is a carbon cycle event of roughly similar time scale, with unambiguous signs of global warming and ocean acidification. It is associated with a significant extinction of benthic foraminifera, but there is no evidence of other major extinctions. What makes these two events so different? The unambiguous co-occurrence of the end-Permian extinction with massive volcanism provides one indication, as does the greater magnitude of the end-Permian carbon isotopic excursion compared to that of the Paleocene-Eocene Thermal Maximum. However, no general distinction, applicable throughout the Phanerozoic, exists.

  Thresholds of catastrophe in the Earth system
  By Daniel H. Rothman
  Science Advances | 20 Sep 2017 : E1700906
  http://advances.sciencemag.org/content/3/9/e1700906.full

  (emphasis mine, removed citation numbers)

Here is an excerpt from a relevant study of Knoll et al. about the affects of end-Permian mass extinction on biomineralization  which includes the extinction percentages of animals that
form skeletons of calcium carbonate and vulnerable to elevated CO2
levels:

  Within the marine realm, animals with active circulation and elaborated gills (or lungs) for gas exchange compensate for elevated PCO2 better than organisms that lack these features. Also, animals that normally experience high internal PCO2 , including infauna and metazoans capable of exercise metabolism at high rates, tolerate experimental increases in carbon dioxide differentially well. And among animals that form skeletons of calcium carbonate, species that can exert physiological control over the pH balance of the fluids from which minerals are precipitated fare better than those with
  limited buffering capacity. Based on these features, Knoll et al. (1996) divided the Late Permian marine fauna into two groups, with high and low expected survival, respectively.

  As predicted, 81% of genera in the “vulnerable” group disappeared at the boundary, while only 38% of nominated “tolerant” genera became extinct (Figure 6A). The selectivity is even more pronounced when skeletal physiology is considered alone (Figure 6B; Bambach and Knoll, in preparation). Fully 88% of genera disappeared in groups that formed massive carbonate skeletons but had limited capacity to buffer fluids (sponges, cnidarians, bryozoans, calciate brachiopods). In contrast, groups that built skeletons of materials other than calcium carbonate lost only about 10% of their genera. Intermediate taxa—groups like mollusks that have a substantial commitment to carbonate skeletons but some physiological capacity to regulate the chemistry of internal fluids—lost 53% of
  their genera. Of these, those genera considered vulnerable on the basis of the other criteria noted above went extinct at twice the rate of those otherwise considered tolerant.

  Biomineralization and Evolutionary History
  By Andrew H. Knoll
  Department of Organismic and Evolutionary Biology
  Harvard University
  Cambridge, Massachusetts, 02138 U.S.A.
  https://web.archive.org/web/20100620222809/http://www.geochem.geos.vt.edu/bgep/pubs/Chapter_11_Knoll.pdf

  (emphasis mine)


What is the name of this strange white caterpillar? My friend found this caterpillar in south-central Tennessee in August. No identification guides or databases I've searched had a similar picture. Does anyone know the name of this species?

It is hard to be sure without clearer pictures, but that looks like something in the genus Eriocampa and it could be a Butternut Woollyworm (Eriocampa juglandis).
Picture taken in Kentucky from BugGuide.net © 2015 by dan40165:

These are the larvae of a sawfly (so not technically a caterpillar) and are about 1 inch long.
You can learn more about this particular species here. To narrow down the exact species it would be helpful to edit more information into your post including the types of plants in the area.


Bioluminescence and photovoltaics I work in the PV industry and was asked a question recently during a presentation. Could Bioluminescence provide enough light to power a PV array during off peak hours? I understand the PV portion and the light spectrums needed to power the photovoltaics, but I have no clue how the science of Bioluminescence works or what type of light is emitted. I have the suspicion that this may be theoretically possible, but would require too much raw material? Any insight would be appreciated.

Here is a report addressing this, I haven't read it in detail, but I've skimmed it and it looks like they've done a pretty good job, and address a number of key points, talk about the emission spectra of certain organisms, etc.
Bioluminescence – a source of marine energy?

From the conclusion: "The low light output of bioluminescent species relative to solar light may render the conversion of bioluminescent light into electrical energy uneconomic as a stand-alone option."

I agree with them that it would be possible to extract energy that way.  I also agree that its not even close to economical.  You lose energy at so many steps, you have chemical energy in whatever the cells eat to grow, then some small fraction of that chemical energy will be turned into light energy, most of that light will shoot out in the wrong direction and just get absorbed by other stuff in the culture.  If you want to use bugs, a better option would probably be a microbial fuel cell, where microbes sit on an electrode, oxidize some chemical, and take that electron and dump it straight onto the electrode.  This is still a pretty inefficient process as far as energy production technologies are concerned, but at least it skips the waste associated with conversion of the chemical energy into light energy and then back into electricity.


Why are tree rings the same if rainfall is different from place to place? I have looked at data from rain gauges and usually the rainfall levels are very different from place to even. Even in adjoining towns or townships the rainfall can exhibit much different patterns.

Nevertheless, all the trees in an area tend to show the same ring patterns. Why is this?

The rings are not only affected by time but also by location. So no, the patterns are not always the same depending where you are. Climate do affect the rings.

Typically a major factor affecting ring patterns is the seasonality. Depending on the number of rainy season, you might observe one or two rings per year.

If interested, here is an introduction to dendrochronology (from the University of Victoria).


Do Schwann cells have Na+/K+ ATPase pump? I was studying "Action Potential" and this question crossed my mind.
Another question is that, "Why does the action potential not occur in Schwann cells, or if it does, how does it occur?"
I know that many animal cell membranes have this pump, but I was not sure about this one.

Yes. Although utilizing the action potential is not in their function, Schwann cells do have Na/K ATPases. In fact all animal cells do. It contributes to the resting membrane potential in neural networks, with regards to Schwann cells, and prevent differences in osmotic pressure from disrupting the cells.

As for your second question, action potentials do not occur in Schwann cells as there is nowhere for this "impulse" to travel to. A localized depolarization is not an action potential. Papers such as this, and this suggest that voltage-gated ion channels in Schwann cells serve complex and specific purposes such as inducing myelin formation.


Why is membrane potential not zero at equilibrium? For the squid giant axon, the membrane potential computed by the Goldman equation is -60mV. And the Nernst potentials are (the differences between the K+ and the Na+'s Nernst potential and the membrane potential let the mechanism work):

  K+ = -74mV
  Na+ = 55mV
  Cl- = -60mV

I am wondering if the membrane potential is 0mV, whether the K+ and Na+ Nernst potentials still cause the mechanism to work, so can 0mV be a reasonable value? (That is, I think the value of potential is not important at all as long as the mechanism works well, is this true?)

The value of the membrane potential does not affect the location of the resting potential.  The membrane potential affects only the fraction of channels that are open, thus allowing net current to change, which allows for the depolarization and repolarization of the membrane (the action potential).  During the action potential, the resting potential does not change.

The value of the resting potential is governed only by the distribution of ions (how many are on one side of the membrane vs. how many are on the other).  This is relatively constant even as ions cross the membrane for the action potential; it is really not a very large fraction of ions moving at all compared to the reservoir they are in, so the reversal potentials are preserved over time.


Can systemic intravascular thrombosis cause brain infarction? I wonder if the thrombus can pass through the brain-blood barrier because I think small molecules like O2, CO2 and ethanol can pass it.
Probably, in some diseases where the permeability of the barrier changes.

Can systemic intravascular thrombosis cause brain infarction?

No, a thrombus would be much too large to pass through the highly selective blood brain barrier.  However, there are some cases where intra-vascular thrombosis can cause stroke.

One example would be non anti-coagulated atrial fibrillation, where the inefficient beating of the heart causes blood to remain stagnant in the left atrium.  This can cause a thrombus to form within the atrium which can then throw off emboli, some of which may enter the cerebral circulation. These may then partially or fully occlude one of the arteries in the Circle of Willis (the brain's circulation system), however the blockage is proximal to the blood brain barrier.

See Management of atrial fibrillation (GY Lip,2007) or for those hitting a pay-wall the professional reference section on AF


Where does the lactate produced by tumors go? Tumors are known to burn glucose and secrete lactate (this is known as the Warburg effect).  Where does this lactate go?

Does it steadily accumulate in the neighborhood of the tumor? This doesn't seem likely. I mean, eventually an equilibrium concentration of lactate in the neighborhood of the tumor must be reached that is balanced by some process taking lactate away from the tumor. The nature of this lactate drain is what I am asking about.

Does it enter the circulation system and is degraded somewhere else in the body (as a part of the Cori cycle)?

Is it consumed by neighboring non-malignant cells?

A combination of all of the above?

Something else?

Most of the lactate produced by tumors probably enters the circulation and is taken up by other tissues (like the Cori cycle, correct). There are several studies like this one measuring glucose uptake and lactate release by tumors in vivo, and it is clear that a substantial amount of lactate is released into the veins draining the tumor site.

Oxidation of lactate by neighboring cells within tumors has been reported as well, but I don't know of any quantitative data on exactly how much lactate this process can consume. But it seems unlikely that this can remove a major fraction of lactate produced by glycolytic tumors, since glycolysis produces lactate at a much higher rate than respiration consumes it (per ATP generated).

It's also true that tumors can accumulate lactate. Some tumors are poorly perfused, with "disorganized" blood vessels and blood flow, and then waste products may not be cleared away efficiently.

So yes, all of the above :)  There are large differences between individual tumors in all these parameters, so there is no generally valid answer I think.


Coalescent theory - independence of coalescent times Let $T_i$ be the time to coalesce from $n(t)=i+1$ to $n(t)=i$, where $n(t)$ is the number of sites that have not coalesced yet. In the below example the maximum $n(0)=6$.

As I understand it, many mathematical developments in coalescent theory depends on the fact that the random variables $T_i$ are independent (but not identically distributed). In other words...

$$f_{T_n, T_{n-1}, …. T_3, T_2}(t_n, t_{n-1},….,t_3, t_2) = \prod_{i=2}^n f_{T_i}(t_i)$$

What are the assumptions for this equation to hold true? Below are some suggestions

No selection
Selection is not varying through time
Stable population size
Random mating
Both sexes have the same genetic background
Both sexes have the same variance in fitness
...

source

As long as members of a generation "randomly choose" their ancestor in the previous generation the law of independent probability (your equation) will hold.
Any study of coalescent theory begins with the Wright-Fisher model. The assumptions are:

finite diploid population of constant size N,
non-overlapping generations (simultaneous reproduction),
random mating,
no mutation, selection, or migration.

These assumptions are consistent with independent non-identically distributed waiting times. An example of an assumption under which independence no longer holds:
Individual B's random choice in generation 2 of ancestor A in generation 1 reduces the probability that individual C in generation 2 will choose A. In other words, the likelihood that A will give its genes to the next generation falls off with each new recipient. Then the independence no longer holds.
See, e.g., Deonier, Computational Genome Analysis (2005, Springer) at pp. 392 ff.
J. Wakely's paper Coalescent Theory: An Introduction (Systematic Biology, 58:1, Feb. 2009) may be one of the best overviews of this immense topic available. He mentions Kingman's 1982 mathematical proof (which I haven't gone through) of the coalescent process (Stochastic Processes and their Applications 13 (1982)--available as a free download from ScienceDirect).


Need / consumption of magnesium Does doing sports makes a human require more magnesium and – if any – how strong is this effect?

Do athletes take magnesium supplements (e.g. pills of magnesium carbonate) because they build muscles and therefore need more of it as their muscle masses increase, or is magnesium consumed by muscle activity (e.g. by causing a chemical reaction which the human body can't undo so it has to excrete the reaction product and get new magnesium from food)?

Strenuous exercise apparently increases urinary and sweat losses that may increase magnesium requirements by 10-20% according to this paper.


Cannot see images beyond a certain magnification with a microscope Using a new microscope with my son, we cannot see images beyond a certain magnification:

Eyepiece: 25x - Objective lens: 4x   --> OK
Eyepiece: 25x - Objective lens: 10x  --> OK
Eyepiece: 25x - Objective lens: 40x  --> not focused
Eyepiece: 25x - Objective lens: 100x --> not focused

In the last two cases, we try moving the stage along all its range, without getting anything.

Same issue using a 10x eyepiece.

On the 100x objective lens "OIL" is written; does it mean the observation needs to be done through oil instead of air? Or just that oil is used inside the objective?

We did not prepare the leaf; we just put a small piece of it between two slides.

Are we doing anything wrong?

Observing a leaf at 250x, we can see tiny round structures (I think barely bigger than what can be possibly seen by our eye): are those the cells?

This is probably the problem: "We did not prepare the leaf; we just put a small piece of it between two slides.".

I suppose you mean you put a leaf fragment between two regular microscope slides, those measuring 26mm * 76mm (1in. * 3in.)?

That won't work. Long story short: microscope optics/objectives are designed with a specific working distance in mind, which is not an entiraly free choice, but dictated by the laws of physics/optics. An average achromat 40/0.65 has a working distance of about 0.6 mm. An average achromat 100/1.25 has a working distance of about 0.2 mm. An average microscope slide has a thickness of about 1 - 1.2 mm...

In the... well... regular microtechnique, a specimen is put on a slide and covered with a very thin coverslip, having a thickness of around 0.15 - 0.17 mm.

Also, as others mentioned, using a 25x eyepiece in combination with a 40/0.65 or a 100/1.25 is kind of overkill. With that combination, you enter the realm of "empty magnification". In short: structures appear larger, but no new structures are revealed and the image becomes more and more fuzzy.

And yes: you need to use immersion oil with the 100x objective, but keep in mind this is a very demanding objective to be used, on the part of the microscopist as well as on the part of the slide preparer.

Using a microscope is not all that simple for novices, but there's an easy way to find out -if no image can be produced-, if it's a microscope problem or an inexperienced user problem: take as a specimen an as thin as possible large object, such as a leaf of cigarette paper, and try to focus on it, using low power and gradually use stronger objectives up to 40/0.65. If an image can be produced, even if it's rather blurred at 40/0.65, the microscope is okay.


Does artificial high intensity light damage permanently dark ecosystems? Popular science features on wildlife typically capture camera images using natural light, or high-speed exposures. This is not possible where the ambient light is extremely poor.
E.g. Caves, Undersea

For beings accustomed to the stygian dark, the high illumination for a video camera and/or the flash of a still camera could both be the equivalent of a 1" spanner wallop on the head or worse. Do we, inadvertently, injure the local ecosystem this way?

I don't know how harmful the exposure to a camera flash could be to organisms that live in complete darkness. However, since the animals that live in this conditions are usually blind, and the time of exposure is quite short, it's reasonable to assume that the damage produced should be minimal.

In the case of caves, permanent artificial illumination is very destructive to the environment, but the effect is due mainly to temperature changes and the introduction of organisms coming from more illuminated parts of the cave (cave organisms are usually slow and react poorly to light, so they are an easy prey if they're under light). In fact, for tourist activity, the use of lanterns or miner helmets is highly recommended.

In the case of abyssal ecosystems, ecological invasions are less likely, since there still exist a vertical barrier based in temperature, oxygen and carbon dioxide concentration and pressure. However, in this ecosystems there exist many animals which are very sensitive to light, due to the prominence of bioluminescence. Some of this animals could be damaged by the kind of light you describe. However, it's very unlikely that the main functioning of this ecosystems could be affected because of its extensive size. Moreover, the low population densities it has implies that even very long submersions would encounter only a few samples (with the exception of volcanic vents and some other geological curiosities which, in fact, are even more isolated from the rest of the biosphere by physical and chemical barriers), so the global effect should be negligible.


When did the mammalian outer ear evolve? All Eutheria and Metatheria have outer ears, and as far as I found out, monotremes once also had them, so they seem to be universal for mammals. Did other synapsids have them, too?

I know that soft tissue doesn't fossilize well, but isn't there any other way to find out, like muscle attachment? Has it something to do with mammalian ear bones?

Yes, it is believed to be linked to the mammalian inner ear bones. Since they act as amplifiers, the faint sounds gathered by the outer ear have a greater benefit. But really early mammals show many adaptations that they were relying very little on sight and a great deal on hearing. External ears just might not be beneficial enough unless you are really relying on hearing. The only other vertebrates that rely that much on hearing, the owls, also have external structures to help gather sound.

The fact that both developed at the same stage is circumstantial evidence that they may be linked as well.


Relationship between food decay and electric current I am planning to do a little experiment on investigating the relationship between food (organic) decay and the electric current.

I am going to place the food (ex.banana) on top of an aluminum foil, then hook the foil to a battery.

However, this doesn't seem convincing that it's going to work.

Is there any better way to experiment this?

I'm not sure if this falls under "biology" category

Also, it doesn't have to be banana, it could be avocado, lettuce, apple etc.

Thank you

Bananas, unless you like mush, become inedible long before any bacterial decay. The brown spots and softening that occur are due to ripening  processes in the banana. Some of the amino acids in the banana are metabolized to produce ethylene. As with other fruits, ethylene acts as a hormone to accelerate the conversion of starches to sugars. The banana gets sweeter while at the same time getting musher. http://www.livestrong.com/article/466183-is-eating-a-banana-with-brown-spots-bad-for-you/

As far as your experimental design, you would need to stick electrodes into the banana to attempt to run a current through it. But I doubt this will work because, to conduct the current inside the banana, there needs to be a certain amount of water, free ions and the structure to allow the ions to move. In my opinion, bananas have too little moisture content for this to occur.

Aiming to affect bacteria on the surface of the banana might be a doable experiment. But the methods that come to my mind involve immersing the banana in an electrolytic solution possibly leading to un-yumminess and not at all guaranteed to work.


Why would glucocorticoids promote glycogenesis and not glycogenolysis? I read in a textbook that glucocorticoids can stimulate the synthesis of glycogen. I do not understand this at all—shouldn’t glucocorticoids try to increase the blood level of glucose? Why would they be storing glucose as glycogen in the liver and muscles like insulin?

Glucocorticoids have a number of physiologic effects on glucose metabolism, inflammation/stress response, bone metabolism, etc. In general they are called glucocorticoids because they were originally found to be associated with increased blood glucose concentrations. Simply put, glucocorticoids antagonize the actions of insulin and create a state of insulin resistance, as well as increasing the expression of enzymes involved in glucose metabolism. They have a number of effects on all sorts of tissues and biological processes.

With regard to your question specifically, it makes sense that glucocorticoids stimulate glycogen synthesis, because it will allow the body to store more glucose as glycogen and increase the body's capacity for liver glucose production (i.e. glycogenolysis). Remember, at the same time glycogen synthesis is being increased, the glucocorticoids are inducing a peripheral insulin resistance that antagonizes insulin action in skeletal muscle and fat that also leads to increasing glucose concentrations in the blood. Moreover, free fatty acid are released from adipose tissue to be carried via the circulation to the liver so they can be oxidized to produce ATP for gluconeogenesis.

There is an excellent chapter that describes the effects of glucocorticoids on glucose metabolism in the major metabolically-active tissues (e.g. liver, white adipose tissue, skeletal muscle) by Kuo et al from Vol 872 of Advances in Experimental Medicine and Biology (pages 99-126). The book is not open access so I can't paste a picture of any of the figures, but they essentially show what I describe above. Here is another link to a very nice review article in the Journal of Endocrinology that has some great figures showing fuel redistribution in response to glucocorticoids as well.


Why people don't harvest Locusts when infestation happeds? We've heard about tremendous amount of money losses even leading to famine due to crop destruction from locust infestation over and over again, but all these grasshoppers are a valuable protein, probably way more valuable than the destroyed crops. Although most people from many cultures won't eat such insects, these can be ground to flour and stored to be fed to omnivore livestock like pigs or sold for profit or exchanged for grains.

Is there edible energy in the insect swarms? Can this be made into livestock feed? If not, is the reason this isn't common practice biological or economical?

Locusts have been harvested in Thailand and Australia they call them sky-prawns. They deep-fry them and consume them happily.

http://www.bugsfeed.com/locust

http://www.fao.org/docrep/017/i3246e/i3246e.pdf

In Thailand Orthoptera or
grasshoppers include Patanga succincta,
Locusta migratoria, Acrida sp.,
Cyrtacanthacris tatarica and Oxya
japonica japonica (Thunb.)
(Hanboonsong et al. 2001; RaƩ anapan
2000). All of them are pests of
economic crops such as maize and
rice. Grasshopper species, parƟ cularly
Patanga succincta and Locusta
migratoria, used to be one of the
major pests of maize and rice. Today
they have become one of the most
popular edible insects since they were
introduced for human consumpƟ on
by entomologists − a campaign to eat
grasshoppers had been launched
because control efforts had been
unsuccessful. For example, in 1983
this was launched by local offi cials and
villagers in Prachin Buri Province
collected more than 10 tonnes for use
as food (Lewvanich et al. 1999).*


How can fennec foxes eat scorpions? I just watched a video of a small desert fox (fennec) that toys and eats a scorpion. Although I am unsure of the exact type of scorpion, it is apparently quite able to sting. Another online instance of the same video states that the scorpion is Androctonus Australis. Not only is this breed severely venomous and claiming, as its name suggests, human lives every year, but it is also well armoured. You can hear it when the fennec chews on it...

Fennec Fox eats Scorpion

So, my question, which might be stupid: how can this fox take the scorpion in its snout again and again? I notice that it lets the scorpion go many times. Is it able to avoid being stung? Is it extremely resistant to venoms? I read in the Wikipedia article, that it eats insects, but was unable to find out more!

I was able to find some information about hedgehogs and snake venom, but nothing similar about canines. In the case of hedgehogs, a partial immunity is apparently due to a protein called erinacin in its muscles.

After a user kindly corrected my spelling, I found some comments beneath YouTube videos, claiming it was nearly immune to scorpion venom. Sadly without additional information.

Very carefully.  First remove the stinger, the rest is relatively easy.  In your video, you see the fox quickly bite at the stinger, then back off.  Over and over until the scorpion's abdomen was loose as a rag, unable to launch the stinger at 3:08 minutes.  3:32 - you can see the stinger is almost off.  3:40 - stinger gone, she can now eat it more calmly.


Are there any other animals that become attached to a non-living object? Do any animals become psychologically attached to any non-living object that is not useful to the animal for any of its physical needs, like some children do to stuffed animals? Some children are so attached to their toys that they take them with them whenever possible, and are upset when the toy goes missing or is taken by another.

So, this is psychological attachment. From the question alone, I thought of physical attachment.

If you provide stuffed animals and human children, then I'd offer the television remote, a chair/sofa and the cellphone for human adults. In general, many adults are far too sedentary for their own health.

Some non-human primates have exhibited behavior similar to that which you describe with the stuffed animals-children example.

In terms of an inanimate object, you can add the Internet. Certain behaviors like over-indulgence in alcohol, sex, gambling, hand-washing, and the like, could, broadly speaking, fit within the question as posed.


What does basipetal succession (of flowers/leaves) mean? The definition says that basipetal succession is the arrangement of flowers such that the older ones are present at upper side and the young flowers are arranged towards base. But in this diagram:

the oldest flower is at the base and the youngest is towards the upper side. Can anyone help me understand this?

The definition you quote is a bit misleading — what matters is where the lateral flowers are connected to the inflorescence axis, not where they are physically in space.

Thus, due to the way these cymes develop (starts with a terminal flower and then a lateral bud grows out to form anther terminal flower, etc.) they must be basipetal because the first flower to develop is the terminal flower.  In other words, for cymes the lateral buds tend to overgrow so it looks like they are above, but what really counts is where they are placed on the inflorescence axis (which is below).

You may find this explanation clearer than the one in your textbook.


Is this experiment to check enzyme reaction rate according to substrate concentration correct? We just had an experiment to check enzyme reaction rate according to it's substrate concentration.
In the experiment, we used a varying amount of substrate and the same amount of enzyme:

(1.5mm enz, 4.0mm water, 0.5mm subs)
(1.5mm enz, 3.5mm water, 1.0mm subs)
(1.5mm enz, 2.5mm water, 2.0mm subs)
(1.5mm enz, 1.5mm water, 3.0mm subs)
(1.5mm enz, 0mm water, 4.5mm subs)

We check the rate by looking at the optical density after 3 minutes.

Upon staring at this, I couldn't help but wonder: We don't only change the substrate concentration! We also change it's amount!

While 3.0/4.5 is a higher concentration than 0.5/4.5, it's also a higher amount resulting in longer reaction time for sure. If we check after 3 minutes, there's a chance that the 0.5mm subs would already be gone.

If we really wished to look at the rate according to concentration, shouldn't we have only changed the amount of water? It also changes the concentration of the enzyme but there is there any way to isolate either of them?

I think there are a few important answers in your question

The concentration of enzyme is the same in each reaction chamber.  The volume of each chamber is 6ml, and you are using 1.5 ml of enzyme in a final volume of 6 ml, so the dilution factor (the same in all chambers) is 1 in 4. So if stock enzyme concentration is 4 micromolar (as an example), the concentration of enzyme is 1 micromolar in each reaction chamber.
The concentration of substrate varies in each reaction chamber.  You MUST take the dilution factor into account when calculating the final substrate concentration.  You do no tell me what the stock substrate concentration is, but if it is 1mM as an example, then in reaction chamber 1 you are taking 0.5 ml of a 1mM solution in a final volume of 6 ml, which is a 1 in 12 dilution.  The substrate concentration in the reaction chamber is therefore 1/12 mM (about 83.33 micromolar).  In a similar way, the concentration in the final reaction chamber (4.5 ml in a final volume of 6 ml, dilution factor of 1.33) is about 750 micromolar.
You are right, measuring the reaction velocity by taking a single time point after 3 minutes is dangerous!  You must of course measure the initial rate if you want to analyze results according to the Michalis-Menten equation. The assumption you are making is that the rate is linear over a period of 3.   minutes for all substrate concentrations.  If this is not so, you will need to redesign your experiment to take a number of time points and take the tangent to the curve. I think you must be interested in determining the Michaelis constant.
In the language of enzyme kinetics you are doing a discontinuous assay with a single time point after 3 minutes as a measure of the initial rate at a series of substrate concentrations.  A better approach if available is to use a continuous assay, for example by continuously monitoring the change of absorbance of NADH with time at 340nm.  But of course continuous assay not always available.
I am surprised that you use water to dilute. Where is the buffer? And how control pH in your chamber?  Maybe the enzyme and substrate stock solutions are made in buffer, is this the explanation?
You should also check that the velocity versus enzyme concentration is linear at all substrate concentrations.


What's the difference between mutation and substitution rates? The Wikipedia section on substitution rates (shown below) isn't clear to me. What's the precise definition and difference between mutation and substitution rates, and how do they relate to each other?

  Substitution Rates

  Many sites in an organism's genome may admit mutations with small fitness effects. These sites are typically called neutral sites. Theoretically mutations under no selection become fixed between organisms at precisely the mutation rate. Fixed synonymous mutations, i.e. synonymous substitutions, are changes to the sequence of a gene that do not change the protein produced by that gene. They are often used as estimates of that mutation rate, despite the fact that some synonymous mutations have fitness effects. As an example, mutation rates have been directly inferred from the whole genome sequences of experimentally evolved replicate lines of Escherichia coli B.

Further context behind this question here.

The mutation rate is the rate at which mutations happen — i.e. the rate at which "mistakes" are generated.

The substitution rate is the rate at which mutations are accepted — i.e. the rate at which "mistakes" become incorporated into a genome.

The difference is due to selection — if a mutation happens that results in an essential protein becoming non-functional that mutation will tend to be purged and thus won't be "accepted".

A relatively clear discussion of these differences:

  Box 1
  Mutation rates versus substitution rates
  It is important to distinguish between the rate at which spontaneous mutations occur and the rate at which genetic changes accumulate in a surviving lineage. The MUTATION RATE reflects the probability of a change in genome sequence between a parent and its offspring. It is the compound result of unrepaired DNA damage, polymerase errors, intragenomic recombination events, movements of transposable elements, and other molecular processes that introduce errors during the transmission of genetic information. However, only those mutations in lineages that persist — typically in the face of selection — contribute to the SUBSTITUTION RATE measured by whole-genome sequencing. The failure to carefully distinguish between these two types of rates is a persistent cause of confusion and misconceptions about whether mutations are random. In the same vein, the frequency of a mutant allele in a population generally does not equal the rate at which the corresponding mutational event occurs.

From: Barrick, J. E., & Lenski, R. E. (2013). Genome dynamics during experimental evolution. Nature Reviews Genetics, 14(12), 827-839.

You may also find the following article to be of interest:
Yi, S. (2013) Neutrality and Molecular Clocks. Nature Education Knowledge 4(2):3
.


How can one identify an organism from its dissymmetry ratio? If I am given the dissymmetry ratio of an organism ((A+T)/(G+C) is a constant), how can I identify the source of the DNA and classify the organism?

It depends what lineage (bacteria, virus, eukaryotes) you are interested in and what level of accuracy you are hoping to reach.

We know the (A+T)/(G+C) ratio for a handful of eukaryotes only. So if you were thinking about eukaryotes, there is no need to look much further. You cannot match a (A+T)/(G+C) ratio to a species because we don't know the (A+T)/(G+C) for the vast majority of species.


Are all Y-chromosomes the same? Since the Y-chromosome can only pass from male to male child, it would seem to pass intact. Thus, a boy's Y-chromosomes would, I guess, be the same as his father's. Going backwards, would not all men have identical Y-chromosomes for this reason, being somewhat like mitochondrial DNA?

Actually, no. There are also recombination prone regions of the Y chromosome that recombine and exchange material with X chromosomes, and these are called pseudoautosomal regions (PARs).

Y chromosomes can be used similarly to mitochondrial DNA to build up profiles of ancestry, but the sequences used for this purpose lie outside PARs, in the non-recombining region.

What about seqeuences outside PARs, do they show genetic variation?

As pointed out in the comments, PARs comprise only 5% of the Y chromosome, but even in the non-recombining regions of the Y chromosome studies in well-characterised populations have found that the mutation rate can approximate autosomal mutation rates in some regions of the chromosome, and exceed them in others.

What processes, other than recombination, drive mutations?

There are loads of different mechanisms by which mutations in general can be generated, including exposure to UV, free radicals, tobacco smoke, aristolochic acid, and perhaps most importantly spontaenous deamination of methylcytosines, which is an age related mutational process, proofreading errors inherent to DNA polymerases. Also, it is well known that in sperm, with age the mutation rate goes up throughout the genome. While UV is unlikely to be a prominent mutagen as was pointed out to me in the comments insofar sperm are concerned, factors like smoking still play a role.

An illuminating read about mutational processes and the mutational footprints they leave in genomes, as understood from studying cancer genomes, is here.


What (if anything) about tuberculosis makes producing a highly effective vaccine difficult? What about tuberculosis makes it difficult to produce a safe vaccine that is effective at producing an immunogenic response in >99% of individuals against all strains of the bacteria?

I am aware of the BCG vaccine which has a variable efficacy depending on how it is measured and am aware of the 4 current vaccine candidates (MVA85A, rBCG30, 72F fusion protein, and ESAT6-Ag85b fusion protein). I am curious about the very specific question of aspects of the bacteria that make the TB vaccine difficult.

Many, many thanks.

Thats an interesting and complex question. First, Mycobacteria tuberculosis is present for a long time in the human population and evolved to evade our immune system. One of the keys are glycolipids and sugars which are part of the bacterial cell wall. These either help suppressing an immune response or help the bacteria to enter host cells in which they can stay without being identified by the immune system. See references 1-3 for details on this topic.

Then most tuberculosis infections are hold of by the immune system, mostly they come up, when the carriers immune system is compromised. M. tuberculosis can successfully hide inside macrophages and multiply there and start an infection from this hiding place. See references 4 and 5 for more details here.

One of the main problems with the development of new vaccines is that this takes quite a long time from successful experiments in the lab to the availability of a usable vaccine. Tuberculosis has been neglected here for decades. Then the market for such a vaccine wasn't deemed lucrative enough from the pharma companies, as this is mostly important for poor and developing countries. For use there, the vaccine needs to be cheap and easy to administer. Additionally humans are the main host for M.tuberculosis which makes chossing appropriate animal models for research and testing not an easy task.

The development of novel vaccine candidates follow different routes. First, there are live vaccinations, which mainly consist of modified strains of the BCG vaccine strain. Then there are vaccines in the development which are supposed to support the immune answer by BCG and finally, there are vaccines which are independent of BCG and are mostly composed from proteins of the outer bacterial cell wall. For an overview about this field, I can recommend the review articles 6 and 7, if you want to go deeper in the field, also the references 8-10.

References

Mycobacterium tuberculosis Cell Wall Glycolipids Directly Inhibit
CD4+ T-Cell Activation by Interfering with Proximal T-Cell-Receptor
Signaling
Divergent Effects of Mycobacterial Cell Wall Glycolipids on
Maturation and Function of Human Monocyte-Derived Dendritic Cells
Interactions between Mycobacterium tuberculosis and host cells: are
mycobacterial sugars the key?
Annulling a dangerous liaison: vaccination strategies against AIDS
and tuberculosis
Macrophages Play a Dual Role during Pulmonary Tuberculosis in Mice
Vaccines against Tuberculosis: Where Are We and Where Do We Need to
Go?
Vaccine against tuberculosis: what’s new
Tuberculosis vaccines: past, present and future.
Childhood tuberculosis: old and new vaccines.
Exploiting the mycobacterial cell wall to design improved vaccines
against tuberculosis


Dimethyltryptamine binding site on Sigma 1 type opioid receptor? I asked this question Dimethyltryptamine and Sigma 1-type opioid receptor interaction but it seems that I didn't express myself well. I was looking for the place on Sigma 1 type opioid receptor where dimethyltryptamine binds rather than the location of Sigma 1 type opioid receptor.

There is no definitive answer to this question since the 3D structure of the receptor has not been determined. In this paper;

  Laurini et al. (2012) Another Brick in the Wall. Validation of the σ1 Receptor 3D Model by Computer-Assisted Design, Synthesis, and Activity of New σ1 Ligands. Molecular Pharmaceutics 9:3107-3126

the authors report the analysis of their molecular model of the receptor. They design 33 new ligands for the putative binding site with binding affinities across five orders of magnitude and then go on to show that the experimentally-determined affinities are in very good agreement with their in silico studies. The paper provides lots of information about the proposed binding site. The paper also describes the use of in silico alanine scanning mutagenesis to assess the relative importance of residues proposed to form the binding site: these are D126,I128,T151,V152,E172,Y173 and L182. Of these D126 and Y173 seem to be critical.

I must stress that this work does not directly investgate the binding of dimethyltryptamine, and the ligands that are used are not based on an indole ring structure. The molecular model used by the authors was first published in an earlier paper.

  Laurini et al. (2011) Homology Model and Docking-Based Virtual Screening for Ligands of the sigma(1) Receptor ACS Medicinal Chemistry Letters 2:834-839

I tried to find out if that paper looks at dimethyltryptamine but unfortunately there seems to be a broken link at the source. Here is the abstract of that paper:

  This study presents for the first time the 3D model of the sigma(1) receptor protein as obtained from homology modeling techniques, shows the applicability of this structure to docking-based virtual screening, defines a computational strategy to optimize the results based on a combination of 3D pharmacophore-based docking and MM/PBSA free energy of binding scoring, and provides evidence that these in silico models and recipes are powerful tools on which virtual screening of new sigma(1) ligands can be based. In particular, the validation of the applicability of docking-based virtual screening to homology models is of utmost importance, since no crystal structure is available to date for the sigma(1) receptor, and this missing information still constitutes a major hurdle for a rational ligand design for this important protein target.


True or False: Dideoxynucleotide sequence analysis Question True or false: Dideoxynucleotide sequence analysis is a template-directed method that makes use of chain terminators that stop DNA synthesis because they lack a 2'OH group.
The answer is false.
However I thought it would be true because dideoxynucleotide sequences stop DNA synthesis due to a lack of an OH group on a 2' and 3' group. What have I misunderstood?

It is false, because DNA synthesis occurs via DNA polymerase,5' to 3'

By hydrolyzing activated nucleotides together. This occurs by nucleophilic attack of 3'-OH, of the last nucleotide in sequence, on alpha phosphate of a corresponding nucleotide triphosphates.


Why is the ability of a virus to get crystallized considered as a "Non living feature of a virus"? My book states that the fact that :"Viruses can be crystallized" is a proof of their "Non living character"
Does that mean living things cannot be crystallized? If yes, why is that so?

Crystallization involves removing extraneous molecules, so that remaining molecules — here, virions, or virus particles — can form a crystalline or ordered structure. https://en.m.wikipedia.org/wiki/Crystallization

As far as cells go, cellular proteins can be crystallized (some more easily than others), as well as nucleic acids, but having those crystals alone is not sufficient for life. You need an input of water, energy, etc.

Making crystals from the constituent parts of cells would effectively kill that lifeform. On the other hand, you can take virus crystals, add a bit of disorder, and they will "wake up" and regain their infectious properties.

Viruses sit on a fine line of what constitutes life. To some extent, the discussion is philosophical in that definitions are chosen and the subject either meets those criteria or not, and some criteria are a bit more arbitrary than others.

Some have argued that viruses in infectious virion form are life, at the stage when infecting a cell and redirecting its machinery to make more virus particles. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2837877/

Over the decades, biology has shifted from a study of cells in Petri dishes, or monks growing peas, to a more abstracted investigation into information science and related fields and subjects: mathematics, entropy, statistics, physics. That perspective started with scientists like Schrödinger, Turing, and Von Neumann, and it continues in the modern day with work by Dawkins, England, and others.

Viruses have and continue to shape the evolution of life around them. In a way, they are frozen information, and the definition of life may be changed over time, as we gain a more broader picture of how things work.


Do single crossovers occur in circular polynucleotides? Single crossovers in circular pieces of DNA do not seem to be a big topic, because if they happened, they would lead to a kind of combined chromosome with two inner strands and one large outer strand. (A bit like an 8)

 ________
|  ____  |
| |    | |
| |____| |
|  ____  |
| |    | |
| |____| |
|________|

But do these single crossovers actually not occur, for example because the crossover machinery is physically not able to do it, or do we just not observe them because they will inevitably lead to cell death and/or the chromosome somehow breaking?

Although crossover events can be observed in mitosis (mitotic recombination), they most frequently occur in prophase I of meiosis (crossing over in bivalents). Circular chromosomes are common in prokaryotes, but eukaryotes have linear chromosomes. Remember what meiosis accomplishes and that prokaryotes reproduce asexually. Prokaryotes don't have a need for -- or engage in -- meiotic division, so crossover events in circular chromosomes can really only be observed in instances of mitotic recombination, and I don't know the frequency of this in prokaryotes.

In prokaryote DNA replication, if any entangling of the two product circular chromosomes occurs, it is resolved by DNA topoisomerase. So perhaps a crossover would present a similar situation and the cell would resolve it by similar means.


I saw these patterns on a hill. Which insect makes such a pattern? Description of the location

It is in India
The place is 300-400 m above sea level.
There is no water body nearby.

Which insect makes these patterns?

It could be an antlion. Antlions are a group of about 2000 species that can be found all around the world (including India). Antlions mainly live in the kind of dry areas you describe and that we see in your picture. I don't think one could be more accurate and tell the genus without a picture of the individual but I might be wrong.

Here is an adult antlion:

and here is a larva antlion

The small pits you see are made by larvae. The larvae make these small trap pits to capture ants (and some other small insects). The larvae is buried in the soil at the center of the pit and simply waits for prey to fall into the pit. Below is a picture of such a pit:


Microscope recommendation for an amateur? I am a mathematics student looking for a hobby and this has come up as a potential hobby. Thus I am interested in buying a high-magnification microscope that is within the limits of my budget.

My first question is, is high-magnification always better? That is, what are some examples, if any, where high-magnification isn't preferred?

Secondly, I am thinking of getting either the "OMAX 40X-2000X Digital Lab LED Binocular Compound Microscope with Built-in 1.3MP USB Camera and Double Layer Mechanical Stage". I have no idea what most of that jargon means, except that it is digital and it can magnify up to 2000x. http://www.amazon.com/40X-2000X-Binocular-Compound-Microscope-Mechanical/dp/B006MX03Q0/ref=pd_sbs_indust_4

Is there any reason I shouldn't get this microscope?

Higher magnification is definitely NOT always better. Indeed, the microscope you are considering is designed for maximum magnification of 1,000x. The 2,000x is achieved by adding 20x eyepieces BUT it creates what is known as 'false magnification'. 2,000x is beyond the resolving power of a light microscope so what happens is that the image is magnified 2,000x but without a corresponding improvement in resolution. In fact, you will notice a degradation in image quality....it's like magnifying a pdf on your computer....it gets bigger but you still can't read it! And in any event, you will never use 2,000x let alone 1,000x! Read this article http://www.microscope.com/education-center/articles/false-magnification/

Second, I advise against buying an integrated digital microscope. Far better to buy a standard trinocular microscope and add a microscope camera. The reason is that the camera will be obsolete within about one year while the microscope should last a lifetime. If anything goes wrong with he camera, you will have to buy an entirely new microscope. Moreover, with separate scope/camera, you can switch cameras on the same microscope or use the camera on a different microscope. For more info read this article http://www.microscope.com/education-center/articles/digital-microscope-options/

Look for a lifetime warranty. A mechanical stage is standard and helps move the slides on the stage.

In full disclosure, I own www.microscope.com so give me a call if you would like any further assistance. You will not find false magnification or false advertising on our website!