interpreting enhancer and promoter regions of a target gene I am reading a paper which talks about promoter/enhancer regions of certain protein coding genes. These genes are for which evidence points to having strong MEF2 transcription factor binding sites.

The paper says

  Sequence data were taken mainly from the international nucleotide
  sequence database. Accession numbers and approximate locations of the
  MEF2 site centers are as follows: human adolase A, X06351 and
  1985/1986, rat adolase A, X04260 and 450/451...

Now, I looked up accession number X06351 but I find no evidence of a enhancer region on that page.

Can someone explain to me how I should be looking for these sites?

The paper is available for free and can be found here: Link to paper
My interest is in the first and third paragraphs of Materials and Methods where the first paragraphs gives a general description of the MEF2 sites and the third paragraphs gives specific accession numbers.

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

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

You can analyse these data for a more detailed information.


Is Batesian mimicry more important for females? Myrmarachne plataleoides  is a jumping spider that mimics the Kerengga or weaver ant (Oecophylla smaragdina) in both morphology and behaviour. However, the two sexes appear different:

Myrmarachne plataleoides (Female)

Myrmarachne plataleoides (Male)

Some links suggest that in dimorphic arthropods the females more exactly mimic the model. Is this true? If so, why would this sex difference exist?

Reference
Phyologenetics of mimicry

In sexually dimorphic ant-mimicking spiders, it depends on the specific species which sex resembles the ant most (Cushing, 2012).

In many cases of sexually dimorphic spider myrmecomorphs, the male is more mimetic than the female, such as in Corinnidae species and the genus Castianeira, Oonopidae and Antoonops.

Such sexual dimorphism may be adaptive if the sexes are exposed to different predation pressures. The spider's mimicry of noxious ant species yields protective benefit from predators who would avoid the ants. However, the mimicry often results in being more conspicuous in their color markings than related spider species that are more camouflaged. Hence, conspicuousness can be considered a cost of Batesian mimicry. A palatable species may be evolutionary maximizing its level of protection for the smallest cost (in terms of conspicuousness). Sexual dimorphism, in which the more active sex (which, in spiders, is typically the males) evolves mimetic resemblance to noxious ants, whereas the other sex remains relatively more concealed and camouflaged behaviorally and morphologically.

Reference
Cushing, psyche (2012); 151989: 1-24


References concerning the relative population sizes of predator and prey In an ecosystem, say there are two species in a predator-prey relationship. What is the most typical ratio of these species' population densities? For instance, it could be that for every fox, there are ten rabbits. Actually, the precise ratios are somewhat irrelevant; mostly I would like to know if we can say that the number of prey is generally larger than the number of predators.

I would like references to articles, textbooks, etc. that contain information about such ratios.

Note that this is aimed at the number of species within a single ecosystem. However, if this information is hard to quantify (perhaps because it is hard to define where an ecosystem ends), global populations could be used as an estimate.

Forgive me if this is ill-defined or trivial, I'm a physicist by training.

Thanks.

You are indeed correct that the prey of predators are usually more common than their predators, especially if you focus on "true" predation (i.e. remove parasitism and parasitoidism). As a rule of thumb, the energy conversion between trophic stages is 10% (first proposed in Lindeman, 1942), which sets one sort of bound on the density relationship between predators and prey. The relationship is extremely variable though, which is easily understood if you consider the density relationships of hares and foxes vs. whales and krill.

For a general reference, Hatton et al (2015, "The predator-prey power law: Biomass scaling across terrestrial and aquatic biomes") might work, even though it is mainly framed in terms of biomass. However, the paper clearly states that biomass and density usually go hand in hand. The main result of the paper is that the biomass relationships between predators and prey collapse to very regular power laws (exponent 3/4) across ecosystems.

As mentioned above, and depending on who you ask, parasitism and parasitoidism are sometimes seen as types of predation. There, the density relationships between "predator" (parasitoid) and "prey" can be very different, especially at certain points in time or at certain lifestages. For instance, in insects it is not uncommon for one "prey" (host) to give rise to a large number of newly hatched "predators". This means that the number of parasitoids can probably outnumber the number of hosts, at least at smaller spatial scales, at some time periods (e.g. late summer, before the parasitoid is hit by high winter mortality).


Does gross production (P) and biomass (B) mean the same? From fundamentals of ecology, Odum 2005:

  ... autogenic succession usually begins with an unbalanced community metabolism, where gross production, P, is either greater than or less than community respiration, R, and proceeds towards a more balanced condition, where P=R. The rate of biomass production  (B/P ) increases during sucession until a stabilised system is achieved, in which a maximum of biomass (or high information content) and symbiosis between organisms are maintained per unit of available energy flow.

Isn't gross production (P) same as biomass (B) ? I can't tell them apart, given that Biomass is the amount of matter living organisms (usually of a specific trophic level) of a given area at a specific time is made up of.

Searching for context from what you wrote, I found this which seems to be an original article later introduced to the textbook you are using. I think this other version is more clear; P refers to photosynthesis, which is also gross production of biomass; B/P is the ratio of standing biomass to new photosynthetic product; rate of biomass production seems wrong unless you expand it to "existing biomass relative to rate of biomass production."

In summary, the correct interpretation should be that P is indeed the gross production, but B/P is simply the ratio of biomass to the gross production. If R is the loss of biomass through respiration and R < P, then both B and B/P will increase (i.e., you will accumulate biomass) until P=R. Probably in this process both P and R also increase, but what is important is that B/P is increasing, which means the new biomass isn't as efficient at new photosynthesis (presumably either because light is a limited resource or because more of the biomass is not held in photosynthetic organisms).

P is in units of mass/time; R is in units of mass/time; B is in units of mass. The equation would be dB/dT = P - R, or another way, B(t1) = B(t0) + (P-R) * (t1-t0), where t1 is some time after t0.


Can fish live in the dark completely? I have got 6 pet fishes in an algae ridden  tank.  My plan is to place the tank completely away from sunlight so the algae dies.  How would this affect my fish?
Edit: Just checked all my fishes died today.  Either its the lack of light or just that i forgot to add the chlorine removal or water pump.

There are lots of fish that live in environments without any light (below 1000m in the ocean there is no useful light for vision), however most aquarium fish have not evolved to live in those sorts of conditions. In the future, I think your best bet would be to remove the fish, clean the tank, and then try to manage your nutrient inputs so that the algae doesn't grow out of control.


Can DNA act as a translation substrate? I get conflicting answers.  One would think if it was true, it would be rather seminal and widely known.

There are papers from Khorana[1], Holland[2], and Bretscher[3] (late 60s) that suggest that it is quite easy in the presence of antibiotics like neomycin.

But more recent papers like this one[4] still openly ask the question, and that the only thing we know is that the initial ribosome binding step is similar between RNA and DNA.

I can't reconcile these papers.

Morgan AR, Wells RD, Khorana HG. 1967. Studies on polynucleotides. LXXIV. Direct translation in vitro of single-stranded DNA-like polymers with repeating nucleotide sequences in the presence of neomycin B. Journal of Molecular Biology, 26(3):477-497, doi:1016.10/0022-2836(67)90316-6.
McCarthy BJ, Holland JJ. 1965. Denatured DNA as a direct template for in vitro protein synthesis. Proceedings of the National Academy of Sciences USA, 54(3):880-886.
Bretscher MS. 1969. Ribosome Initiation and the Mode of Action of Neomycin in the Direct Translation of Single-Stranded fd DNA. Cold Spring Harbor Symposia on Quantitative Biology, 34:653-651, doi:10.1101/SQB.1969.034.01.075.
Damiana L, Marty-Detravesa C, Winterhalterc M, Fourniera D, Paquereaua L. 2009. Single-strand DNA translation initiation step analyzed by Isothermal Titration Calorimetry. Biochemical and Biophysical Research Communications, 385(3): 296-301, doi:10.1016/j.bbrc.2009.05.044.

As far as I can tell from the paper you linked to (Damiana et al) it is possible but inefficient:

  Naturally, we tried to translate ssDNA, but as previously described
  elsewhere, direct DNA translation was not really efficient in absence
  of antibiotics such as neomycin [5] and [6]. It seemed that the
  elongation phase was the limiting step in the direct translation of
  single-stranded DNA. Whether direct participation of DNA in protein
  synthesis could play any role in vivo must be excluded, although such
  a role could be attractive for modelling the evolution of the earliest
  forms of life.


What would kill you first water or cola? After discussing this with some colleagues, I devised the theory that you could drink more coca-cola in a single sitting than you could water, without killing you.

Defining the volume it would take for one of the liquids to kill you as the 'x volume'.

Thus the hypothesis goes that the x volume for water would be lower than that of coke.

This is based on the notion that water would affect the body's water potential significantly more than the cola solution. For instance, the large volume of water would diffuse, via osmosis, into your blood and this would reduce the water potential of the blood, which would in turn diffuse into your cells which would in turn damage the micro environments and prevent proper enzymatic activity in all aspects of the cell cycle: which would have devastating affects on the brain function. Given enough water: something that can be read about here (water intoxication).

Coca-cola on the other hand which has an acidic pH -- though I'm not entirely sure of it's water potential -- would not have the same disturbance on somatic cells in the body due to the acids and sugars. However, although the large consumption of cola may have longer term effects: would the x volume of coca cola be higher than that of water?

The LD 50 listed on the wikipedia page you link to is 90 mL/kg, which would be about 6 liters for a 68 kg (150 lb) person. This is consistent with at least one report, where someone died from drinking 7 liters of water in 1.5 hours.

The mechanism by which water kills people is by lowering the amount of ions (chiefly sodium) in the blood. A condition called hyponatremia.

Coke contains four relevant looking ingredients: Water, sugar, phosphoric acid, caffeine. Coke also has carbonic acid from the carbonation, but I'll assume we're either talking about uncarbonated Coke, or that the carbonation does not contribute to toxicity (perhaps a bad assumption).

Before worrying about whether the water will kill you, let's verify that the caffeine and sugar won't kill you first.

It seems unlikely that the caffeine in the coke would kill you before the hyponatremia. The concentration of caffeine in coke is about 0.1 mg/mL, and the LD50 is > 150 mg/kg, so for the same 68 kg person, it would take about 100 L of coke to get a lethal dose of caffeine.

The sugar in coke is more deadly, but still not as bad as pure water. There are about 0.11 g sugar per mL of coke. The LD50 of sucrose is apparently around 30 g/kg. So it would take about 2 kg of sucrose to kill our 68 kg person. That is about 18.5 L of Coke.

The concentration of phosphoric acid in Coke is about 5 mM which is about 0.5 mg/mL. The LD50 is about 1530 mg/kg. Which works out to about 212 L of Coke to kill by phosphoric acid.

Now that we've ruled out some other possibilities, lets get back to whether coke will kill you faster or slower via hyponatremia than pure water will.

Take another look at the the nutrition information for Coke. Notice that Coke actually contains some sodium, about 0.13 mg/mL in fact. A drink called "Powerade Isotonic"  which claims to have a proper electrolyte balance contains sodium at 0.28 mg/mL.

So given that (A) what kills you first from drinking too much water is hyponatremia. (B) Coca-cola contains a non-trivial (but still less than many electrolyte drinks) amount of sodium. and (C) other potentially toxic components of Coca-Cola, such as acid and caffeine, require much higher doses to be toxic. It seems reasonable to conclude that Coca-Cola has a lower acute toxicity than distilled water.

Caveats:
I did not consider osmolarity. There could be some effect here that I'm overlooking.
I did not consider the effects of carbonation (soluble carbonic acid).
For people with certain medical conditions, such as diabetes or caffeine sensitivity, Coca-Cola may be toxic at much lower doses than for other people.


BLAST, using Smith-Waterman in the last step and S-score In my bioinformatics course we studied the BLAST agorithm. After finding the HSP's and joining the HSPs together that are close enough and in a correct diagonal trend, we perform a next step: namely a Smith-Waterman alignment. Why do we do this? Didn't BLAST already find the alignment by joinging the HSPs?

I also have a second question about BLAST. When calculating the E-value with the formula:

$E=K \times m \times n \times e ^{\lambda S}$

Which score is this S exactly? Is it the score found for the HSP with the used substitution matrix? What is the score if we have multiple HSPs in one database entry? Is the E-value, and thus the S-score, calculated seperatly for every HSP or is it a value for the entry in total?

The BLAST algorithm is a heuristic to find which the path through the matrices formed between a query sequence and a target sequences from the database is ‘best’. Such paths represent an alignment which is has a completely different basis to that of the Smith-Waterman dynamic programming algorithm. Not only is it ungapped, but it based on comparison of tuples with matches scored according to frequency, and then proceeds by trying to join those with certain relative scores.

The speed of the program is partly the result of rapidly discarding unpromising paths, storing and continually refining only the current best candidates. The alignments will not be Smith-Waterman alignments, but there is no point in performing a Smith-Waterman alignment on each high-scoring sequence pair as this is not the basis of inclusion in the pool of best candidates. Performing such an alignment would be a waste of time for those candidates that will ultimately be discarded.

Only when the run is complete is it appropriate to perform the Smith–Waterman alignment on the final top candidates to produce a gapped alignment from which statistics such as the E-value are calculated (using S, the raw score from such Smith–Waterman alignments).


Do all mushrooms have the same multicellular ancestor? Do all mushrooms have the same multicellular ancestor? Did that ancestor feature common mushroom elements such as cap, stem, sporofore, vulva, bulb, etc.

All fungal species within the kingdom have the same common ancestor, which is unicellular (thought to be protistan). This common ancestor is the point at which it is thought that animals diverged, as suggested by this article.
In their words:

  It is now well established that animals share a common single-celled ancestor with fungi, and that in the two sister lineages multicellularity arose independently

A fungal phylogenetic tree is shown below, which originated from this paper.

Note: all colored areas represent different phyla of fungi.

EDIT:

I will respond to a few questions addressed in the comments.

  Is there a unique multicellular ancestor to all mushrooms?

I am rather sure (but can't explicitly confirm with a reference) that multicellularity in fungi only evolved once. If this were true, I would also hypothesize that mushroom-like characteristics also evolved only once, thus indicating that there is a multicellular ancestor to all mushrooms.

  Are there multicellular fungi outside dikarya?

No. One branch of dikarya seems to consist of only unicellular organisms, suggesting that multicellularity evolved at some point within organism under only one dikaryan branch.

  Was the common ancestor of Dykarya multicellular?

No. See previous answer.

  Are those unicellular dykaria secondary unicellular or not? Given that the both branches of dykaria show similarities in fruiting bodies, it seems to be plausible that the common ancestors of dykaria had a similar structure.

I am not exactly aware of the similarities in fruiting bodies in both branches, but if the physiology behind fruiting bodies are similar, it is very likely because the dikaryan common ancestor had a similar mechanism.


Diet of free-range herbivores Giving minimal credence to estimates in popular media of the average biomass of  insects/arachnids, etc. in an acre of land, it seems that a "free-range" cow (I don't mean to pick on cows) might be something of an omnivore. Is there any evidence that herbivores derive essential parts of their diet from sources other than cellulose? Or that they do not?

One key nutrient worth thinking about in the context of this question is vitamin B12. Herbivores such as cows and sheep will derive this directly from the bacteria in their rumen. Rabbits produce two types of feces - soft and hard - and they eat the soft variety, rich in gut bacteria, as a source of nutrients like vitamin B12. Gorillas are primarily herbivores, but are thought to derive their vitamin B12 from insects, eaten purposefully or inadvertently.

So yes, herbivores derive this particular nutrient from non-plant sources.


Why does asbestos cause cancer? We are probably all familiar with the dangers of asbestos in your rooftop or in various pieces of old equipment as it has been shown that the microscopic asbestos particles reach our lungs and can then potentially cause lung cancer.

Now smoking (for example) can cause cancer because of various carcinogens chemically interacting with DNA, but how can these asbestos particles, specifically prized for being quite unreactive, damage DNA to the point of triggering cancer?

More basic answer; the asbestos crystals have hooks. So the cilia in the lungs have difficulty moving them out with the other dust. This irritates the tissue causing the effects of the first answer. So it is a matter of time and number of asbestos particles that increases the probability of a cancer. Decades ago , the asbestos miners in Africa typically worked for years ( eg 20 years) before getting cancer.


Why are some chemical dangerous to aquatic environment only? Recently I was changing the thermal grease on my PC. I have noticed on the back of box, that the grease is not dangerous when ingested or when touched. But there was specifically stated, that is dangerous to aquatic organisms.

What is so special about aquatic chemistry, that the grease is dangerous to them? I would guess that the chemistry of mammals, reptiles, and birds would be quite similar to that of fish.

From some of the MSDS (1, 2) I come across, a major component of thermal grease is aluminum oxide.

Risk Management for Hazardous Chemicals by Jeffrey Wayne Vincoli states in page 101 that aluminum oxide has both acute and chronic toxic effects to aquatic life; it also states that aluminum oxide has a half-life longer than 200 days in water; finally, it acknowledges that the short term toxicity data for non-aquatic animals are insufficient.

From this, the reason thermal greases have special notification regarding to fishes can be attributed to those following points:

The long half life makes fishes exposure to it longer and therefore makes them more susceptible.
We simply do not understand how aluminum oxide effect non-aquatic animals.

(According to Risk Management for Hazardous Chemicals, bioaccumulation in food chain might not be the concern.)


Can anyone help to identify this fruit? It stays the same color when ripe. It's about the same size as a pear. Grows in sub tropical climate of Meghalaya, India.

I think this looks a lot like a pale variety of Solanum Muricatum or Pepino dulce/melon/pear.

It's native to South America, but I think that it would be able to be cultivated in India as well.


aspartame in relation to generating methanol So I posted another question with respects to methanol and aspartame in metabolism with respects to toxicity.  So another question I have is "Why is aspartame used as a dietary component to generate methanol following metabolism?"  This is a topic of discussion in my thermonuclear pharmaceuticals class at my institution, and more or less it's also part of an active assignment that we're expected to cover for a weekly discussion which is no graded; otherwise I wouldn't seek free advice on this.  As much as I read in my book it does not go into detail and I am curious if anyone out there has any advice on this or perhaps you could point me towards relevant articles?

Aspartame is the methyl ester of the aspartic acid phenylalanine dipeptide. Esters are very easily hydrolyzed by esterase enzymes in the body. This will create an acid and an alcohol. In this case the alcohol is methanol, because it was generated from the methyl group. I'm not familiar with why thermonuclear pharmaceuticals would be concerned with aspartame, generally thermoncuclear refers to nuclear fusion, and even radioactive drugs don't undergo fusion.

Anyway, some people are afraid that aspartame is toxic because the methanol it generates is toxic. This fear is unrealistic because the amount of methanol it takes to cause blindness is about 10mL, and the smallest amount needed to kill someone is about 30mL 2. To generate this much pure methanol from aspartame would require you to eat an impossible amount of aspartame.


bunsen vs meker for best sterile field I need one bunsen and i have a friend that sells me a bunsen-meker burner.
I see that bunsen-meker burners have more flame diameter, so should have more diameter of sterile field, but i dont know XD
Is good for sterile field? or i should buy a typical bunsen?
thanks.

The difference in flame diameter between a Bunsen and Meker (or Fisher) burner really isn't that much, so I'm not sure how much larger the sterile field would be. On the other hand, Fisher burners can be tuned to be much hotter than standard Bunsen burners, so that may impact the size of the field as well. But, at the same time, they use more fuel, so you have to think of that as an additional cost.
If you're just sterilizing inoculating needles/loops, flask necks, etc., a Bunsen is perfectly fine. However, if you're trying to create a larger "sterile" field, there are too many variables to make a definitive recommendation. Are you setting up in an area with relatively little airflow, or are there cross-breezes? How large of a field do you actually need - what is the area where you'll be working with open containers of sterile media?
All in all, to be safest, you'd probably want the Fisher burner, but I don't know what the cost differential is and what your budget is. If you're careful with media manipulation and have a good still area to work in, a Bunsen should be fine, though.


Are phylogenetic tree construction algorithms any different than general clustering algorithms? I suspect the answer is no. But I don't know enough to be sure that that is the case. Of course phylogenetic tree construction uses biological knowledge, e.g special distance metrics, but does it brings anything new at the level of clustering agorithm (e.g hierarchical, neighbor-joining etc).

One difference is that phylogenetic tree construction algorithms will typically try to jointly estimate the tree and the transition parameters.  A general clustering algorithm might assume that a difference in one feature would make the same contribution to 'distance' between clusters as a difference in another feature. In phylogenetic tree construction, it is explicit that not all differences between taxa represent the same evolutionary distance between taxa, and the parameters governing the distribution of distance/difference may be jointly estimated with the tree.


What is the quality rate of intrinsic autoregulation in the heart? Autoregulation is the maintenance of constant blood flow to an organ in spite of fluctuations in Blood pressure.
It involves the relaxation of myocardium and contraction.
It is local.

I know that autoregulation is best done in the brain, well in kidneys and badly in skeletal muscle.
I am interested how it is in the heart.
I think it should be at least good.
Brain can be thought more important.
However, I am not sure.

How good is the autoregulation of the blood flow in the heart?

My conjecture: Intrinsic regulation is done in the heart the second best, after the brain.
This idea is based on the fact that the brain controls heart's some autonomic functions.

It is an open research question how the autonomic nervous system affects the intrinsic functions of the heart - and the reverse is true too.

To answer this question, we need to understand the autonomic regulation of the heart better i.e. the inner-physiology of the heart's electrical activity.


Why do stomata close in low intensity light? Stomata close during high intensity light to prevent excessive transpiration but why did they close during low intensity of light? Please explain in easy- understand language because i'm  in just 10th standard.

The primary function of open stomata is to promote gas exchange in leaf tissue: atmospheric carbon dioxide is a substrate for photosynthesis. A side effect of opening the stomata is an increase of water loss through transpiration. If light intensity is low then photosynthesis will be depressed: under these conditions it makes sense to close the stomata to conserve water.


How do animals learns seductional behaviour? I was curious how the gender behaviour, the male role or female role, is known in mammals. Do mammals instinctively know how to do seduce the opposed sex or do the animals learn it from their parents/companion of the same sex (e.g. by imprinting)?

Some behavior can be traced to the genome. In Drosophila there are many interesting studies that show how genes and courtship behavior are related Example.

In mammals, the environmental component in determining courtship behavior is for sure, much more relevant than in Drosophila.


Why was polyploidy not lethal in certain octodontid rodents? As discussed in Why is polyploidy lethal for some organisms while for others is not?, polyploidy is normally lethal in mammals.

However, two species of Octodontidae (South American rodents), are tetraploid due to a recent doubling of all chromosomes:

Tympanoctomys barrerae: 4x = 102
Pipanacoctomys aureus: 4x = 92 (apparently some chromosomes were lost after the polyploidy event)

See the paper discussing T. barrerae, the first of these tetraploid rodents discovered.

According to the Wikipedia article, both are believed descended from the same species, Octomys mimax (or possibly now-extinct close relatives thereof), which has 2x = 2n = 56 chromosomes, half those of T. barrerae.

What was special about Octomys that allows it to survive polyploidy, unlike most mammals?

Interesting:

  The sperm head of Tympanoctomys is is by far the largest naturally occurring in mammals, and its size is causally related to the double genome size it has to accomodate.

Actually, that is not what is discussed in the question you linked to. The following is a quote from the very comprehensive accepted answer (emphasis mine):

  Polyploidy arises easily in both animals and plants, but reproductive
  strategies might prevent it from propagating in certain circumstances,
  rather than any reduction in fitness resulting from the genome
  duplication.

In fact, try rereading that answer and the references therein, it answers your general question.

There is a popular theory (mostly accepted) that there have been whole genome duplication events (WGDs) in the vertebrate ancestry. If true, it means that all mammals are the descendents of polyploid ancestors. For a very nice review of WGDs in vertebrate evolution, see here [1]. Octomys is simply the only known mammal with a more recent WGD event. As for what makes it special (taken from [2]):

  Our data demonstrate that parental-specific silencing of at least one
  gene and normal X chromosomal dosage mechanism are conserved in the
  tetraploid genome. We hypothesize a concerted action of genetic and
  epigenetic mechanisms during the process of functional diploidization
  of this tetraploid genome.

1) Van de Peer Y, Maere S, Meyer A., The evolutionary significance of ancient genome duplications., Nat Rev Genet. 2009 Oct;10(10):725-32.

2) Bacquet C, et al., Epigenetic processes in a tetraploid mammal, Mamm Genome. 2008 Jun;19(6):439-47.


Why is the function of lacA (encoding thiogalactoside transacetylase) not clearly understood? It's almost half a century since the lac operon was discovered but isn't it weird that the precise role of transacetylase isn't clearly understood ?

Here a wikipedia article with a link to a journal article which proposes a function of this enzyme. This article was written in 2002 but in most of the text books I have referred to ( written well after 2002 ), no function is mentioned.

MY QUESTION : What are the difficulties that are not allowing us to understand the precise role of this enzyme ?

Note: This is NOT my field. However, given @biogirl's question, it appears that there aren't many people in this field in the first place. From what I can gather, here are the reasons why I think it has been difficult to study.

I. The lac operon has strong polarity. By this I mean that when the lac operon is induced, lacZ (the first gene in the operon) is translated much more than lacA (the last gene in the operon). Measurements have recorded the molar ratio of $\beta$-galactosidase : thiogalactoside transacetylase (the protein products of lacZ and lacA) upon induction of the operon at 3:1 to 5:1; i.e. when the lac operon is induced 3 to 5 molecules of $\beta$-gal are produced for every one of the transacetylase. If you factor in the relative length of each of these proteins ($\beta$-gal is 1024 a.a.s, transacetylase is 203), it works out that lacZ is being translated at least 10 times faster than lacA when the lac operon is induced. Sidney Altman's lab has attributed this to the fact that there is a cleavage site between lacY and lacA where RNAses can cleave the nascent mRNA transcript, removing lacA from the operon and reducing the production rate of transacetylase. So it appears the cell needs quite a bit less lacA than lacZ---if indeed they need it at all, see point 2---which makes it harder to study.

Sources: Brown JL, Brown DM, Zabin I. (1967). J Biol Chem. 242(18):4254-8.

Li Y, Altman S. (2004). J Mol Biol. 339(1):31-9.

II. lacA seems to provide only a small fitness advantage under somewhat contrived conditions. In A paper from the 70s researchers presented competition experiments between $lacA^{+}$ and $lacA^{-}$ strains in media with $\beta$-galactosides as the only carbon source. For 50 generations there was no competitive advantage of one strain over the other (ratio of $lacA^{+}$ : $lacA^{-}$ stayed at 1). When after 50 generations the researchers added a lot of IPTG, a non-hydrolyzable $\beta$-galactoside, $lacA^{+}$ outcompeted $lacA^{-}$; the absolute fitness of wild-type:mutant could be calculated to be $\approx 1.05$. This means that the wild-type produced 105 cells for every 100 produced by the mutant. I am not a population geneticist, so I don't know if that is a large value or not. For comparison, I used to work in cyanobacterial circadian rhythms, and the absolute fitness advantage for having a circadian clock with the same period as the light-dark cycle in the environment works out to $>1.11$, which is twice as advantageous as the one reported for $lacA^{+}$ over $lacA^-$. In any case, the experimental situation in which $lacA^+$ has a competitive advantage seems rather contrived: growing with $\beta$-galactosides as the sole carbon source with a significant amount of non-hydrolyzable analoges around gumming up the $\beta$-galactoside metabolic machinery.

Source: Andrews KJ, Lin EC. (1976). J Bacteriol. 128(1):510-3.

My read from these observations is that the physiological role of lacA is challenging for a biologist to untangle due to the small size of its effect on bacterial physiology. Fitness advantages of 5% may certainly be useful on evolutionary timescales, but they suggest that the benefit afforded by the enzyme will be very hard to discriminate from noise or other confounding factors in the system. The fact that lacA production is much lower than lacZ in times of lac operon induction also would make it hard to measure.

A postdoc I used to work with advised me, "don't go looking for 2-fold changes in biology," by which he meant don't spend too much time on questions where the size of the effect you are looking at is minor and very difficult to distinguish from noise, bias, measurement error, or other confounding variables. Obviously there are limitations to this advice; a lot can be learned from the the combination of several seemingly minor effects that have big cumulative consequences for an organism. But as a rule of thumb, it's so hard to get strong results when your effect size is so small that going after small effects is justifiable only if you have a good reason to believe there is some profound, fundamental biology behind them. My view is that the consensus of the scientific community up to this point has been that untangling the role of lacA in the lac operon and more broadly in bacterial physiology would involve too much work for too little payoff.


Why do eyes change colour after death? Why exactly do eyes turn black when we die? (Or even change colour at all).
The source of inspiration to this question is due to this video https://www.youtube.com/watch?v=6mNs_TcUyHc&t=627s (it's a cow's eye being dissected). The man explained how the cornea is crystal clear in an actual cow but since it's been preserved, the preservative has denatured the protein causing it to turn cloudy.

So why does our eye change colour when we die when no preservative is used?
I know this is a pretty gruesome question to ask but curiosity has the best of me haha.

Living tissues are not usually transparent. Obviously, the crystalline lens needs to be in order to let light go through. This is done by a fairly complicated system that requires active pumping of ions in and out. When that system stops, the lens becomes opaque resulting in that white cloudy appearance. This can happen in living animals (including humans) too, such as in cataract.


How does one determine intracellular concentration? The TL;DR version

Is there a fast way to determine what the cell environment of a particular cell (E.g RBC) is? (in terms of solute/ionic concentration)

I'm not sure if the question belongs here, but hear me out. I was doing revision and I kept coming across the line "put the cell in a solution which has the same solute/ionic concentration to prevent the cell from bursting or shrinking"

I get that concept, basically it's sort of replicating the internal environment of the cell with the buffer/solution so that the cell feels "at home."

Then my question is, how does one go about finding out how much exactly for each cell? I would think different cells have different internal environments and I don't believe that scientists actually just have stock solutions of buffers ranging from 0.00001M to 100M and trying every single solution until they find the perfect concentration.

In fact the line that you quote doesn't mean that the solution is formulated to be identical to the cytosol. All that it means is that the solution should be buffered to physiological pH (typically slightly alkaline); should contain a relatively high concentration of sodium ions and a low concentration of potassium ions; and should be isotonic (i.e have the same osmolarity as the cytosol) to avoid osmotic effects such as plasmolysis (shrinkage due to loss of water) or osmotic lysis (bursting due to uptake of water).

There are many such solutions, but a commonly used simple one is phosphate buffered saline. Another is Ringer's solution. If the aim is to keep the cells metabolically active these are often supplemented with glucose or lactate, depending upon the cell type.

Addendum in response to comment from OP

According to the WP entry for Ringer's solution, Sydney Ringer determined the requirement for Na, K and Ca salts in a specific proportion when carrying out experiments with perfused frog hearts. This was in the late 19th century. A  Google search measurement of intracellular ion concentrations reveals current methods.

This review starts off with a discussion of early measurements of intracellular pH (see page 298). Basically these all consisted of making cell lysates, with various attempts to prevent post-lytic changes. If you do a Google search determination of intracellular pH you will find lots of current methods.


Are there axon branches that go up to cortex layer 1 and spread there? I found the following pictures of axon trees:

source

source (axons are red)

but didn't find a concise answer to the following question:

  Are there axon branches that go up to cortex layer 1 and spread there?
  (This is not indicated in the pictures above, maybe because there are no.)

Short answer: It depends on the layer.

Axons of some neurons in deep layers will project back to L1 (Brecht et al. 2003a, Oberlaender et al. 2011), but neurons of superficial layers extend their axons laterally (Brecht et al. 2003b).

Besides focusing on specific pyramidal cell sub-classes it's worth considering what proportion of inputs to L1 comes from intracolumnar or extracolumnar inputs. From the wikipedia article on the cerebral cortex:

  Layer I, the molecular layer, contains few scattered neurons and consists mainly of extensions of apical dendritic tufts of pyramidal neurons and horizontally oriented axons, as well as glial cells. [...] Inputs to the apical tufts are thought to be crucial for the ‘‘feedback interactions in the cerebral cortex involved in associative learning and attention. While it was once thought that the input to layer I came from the cortex itself, it is now realized that layer I across the cerebral cortex mantle receives substantial input from ‘‘matrix or M-type thalamus cells (in contrast to ‘‘core or C-type that go to layer IV).

Most of the inputs to layer 1 (L1) are indeed thought to come from the "non-specific" thalamus and other cortical areas, such as the primary motor cortex in the case of primary sensory areas.[citation needed] I am only aware of circumstantial evidence for the relative prevalence of thalamic inputs in L1. According to staining for different vesicular transporters of glutamate (type I is thought to label mostly cortical neurons in adult animals, type II subcortical), about half of the input to L1 is subcortical (Kubota et al. 2007). It's worth noting that the slender-tufted neurons described by Oberlaender et al. (2011) to project heavily in L1 are considered to be the main targets of the "non-specific" thalamus in the cortex (Brecht et al. 2003a). The extracolumnar origin of cortical inputs to L1 matches with the overall trend observed accross layers for the majority of inputs to come outside the cortical column (Stepanyants et al. 2009).


What is the cause of muscle cramps? According to Wikipedia, muscle cramps are caused by the inability of myosin fibers to break free from the actin filaments during contraction, resulting in a prolonged contraction.

A lack of ATP would obviously produce cramping, as myosin requires ATP to become free from actin.

However, I have heard that potassium and sodium are useful for treating cramps and that their deficiencies can lead to cramping.

So, how does a deficiency in sodium or potassium result in the inability of myosin fibers to break free from the actin filaments during contraction?

The quick and simple answer:

Cramps of a hypokalemic origin are much more common than those of a hyponatremic origin because the Na-K pump is more effective at moving potassium in comparison to sodium.
At the onset of a muscle contraction, the presence of calcium triggers the opening of the Na-K channels in the membrane. Potassium is a calcium inhibitor, so as the potassium flows out of the cell, it eventually reduces the presence of calcium. This causes the closure of the Na-K channel (negative feedback mechanism). In a hypokalemic state, the lack of sufficient K doesn't inhibit the calcium channel, and in turn doesn't properly terminate the muscle contraction at the cellular level.

The continued presence of calcium, which has a lot to do with nerve impulses, means that the nerves keep firing, and in some cases such as a 'charlie horse', these impulses fire fast and continuously. The body at this point is reaching a small local state of metabolic acidosis resulting from the extremely high oxygen consumption, increasing levels of CO₂ (the acidosis component) and reducing blood partial oxygen levels. Since the oxygen is no longer as abundant as it was, it inhibits the bodies ability to locally produce the ribose and phosphate necessary for ATP. Less ATP = more myosin that can't be disconnected from actin = continued muscle cramp.


Coefficient of Inbreeding - implementation issue The formula for the coefficient of inbreeding is as follows...

I have a family tree going back 9 generations. Say I find a common ancestor X in the 4th generation on the mothers side and in the 5th generation on the fathers side. I can work out that constituent of F... but what do I do about all the ancestors of X (they will all also be common ancestors). Do I also work out their values and add them to F?... or do I ignore them? The descriptions of the COI I have seen do not make this clear.

The $F_i$ term is the term that accounts for inbreeding of your common ancestor X. If that common ancestor is not inbred then the term is 0 and the calculation is a little easier. Using the example you have given:

 X ─┬─ Y
    │
 ┌──┴──┐
GGGF  GGM
 │     │
GGF    │
 │    GM
GF     │
 │     │
 F ─┬─ M
    │
   Mick

In this case, the common ancestors are not inbred so the $F_i$ terms go away ($1+F_i = 1$). There are two paths of common ancestry (via X and Y), therefore the calculation of the two paths from the father (F) and mother (M) to X and Y is:

$F_{Mick} = \frac12^{n_{F,X}+n_{M,X}+1}(1+F_X)+\frac12^{n_{F,Y}+n_{M,Y}+1}(1+F_Y) $

$F_{Mick} = \frac12^{4+3+1}(1+0)+\frac12^{4+3+1}(1+0) $

$F_{Mick} = \frac{1}{256} + \frac{1}{256} = 0.0078 = 0.78\% $

In a more complex case, such as where ancestor X was inbred, $F_i$ cannot be ignored. In the following example, X's parents were first cousins:

  U ─┬─ V
     │
  ┌──┴──┐
 XGF   XGM
  │     |
  XF─┬─XM
     │
     X ─┬─ Y
        │
     ┌──┴──┐
    GGGF  GGM
     │     │
    GGF    │
     │    GM
    GF     │
     │     │
     F ─┬─ M
        │
       Mick

For this, we must first calculate $F_X$ (i.e. how inbred X is):

$F_X = \frac12^{n_{XF,U}+n_{XM,U}+1}(1+F_U)+\frac12^{n_{XF,V}+n_{XM,V}+1}(1+F_V) $

$F_X = \frac12^{2+2+1}(1+0)+\frac12^{2+2+1}(1+0)$

$F_X = \frac{1}{32} + \frac{1}{32} = 0.0625 = 6.25\% $

Then we can input this $F_X$ into the same calculation as done before for the simple case:

$F_{Mick} = \frac12^{n_{F,X}+n_{M,X}+1}(1+F_X)+\frac12^{n_{F,Y}+n_{M,Y}+1}(1+F_Y) $

$F_{Mick} = \frac12^{4+3+1}(1+0.0625)+\frac12^{4+3+1}(1+0)$

$F_{Mick} = 0.00415 + \frac{1}{256} = 0.0081 = 0.81\% $

A good explanation of these calculations with further examples can be found here: The Coefficient of Inbreeding (F) and its applications. The calculations can get quite complicated even with relatively simple inbreeding.


Are erythrocytes lysed during alpha hemolysis? Wikipedia says:

  When alpha hemolysis (α-hemolysis) is present, the agar under the colony is dark and greenish. Streptococcus pneumoniae and a group of oral streptococci (Streptococcus viridans or viridans streptococci) display alpha hemolysis. This is sometimes called green hemolysis because of the color change in the agar. Other synonymous terms are incomplete hemolysis and partial hemolysis. Alpha hemolysis is caused by hydrogen peroxide produced by the bacterium, oxidizing hemoglobin to green methemoglobin.

From this it seems that in alpha hemolysis , it's not the lysis that's the defining event rather the chemical change of the hemoglobin molecule.

Wikipedia states:

  Beta hemolysis (β-hemolysis), sometimes called complete hemolysis, is a complete lysis of red cells in the media around and under the colonies: the area appears lightened (yellow) and transparent.

I am unsure of the reason for color change (blood agar plate) in beta hemolysis, my guess it's due to diffusion as I have found no mention of chemical change in hemoglobin molecule anywhere (yet).
So far my position is chemical change in hemoglobin without lysis is alpha hemolysis and lysis followed by diffusion of the hemoglobin molecule is beta hemolysis. Problem is my support is shaky at best.

Alphahemolysis simply oxidizes hemoglobin to methemoglobin and causes a color change on blood-agar. The RBC membrane is left in tact as far as I know. If you look at a picture of the 3 types of hemolysis, you will see that there is no zone of clearing in the alphahemolysis plate. Compare that to the obvious zone of clearance observed on the betahemolysis plate, in which complete lysis occurs. Here is a nice picture


What exactly is "chromosome topology"? I've been reading a lot about Hi-C lately, and this has been bothering me.  So far as I can tell from reading around, the topology is related to the conformation of the linear chromosome.  This seems like a fairly pointless description however, as they should all have the same topology.  A "conformation", in my understanding, is the chromosome being folded into a particular geometry.
On the other hand though, I guess if two genes were brought together to form a loop, they would also form a "hole" (the gap in the loop).  But this seems like a weak connection to make, just because two chromosome regions are paired doesn't necessarily mean they were bound and formed a loop.  It seems the "topology" would "best" be seen after a 3D reconstruction from the pairs data, showing the predicted geometry, and from there you could see how many putative loops and such there are, and thus start to determine the topological properties.
The last possibility I was thinking was that this is in reference to network topology implied by a contact matrix.  This seems the most likely to me, but also the least implied (to me, at least) in the literature I've ever read.
All of this has me wondering if I've missed something about the meaning of "topology" here, as opposed to just "conformation".  I'm wondering if there is a consensus on the precise meaning of topology in the genomics/Hi-C context.

I think that there are a few things going on in this question, I'm going to try to answer the ones that I think are most pertinent:

We should not expect "topology" as used in the Hi-C field to have a rigorous mathematical interpretation. Most of the people thinking about it are ultimately biologists who are interested in biological problems. As suggested in the comments, they are basically interested in the shape of DNA in the cell; e.g. which pieces of DNA are close together and which are far away. You can use this information for a lot of different purposes of course, but most people using the technique are satisfied with viewing topology as "the set of pairwise distances between all DNA chunks" (and whatever things you can infer from that set).

Your sense (from the comment) that the linear chromosome ordering is the main interesting feature of topology is (IMO) absolutely correct. However, it is not a given that every chromosome is put together the same way. This is related to the most useful application of Hi-C data that I know of, which is to either (A) scaffold genomes (put discontinuous sequences into the right order) or (B) deconvolute mixed populations of genomes into groups of sequences that belong to the same cell. The linear order of DNA is by at least an order of magnitude the dominant signal in the data, and is therefore the most trustworthy thing in there.

Network topology is sometimes implicit but generally central as a feature of algorithms using Hi-C data. I don't know that we can say that all workers in the field are thinking of this when they talk about topology, but I certainly am. Some random papers that make it fairly obvious: here, here, here.

(Full disclosure: I work for a company that sells Hi-C kits and services.)


Do creatures exist which can stop their hearing at will? Many people would love to have the ability to shut out noise while sleeping, in the same way that we have eyelids to shut out light. If this capability exists in nature, it could offer clues to researchers in the field of sound proofing.

Are there creatures which are capable of 'switching on or off' their hearing capabilities at will? At least partially?

I don't see why this cannot be evolutionarily possible. If perception of sound was necessary to know a predator was approaching while the creature slept, then according to evolution, creatures would not have had the ability to shut out vision either.

Yes
Many echolocating bats use the stapedius muscle to separate the inner ear bones
when they emit their call so they are not deafened by their own call. Their ears are highly sensitive to the very frequency they are making so they need a way to protect against it. They are only deafened for 2-8ms but that is enough to protect their hearing while still being able to hear any echo.
Source


Specific mechanism behind lethality of yellow coat color in mice Our high school genetics chapter has some extra information about L.Cuenot. It only covered his research, and the fact that mice homozygous for yellow coat color would die before birth. It was an example of a lethal allele.
We have learned about sickle cell anemia, thalassemia, and hemophilia. All of them had a specific reason/mechanism which caused damage. For example, it's not the shape of the red blood cell in itself which is problematic, it is the fact that it can't carry enough oxygen. Therefore the cell will die off much quicker than normal cells.
I asked few of the biology teachers why the yellow coat color was lethal, but they couldn't provide any answer.
My question is, what causes the mice to die before birth?
Links to relevant articles or excerpts from them are highly appreciated.

Really interesting question: The lethal yellow mutation (also abbreviated Ay) affects the agouti signalling protein which plays a major role in pigmentation. Heterozygous expression of it leads to the dominant expression of pheomelanin (which is yellow), causing the mice to express this color (among other effects). To understand why it is homozygous embryonic lethal, we need to take a further look at the gene and its organisation.
Agouti is located on chromosome 2 of the mouse genome and downstream of a gene called "Raly" (synonymous also MERC)(Image from NCBI Genes)

The Ay mutation now deletes a large chunk of DNA, removing about 170kb between these genes. This removes parts of the coding sequence of the Raly gene and the complete promoter and (non-coding) exon1 of the Agouti gene and results in a fusion protein in which the agouti gene is put under the control of the Raly promoter. This leads to the expression of Agouti every time when Raly should be turned on.
Schematically, this looks like this (figure 4 from reference 2):

Raly is an RNA binding protein, which is highly expressed in embryonic tissues. The mutation leads to the expressing of Agouti there instead. According to reference 3 this leads to embryos which do not develop further than the blastocyst stage leading to premature death of the embryo.
So in short, the deletion removes the expression of Raly, a protein important for embryonic development. Im homozygous mice this is embryonical lethal, in heterozygous mice this can obviously be compensated. However, these mice tend to be obese and are more susceptible for certain tumors (reference 4).
References:

The embryonic lethality of homozygous lethal yellow mice (Ay/Ay) is
associated with the disruption of a novel RNA-binding protein
A molecular model for the genetic and phenotypic characteristics of
the mouse lethal yellow (Ay) mutation.
Pleiotropic effects of the mouse lethal yellow (Ay) mutation
explained by deletion of a maternally expressed gene and the
simultaneous production of agouti fusion RNAs
The molecular basis for dominant yellow agouti coat color mutations


Relation between trigeminal and facial nerve in sympathetic response In my neuro-anatomy course notes I found that the facial nerve "uses" the trigeminal nerve to reach its targets. However, I have yet to find any diagram or reference that indicates how this is done. How is the trigeminal nerve "used" by the facial nerve?

Certain parts of the facial nerve cooperatively share structure of trigeminal nerve. For example, to reach the sublingual gland, the chorda tympani of the facial nerve joins the mandibular branch of the lingual nerve. Additionally, to reach the lacrimal gland of the eye, the greater petrosal nerve branch of the facial nerve joins the structure of the maximallary branch of the trigeminal nerve.

For a pictorial demonstration of this, please refer to page 1069 of Clinically Oriented Anatomy 7th edition by Moore.


Can a rotten egg actually hatches to a real life? First of all, I'm no expert in biology. I failed a lot in high school. Please bear with it if it's a stupid question.

For the past few days, I got a rotten smell as if an animal died in my kitchen. I cleaned and didn't find anything until I found the culprit today: leakage of rotten eggs.

There were two eggs in a hard plastic container, and one of them leaked a bit. Then I saw around 4-5 insects-kind of thing lurking around. It looks like a worm and if you ask me how those things look like, it's as if the egg yolk itself separated into the shape of worms and started moving. If I remember correctly, I believe I saw a pair of white dots (their eyes) in each.

Did those eggs (which was stored in a warm place) actually hatched and gave to a life? I threw all of them away, but I still feel really sick. Is it because of my carelessness that the egg yolk actually became alive in such shape?

Thanks beforehand.

A chick can't develop outside of it's egg, so you won't see an embryonic chick growing and wiggling in a pool of substance leaked from a cracked egg.

Centuries ago, people believed in spontaneous generation: that life can arise from non-living things. A common example of this was the fact that maggots would "arise" from rotting meat if left to rot.

Although this theory was disproved, it is not rare to find someone that still believes it, because they seem to see it happen.

In the 1800's, before DNA was discovered, it became accepted that "like gives rise to like" - that is, chicken eggs will hatch chicks (not peacocks or mice), pea seeds will always give rise to peas, etc.

DNA was 'discovered' in the late 1800's by Johann Friedrich Miescher. He extracted a new king of organic moleculr out of cell nuclei, which he called "nuclein". Although Miescher did develop some hypotheses about how "nuclein" might be involved in heredity, he ascribed to the view at the time that any one type of molecule would be too simple to account for all the variation seen within species.

It would be about 75 years before the magnitude of Miescher's discovery would be fully understood, and that DNA is the basis for heredity.

Chicken eggs, if they give rise to anything (which will depend on if it is fertilized and properly incubated) can only give rise to chickens. Whether they are fertilized or not, they can't give rise to worms. A chick can't develop outside of it's egg, so you won't see an embryonic chick growing and wiggling in a pool of substance leaked from a cracked egg.

If you buy bananas and let them ripen and rot on your kitchen counter, you will suddenly find a lot of fruit flies in the house. The fruit flies did not spontaneously arise from the bananas; they came from eggs laid on the bananas before you bought them.

If you buy bananas and wash them well when you get home, and let them rot, you will not find fruit flies buzzing around them.

That is why your rotten egg didn't give rise to those little worm things.


Are there fishes with a double circulatory system? Our courseware materials say there are such fishes, but my Internet searches suggests fishes only have a single circulatory system.

It seems that lungfish display the beginnings of a double circulatory system:


Why a cell contains all DNA when it only needs a few genes? Is that what they called junk? Why does a simple cell have the DNA code for everything else when it just needs a few codes to function? Wouldn't that be a wasteful?

Why does a cell contain all DNA when it only needs a few genes ?

I interpret this question to mean "why does every cell contain the whole human genome even though it doesn't use it all, i.e. why does a liver cell contain the genes for eye color?"

If that is what you meant, then we can easily answer the first question in your actual text:

  Is that what they called junk?

No, that is not what is called "junk DNA". "Junk DNA" can refer to many concepts, but generally it refers to parts of DNA that serve no function in the body: they are not transcribed into proteins, they don't serve to regulate other genes, and if you remove them or change their sequence this will have no effect on the overall organism. This means it refers to parts of DNA that are used nowhere in the body, not parts that are used in one place but not in others.

How much DNA is "junk", how useless it actually is, and why we have it are complex questions that don't all have known answers, but it is completely different from your headline question.

I don't have the time to look up a detailed answer to your first question so I will leave that to others, but here are some elements that might help:

1) I think cells use more genes than you realize. I don't know the proportion of genes that are used for the cell to live as a cell vs those that are used for the specific tasks this cell needs to do beyond maintaining itself and reproducing, but I'm pretty certain there is no cell in the body that "only needs a few genes". I would even guess all cells in the body use most of the genes they contain.

2) not all cells contain an unmodified copy of the whole genome. Some cells lose their nucleus, i.e. their DNA entirely (red blood cells); others multiply some genes that they use a lot.

3) having said all that, I would guess that liver cells indeed don't need the genes for eye color, yet they might have them. Consider that cells reproduce by copying themselves, and copying their whole genome. Is it more of a waste to keep the copy as it is, or to go around before or after the copying cutting out all the bits this specific cell won't use? Do I go around editing the code of my text editor and recompiling it to get rid of all the functionalities I don't use? I might save some space on my hard drive but it is very obviously not worth my time to do that either. If the extra DNA doesn't do enough harm, there is no reason it would be taken out; indeed the wasteful thing would be to do so.


What traits make mountain goats so well adapted to mountain living? I've never really understood how mountain goats manage to survive so well in mountainous regions. I've seen them scale almost sheer cliff faces with apparent ease, and they can almost sprint vertically downwards without losing their balance.

How do they manage to do this? I can't see any discernible characteristics that would make them able to achieve this particularly well. For example, snow leopards achieve similar feats, but they have incredibly long tails and large paws to help with balance and agility, yet the skinny legs and hooves of mountain goats seem largely unfit for this purpose.

What adaptations do mountain goats have that allow them to survive in mountainous regions, and how do they work?

I'm hoping mostly for information on how they perform such feats of agility as to move around on very precarious outcroppings and such, but am also interested to hear about any other qualities that they may have to deal with the other mountain conditions (altitude/ cold etc.).

Mountain goats belong to the subfamily Caprinae, or goat-antelopes. The higher family is the Bovidae (cloven-hoofed mammals).
Now members of Caprinae are pretty stocky in their build and have thicker fur both of which help them survive in the higher altitude. Their ability to scale/descend sheer cliffs with such agility comes down to their cloven hooves. Their hooves enable them to grasp onto the the face of the mountain in areas other animals could not as well as shift direction very quickly. Despite the fact that cloven-hooves are not unique to mountain goats or other members of Caprinae it is a trait essential for them to be able to inhabit those harsh environments.

Nubian Ibexes (also a member of subfamily Caprinae) are experts at climbing as well; one of the best Caprinae members in my opinion. Nubian Ibex baby and fox


Reason behind colour of hibiscus and sunflower What is the reason for the red colour of hibiscus and the yellow colour of sunflower?

Flower color is result of reflection of light due to various color pigments. Evolutionary such pigments were selected due to various reasons like to attract pollinators (Dyer et al 2012). There are two major types of flowers pigments

Carotenoids (produces yellow, orange and red colors)
Flavonoids (produces red, purple, magenta and blue colors)

However, flower color is affected by various other factors (e.g. other pigments, metal ions and its chemistry etc.) along with above pigments.

Hibiscus' dark red color is outcome of Anthocyanins which is water soluble flavonid (Grajeda-Iglesias C et al 2016). However, this pigment is highly unstable and depending on pH of the surrounding it can be red, purple, blue or black. (More details in this book). Hibiscus contains majorly delphinidin-3-O-sambubioside (Dp-samb) and cyanidin-3-O-sambubioside (Cy-samb) as the major anthocyanins (DU and Francis 1973). Chemical reaction responsible for generation and utilisation of these pigment is shown below (borrowed from Grajeda-Iglesias C et al 2016)

In above image, at low pH values $AH^+$ produces red color while  and $(A)$ produces purple/blue, which is thermodynamically unstable. In addition to that co-pigments like Hydroxylatedbenzoic and cinnamic acids, hydroxyflavones (which all are colorless) are also responsible for not only stabilizing these chemical products but enhances the color (Grajeda-Iglesias C et al 2016).


Why does low sequence diversity cause sequencing problems When sequencers are processing sequence fragments, if there is little diversity at a particular bp locus this can cause problems for the sequencer. I have the superficial understanding that when a flow cell contains a significant percentage of a single base on any given cycle, it has difficulty deciding what base is present in each sequence. Why is this?

I think the problem is more that the software has a hard time identifying individual clusters if way more than a quarter of them are lighting up for a given base.  If you have more diversity in the first few cycles, when the cluster coordinates are being identified, I think this is less of a problem.


How does electrolarynx work? I have heard that this is an effective replacement for patients who have a dysfunctional larynx, partly due to cancer.

I am curious to know the inner working of this device and why such a robotic voice comes out?
What is the basic principle of this device. Does it simply captures vibrations and converts it to sound? Just like how a mic does?

Thank you.

Your vocal chords vibrate to produce a tone, but your mouth shapes that tone into the sounds that make up voice. If your vocal chords fail or are removed, the electrolarynx can be used to vibrate the throat for you, but your mouth still needs to shape that sound into words. Because the electrolarynx produces a mechanical buzzing vibration, you get mechanical buzzing words. This is similar to how the talkbox works with electric guitars, the guitar sound is piped through a tube into the musicians mouth, they have to shape that sound into words with their mouth. Go listen to Peter Frampton for a good example.


What is the meaning of depth relation and EM in this excerpt? In the excerpt below from Morphology of Invertebrate Neurons and Synapses

  For the better part of a century, conclusions were made largely by matching the depth relations between the terminals of input neurons and the dendrites of their presumed targets; this practice became transferred to arthropods and cephalopods. The practice may be true for particular terminals or dendrites, and in vertebrates, but it has been long gainsaid by many examples in invertebrates. In the particular case of Drosophila, now known from dense reconstructions, EM denies any such simple dichotomy in important details, with many terminals having postsynaptic sites and many dendrites that are presynaptic as well as postsynaptic (Takemura et al., 2008).

I'm having trouble understanding what the acronym "EM" stands for, the author seemed to throw it in without prior definition (my guess is it's some neuroscience jargon). I also don't understand what the author means by "depth relation". Could someone explain to me the two terms assuming a college intro level background in neuroscience?

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

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

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


moltype controlled vocabulary? In submitting sequences using tbl2asn to NCBI/GenBank, the documentation states that there is a controlled vocabulary for the key "moltype", but no where on the Internet can I find a full list of that vocabulary.  "mRNA" and "genomic" are given as examples on several pages, and I can see from Sequin documentation what the GUI descriptors of all the vocabulary terms are (e.g., "genomic DNA"), but I can't find the terms themselves.  Any ideas where I can find this list?

There is this "Controlled vocabulary for /mol_type qualifier" page created by the International Nucleotide Sequence Database Collaboration in 2013.  It says the allowed values are:

  "genomic DNA", "genomic RNA", "mRNA", "tRNA", "rRNA", "other RNA", "other DNA", "transcribed RNA", "viral cRNA", "unassigned DNA", "unassigned RNA"

I found this as the second result of a Google search on moltype vocabulary.


What is the conical mouthpart of a soldier termite and what does it do? I'm trying to get a visual understanding of termite anatomy and I'm getting quite confused on the protruding mouthpart area (it looks like a beak) located between the pincers.

What does it do / what is it for? It does not look like a chewing mouthpart.

Further, is it related to the mouthparts of the worker / females termites?

Oddly enough, I found "Conehead" termites with what appears to be a far more profound version of this part (though it might not be) and again I see no purpose for it.

Is there a place on the internet where the breakdown of termites can be found? This would be very useful.

What is between the pincers?

This is actually the termite's labrum. Its quite big in termites. Does not have value in telling male from female.


Is my cell-culture contaminated with mold? I am growing cell cultures at the moment, and I sometimes find 1-2 of these elongated, black structures in one of my 8 wells. Should I be concerned?

I have been growing these for about 5 days at this point, replacing the media every the other day. I figure that the life-cycle of mold is pretty fast, and that if it were truly mold that it would overpopulate the well pretty quickly. Perhaps it's just debris?

Most of the time you can find shards of plastic, defects in the plate and other non-cellular debris in brightfield that look suspicious. Even some cellular debris can look suspicious, like when your viability is really poor. That doesn't look like anything to me. You'd know if you had contamination because it would be in more than 1 field, you'd have more than 1-2 of them, and your culture would either change in color, turbidity or smell. If it's a plate defect, you probably wont see it move if you re-suspend the well, either.


Why do we get bored of certain food items after repeatedly eating them? Why do many people not like certain food items after eating them for long? They seem tasty first, and after eating many times, it feels like we get bored.

Humans inadvertently try to balance neophilia and neophobia - fancy names for preferring the new and fearing the new. With regards to food, most humans, and animals, take an overall stance of cautious curiosity. Curiosity as in discovering a new edible food that helps them survive and thrive, and caution as in any new food item may cause harm. Certain individuals will have less curiosity, being content with just eating a few foods, while others will seek new experiences when they can. That's part of the variety in humanity.

For example, people from the Eastern countries rarely ever get bored of certain foods, as they are a primary source of fuel, such as rice or noodles. Or like people from western countries, many of them eat bacon, eggs, and toast every morning for sixty years. They eat it repeatedly, almost everyday, yet they continue to do so without complaining of boredom.

The scientific explanation is just that the brain will get tired of the same thing. That's why do many fast foods are engineered so carefully tantalize (bliss factor) and yet not go over the point when the brain gets overloaded. This phenomenon doesn't really count as a factor of boredom, rather more like insensitive to repeated exposure. It's like when you are exposed to a strong smell (e.g. Perfume) for a longtime. The brain, neurotransmitters and olfactory receptors just ignores it and doesn't register it. It is suggested why we females keep putting more and more layers of perfume on, we just don't smell it anymore .

Hope that helps <3.


Textbook/lab manual for mammalian cell culture For general techniques involving molecular biology, I know of Sambrook and Maniatis Molecular Cloning which covers many of the standard cloning techniques.

However, mammalian cell culture has many significant differences from bacterial cell culture, some of which include the many different variants of cell culture media as well as the relatively complex systems which cannot be provided using standardised media such as LB or TB in E. coli culture.

Are there any similar textbooks/lab manuals for cell culture? Alternatively, good review papers covering the different kinds of media used in mammalian cell culture and their relative benefits would also be a good answer to this question.

Culture of Animal Cells: A Manual of Basic Technique and Specialized Applications by Ian Freshney is the most popular book on the topic of animal cell culture.

You can also refer to ATCC animal cell culture guide which also has information about media formulations.


Do You Need Vitamin B12 To Utilize Folate Just wondering if Vitamin B12 is necessary for the body to utitlize folate. My husband is on Methotrexate for rheumatoid arthritis, a medicine which is known to destroy folate. The doctors therefore prescribe high dose folic acid. He also, however, has a geographic tongue which is supposedly due to B12 defiency. If he is deficient in B12, and yet if B12 is necessary for folate absorption, the extra folic acid is presumably doing no good. Whether the two vitamins are essential co-factors is interesting to know because I've just read that folic acid deficiency gives people a 69% higher risk of heart disease. And he's just had a massive heart attack.

I can't seem to find the answer on standard search engines, would be grateful to know whether B12 is needed to utilize folate. Many thanks.

B12 is not necessary to utilize folate but it is necessary to replace B12 before repleting folate as otherwise you can induce subacute combined degeneration of the cord.  There are multiple mechanisms of folate absorption from the small bowel and large bowel which don't require B12.

Geographic tongue is not caused by B12 deficiency, and the actual cause is not known.  It does cause raw beef tongue.

You don't normally need to prescribe mega doses of folic acid with methotrexate.  Common doses are 5 mg per week, and 0.8 mg daily, though some physicians don't bother using folic acid at all.  Although folic acid was commonly prescribed because it was believed that methotrexate works by virtue of its ability to antagonize folic acid, it is now known that this is not true. It works as an adenosine antagonist, and so you can take the folic acid on the same day as the methotrexate if you wish.


Do DNA supply houses maintain a watch list for dangerous oligos (Anthrax, Smallpox, etc.)? The recent work by DeLoache, et al. on a synthetic opiate-precursor production pathway in yeast has generated a lot of scare stories in the media about people homebrewing heroin as easily as they would beer.

In connection with DeLoache and coworkers' research, the New York Times has claimed

  Their DNA could be put on a watch list, as sequences for anthrax and smallpox are, so any attempt to buy them from DNA supply houses would raise flags.

I have never heard of such a watch list, and a thorough googling turned up nothing relevant save for the NYT article itself. Does this watch list exist?

I don't know how generally such things are followed, but in at least one contract gene synthesis provider's FAQ, they address this issue, and mention two such government-provided resources:

  Q: Does GENEWIZ have a procedure in place to address potential biosecurity
          concerns for gene synthesis projects?

  GENEWIZ is fully aware of all risks and benefits associated with gene synthesis research. With the knowledge that gene synthesis technologies have the ability to enable de novo reconstruction of dangerous pathogens, GENEWIZ employs rigorous quality control policies and procedures to safeguard against abuse of the genes we synthesize. GENEWIZ actively monitors the Screening Framework Guidance for Synthetic Double-Stranded DNA Providers [link], drafted by U.S. Department of Health and Human Services (HHS), as well as the Select Agents and Toxins list put forth by the U.S. Government.


Are all endocrine glands associated with common human feelings? I was looking at endocrine glands and found it interesting that a few of them have some very understandable feelings/mentalities associated with them.  In particular:

Gonads: arousal/romance
Pancreas: hunger (glucose)
Adrenal glands: fight or flight
Pineal gland: sleepiness (melatonin)

Of course, there is a lot more complexity to how these glands work and what they do, but I find the notion of being able to empathize with a part of the body interesting.

As a counter-example, if something is wrong with my spleen, there may be feelings associated with that (ie pain), but they aren't so profound as things like hunger, fear, and arousal.

Anyways, my curiosity here is: do all endocrine glands have a feeling associated with them?

Here's the list of all glands:

Pituitary gland
Thyroid gland
Parathyroid glands
Adrenal glands
Pancreas
Gonads
Pineal gland

Also, I know this is a silly question, but please bear with me here.  It's piqued my interest, and I just want to fulfil some curiosity.

You may not be able to feel or be aware of the actions of all endocrine glands at the time they occur.

The parathyroid gland secretes parathormone, which affects calcium absorption in the intestine, kidneys and bones, phosphate excretion in the kidneys and vitamin D production in the kidneys. I'm not sure if one can feel these actions or its consequences.

The adrenal cortex secretes aldosterone, which maintains sodium and potassium blood levels, which is related to blood pressure and urine excretion. It also secretes cortisol, which affects glucose utilization, fat breakdown and inflammation and affects the actions of some other hormones, but within normal physiological range, you don't feel these effects. Cortisol is also known as a stress hormone, but its actions are much more subtle (on the level of metabolism) than those of adrenaline (heart rate, excitement). Saying that, cortisol secretion can be related to sleep and appetite. There is a lot of speculation how it might affect mood or "energy levels" (adrenal fatigue).

There are many gastrointestinal hormones (gastrin, secretin, cholecystokinin, ghrelin), some of which affect digestion, some peristalsis and some appetite and you may not be consciously aware of all of that.

Some pituitary gland hormones (ACTH, TSH, FSH, LH) stimulate the secretion of hormones from other glands (adrenal, thyroid, gonades) and some (growth hormone, ADH, oxytocin) act directly on organs - I don't think you can say that you can feel these effects.

Some hormones have effects on other hormones (cortisol > adrenaline ; thyroxine > growth hormone, etc.), so it may not always be possible to pinpoint which feeling is directly related to which hormone.

Common human feelings related to hormone secretion:

Excitement or stress response, including fast heart rate and breathing and anxiety: short term response: adrenaline; long-term response: cortisol
Appetite: ghrelin, leptin, adiponectin, cholecystokinin, insulin, glucagon-like peptide, gastrointestinal peptide...
Sexual drive: sex hormones, mainly testosterone and estradiol
Sleepiness: melatonin, cortisol
Depression: cortisol, sex hormones (mainly in women)

The point of this answer is to show that some of your feelings can be simply affected by hormones, which are note some ultimate forces, and that being aware of that can help you to control them to some extent.


Why do earthworms surface after a rain? Googling, I find two different explanations for why earthworms tend to surface after a rain.

This page from UCSB, for example, gives both answers, contradicting itself:

The first explanation is that worms can breathe fine when it's wet underground, but surface after rain because it's their only chance to surface without drying out:

  Worms, like all other animals need to breathe, but since worms do not have mouths, they have a different way they breathe. Worms breathe directly through their skin, but they can only do so if their skin remains moist. Deep down in the soil, where worms typically live, it is normally moister than the surface. For this reason, worms prefer to live underground. After it rains, the surface becomes wet enough to support worm life, so they can come above ground to explore new areas more quickly. Fun fact: worms actually don’t come above ground after it rains to avoid drowning. Earthworms can live underwater for approximately two weeks. Thank you very much for your question!

The second answer is that worms drown if they stay under ground after a rain

  Worms are animals and, like you and me, they require oxygen to live. Instead of breathing air though their mouth into lungs, worms absorb oxygen from the air across their skin. Worms eat dirt. They burrow into the soil and normally live underground, where they are protected from the sun and so won't dry out. If you've ever played in the dirt by digging holes, you probably noticed that there are small holes or tiny pockets of air. The worms use that air, and the air that enters through their burrow holes, to breathe. When it rains and the dirt absorbs a lot of water, those air holes disappear, and the worms' burrows fill with water. If the worms do not come to the surface during a heavy rain, they will suffocate. Likewise, if they do not return to the soil after the sun comes out, they will dry out and die.

Which of these two is correct?

It looks like certain species of earthworms need to surface because they have higher oxygen consumption, while other species do not need to surface because of their lower consumption.

In particular, specimens of Amynthas gracilis were found to have low water tolerance, hence they

  crawl out of the waterlogged soil, especially at night when their oxygen consumption increases

while Pontoscolex corethrurus

  survived longer under water and was never observed to crawl out of the
  soil after heavy rain

Role of diurnal rhythm of oxygen consumption in emergence from soil at night after heavy rain by earthworms


Identification of small fuzzy flying insect (pic) These critters were flying around the neighborhood on an autumn evening in Seattle, WA, USA. Their most notable feature was the small amount fuzz on them. They were quite slow in their flight compared to similar-sized fruit flies.

Any ideas?

Here are two close-ups:

One one for size comparison:

To me, it looks like a male Aphid (males are winged, and have four wings) from the genus Eriosoma (wooly aphids). The white feathery substance is a wax secretion.

Have a look at Bugguide: Eriosoma, InfluencialPoints: Eriosoma and this page from the Uni of Minnesota for some more info.

A picture of a species from the genus:


Are Asians more genetically homogenous than other races? I've heard that Asians (I'm not entirely sure which subgroup was being referred to) tend to be more genetically homogenous than other races, with people of African lineage being on the other end of the spectrum being the least homogenous.

Is there any truth in the claim that Asians or a specific subcategory such as South East Asians have less genetic variance than other races?

I've seen papers like Extreme mtDNA homogeneity in continental Asian populations for example, but I don't understand enough to know if that answers my question.

If Asians have less genetic variance, would that lead to less variance in phenotypes?

I will side-step the question of 'race', as you seem to be using it (like most people) in the sense that has no scientific basis, but the answer to your question goes something like this:

The amount of genetic variation in a given population is mostly the function of the geographical distance from Africa. Roughly, populations in Africa are most genetically variable as they are the oldest (they have been there for the longest time in human evolutionary history and therefore there was a long time for mutations to accumulate in their genomes). Because all the other populations in the world have originated from these original African populations, they have a subset of that original variation - they are less variable. The further you get from Africa the less variation remains (a very simplistic scenario: a group of Africans left and settled down in the Middle East; then a group of Middle Easterners went further up to Europe and further east to India; then the Indians moved further north and east etc. etc.; in each stage, only a subset of the previous variation would be travelling along).

A famous image depicting this phenomenon is in Ramachandran, S. et al. (2005). Support from the relationship of genetic and geographic distance in human populations for a serial founder effect originating in Africa. Proceedings of the National Academy of Sciences of the United States of America, 102(44), 15942–15947. doi:10.1073/pnas.0507611102 figure 1B

On the Y axis you have a measure of genetic relatedness (more relatedness = less variation) and on the X axis you have rough geographic distance that takes into account major geographic barriers (like seas etc.). Green is Eurasia and blue is Australia and Oceania. Red is variation within the groups (so, Europeans only, Australians only etc.) The variation  between the populations explained by this geographic distance is close to 80% - which is huge. If I get this right, it means that most of the genetic differences between people in different populations are a simple consequence of living outside Africa. And the variation within each population is tiny (12%) compared to the between population.

This is a simplified view, because we now know that there were other species of humans that lived when our ancestors left Africa, and that thay had sex together as our ancestors spread around the globe, so a small portion of the others' DNA is still present in us today. Also this picture may be slightly different depending on what region of the genome you're looking at. But the major picture stands.

Going back to your question - "Asians" (populations with ancestry in east Asia) are on average more genetically homogenous than "Australians", "Americans", and "Africans".

EDIT: A paper I like that should explain all this much better: Barbujani, G., & Colonna, V. (2010). Human genome diversity: frequently asked questions. Trends in genetics : TIG, 26(7), 285–295. doi:10.1016/j.tig.2010.04.002 link


What made this black cluster on a leaf? I found this black slug-shaped thing on a leaf by my pond in western Sweden. It's about 15 mm long, positioned on a vertical leaf (I bent it to take the picture).

And I don't even know where to start looking. I was thinking it might be an egg cluster, but can't find anything useful without knowing at least what kind of organism made it.

After a lot of scrolling through image searches I stumbled upon the answer: this is the egg mass of some sort of horse-fly (Tabanidae). Almost identical egg mass here: http://bugguide.net/node/view/21171

I'm assuming I won't get a more specific answer than this.


What role does the eardrum and ossicles play in hearing, versus cilia? Modern electronic sound recording equipment employs a physical membrane that triggers the piezoelectric effect in a metallic element, to transform sound waves into electric signals.
I had always thought that the eardrum (or tympanic membrane) was the main instrument of hearing in vertebrates, that it physically transduces sound waves into nerve signals. However, in looking into it, I find that the eardrum transmits sounds to inner ear anatomy, where more structures are encountered before the sound waves become nerve signals.
I also find that small hairs, cilia, are sensitive to sound, and appear to be what actually turns sound waves into nerve signals, perhaps analogously to rod and cone cells in the eye. These cells line the ear canal, and when I read about them, they seem to be the real mechanism of hearing, and not the ear drum or inner ear bones.
At this point I'm confused as to actually how sound waves are transduced into nerve signals in vertebrates. Can someone explain the the roles of the various parts of anatomy in vertebrate hearing, in the overall, big picture? What roles do the large parts play, versus the microscopic cilia?

Sounds are pressure waves in air, but the inner ear is a liquid-filled space. This presents an impedance matching problem where sound is reflected rather than transmitted.
The eardrum and inner ear bones perform this mechanical impedance matching/transduction of air-to-liquid sound. From Purves' Neuroscience:

Sounds impinging on the external ear are airborne; however, the environment within the inner ear, where the sound-induced vibrations are converted to neural impulses, is aqueous. The major function of the middle ear is to match relatively low-impedance airborne sounds to the higher-impedance fluid of the inner ear. The term “impedance” in this context describes a medium's resistance to movement. Normally, when sound travels from a low-impedance medium like air to a much higher-impedance medium like water, almost all (more than 99.9%) of the acoustical energy is reflected. The middle ear (see Figure 13.3) overcomes this problem and ensures transmission of the sound energy across the air-fluid boundary by boosting the pressure measured at the tympanic membrane almost 200-fold by the time it reaches the inner ear.

Some sources will refer to this as "amplification" which is correct in some ways (without it, sound would be too "weak" in the inner ear) but doesn't quite explain the whole problem.
Inner hair cells do the actual sensory transduction, converting vibrations into electrical signals when the "hairs" are stretched apart mechanically, causing a fragile "tip link" to pull on a physical channel, opening it and allowing ions to flow through. The cochlea is a frequency-analyzer, vibrating at different frequencies along its length and allowing different hair cells to respond maximally to different frequencies of sound.

As a side note, although you asked about vertebrates, aquatic vertebrates like fish don't have these middle ear bones, their hearing is quite different from the mammalian ears I am most familiar with. I'm not sure at all about hearing mechanisms in aquatic mammals that evolved from terrestrial ancestors, like whales and dolphins, but that might be a good subject of a later question.


Why should collected blood from patients be analyzed as soon as possible? I'm looking for the possible factors influencing blood samples. What happens to the blood cells esp. WBCs/PBMCs after 8 hours of blood draw? For example, I know that granulocytes may cause oxidative stress and that may affect the viability of WBCs. What else could have an effect on blood samples that we can't store them for a long time at room temperature?  Thank you.

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

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


Do the BLAST scores have any relation between them? Is there any relation among the BLAST scores (E-value, similarity, identity, gap, bit score)?  Is the e-value score for an alignment proportional to other scores, such as similarity score (i.e. the lower the e-value, the higher the similarity)?

Thank you!

Yes there is a relationship between them but you may not be able to observe correlation between some of them.

Number of matches and score are definitely proportional, however higher similarity would translate to higher score only if the lengths of the scoring pairs are the same. Gap would have a negative effect on the score but it totally depends on what your scores/penalties are (see BLAST help and documentation).

E-value is basically the likelihood of two random sequences having a certain match score from a given database. So whether or not it is low for a hit depends on the score distribution of the database. Lower E-value does not mean higher similarity. It means that a hit of this score has a low likelihood to be found by random chance. The score distribution is generally skewed towards low scores and so high scores usually have low E-value but what a "high" score is totally dependent on your queries and therefore this statement cannot be generalized.

From BLAST docs:

  $$E=K.m.n.e^{-\lambda.S}$$

  This formula makes eminently intuitive sense. Doubling the length of
  either sequence should double the number of HSPs attaining a given
  score. Also, for an HSP to attain the score 2x it must attain the
  score x twice in a row, so one expects E to decrease exponentially
  with score. The parameters K and lambda can be thought of simply as
  natural scales for the search space size and the scoring system
  respectively.


mRNA bonding to itself Does a mRNA molecule bond to itself? I heard that only tRNAs have hydrogen bonds that let them have second structures, but after searching the web i found multiple answers. If yes, does anybody have a credible reference for that?(books, articles etc.)

It is very common!

Let's have a look at a few examples.

In bacteria, a lot of the genetic expression is regulated at the mRNA level. Certain mRNAs can form complex secondary structure that prevent or allow translation, and can switch from one structure to another based on the presence or absence of a signal molecule. These structures are called riboswitches; a very well-described example is the riboswitch regulating the expression of genes responsible for the biosynthesis of tryptophan.
For more details see this short article or this one.
Some mRNAs include internal ribosome entry sites (IRES), usually just upstream of coding sequences in mRNAs that code for several distinct proteins (polycistronic RNAs). IRES are highly structured RNA structures recognized by ribosomes that allow translation to start at a point in the middle of the mRNA. They are very widespread, especially in viral genomes. You can find a detailed explanation in the case of viral genes here:
In eukaryotes, mRNA molecules undergo a maturation process called RNA splicing that results in the excision of unnecessary internal sequences. During splicing, the mRNA forms a loop and a covalent bond is created at the future junction point; this bond is very transient but absolutely necessary for mRNA maturation and correct gene expression. See here for more explanations.
What about engineered RNA molecules? Self-hybridization of mRNAs is very useful in biological engineering. People reprogram riboswitches and IRES, but also use very useful tools based on mRNA self-binding. For example: based on a similar principle as the riboswitches, the transcription starting site can be masked by articificially introducing a (fairly simple) secondary structure called toehold switch that hides the ribosome binding site; however when a competing RNA sequence (which nature is specified by the sequence of the toehold) is present it opens and binds a part of the toehold, thereby making the ribosome binding site available for gene expression. This website shows an explanation and a real-life application of toehold switches for diagnostics.

These are only a few examples of mRNA self-binding processes; all of these have been extensively studied and are well described in many articles and books. There are many others types of self-hybridization in mRNA, and in pretty much all other types of RNAs too!