Is cyanocobalamin toxic? I see that cyanocobalamin is not naturally occurring, and is synthesized in vivo to methylcobalamin. As part of the synthetic pathway, cyanide is broken off. All opinions I can find are that this isn't a problem as cyanide is naturally occurring in many foods anyway, and is safely detoxified via the the Rhodenase pathway.

However, given its synthetic creation and vast prevalence as the primary B12 source in nearly all supplements, I was curious if any actual studies did exist to rule out potential (albeit minor) long term cyanide toxicity for this synthetic form of B12. I'm unable to find a single study where cyanide toxicity  was directly tested for, only studies stating that RDA in excess of 1000 times the daily dosage isn't lethal.

I understand no evidence currently exists for cyanocobalamin toxicity, but this wouldn't be surprising if there aren't any studies done in the first place.

Would anyone be able to reference an actual study that directly measured levels of potential cyanide toxicity for cyanocobalamin in any animal or humans?

Potassium cyanide is added to the cobalamins produced by bacteria to give rise to cyanocobalamin. CN is strongly bonded to Co and will not easily dissociate, thereby making this form of B12 inactive. Therefore, it has been argued that cyanocobalamin is not a good vitamin supplement and other variants such as hydroxycobalamin or methylcobalamin should be used. Displacement of CN from the complex would be energy expensive and even if the reaction is efficient the amount of cyanide released would not be in the toxic concentration. The CN-Co bond is so strong that hydroxycobalamin is used as an antidote for cyanide poisoning; it forms cyanocobalamin by displacing OH with CN.

 Source: Wikipedia and the cross references.


Neuronal coordinates of C.elegans Is there a list of neural coordinates for C.elegans? I need it to build a 3D model.

Update:
What is available at the moment is:

full connectome for example, at openconnectome;
neuron description with images of relative position at wormatlas;
2d position data at dynamic-connectome.

Update 2:

I've created very simple 3d model that consists of three layers (left, right and center) based on neuron labels. This shouldn't be considered as a real biological, but better than nothing. Code and data is on github.

Clarification:

The question is still there, I've provided very basic model and everyone are welcome to use it. But it still would be interesting to get experimental results. I'll keep the question open in case someone could share the data.

The Worm Atlas you cited is NOT just a "model." The neuronal cell coordinates were determined from an actual 3-D reconstruction of a worm based on serial thin section electron micrographs.  The serial sections were manually digitized to permit annotation and analysis using computer graphics. The annotation (over a period of years) established the synaptic connectivity, published by John White et al. in 1986 in the Proceedings of the Royal Society of London.


Is this a crayfish hole? or wasp nest? I'm suspicious that it might be crayfish, which I'd think was insane (I still kind of do), if I hadn't found a dead one around  my house earlier this summer.

Is that definitely what it is, or do I have to worry it might be wasps?

I'm located in Michigan.

This is the nest of a cicada killer wasp, Sphecius speciosus.

  Harmless, solitary and  Cicada-killer wasp holes are ½ half to 1-inch around with thinly scattered loose soil, usually where there is no grass. Cicada-killer burrows have a U-shaped mound of soil at the entrance. Adults emerge June/July.

Source: All the Dirt on Gardening blog

According to the Wikipedia article linked above:

  this species occurs in the eastern and midwest U.S. and southwards into Mexico and Central America.

so being in Michigan, you are certainly within the region in which the insect is found.

Parenthetically, also according to the blog from above:

  Crayfish holes are 1-inch wide, 2-inches high and made of mud balls.

and the texture of that hole looks more even.

Related Bio.SE question:  Cicada Killer Behavior


Bird diversity and the avian flu From Learning from the Octopus 1 (p. 201):

  A complimentary line of defense would be to lower the chance of infection by lowering the prevalence and virulence of diseases…just keep the variability of nature intact…West Nile virus increases its prevalence when bird diversity declines.

and on p. 212:

  A high diversity of bird species has recently been shown to be a key factor in reducing transmission of some diseases such as avian flu.

Why is this so?

What does bird diversity have to do with reduced disease transmission?

Biodiversity is the opposite of monoculture, and we know that one possible consequence of monoculture is disease transmission -- bananas being the modern poster child for monoculture leading to disease spread.

The concept seems to have been most clearly presented in

Schmidt, K.A. & Ostfeld, R.S. Biodiversity and the dilution effect in disease
ecology. Ecology 82: 609–619 (2001)

  A community of abundant alternative hosts with reduced competence mitigates Lyme disease risk in this system by decreasing the average infection prevalence of ticks. When alternative hosts have net negative impacts on the most competent reservoirs, via competition and predation, the dilution effect is compounded. We believe this dilution effect to be a general phenomenon of disease ecology because the majority of vector-borne zoonoses are characterized by the fea- tures necessary for it to occur.

There are many articles following up on this one, such as Declining ecosystem health and the dilution effect:

  The “dilution effect” implies that where species vary in susceptibility to infection by a pathogen, higher diversity often leads to lower infection prevalence in hosts. For directly transmitted pathogens, non-host species may “dilute” infection directly (1) and indirectly (2). Competitors and predators may (1) alter host behavior to reduce pathogen transmission or (2) reduce host density. ... Our study provides further evidence for dilution effect ...

However, not all agree that this is a general or even a real effect.  For example:

  How changes in biodiversity alter the transmission of infectious diseases is presently under debate. Epidemiologists and ecologists have put a lot of effort to understand the mechanism behind biodiversity–disease relationship. Two important mechanisms, i.e. dilution and amplification theories have in some manner made it clear that biodiversity and disease outcome have an intimate relationship.... We suggest a multidimensional approach whereby the same disease system needs to be studied in different ecological zones and then the effect of biodiversity on disease outcome needs to be ascertained. Nonetheless, caution is to be taken while jumping to any conclusion as biodiversity–disease relationship is a multifactorial process.

--Does alteration in biodiversity really affect disease outcome? – A debate is brewing

The book seems to be making the specific claim that biodiversity reduces transmission of avian influenza, and without a reference I can't evaluate that, but I couldn't find any articles supporting the claim. I'd be skeptical about that claim without some good  evidence, because avian influenza viruses are exceptionally good at crossing species barriers, so biodiversity should be much less of an obstacle for them than more species-constrained pathogens.


Is there a link between autoimmune diseases and X-chromosome inactivation? I was reading about the necessity of niche formations to adequate development of blood progenitors and this idea reminded me of the patchy inactivation of the X chromosome which followed that maybe, if some of these pathways passed through X coded proteins, this might make women have different niches, that could account for the seemingly greater occurrence of auto-immune diseases in women.

Is there any sense to this idea? Was this ever researched?

Yes, here is an article on it: "The role of X-chromosome inactivation in female predisposition to autoimmunity"

Below see the method and results summarised.

  Using a DNA methylation assay, we have examined the X-chromosome
  inactivation patterns in peripheral blood from normal females (n =
  30), female patients with a variety of autoimmune diseases (n = 167).
  No differences between patients and controls were observed. However,
  locally skewed X-chromsome inactivation may exist in the thymus, and
  therefore the underlying hypothesis remains to be disproved.


How is a portion of DNA selected and unwound from nucleosome? If I understand this correctly during interphase most of the DNA strand is tightly wound around histones in the form of nucleosomes, to conserve space in the nucleus. Yet RNA polymerase in order to work needs a part of DNA to be temporarily unwound. How does the polymerase find the particular part of the DNA (and especially the promoter for a gene coding the protein needed to be synthesised) in this mass of tightly wound DNA?

This answer will be a very broad overview and is based largely on information from the textbook "Molecular Biology of the Gene" by Watson et al. (which I highly recommend).

Nucleosomes are dynamic structures.

The interactions between DNA and histones are non-specific and dynamic. Regions of DNA can be transiently unwrapped from the nucleosome and thus recognized by DNA binding proteins. In fact, because of the non-specific nature of the interaction, DNA can slide relative to the histone core and expose different sections of DNA. This can be facilitated by nucleosome remodelling complexes which can also catalyze complete ejection of histone octamers to expose even more DNA.

Nucleosomes can be positioned specifically.

The association of DNA binding proteins with specific sequences can prevent or control nucleosome formation at specific loci and leave tracts of exposed DNA accessible to the transcription machinery. Additionally, certain DNA sequences that form bent helices are preferentially bound by nucleosomes.

Chromatin compaction is highly regulated.

Two broad classes of chromatin are present in the interphase nucleus: highly condensed, transcriptionally inactive heterochromatin and less condensed, transcriptionally active euchromatin. Chromatin compaction is regulated by post-translational modification of histone tails, and modifications such as acetylation and phosphorylation, especially of the N-terminal tails, can prevent higher order, repressive chromatin compaction. The specific pattern of histone modification is referred to as the histone code and certain modifications are associated with gene expression. These modifications can be recognized by remodelling complexes and even transcription factors.

Further Reading:

Becker PB, Workman JL. 2013. Nucleosome Remodeling and Epigenetics. Cold Spring Harb Perspect Biol 5(9):a017905.


Effect of forced breathing on RBC size Microcytosis, i.e. decrease in the size of RBCs occurs:
– In iron deficiency anaemia,
– During prolonged forced breathing and
– When osmotic pressure of the blood is increased.

I am unable to understand how forced breathing results in microcytosis.

My attempt: I think prolonged forced breathing results in low CO2 concentration in blood which would lead to low H+ ion concentration , but this would lead to hypo-osmic plasma, which would certainly produce macrocytosis.

Source:Textbook of physiology

Forced breathing, a.k.a hyperventilation, causes hypertonic dehydration.

According to Greger and Windhorst, Comprehensive Human Physiology (2014):

  Loss of more water than NaCl leads to hypertonic dehydration and hypernatremia. In this condition the intracellular volume is marked decreased, whereas the extracellular volume is less compromised. Possible causes of hypertonic dehydration include excessive loss of hypotonic fluid (e.g., sweat) or hyperventilation.

Therefore, the decrease of the size of red blood cells is due to the dehydration following hyperventilation.

Source:

Greger, R. and Windhorst, U. (2014). Comprehensive Human Physiology. Berlin: Springer Berlin.


Indoor plants acidic soil I have a ponytail tree plant. The new growth look anemic, pale and thin. And several leave have browned from the midway to the ends of the leaves. The stem is woody and firm. Though it is in a solid pot, the soil tests dry, and there seems to be reasonable space for root growth. I have just moved it so it can get eastern morning sun for several hours. I have tested the pH of the soil and it tested to be a pH of 4.0. Can someone help me diagnose and treat my plant.

Thank you.

That's a super low pH, and I kinda doubt it's real. If you used a cheap home test, it's more likely analytic error (not necessarily your fault, it's just a hard thing to measure) than a real result. 4.0 pH is lower than most plants can tolerate--it's in the range of vinegar. Most plants (I have no experience with this species) prefer a slightly acidic soil, ~6.8pH. So, if your pH is really 4.0, then that's almost certainly a problem. It messes up the cation-exchange capacity of the soil, so even if you fertilize, the plant can't access the nutrients.

You can easily amend with some lime--if you don't want to dig it up, you can just scratch it into the top of the soil, and water through it. It will leech down through the pot. Hope that helps.


How to measure heat loss in Tardigrades I want to measure metabolism in tardigrades (a jar of 30 tardigrades). I know that an easy way to measure metabolism is heat loss; I can just measure the temperature of the water before and after a certain period of time and take the difference. I have a few questions:

1) Is this a viable way?

2) Do I need to put the tardigrades in a controlled system (or is the outside environment a constant)?

3) Will the measurements be really really small (so I would need a very precise thermometer?)

4) How long should I wait between the two measurements?

1 and 2) You need to build/use a calorimeter : http://en.wikipedia.org/wiki/Calorimeter
Different types exist, depending on your constraints.

3 and 4) It will depend on the size of your system.

If you decide to use an adiabatic calorimeter: First have an estimate of their metabolism (see e.g. [1]), then divide the energy spent over the duration you think you'll use by the heat capacity of the water volume you have, you get the temperature elevation.

If you use a flux calorimeter, then you don't multiply by the duration but check that the calorimeter will be sensitive enough.


Is there a protocol for freezing and thawing Bacillus subtilis cells? There is a book that says to store Bacillus spores in 50% glycerol at -70 degrees Celsius (doesn't mention if the 50% is final concentration or not). But from what I know, the cells themselves can be stored in any % glycerol as long as the final glycerol concentration is 15% (v/v) at -80 degrees Celsius.

Is there a difference between preserving spores and cells? Because the book said to preserve the cells at a certain glycerol concentration and the spores at a different glycerol concentration.

Also, say I scrape some B. subtilis out from the cryovial for reuse, and they are frozen. Do I wait for the scraped cells to thaw and then plate them, or plate them while they are still frozen?

And if I want to sporulate these cells, should I recover these frozen cells by plating and incubating overnight, or can I just drop them directly into the sporulation medium? I want to get the details down properly.

While I have never done bacterial stock cultures from spores, I don't think it is necessary, as the standard procedure for making bacterial stocks should work without problems.

For that you grow your bacteria in liquid culture until you reach the late log phase (so you have a lot of bacteria in your media), take 1 ml of the culture, mix it with 100% glycerol to reach a final glycerol concentration of 50% and then freeze it a -80°C. At this you can store it for long times (probably not indefinitely but for years is possible).

When you want bring your cultures back to life, take the tube and either use an inocculation loop or a pipette tip to scrape a bit of the frozen culture and plate it on an appropriate agar plate. If you want to scale up, pick one colony from the plate into liquid media.

Since glycerol is a pain to pipette (and can also have sterility problems), I have switched over to DMSO as a cryo-protective agent for bacterial cultures as well. Simply add 15% (end concentration) DMSO into the cryo vials (so 150ul DMSO to 850 of culture), mix and then freeze the cells. In my experience this works as good as glycerol.


human body in an environment where temperature is above body temperature What would happen if humans were to live in an environment where the temperature is above the body temperature?

Does the human body have a mechanism to cool the body?

When the surrounding temperature is below the body temperature, the body has a mechanism to heat up. When the surrounding temperature is above the body temperature, the body would require some mechanism to cool down since there will be a net heat transfer into the body.

There are many ways by which a healthy human body deliberately dissipates heat. First, it is important to note bodily temperature is not uniform. Our skin is generally colder or warmer than the rest of the body, which is the reason why we place the thermometer between our armpit or inside our mouth, instead of just placing it in our say, fingernails.
Vessel dilation
Arterioles can tighten or relax, increasing or reducing blood flow. High CO2 concentrations and heat cause the arteriolar diameter to increase, allowing larger blood flow. High oxygen concentration and cold cause the opposite effect. At normal conditions, about 0.2 to 0.5 liters of blood pass through the skin. But under stress, this can rise up to 8 liters per minute. What this response entails is an increase in cardiac load.
Sweating
We have up to 4 million eccrine sweat glands. Normally, they secrete an extremely filtered version of blood plasma, which is odorless. Exercising or heat changes this. As it is mostly water, which has a specific heat of 4.2 joule per gram, its evaporation releases quite a bit of heat. So what this mechanism requires is greater hydration, or else there is risk of hyperthermia (increase in core body temperature unrelated to fever).
References
This text is a very resumed version of this article:
Physiological Responses to the Thermal Environment


Why does yawning trigger tears? I'm just wondering when I yawned, there are tears coming out from my eyes, which makes me look like I'm crying.

So my question is how does yawning give out tears?

When you yawn, the muscles surrounding the glands which are responsible for bringing tears, i.e. the Lacrimal glands get squeezed leading to teary eyes. This is the location of Lacrimal gland (it's present at the top left corner in this image):

https://upload.wikimedia.org/wikipedia/commons/c/cf/Gray896.png

These glands actually work all the time as they've the responsibility to coat the surface of our eyes (that's the reason our eyes appear glistening). When they get squeezed, due to the tightening of facial muscles surrounding the eye, or maybe because your closing eyelids too tightly while yawning, they release a small amount of "tears" they would have otherwise used at a later moment.

Also, as a side note, there are more than one type of tears, this specific type of tears are called reflex tears. Quoting a Wikipedia article as a reference (https://en.wikipedia.org/wiki/Tears#Types):

  $\ldots$ It can also occur with bright light and hot or peppery stimuli to the tongue and mouth. It is also linked with vomiting, coughing and yawning. These reflex tears attempt to wash out irritants that may have come into contact with the eye.


What plastic eating organisms are there to help with plastic in landfills problem? I see some popular science articles on the plastic eating bacteria and fungi appearing on the web since 2009. Most of the articles praise discoveries, because such organisms promise to break down plastics which were previously thought to be indestructible. However, from the articles it is hard to understand the total number/names of promising organisms that can biodegrade plastic.

Additionally, it's hard to gather from the dated articles if these plastic eating organisms have passed safety testing - for example that they don't break down plastic into something volatile and toxic.

My question is - which organisms as of 2013 are seriously considered for solving the plastic in landfills problem?

I remember this link - about a high school student who's science fair project was a basic but effective selection experiment.  He cut up plastic and put it in a yeast medium (growth medium for microorganisms) for a few weeks.  It says he tweaked the temperature and other incubation conditions for a few weeks and got a significant degradation of the plastic in the media.  The microorganisms in the media were not characterized.

That article is great because the bloggers compiled a list of similar work.

There are a couple of links that point to styrene degradation by Pseudomonas putida variants.  Pseudomonas putida is a likely candidate from bacteriology - it was first isolated near chemical and petroleum spills - they can degrade petrochemicals and organotoxics, so researchers might tend to start with this bacteria or an isolate of it.

This paper identifies Phanerochaete chrysosporium, a white rot fungus as an organism that can degrade phenolic resins.  White rot fungi are found in wood rot and can degrade lignin which is derived from a poly-phenolic like biosynthesis pathway.  So this is also an interesting lead.  It doesn't always grow to industrial scale - I've known people working on this even in the early 80s.

So it seems despite the fact that plastic never seems to go away, there are organisms in the wild that will chew away at the plastic, and with a little bit of selection work you can pick them out pretty easily.  This survey of the plastic dump in the Pacific gyre found that there were marine microorgs that might be eating plastic there too.  They had a preliminary report:

  So far, the DNA sequences obtained by her lab show that almost 25% of the bacteria on one polyethylene surface were vibrios

A survey of the tropical rainforest also found a collection of fungi that can subsist on polyurethane. These included Pestalotiopsis microspora which seems to be have the so far unique property of anaerobic degradation of polyurethane.

Overall it seems that finding organisms in the wild is of ongoing interest.  This may be because biodegradation of plastic tends to be slow, which makes sense because if it were quick there would be no problem with dumping it into the dirt of into the ocean, but it would also rot over time in the back yard or in your boat.  While its possible that more fishing trips may find the perfect plastic eater, its also possible that industrial processes for the bioremediation of plastics may have to wait for some engineered organisms.


how to close a severed artery/vein? This is a medicine-related question that I've been wondering about. I've been watching medical lectures on YouTube regarding the human body and was wondering about how surgeons treat a severed artery or vein (think Juggular or Carotid)? Specifically I was curious about what kind of tools they use and what the technique is for performing this operation.

And before anyone asks, no, I don't need to treat someone with this kind of injury :).

Thanks,
mj

I'm going to take a shot at putting a whole lot of information into a small answer, so let me know what parts need more explanation.  To any others experienced with closure, I am certainly skipping plenty of steps and ideas in attempt to convey the general.

******A general warning that graphic surgical images are used below.******

The Setup:

You asked about "severed" jugular and carotid injuries, so we will focus on neck injuries, with a focus on insults to the R/L common carotid arteries (CCA) and the R/L internal jugular vein (IJV).  To get everyone on the same page visually, we are talking about the large blood vessels in this image:

For the sake of simplicity, we will deal with injuries that are focused directly on these vessels.  In reality, there are so many different and important tissues tightly packed in the neck that there are often many complications and multiple vessels that need to be dealt with near simultaneously.  Further, we will suppose that our patient (pt) is unlucky to have a "severed" vessel in his neck, but lucky enough to have immediate access to ATLS.

Just like you should have learned in your basic neighborhood CPR/aid class, you address the ABC's (MD's add DE): A irway, B reathing, C irculation (D isability, E xposure).  In reality when presented with a pt bleeding from the neck, you will almost always begin by applying pressure at the wound site, while you address the airway.  When I say "applying pressure" I literally mean a nurse or medic putting their fingers up against where it is bleeding and trying to stop it like a hose.

We will assume that a clear airway is established, the pt is breathing normally enough, and under general anaesthesia.  We will also give us the advantage of having the head, and to a little lesser extent body, packed down with ice.  This will give us precious time, and help prevent brain damage.  All else is presumed to be well with the pt, and all we need to do is fix the bleed in his neck.

Identifying the problem:

Now that we have our idealized pt ready to fix, the first thing you have to do is to identify where the bleed is.  Assuming you have serious bleeding, like one would come from a "severed" CCA or IJV that normally means cutting open the wound quickly and in a controlled manner.  Again, the neck is full of tissue you don't want to damage, so a anterior sternocleidomastoid incision is normally called for when you are looking for where the CCA or IJV is damaged.  As opposed to coming from the top the way we would dissect a cadaver (as in the drawing above), the sternocleidomastoid incision will give us a side view into the neck like this:

The point at this stage is to gain control of the bleed.  You don't want to just go digging in where the vessel is bleeding, because you are likely to cause more damage than help (and in this case, loose the pt).  Instead you are going to clamp above and below where the vessel is bleeding.  This will let you suck out the blood and see what's going on.  If you happen to have a large wound in a large vein, there's a chance that a clamp won't give you sufficient control of the bleeding.  In that case you have to also use a catheter to stop the bleeding (in obtaining distil control to be specific).

In our case, this means dissecting the carotid sheath.  This needs to be done very carefully so that you don't damage the vagus nerve.

You may have noticed I kept putting "severed" in quotes.  That's because it matters how the vessels are damaged.  Were they crushed or ground apart? Cut jagged or cleanly? Transverse or longitudinal?  All of these change the exact procedures into how you go forward.  Clearly a vessel that has a small tear is easier to repair than one that has been totally separated with jagged shredding from a crush injury.  Veins and arteries won't retract from the insult in the same way either, so how you find them can be a bit different.  Here is a flow chart that shows the basic decisions:

Put it back together Doc: [warning of graphic images]

You may notice that there are basically two end points for either veins or arteries: repair it or ligate it.  There are many different technical/specific ways either can be done, but those are beyond the scope of this answer.  If the sight of open wounds bothers you, note I am going to start using actual surgical photos below.

When it's possible it's better to repair the vessel.  That means that you can close the artery where it is.  If there is just a small hole, you can suture the hole closed.  With the CCA or IJV it's more likely that you are going to need a patch.  This means that you take another piece of vein or a synthetic replacement, and suture it into the hole.  I always like to tell people surgery is a lot more tailoring than most people realize (not that this is as easy as sewing fabric).  Below is an example of where a patch would be used in the CCA:

First the tear in the artery:

And after the patch has been added:

Suturing and patching can only be used to close the vessels when tension isn't needed to repair the wound.  If the laceration or severing of the vessels are such that it has come mostly (not completely) apart, but you can still get the ends together with NO tension,  end-to-end anastomosis repair can be utilized.  This means that you take the two ends, with branches if there are any at the wound, and suture them back together.

Again here is an example of the opening in the artery (popliteal):

And here it is again after end-to-end anastomosis repair:

Now let's say that you really did get the vessel cut in half.  That's a bit of bad news for you, you're going to have to ligate the vessel.  That means sewing up the end of it to close it down.  You start above the injury in arteries and below in veins, and then you tie at least three loops--many prefer five loops--down on the vein, and make a clean cut leaving at least two loops on the part staying in the body.  Then you do the same thing on the other side of the injury.  I think this is best displayed by a video, unfortunately most of the good ones I know of are not available to the public.

This video certainly not the best technique I've ever seen but it get's the idea across.  I will search for a better video as I have time.

Now if it is possible, a surgeon will try to make a graft deal with the ligation.  The first choice is a interposition graft.  This means taking a larger vein graft and connecting the two ends of the severed vessel.  You do this after making clean ends with the ligations from above.

Here we have the femoral artery prepped for an interposition graft:

And here is interposition graft in place:

In certain cases, this is not possible.  As strange as it sounds, the ligation may just be left in place, depending on where it is.

Is that all?

No, not by a long shot, but that is the basics.  There are many different techniques that can be used, with new and better ones being invented often.  For example instead of suturing, chemical cauterizing of the ligation can be used and is quicker.  That also allows the surgery to be done through a scope.  But the basics remain the same:

Stop the bleeding, gain basic access, get full control of the bleeding, obtain full exposure/access, sew up the problem, put everything back, close up, give fluids, and send them to ICU.  Even after getting everything right in surgery, the recovery can be quite difficult.

Sources and Further Reading

Note: I will try to come back with primary sources, I started from knowing what to do and searched for sources.  Here are two great sources which contain more complete information:

1) Trauma.org  This is a great site for use by actual medical professionals when addressing trauma.  They don't really cover the basics, but they do give wonderful care write ups.  Here is the relevant reference for this answer:

Karim B, 'Peripheral Vascular Trauma' trauma.org 7:3, March 2002. http://www.trauma.org/archive/vascular/PVTmanage.html

2) Acssurgery.com  Even more than Trauma.Org, this site is designed for use by clinicians.  Relevant reference:

Wisner DH, Galante JM, INJURIES TO THE NECK acssurgery.com 7:4, 2010. http://www.acssurgery.com/acssurgery/institutional/getChapterByIDHTML.action?chapId=part07_ch04&type=tab


Osmotic Pressure and Enzyme Activity Is it true that in an enzyme-catalyzed reaction, the rate of reaction does not vary with varying osmotic pressure?

Instead of just a true or false answer, why does it, or why does it not vary with osmotic pressure?

This paper is a compelling example of an effect of osmotic pressure on enzyme function. Restriction enzymes are normally very selective in the base sequences of sites at which they cut DNA, but in some conditions they show cutting at off-target sites, called "star activity." "Star activity" increased for some restriction enzymes almost linearly with osmotic pressure generated by a range of non-ionic solutes. Supporting the idea that the higher osmotic pressure was directly responsible, increased hydrostatic pressure reversed the effect of increased osmotic pressure.

Increasing the osmotic pressure is essentially decreasing the chemical activity of the water in the system. So it's not surprising that any enzyme reaction might be affected, particularly if the structures of active sites of enzymes are altered as suggested by the authors of the paper cited above.


Repeating sequences of genomes How can we estimate what portion of a genome is repeating sequences without sequencing it?

Thank you

Yes, it is possible to estimate the amount of repetitive DNA in a genome without sequencing. This was an important technique in the 1960s, referred to as C₀t analysis and pioneered by Roy Britten.

The approach taken is to study the kinetics of renaturation of heat-denatured genomic DNA (in a fragmented form). As you can see in this idealised Figure taken from the Wikipedia article on the technique there are components which renature rapidly whilst other components renature more slowly:

The interpretation of this is that repeated sequences renature rapidly because they are at a higher concentration than are single-copy sequences.

As stated at the linked Wikipedia article:

  ...it was through C₀t analysis that the redundant (repetitive) nature of eukaryotic genomes was first discovered.

And finally here is a quotation from Britten and Kohne's 1968 paper in Science:

  The rate of reassociation of the complementary strands of DNA of viral and bacterial origin is inversely proportional to the (haploid) DNA content per cell. However, a large fraction of the DNA of higher organisms reassociates much more rapidly than would be predicted from the DNA content of each cell. Another fraction appears to reassociate at the expected rate. It is concluded that certain segments of the DNA are repeated hundreds of thousands of times. A survey of a number of species indicates that repeated sequences occur widely and probably universally in the DNA of higher organisms.


How can I clean phenol extracted RNA? I extracted RNA from skin and quantified it in an Nanodrop machine. The 260/230 ratio was very low and two peaks appeared in the absorbance curve, but the RNA is ressuspended in RNAse free water. How can I clean it?

Phenol absorbs at 230 nm, this is the most likely contamination in your case. You should try to avoid pipetting from the phenol phase, or use a phase lock gel to make this easier. I assume you washed it a few times with pure chloroform after the phenol/chloroform mixture, that should help to get rid of the phenol.

I only precipitate my RNA with 1-1.5 volumes of isopropanol after the chloroform/phenol extraction, that should be sufficient for most uses. Just add the isopropanol, keep it at -20°C for 30 minutes and then centrifugate it at 9000 g for 20 minutes, redissolve the pellet in water.


Is feeding birds only after a snowstorm helpful or harmful? We had a very rare snowstorm here which left the ground covered in 8" of snow and trees covered in snow and ice. It'll likely all melt away in the coming days as we have sunny days and temps rise above freezing.

I noticed some birds poking around the snow on my back deck, so I cut up some raw untoasted walnuts and almonds into small pieces and and scattered them out on the deck and have seen a number of small birds stopping by to feed.

I travel away from home a lot and can't reliably keep a bird feeder stocked, so I'm wondering if this temporary food source is helpful or harmful to the birds since I'm not going to keep it up after the snow melts.

My concern about harm is about causing them to change their behavior and training them to keep looking for food on my deck after I stop feeding them in a few days. I'm assuming that the raw nuts I'm feeding them won't cause any harm even if it's not a well balanced diet, but I don't really have anything more suitable.

I don't know what type of birds they are, they are around 3" high, typical Pacific Northwest birds, I guess.

Feeding for a short period should be helpful, not harmful to the birds, particularly if it is during or following a cold storm.  (Ground feeding birds, such as the Junco or Towhee shown in your picture have particular difficulty after a storm covers the ground with snow.)  A concern people have with feeding is that feeding will create a dependency of the birds on the artificially supplied food.  The worst case of this would be expected to occur during fall migration, where an unusual supply of food might delay birds from migrating, which may be detrimental if they cannot survive the colder weather they may encounter because of the delay.  Other than that period, short term feeding should not be problematic since the birds will not develop a strong visiting habit over a short period.

Dependence on human feeding was studied by Brittingham and Temple in an article "Does Winter Bird Feeding Promote Dependency?".  This study evaluated chickadees in two areas, one which had supplemental food available for a year.  The next year, without food available for either area, showed no difference between the resident birds of the two areas.  Although they didn't test suddenly discontinuing food in midwinter, they do comment on that scenario:

  We did not test what happens when feeders are removed unexpectedly from a site in the middle of winter, but we suspect that this would not be as detrimental as is typically thought. In winter, a natural food patch may disappear suddenly as a result of a winter snow or ice storm or the foraging activities of other flock members. As a result, chickadees apparently track a number of food patches at all times and sample a number of areas continuously no matter how abundant food is in any one patch. This strategy is necessary for surviving in an unpredictable and fluctuating environment. People consider bird feeders to be a very predictable food source, but in terms of evolutionary time, they have only been available for a very short time. For birds, they are probably no different than any other food patch.


Is there a biological reason for spreading food intake into breakfast-lunch-dinner? I keep hearing over an over how humans can satisfy their entire daily caloric need in one sitting at a fast food restaurant. At the same time I'm looking at the kitchen plates, cups, etc, and they also seem to be getting bigger.

This makes me ask the question - was breakfast-lunch-dinner a concept invented because people:

Could not make enough food?
Could not make food fast enough?
Could not make food with high enough caloric intake?

I'm thinking along the lines of: you can make only so much tasteless porridge and stuff it in your mouth before it gets cold. At the same time I know that gorillas and some other primates have a very long (8 hours?) feeding session of eating raw vegetation throughout the day.

Is there a biological explanation why human food intake should be spread into X distinct sittings?

The three meals a day seems to be a cultural trait. Then what is the optimal number of meals a day? It is not known. Here are the results of some studies:

Reduced meal frequency:

It was found that the body can adapt to a single meal a day by modifying circulating hormone levels and glucose tolerance [1]. However it does not modify lipogenesis rates [2]. It may support cardiovascular disease risk factors [8].

Increased meal frequency:

Although there are studies that claim 5-6 meals a day help in maintenance of weight loss [3], others claim this habit increases hunger and the desire to eat and has no significant effect on fat oxidation [4]. A higher number of daily meals is recommended to the elderly suffering from cardiovascular diseases [5] because less but square meals lead to a redistribution of blood to the gastro-intestinal tract to increase absorption, which causes reduction of blood pressure [6].

Conclusion:

Energy balance is more important than meal frequency. As this study says [7]:

  ... there is no evidence that weight loss on hypoenergetic regimens is altered by meal frequency. We conclude that any effects of meal pattern on the regulation of body weight are likely to be mediated through effects on the food intake side of the energy balance equation.

References:

Carlson O, Martin B, Stote KS, Golden E, Maudsley S, Najjar SS, Ferrucci L, Ingram DK, Longo DL, Rumpler WV, Baer DJ, Egan J, Mattson MP. Impact of reduced meal frequency without caloric restriction on glucose regulation in healthy, normal-weight middle-aged men and women. Metab. Clin. Exp. 2007 Dec;56(12):1729-34. doi: 10.1016/j.metabol.2007.07.018. PubMed PMID: 17998028.
Jones PJ, Namchuk GL, Pederson RA. Meal frequency influences circulating hormone levels but not lipogenesis rates in humans. Metab. Clin. Exp. 1995 Feb;44(2):218-23. PubMed PMID: 7869919.
Bachman JL, Phelan S, Wing RR, Raynor HA. Eating frequency is higher in weight loss maintainers and normal-weight individuals than in overweight individuals. J Am Diet Assoc. 2011 Nov;111(11):1730-4. doi: 10.1016/j.jada.2011.08.006. PubMed PMID: 22027056.
Ohkawara K, Cornier MA, Kohrt WM, Melanson EL. Effects of increased meal frequency on fat oxidation and perceived hunger. Obesity (Silver Spring). 2013 Feb;21(2):336-43. doi: 10.1002/oby.20032. PubMed PMID: 23404961.
Ortega RM, Redondo MR, Zamora MJ, López-Sobaler AM, Quintas ME, Andrés P, Gaspar MJ, Requejo AM. [Relationship between the number of daily meals and the energy and nutrient intake in the elderly. Effect on various cardiovascular risk factors]. Nutr Hosp. 1998;13(4):186-92. PubMed PMID: 9780751.
Westenend M, Lenders JW, Thien T. The course of blood pressure after a meal: a difference between young and elderly subjects. J Hypertens Suppl. 1985 Dec;3(3):S417-9. PubMed PMID: 2856754.
Bellisle F, McDevitt R, Prentice AM. Meal frequency and energy balance. Br. J. Nutr. 1997 Apr;77 Suppl 1:S57-70. PubMed PMID: 9155494.
Stote KS, Baer DJ, Spears K, Paul DR, Harris GK, Rumpler WV, Strycula P, Najjar SS, Ferrucci L, Ingram DK, Longo DL, Mattson MP. A controlled trial of reduced meal frequency without caloric restriction in healthy, normal-weight, middle-aged adults. Am. J. Clin. Nutr. 2007 Apr;85(4):981-8. PubMed PMID: 17413096.


Why does the mixture of infant formula with saliva provide an ideal breeding ground for disease-causing micro-organisms? From: http://www.nal.usda.gov/wicworks/Topics/FG/Chapter4_InfantFormulaFeeding.pdf

  Discard any infant formula remaining after a feeding. The mixture of infant formula with saliva provides an ideal breeding ground for disease-causing micro-organisms.

Why is this so? Doesn't Saliva contain anti-bacterial properties?

Doesn't Saliva contain anti-bacterial properties?

Yes, in particular some IgA antibodies and lysozyme, but there are also plenty, and I mean plenty of bacteria in your mouth at any given point; we do, after all, still have to brush our teeth!  In fact, animal (including human) bites should be treated lest they lead to sepsis.  Those bacteria would love all the magnificent nutrients in infant formula.  Contact with an infant's mouth will introduce bacteria to the formula, as will exposure to air, contact with your hand, and anything else it experiences.  As an example, in the past few years, there have been some cases (from China, I believe, someone correct me if I'm wrong) of formula contaminated with bacteria, which were more than happy to stick around.


For how long and how cold should I perform ethanol/isopropanol precipitations of RNA or DNA? Precipitating nucleic acids using either isopropanol or ethanol is a very common operation, and I've read some very different protocols on the duration and temperature the precipitation should be performed.

I've seen anything from precipitating at room-temperature and centrifugating immediately without any delay to precipitating at -20 °C over night in various protocols.

Is there any published data about the influence of duration and temperature on the yield of the nucleic acid precipitation?

I always did mine at -80 C, but I never compared the results to other protocols (I don't fix what's not broken). But, I was curious about the same thing, so I looked around. I found one paper discussing this: Paithankar and Prasad, Nuc Acids Res 19(6):1346 (1991)

It shows that at low concentrations, EtOH at RT actually outperforms the precipitations at both 4 C and  dry ice/ethanol bath. That difference is quite big at 100ng/ml DNA and lost when there is more than 10 ug/ml DNA. For typical extractions, based on this data, I'd do it at RT.

On the other hand, Hilario and Mackay say in their book that:

  for genomic DNA isolation, different DNA precipitation temperatures
  and incubation times have little effect on recovery rates. One can
  directly centrifuge after adding ethanol without the -20 C incubation,
  and, it -20 C ethanol is not available, room temperature ethanol can
  be used.

They do not, however, provide any citation for that statement.


How is tolerance to an allergen developed? My question is mainly about how allergy shots work.

I did some basic research before posting here, however I could not find an explanation of what occurs at a cellular level.

Is it the persistance of the antigen which somehow induce immune tolerance?

The allergy shot in itself is a form of therapy called allergen immunotherapy (AIT). In it's essence, we're trying to get someone to develop immunologic tolerance to a given allergen such as pollen, okay! So how does it happen at the cellular level? (Assuming the treatment protocol is known)

Understanding The Mechanism Of Allergen Immunotherapy, as an article is kind of a broad overview. Thus there are phases to AIT that include early, intermediate and late phases. The process begins with a downregulation of mast cell and basophil activity, followed by induction of allergen specific Treg cells, a decrease in Th2 cells, and then a decrease in IgE production with an increase in IgG4/IgA.

Mechanistically, it doesn't look like it's well known how basophils and mast cells get regulated by AIT, but the theory is that the mechanism may resemble H2R (a histamine receptor) receptor activity during venom immunotherapy: H2R becomes highly upregulated after therapy start, and inhibits Fcε-R1 activation of mast cells and basophils, even in the presence of IgE (2, paywall on this one).

They provide an impressive table in Akdis & Akdis 2014 as to the role of immune cells in AIT:

So in the process of encountering the allergen, the immune system produces Treg cells as a result of dendritic cell antigen presentation. An inducible type of Treg called Tr1 is capable of abrogating the response of Th2 and Th1 cells through the secretion of TGF-ß and IL-10. They have a good table for this, too:

There's an effect in there due to TGF-ß exerting its effect on B cells that ends up inhibiting class switching to most other immunoglobulins except mucosal IgA. In conjunction with IL-4, IL-10 is capable of promoting the class switch of preceding B cells to IgG4. So the classes of Ig will largely become IgG4 and IgA in response to the allergen of interest. The B cells will also begin to produce their own IL-10, and in a way become a regulatory type of B cell, or Breg, that propagates the tolerogenic response.

And so the big conclusion: (1) the mast cells/basophils aren't as prone to causing anaphylaxis, (2) the effector cells specific for the allergen have actually shifted to populations of tolerogenic DCs, Tregs and Bregs, and (3) antibody production has shifted to IgG4/IgA from IgE. The net result is due to the repeated exposure to the allergen at some optimal concentration, but the key is they performed the treatment slow enough that the immune system had time to build up tolerance without going crazy. It's also likely that we don't know how long the system stays tolerant for after successful treatment.

It's much more complicated and if you can get past the paywall on source 2 there's really good, detailed info. I didn't want to go into a novel here, but let me know if you need clarification anywhere.


Low-cost simple water testing for faecal contamination I live in Indonesia and there are lots of sewage pipes discharging directly from homes/restaurants/etc directly into the river. It's also common to wash clothes and so on, so there is likely detergent in there as well.
Some water courses that people bathe in seem to be more s**t than water, if you see what I mean, in that it starts off in the river, then diverts into various smaller canals which often end up with trash, diapers, and so on.
I'm wondering what I could do to test/measure this in simple & low-cost fashion, so that I could test in different places and on different dates, and possibly to include quantative values such as 'how much dirtier' the river is when there are many people bathing in it, or when it is dry season, or whatever.
I think I don't need to test for every pathogen so it might be sufficient to just test for E coli? [I think S. aureus is also common, as skin boils tend to occur after bathing in dirty water.]

The best and most common would be the "multiple fermentation tube” or “most probable number” technique. Rather than testing for all pathogenic bacteria, it uses indicator microorganisms to assess the potability of the water. You'll need a lab to do this but if you have access to one, I'm sure that all the needed materials are common there. Here's a copy of the method: https://www.who.int/water_sanitation_health/resourcesquality/wqmchap10.pdf


Enzymes extracted from diferent tissue, may have diferent $K_m$ values under the same conditions? My laboratory team has been used succinate dehydrogenase (1.3.5.1) from Gallus gallus domesticus breast (the most meated part of the chicken, where you will obtain nuggets) to determine $K_{m}$ and $V_{max}$ under 3 linearization methods.

But, in BRENDA page, I found various values for many organisms, like Bos taurus, and they select other tissues like liver tissue.

Why the difference?

PD. Any reference about where to find this values for Gallus gallus mesticus will be very appreciated.

EDIT: The reaction consists on dehydrogenating succinate to fumarate, on the tricarborxilic acid cycle. Include the creation of a trans-double bond.

Describing my laboratory practice, we macerate the meat with glass sand, and divide this mixture on 2 kinds: one with methylene blue and trichloroacetic acid (TCA) and one without TCA. Now I know that TCA is a protein precipitant, and methylene blue is an indicator; the less blue, the less succinate. So, with absorbance tests, we can elucidate [Succinate] vs time plot, and approximate the ratio $V_{max}/K_m$ from the michaelian equation for substrate concentration decay:
$$S(t)=S_0 e^{-\frac{V_{max}}{K_m}t}$$
Also, i think it will be possible modeling instantaneous velocity with its derivate and make the linealization plots, but i'm not very sure of this.

EDIT2: Thanks for the help with my practice report (I really appreciate it), but I still wanna know if it's possible to have different $K_m$ values on the same enzyme, only changing the tissue for reaction.

You would not expect the same enzyme from different tissues to have different Km values if the enzymes are truly identical.

In addition, you would not expect the Km value to change during purification: the Michaelis constant for the purified enzyme should be the same as that determined with a crude sample.  If this is not true, it might mean that the enzyme has become modified during purification, perhaps by proteolysis (not something you want your examiner to point out or suggest!).

One advantage of the Michaelis constant is that it is independent of enzyme concentration (and so does not depend on the degree of purity).

Having said that, I think it would not be considered too unusual for enzymes isolated from different tissues to have different Km values.

Possible reasons are:

The assay conditions are not really the same. pH, ionic strength, temperature and buffer composition may all affect  Km.  The Michaelis constant determined at pH 7 in 100mM phosphate at 37oC may be very different from that determined in 50mM Tris pH 7 and 25oC
Post-translation modification may be important.  The enzyme from one tissue may be phosphorylated, for example. One laboratory may have isolated the modified from, whereas another laboratory may routinely include phosphatase inhibitors.
Proteases present in the crude tissue preparation may have modified the enzyme.

In the case of succinate dehydrogenase, there are two other important considerations.

Succinate dehydrogenase is a membrane-bound enzyme (containing a covalently bound flavin) and the method of extraction will be all-important, and a key area to examine is whether extraction conditions may account for the difference in Km.
Finally, and this one is important I think.  SDH is a two-substrate enzyme and the Km for substrate A will depend on the concentration of substrate B ! To determine the 'true' Michaelis constant for a two-substrate enzyme (assuming no substrate inhibition), we must extrapolate to 'infinite' concentrations of the co-substrate. Otherwise we are dealing with apparent Km values.

I'll bet the last point is important. Is the problem that at least some of the reported Kms are apparent values, ie the concentration of co-substrate is different under the different experimental conditions?


Evolution & Celluar Chemistry I'm new to this site but had a question on evolution, apologies if some of these questions seem basic but they are from a book i am reading challenging the role of chance in evolution.

Taking the example of Polar bears in the Arctic, how does evolution determine that it was white fur that was a beneficial trait rather than any other colour of fur? Is this a random change in cellular chemistry?

The book argues that there should be more evidence of polar bears of all shapes and sizes but with no evidence, asking "why should the creative factors provide only single options in the polar habitat and let natural selection sit idly by?"

The question is quite unclear but I'll try to say a few words that may help you.

You seem to be considering evolution as an individual that decides what is good and what is not. You seem to be considering the evolution as determing at any time point what will be good for a given species. That sounds very wrong.

Evolution is much more than Natural Selection (NS) but for the purpose of this answer I will talk only about NS. NS is a differential of fitness. Fitness is a function of both the expected reproductive success and expected survival of an individual. The environment is part of what determines the fitness of an individual.

So the question, you might be willing to ask is why is having white fur advantageous for a polar bear. The answer is on this post. In short, polar bear live in a very cold climate and their white fur is actually made of clear tubule which let the sun get through and reach their black skin. If it is unclear for you why dark matter warms up faster than lighter matter, you might want to follow a short physics lecture on light.

I would recommend that you have a look at a very introductory class to evolutionary biology such as Understanding Evolution by UC Berkeley for example. It is pretty short (much shorter than reading the book you're reading and you will learn so much more about evolution).

EDIT

I will not be able to explain you the basics of evolution theory entirely as it would not fit in a single post. So, I am reacting to your first comment but for the follow-up questions, please just have a look at an introductory source of information first and we will all gain lots of time. (No aggressivity here, I just want to avoid spending my day on this single post). Once you've finished an introductory course you are very welcome to ask further questions. Btw, evolutionary biology is a very big field. There are a large number of researchers (me and other users on this website included) who work during their whole to further our understanding of evolutionary processes.

  Natural selection must wait for these painstakingly slow changes to provide a large variety of options for it to choose from

This is wrong for two reasons. 1) NS tends to be a relatively fast process for rising the frequency of beneficial mutations. 2) NS does not give options to chose from. It is even the opposite NS remove options to keep only some of them. Mutations create options. In more correct terms, mutation increase the genetic variance while NS (and genetic drift that I haven't talked about yet) remove variation.

A1 allele is a very simple software for students in evolutionary biology that help the to simulate the action of NS and genetic drift on an already polymorphic locus. You might not understand what is meant by "polymorphic locus" but this just mean you need to have a look at an introductory course to evolutionary biology.

  if random changes in the cellular chemistry can suddenly alter the colour of hair from black to white, why cannot they change the colour of the hair from black to blue or red or crimson or violet or green, how did cellular chemistry know that what was needed in the arctic climate was only white?

Well, again the hairs aren't really white!

Mutation are random (although this statement can be misleading because there is variation in mutation rate). A mutation is just a "mistake" done during the replication of DNA. An organism does not make mutations to achieve a particular goal. It just make mutations. This is why the vast majority of mutations are deleterious (=decrease the fitness of the individual carrying it).

Now, some mutational effect (in terms of phenotype and not fitness) are more likely than others. For example, a polar bear may already produce a number of pigments that it could "easily" use for colouring its hairs. For example, a polar bear already produces dark pigments (such as melanin) and it is reltaively likely for that a single mutation could darken the fur of the polar bear. If having darker fur was beneficial then this mutation would increase in frequency in the population(assuming no genetic drift which is wrong but this is a story for another time). On the other hand, a polar bear does not produce violet pigments (to my knowledge). As a consequence, it would take a much larger number of mutation (each of which aren't necessarily beneficial) for a population of polar to have a light violet fur (and we would need to assume that having a light violet fur is beneficial).


Is it possible to extract tissue-culture material from a seed? Here is the problem: Tissue culture is cloning, and all plants from the same mother plant are identical. On the other hand, plants grown from seed are all different. If parent plants are genetically diverse (not inbred), growing from seed is the best thing in the long run.

The problem starts when some plants have a low germination rate, or are difficult to grow from seed. We want to grow a large number of plants as fast as tissue culture does, but we want diversity. Suppose the plant can produce a large number of seeds or at-least can produce them easily.

Can we extract cells from the seed and grow them via tissue culture? Which part of the seed should be used, and how different it is from using vegetative parts such as the apical meristem?

Yes. It's quite common, to the degree that it's done by some hobbyist plant breeders. See en.wikipedia.org/wiki/Embryo_rescue  However, AFAIK (I'm not an expert), it wouldn't be done for raising multitudes of plants, like tissue culture.

Rather, it's used in hybridization, where you hope to produce hybrids from plants that don't readily hybridize.  You would typically rescue a number of embryos, grow them on until mature, then perhaps use tissue culture to mass-propagate the ones that have interesting characteristics.


Why do bumble bees run repeatedly into walls? I have noticed on dozens of occasions that bumble bees will run repeatedly into a wall. Usually between 1 - 5 times before clearing the obstacle or flying away.

 Credit: Spine Films

This source suggests that this might be due to "unpredictable, unsteady airflow ... [that results in them being] buffeted back and forth by wind."

However, I've seen this occur in very clear, calm weather.

Further, I do not see other genera of bees colliding into things with anywhere near the frequency of bumble bees.

So what's going on here?

(FYI: their eyes, though primitive, are not likely the reason. Nor is their intelligence).

Crall et al., 2015, studied bumblebee collision avoidance (note the senior authors are the same from your link). It seems that, contrary to popular belief and experience, bumblebees are actually quite good at avoiding collisions, but they are also in an environment that has a lot of obstacles, so collisions still happen frequently.

There is a lot of interesting content in that paper, but one of the interesting discussions was about types of collision avoidance by body size. The authors note that for larger animals, collision avoidance strategies tend toward reversal/slowing down to reduce impact, whereas in smaller animals, strategies tend toward direction-change. This might be because collisions at high speeds are more dangerous for larger animals, so slowing down is the priority. Accelerating in a lateral or vertical direction, instead, would result in a full-force collision if the acceleration was insufficient to avoid the object (I have to admit, though, your gif doesn't seem to show any deceleration).

Larger individuals in their study performed more slowly on their obstacle course than smaller ones, but it seemed like all the bees were pretty good at avoiding obstacles.

Based on this study, I don't know that we can conclude definitively why bumblebees repeatedly run into walls, but given how well they navigate an obstacle course like this I am guessing it isn't simply because they are incapable, but rather has to do with a few things:

Walls are somewhat unexpected obstacles; bumble bees are probably best evolved for navigating around foliage that has a limited horizontal size, and once headed home they are expecting a direct route to be most efficient. A good transit strategy in that case would be to fly slightly laterally in the event of a collision to find a new opening, but not deviate too much from the original path of travel.
Speed/collision tradeoff. Getting home fast can have some obvious advantages because it increases the effective foraging potential. If collisions can be mitigated or aren't damaging, it might make sense to fly at high speed and just deal with the collisions as they come.
Bumblebees are big. Therefore, it's harder for them to stop, and they might use a strategy for collision avoidance that reduces impacts rather than avoids impacts altogether.
Cognitive biases in humans. Bumblebees make quite the racket when they run into things. You're going to hear it each and every time if you are nearby. The same isn't necessarily true for other bees or other insects.

References

Crall, J. D., Ravi, S., Mountcastle, A. M., & Combes, S. A. (2015). Bumblebee flight performance in cluttered environments: effects of obstacle orientation, body size and acceleration. Journal of Experimental Biology, 218(17), 2728-2737.


What factors affect the rate of siderophore production by microbes? Microbes produce siderophores which are chelators and bind to iron. This is how microbes absorb iron from soil or rock. What causes microbes to increase or decrease the rate of production of siderophores?

I think that you are interested in how bacteria regulate the expression of genes that produce siderophores. For a technical reference you can see this paper studying Vibrio, or this paper studying Pseudomonas. For a more general review see here.

Note that this is a diverse piece of metabolism and therefore there are likely to be a diversity of mechanisms by which siderophore production occurs, though superficially it appears that there are some general principles you can draw. I recommend looking at those papers and trying to understand the commonalities.


What are the negative consequences of a narrowed biodiversity to the planet? In this question about the fires in the Amazon rainforest, a user responds with

  It [the Amazon] is still a part of nature and burning it can narrow
  the diversity of both plants and animals, which can have consequences
  on the whole planet.

What are the negative consequences of a narrowed biodiversity to the planet?

From an ecological sense, cycles of living beings are intertwined. Breaking cycles affects life being able to live, reproduce, and die in a manageable way. Insects, animals, and plants help feed each other and help them reproduce. Fewer insects are less of a food source for animals and can't pollinate plants as much. Reduced animal populations are less of a food source for scavenger insects and don't feed plants through manure or decay after death. Fewer plants means less food and protection of insects and animals from predators. Predators overload on newly-available prey and their populations crash. It all intertwines.

From an environmental sense, the results of a narrowed biodiversity include putting more carbon into the atmosphere. In addition to warming the planet and the ocean, the ocean acts a carbon sink, acidifying in the process. This damages existing sea life that can only live within a certain pH and temperature range without sickening or dying. Some fish are trying to migrate and are dying off, due to lack of food where they are headed.

From a medical sense, burning down forests is stupidity. There are drugs that are naturally found in their rare plants, which have been developed into medications that save lives, e.g. Paclitaxel or Taxol. Only 1% of remaining rainforests have been explored for these plants and their compounds and we're stupidly burning them up. Nature has evolved many useful remedies, but we'll never know about the ones we destroyed, and that means more sickness and death.

For people obsessed with money, that medical sense translates just as well into pharmaceutical products and the resulting loss of jobs and profits.

All of these factors are linked together, hand-in-hand.


How were we able to determine the age of the first cell? I heard in episode 20 of Youtube channel CrashCourse's biology series that every living organism descended from a single microorganism 3.8 billion years old. I'm astonished by that figure. Even though it leaves a good 100 million years of wiggle room.

As a mathematician I happen to have a fair background in physics so I have been able to grasp the concept of carbon dating and a few other techniques, none of which seem to me to explain how this was determined. What trace could we possibly have of such an organism ? I can't imagine a team finding a fossilised cell and shouting "We've found the first cell !".

Might it have something to do with a well determined evolutionary rate conjectured to be constant and leading back to that particular time ?

I can't imagine a team finding a fossilised cell and shouting "We've found the first cell !"

Well... not the very first cell, but one old cell, yes!

Most of these very old fossils are microorganisms found in seafloor hydrothermal vent precipitates, in stromatolite or in very old sedimentary rocks typically in Greenland but also in eastern Canada. There were also very old fossils found in sandstone in Australia.

  Might it have something to do with a well determined evolutionary rate conjectured to be constant and leading back to that particular time ?

No, that's now how we do. We just look for very old fossils. The reason we can't do such simple regression is three-fold.

As measure of 'evolutionary rate', we would typically use the substitution rate at neutral loci. The method is referred to as "molecular clock". The principle is easy (the stats and detailed implementation are a bit less easy). Consider a diploid population of size $N$. Each generation $2N\mu$ mutations are being created at a given locus, where $\mu$ is the mutation rate at this locus. If those mutations are neutral, then a fraction of $\frac{1}{2N}$ of these mutations are going to fix (fixing means reaching a frequency of 1 in the population). This result can be demontrate with a number of technics (incl. diffusion equations and branching processes) but I am not going to detail that now. This means that $2N\mu \frac{1}{2N} = \mu$ mutations will fix every generation in a population. If each substitutions occur at a new locus, then the number of substitutions accumulated over $t$ generations is $2t\mu$. For the substitution rate at neutral loci to scale with time we need constant mutation rate.

The assumption of constant mutation rate is very likely violated on such time interval.
For very distantly related lineages, substitutions won't always occur at new loci. There are tricks to deal with that but there's a point after which, all substitutions will occur at loci that have already received substitutions and there is no signal left to analyse.
We need two lineages to compare their number of substitutions but there is no reason to think that the oldest forms of life quickly separated in different lineages that would have survived until today

Was it really 3.8 billions years ago?

The date of 3.8 billions years ago that you got from CrashCourse (or that you may have read somewhere) is not as accurate as the Green brothers (authors of CrashCourse) may have made you think it is. There is much more than a 100 million years of wiggle room. The only think we can do is find a very old fossil of something that looked like a living thing, date it and claim that life is at least as old as this fossil is.

We think life appeared after the formation of the ocean (which happened 4.41 billions years ago), so any fossil older than that would be quite an extraordinary discovery. The earth was formed about 4.54 billions years ago, so of course we won't find any fossil older than that.

Papineau et al. (2017) is good read on very old fossil (and potential fossils) that we've found. From their abstract

  Here we describe putative fossilized microorganisms that are at least 3,770 million and possibly 4,280 million years old in ferruginous sedimentary rocks, interpreted as seafloor-hydrothermal vent-related precipitates

You will notice that we don't quite know the exact date of when abiogenesis happened. I recommend you having a look at this paper if you want to learn more.


"Prime" structure of DNA Double Helix: Confusion In this video on DNA replication, the diagram shows the unwound DNA as still being anti-parallel, but the first diagram in this post on Biology SE shows that the individual strands are 5'____5' and 3'_____3'. So my question is the following:

Does a single, unwound strand of DNA run as either 5'______3' or 3'_______5', or does it run either 5'______5' or 3'________3'?

A single, unwound strand of DNA runs 5' to 3', the video is correct. When wound properly, the strands run in reverse directions, 5' to 3' for the first, 3' to 5' for the other. That diagram is not helpful, though the post itself is quite good.


Why does size decrease across the sequence of human chromosomes? The following graph shows a decrease in the number of base pairs per chromosome across the sequential set of human chromosomes:

Is this because chromosomes were originally numbered by their size on the karyotype?

You nailed it!

Nomenclature

Autosomal chromosomes

Chromosomes are numbered based on their size (in base pairs).

Sexual chromosomes

Sexual chromosomes (when they exist) are defined as the largest number regardless of their length. Note that the definition of a sex chromosome can sometimes be a little bit troublesome (see this book).

Exceptions

It sometimes happens that the first approximation of the length of a chromosome is inaccurate and that chromosomes are therefore numbered wrongly. In such case, when we realize the mistake, we just keep numbering the chromosomes the same way we did before even if it doesn't follow the standard nomenclature! This is, for example, the case of chromosomes 19 and 20 in Homo sapiens as you can see on your barplot. Chromosome 20 is actually a little bit longer (by about 4.5 Mb) than the chromosome 19. There are many other types of exceptions as well. Thanks to @Dexter  pointing out int he comments that in Drosophila melanogaster (model organism) the sex chromosome is numbered before the automosomes (autosome = non-sexual chromosome).


What is the equivalent of shutter-speed in Human eye? I just learned that in video cameras, every frame of the video has its own shutter speed.

And I know how frame-rate in human eye works out, well, not completely, hence the question.

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

  The human eye and its brain interface, the human visual system, can process 10 to 12 separate images per second, perceiving them individually.

How much (or what is the equivalent of) shutter-speed in those individual images?

The light receptor of the eye is a protein called Rhodopsin.  To me the equivalent of shutter speed for the eye is the (de)sensitization of rhodopsin by phosphorylation.  The brighter the light, the more sites on rhodopsin are phosphorylated, diminishing the intensity of the signal coming from the photo receptor via the transducin G protein that conveys the visual signal onward.

This process takes a few seconds, but then its possible to see when stepping into sunlight or in a darkened room.

This is more like a volume knob than a shutter speed since the same signal comes out at the same rate of each light sensor, but it has a similar effect - it modulates the intensity of the image.


Mouse Colony Software I am looking for a good mouse colony census program that tracks the mice we have in the lab, breeding success of breeders, lineages, multiple user access, etc. Jackson labs has a program that does this but is is cumbersome and a bit pricey (softmouse is also an option, though a pricey one). I figured that since colony management is so pervasive there must be a good piece of software to deal with this, but have mostly been out of luck. It would also be great if it is currently supported software that isn't outdated and free or sold at a relatively cheap price. Thanks.

Here is a list of programs that could work:

E-mouse Lab: http://e-mouselab.com, seems like the best fit for your requirements.
ZooEasy: http://standalone.zooeasy.com/en/pedigree-software/breeding-mice/breeders/index.html, Cheaper, good for breeding and pedigrees.
LabGuru: http://www.labguru.com, seems very professional and great for mice specimens as well.
MouseHouseApp: http://www.mousehouseapp.com, This is an iPhone and iPad app, so this would be good in the lab, but it depends on whether or not you have an iOS device.

Also, from what I found, Jackson Labs actually offers free mouse colony management programs. It does seem like it is cumbersome, but also a great program.

I will add more when I get time.


Why we can't feel the different parts of ear during hearing which is mentioned in all biology books? We can't feel our outer ear, middle ear and inner ear during hearing something. Why is that such a complex phenomenon is happening all the time but still we don't have any clue regarding that in our practical life?  We just get the sensation of hearing something and get no sensation/feeling how  different parts of our ear work all together .why all these happening within our ear and we never conscious about them ? In fact , we can know them only after studying biology.

Going to be productive instead of posting unhelpful snarky comments and downvoting.

You can only perceive what you have nerves for. Considering humans are unaware of all the rattling going on between the eardrum and inner ear, the only logical explanation is that there are no nerves in the region made to perceive said rattling.


Y-chromosome and phenotype I have a male colleague which has a son that does not resemble its father in any degree (apart of being male). The "father" is thin, tan-skinned, brown-eyed and the "son" has blue eyes, blond and already slightly overweight boy. Their faces have no any signs of similarity.

Since, the son gets Y-chromosome from a father, it is interesting to know if the Y-chromosome possesses any phenotypical feature apart of testicular development?

I did not find any Y-gene that influences the phenotype.

So, the second part of the question: Can other 22 parental chromosomes be so "recessive" that a child will have no "any" external signs resembling its biologic father.

The Y-chromosome only really contains genes relevant to sex determination[1], with estimates of protein-coding genes ranging from 50-450. For instance the SRY gene, also known as the testis-determining factor [2], is only found on the Y-chromosome.

Phenotypes such as eye colour are coded on the autosomes (i.e. not the sex chromosomes), and as such are determined by alleles inherited from both parents. As Koustav Pal mentions in his comment, many such traits are multi-allelic (i.e. determined by multiple regions of the genome), and are therefore more complex than first appear; eye-colour can change over time, and there are many more complexities that do not fit into the simple "blue", "brown", "green/hazel" categories [3]. This also applies to hair, so the child you mention could become more like their father as they grow older (or not!).

Because each individual posesses two alleles for each possible trait (one from their mother, one from their father - we each have two whole copies of the human genome in our cells*) a person can be a carrier for traits, such as blue eyes, whilst themselves having brown eyes. In fact the situation is so complex (>15 genes affect eye colour) that two blue-eyed parents could have a child with brown eyes [4] - the historical perspective was the brown eyes were dominant over blue eyes.

I have focussed on eye colour because it is a good case-in-point: there are clear genetic determinants and heritability, and it is more complex than the popular perception. Regarding hair (or skin) colour, single-gene mutations can cause pale skin and red hair [5], but beyond these cases the same rules seem to apply; that there are multiple genetic determinants (which means the Mendelian single-allele dominant/recessive model does not really apply) that affect the amount of eumelanin (which is dark brown) and pheomelanin (which is reddish) produced, with together combine to make the spectrum of colours we see in the population - it is not true to say that there are only blond OR brown haired people, as many people lie somewhere between [6].

This has not been an exhaustive review of these topics by any means, and there may be further evidence either way, but it seems quite clear that it is not unusual for offspring to not actually take the appearance of one or both parents. There are many traits you mention (such as build) that I don't go into detail, but there is emerging evidence that these are incredibly polygenic (caused by many small-effect genetic variants - e.g. height [7]) and as such could lead to the same phenomenon.

http://ghr.nlm.nih.gov/chromosome/Y
http://www.ncbi.nlm.nih.gov/gene/6736
http://udel.edu/~mcdonald/mytheyecolor.html
https://www.uq.edu.au/news/article/2007/02/eyes-have-it-multiple-gene-question
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3095693/
http://udel.edu/~mcdonald/mythredhair.html
http://www.nature.com/ng/journal/v46/n11/full/ng.3097.html

* well, most cells - red blood cells and gametes do not.


Help me identify this insect found in fishtank This bug appeared in my fish tank,transparent 6 legged with 3 tail insect. Anyone able to identfy this, please help. Many thanks

This is a Damselfly, suborder Zygoptera. Together with the Anisoptera (true dragonflies) they belong to the order Odonata, usually also named dragonflies.

Damselflies are smaller and more slender then Dragonflies, both as larva and as adult, although there are exceptions (mostly tropical species).

It can be distinguished from mayflies by it's broad head and the broad, flat lamellae; the 3 'tails' as you call them.

Some beautiful pictures can be found here


What kind of fruit is this? Just spotted this fruit while walking to school. It's the size of a small coin.The taste is almost sour and tangy and somewhat sweet (I only tried one of them and very little of it).  I admit, I've never seen it before. Does anyone know what this is?

Update: Location is two or three blocks north of UC Berkeley (Berkley, CA, USA).

It's probably Arbutus unedo, strawberry tree. Native to Mediterranean region and some part of western Ireland.

Edit: I've just spot that you found it in California, so it's probably one of north american Arbutus species, eg. Arbutus menziesii.


Definition of species - location of gene I know that species have been classified on basis of reproduction , DNA similarity , niche, etc.

Has there been a classification based on locus of genes ? What are the drawbacks/shortcomings of classifying this way ?

Isn't it simple to classify on this basis as - a species can have variation at a locus but the position of that locus with respect to a chromosome is fixed in every individual of that species. This fact can eliminate the subjective criteria of DNA similarity.

But I think this isn't valid for bacteria as there is so much recombination going on.

The position of a gene is not always fixed neither within nor between species. There are Copy Number Variation for example. A great part of the variation within humans is due to CNV. I agree that it is important to consider other genetic variations than only the alleles though. CNV, position of genes, regulatory sequences and other stuff are important too in the description and the functionality of a lineage.

The concept of species is a poor concept which is old as Aristotle and important in the christian culture but we have to accept that this concept is not a natural category. For french speaker people this podcast(Follow: Biodiversité: Plus qu'une simple histoire de conservation/Pierre-Henry Gouyon) is of interest. You won't find the perfect objective definition of what is a species. Here and here are posts that discuss the definition of species.


How correlated are proximally related CpG sites in human DNA? Cytosine residues in DNA that can be methylated (i.e. CpG sites) are likely to be in the same methylation state if they are geographically (proximally) close together.

I can only find one paper that states this empirically (1), that 90% of CpG sites within 50bp of one another are in the same methylation state - see below graph.

However this study is quite dated now (in the fields of epigenetics at least), and is very general.

I would like to know whether CpG's in different regions of the genome are more/less likely to be correlated than in other regions (say, exons vs. promoter regions). It would also be interesting to know whether the correlations change with age, and whether this is related to any disease processes?

Thanks for the input.

Eckhardt, et al, 2006. Nature Genetics. doi: 2010.1038/ng1909

I've got to dash off so I won't be able to give a fully in-depth answer today, but this basically boils down to the concept of CpG islands.  Something like 70-80% of CpGs are methylated in humans, so if they were randomly scattered around the genome there is already a pretty high chance nearby CpGs are in the same state.  However, because of CpG islands, CpGs of similar state are indeed grouped together, depending on promoter activity (to simplify things a bit).

That being said, if you look for articles that cite your article, a plethora of useful references show up.  In particular, this bad boy has a handy figure 1 which displays the overall landscape.  Maybe that's too broad of a view, but in general, like methylation patterns cluster together; otherwise, there'd be no such thing as a methylation pattern!  This paper has a neat figure which sums it all up nicely:

Basically, it's usually high-methylation or low-methylation; rarely is there anything in between.  There's a lot more in there so I'd recommend going through some of them; I'll try to get back to this later.


How did this spider evolve to mimic exactly a human face and arms? So I came across something terribly amazing today, that is, a video showing this species of peacock-spider, that literally, transforms into a human face waving his arms about.

What could have possibly given rise to this?

I can understand the arms waving around, but why the uncanny human-face template, complete with eyes, nose, mouth, etc.

I do not believe this to be a case of anthropomorphism on my part, (seeing what I am familiar with), because I cannot imagine any other natural case where such symmetry in a pattern would closely resemble a human face.

Would appreciate any explanation. Thanks!

I think this really is just a case of what you refer to in your question as anthropomorphism. We are very, very good at seeing faces. Here are some more examples.

Addendum

This site has pictures of quite a few peacock spiders, and as far as I can tell these are all the same species (The only peacock spider mentioned on Wikipedia is Maratus volans).

The remarkable thing about these images is that individual spiders seem to have very different patterns on thorax and abdomen, and many of these are much less like human faces. This seems to me to weaken the case for some sort of mimicry.

Interesting fact: seeing faces and other forms where they do not exist is a psychological phenomenon called pareidolia.


Is it feasible to grow edible crops for lawns? Is it possible to grow some type of plant that functions well as a lawn (e.g. is somewhat grass like), but that is humanly edible?  Would anything that currently exists fit this role?  For example possibly spinach or lettuce might work somewhat, but probably wouldn't be ideal.  If not, could we bioengineer something to fit that role?  I am thinking if we can, this could solve world hunger!

There are lots of things that you can eat that you could grow as a lawn.  That probably are growing in your lawn now.  My yard is about half violets and they are edible.  Purslane is a delicious succulent lawn weed.  Grab some, rinse it off and eat it.  It is crunchy!  I am telling you from experience you can eat a lot of it and you will not get sick.

Purslane image from here.
http://www.livescience.com/15322-healthiest-backyard-weeds.html

This backyard weeds link says lambs quarters are edible and I did not know that.  They are also volunteers but I did not know they were good for anything and so I was pulling them up.

We are surrounded by things we could eat and which our ancestors ate all the time but which we do not eat.  If you are in school, Johnathan, and this sort of thing interests you it would be a stellar project.  You have all summer to grow weeds in pots and then at the science fair you could have people taste them.


Is ebola non-contagious until symptoms appear? Why? There's been a lot of talk lately about the man who recently came down with ebola in Dallas, Texas. While I live elsewhere, I keep hearing quotes from CDC and state officials that ebola is not contagious until a person shows symptoms. This is generally used in the context of "Don't worry too much; we have the situation under control." Is this true in all cases? Why?

First, confirmation from the World Health Organisation:

  The incubation period, that is, the time interval from infection with the virus to onset of symptoms is 2 to 21 days. Humans are not infectious until they develop symptoms.

But

  People remain infectious as long as their blood and body fluids, including semen and breast milk, contain the virus. Men who have recovered from the disease can still transmit the virus through their semen for up to 7 weeks after recovery from illness.

They also state that deceased people may still transmit the virus via body fluids.

As to why the patients become infectious only when symptoms show, there are several related ideas.  For example, from the CDC:

  Ebola virus enters the patient through mucous membranes, breaks in the skin, or parenterally and infects many cell types, including monocytes, macrophages, dendritic cells, endothelial cells, fibroblasts, hepatocytes, adrenal cortical cells and epithelial cells. The incubation period may be related to the infection route (i.e., 6 days for injection versus 10 days for contact). Ebola virus migrates from the initial infection site to regional lymph nodes and subsequently to the liver, spleen and adrenal gland.

According to Dr. Ray Schilling:

  Ebola virus disease has an incubation time of 8 to 10 days where the person may complain of some tiredness, but is not sick yet. This is the time when the Ebola virus multiplies. It  paralyzes the immune system and distributes itself through the organ system.

From there, the symptoms and effects of Ebola are fast, according to the article "Ebola Virus Pathogenesis: Implications for Vaccines and Therapies" (Sullivan et al. 2003):

  Ebola virus replicates at an unusually high rate that overwhelms the protein synthesis apparatus of infected cells and host immune defenses


can you identify this plant? I would like to learn how this plant is called. It grew together with the beans I had planted. The body of the plant grew overnight while the leaves took a couple of days to develop. I decided to keep it in a small pot I had laying around to see if it will develop any further....

Looks a lot like a radish seedling to me.

However, if I'm not mistaken, it doesn't even have its first true leaves yet, making identification very tenuous.

It can also be any number of brassica species, e.g. mustard (l) or cabbage (r):

If you can't wait to see what it grows into, smash one of the "leaves" between your thumb and a finger. If it's a radish, it will smell like one. If it does, taste the other leaf. If it tastes radishy, you have your answer without waiting. If you want to wait, however, doing that would kill the seedling.

Brassica seedlings will also taste spicy, but not like a radish.

Based on the number of "weeds" in the brassica family, I'd guess it belongs in that group.

I included these diverse possibilities to illustrate how difficult identifying a plant without true leaves is. :)


Does DNA polymerase always go the same direction? I read that mutations are more likely to occur on "the strand that DNA polymerase replicates discontinuously". Does DNA polymerase always replicate the same strand discontinuously and, if so, how/why?

Summary:
In bacteria or organisms with only one well defined replication origin and a circular chromosome, yes for a given DNA region the same strand is replicated discontinuously.
In high order animals, which replicate chromosomes using several origins of replication (ori), this is less clear as the way ori are recognized is still not fully understood but seems to involve DNA structure. Chromatin structure is dynamic which means ori are also likely dynamic which results in defined regions of the DNA not likely to always be replicated discontinuously from a well defined strand (i.e. DNA replication might not always start at the exact same sites).

First off, as you probably know, DNA is always transcribed in a 5' to 3' direction. The why is nicely answered in this post.
DNA replication forks start at replication origins. Replication origins are recognized by origin recognition complexes. The way DNA replication occurs is by having two DNA polymerase complexes traveling in opposite direction (i.e. two bidirectional replication forks) from the origin as shown in the following schema:

This means that given constant origins of replication in an organism (like bacteria which usually only have only a single origin of replication) and given the DNA is replicated in a 5'-3' direction, same strands will be replicated discontinuously from the origin (i.e. in the schema, the bottom one on the left and the top one on the right). A global view of the replication at the chromosome level in bacteria is shown here below:

Now for more complex organisms, the origin of replication is not a single site but rather multiple ones across chromosomes (30'000-50'000 ori in humans). Where does DNA replication starts exactly, this is still not fully understood. DNA sequence is likely to play a role but no highly conserved consensus sequences were found and it is believed that origins of replication are linked to the structure of the DNA instead. In essence the chromatin structure is what seems to dictate where DNA replication starts and as the chromatin structure is dynamic within a cell, it is likely that origins of replication are also dynamic therefore making the identification of the discontinuously replicated strands very difficult (Méchali M, 2010).
Finally if you wonder what happens when two replication forks collide, well the answer is simple, replication stops and the two DNA polymerase complexes leave the DNA.


Western blot alternatives Given an in vivo sample from an experimental infection, I would like to see if a bacterial protein is present.

I've been thinking about Western Blot using sera from animals infected with the bacteria. However, this strategy needs a positive control that requires prior gene cloning and expression.

There is maybe a shorter path.

Thanks

I think that enzyme-linked immunosorbent assay (or ELISA) is the best way to do so, given you have an antibody against the protein to coat the sample wells with... You could use mice to create polyclonal antibodies against your protein by injecting the protein and collecting the serum and purifying it...as long as there isn't similar proteins to the bacterial one in the sample you are testing for...but to diagnose an infection you could use something like q-PCR assuming you can get the bacterial DNA from the sample (you could use typical bacterial DNA extraction techniques).

For more on ELISA go here. Here is a good animation on ELISA:
http://highered.mheducation.com/sites/0072556781/student_view0/chapter33/animation_quiz_1.html


What species is this fly? I am looking for an ID of this fly at genus or preferably species level.
Location: The Netherlands.
Size: approx. 7-8mm
Habitat: indoors, attic.
Timing: usually appears late winter, early spring

Apparently, this is a Pollenia sp
https://forum.waarneming.nl/smf/index.php?topic=447650.0.

One of the common species from this genus, Pollenia rudis, is often found overwintering in groups in attics and is therefore known as the cluster fly or attic fly.


Examples of how the presence or absence 2'-hydroxyl groups influence physicochemical properties of DNA and RNA I know, for instance, that RNA is much more succetible to alkaline hydrolysis than DNA and this difference is determined by the presence of 2'-hydroxyl group in ribose.
I have also heard that "DNA is more stable" and thus was selected as the repository of genetic information. Though, I still haven't understood why the lack of just one hydroxyl would lead to more stability...

As user137 said, the general base abstracts a proton from the 2'OH and subsequently the 2'O- renders a nucleophilic attack on the δ+ Phosphorous, leading to the hydrolysis of the phosphodiester bond. There can be slight variations in the mechanism and the intermediates; for details see this review.

After hydrolysis both 2'- and 3'- phosphates can form.
RNA is not thermodynamically unstable; apart from being unstable in the presence of a strong base RNA is biochemically unstable too. This is because there are several RNAses and most of them degrade RNA by a mechanism similar to alkaline hydrolysis (they cannot act on DNA). Also see this post.


Is galvinoxyl antioxidant assay possible using NMR spectroscopy? I would like to perform an antioxidant assay using the galvinoxyl protocol. The protocol states that we need EPR spectroscopy, but only NMR spectroscopy is available at my institution. Is there an alternate way where I perform a galvinoxyl assay using NMR spectroscopy.

Galvinoxyl is a free radical, which means it has an unpaired electron that can be detected with EPR. Antioxidants reduce the radical, which is then not detectable in the EPR anymore as it doesn't have an unpaired electron. What you need the EPR for in the assay is to determine how much of the galvinoxyl is still a radical.

Paramagnetic molecules like galvinoxyl are problematic for NMR, they bleach signals in close proximity to the radical and cause line-broadening. You still might be able to quantify the amount of oxidized and reduced galvinoxyl, but I'm not sure how reliable this would be. The oxidized galvinoxyl would probably be not visible in the NMR, while the reduced version would give a signal. You'd have to measure a few spectra to see if you can determine the percentage of reduced galvinoxyl from the NMR spectra.

EPR is the far easier method here, while I don't think doing this with NMR is impossible, there are quite a few ways it could be inaccurate. I'd strongly recommend to either use an EPR machine somewhere else, or use an entirely different assay that doesn't require such specialized equipment. I have no experience with antioxidation assays, but I'd guess that some exist that don't require EPR.


How do homologous pairs find each other If I'm not mistaken the only time homologous pairs of chromosomes need to find each other is during gamete formation in preparation for crossover recombination.
How do they find each other?

I found this review from 1999.  From the abstract:

  It is concluded that DNA-DNA interactions cannot bridge the distances between homologous chromosomes in the nucleus, and it is suggested that protein chains are formed between homologous segments. These attach to homologous chains emanating from homologous sequences in other chromosomes, and the chains move along each other until the homologous DNA sequences meet.

For more recent publications, you can search the citing articles here.