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

Yes. Although utilizing the action potential is not in their function, Schwann cells do have Na/K ATPases. In fact all animal cells do. It contributes to the resting membrane potential in neural networks, with regards to Schwann cells, and prevent differences in osmotic pressure from disrupting the cells.
As for your second question, action potentials do not occur in Schwann cells as there is nowhere for this "impulse" to travel to. A localized depolarization is not an action potential. Papers such as this, and this suggest that voltage-gated ion channels in Schwann cells serve complex and specific purposes such as inducing myelin formation.

Please do add some references.

"All three α-subunit isoforms are expressed in the CNS but to varying extents in different regions and cell types. The α1 isoform appears in glia, Schwann cells, choroid plexus epithelium and some neurons." link

Sorry put simply yes. Schwann cell, also called neurilemma cell, any of the cells in the peripheral nervous system that produce the myelin sheath around neuronal axons. Schwann cells are named after German physiologist Theodor Schwann, who discovered them in the 19th century. As such of it function an action potential is needed.
The principal primary active transport system in neurons, as in most other animal cells, is a P-type pump that concurrently extrudes Na+ and accumulates K+. For brevity, we will refer to it as the Na,K-ATPase. Depending on their functions, different tissues have vastly different requirements for pumping Na+ and K+. Transport by Na,K-ATPases is specifically inhibited by cardiac glycosides, such as ouabain.
http://study.com/academy/lesson/the-myelin-sheath-schwann-cells-nodes-of-ranvier.html
enter link description here

The purpose of the Schwann cells is to promote saltatory conduction whereby the action potential, in the neuron, "skips past" the Schwann cell to initiate an action potential at the next node between Schwann cells. The diffusion of ions in the short distance between Schwann cells is faster than the contiguous propagation of the action potential.

@Martin Anderson, -1 as you haven't answered the question of whether schwann cells have Na,K-ATPase pumps. I don't believe they do as it is unnecessary for their function (which bpedit outlines above). If you edit the answer I'll change the downvote to an upvote.

-1. You seem to have just pieced together unrelated facts about Schwann cells and copy-pasted citation text without reference to the question at all. Consider deleting your response.


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What are the on-rate and off-rate constants for 5-HT1 receptors binding 5-HT?
The class of 5-HT1 receptors binds serotonin (5-HT) reversibly (Wikipedia). I'm interested in the on-rate and off-rate constants $k_{\text{on}}$ and $k_{\text{off}}$ of this process.
So my question is: Have these constants already been determined experimentally for any member of the 5-HT1 receptor family, and, if so, what where the values observed?

Edit: Since this question didn't get much attention yet: Instead of the on-rate and off-rate, maybe the dissociaton constant/binding constant of the binding process is known?

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sort: votes


text:
Does every nerve ending send information to the brain separately?
Does every nerve ending send information to the brain separately? Is there a nerve path (I don't know their scientific name) from every nerve ending to the brain; or are they sent to brain from the same paths in the dorsal root ganglion? If not, how can we determine the (almost) exact location of pain in our hand?
I am not very familiar with the biology except the lessons I had taken in the high school. So please try to use daily language explaining this.

This depends on what you mean by a nerve ending. An entire nerve [bundle] such as the sciatic nerve? An individual neuron within the bundle? The dendritic branches at the terminal end of the neuron?

Nerve cells typically have many - sometimes thousands - of endings, called dendrites.  The inputs from these are integrated, and cause a spike to travel along the axon.  (This is a considerable oversimplification: look up "dendritic tree" for more info.)

sensory neurons often have a single dendrite, either synapsed to a sensory receptor cell, e.g. type I spiral ganglion neurons and inner hair cells in the cochlea. Or, the sensory neuron may have a specialised sensory dendrite, e.g. merkel's discs.

There are two main structures in the human nervous system:

The central nervous system, which includes the brain and spinal cord
The peripheral nervous system, which is all of the nerves in the rest of the body (fingers, arms, feet, etc.)

The signals taken by the peripheral nerves mainly travel to the brain through the spinal cord, and the brain sends signals back to the peripheral nerves through the central nervous system.
There are a lot more complex mechanisms and various exceptions, but essentially: the nervous system is a vast network of signals, and the majority of these signals travel through the spinal cord to the brain and from the brain to the target nerves.
The signals travel via different nerve "branches" — think of it like a tree of nerves, with the common root being the brain.
For more information please see:
Overview of the nervous system for dummies
Wikipedia (with strong references and lots of detailed information)

As commented, a nerve ending is really the ending of a neuron, some sensory neurons travel directly to the brain, some form synapses in the spinal cord (most touch and pain neurons from the body), then spinal cord neurons carry the information to the brain. (Note that facial sensation is carried by cranial nerves from the brain stem).
Some, e.g. in the retina undergo some quite intensive processing before ganglion cells carry any information to the brain.

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Genetics problem, test-crossed

Image description: text reads "An $F_1$ x $F_1$ self gives a 15:1 phenotypic ratio in the F2. What phenotypic ratio would you expect if you test-crossed the F1?"
How do I find out the $F_1$ phenotypic ratio by using the given $F_2$ phenotypic ratio?
What method should I use to solve?

Please show an attempt at solving this question or it may be closed.

Test-crossed f1 : AaBb X aabb
AaBb:1/4
Aabb:1/4
aaBb:1/4
aabb:1/4
ratio is 1:1:1:1

I have no idea what should i do next

PLEASE DO NOT POST TEXT AS IMAGES. Copy and paste the text into your question. Images are not searchable, and can not be interpreted by screen readers for those with visual impairments. Use the [edit] link to modify your question. See this for more information.

The 15:1 phenotypic ratio resulting from the self cross suggests duplicate dominant genes without cumulative effect.
In other words, two genes with complete dominance and dominant alleles producing the same phenotype, but independently, meaning that dominance at one locus ~ dominance at the other locus ~ dominance at both loci as far as phenotype is concerned.
So, in the self cross:
AaBb x AaBb =>
9 A_B_  double dominance = dominance
3 A_bb dominance from A
3 aaB_ dominance from B
1 aabb recessive
So that's where you get your 15:1 dominant:recessive phenotypic ratio.
Now, with a testcross, you were on the right track:
AaBb x aabb =>
1 AaBb
1 Aabb
1 aaBb
1 aabb
So, comparing this to the selfing results above, you'd get 3 dominant : 1 recessive for your phenotypic ratio.

Let me know if this answers your question!


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Restriction enzymes
Why are those restriction enzymes which cut the DNA strands a little away from the centre of the recognition sequence more useful in the construction of recombinant DNA?

Why do you think? What would be the use of overhanging (hint: sticky) ends vs a blunt cut?

I've read this and there should be and is a reason behind it

Yes, there is, and I'm trying to help you answer your own question. So, we're constructing recombinant DNA, which means we're splicing a linear piece of double-stranded DNA into a spot (most likely) in a plasmid. Why would you want sticky ends, and where would you want them?

Also important - would you want the same sticky ends everywhere, or only certain places?

I'm Confused*****

There is two main ways to cut DNA, creating Blunt ends or Sticky ends.
Blunt end example of SmaI recognition site:
("|" is the cutting site)
5'---CCC | GGG---3'
3'---GGG | CCC---5'
Sticky end example of EcoRI recognition site:
5'---G  |   AATTC---3'
3'---CTTAA    | G---5'
In blunt end example, the only way you can attach both pieces of DNA is one after the other, which is harder to do and not specific at all since any bases can go one after the other.
5'---CCC --> <-- GGG---3'
3'---GGG --> <-- CCC---5'
In the sticky example, the sequences will recognize its homologous sequence and attach to it (The TGGG will attach to the ACCC part, making a strong bond). When attaching one strand of DNA on the other, the bases must be homologous (A-T, G-C), this gives specificity since the strand can only be attached with specific sequences.
5'---GAATTC---3'
3'---CTTAAG---5'
Here is some good references on restriction enzymes:

Wikipedia(Complete informations with strong references)
Biotech Learning Hub (Basics easily understandable)


text:
What makes the hepatic portal vein unique?
What makes the hepatic portal vein unique?, is it because it begins and ends with capillaries or because it carries digested food.

Homework questions and questions that show little or no prior research effort are off-topic on Biology unless you have shown your attempt at an answer. For more information see our homework policy.


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What decides whether an ulcer/chancre is painful or painless?
In sexually transmitted infections, it is important to differentiate a painful ulcer from a painless one. This is because painless ulcers are seen in the chancre of primary syphilis while painful tender ones are seen in Herpes and though rare, in chancroid (H. ducreyi).
I can guess that it must be due to peripheral nerves, but how does this happen?

My hat's off to you. Not only have I never wondered about this, but having consulted Cecil's, Harrison's, several neurology texts, and other scholarly sources, not a single source addresses this.

It is small things like these that we generally ignore.. Thanks :') @anongoodnurse


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Is the enteric nervous system found only in vertebrates?
The enteric nervous system is distinguished by being autonomous from the central nervous system and capable of independent action, such as the peristaltic reflex. For this reason the the intestines can be removed from the body of a vertebrate creature and they will still function.
Is this type of nervous system unique to vertebrates, or is it found in invertebrates and insects as well?

A Google search of "enteric nervous systems of invertebrates" yields rich results, such as How To Innervate A Simple Gut: Familiar Themes And Unique Aspects In The Formation Of The Insect Enteric Nervous System. Searching before posting is always a good practice.


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Light microscope specimen size
I was going through sample questions for Science Olympiad, and one of the questions went like this:

A cell is observed through a light microscope at 4x magnification. The cell takes up about half of the visual field. What is the approximate length of this organism?

I know from prior knowledge that a cell can be anywhere from $10$ to $100$ micrometers, but I don't know how to figure out a cell's size with the information I'm given. Usually when I do problems like this, I am given the size of the field of view. Is that not needed to solve this problem?

http://pob.k12.ny.us/cms/lib/NY01001456/Centricity/Domain/517/Measuring%20%20With%20a%20Microscope%20SB201312_9_13.pdf Have a look his should help..

@Polisetty Those slides just pretty much review what I already know... is there something I missed?

Is this an mcq? since the question says, "approximate", you can assume the fov to be 5mm for 4x. Though it changes also with the magnification of your eyepiece. We were told to remember the fov values for 4x, 10x, 40x, 100x.. approximately - 5mm, 2mm, 0.5mm, 0.2mm These were approximates. This was a long time back.. maybe someone else can answer better.. Here's a full table - http://www.seoenterprises.com/shop/pages.php?pageid=12

@Polisetty thanks for the chart; also what's a mcq?

a 'multiple choice question'. huehuehue.

@Polisetty lol, no

Some cells can be much larger than the range you listed, examples that come to mind are some eggs (the yolk of a normal chicken egg is a favorite example), some algae, and I believe some amoebae too; not a bad rule of thumb for mammalian somatic cells but just a hint to not be overly focused on what is "typical" if the question doesn't define or depend on it.

@BryanKrause Never thought of that...biology textbooks always say cells are between 10 and 100 micrometers

@suomynonA Do you have a source for that? I wouldn't be surprised if there was a "typically" in that sentence, or if the topic was clearly relating to non-gamete animal cells, or something like that, because that certainly isn't true overall.

@BryanKrause The science olympiad rules, I copied it verbatim

@suomynonA I meant for your statement that "biology textbooks always say..." - I'm assuming that isn't written in the science olympiad rules?

@BryanKrause I just checked Campbell biology, it says "most cells" so I guess there are exceptions

The best  "approximate" answer in my opinion is: 2 times the length of the visual field :P


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Number of chromatids Before S
Is it better to say 0 chromatids or 46 Chromatids in a human cell?
Because most of the webpages I have seen say 46 chromatids and some clarified that it is infact according to the definition 0 but 46 is more commonly used

Please add some citations to your sources.

Just as MattDmo said add some citation, the chromatids (you mean sister chromatids?) are synthesised IN the S phase so there are no chromatids before the S phase, I don't understand your confusion?


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Can fruit fly larvae eat plastic?
I highly doubt that fruit flies or their larvae can digest any plastic used in everyday products. But are there any documented cases where they attempted to eat plastic? I ask this because last Sunday I was setting up a Wii U at my grandparent's house. It had been in this plastic bag that has been sitting in the same room for about three weeks because I only use it at other people's houses and is never set up in my house. This plastic bag was similar in shape and size to many re-suable grocery bags that supermarkets distribute, example Whole Foods. But this bag was made entirely out of plastic. Of course I don't know what type because it wasn't recyclable. It was also more rounded on the edges. Okay, here comes the biology part. I took the Wii out and there were light-brown, rice-shaped and approximately rice-sized "things" on some of the controllers, the power adapter and on the inside of the bag. There were a couple of fruit flies flying around when I took everything out. This immediately led me to believe that the "things" were fruit fly larvae, or dead larvae. I came to this assumption because in the past few weeks there have been more fruit flies than normal in my house, probably because of compost staying inside for too long (in a container in the kitchen sink) and a few too many rotting bananas that weren't eaten or disposed of for a while. And after seeing two or three live flies flying around the controllers I assumed that's what it must be. When searching for fruit fly larvae on Google Images the best picture that represents what I'm describing is this. There were also smaller brown dots where the larvae were and in some places they were not. I don't know what these are. They are smaller than 1mm in diameter. I understand that the flies probably thought that the bag was a dark and safe place to reproduce, but there are two things that I could not figure out, and they seem to be related. One of the Wii remote controller's strings (handles?) was dark brown and slightly wet. It looked like it had been soaking in muddy water. I was very confused by this. I took the bag outside to try and empty it but the supposed larvae were stuck to the inside of the bag. What did fall out of the bag that I missed before was a black ball about two inches in diameter that was also slightly wet upon touching it and was apparently plastic. There were a couple larva on it as well. The bottom of the bag looked like it had some plastic removed from it. This led me to believe that larvae had eaten some of the bag and detached it from the bottom. And somehow this ended up in the form of a ball. (Not a perfect sphere, but round.) I really wish I had taken more time and examined it more to confirm that it was from the bag. I don't have pictures of any of this because everyone was pressuring me to throw out the bag and clean off the equipment, apparently not caring about what actually happened. I also don't have pictures of the Wii remote string because I cut that off and threw it away as well. I later realized that I should have taken pictures because it is so difficult to describe. I began thinking of explanations for each part of what happened. My hypothesis is: Fruit flies in our house reproduced until there were too many to be sustained by the amount of food that was available. This probably happened when there were no bananas left or compost had just been taken outside. Some found the bag which was dark and safe, so they reproduced there. There wasn't any food for the larvae so they tried to eat the plastic that they were on but couldn't digest it, so they died.
This is way longer than I wanted to it to be...
So it comes down to these questions:
1. Would fruit flies lay eggs where there is no food?
2. Would fruit fly larvae attempt to consume something that clearly wasn't food?
3. What are the small dots on the adapter?

the dots look more like the fruit fly poop...

That's what I was thinking. Still doesn't answer if they were eating the plastic though...

Why do you think they eat plastic? I'm not able to find anything about that, I doesn't seems logical for me because the fruit flies lay their eggs in the fruit because their larvae need fermenting fruit to develop.

Can you give a better description of the 'black ball about two inches in diameter'? The most obvious explanation would be that it was a piece of fruit of some sort. It rotted, leaked on the remote before it dried out and the associated fruit fly population then starved (after crapping on everything). The photo definitely shows fly excreta, and flies can't eat plastic, so they were eating something...

arboviral - I think you might be right about the fruit. I don't know why I hadn't thought about that before. It seems so obvious now. There must have been some sort of fruit, probably a piece of a banana that was in the bag and stayed there for a while. It don't remember it smelling like any particular fruit at the time but maybe that's because it had been eaten. And the fruit must have stained the bottom of the bag and that's why it looked damaged. I left a banana in a plastic lunch bag one time for a few days and after it rotted I couldn't get the stain out.

As someone commented, it seems likely that this was just caused by a piece of fruit that had been accidentally left in the bag. It attracted fruit flies and for weeks they were reproducing.


text:
Differences in the action of Scopolamine and Atropine
Both Scopolamine and Atropine are muscarinic antagonists, having essentially the same action: blocking parasympathetic nerve receptors.
The action on the brain by muscarinic antagonists is presumed to be caused by dilation of blood vessels, thus we might expect the effect on the brain by the two compounds to be similar.
However, in actuality the action of the two compounds on the brain is somewhat different. Scopolamine begins causing strong psychotropic effects even in very small doses before it has any effects on the skeletal nervous system. Conversely, atropine begins having effects on the muscular system long before it begins having psychotropic effects and in fact, potentially toxic doses of atropine have to be administered before significant psychotropic effects begin manifesting.
If the apparent biochemical action of the two compounds is similar, why do we see this difference in the effects between the two with regards to the brain?

It seems that the reason for the different effect of Atropine and Scopolamine on the brain is related to the structural difference between them.
From the chemical structures below it is evident that the two molecules are almost identical, save for an epoxide group that is found in Scopolamine but not in Atropine.

According to Brody's Human Pharmacology: Molecular to Clinical, 5th edition, 2010, pp. 113-115, this epoxide reduces Scopolamine's base strength and enables it to penetrate into the brain more readily than Atropine.
Faster penetration into the brain = earlier appearance of psychotropic effects.


text:
Widest angular of binocular vision

Which out of eagle, rat, duck or owl has the widest angle of binocular vision?

I am pretty sure it's not rat and duck but I am confused between owl and eagle. Can anybody help me figure out which one would have the widest angle of binocular vision?

This sounds like a homework question. Did you do any research yourself on binocular vision?

@Ebbinghaus I did but couldn't really find anything. This is not a homework question I found it in a question paper and wasn't able to find the answer

Take a look at some pictures of eagle and owl and observe their beaks. It will help you in concluding which might have the widest binocular vision angle.


text:
Moss CO2 consumption
I wish to calculate how much CO2 would a sq m of moss fixes to glucose in one day, taking about 20 degrees C average temperature, 55% humidity and a regular 8 hour day. Water and nutrients are at optimal amounts. Is there a formula I could use? I can't seem to find anything online.


text:
Plasmid specific DNA degradation
I'm interested if there is a way to degrade the plasmid DNA inside an E.Coli cell specifically so that the method does no harm to the chromosomal DNA. First I was thinking about restriction endonucleases but I'm afraid that;

it isn't specific enough and kills the cell
or it does nothing, because the E.Coli methylates the plasmid DNA too

My second thought was the CRISPR/Cas9 system but it sounds like an overcomplication of the problem. Any simpler ideas? (For eg. specific enzymes)
EDIT: the main idea is to create more competent E.Coli cells with directed evolution. Currently this is just a thought experiment, so there is no specific plasmid sequence. In details; I would transform the plasmid into the cells, then do the selection part with an antibiotic and let them grow, then transfer the cells into a medium where there is no antibiotic and add IPTG to induce the plasmid-DNA-hydrolase enzyme, then maybe an other selection part could be performed to remove the cells which still contain the plasmid (for example with FACS if there is a GFP gene on the plasmid), then make the cells competent again with CaCl2 and do this whole process over and over again.

There are a lot of (simple) solutions, but I'm not really sure what you want to achieve. Can you clarify?

Why do you want to do this? To get rid of the plasmid and re-use the cells for something else?

@Chris Exactly, the core idea was that if such an enzyme exists then I could elevate the competitive ability of the cells by directed evolution.

Do you know the sequence of the plasmid? It would not be straightforward to get rid of the plasmid especially if it is high-copy number.

@VonBeche I tried to clarify it in the question details. What are those simple solutions?

traditional method to remove a plasmid from E. Coli is to grow the cells with Etidium bromide.
http://vlab.amrita.edu/?sub=3&brch=186&sim=1097&cnt=1

Done. But really... this is like needing to reference plasmid extraction by alkaline lysis or pouring an agarose gel.


text:
Choosing PCR conditions
How does one choose PCR conditions? Does it depend on the taxon, on the DNA concentration, on the primers or anything else?

You need to first build an initial protocol and then optimize it.
The most important to determine the conditions is the polymerase used. Some polymerases work at higher or lower temperatures and will work faster or slower. Find the default protocol from the polymerase seller and this will give you a good idea where to start.
The second most important is the primers used. Depending on the GC % in the primers and their length, the times or temperature of each step will change, or if you prefer will need to be Optimized.
The length of the DNA fragments will also determine the length of the cycles. Most polymerase sellers will includes steps to optimize the reaction depending on the quantity of DNA used, primer length and other parameters.
For more information:
Designing primers:
Taq DNA polymerase protocol example:
Optimizing PCR

PCR thermal profile, Deoxynucleoside Triphosphates and Primers are interesting paragraphs

Use primer3 to design your primers, then just use whatever protocol your lab usually used for PCR.
A high annealing temp solves many problems, and a good enough taq won't mind.
I successfully sanger sequenced thousands and thousands of mammalian exons, with primer3 designed primers, a HotStar Taq, and a 60 degree annealing temp.  Worked almost every time.
Obviously if you are doing long PCR, or working with a very high GC or low GC species, that might requires more optimizing.

According to my knowledge the main thing in annealing temperature in PCR
Primers annealing temperature should be selected by keeping in 5° less than the lower melting temperature of primers
Secondly MgCl2 working Concentration also plays a major role in PCR optimization

As you are probably aware there's a lot more to designing a PCR, as the previous answers have suggested.

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Phylogenetic tree with tagging
I'm working for a software company. For one of our projects, we need software to cluster nodes in a phylogenetic tree by a certain kind of similarity and give them a user-defined tag. Preferably, the tag would consist of two different values: a unique ID and a human-readable name. It would also be nice to set multiple tags for one or several nodes.
Some more in depth information:
We get sequenced data from a laboratory. The first thing the software has to do is an alignment. Based on the aligned data we need a phylogenetic tree. The software then has to give us the possibility to set one or more tags on one or more nodes. After the tagging, the data has to be exported from the software, so that we can give our clients enriched data.
Phylogenetic tree:

                                       ________ M.HpyFI.dna
                                      |
                                      |_______________ M2.HpyFXIII.dna
                                      |
                                      |___________ M.HpyFII.dna
                                      |
                                      |        ___ M.HpyFIII.dna
                                      |_______|
                                      |       |__________ M.HpyFIV.dna
                                      |
                                      |  ________________ M.HpyFVII.dna
                                      |_|
                                      | |__________ M.HpyFXII.dna
______________________________________|
                                      |____________ M.HpyFIX.dna
                                      |
                                      |    ________ M.HpyFVI.dna
                                      |___|
                                      |   |_________ M.HpyFVIII.dna
                                      |
                                      |_____________ M.HpyFORFX.dna
                                      |
                                      |   _________ M.HpyFV.dna
                                      |__|
                                      |  |____________ M.HpyFXI.dna
                                      |
                                      |____ M1.HpyFXIII.dna

Phylogenetic tree with tags:
This graphic shows what we want to achieve. Every node should get a tag. In the shown case, it could also be possible that all nodes would get a second tag of Citrobacter.

                     ________ M.HpyFI.dna
                    |
                    |_______________ M2.HpyFXIII.dna
                    |
                    |___________ M.HpyFII.dna
                    |
                    |        ___ M.HpyFIII.dna
                    |_______|
                    |       |__________ M.HpyFIV.dna
                    |
                    |  ________________ M.HpyFVII.dna
                    |_|
                    | |__________ M.HpyFXII.dna
____________________|
                    |____________ M.HpyFIX.dna
                    |
                    |    ________ M.HpyFVI.dna (Citrobacter koseri)
                    |___|
                    |   |_________ M.HpyFVIII.dna (Citrobacter koseri)
                    |
                    |_____________ M.HpyFORFX.dna (Citrobacter koseri)
                    |
                    |   _________ M.HpyFV.dna (Citrobacter freundii)
                    |__|
                    |  |____________ M.HpyFXI.dna (Citrobacter freundii)
                    |
                    |____ M1.HpyFXIII.dna (Citrobacter freundii)

Our company has already developed a software which fits our needs for the alignment and the phylogenetic tree, using the Biopython package.
The question is: is there already a software (preferably open source) which does everything that we want — align imported data and create a phylogenetic tree and tag and export data? Or do we need to improve our own software by adding the ability to tag?
I hope it is clear what we want to achieve and what we are searching for.
Edit:
The text above mainly explains what we have. How we implemented everything with Biopython isn't relevant to this question. I only posted it to show our workflow.
At the moment, our software is not able to place user-defined tags, as shown in the second phylogenetic tree. It is no problem for us to improve our software so that it can do the tagging. But, if a software which can align data, create a phylogenetic tree, add user-defined tags, and export the data, we would prefer to use this software instead of modifying our own.
As a possible hint, the software MEGA (http://www.megasoftware.net/) can align data and create a phylogenetic tree, but it doesn't allow for editing/adding tags.
I hope this question is now clearer.
In case you want to know, the algorithm we used to create the phylogenetic tree was Maximum Likelihood

It's not clear what you're searching for. Please clearly lay out what Biopython doesn't do that you still want to do. Please also be aware that questions regarding analytical methods, such as those related to bioinformatics or biological simulation, that do not ask explicitly about the underlying biology are considered off-topic. Please [edit] your post to address only your question relating to biology or delete it and visit another Stack Exchange site such as [so] for programming, [stats.se] for statistics, etc. You may also find Biostars helpful.

In case you might be interested, here are some python-based tools that include tree manipulation functions:
http://etetoolkit.org/
http://p4.nhm.ac.uk/


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Travelling with tissue samples in RNAlater
I've been in Brazil collecting some samples (ants) and need to travel back to to the UK with - I've got their brains stored in RNAlater, which have been in the freezer at -4C for a bit less than a month. On the Fisher Scientific website it says that they can be left at 37C for a day in solution before the RNA can begin to degrade. I've got a long journey home which could take up to 3 days in the heat (it's around 38C at the moment here) and involves stopping off through Morocco.
Has anyone travelled with samples in RNAlater like this before in elevated temperatures and got good results from their RNA extractions? Would you reccomend trying to source some dry ice for the journey?

Though I have not really tried it, I think that keeping the suspended tissues at 37⁰C for three days is not a good idea. You can try getting some ice from local shops and keep the samples in ice inside a thermocol box. IMO, the best option would be to courier your samples from Brazil to UK.


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Are Pond Algae Edible for Humans?
I've been farming freshwater fishes. After some time, i found some green algae grows there. When the algae dried, it looks like nori (which commonly used for sushi wrapping).
So, i wonder if those algae edible for human. Are the algae safe to eat?
Here's the picture:

Can you advise where you are at (not an address or anything, just what state/region/country something like that)?

I live in Indonesia

Don't risk it. However to me it looks like sort of  filamentous chlorophyta; still it is impossible to identify without microscopy.

If you really would like to eat it without causing you problem, your best chance would be to eat a very small amount first, get accustomed to it and gradually increase the amount you eat. Given that the pond is relatively clean :)

Looks like blanket weed (various green algae) to me.

If the fish dont, it not nutritious. Grow cress or nutritious species.

I came across a this Wikipedia page which said blue green algae from ponds can be used as dietary supplement (in tablet form).
Many other articles on the internet like  here suggest it is included in many diets in many places across the globe.
However, without proper regulation one can include a heavy metal contaminated vegetable to their diet which is detrimental to health. Furthermore cyanobacteria are known to produce toxic substances known as microcystins which can cause damage to human organs as well.
So unless you are certain of the biochemical balance of your pond I would  recommend not integrating it in your diet. Rather you can find commercially available ones which your local regulatory authority(s) recommend for dietary purposes.

First off: Don't risk it
I'm not an ecologist but I believe the type of algae you are holding tends to be cyanobacteria.
Cyanobacteria make all kinds of toxins, check the first table in this article.
Some cyanobacteria are eaten like Arthospira (commonly called spirulina) but I would not eat any random filamentous cyanobacteria. They also tend to be quite hard to digest so at best you will have increased your dietary fibre level and at worst ... well make sure your sanitary facilities have enough capacity.


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Why are H+ ions pumped out instead of in during cellular respiration
During cellular respiration in both mitochondria and aerobic prokaryotes, the Electron Transport Chain pumps H+ ions out of the matrix or cytoplasm to create a H+ concentration gradient. This forces the H+ ions back into the matrix or cytoplasm forcing ATP synthase into action.
I was wondering, however, why the H+ ions are pumped out of the matrix or cytoplasm, instead of into it. For aerobic prokaryotes, and the early mitochondria (which were prokaryotes living on their own) pumping the H+ ions out of the matrix or cytoplasm means pumping them into the outside world, a very uncontrolled environment. There is nothing to prevent the H+ ions from diffusing out, making the pumping completely inefficient, if not pointless. Wouldn't it make more sense to pump the H+ ions into the matrix or cytoplasm, where the H+ ions cannot diffuse, resulting in much higher efficiency?

But they aren't pumped out in the surroundings they are pumped between inner and outer membrane? Add some references about your statements

@KingBoomie the OP is talking about when mitochondria were still free living bacteria

Mitochondria pumps out the H+ perhaps just because there is no disadvantage of it. Once they've evolved such a machinery with complex network; they weren't threatened to evolve any opposite-system.
Any opposite system too; would not plausibly disadvantageous; and really happens in case of chloroplast; another sort of cell-organelle.

1: image from Plant Biochemistry, by Hans Walter Heldt, 3rd Edition.
2:  picture including all chloroplast membranes.

But if any organelle used cytosol as the H+ pool; probably that would made cytosol acidic as wel disrupt metabolic processes on cytosol. (usually the cytosol have very mildly alkaline pH.)

Reference: Plant Biochemistry by Hans Walter Heldt, 3rd Edition, Academic Press.

Probably someone can dig up an answer that answers this question, but I'll just repeat it here shortly:
You'll get the same gradient if you pump protons out or in. You're not specifically decreasing the outside pH when you pump protons, you're mainly increasing the inside pH. As long as there is a gradient that can be used to achieve other things for the cell, it doesn't fundamentally matter if protons want to flow in or out the cell, as long as they want to flow across the membrane.

If the protons would flow into the cell the pH would rise here, this could be a problem for the protiens present here

@RickBeeloo the reverse is also true, so your statement is not a valid argument.

but the reverse is happening in the mitochondria.... and we all still live so what do you mean? @LiuTianyi?

Because the proteins in the mitochondria have adapted for that reason? Evolution could very well occur such that proteins in the cell would be suited to work in low ph (ph decreases when protons flow into the cell, not rise) levels, which is the case for, eg lysosomes. You reject your hypothetical statement on the basis that it does not occur in the real world, exactly because it is hypothetical. That line of argument does not make sense. @RickBeeloo

Coult you cite you reference on "Because the proteins in the mitochondria have adapted for that reason"?

Here is my reference, good sir. but the reverse is happening in the mitochondria.... and we all still live

I mean a article on where to find that? You have a good point so I'm interested in why the evolution should prefer the adaption of the proteins in the matrix instead of inside the cell? @LiuTianyi . This Could be helpfull for the asker of this question.

That is exactly the point to discuss.  Why should "evolution prefer proteins adapt to basic environments over acidic environments". That answers the question. I did not add additional content on this topic. I merely said that this could be a problem for the protiens present here is not a valid reason, as the presense of proteins that adapt to high pH is inherently linked to the premise of "there is high pH in intracellular environments". I'm pointing out a logical fallacy, not a content fault. @RickBeeloo

I'll just post one more example in hopes of you understanding. Let's say chairs have 4 legs. "Why do chairs not have 3 legs?" "Because if they do, they wouldn't have 4 legs". The answer is part of the premise, it does not answer anything. If you need more explanation, feel free to discuss over chat. I'm not interested in discussing this question per se, but I feel obliged to explain why your point does not help OP.

I don't know if this is a proper answer... and this answer is really late... but if I remember correctly, the mitochondria pump H+ out to better compartmentalize the activities of the TCA and other oxygen-dependent metabolic processes within the mitochondria. This compartmentalization helps further minimize the possibility of a process or reaction to take place before the cell is ready. It also helps keep proteins that have closely related functions (as in they function in the same or complementary pathway) spatially close to each other.
Interestingly, prokaryotes have been observed to localize cellular activities as well. It is hypothesized that this occurs for the same or a similar reason as described above for eukaryotic cells, albeit it is likely less effective. This is accomplished through intracellular scaffolding of some kind of cytoskeleton. My guess is that prokaryotic cells can utilize this cytoskeleton to localize their proteins, but can't use it to localize H+ due to a lack of "binding" region (speculative).
Also, majority of prokaryotic organisms will pump the H+ into their periplasm (inter membranous space, not the "chaotic" external environment) as Rick Beeloo mentioned. This periplasm is a smaller environment than the cytoplasm and is more densely filled with proteins (and possibly others molecules) as well. I think the periplasm is more viscous as well - whether a result of solvent composition, high protein or other molecule concentration, or something else entirely, I'm not sure (relatively unfounded statement). Regardless, all these factors actually make it more difficult H+ molecules to diffuse away in the periplasm than in the cytoplasm.
Another argument against why the H+ must be pumped to the side opposite of the proteins is that ATP inhibits the TCA and other oxygen dependent metabolic processes. The ATP synthase creates ATP on the side that the H+ ion passively flows to. This causes feedback inhibition is much more temporally sensitive as ATP synthase synthesizes ATP on the same side as the proteins involved in ATP synthesis. I think that ATP synthase cannot produce ATP on the same side as the H+ ions because their is no energy to make the ATP with until the H+ ion has flowed down the concentration gradient across the membrane; by this I mean the energy used to create ATP can only be harnessed on the low-energy side of membrane (I'm guessing on this last sentence...).
As a result of these reasons and maybe more, I'm led to believe these are some reasons that it is advantageous to pump H+ ions out of the cell/mitochondria interior than in. Although 2 years late and by no means a definitive answer, I hope this adds some new perspectives or ideas to the discussion on why this process occurs as it does.

Can you add sources to your answer to allow other users to background read on your material. +1 for the elaborate answer.

Okay, I will work on that over time. It's been a while since I've gone through cell bio/biochemical engineering. It might take me a lot of time to pull stuff together, but I hope I can still find everything!

You don't have to add a zillion citations, but an image helps a lot and a few web-links here and there that back up your major claims and explain key terms would make a more satisfactory post and will give you your deserved #upvotes too. See the most upvoted answer above for example (not the best ever answer, but, well... better organized than yours for now :-).

I cannot completely vouch for how accurately my answer does answer your question. I will however try to explain the best that I can.
Here is a picture:

(source: els-cdn.com)
Firstly, in the electron transport chain the reactions that happen to metabolize the substrate are Redox reactions. As the complexes are oxidized by the release of electrons, protons are also released for counterbalancing. Statistically, the most effective route of ejection of the protons is through the H+ uniporters. There is a need for the protons to catalyze the reactions for synthesis of Hydrogen Sulfide which is required for stimulating the ATP synthase (you can check out the figure).
I am attaching some links which you can go through.
http://www.sciencedirect.com/science/article/pii/S1043661816304820 (This paper gives a detail overview of the H2S mechanism.
You can also go through this wiki article.
https://en.wikipedia.org/wiki/Electron_transport_chain
Hope I could clarify your question!
Thanks!


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How to determine whether changes of an allele's frequency are due to genetic drift or selection?
Given that both natural/artifical selection and genetic drift are evolutionary mechanisms that influence how allele frequencies shift in a population:
Are there ways to determine whether a frequency shift for a specific gene/allele is due to genetic drift or selection? In other words: when we see an allele take over a population, is there a way to know whether it was selected or just 'got lucky'?
UPDATE: since apparently this issue is quite complex in experimental biology I want to clarify why I'm asking this and what I hope to learn.
I'm looking for a 'theoretical way' of determining whether the changes in allele frequencies in subsequent generations are the product of selection or mere drift.
I'm applying a genetic algorithm to the optimisation of websites, where each gene determines an aspect of the user experience of that website. The question is whether the alleles I see emerging in the fittest solutions (= the best user experience, rated by visitors) got there by chance or actually contribute to the fitness of the candidate solution (= make a difference in shaping the user experience).

Is there a way to disentangle selection from drift
Yes, there are actually many ways...so many so different ways that it is impossible to correctly answer this question. Hopefully, below answer will give you some appreciation of why there is such a diversity of methods and wil give you sources to further your knowledge on the question.
It depends upon the data you have
The answer very much depends on the data you have in mind. Are you looking at a

panmictic population
a structured population
are you comparing a large number of lineages along a phylogeny
do you have information about a proxy for fitness in this population
can you perform an evolution experiment (depends a lot on the generation time)
do you have genetic data that are temporally separated
...

Also, what type of selection are you thinking of?

balancing selection
Are you trying to find epistasis for selection
Are you looking at some form of balancing selection
Local selection
...

Also depends upon whether you have data about potentially correlated variables such as

phenotypic data
ecological data

There are tens (or even hundreds of methods esp. when having data about related lineages) under each bullet point above, so your question is definitely quite broad.
Source of information
Statistical tests that test to the null that there is no selection are often called "test of selective neutrality". You might want to read Nielsen 2001  and Nielsen 2005 to get an overview of tests of selective neutrality in panmictic populations.
You might want to have a look at this answer, this answer and especially this answer.
What does it take to understand the methods for disentangling selection from drift?
Understanding the tests of selective neutrality can be a bit demanding as it requires having good knowledge in classical statistics, bayesian statistics, MCMC, Approximate Bayesian Computation and even machine learning algorithms. It also requires good knowledge in population genetics (typically incl. coalescent theory) and statistical phylogenetic.
A specific example
Unfortunately, I can't think of any specific example of a test which is really easy to grasp without a priori knowledge. A classical, not too hard and historically example test for neutrality in panmictic population is the used of Tajima's D (which derivation require basic knowledge in branching processes). You might want to learn about it to have a specific example. I recommend Gillespie's book Population Genetics: A Concise Guide to learn about this test. More book recommendation can be found here.

I'm looking for a 'theoretical way' of determining whether the changes in allele frequencies in subsequent generations are the product of selection or mere drift. I'm applying this to the behaviour I see in applying a genetic algorithm where each gene determines an aspect of the user experience of a website. The question is whether the alleles I see emerging in the fittest solutions got there by chance or actually contribute to the fitness of the candidate solution. I probably should have clarified this in my question but didn't because I didn't realise the complexity of this issue.

I would suggest that you open a new post for this more specific question. Don't forget to clearly define your algorithm model. A priori, if I were you, as a first step, I would examine the site frequency spectrum and perform a Tajima's D test.


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Fruit identification
On the way from school to home, I came across this strange looking fruit that looks similar to a potato and it grows on a tree. Can you identify it?

Where is this image taken?

it looks like medlar. Medlar is a fruit sized about 4cm (1 1/2 inch). it must be common medlar.

You can find out more about this interesting fruit here at Wikipedia.

The medlar was already being cultivated about three thousand years ago in the Caspian Sea region of northern Iran and Azerbaijan. It was introduced to Greece around 700 BC, and to Rome about 200 BC. It was an important fruit plant during Roman and medieval times. By the 17th and 18th centuries, however, it had been superseded by other fruits, and is little cultivated today.

Looks like that to me too. +1. Don't know exactly why you got a down vote. Don't think this correct answer deserved it. Perhaps because it is heavily link-dependent, and link rot can destroy it? I'll edit the picture in for you.

first answered "it looks like medlar but dont sure about details i dont even touched before" i was trying to say "i saw multiple times but never look that close" i guess first answer deserved that down vote. edited and added wikipedia image link because of that down vote :) there is also another fruit called japanese medlar or loquat but it is in different genus. and there is a nice coincidence have to tell, yesterday went to grocery for buying some potatoes and saw medlar went back to home and after surfing little bit saw question when just asked. and i hardly remembered what was its name :)


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What is the actual size of a nucleotide?
I found in this website that the dimension of a nucleotide is 0.34 nm. Is there any experimental paper confirming this statement?

This site might be able to help you: https://en.m.wikipedia.org/wiki/Molecular_Structure_of_Nucleic_Acids:_A_Structure_for_Deoxyribose_Nucleic_Acid.  If you are collecting facts at Yahoo Answers, why not ask the people who posted there where they got their numbers?

What exactly do you mean by dimension? The molecule is not circular; do you mean the longest dimension? or the van der Waals radius?

I know it is not circular, rather a flattish molecule with different conformations; but a sphere is still a good approximation. Van der Waals is probably the best measure.

If you want experimental papers, we should be precise about what we're measuring. "The dimension of a nucleotide" is rather imprecise, as a nucleotide is a rather oblong, knobbly thing.
0.34 nm is a relevant measurement related to nucleotides, but it's specifically the distance between consecutive bases in a standard B-form DNA helix - that is, what's the spacing between the "rungs" on a DNA ladder.
This measurement can be confirmed by several experiments, primarily those involving X-ray or neutron crystallography or scattering. For example, both the Wilkins and Franklin papers that were published back-to-back with the famous Watson & Crick DNA structure paper referrence the strong 0.34 nm reflections from X-ray fiber diffraction which Watson & Crick reference as the spacing of the bases in their model of DNA structure. Other papers have confirmed the measurement. This 1983 Biomed Biochim Acta paper uses wide-angle X-ray scattering to find it. Additionally, there are a large number of structures in the Protein Databank which contain DNA structures - these have been determined by a number of different approaches (X-ray crystallography, neutron diffraction, NMR, electron microscopy, etc.) and all of which are consistent with the 0.34 nm average spacing of base pairs. (Modulo minor structure-to-structure variations.)

this is for a polymer of nucleotides, how big is an individual nucleotide though?

It's for an individual nucleotide within a polymer, yes. But if that doesn't work for you, how do you want to measure it? As mentioned, a nucleotide is a rather oblong knobbly thing - the size depends on which direction you're measuring it in. Additionally, molecules don't have well-defined surfaces, being made mostly of electron clouds. There's conventions for the standard surface, but if you want experimental references, you have to specify an experimentally measurable distance.


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where does genetic material for antibody production come from?
All antibodies are proteins and like every other protein, mRNA codes for them. So acquired immunity, is acquired, which means that information was not previously present in our DNA before exposure to the pathogens.
So my question is, does our DNA in some way get modified or something else? Where does the new genetic material come from?

Does our DNA in some way get modified or something else?

Yes. The DNA gets modified. VDJ recombination and somatic hypermutation are the mechanisms by which this happens.
You can find an entire book chapter/review on these topics. So I shall not elaborate further.

thank you ... i don't mean to delve further into this I just wanted to know the broad concept . thanks a lot


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Identification of Bioluminescent Species in South Carolina Marshlands
I was in the brackish marshlands in South Carolina and the water was lit with short flashes of greenish bioluminescent light from a species that seemed to be floating in the current.  The lights seemed to be associated with a crackling noise as well but I'm not 100% sure that the light and sound were related as there were so many flashes going off at a given.
When I turned a flashlight on I saw some quarter inch long bugs moving in the water but the light was too bright to confirm that the bioluminescent light was coming from those bugs.

Do you have a picture?

Quarter of an inch is quite large but it sounds like bioluminescent plankton. All lumped together by their behavior when we call them "plankton", there is tremendous variety of species of these animals and plants. Unfortunately, I think it might be impossible to identify which species you observed without a clear photograph or a microscopic image from a sample taken.

We tried to take a movie but it didn't come out.   The lights were just short flashes and a ton of them in the water, but they were spaced out fairly well. The plankton idea is probably correct we were thinking small pistol shrimp (Alpheidae) given the sound, but the light the cavitation produces is not supposed to be visible.

Confirmed by a number of locals later on to be a small species of pistol shrimp. It was a pretty cool phenomenon.  Thanks for the help here.


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Cough at 1000 km/h?
How fast does air move in the airways during a cough?
The following passage is from Talley and O'Connor's Clinical examination: a systematic guide to physical diagnosis (emphasis mine):

Cough is a common presenting respiratory symptom. It occurs when deep inspiration is followed by explosive expiration. Flow rates of air in the trachea approach the speed of sound during a forceful cough. Coughing enables the airways to be cleared of secretions and foreign bodies.

The speed of sound claim is unreferenced. I have found mention of coughs approaching the speed of sound in numerous popular sources (e.g. here, here, here (where it says 1000 km/h), and here), and innumerous books (e.g. here, here, here, here, here, and here); none of these references the claim. The same claim is also here. This book has a more exact (unreferenced!) claim:

Velocities as great as 28 000 cm/s (85% of the speed of sound) have been reported, but it is impossible to determine the gas velocity at points of airway constriction, where the greatest shearing forces will be developed. During this phase there is dynamic collapse in the bronchial tree, with large pressure gradients across the collapsed segment.

That speed is just over 1000 km/h. When I have searched for research literature behind this, I've only found much lower velocities at the mouth (rather than at a narrower location like the glottis), e.g. a peak cough velocity of 22m/s, also 11.2m/s, and 28.8m/s. The closest to a reference I found was this book with the following:

A cough comprises: ... sudden opening of the glottis, causing air to explode outwards at up to 500 mph or 85% of the speed of sound (Irwin et al, 1998), shearing secretions off the airway walls.

Irwin et al isn't primary literature either, and references Comroe JH, Jr. Special acts involving breathing. In: Physiology
of respiration: an introductory text. 2nd ed. Chicago:
Year Book Medical Publishers, 1974; 230-31. I don't have access to this book (does anyone here?), but I expect the references only continue from there.

My question is this: how fast is a cough in the airways (I am interested because such an explosive rush of air could explain the substantial damage seen in chronic cough), and does anyone know where the 1000 km/h claim comes from, or can point me to a legitimate reference?

If you are asking about whether a claim is correct/or not and where it comes from, you might receive more feedback on the skeptics stackexchange.

Perhaps. I'm not a skeptic though, I'm sure the claim is probably true; I would just be interested to find a reference for it so I can see how it was measured. I thought it would be more relevant on biology.SE.

This reference from CHEST lists 21 clinically measured peak flow rates during various modes of coughing. Of these patients, and for unassisted cough, the highest peak flow is about 4 liters/sec. The human trachea ranges from 13 to 27 mm diameter. The relationship between velocity, $V$ and flow $Q$ is
$$ V=\frac{Q}{A}$$
Assume the 4 liters/sec = 4000 cm^3/sec and minimum diameter, 13 mm = 1.3 cm, the cross section area being
$$A = \pi (D/2)^2 = 1.3 cm^2$$
Plugging in
$$ V=\frac{4000}{1.3} = 3077 cm/sec$$
which is a far cry from 28,000 cm/sec, so at this point I'm skeptical.
Things to consider is that the data taken in the paper was from sick humans so perhaps a healthy (and athletic) person may be able to exert much higher flow rates. But then healthy people generally are not stimulated to cough as much as a sick person with an airway compromised by sputum.
Although lower airways do have smaller diameters, the flow measured at the trachea is divided among them, so you wouldn't expect to see peak velocities in the lower airways, but rather the accumulation in the trachea.

Nice answer +1. I did a similar calculation to you, but I thought perhaps using that size for the trachea wasn't legitimate; a cough begins with a closed glottis, so in principle the airflow in the first moments is through a very narrow opening between the vocal folds and so in principle the flow rate could be higher. The flows in your paper are at the mouth which would potentially lead to a slower pickup in velocity at the beginning (if the actual speed were actually near the speed of sound which is the maximum speed that an impulse can be transmitted in air). I agree about smaller airways.


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Are there any photosynthetic catalysts in use other than chlorophyll?
When I search for catalysts other than chlorophyll on Google, I only get references to artificial photosynthesis. When I look up photosynthesis, I see accessory pigments mentioned, but it appears that the chlorophyll family is crucial.
These chlorophyll variants all have the chlorin (not to be confused with chlorine) ring in common.
Are there any photosynthetic organisms that do not use a chlorin derivative? Why is chlorin so predominant?

There are photosynthetic organisms that use retinal-rhodopsin complex. However, the mechanism of photosynthesis is different in these organisms than those that employ chlorophyll dependent photosystems. In these organisms, the light causes the rhodopsin-like membrane proteins to pump proton out of the cell and create a proton gradient which in turn is used by the ATP synthase to make ATP.
See this post too Why are there no known photosynthetic archaea?
This mechanism of "photosynthesis" is not as efficient as the chlorophyll dependent one (page 22, Baltscheffsky, 1997†). Moreover, it does not produce NADPH.

† Baltscheffsky, Herrick. Origin and evolution of biological energy conversion. New York etc: VCH, 1996. Print. ISBN: 978-0-471-18581-9

What is the efficiency of that process, compared to chlorophyll photosynthesis?

I think you would do better to ask that as a separate question, rather than commenting on a four-year old answer.

I would say even photolyase counts since it uses light to change chemical bonds in DNA repair.


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What is the meaning of Dimer Catastrophe?
What is the meaning of Dimer Catastrophe?  I still don't understand it even I've already read the paper about it.  Here's the link to the paper origin NCBI

A "plasmid dimer" is defined as a plasmid that has two origins of replication instead of the usual one origin of replication. This can happen if two copies of the same dimer undergo recombination resulting in one plasmid with two origins and one with zero. I hadn't seen this term before, but it seems to be the meaning with which it's used in this paper and a few others I saw.
The "dimer catastrophe" hypothesized in this paper refers to the idea that over time this would lead to a reduction in overall plasmid copy number (and thus an increased probability of plasmid loss), since dimers may be more likely to replicate than monomers (due to having more origins of replication).
For what it's worth, I also found the paper you linked a bit hard to understand, but I found this one more explanatory (your mileage may vary): Multicopy plasmid stability: Revisiting the dimer catastrophe.


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Has anyone tried using luminescent conjugated oligothiophenes to detect cellulose in a microbial biomass? If so is it accurate?
I recently found this paper http://www.nature.com/articles/srep35578 which describes a "new" method for detecting cellulose. As I'm not an expert in the field I was wondering if other people have used this to detect cellulose in microbial biomass (specifically E. coli biofilm) and not just plants. It seems like it should work but maybe I'm missing something.


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Is the whole MHC haplotype expressed and so their proteins are exhibited on each nucleated cell membrane?
Am I correct if I guess the following (?):
If we inherit both maternal and paternal MHC haplotypes, the functional (non-pseudo)genes are expressed and all of their products (MHC molecules) are exhibited on the cytoplasmic membrane of any nucleated cell.
In case of MHC type I molecules our all nucleated cells bear one (or more? how many?) types of polypeptide(s) (corresponding to and) encoded by the inherited allels of each of A, B, C, E, F, G MHC-I genes.
In other words each nucleated cell expresses all MHC type I molecules encoded by our inherited MHC haplotype.
Is it true?
Thank you.


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What properties (if any) do AT rich regions of DNA have?
I was looking up the fluorescent stain DAPI and seeing that it
binds strongly to A-T rich regions in DNA.

That made me wonder what is special about AT-rich regions.

In bacteria AT-rich regions are usually binding sites for initiation of replication proteins.

I edited your title as "traditional" didn't make sense. Not clear what you actually meant, but I think question works ok without it.

With regards to DAPI itself, one could tell that the molecule itself has a shape complementary to the shape of A-T rich DNA. So in this case it's "special" because DAPI happens to have the structure to form bonds to A-T rich DNA regions. (There can very well be another organic molecule that binds to C-G rich regions). A quick google search will show how it looks like

With regards to A-T in general, A-T share 2 hydrogen-bonds. However, this is not the reason why it's easier to break A-T rich regions. A-T rich regions destabilize the DNA double-helix. Refer to this http://nar.oxfordjournals.org/content/34/2/564.long. Transcription initiation occurs near T-A rich regions, e.g. TATA box in eukaryotes and Pribnow box in prokaryotes.


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How does the composition of blood cell types in human blood change during our lifetimes?
I was reading the paper Age-related accrual of methylomic variability is linked to fundamental ageing mechanisms.
There they do additional checks to see that their results are not due to differing cell type composition in blood that happens as we age.
That made me wonder, how does the cell type composition of our blood change as we age? Is it known? (I guess we would get less hematopoietic stem cells, but I do not think they are in the blood themselves.)


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Rate-determining steps in enzyme catalysed reactions
According to my chemistry book, there are 3 simplified steps within an enzyme catalysed reaction:

S + E → ES
ES → EP
EP → E + P

Where S is substrate, E is enzyme, ES is enzyme substrate complex, EP is enzyme product complex and P is product.
It is my understanding that at first, when substrate concentration is low the rate determining step is step 1, as this is the slowest step in the mechanism.
When you increase substrate concentration to a certain level, where there are no free enzymes remaining to bond with them, adding more substrate will not make the reaction faster, so the order has become 0 with respect to substrate conc.
Is the rate determining step now 2 or 3? I thought it would be 3 as that is the step that frees up more enzymes which could go on to catalyse more reactions. My book says that it is step 2, as "it depends on how fast the ES can convert into EP". But surely this step won't free up more enzymes to catalyse reaction further?
Is the book correct? Can anyone help me understand this?

This is enzyme and substrate concentration specific, since the reaction rate depends on the reaction rate constant k that depends on the enzyme. However if there is a large amount of P present in the solution the EP -> E + P reaction slows down so this can be the rate determining step. On the other hand if you dynamically remove the P molecules from the system the ES->EP can be the rate determining step.

Is it enzyme specific, or is it related to the amount of P in solution? Your first sentence and the second two seem to be be giving two separate answers. -- FWIW, I agree with the answer of "enzyme specific". Even in the absence of appreciable amounts of product there are enzymes which have a slow off rate of product release, and it's this product release which is the rate limiting step.

@R.M. You are right, my explanation was poorly constructed. I wanted to say that it is both enzyme specific and depends on the concentration since the reaction speed depends on a k constant and on the concentrations of the reactants. This constant depends on the enzyme.

You can (and should) edit your answers to add additional information and to clarify things that might be confusing. (Edits are not just for typo correction.) Just click the "edit" link in the bottom left of your answer.


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Are MHC Proteins the Most Polymorphic Human Proteins Known?
There is a paragraph titled "MHC Proteins Are the Most Polymorphic Human Proteins Known" in the "Molecular Biology of the Cell" by Alberts et al. 6th ed. 2014.
But someone has recently told me that it is not the case making an example of a set of genes helping to identify persons in forensic medicine. (I didn't remember the genes.) Is it true?
Are MHC proteins the most polymorphic human proteins known?

In addition to the excellent answer given by @Amory, it might be of interest for you that this not only applies to modern humans but also appears to be true for archaic humans (Neandertal and Denisova), even though the latter had far lower overall genetic diversity.

I don't think the markers used in forensic DNA fingerprinting code for proteins.

Are we restricting things to germ-line polymorphism, or is there some other reason to exclude immunoglobulins?

@AlexDeLarge: you mean MHC locus was also diverse in the archaic humans? Thank you for your comment.

@swbarnes2: primarily the emphasis was on genes.

@stan: Yes, looking at archaic genomes one also finds MHC genes to be among genes with highest diversity.

Yes.  There are many MHC (MHC in humans is called HLA) genes.  The classical loci — Class I A, B, and C, and Class II DP, DQ, and DR — are the most polymorphic.
Here's a table from a 2002 article which clearly shows the number of polymorphisms.  It's no contest.

It's worth me pointing out that those numbers are wildly out of date.  The IPD-IMGT/HLA can provide full lists of known HLA alleles, but the exact numbers are in the tens of thousands:

The person you spoke with was probably referring to sequences called microsatellites.  These are small regions that are polymorphic and quite variable between individuals, and using a number of these together can be useful for genetic fingerprinting, but each individual microsatellite will not be as polymorphic as HLA class I A, for example.


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Evolutionary Midways
Given that the mechanism of natural selection is sensitive, how do species survive in an evolutionary midway? The ability to breath in air requires complex protein systems. An animal that is developing these organs would not be able to utilize its function until it fully evolves. While it doesn't, wouldn't the wasted resources used in growing half-developed lungs be.. wasted? Or is all evolution continuous?

I have this very question in my mind as I take H2 biology. It is not from homework.

It is a common question
Statements of the kind "Evolution is impossible because of intermediate state" are common from religious extremists literature. There is therefore a lot of resource online that already debunk this type of statement but I guess, I'll just quickly write one more! Of course, I am not suggesting that you are taking an opinion-based position, you might well be genuily seeking for an understanding of the world.

Quickly speaking there are a series of concepts that are necessary to understand in order to answer this question.
Fitness landscape and fitness valley
The term "evolutionary midways" is not used in biology but one can rephrase it with the concept of fitness landscape and fitness valley.

Fitness landscape

The fitness landscape is the function that maps fitness (generally represented in y-axis) to phenotypic trait value (typically multi-dimensional but often represented on a single axis for simplicity). Fitness landscape may also refer to the mapping from genotype to fitness but we will not be concerned with that for this answer.

Fitness valley

A fitness valley refers to a region of low fitness on the fitness landscape. The movement from one locally high fitness state to another locally high fitness peak might well get through a region of low fitness. This is what you call fitness valley and on the fitness landscape and this is what you are interested in.

Is there always a fitness valley?
Let's first consider reasons for which a population might not experience such fitness valley

Logical Fallacy: Argument to ignorance

It is common for a layman to assume that intermediate states ought to be associated with low fitness. In reality the intermediate states might well be neutral or only slightly deleterious (and therefore be mainly affect by genetic drift) or might even be directly beneficial. It appears to be a mistake to assume such fitness valley are more common than they are in reality just because you fail to imagine how a trait may have evolved. In philosophy of logic, this is called an argument to ignorance. Of course, fitness valleys do exist. So, when they exist, do populations ever manage to get over them?

Assuming there is a fitness valley (for a given trait), can populations just "jump over it"?

Do populations need to get through an intermediate state?

Darwin framed his theory into the idea that evolution is a very gradual process. As we know today, this is far from being true. Evolution can actually occur through a big steps. There are single mutations that double the amount of genetic material, there are single mutations that completely affect the physiology or anatomy of an individual. There are cases of horizontal gene transfer (transfer of genetic material between species) as well that can cause sudden important change without having to get through intermediate stages. It is sometimes wrong to assume that there must be intermediate steps.

If there is a fitness valley and the population will not "jump over it"...
Let's assume a fitness valley (for a given trait, for a given population) and let's assume that the population will not "jump over it" thanks to a mutation of big effect.

Shifting Balance Theory

There are a number of different forces that affect evolutionary processes. Layman often think of natural selection as being the only force causing evolution but this is wrong. Genetic drift is another very important process that affect evolutionary process. Genetic drift refers to the random sampling of individual at one generation to build up the successive generation. The relative importance of drift to natural selection in driving evolution of a population depends on the effective population size. Have a look at Why is the strength of genetic drift inversely proportional to the population size?. Genetic drift can typically randomly yield a population toward a fitness valley, from which natural selection will yield the population to either come back or start climbing the opposite fitness peak. This concept is called shifting balance theory. There has been a lot of work on shifting balance theory suggesting that it well be much more common than previously thought.

Phenotypic flexibility

One may wrongly assumed that if a mutation occurs to make, say, a bone a big longer, then one organism would simultaneously need mutations that would make muscles, nerves and other tissues longer accordingly. In reality our developmental process is very flexible to an environmental change or to a mutational change. This flexibility is very much used in medicine and agriculture. If a bone gets a bit longer, muscle might just stretch a little more and end up developing in accordance to the new mutation. It would therefore be wrong to assume that because we are made of a complex interaction of traits, that a mutation cannot bring anything that would not be beneficial. If you are interested in the evolution of complex system you might want to have a look at the post How did the cardiovascular system evolve? for example.

Source of information
I would recommend that you have a look at a very short and introductory course to evolutionary biology such as Understanding Evolution by UC Berkeley for example and you will be able to understand much more about what evolution is and how it occurs.

https://en.wikipedia.org/wiki/Irreducible_complexity Seems to be what I was writing about. (Just found this out). Thanks for your answer too.

No, I am not at all writing about Irreducible Complexity. Irreducible Complexity has nothing to do with science. It is a fallacy (or set of fallacies) build by creationists. As the wikipedia article you link says: Irreducible complexity [..] is rejected by the scientific community, which regards intelligent design as pseudoscience. If your aim is to learn about evolution, I would recommend reading from the popular science literature (and not pseudo-science and other sources of unjustified arguments). There are many good sources of knowledge, one of them being linked in the post.

Yes you weren't writing about it but I was asking about it. I had thought that complex systems are irreducible, therefore midways are impossible. But I was wrong.


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Why cannot machines use energy stored in a way similar to biological systems' energy storage?
Owing to the generality of the question I am interested merely in key problems so that I could do further reading.
As I understand man-made energy storages are significantly less efficient than biological ones. I would like to focus on quickly available energy for small systems (human scale or smaller) - after all we can say that hoards of coal are a pretty nice energy reservoir.
For example, a robotic bee:
https://www.youtube.com/watch?v=lJCMIsLuGpg
What can we see here? A wire - and I think we cannot expect to have a long lasting independent robotic bee with the current technology due to inefficiency of our energy storage.
How do biological systems store the energy then? https://en.wikiversity.org/wiki/Energy_Storage_in_Biological_Systems

Living organisms use two major types of energy storage. Energy-rich
  molecules such as glycogen and triglycerides store energy in the form
  of covalent chemical bonds. Cells synthesize such molecules and store
  them for later release of the energy. The second major form of
  biological energy storage is electrochemical and takes the form of
  gradients of charged ions across cell membranes. This learning project
  allows participants to explore some of the details of energy storage
  molecules and biological energy storage that involves ion gradients
  across cell membranes.

To be more specific let me give an example: why cannot we have a machine that would have an input for carbohydrates, a converter to say glucose and then ATP which would finally break down and release the needed energy?
Why is it not viable? Do we lack technology to do this? Which step is problematic? Are we far from having biological-like storages?

We built it. It's called the methane fuel cell. It can run in reverse.

The activation energy of breaking these covalent bonds is high. Biological systems use phosphorylases to couple ATP to glycogen such that the high energy phosphate bonds then supply some of their energy to break the covalent glycosidic bonds in glycogen
So problem 1, high activation energy.
Secondly, how are you going to store the energy in the machine? Conventional electrochemical cells use something like what was written about membrane potential. Their energy is accessible as it is in a form of an electrical potential. When you expend energy to break storage molecules into glucose, there's not much for you to do on the glucose other than to burn it. Burning it is extremely inefficient and makes up a huge amount of energy loss to wasted heat. The other way would be to oxidize it. You'll need something to accept the electrons (NADH and FADH in biological systems), something to overcome the high activation energy of oxidizing the bonds at every stage (more ATP coupling), something to harness the high-energy electrons from glucose (electron transport chain/chemiosmosis). In all, it is too complicated to be replicated efficiently.
So problem 2, there are many complicated steps involved.
This is why only simpler versions of the above exist. Power to gas shows us the splitting of H2O into H2 and O2. This is akin to only one stage of bond-breakage in respiration, and is simple enough to carry out (through electrolysis). H2O donates and another H2O accepts the electron. Energy is supplied as a electrical potential in the circuit instead of ATP coupling from enzymes.
Last problem is, there really isn't a need to store energy in other forms than an already-existing energy storage molecule. Most of our energy storage is in the form of carbon compounds, and electricity. Carbon compounds are high energy density, and electricity is easy to manipulate. It is perhaps trivial to the world to attempt condensing table sugar (glucose) into starch. It is not efficient enough to be impactful. Biological systems need to do this because storage is on a scale comparable to the cell body, and directly relates to survival. High blood glucose in animals might lead to hyperglycemia, triose phosphate (product of respiration) is used for lipid formation and in turn building of cell membranes, glucose molecules are used as monomers in the production of cellulose, aka cell wall in plants, (a heck ton of other metabolic pathways exist), etc.
This link shows us the different ways of energy storage in our world. We're not limited by biological constraints, so even compressing H2 into a liquid, will be more efficient than interconverting that into other forms of chemical energy, if you're talking about for pure "storage"'s sake.
I highly recommend reading up on photosynthesis, to see how biological systems harness energy from the sun, and store that into covalent bonds between CO2 molecules. More specifically you can look up Krebs Cycle.

Yes. Gibbs free energy when it comes to spontaneity of the reaction. Thank you for your clarification. The "high energy" bond was referring to the high energy electrons shuttled by the reduced coenzymes as they travel down the ETC. Probably bad phrasing.

The OP's question is a bit broad and vague, so let's focus on his example, an insect. Bees (let alone butterflies) can fly miles with the chemical energy stored in their bodies. Why can't small mechanical flying objects? The reason is clearly not storage (as opposed to what the OP's title suggests); we can store sugar and fat perfectly well. But using it for mechanical work as efficiently as a biological system does seems impossible for now; we tend to explode and burn stuff, which is terrible.


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What properties of DNA and Chromosones do birds have?
What properties of DNA and Chromosones do birds have? How many chromosones do males and females have? Are the nucleotides the same (CGAT)?
There are a lot of different kinds of birds. Maybe the DNA varies a lot among them, so I want to specify: Fowls (gamefowl/landfowl/waterfowl).

Yes. Birds do have DNA. I don't understand what you mean by the type. If you mean by geometry, I suppose they should be having all 3 A, B, Z- DNA. Chromosome number varies with species. 'Birds' is a class of animals with many many species.. so ya - you can't generalize. Sex determination also varies. Since you ask for the fowl - males are homogametic - ZZ and females are heterogametic with ZW. So in a way, it is opposite to that in humans. I don't understand why you expect birds to be that different

-1, the most basic search will confirm that birds, and indeed all life above eukaryotes, have genomes encoded by DNA.

@Michael_A Which is why I asked "what kind of DNA"---and specified the properties I'm interested in, instead of asking "do they have DNA at all?".

Then, what are the 'kinds' of DNA u r looking for?

@DrZ214, My comment is specific to these two questions. Is it really DNA, or rather RNA, or something else? Are the nucleotides the same (CGAT)? You have posed 4 questions which confuses the issue. Polisetty's question is a good one, I also don't understand what you mean by kind of DNA.

@Polisetty I specified in the OP: chromosones, nucleotides, and DNA or RNA. Those 3 things are what I mean by "kind".

Then everthing is the same. Just chromosome number varies

@DrZ214 Not to be offensive, but knowledge about DNA is probably one of the most basic things when it comes to biology. Exactly because it is basic, it is also easy to find on the internet, e.g. Wikipedia page on DNA. DNA is not RNA. DNA and RNA are made up of nucleotides. Chromosomes are condensed DNA packaged by histones and scaffolding proteins. You have contradicted your own question by listing those "kinds" of DNA. DNA has probably only two qualifiers: linear/circular, single-stranded/double-stranded.

@LiuTianyi I made some edits.

The class "Aves" fall under the kingdom Animalia. Therefore, they are multicellular eukaryotic organisms. Being eukaryotes, their genetic information is encoded in linear double stranded DNA.
What is their chromosome number? Fowls (gallus Domesticus) have approximately 36. It varies from bird species to bird species as much as it does from humans (46) to gorrilas (48). Chickens have 78, and so on.
The genetic code is universal. It is used by virtually all known organisms, save some very specific outliers.


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How is the site of administration of a vaccine decided?
Vaccines can either be given intramuscular or subcutaneous or intradermal. I know the technique used is specific for each organism. What decides this?
I understand the reason for oral vaccines in polio but, why should a vaccine that is given s/c not be given im?
If there is a logic to this (which I am sure there is), it would be a lot easier to remember the same.

When the effectiveness of subcutaneous is comparable to intramuscular, then the choice is made based on the degree of discomfort and adverse reactions.
In many situations intramuscular will outperform subcutaneous delivery due to subcutaneous fat having poor vascularity which may result in slow mobilisation and processing of antigen(source).
Disclosure: I am not a biologist so this is outside my field of expertise.


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MS/MS for complex samples
I saw this figure in this atricle:

It's a really nice representation of what happens when using MS/MS. However I was wondering how this works when there are more proteins present in the gel spot. How would you be able to select the parent ion(because there are multiple of them)?

Liquid chromatography (LC) allows the peptides from a complex sample to be fed into the mass spectrometer over time. The bottom half of the image shows an MS spectrum from a single precursor scan and the machine is programmed to select the three most intense peaks (parent ions or precursor ions) from this scan for MS/MS (MS2).

This process is repeated throughout the LC-MS/MS run and programs usually include exclusion criteria where a parent ion is ignored for 30 - 90 seconds once it has been scanned 1 - 2 times. Usually the machine will also ignore singly charged parent ions as many of these ions will be inorganic contaminants and you want the machine to be busy with peptides.
Efficient use of machine time is critical to getting good coverage of the proteins in the sample. Proteins that are small create fewer peptides that are amenable to sequencing so these can be missed. Also those proteins that are less abundant may produce peptides that stay below the selection criteria. Good chromatography and efficient use of machine time are critical to getting good results and even in good conditions most peptides will not be subjected to MS2 sequencing. This estimates that of 100 000 peptides with only 16% were 'sequenced'. This explains why proteomics labs are speed freaks, and has driven the development of faster machines. The ~ 1 hour yeast proteome paper demonstrates the 'work' that the newer machines can get through;

Over a 1.3 h chromatographic method .... collected an average of 13,447 MS1 and 80,460 MS2 scans (per run) to produce 43,400 peptide spectral matches and 34,255 peptides with unique amino acid sequences (1% false discovery rate (FDR)).

Thankyou! One thing isn't clear for me, from the MS spectra 3 peaks were selected(for peptide fragmentation). But how are the parent peaks detected? e.g. how could the program "know" if a peak is a parent ion peak or not? Because in the spectra (bottom right) all the peaks (from three peptides) are mixed up.

Precursors are selected for MS2 based on their intensity, the three in the image are the three tallest (most intense) peaks. The machine switches between MS1 where the precursors are screened and MS2 where mass filters close to the source (entrance to machine) only allow precursors within the precursor window to continue to the fragmentation and measurement sections of the machine.

So the precursors are selected based on their intensity and if they "match" the mass of the input (which makes sense to me because they only differ by one H atom)? @Michael_A

I'm not able to find information about the determination of the input mass you mentioned. Can you please add some information about the determination of these parent ion peaks, that would be great!

No shotgun sequencing relies on collecting the most abundant precursors that are in the machine at any given time. This bit is not true for shotgun sequencing; and if they "match" the mass of the input (which makes sense to me because they only differ by one H atom)? The bracketed portion is only true of singly-charged precursor ions. I said mass filters in my previous comment but it is really an m/z filter. If you can quote where I mention "determination of the input mass" as I can't see where you got that from but I clearly need to improve my answer so it's clearer.

Sorry I didn't meant you said that specifically it was about "mass filters close to the source (entrance to machine)" However it would be great indeed if you improve your answer on how the three precursors ions are selected @Michael_A

The precursors are selected for MS2 because they are the most intense, this is a programmatic consideration. I assume you have understood this so it's not the how that you mean? The question of "How do MS allow molecules of a specific m/z to pass to the next part of the machine?" is physics which doesn't belong in SE biology. If you don't understand the physics you need to accept that the machine can do what we say it does. This guy does a great job explaining how quadripoles select a specific m/z window.

Thankyou for the link! What I mean is I see one large peak (the middle precursor peak), in my opinion the left precursor peak could just be a fragment of that middle precursor peak? @Michael_A

No, that is an MS1 scan. There is no fragmentation occurring.

I understand, I mean there are 4 proteins in the beginning --> which are digested --> peptides --> MS. So in this spectrum we got the peptides of ALL 4 proteins. But you don't know how many proteins there are at the beginning so the peak on the left could be just a peptide of the same protein as where the middle came from e.g? Sorry for all these questions but I can't get it clear

Let us continue this discussion in chat.


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Reverse evolution to gain back lost traits
Many animals return to shapes similar to their ancestors like mammals and reptiles growing fins and fish tails or animals losing limbs they just grew and so on.
But I notice that once an animal loses a feature it doesn't actually grow back... they con only mimic it, no reptile or mammal has fins but only limbs that look like fins... and no aquatic mammal or reptile seems to regrow back their lost legs or arms.
No animal seems to regrew its ancestral gills even though they live 100% of their lives inside deep waters.
If some organs can be so useful to have back, with evolutionary pressure at maximum, why don't they ever return?
What blocks animals from re-evolving something they lost?

I suggest that you check out the answers provided here: http://biology.stackexchange.com/questions/1754/can-species-back-evolve?rq=1  The main points are that there is no forward and backward in evolution, just a constant adaptation to one's environment.

@Forest, I am not sure that Koume is under that impression that there is a forward or backward in evolution. Instead, I think that Koume is under the impression that an organism is unable to re-attain a trait previously lost due to selective pressure, possibly partly because of the examples being somewhat scarce or inaccessible to the layman.

@niobe From what I understand, the idea of backwards evolution comprises the reacquisition of a lost trait, such as a previous form of some organ. In either case, selective pressures drive the evolution of that trait, whether it's something entirely new, or a return to something previously seen.

@Forest, It seems we are in agreement then.

Back evolution
Evolution do not strictly keep a history of how they were before. There is no way for a population to specifically produce mutations to reverse previously fixed mutations in order to evolve back in time. This has sometimes been called Dollo's law but very few people actually use this term today.
Note however that a population may have kept pseudogenes or specific developmental pathway or case of atavism that make the evolution of some traits similar to previously existing trait "easier". A very nice example of such mechanism is the case of Membracidae (treehoper).
Example of Membracidae
insects have evolved flight once. The first flying insect had 3 pairs of wings, one pair on each of the 3 segments of the thorax. Today, there exist no insects with 3 pairs of wings. In all lineages descendent of this flying ancestor many have no wings and many have 2 pairs of wings only. Here is a schema showing a typical insect with 2 pairs of wings.

As you can see there is no pair of wings on the first segment of the thorax (called prothorax) as it has been lost through evolution. Note that the diptera (true flies) have lost a second pair of wings (the one on the metathorax which has been replaced by halters).
Membracidae (treehoper) is a family of wingless insects. They use previously existing developmental pathways and previously existing genes (Prud'homme et al. 2011) for developing wings on the protothorax but instead of making wings, they make all kind of funny shape for defense purpose. Here are a few examples

I don't remember why I didn't accept this answer back in 2016

Just curious Remi.b, what evidence supports that the first flying insect had 3 pairs of wings?

May I suggest 2 keywords that might help you get started. Atavism and Dollo's Law
Attempting to answer your question:
In fact there are examples of where animals "re-evolve" a previously lost trait. There is a hypothesis called Dollo's law which posits that the evolution of an organism is not reversible, but as you can see there are exceptions.
Speaking to the likelihood of rediscovering a trait previously lost, assuming it is favorable. From what I can gather, when a trait is deemed to be impossible to rediscover, it would be because the genetic information that expressed that trait has been subject to sufficient mutation and selection so that it has very little resemblance to its previous underlying genetic information. Put differently, it is because the genetic "distance" between what currently is and what used to be is sufficiently great to make rediscovery by mutation and selection very unlikely.
Full disclosure: I am not a biologist and I draw most of my knowledge from studying genetic algorithms in computer science. So let me know if there are any glaring errors that I need to correct.


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What is the name/type/species of this spider?
Below are images of it, specimen found in the western region of the Pacific Northwest - North America.

I presume it is Eratigena atrica, commonly called the giant house spider.
It belongs to      Agelenidae family.

E. atrica is found in Europe, Central Asia and Northern Africa. It was unwittingly introduced to the Pacific Northwest of North America circa 1900 due to human activity and has strongly increased in numbers for the last century.

Reference: Wikipedia

This is, indeed, a giant house spider. But the species known to be established in the Pacific Northwest is Eratigena duellica, not E.atrica. (E.duellica is still part of the "E.atrica complex")


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What is a PCR test?
I know that PCR is used to amplify DNA, but what do people mean when they mention 'PCR tests' for diagnosis of disease? And what does a positive/negative PCR test mean?

Whether or not the amplified DNA fragment is present

So we add in known sequences (primers), and if the initial DNA is amplified, that's how we know that the original sample contains the sequence of interest?

PCR tests would involve amplification of DNA before actual tests happen. PCR tests actually refer to tests that occur after PCR has been done. Most of the time when you look at PCR tests you see images like this

This is the result of gel electrophorosis, and not specifically PCR, as PCR only increases the content of DNA so that it is sufficient for gel e. to take place (if not you won't be able to visualize the bands, etc).
Diagnosis of genetic diseases are made available through similar processes (gel e., RFLP analysis). They are just categorically termed under PCR. They detect the presense of mutant or healthy alleles and subsequently whether the subject is tested positive or negative for the disease.